Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1024
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: 1774716
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 201941 characters in sequence are not A, C, G, or T
File 6 of 5
Found at i:1631534 original size:28 final size:28
Alignment explanation
Indices: 1631055--1631531 Score: 465
Period size: 28 Copynumber: 17.0 Consensus size: 28
1631045 CGAAAGAGGA
* * *
1631055 CAACTAACCTCATCGATTGTTAATTAGT
1 CAACTAACCTCATCGATAGGTAATTGGT
* * *
1631083 CAACAAACTTTATCGATAGGTAATTGGT
1 CAACTAACCTCATCGATAGGTAATTGGT
* *
1631111 CATCTAACCTCATCGATACGTAATT-GT
1 CAACTAACCTCATCGATAGGTAATTGGT
* *
1631138 ACAACTAACCTCATCGCTTGGTAATTGGT
1 -CAACTAACCTCATCGATAGGTAATTGGT
** * * **
1631167 CAACTAACCTCATAAAAAGGCAATAAGT
1 CAACTAACCTCATCGATAGGTAATTGGT
* * * * **
1631195 CCACTAACCTTATCTATAGGAAATAAGT
1 CAACTAACCTCATCGATAGGTAATTGGT
1631223 CAACTAACCTCATCGATAGGTAATTGGT
1 CAACTAACCTCATCGATAGGTAATTGGT
* * * *
1631251 TAGCTATA-CTCTTCGATATGTAATTGGT
1 CAACTA-ACCTCATCGATAGGTAATTGGT
* *
1631279 CAACTAAACTCATCGATGGGTAATTGGT
1 CAACTAACCTCATCGATAGGTAATTGGT
* *
1631307 CAACTAACCTTATCGATAGGTAATAGGT
1 CAACTAACCTCATCGATAGGTAATTGGT
* * *
1631335 CAACTAACCTTATCGATAGGTAAGTAGT
1 CAACTAACCTCATCGATAGGTAATTGGT
* *
1631363 CAACTAACCTCTTCGATAGGTAATTCGT
1 CAACTAACCTCATCGATAGGTAATTGGT
* *
1631391 CTACTAACCTCATCGATAGATAATTGGT
1 CAACTAACCTCATCGATAGGTAATTGGT
* * **
1631419 CAACTAACCTTATCGAAAGGTAATAAGT
1 CAACTAACCTCATCGATAGGTAATTGGT
* *
1631447 CAACCAACCTCATCGATAGGTAGTTGGT
1 CAACTAACCTCATCGATAGGTAATTGGT
* * *
1631475 CTACTGACCTCATCGAAAGGTAATT-GT
1 CAACTAACCTCATCGATAGGTAATTGGT
* * *
1631502 ACCACTAACCTCATCAAAAGGTAATTGGT
1 -CAACTAACCTCATCGATAGGTAATTGGT
1631531 C
1 C
1631532 CACGTTGAGG
Statistics
Matches: 364, Mismatches: 79, Indels: 12
0.80 0.17 0.03
Matches are distributed among these distances:
27 5 0.01
28 354 0.97
29 5 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.30
Consensus pattern (28 bp):
CAACTAACCTCATCGATAGGTAATTGGT
Found at i:1641060 original size:99 final size:100
Alignment explanation
Indices: 1640889--1641179 Score: 388
Period size: 104 Copynumber: 2.9 Consensus size: 100
1640879 GAAATCTAAC
* * **
1640889 AAAAAGCTTAGTGATTATA-TAATCTTGAAAAATAAAGTCGGTCATGTTTAGCTATCTTAGTGTT
1 AAAAAGCTTAGTGATTATAGAAACCTTGAAAAATAAAGTCGGTCATGTTTAGAAATCTTAGTGTT
*********
1640953 ATCTTTTTAGAGGGTTAATGTTTTT-TTTTTTTTT
66 ATCTTTTTAGAGGGTTAATGTTTTTAAAAAAAAAA
* * *
1640987 TAAAAGTTTAGTGATAATAGAAACCTTGAAAAATAAAGTCGGTCATGTTTAGAAATCTTAGTGTT
1 AAAAAGCTTAGTGATTATAGAAACCTTGAAAAATAAAGTCGGTCATGTTTAGAAATCTTAGTGTT
1641052 ATCTTTTTAGAGGGTTAATGTTTTTAAAAAAAAAAAAA
66 ATCTTTTTAGAGGGTTAATGTTTTT---AAAAAAAAAA
1641090 AAAGAAGCTTAGTGATTATAGAAACCTTGAAAAATAAAGTCGGTCATGTTTAGAAATCTTAGTGT
1 AAA-AAGCTTAGTGATTATAGAAACCTTGAAAAATAAAGTCGGTCATGTTTAGAAATCTTAGTGT
1641155 TATCTTTTTAGAGGGTTAATGTTTT
65 TATCTTTTTAGAGGGTTAATGTTTT
1641180 GCTGTAAAGT
Statistics
Matches: 168, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
98 16 0.10
99 66 0.39
103 2 0.01
104 84 0.50
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (100 bp):
AAAAAGCTTAGTGATTATAGAAACCTTGAAAAATAAAGTCGGTCATGTTTAGAAATCTTAGTGTT
ATCTTTTTAGAGGGTTAATGTTTTTAAAAAAAAAA
Found at i:1643692 original size:10 final size:10
Alignment explanation
Indices: 1643677--1643705 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1643667 TCATTTGGGT
1643677 CCCTCTTTGC
1 CCCTCTTTGC
1643687 CCCTCTTTGC
1 CCCTCTTTGC
1643697 CCCTCTTTG
1 CCCTCTTTG
1643706 TTTGATGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.48, G:0.10, T:0.41
Consensus pattern (10 bp):
CCCTCTTTGC
Found at i:1655250 original size:26 final size:25
Alignment explanation
Indices: 1655221--1655275 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
1655211 GTTTGTAATA
1655221 TTTTAATGATGTCCCGTGTACGCAGG-
1 TTTTAAT-A-GTCCCGTGTACGCAGGC
**
1655247 TTTTGGTAGTCCCGTGTACGCAGGC
1 TTTTAATAGTCCCGTGTACGCAGGC
1655272 TTTT
1 TTTT
1655276 GTAAATTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 16 0.62
25 5 0.19
26 5 0.19
ACGTcount: A:0.15, C:0.20, G:0.27, T:0.38
Consensus pattern (25 bp):
TTTTAATAGTCCCGTGTACGCAGGC
Found at i:1656100 original size:11 final size:11
Alignment explanation
Indices: 1656078--1656108 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
1656068 CTTAATGAAG
1656078 AAATTAATATAT
1 AAATT-ATATAT
1656090 AAATTATATAT
1 AAATTATATAT
1656101 AAATTATA
1 AAATTATA
1656109 CCCAGAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATTATATAT
Found at i:1664220 original size:2 final size:2
Alignment explanation
Indices: 1664213--1664259 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1664203 TTACTAGTCT
1664213 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
1664255 GA GA G
1 GA GA G
1664260 TCGCTTGGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1665323 original size:12 final size:13
Alignment explanation
Indices: 1665296--1665324 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1665286 GGCAAATAGT
1665296 TTTTTAAAATTGA
1 TTTTTAAAATTGA
1665309 TTTTTAAAATT-A
1 TTTTTAAAATTGA
1665321 TTTT
1 TTTT
1665325 GTTAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
TTTTTAAAATTGA
Found at i:1667002 original size:2 final size:2
Alignment explanation
Indices: 1666997--1667048 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1666987 AGAGATTATG
1666997 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
1667039 GA GA GA GA GA
1 GA GA GA GA GA
1667049 TAAGACAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1668446 original size:2 final size:2
Alignment explanation
Indices: 1668439--1668479 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1668429 GAATGCACTG
1668439 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1668480 TATATTAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1673059 original size:14 final size:14
Alignment explanation
Indices: 1673040--1673067 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1673030 GGATGTCAGG
1673040 CCCCTTTTCCCAAC
1 CCCCTTTTCCCAAC
1673054 CCCCTTTTCCCAAC
1 CCCCTTTTCCCAAC
1673068 ATTAGATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.57, G:0.00, T:0.29
Consensus pattern (14 bp):
CCCCTTTTCCCAAC
Found at i:1675445 original size:4 final size:4
Alignment explanation
Indices: 1675436--1675517 Score: 53
Period size: 4 Copynumber: 20.0 Consensus size: 4
1675426 TGATTTGTAT
* * *
1675436 ATTG ATTG ATTG ATTG ATTG AAAT- ATTG TTTG AATT- -TTG ATTG GTTG
1 ATTG ATTG ATTG ATTG ATTG -ATTG ATTG ATTG -ATTG ATTG ATTG ATTG
* *
1675483 ATTTC ATTG ATTG ATTC ATCTTG ATTG ATTG ATTG
1 A-TTG ATTG ATTG ATTG A--TTG ATTG ATTG ATTG
1675518 TTTGGGTCAT
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
2 2 0.03
3 2 0.03
4 46 0.77
5 7 0.12
6 3 0.05
ACGTcount: A:0.24, C:0.04, G:0.21, T:0.51
Consensus pattern (4 bp):
ATTG
Found at i:1682787 original size:2 final size:2
Alignment explanation
Indices: 1682780--1682810 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1682770 CAAAGATGTT
1682780 GA GA GA GA GA GA GA GA GA G- GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1682811 AAAGCCATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1688175 original size:4 final size:4
Alignment explanation
Indices: 1688166--1688208 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
1688156 CTTGCCCCTC
1688166 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
1688209 CCAATGCACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TCTT
Found at i:1689025 original size:4 final size:4
Alignment explanation
Indices: 1689016--1689054 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
1689006 TTATCATCCC
1689016 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
1689055 CCATCGGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TCTT
Found at i:1694346 original size:20 final size:20
Alignment explanation
Indices: 1694309--1694346 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1694299 TATGTTCACA
*
1694309 TTTAACTTTTATTCAACAGG
1 TTTAACTTTCATTCAACAGG
*
1694329 TTTAACTTTCATTGAACA
1 TTTAACTTTCATTCAACA
1694347 ATGATATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.45
Consensus pattern (20 bp):
TTTAACTTTCATTCAACAGG
Found at i:1706248 original size:21 final size:21
Alignment explanation
Indices: 1706222--1706286 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
1706212 TTTTTCTATC
1706222 AAATATGTCAACATGCAAGAT
1 AAATATGTCAACATGCAAGAT
*
1706243 AAATATG-CTGACATGCAAGAT
1 AAATATGTC-AACATGCAAGAT
* *
1706264 -AGTAATGTCAACATGCAACAT
1 AAAT-ATGTCAACATGCAAGAT
1706285 AA
1 AA
1706287 CTACATTGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
20 3 0.08
21 31 0.86
22 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (21 bp):
AAATATGTCAACATGCAAGAT
Found at i:1706521 original size:42 final size:42
Alignment explanation
Indices: 1706421--1706523 Score: 161
Period size: 42 Copynumber: 2.5 Consensus size: 42
1706411 TGATGTATGA
*
1706421 CATGTCGACATAAATAAGTTGCATGTAAACATAAATTAGTTG
1 CATGTCGACATAAATAAGTTGCATGTAAACATAAATAAGTTG
* *
1706463 CATGTCAACATAAATAAGTTGCATGTCAACATAAATAAGTTG
1 CATGTCGACATAAATAAGTTGCATGTAAACATAAATAAGTTG
* *
1706505 CATGTCGACTTCAATAAGT
1 CATGTCGACATAAATAAGT
1706524 AACATCCAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.30
Consensus pattern (42 bp):
CATGTCGACATAAATAAGTTGCATGTAAACATAAATAAGTTG
Found at i:1706523 original size:21 final size:21
Alignment explanation
Indices: 1706421--1706510 Score: 153
Period size: 21 Copynumber: 4.3 Consensus size: 21
1706411 TGATGTATGA
*
1706421 CATGTCGACATAAATAAGTTG
1 CATGTCAACATAAATAAGTTG
* *
1706442 CATGTAAACATAAATTAGTTG
1 CATGTCAACATAAATAAGTTG
1706463 CATGTCAACATAAATAAGTTG
1 CATGTCAACATAAATAAGTTG
1706484 CATGTCAACATAAATAAGTTG
1 CATGTCAACATAAATAAGTTG
1706505 CATGTC
1 CATGTC
1706511 GACTTCAATA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (21 bp):
CATGTCAACATAAATAAGTTG
Found at i:1706634 original size:21 final size:21
Alignment explanation
Indices: 1706598--1706670 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
1706588 ATTGTAATTT
* **
1706598 TCTTGCATGATAACATAGTTA
1 TCTTGCATGTTAACATAACTA
* *
1706619 TGTTGCATGTTGACATAACTA
1 TCTTGCATGTTAACATAACTA
*
1706640 TCTTGCATGTCAACAT-ACTTA
1 TCTTGCATGTTAACATAAC-TA
*
1706661 TCTTACATGT
1 TCTTGCATGT
1706671 CGATATATTT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 2 0.05
21 40 0.95
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (21 bp):
TCTTGCATGTTAACATAACTA
Found at i:1708142 original size:21 final size:20
Alignment explanation
Indices: 1708116--1708173 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
1708106 TTAGAGTATC
1708116 ATTCGTAAACTATAGTTAACG
1 ATTCGT-AACTATAGTTAACG
* **
1708137 ATTCGTTAACTATGGTTTGCG
1 ATTCG-TAACTATAGTTAACG
*
1708158 GTTCGTAACTATAGTT
1 ATTCGTAACTATAGTT
1708174 CAAAATAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 10 0.32
21 20 0.65
22 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGTAACTATAGTTAACG
Found at i:1719223 original size:10 final size:11
Alignment explanation
Indices: 1719198--1719236 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1719188 TTAAGTTCTC
*
1719198 CTTAAAGATAG
1 CTTAAAGGTAG
*
1719209 CTTAAATGT-G
1 CTTAAAGGTAG
1719219 CTTAAAGGTAG
1 CTTAAAGGTAG
1719230 CTTAAAG
1 CTTAAAG
1719237 ACGATCTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (11 bp):
CTTAAAGGTAG
Found at i:1719287 original size:11 final size:11
Alignment explanation
Indices: 1719271--1719323 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
1719261 TATATGTGTT
*
1719271 GCTTAAAGGTA
1 GCTTAAAGATA
1719282 GCTTAAAGATA
1 GCTTAAAGATA
* *
1719293 GCGTAAAGATG
1 GCTTAAAGATA
**
1719304 GCTTAAAGGCA
1 GCTTAAAGATA
1719315 GCTTAAAGA
1 GCTTAAAGA
1719324 CTATCTTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23
Consensus pattern (11 bp):
GCTTAAAGATA
Found at i:1719344 original size:11 final size:11
Alignment explanation
Indices: 1719328--1719356 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1719318 TAAAGACTAT
1719328 CTTTAAGCCAC
1 CTTTAAGCCAC
1719339 CTTTAAGCCAC
1 CTTTAAGCCAC
1719350 CTTTAAG
1 CTTTAAG
1719357 GACAACTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:1719404 original size:11 final size:11
Alignment explanation
Indices: 1719388--1719452 Score: 112
Period size: 11 Copynumber: 5.9 Consensus size: 11
1719378 GTCCAAACTT
1719388 CTTTAAGCCAC
1 CTTTAAGCCAC
*
1719399 CTTTAAGCTAC
1 CTTTAAGCCAC
*
1719410 CTTTAAGCTAC
1 CTTTAAGCCAC
1719421 CTTTAAGCCAC
1 CTTTAAGCCAC
1719432 CTTTAAGCCAC
1 CTTTAAGCCAC
1719443 CTTTAAGCCA
1 CTTTAAGCCA
1719453 TTAATAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 52 1.00
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.31
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:1719570 original size:14 final size:14
Alignment explanation
Indices: 1719551--1719588 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1719541 TTCTAGGAAG
1719551 AAAAAAAAACAAAA
1 AAAAAAAAACAAAA
1719565 AAAAAAAAACAAAA
1 AAAAAAAAACAAAA
*
1719579 CAAAAAAAAC
1 AAAAAAAAAC
1719589 GCCCACGGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAACAAAA
Found at i:1719578 original size:19 final size:18
Alignment explanation
Indices: 1719551--1719587 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
1719541 TTCTAGGAAG
1719551 AAAAAAAAACAAAAAAAA
1 AAAAAAAAACAAAAAAAA
1719569 AAAAACAAAACAAAAAAAA
1 AAAAA-AAAACAAAAAAAA
1719588 CGCCCACGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAAAAACAAAAAAAA
Found at i:1721189 original size:112 final size:112
Alignment explanation
Indices: 1720992--1721205 Score: 401
Period size: 112 Copynumber: 1.9 Consensus size: 112
1720982 AACCCTGACG
* *
1720992 TGCACCTGGGCACACGACACACCTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
1 TGCACCTGGGCACACGAAACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
*
1721057 TTCTTAAGTTGGACAAACAATAGACTTTAATTAGATATACACAAACC
66 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACC
1721104 TGCACCTGGGCACACGAAACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
1 TGCACCTGGGCACACGAAACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
1721169 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATA
66 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATA
1721206 CTTTATTAGT
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 99 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (112 bp):
TGCACCTGGGCACACGAAACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACC
Found at i:1728567 original size:22 final size:22
Alignment explanation
Indices: 1728533--1728586 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
1728523 CAAACGTTAC
* * *
1728533 GCCAACGTCGAACTAATATTGG
1 GCCAACGTTGAACTAACATTAG
* *
1728555 GTCAACGTTGAACTCACATTAG
1 GCCAACGTTGAACTAACATTAG
1728577 GCCAACGTTG
1 GCCAACGTTG
1728587 GACCAATGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (22 bp):
GCCAACGTTGAACTAACATTAG
Found at i:1730083 original size:7 final size:7
Alignment explanation
Indices: 1730071--1730100 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1730061 AGAAAACTTC
1730071 ATTAATT
1 ATTAATT
1730078 ATTAATT
1 ATTAATT
*
1730085 ATTAAGT
1 ATTAATT
1730092 ATTAATT
1 ATTAATT
1730099 AT
1 AT
1730101 ATAAACCTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (7 bp):
ATTAATT
Done.