Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold3
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1336734
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 151046 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1234595 original size:21 final size:21
Alignment explanation
Indices: 1234554--1234597 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1234544 ATAGTTCGTA
*
1234554 TAACGTGGGTGATCGTTCGTG
1 TAACGTGGGTGATCGTGCGTG
1234575 TAACGTGCGG-GATCGTGCGTG
1 TAACGTG-GGTGATCGTGCGTG
1234596 TA
1 TA
1234598 TCAGGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.16, C:0.16, G:0.39, T:0.30
Consensus pattern (21 bp):
TAACGTGGGTGATCGTGCGTG
Found at i:1235620 original size:11 final size:11
Alignment explanation
Indices: 1235604--1235639 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1235594 GATCATGCGT
1235604 TATCGTTCGTG
1 TATCGTTCGTG
*
1235615 TATCGTGCGTG
1 TATCGTTCGTG
1235626 -ATCGTTCGTG
1 TATCGTTCGTG
1235636 TATC
1 TATC
1235640 AGAATCGTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.11, C:0.19, G:0.28, T:0.42
Consensus pattern (11 bp):
TATCGTTCGTG
Found at i:1235629 original size:21 final size:21
Alignment explanation
Indices: 1235599--1235639 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1235589 TTAGTGATCA
*
1235599 TGCGTTATCGTTCGTGTATCG
1 TGCGTGATCGTTCGTGTATCG
1235620 TGCGTGATCGTTCGTGTATC
1 TGCGTGATCGTTCGTGTATC
1235640 AGAATCGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.20, G:0.29, T:0.41
Consensus pattern (21 bp):
TGCGTGATCGTTCGTGTATCG
Found at i:1237166 original size:161 final size:160
Alignment explanation
Indices: 1236556--1237548 Score: 1239
Period size: 160 Copynumber: 6.1 Consensus size: 160
1236546 GGTCCACCAA
* * *
1236556 CAGTTTCCGTTCATTTTCTTTGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
1 CAGTTTCCGCTCATTTTCTTCGCAGGGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
* * *
1236621 TCATGATAAAATCTAGGTCAAGTGTGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGG
66 TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG
1236686 CCCTTGGACATAGAAAATTTCCAGTTATTTG
131 CCCTTGGACATAGAAAA-TTCCAGTTATTTG
** * *
1236717 CAGTTTCAACTCATTTTCTTCGCAGGGGATGAACATATTGTAATGAAATTTGGTA-AAAGGTTTA
1 CAGTTTCCGCTCATTTTCTTCGCAGGGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
* *
1236781 TCATGATGATATCTAGGTCAAGTTTGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGG
66 TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG
1236846 CCCTTGGACATAGAAAATTTCCAGTTATTTG
131 CCCTTGGACATAGAAAA-TTCCAGTTATTTG
** * *
1236877 CAGTTTCAACTCATTTTCTTCGCAGGGGATGAACATATTGTAATGAAATTTGGTA-AAAGGTTTA
1 CAGTTTCCGCTCATTTTCTTCGCAGGGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
* * * *
1236941 TCATGATGATATCTAGGTCAAGTTTGATATTGGGTATGATAGAGCAATTTTCAAACAGAGTTATG
66 TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTC-GACAGAGTTATG
*
1237006 GCCCTTGGACTTAGGAAAATTCCAGTTATTTG
130 GCCCTTGGACATA-GAAAATTCCAGTTATTTG
*
1237038 CAGTTTCCGCTCATTTTCTTTGCAGGGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
1 CAGTTTCCGCTCATTTTCTTCGCAGGGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
* * * * * *
1237103 TCATGATAATATCTAGGTCAAGATCGATATTGGATACGATCAAGGAATTTTCGACAAAGTTATGG
66 TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG
*
1237168 CCCTTGGACTTAGAAAAATTCCAGTTACATTGTATATG
131 CCCTTGGACATAG-AAAATTCCAGTT--A---T-T-TG
* * * *
1237206 CAGTTTACGCTCATTTTCTTTGCAGAGGATGAACATATTG--ATGGAAATTTAGTATACAGGTTT
1 CAGTTTCCGCTCATTTTCTTCGCAGGGGATGAACATATTGAAAT-GAAATTTGGTATACAGGTTT
* *
1237269 ATCATGTTAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATG
65 ATCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATG
* *
1237334 GCTCTTGGACGTAGAAGAATTCCAG-T-TTTG
130 GCCCTTGGACATAGAA-AATTCCAGTTATTTG
* * * *
1237364 CAGTTTCCGCTCATTTTCTTCGCAGAGGG-TGCACATATTGATATGAAATTTGGTATACAGCTTC
1 CAGTTTCCGCTCATTTTCTTCGCAG-GGGATGAACATATTGAAATGAAATTTGGTATACAGGTTT
* * * * *
1237428 ATC-TAAATAATATCTAGGTCAAGTTTGAT-TTTGGTATGATGGAGCAATTTTTGTCAGAGTAGA
65 ATCAT-GATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAA--TTT-TC-GA-CAGA
* * * **
1237491 GTTATGTCCCTTGGACTTACAAAAATTCCAAATATTTG
124 GTTATGGCCCTTGGACATA-GAAAATTCCAGTTATTTG
* * *
1237529 CAGTTTACGTTCAATTTCTT
1 CAGTTTCCGCTCATTTTCTT
1237549 TGTGGATGTT
Statistics
Matches: 744, Mismatches: 63, Indels: 46
0.87 0.07 0.05
Matches are distributed among these distances:
158 51 0.07
159 44 0.06
160 221 0.30
161 173 0.23
162 59 0.08
163 27 0.04
164 3 0.00
165 21 0.03
166 6 0.01
167 99 0.13
168 40 0.05
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (160 bp):
CAGTTTCCGCTCATTTTCTTCGCAGGGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG
CCCTTGGACATAGAAAATTCCAGTTATTTG
Found at i:1239944 original size:33 final size:33
Alignment explanation
Indices: 1239906--1239994 Score: 169
Period size: 33 Copynumber: 2.7 Consensus size: 33
1239896 TCACAGGAAC
1239906 AGACTCCTCCAATATCCACAGAAGAACAGACAG
1 AGACTCCTCCAATATCCACAGAAGAACAGACAG
*
1239939 AGACTCCTCCAATATCCACAGAGGAACAGACAG
1 AGACTCCTCCAATATCCACAGAAGAACAGACAG
1239972 AGACTCCTCCAATATCCACAGAA
1 AGACTCCTCCAATATCCACAGAA
1239995 AATGAAATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.40, C:0.31, G:0.15, T:0.13
Consensus pattern (33 bp):
AGACTCCTCCAATATCCACAGAAGAACAGACAG
Found at i:1240401 original size:6 final size:6
Alignment explanation
Indices: 1240390--1240453 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
1240380 AGAAGAGAGG
* ** *
1240390 GAGGAA GAGGAA GAAGACA GAGGAA GTTGAA GAGG-- G-GGAG GAGGAA
1 GAGGAA GAGGAA GAGGA-A GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA
*
1240436 GAGGAA GAAGAA GAGGAA
1 GAGGAA GAGGAA GAGGAA
1240454 CTGCCAACCA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 1 0.02
6 36 0.80
7 5 0.11
ACGTcount: A:0.47, C:0.02, G:0.48, T:0.03
Consensus pattern (6 bp):
GAGGAA
Found at i:1242566 original size:2 final size:2
Alignment explanation
Indices: 1242559--1242618 Score: 90
Period size: 2 Copynumber: 31.5 Consensus size: 2
1242549 TTTAAAAGTT
*
1242559 GA GA GA GA -A GA CA G- GA G- GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1242598 GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA G
1242619 CAAGCTTGCT
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
1 3 0.06
2 50 0.94
ACGTcount: A:0.48, C:0.02, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1249324 original size:2 final size:2
Alignment explanation
Indices: 1249317--1249401 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
1249307 ATGATTTAGC
1249317 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1249359 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1249401 A
1 A
1249402 TTTTTAAAAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1251453 original size:8 final size:7
Alignment explanation
Indices: 1251428--1251557 Score: 63
Period size: 8 Copynumber: 17.7 Consensus size: 7
1251418 GCCTTTAGGT
1251428 CGAAGATG
1 CGAAG-TG
1251436 CGAGAGTG
1 CGA-AGTG
1251444 CGAAGTTG
1 CGAAG-TG
1251452 CGAAG-G
1 CGAAGTG
1251458 CGAAAGTG
1 CG-AAGTG
*
1251466 CGATGGTG
1 CGA-AGTG
*
1251474 CGACG-G
1 CGAAGTG
*
1251480 CGAAGGAG
1 CGAA-GTG
1251488 CGAAAGTG
1 CG-AAGTG
1251496 CGAAGATG
1 CGAAG-TG
*
1251504 CGACG-G
1 CGAAGTG
*
1251510 CGAAGCG
1 CGAAGTG
*
1251517 CGGAGATG
1 CGAAG-TG
*
1251525 CGATG-G
1 CGAAGTG
1251531 CGAAAGTG
1 CG-AAGTG
1251539 CGAAGGTG
1 CGAA-GTG
1251547 CGAAG-G
1 CGAAGTG
1251553 CGAAG
1 CGAAG
1251558 GAGCGATATT
Statistics
Matches: 97, Mismatches: 11, Indels: 30
0.70 0.08 0.22
Matches are distributed among these distances:
6 21 0.22
7 21 0.22
8 51 0.53
9 4 0.04
ACGTcount: A:0.29, C:0.16, G:0.45, T:0.10
Consensus pattern (7 bp):
CGAAGTG
Found at i:1251465 original size:22 final size:22
Alignment explanation
Indices: 1251435--1251556 Score: 82
Period size: 22 Copynumber: 5.2 Consensus size: 22
1251425 GGTCGAAGAT
* *
1251435 GCGAGAGTGCGAAGTTGCGAAG
1 GCGAAAGTGCGAAGGTGCGAAG
* *
1251457 GCGAAAGTGCGATGGTGCGACG
1 GCGAAAGTGCGAAGGTGCGAAG
* * *
1251479 GCGAAGGAGCGAAAGTGCGAAG
1 GCGAAAGTGCGAAGGTGCGAAG
* * * *
1251501 ATGCGACGGCGAAGCGCGGAGATGCGATG
1 --GCGA-----AAGTGCGAAGGTGCGAAG
1251530 GCGAAAGTGCGAAGGTGCGAAG
1 GCGAAAGTGCGAAGGTGCGAAG
1251552 GCGAA
1 GCGAA
1251557 GGAGCGATAT
Statistics
Matches: 74, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
22 54 0.73
24 4 0.05
27 4 0.05
29 12 0.16
ACGTcount: A:0.29, C:0.16, G:0.45, T:0.10
Consensus pattern (22 bp):
GCGAAAGTGCGAAGGTGCGAAG
Found at i:1251475 original size:30 final size:30
Alignment explanation
Indices: 1251457--1251514 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1251447 AGTTGCGAAG
*
1251457 GCGAAAGTGCGATGGTGCGACGGCGAAGGA
1 GCGAAAGTGCGATGGTGCGAAGGCGAAGGA
* * *
1251487 GCGAAAGTGCGAAGATGCGACGGCGAAG
1 GCGAAAGTGCGATGGTGCGAAGGCGAAG
1251515 CGCGGAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.17, G:0.45, T:0.09
Consensus pattern (30 bp):
GCGAAAGTGCGATGGTGCGAAGGCGAAGGA
Found at i:1251524 original size:21 final size:21
Alignment explanation
Indices: 1251495--1251557 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
1251485 GAGCGAAAGT
*
1251495 GCGAAGATGCGACGGCGAAGC
1 GCGAAGATGCGAAGGCGAAGC
* * *
1251516 GCGGAGATGCGATGGCGAAAGT
1 GCGAAGATGCGAAGGCG-AAGC
*
1251538 GCGAAGGTGCGAAGGCGAAG
1 GCGAAGATGCGAAGGCGAAG
1251558 GAGCGATATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.29, C:0.17, G:0.46, T:0.08
Consensus pattern (21 bp):
GCGAAGATGCGAAGGCGAAGC
Found at i:1252569 original size:8 final size:8
Alignment explanation
Indices: 1252546--1252608 Score: 57
Period size: 8 Copynumber: 8.6 Consensus size: 8
1252536 GATAGTAGTA
*
1252546 TCGCTTCT
1 TCGCATCT
1252554 TCGC--CT
1 TCGCATCT
*
1252560 TCGCAACT
1 TCGCATCT
1252568 TCGC--CT
1 TCGCATCT
1252574 TCGCATCT
1 TCGCATCT
1252582 TCGCATCT
1 TCGCATCT
*
1252590 TCGC--CG
1 TCGCATCT
1252596 TCGCATCT
1 TCGCATCT
1252604 TCGCA
1 TCGCA
1252609 CTTTCACTCC
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
6 17 0.36
8 30 0.64
ACGTcount: A:0.10, C:0.41, G:0.16, T:0.33
Consensus pattern (8 bp):
TCGCATCT
Found at i:1252569 original size:14 final size:14
Alignment explanation
Indices: 1252552--1252585 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1252542 AGTATCGCTT
1252552 CTTCGCCTTCGCAA
1 CTTCGCCTTCGCAA
*
1252566 CTTCGCCTTCGCAT
1 CTTCGCCTTCGCAA
1252580 CTTCGC
1 CTTCGC
1252586 ATCTTCGCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.09, C:0.44, G:0.15, T:0.32
Consensus pattern (14 bp):
CTTCGCCTTCGCAA
Found at i:1252583 original size:22 final size:22
Alignment explanation
Indices: 1252558--1252608 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1252548 GCTTCTTCGC
*
1252558 CTTCGCAACTTCGCCTTCGCAT
1 CTTCGCAACTTCGCCGTCGCAT
*
1252580 CTTCGCATCTTCGCCGTCGCAT
1 CTTCGCAACTTCGCCGTCGCAT
1252602 CTTCGCA
1 CTTCGCA
1252609 CTTTCACTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.12, C:0.41, G:0.16, T:0.31
Consensus pattern (22 bp):
CTTCGCAACTTCGCCGTCGCAT
Found at i:1252606 original size:30 final size:30
Alignment explanation
Indices: 1252571--1252641 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
1252561 CGCAACTTCG
1252571 CCTTCGCATCTTCGCA-T-CTTCGCCGTCGCA
1 CCTTCGCA-CTT-GCACTCCTTCGCCGTCGCA
* *
1252601 TCTTCGCACTTTCACTCCTTCGCCGTCGCA
1 CCTTCGCACTTGCACTCCTTCGCCGTCGCA
1252631 CCTTCGCACTT
1 CCTTCGCACTT
1252642 TCGCCTTCGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 2 0.06
29 4 0.11
30 30 0.83
ACGTcount: A:0.10, C:0.44, G:0.14, T:0.32
Consensus pattern (30 bp):
CCTTCGCACTTGCACTCCTTCGCCGTCGCA
Found at i:1252639 original size:8 final size:8
Alignment explanation
Indices: 1252557--1252671 Score: 59
Period size: 8 Copynumber: 15.4 Consensus size: 8
1252547 CGCTTCTTCG
1252557 CCTTCGCA
1 CCTTCGCA
*
1252565 ACTTCG--
1 CCTTCGCA
1252571 CCTTCGCA
1 CCTTCGCA
*
1252579 TCTTCGCA
1 CCTTCGCA
*
1252587 TCTTCG--
1 CCTTCGCA
*
1252593 CCGTCGCA
1 CCTTCGCA
*
1252601 TCTTCGCA
1 CCTTCGCA
* * *
1252609 CTTTCACT
1 CCTTCGCA
1252617 CCTTCG--
1 CCTTCGCA
*
1252623 CCGTCGCA
1 CCTTCGCA
1252631 CCTTCGCA
1 CCTTCGCA
*
1252639 CTTTCG--
1 CCTTCGCA
1252645 CCTTCGCA
1 CCTTCGCA
*
1252653 ACTTCGCA
1 CCTTCGCA
1252661 -CTCTCGCA
1 CCT-TCGCA
1252669 CCT
1 CCT
1252672 CGACCTAAAG
Statistics
Matches: 79, Mismatches: 18, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
6 19 0.24
7 2 0.03
8 56 0.71
9 2 0.03
ACGTcount: A:0.11, C:0.44, G:0.14, T:0.30
Consensus pattern (8 bp):
CCTTCGCA
Found at i:1252644 original size:22 final size:22
Alignment explanation
Indices: 1252619--1252667 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1252609 CTTTCACTCC
*
1252619 TTCGCCGTCGCACCTTCGCACT
1 TTCGCCGTCGCAACTTCGCACT
*
1252641 TTCGCCTTCGCAACTTCGCACT
1 TTCGCCGTCGCAACTTCGCACT
*
1252663 CTCGC
1 TTCGC
1252668 ACCTCGACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.10, C:0.45, G:0.16, T:0.29
Consensus pattern (22 bp):
TTCGCCGTCGCAACTTCGCACT
Found at i:1252661 original size:30 final size:28
Alignment explanation
Indices: 1252588--1252651 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 28
1252578 ATCTTCGCAT
* *
1252588 CTTCGCCGTCGCATCTTCGCACTTTCACTC
1 CTTCGCCGTCGCACCTTCGCACTTT--CGC
1252618 CTTCGCCGTCGCACCTTCGCACTTTCGC
1 CTTCGCCGTCGCACCTTCGCACTTTCGC
1252646 CTTCGC
1 CTTCGC
1252652 AACTTCGCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 8 0.25
30 24 0.75
ACGTcount: A:0.08, C:0.45, G:0.16, T:0.31
Consensus pattern (28 bp):
CTTCGCCGTCGCACCTTCGCACTTTCGC
Found at i:1252668 original size:30 final size:29
Alignment explanation
Indices: 1252588--1252669 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 29
1252578 ATCTTCGCAT
*
1252588 CTTCGCCGTCGCA-TCTTCGCACTTTCACTC
1 CTTCGCCGTCGCACTCTTCGCACTTT--CGC
1252618 CTTCGCCGTCGCAC-CTTCGCACTTTCGC
1 CTTCGCCGTCGCACTCTTCGCACTTTCGC
*
1252646 CTTCGCAACTTCGCACTC-TCGCAC
1 CTTCGC--CGTCGCACTCTTCGCAC
1252670 CTCGACCTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
28 8 0.17
30 37 0.80
31 1 0.02
ACGTcount: A:0.11, C:0.45, G:0.15, T:0.29
Consensus pattern (29 bp):
CTTCGCCGTCGCACTCTTCGCACTTTCGC
Found at i:1261220 original size:2 final size:2
Alignment explanation
Indices: 1261213--1261254 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1261203 ACCTGCATAA
1261213 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1261255 AAAATCAGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1273613 original size:15 final size:15
Alignment explanation
Indices: 1273593--1273623 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1273583 ACGCACTTCG
1273593 TGAAAAAAAAATCAA
1 TGAAAAAAAAATCAA
*
1273608 TGAAAAAATAATCAA
1 TGAAAAAAAAATCAA
1273623 T
1 T
1273624 CAAACGACGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (15 bp):
TGAAAAAAAAATCAA
Found at i:1294189 original size:16 final size:16
Alignment explanation
Indices: 1294168--1294227 Score: 84
Period size: 16 Copynumber: 3.8 Consensus size: 16
1294158 GACCCGCCTT
*
1294168 GGCCGAGGAGTCCTGG
1 GGCCGAGGTGTCCTGG
*
1294184 GGCCGAAGTGTCCTGG
1 GGCCGAGGTGTCCTGG
* *
1294200 GGCCGAGGTGTCGTTG
1 GGCCGAGGTGTCCTGG
1294216 GGCCGAGGTGTC
1 GGCCGAGGTGTC
1294228 TGACATTCGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.10, C:0.23, G:0.48, T:0.18
Consensus pattern (16 bp):
GGCCGAGGTGTCCTGG
Found at i:1299341 original size:203 final size:202
Alignment explanation
Indices: 1298992--1299396 Score: 801
Period size: 203 Copynumber: 2.0 Consensus size: 202
1298982 TGTACAATTG
1298992 TCCAGGCATGACTGTTTTCATGGATGGTGGTATTGTGAGGTCCCCAATGACAAATTCATACGTAC
1 TCCAGGCATGACTGTTTTCATGGATGGTGGTATTGTGAGGTCCCCAATGACAAATTCATACGTAC
1299057 TTCCCTGTGATTTGTGTGCCGTTATACCAAAGGCTGGAACAATAGGAAACATTGTTCTTTCCACC
66 TTCCCTGTGATTTGTGTGCCGTTATACCAAAGGCTGGAACAATAGGAAACATTGTTCTTTCCACC
1299122 TGAACAGGAGATTTTGCTGTTAATAAGAAGTTCACTGTCACTGCCTTTATAGGAACACTTCCTTT
131 TGAACAGGAGATTTTGCTGTTAATAAGAAGTTCACTGTCACTGCCTTTATAGGAACACTTCCTTT
1299187 CAGACGC
196 CAGACGC
1299194 NTCCAGGCATGACTGTTTTCATGGATGGTGGTATTGTGAGGTCCCCAATGACAAATTCATACGTA
1 -TCCAGGCATGACTGTTTTCATGGATGGTGGTATTGTGAGGTCCCCAATGACAAATTCATACGTA
1299259 CTTCCCTGTGATTTGTGTGCCGTTATACCAAAGGCTGGAACAATAGGAAACATTGTTCTTTCCAC
65 CTTCCCTGTGATTTGTGTGCCGTTATACCAAAGGCTGGAACAATAGGAAACATTGTTCTTTCCAC
1299324 CTGAACAGGAGATTTTGCTGTTAATAAGAAGTTCACTGTCACTGCCTTTATAGGAACACTTCCTT
130 CTGAACAGGAGATTTTGCTGTTAATAAGAAGTTCACTGTCACTGCCTTTATAGGAACACTTCCTT
1299389 TCAGACGC
195 TCAGACGC
1299397 GAAGGTGTTG
Statistics
Matches: 202, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
203 202 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (202 bp):
TCCAGGCATGACTGTTTTCATGGATGGTGGTATTGTGAGGTCCCCAATGACAAATTCATACGTAC
TTCCCTGTGATTTGTGTGCCGTTATACCAAAGGCTGGAACAATAGGAAACATTGTTCTTTCCACC
TGAACAGGAGATTTTGCTGTTAATAAGAAGTTCACTGTCACTGCCTTTATAGGAACACTTCCTTT
CAGACGC
Found at i:1304716 original size:69 final size:69
Alignment explanation
Indices: 1304642--1305136 Score: 578
Period size: 69 Copynumber: 7.2 Consensus size: 69
1304632 ACTTTTCCTT
* **
1304642 TTCTTATCTTTGTCATTATCTGAGGTGATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCAT
1 TTCTTATCTTTGTCATTGTCTGAGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCAT
1304707 CCAA
66 CCAA
* * * * * * *
1304711 TTCTTATTTTTGGCATTGTCTTAGGCCATTTGAGCTGGTGTTCTTGAGTCACGAGAGTCACTCTT
1 TTCTTATCTTTGTCATTGTCTGAGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCAT
* **
1304776 TCTT
66 CCAA
* *
1304780 TTTTTATCTTTGTCATTGTC-GTAGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGACAATCA
1 TTCTTATCTTTGTCATTGTCTG-AGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCA
1304844 TCCAA
65 TCCAA
* * * * * * * *
1304849 TTCTTATTTTTGGCTTTGTCTGAGGCCACTTGAGCTGGTGTTCTTGAGTCACGAGAGTCACTCTT
1 TTCTTATCTTTGTCATTGTCTGAGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCAT
* **
1304914 TCTT
66 CCAA
* * *
1304918 TTCTTATCTTTGTCATTATCTGAGGCAATTTGAGCAGGTGTTCTTGAGCCCCGAGAGTCAATCAT
1 TTCTTATCTTTGTCATTGTCTGAGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCAT
1304983 CCAA
66 CCAA
* * * * * * * *
1304987 TTCTTATTTTTGTCTTTGTCTGAGGCTACTTGAGCTGGTGTTCTTGAGTCACGAGAGTCACTCTT
1 TTCTTATCTTTGTCATTGTCTGAGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCAT
* **
1305052 TCTT
66 CCAA
* * *
1305056 TTCTTATCTTTGTCATTATCTGAGGCAATTTGAGCAGGTGTTCTTGAGGCACGAGAGTCAATCAT
1 TTCTTATCTTTGTCATTGTCTGAGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCAT
1305121 CCAA
66 CCAA
*
1305125 TTCTTATTTTTG
1 TTCTTATCTTTG
1305137 NNNNNNNNNN
Statistics
Matches: 346, Mismatches: 78, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
69 345 1.00
70 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (69 bp):
TTCTTATCTTTGTCATTGTCTGAGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCAT
CCAA
Found at i:1304812 original size:138 final size:138
Alignment explanation
Indices: 1304630--1305136 Score: 865
Period size: 138 Copynumber: 3.7 Consensus size: 138
1304620 AGCTCTTGAA
**
1304630 TCACT-TTTCCTTTTCTTATCTTTGTCATTATCTGAGGTGATTTGAGCAGGTGTTCTTGAGCCAC
1 TCACTCTTT-CTTTTCTTATCTTTGTCATTATCTGAGGCAATTTGAGCAGGTGTTCTTGAGCCAC
* * *
1304694 GAGAGTCAATCATCCAATTCTTATTTTTGGCATTGTCTTAGGCCATTTGAGCTGGTGTTCTTGAG
65 GAGAGTCAATCATCCAATTCTTATTTTTGGCTTTGTCTGAGGCCACTTGAGCTGGTGTTCTTGAG
1304759 TCACGAGAG
130 TCACGAGAG
* * *
1304768 TCACTCTTTCTTTTTTTATCTTTGTCATTGTC-GTAGGCCATTTGAGCAGGTGTTCTTGAGCCAC
1 TCACTCTTTCTTTTCTTATCTTTGTCATTATCTG-AGGCAATTTGAGCAGGTGTTCTTGAGCCAC
*
1304832 GAGAGACAATCATCCAATTCTTATTTTTGGCTTTGTCTGAGGCCACTTGAGCTGGTGTTCTTGAG
65 GAGAGTCAATCATCCAATTCTTATTTTTGGCTTTGTCTGAGGCCACTTGAGCTGGTGTTCTTGAG
1304897 TCACGAGAG
130 TCACGAGAG
*
1304906 TCACTCTTTCTTTTCTTATCTTTGTCATTATCTGAGGCAATTTGAGCAGGTGTTCTTGAGCCCCG
1 TCACTCTTTCTTTTCTTATCTTTGTCATTATCTGAGGCAATTTGAGCAGGTGTTCTTGAGCCACG
* *
1304971 AGAGTCAATCATCCAATTCTTATTTTTGTCTTTGTCTGAGGCTACTTGAGCTGGTGTTCTTGAGT
66 AGAGTCAATCATCCAATTCTTATTTTTGGCTTTGTCTGAGGCCACTTGAGCTGGTGTTCTTGAGT
1305036 CACGAGAG
131 CACGAGAG
*
1305044 TCACTCTTTCTTTTCTTATCTTTGTCATTATCTGAGGCAATTTGAGCAGGTGTTCTTGAGGCACG
1 TCACTCTTTCTTTTCTTATCTTTGTCATTATCTGAGGCAATTTGAGCAGGTGTTCTTGAGCCACG
1305109 AGAGTCAATCATCCAATTCTTATTTTTG
66 AGAGTCAATCATCCAATTCTTATTTTTG
1305137 NNNNNNNNNN
Statistics
Matches: 349, Mismatches: 17, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
137 1 0.00
138 344 0.99
139 4 0.01
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.41
Consensus pattern (138 bp):
TCACTCTTTCTTTTCTTATCTTTGTCATTATCTGAGGCAATTTGAGCAGGTGTTCTTGAGCCACG
AGAGTCAATCATCCAATTCTTATTTTTGGCTTTGTCTGAGGCCACTTGAGCTGGTGTTCTTGAGT
CACGAGAG
Found at i:1317374 original size:52 final size:52
Alignment explanation
Indices: 1317318--1317421 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
1317308 CATACCTAAA
*
1317318 TGATTACTGAATGAATTGACCCTAATTTGGGAAGCACCCAAATCCCACAGAC
1 TGATTACTGAATGAATTGACCCTAATTGGGGAAGCACCCAAATCCCACAGAC
* * *
1317370 TGATTACTGATTGAATTGACCCTTATTGGGGAAGCGCCCAAATCCCACAGAC
1 TGATTACTGAATGAATTGACCCTAATTGGGGAAGCACCCAAATCCCACAGAC
1317422 CTGTTTTGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (52 bp):
TGATTACTGAATGAATTGACCCTAATTGGGGAAGCACCCAAATCCCACAGAC
Found at i:1323196 original size:46 final size:46
Alignment explanation
Indices: 1323129--1323220 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
1323119 TGATGACATT
1323129 TCATCTCTGTTACTAAGCATGTGTAAAGATGCAATGTGTCTCACTG
1 TCATCTCTGTTACTAAGCATGTGTAAAGATGCAATGTGTCTCACTG
1323175 TCATCTCTGTTACTAAGCATGTGTAAAGATGCAATGTGTCTCACTG
1 TCATCTCTGTTACTAAGCATGTGTAAAGATGCAATGTGTCTCACTG
1323221 ACGTCAGCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (46 bp):
TCATCTCTGTTACTAAGCATGTGTAAAGATGCAATGTGTCTCACTG
Found at i:1334785 original size:47 final size:47
Alignment explanation
Indices: 1334734--1335294 Score: 804
Period size: 47 Copynumber: 11.7 Consensus size: 47
1334724 GCAGTGTTCA
* * * *
1334734 AAGTTTTCAAAATTGTATTCATTCAAGGTTCTGAATAGTTGTGCTCC
1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAGTTGTTCTCC
* *
1334781 AAGTTCTCAAAATTGTGTTCATTCAAAGTGCTCAATAGTTGTTCTCCAACTCC
1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAGTTG-T-T----CTCC
1334834 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAAG-TGTTCTCC
1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAAT-AGTTGTTCTCC
*
1334881 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAATTGTTCTCC
1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAGTTGTTCTCC
1334928 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAAG-TGTTCTCC
1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAAT-AGTTGTTCTCC
*
1334975 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAATTGTTCTCC
1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAGTTGTTCTCC
*
1335022 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAATTGTTCTCC
1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAGTTGTTCTCC
1335069 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAAG-TGTTCTCC
1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAAT-AGTTGTTCTCC
* *
1335116 AAGTTCTCAAAATTGTATTTATTCAAAGTTCTCAATAATTGTTCTCC
1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAGTTGTTCTCC
* * *
1335163 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTTAATAATTGTGCTCC
1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAGTTGTTCTCC
* * * *
1335210 AAGTTTTCAAAATTGTGTTCATGCATTCAAAGTTCGCAATAGTTGTGCTCC
1 AAGTTCTCAAAA-T-TG-T-ATTCATTCAAAGTTCTCAATAGTTGTTCTCC
* *
1335261 AAGTTTTCAAAATTGTGTTCATTCAAAGTTCTCA
1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCA
1335295 TAAATTGTAA
Statistics
Matches: 473, Mismatches: 25, Indels: 32
0.89 0.05 0.06
Matches are distributed among these distances:
46 3 0.01
47 376 0.79
48 5 0.01
49 4 0.01
50 2 0.00
51 40 0.08
52 1 0.00
53 40 0.08
54 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.39
Consensus pattern (47 bp):
AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAGTTGTTCTCC
Found at i:1335226 original size:21 final size:22
Alignment explanation
Indices: 1334859--1335226 Score: 185
Period size: 22 Copynumber: 15.8 Consensus size: 22
1334849 TATTCATTCA
* *
1334859 AAGTTCTCAATAAGTGTTCTCC
1 AAGTTCTCAATAATTGTGCTCC
* *
1334881 AAGTTCTCAA-AATTGTATTCATTCA
1 AAGTTCTCAATAATTG--TGC--TCC
*
1334906 AAGTTCTCAATAATTGTTCTCC
1 AAGTTCTCAATAATTGTGCTCC
* *
1334928 AAGTTCTCAA-AATTGTATTCATTCA
1 AAGTTCTCAATAATTG--TGC--TCC
* *
1334953 AAGTTCTCAATAAGTGTTCTCC
1 AAGTTCTCAATAATTGTGCTCC
* *
1334975 AAGTTCTCAA-AATTGTATTCATTCA
1 AAGTTCTCAATAATTG--TGC--TCC
*
1335000 AAGTTCTCAATAATTGTTCTCC
1 AAGTTCTCAATAATTGTGCTCC
* *
1335022 AAGTTCTCAA-AATTGTATTCATTCA
1 AAGTTCTCAATAATTG--TGC--TCC
*
1335047 AAGTTCTCAATAATTGTTCTCC
1 AAGTTCTCAATAATTGTGCTCC
* *
1335069 AAGTTCTCAA-AATTGTATTCATTCA
1 AAGTTCTCAATAATTG--TGC--TCC
* *
1335094 AAGTTCTCAATAAGTGTTCTCC
1 AAGTTCTCAATAATTGTGCTCC
** *
1335116 AAGTTCTCAA-AATTGTATTTATTCA
1 AAGTTCTCAATAATTG----TGCTCC
*
1335141 AAGTTCTCAATAATTGTTCTCC
1 AAGTTCTCAATAATTGTGCTCC
* *
1335163 AAGTTCTCAA-AATTGTATTCATTCA
1 AAGTTCTCAATAATTG--TGC--TCC
*
1335188 AAGTTCTTAATAATTGTGCTCC
1 AAGTTCTCAATAATTGTGCTCC
*
1335210 AAGTTTTCAA-AATTGTG
1 AAGTTCTCAATAATTGTG
1335227 TTCATGCATT
Statistics
Matches: 284, Mismatches: 27, Indels: 71
0.74 0.07 0.19
Matches are distributed among these distances:
21 39 0.14
22 93 0.33
23 18 0.06
24 17 0.06
25 84 0.30
26 33 0.12
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (22 bp):
AAGTTCTCAATAATTGTGCTCC
Done.