Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold301
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: 1229110
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 128216 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1153414 original size:18 final size:18
Alignment explanation
Indices: 1153391--1153820 Score: 274
Period size: 18 Copynumber: 23.9 Consensus size: 18
1153381 CGTTTCCGTT
* *
1153391 ATTTCCTCCATTCCCACC
1 ATTTCCACCATTACCACC
1153409 ATTTCCACC-TTGACCACC
1 ATTTCCACCATT-ACCACC
* * *
1153427 ATTTCCTCCGTTACCACT
1 ATTTCCACCATTACCACC
1153445 ATTTCCACCATTACCACC
1 ATTTCCACCATTACCACC
* * *
1153463 ATTTCCCCCGTTTCCACC
1 ATTTCCACCATTACCACC
*
1153481 ATTTCCGCCATTACCACC
1 ATTTCCACCATTACCACC
* * * * *
1153499 ATTTCCTCCGTTGCCGCT
1 ATTTCCACCATTACCACC
1153517 ATTTCCACCATTACCACC
1 ATTTCCACCATTACCACC
*
1153535 ATTTCCACC-TTGACCTCC
1 ATTTCCACCATT-ACCACC
* * * *
1153553 ATTTCCTCCGTTCCCACT
1 ATTTCCACCATTACCACC
*
1153571 ATTTCCACCATTACCGCC
1 ATTTCCACCATTACCACC
*
1153589 ATTTCCACC-TTGGCCACC
1 ATTTCCACCATT-ACCACC
* * * *
1153607 ATTTCCTCCGTTCCCACT
1 ATTTCCACCATTACCACC
*
1153625 ATTTCCGCCATTACCACC
1 ATTTCCACCATTACCACC
* * *
1153643 ATTTCCTCC-TTGCCCTCC
1 ATTTCCACCATT-ACCACC
* * * * *
1153661 ATTGCCGCCGTTTCCGCC
1 ATTTCCACCATTACCACC
* ** * * **
1153679 CTGACCTCCATTGCCATT
1 ATTTCCACCATTACCACC
*
1153697 ATTTCCACCATTTCCACC
1 ATTTCCACCATTACCACC
* *
1153715 ATTTCCGCCATTGCCACC
1 ATTTCCACCATTACCACC
* * *
1153733 GTTTCCACCATTTCCTCC
1 ATTTCCACCATTACCACC
* *** *
1153751 GTTTCCGTTATTCCCACC
1 ATTTCCACCATTACCACC
* *
1153769 ATTTCCGCCATTGCCACC
1 ATTTCCACCATTACCACC
* * *
1153787 ACTTCCCCCGTTACCACC
1 ATTTCCACCATTACCACC
*
1153805 ATTTCCACCGTTACCA
1 ATTTCCACCATTACCA
1153821 TTAGAGCCAG
Statistics
Matches: 318, Mismatches: 86, Indels: 16
0.76 0.20 0.04
Matches are distributed among these distances:
17 8 0.03
18 302 0.95
19 8 0.03
ACGTcount: A:0.17, C:0.44, G:0.07, T:0.32
Consensus pattern (18 bp):
ATTTCCACCATTACCACC
Found at i:1153431 original size:36 final size:36
Alignment explanation
Indices: 1153391--1153820 Score: 312
Period size: 36 Copynumber: 11.9 Consensus size: 36
1153381 CGTTTCCGTT
*
1153391 ATTTCCTCCATTCCCACCATTTCCACC-TTGACCACC
1 ATTTCCTCCATTACCACCATTTCCACCATT-ACCACC
* *
1153427 ATTTCCTCCGTTACCACTATTTCCACCATTACCACC
1 ATTTCCTCCATTACCACCATTTCCACCATTACCACC
* * * *
1153463 ATTTCCCCCGTTTCCACCATTTCCGCCATTACCACC
1 ATTTCCTCCATTACCACCATTTCCACCATTACCACC
* * * *
1153499 ATTTCCTCCGTTGCCGCTATTTCCACCATTACCACC
1 ATTTCCTCCATTACCACCATTTCCACCATTACCACC
* * * * * *
1153535 ATTTCCACC-TTGACCTCCATTTCCTCCGTTCCCACT
1 ATTTCCTCCATT-ACCACCATTTCCACCATTACCACC
* * *
1153571 ATTTCCACCATTACCGCCATTTCCACC-TTGGCCACC
1 ATTTCCTCCATTACCACCATTTCCACCATT-ACCACC
* * * *
1153607 ATTTCCTCCGTTCCCACTATTTCCGCCATTACCACC
1 ATTTCCTCCATTACCACCATTTCCACCATTACCACC
* * * * * * *
1153643 ATTTCCTCC-TTGCCCTCCATTGCCGCCGTTTCCGCC
1 ATTTCCTCCATT-ACCACCATTTCCACCATTACCACC
* ** * ** *
1153679 CTGACCTCCATTGCCATTATTTCCACCATTTCCACC
1 ATTTCCTCCATTACCACCATTTCCACCATTACCACC
* * * * *
1153715 ATTTCCGCCATTGCCACCGTTTCCACCATTTCCTCC
1 ATTTCCTCCATTACCACCATTTCCACCATTACCACC
* * * * *
1153751 GTTTCCGT-TATTCCCACCATTTCCGCCATTGCCACC
1 ATTTCC-TCCATTACCACCATTTCCACCATTACCACC
* * * *
1153787 ACTTCCCCCGTTACCACCATTTCCACCGTTACCA
1 ATTTCCTCCATTACCACCATTTCCACCATTACCA
1153821 TTAGAGCCAG
Statistics
Matches: 312, Mismatches: 73, Indels: 18
0.77 0.18 0.04
Matches are distributed among these distances:
35 6 0.02
36 298 0.96
37 8 0.03
ACGTcount: A:0.17, C:0.44, G:0.07, T:0.32
Consensus pattern (36 bp):
ATTTCCTCCATTACCACCATTTCCACCATTACCACC
Found at i:1153456 original size:54 final size:54
Alignment explanation
Indices: 1153391--1153672 Score: 309
Period size: 54 Copynumber: 5.2 Consensus size: 54
1153381 CGTTTCCGTT
* * * *
1153391 ATTTCCTCCATTCCCACCATTTCCACC-TTGACCACCATTTCCTCCGTT-ACCACT
1 ATTTCCTCCGTTCCCACTATTTCCACCATT-ACCACCATTTCCACC-TTGACCACC
* * * * * * * *
1153445 ATTTCCACCATTACCACCATTTCCCCCGTTTCCACCATTTCCGCCATT-ACCACC
1 ATTTCCTCCGTTCCCACTATTTCCACCATTACCACCATTTCCACC-TTGACCACC
* * *
1153499 ATTTCCTCCGTTGCCGCTATTTCCACCATTACCACCATTTCCACCTTGACCTCC
1 ATTTCCTCCGTTCCCACTATTTCCACCATTACCACCATTTCCACCTTGACCACC
* *
1153553 ATTTCCTCCGTTCCCACTATTTCCACCATTACCGCCATTTCCACCTTGGCCACC
1 ATTTCCTCCGTTCCCACTATTTCCACCATTACCACCATTTCCACCTTGACCACC
* * * *
1153607 ATTTCCTCCGTTCCCACTATTTCCGCCATTACCACCATTTCCTCCTTGCCCTCC
1 ATTTCCTCCGTTCCCACTATTTCCACCATTACCACCATTTCCACCTTGACCACC
* *
1153661 ATTGCCGCCGTT
1 ATTTCCTCCGTT
1153673 TCCGCCCTGA
Statistics
Matches: 197, Mismatches: 29, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
53 2 0.01
54 193 0.98
55 2 0.01
ACGTcount: A:0.17, C:0.44, G:0.06, T:0.33
Consensus pattern (54 bp):
ATTTCCTCCGTTCCCACTATTTCCACCATTACCACCATTTCCACCTTGACCACC
Found at i:1153711 original size:9 final size:9
Alignment explanation
Indices: 1153697--1153813 Score: 99
Period size: 9 Copynumber: 13.0 Consensus size: 9
1153687 CATTGCCATT
1153697 ATTTCCACC
1 ATTTCCACC
1153706 ATTTCCACC
1 ATTTCCACC
*
1153715 ATTTCCGCC
1 ATTTCCACC
*
1153724 ATTGCCACC
1 ATTTCCACC
*
1153733 GTTTCCACC
1 ATTTCCACC
*
1153742 ATTTCCTCC
1 ATTTCCACC
* ***
1153751 GTTTCCGTT
1 ATTTCCACC
*
1153760 ATTCCCACC
1 ATTTCCACC
*
1153769 ATTTCCGCC
1 ATTTCCACC
*
1153778 ATTGCCACC
1 ATTTCCACC
* *
1153787 ACTTCCCCC
1 ATTTCCACC
* *
1153796 GTTACCACC
1 ATTTCCACC
1153805 ATTTCCACC
1 ATTTCCACC
1153814 GTTACCATTA
Statistics
Matches: 79, Mismatches: 29, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
9 79 1.00
ACGTcount: A:0.16, C:0.45, G:0.07, T:0.32
Consensus pattern (9 bp):
ATTTCCACC
Found at i:1153716 original size:27 final size:27
Alignment explanation
Indices: 1153422--1153792 Score: 138
Period size: 27 Copynumber: 14.1 Consensus size: 27
1153412 TCCACCTTGA
* * * *
1153422 CCACCATTTCCTCCGTTACCACTATTT
1 CCACCATTTCCGCCATTGCCACCATTT
* * * * *
1153449 CCACCATTACCACCATTTCCCCCGTTT
1 CCACCATTTCCGCCATTGCCACCATTT
*
1153476 CCACCATTTCCGCCATTACCACCATTT
1 CCACCATTTCCGCCATTGCCACCATTT
* * * * * *
1153503 CCTCCGTTGCCGCTATTTCCACCATTA
1 CCACCATTTCCGCCATTGCCACCATTT
* *
1153530 CCACCATTTCCACC-TTGACCTCCATTT
1 CCACCATTTCCGCCATTG-CCACCATTT
* * * * * * *
1153557 CCTCCGTTCCCACTATTTCCACCATTA
1 CCACCATTTCCGCCATTGCCACCATTT
* *
1153584 CCGCCATTTCCACC-TTGGCCACCATTT
1 CCACCATTTCCGCCATT-GCCACCATTT
* * * * * * * *
1153611 CCTCCGTTCCCACTATTTCCGCCATTA
1 CCACCATTTCCGCCATTGCCACCATTT
* * *
1153638 CCACCATTTCCTCC-TTGCCCTCCATTG
1 CCACCATTTCCGCCATTG-CCACCATTT
* * * *
1153665 CCGCCGTTTCCGCC-CTGACCTCCA-TT
1 CCACCATTTCCGCCATTG-CCACCATTT
* *
1153691 --GCCA-TT-----ATTTCCACCATTT
1 CCACCATTTCCGCCATTGCCACCATTT
*
1153710 CCACCATTTCCGCCATTGCCACCGTTT
1 CCACCATTTCCGCCATTGCCACCATTT
* * * *** *
1153737 CCACCATTTCCTCCGTTTCCGTTATTC
1 CCACCATTTCCGCCATTGCCACCATTT
*
1153764 CCACCATTTCCGCCATTGCCACCACTT
1 CCACCATTTCCGCCATTGCCACCATTT
1153791 CC
1 CC
1153793 CCCGTTACCA
Statistics
Matches: 246, Mismatches: 83, Indels: 30
0.69 0.23 0.08
Matches are distributed among these distances:
18 5 0.02
19 3 0.01
21 3 0.01
22 2 0.01
23 2 0.01
24 3 0.01
26 7 0.03
27 217 0.88
28 4 0.02
ACGTcount: A:0.16, C:0.44, G:0.07, T:0.32
Consensus pattern (27 bp):
CCACCATTTCCGCCATTGCCACCATTT
Found at i:1153950 original size:30 final size:30
Alignment explanation
Indices: 1153917--1154090 Score: 228
Period size: 30 Copynumber: 5.8 Consensus size: 30
1153907 ATTTGGACCT
* * *
1153917 GTTGGGGGTTT-TTGGTTTGGCTTTCCTCCT
1 GTTGGGGGTTTGTT-GTTAGGTTTTCCTCCA
* *
1153947 GTTGGGGGCTTT-TGGTTTGGTTTTCCTCCA
1 GTTGGGGG-TTTGTTGTTAGGTTTTCCTCCA
*
1153977 GTTGGAGGTTTGTTGTTAGGTTTTCCTCCA
1 GTTGGGGGTTTGTTGTTAGGTTTTCCTCCA
1154007 GTTGGGGGTTTGTTGTTAGGTTTTCCTCCA
1 GTTGGGGGTTTGTTGTTAGGTTTTCCTCCA
1154037 GTTGGGGGTTTCG-TGTTAGGTTTTCCTCCA
1 GTTGGGGGTTT-GTTGTTAGGTTTTCCTCCA
* *
1154067 GTTGGGGGTTTATTGTTTGGTTTT
1 GTTGGGGGTTTGTTGTTAGGTTTT
1154091 GTGTTCGGTT
Statistics
Matches: 131, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
29 3 0.02
30 123 0.94
31 5 0.04
ACGTcount: A:0.05, C:0.13, G:0.33, T:0.48
Consensus pattern (30 bp):
GTTGGGGGTTTGTTGTTAGGTTTTCCTCCA
Found at i:1154095 original size:12 final size:12
Alignment explanation
Indices: 1154080--1154119 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1154070 GGGGGTTTAT
*
1154080 TGTTTGGTTTTG
1 TGTTCGGTTTTG
1154092 TGTTCGGTTTTG
1 TGTTCGGTTTTG
*
1154104 TGTTCGGTTTCG
1 TGTTCGGTTTTG
1154116 TGTT
1 TGTT
1154120 GGCTTTCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.07, G:0.33, T:0.60
Consensus pattern (12 bp):
TGTTCGGTTTTG
Found at i:1157319 original size:1 final size:1
Alignment explanation
Indices: 1157313--1157360 Score: 96
Period size: 1 Copynumber: 48.0 Consensus size: 1
1157303 TTGTTGCTGA
1157313 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1157361 GGTCAGTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1159463 original size:2 final size:2
Alignment explanation
Indices: 1159458--1159513 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1159448 TTTTTATTAA
1159458 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
1159500 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
1159514 CTAGACCGAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1170723 original size:15 final size:15
Alignment explanation
Indices: 1170703--1170735 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1170693 TTTCAGAGGT
1170703 AACAATGCATAATTG
1 AACAATGCATAATTG
1170718 AACAATGCATAATTG
1 AACAATGCATAATTG
1170733 AAC
1 AAC
1170736 TCTTTCCGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.24
Consensus pattern (15 bp):
AACAATGCATAATTG
Found at i:1175979 original size:2 final size:2
Alignment explanation
Indices: 1175972--1176016 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1175962 GTGCCACATC
1175972 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1176014 CT C
1 CT C
1176017 AATGTAATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1180725 original size:2 final size:2
Alignment explanation
Indices: 1180718--1180772 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1180708 CGTTAAAAAC
1180718 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
1180760 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
1180773 TTTACTTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1189224 original size:5 final size:5
Alignment explanation
Indices: 1189205--1189340 Score: 163
Period size: 5 Copynumber: 27.4 Consensus size: 5
1189195 CTGTAAAGTG
1189205 CGAAA CGAAA TCGAAA CGAAA CGAAA CGAAA TCG-AA CGAAA CGAAA CGAAA
1 CGAAA CGAAA -CGAAA CGAAA CGAAA CGAAA -CGAAA CGAAA CGAAA CGAAA
* * * *
1189256 CCAAT CGAAA CGAAA CGAAA CCAAT CGAAA CGAAA CGAAA TC-AAA CGAAA
1 CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA -CGAAA CGAAA
* *
1189306 CGAAA CCAAA --AAT CGAAA CGAAA CGAAA CGAAA CG
1 CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CG
1189341 GAATTTAAAC
Statistics
Matches: 113, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
3 2 0.02
4 3 0.03
5 100 0.88
6 8 0.07
ACGTcount: A:0.57, C:0.22, G:0.17, T:0.04
Consensus pattern (5 bp):
CGAAA
Found at i:1189595 original size:2 final size:2
Alignment explanation
Indices: 1189588--1189666 Score: 142
Period size: 2 Copynumber: 40.0 Consensus size: 2
1189578 ACGTTTTGGG
1189588 GA GA GA GA GA GA GA GA GA GA 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
*
1189630 GA GA GA GA GA GA AA 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
1189667 AATGCCTTAA
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 73 0.99
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1189761 original size:3 final size:3
Alignment explanation
Indices: 1189753--1189784 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1189743 ATATAGAGAT
*
1189753 ATG ATG ATG ATG ATG ATG ATG ATG ATG GTG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1189785 AAATATAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:1190537 original size:5 final size:5
Alignment explanation
Indices: 1190527--1190608 Score: 103
Period size: 5 Copynumber: 16.2 Consensus size: 5
1190517 AAACATACAG
* * * *
1190527 GTTTC GTTTC GTTTG GTTTT GTTTC GTTTC GATTG GTTTC GTTTC G-TTC
1 GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC
1190576 GATTTC GTTTC GTTTC GTTTC GATTTC GTTTC G
1 G-TTTC GTTTC GTTTC GTTTC G-TTTC GTTTC G
1190609 CACTTTACAG
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
4 4 0.06
5 54 0.81
6 9 0.13
ACGTcount: A:0.04, C:0.16, G:0.23, T:0.57
Consensus pattern (5 bp):
GTTTC
Found at i:1195795 original size:48 final size:48
Alignment explanation
Indices: 1195717--1195910 Score: 208
Period size: 48 Copynumber: 4.0 Consensus size: 48
1195707 GTGCTCTAAT
* * * *
1195717 CTTGTCATGCAAATTAACTACGACTATAGCTTTCTACTTCTTTATACA
1 CTTGTCATGCAAATTAACTCCGAATATAGCTTACTATTTCTTTATACA
* * *
1195765 CTTGTCCTGCAAATTAACTCCGAATTTAGCTTACTATTTCTTGATACA
1 CTTGTCATGCAAATTAACTCCGAATATAGCTTACTATTTCTTTATACA
* * * * * * *
1195813 CTTGTCGTGCAGATTAATTCCGAATAAAACTCAATATTTCTTTATACA
1 CTTGTCATGCAAATTAACTCCGAATATAGCTTACTATTTCTTTATACA
* * * * * *
1195861 CTTGTTATGCAAGTTAACTCCGATTAAAGATTACTATTTCTATATACA
1 CTTGTCATGCAAATTAACTCCGAATATAGCTTACTATTTCTTTATACA
1195909 CT
1 CT
1195911 GGTGTTTTGA
Statistics
Matches: 119, Mismatches: 27, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 119 1.00
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (48 bp):
CTTGTCATGCAAATTAACTCCGAATATAGCTTACTATTTCTTTATACA
Found at i:1207991 original size:17 final size:16
Alignment explanation
Indices: 1207973--1208031 Score: 73
Period size: 17 Copynumber: 3.5 Consensus size: 16
1207963 ACTGTCCGTT
*
1207973 TAGTGTAATCGCCCATT
1 TAGTGTAA-CGCCCATG
*
1207990 TAGTGTAACCGTCCATG
1 TAGTGTAA-CGCCCATG
1208007 TAGTGTAACTGCCCATG
1 TAGTGTAAC-GCCCATG
1208024 TAGTGTAA
1 TAGTGTAA
1208032 GACTAGTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
16 1 0.03
17 36 0.97
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (16 bp):
TAGTGTAACGCCCATG
Found at i:1208259 original size:37 final size:36
Alignment explanation
Indices: 1208195--1208266 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 36
1208185 GGTTCATATT
* * *
1208195 GAATTGTTCCTAATTCGTTGTGGAATTATCTATGTG
1 GAATTGTTCCCAAGTCGTTGTGGAATTATCCATGTG
**
1208231 GAATTGTTCCCAAGTCTGTTGTTTAATTATCCATGT
1 GAATTGTTCCCAAGTC-GTTGTGGAATTATCCATGT
1208267 TCAGGTTTAG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 14 0.47
37 16 0.53
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.44
Consensus pattern (36 bp):
GAATTGTTCCCAAGTCGTTGTGGAATTATCCATGTG
Found at i:1210041 original size:2 final size:2
Alignment explanation
Indices: 1210034--1210058 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1210024 NNATAAATGA
1210034 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1210059 GACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1210065 original size:2 final size:2
Alignment explanation
Indices: 1210060--1210086 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1210050 ATATATATAG
1210060 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1210087 AATGTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1212084 original size:35 final size:35
Alignment explanation
Indices: 1212038--1212492 Score: 597
Period size: 35 Copynumber: 12.8 Consensus size: 35
1212028 CTACGTGCCT
1212038 GTTATTGCTTCTACTGTCAGATACAAACTATTATC
1 GTTATTGCTTCTACTGTCAGATACAAACTATTATC
1212073 GTTATTGCTTCTACTGTCAGATACAAACTATTATC
1 GTTATTGCTTCTACTGTCAGATACAAACTATTATC
*
1212108 GTTATTGCTTCTACCGTCAGATACAAACTATTATC
1 GTTATTGCTTCTACTGTCAGATACAAACTATTATC
* *
1212143 GTCATTGCCTCTACTGTCAGATACAAACTATTATC
1 GTTATTGCTTCTACTGTCAGATACAAACTATTATC
* * *
1212178 GTTATTGCCTCTACCGTCAGATACAAACTATTGTC
1 GTTATTGCTTCTACTGTCAGATACAAACTATTATC
* *
1212213 GTTATTGCTTCCACCGTCAGATACAAACTATTATC
1 GTTATTGCTTCTACTGTCAGATACAAACTATTATC
1212248 GTCT-TTGCTTCTACTGTCAGATACAAACTATTATC
1 GT-TATTGCTTCTACTGTCAGATACAAACTATTATC
** * *
1212283 GGCATTGCCTCTACTGTCAGATATAAACTATTATC
1 GTTATTGCTTCTACTGTCAGATACAAACTATTATC
* *
1212318 GTTATGGCTTCTACCGTCAGATACAAACTATTATC
1 GTTATTGCTTCTACTGTCAGATACAAACTATTATC
** ** *
1212353 GCCATTGCTTCTACACTCTGATACAAACTATTATC
1 GTTATTGCTTCTACTGTCAGATACAAACTATTATC
* * * *
1212388 GTTATTGCCTCTACCGTCAGATACAAAATTTTATC
1 GTTATTGCTTCTACTGTCAGATACAAACTATTATC
*
1212423 GTTATTGCTTCTACTGTCAGATTCATACTACATGTGTATTATC
1 GTTATTGCTTCTACTGTCAGATACA-A--AC-----TATTATC
*
1212466 GTTATTGCCTCTACTGTCAGATACAAA
1 GTTATTGCTTCTACTGTCAGATACAAA
1212493 ATTTTATCAG
Statistics
Matches: 367, Mismatches: 43, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
35 333 0.91
36 2 0.01
38 1 0.00
40 1 0.00
42 1 0.00
43 29 0.08
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (35 bp):
GTTATTGCTTCTACTGTCAGATACAAACTATTATC
Found at i:1212546 original size:35 final size:35
Alignment explanation
Indices: 1212499--1212801 Score: 318
Period size: 35 Copynumber: 8.4 Consensus size: 35
1212489 CAAAATTTTA
* * *
1212499 TCAGATATAAACTATTATCGTTATGGCTTCTACCG
1 TCAGATACAAACTATTATCGTTATTGCTTCTACTG
** **
1212534 TCAGATACAAACTATTATCGCCATTGCTTCTACAC
1 TCAGATACAAACTATTATCGTTATTGCTTCTACTG
* * *
1212569 TCTGATACAAACTATTATCGTTATTGCCTCTACCG
1 TCAGATACAAACTATTATCGTTATTGCTTCTACTG
* *
1212604 TCAGATACAAAATTTTATCGTTATTGCTTCTACTG
1 TCAGATACAAACTATTATCGTTATTGCTTCTACTG
* *
1212639 TCAGATTCATACTACATGTGTATTATCGTTATTGCCTCTACTG
1 TCAGATACA-A--AC-----TATTATCGTTATTGCTTCTACTG
* * * *
1212682 TCAGATACAAAATTTTATCGTCATTGCCTCTACTG
1 TCAGATACAAACTATTATCGTTATTGCTTCTACTG
* *
1212717 TCAGATACAAACTTTTATCGTTATTGCTCCTACTG
1 TCAGATACAAACTATTATCGTTATTGCTTCTACTG
* * *
1212752 TAAGATGCAAACTATTATCGTAATTGCTTCTACTG
1 TCAGATACAAACTATTATCGTTATTGCTTCTACTG
*
1212787 TCAGATGCAAACTAT
1 TCAGATACAAACTAT
1212802 AAGAGCTCGG
Statistics
Matches: 225, Mismatches: 35, Indels: 16
0.82 0.13 0.06
Matches are distributed among these distances:
35 192 0.85
36 1 0.00
38 1 0.00
40 1 0.00
42 1 0.00
43 29 0.13
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (35 bp):
TCAGATACAAACTATTATCGTTATTGCTTCTACTG
Found at i:1212779 original size:148 final size:148
Alignment explanation
Indices: 1212511--1212792 Score: 395
Period size: 148 Copynumber: 1.9 Consensus size: 148
1212501 AGATATAAAC
* * * *
1212511 TATTATCGTTATGGCTTCTACCGTCAGATACAAACTATTATCGCCATTGCTTCTACACTCTGATA
1 TATTATCGTTATGGCCTCTACCGTCAGATACAAAATATTATCGCCATTGCCTCTACACTCAGATA
* * *
1212576 CAAACTATTATCGTTATTGCCTCTACCGTCAGATACAAAATTTTATCGTTATTGCTTCTACTGTC
66 CAAACTATTATCGTTATTGCCTCTACCGTAAGATACAAAATATTATCGTAATTGCTTCTACTGTC
1212641 AGATTCATACTACATGTG
131 AGATTCATACTACATGTG
* * * * **
1212659 TATTATCGTTATTGCCTCTACTGTCAGATACAAAATTTTATCGTCATTGCCTCTACTGTCAGATA
1 TATTATCGTTATGGCCTCTACCGTCAGATACAAAATATTATCGCCATTGCCTCTACACTCAGATA
* * * *
1212724 CAAACTTTTATCGTTATTG-CTCCTACTGTAAGATGCAAACTATTATCGTAATTGCTTCTACTGT
66 CAAACTATTATCGTTATTGCCT-CTACCGTAAGATACAAAATATTATCGTAATTGCTTCTACTGT
1212788 CAGAT
130 CAGAT
1212793 GCAAACTATA
Statistics
Matches: 116, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
147 2 0.02
148 114 0.98
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (148 bp):
TATTATCGTTATGGCCTCTACCGTCAGATACAAAATATTATCGCCATTGCCTCTACACTCAGATA
CAAACTATTATCGTTATTGCCTCTACCGTAAGATACAAAATATTATCGTAATTGCTTCTACTGTC
AGATTCATACTACATGTG
Found at i:1216394 original size:2 final size:2
Alignment explanation
Indices: 1216387--1216425 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1216377 GTTGTGACAT
1216387 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1216426 TTTAATACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.