Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold23
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3125668
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 362582 characters in sequence are not A, C, G, or T
File 11 of 18
Found at i:1561244 original size:52 final size:53
Alignment explanation
Indices: 1561159--1561328 Score: 172
Period size: 52 Copynumber: 3.3 Consensus size: 53
1561149 TTATTTCTGA
* * * *
1561159 GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAATTTTTCCATAATC
* * * * *
1561211 GGGGATACTTCAA-TCCTGGTTTTATTTTC-AAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAATTTTTCC-ATAATC
*
1561263 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CATAATC
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCCATAATC
*
1561315 GAGGATACTCCAAC
1 GGGGATACTCCAAC
1561329 CTCGTTATTT
Statistics
Matches: 98, Mismatches: 13, Indels: 14
0.78 0.10 0.11
Matches are distributed among these distances:
51 9 0.09
52 71 0.72
53 13 0.13
54 5 0.05
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (53 bp):
GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCCATAATC
Found at i:1561348 original size:28 final size:28
Alignment explanation
Indices: 1561312--1561388 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
1561302 ATTTTTCATA
* * *
1561312 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
1561340 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
1561368 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1561389 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:1561362 original size:212 final size:212
Alignment explanation
Indices: 1560988--1561395 Score: 590
Period size: 212 Copynumber: 1.9 Consensus size: 212
1560978 TTATCAATTC
* *
1560988 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATTGGGGA
1 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
1561053 TACTCTAACTCCGATTTTATTTCCAAAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAAC
66 TACTCCAACTCCGATTTTATTTCC--AAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* * * *
1561118 CCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACTCCGGTTTTA
129 CCCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTA
1561183 TCGCTAAAACACTAATTTT
194 TCGCTAAAACACTAATTTT
* * * *
1561202 TCCACAATCGGGGATACTT-CAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGG
1 TCCACAATCGAGGATA-TTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGG
* *
1561265 GGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCATAATCGAGGATACTCCAA
63 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
* *
1561328 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTT
128 CCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTT
1561393 TAT
192 TAT
1561396 TCCCAAAATA
Statistics
Matches: 174, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
211 27 0.16
212 67 0.39
213 3 0.02
214 41 0.24
215 36 0.21
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (212 bp):
TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
GCTAAAACACTAATTTT
Found at i:1561460 original size:107 final size:108
Alignment explanation
Indices: 1561263--1561470 Score: 240
Period size: 107 Copynumber: 1.9 Consensus size: 108
1561253 TCCTTTAATC
* * *
1561263 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCATAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCATAATCGAGGATACTCCAA
* * * * *
1561328 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCCATTATTTCATAGGGAACACTCCAACCCCGTTACTTCCGA
* * *** * * *
1561371 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAG
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCATAATCGAGGATACTCCAA
*
1561435 CCCCATTATTTTCA-AGGGAACACTCCAACCCTGTTA
66 CCCCATTA-TTTCATAGGGAACACTCCAACCCCGTTA
1561471 TTATCTCCAA
Statistics
Matches: 82, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
107 56 0.68
108 26 0.32
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (108 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCATAATCGAGGATACTCCAA
CCCCATTATTTCATAGGGAACACTCCAACCCCGTTACTTCCGA
Found at i:1562581 original size:20 final size:20
Alignment explanation
Indices: 1562556--1562613 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
1562546 CTGCCAGTTT
*
1562556 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTA
* *
1562576 CATGTATTGATACAA-TGAA
1 CATGTATCGATACAATTGTA
1562595 CATGTATCGATAC-ATTGTA
1 CATGTATCGATACAATTGTA
1562614 TCGATACAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 1 0.03
19 17 0.53
20 14 0.44
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:1562615 original size:13 final size:13
Alignment explanation
Indices: 1562597--1562621 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1562587 ACAATGAACA
1562597 TGTATCGATACAT
1 TGTATCGATACAT
1562610 TGTATCGATACA
1 TGTATCGATACA
1562622 AAACATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1563305 original size:25 final size:25
Alignment explanation
Indices: 1563255--1563319 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
1563245 TTAATACTTT
1563255 AAAT-ACATGAAGAAATAACACGAAAA
1 AAATAACATGAA-AAATAACAC-AAAA
* * *
1563281 TAA-AATATGAAAAATAACATAAAA
1 AAATAACATGAAAAATAACACAAAA
1563305 AAATAACATGAAAAA
1 AAATAACATGAAAAA
1563320 ACTATAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 6 0.19
25 18 0.56
26 8 0.25
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (25 bp):
AAATAACATGAAAAATAACACAAAA
Found at i:1563326 original size:16 final size:13
Alignment explanation
Indices: 1563290--1563320 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
1563280 ATAAAATATG
1563290 AAAAATAACATAA
1 AAAAATAACATAA
1563303 AAAAATAACATGAA
1 AAAAATAACAT-AA
1563317 AAAA
1 AAAA
1563321 CTATAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.13
Consensus pattern (13 bp):
AAAAATAACATAA
Found at i:1566204 original size:3 final size:3
Alignment explanation
Indices: 1566198--1566233 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1566188 AAGCACTATC
1566198 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1566234 TATAAAGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1566310 original size:16 final size:16
Alignment explanation
Indices: 1566285--1566427 Score: 91
Period size: 16 Copynumber: 9.2 Consensus size: 16
1566275 ATATGTTTTA
1566285 AAATATAAAATTATTT
1 AAATATAAAATTATTT
* *
1566301 AAATA-AAAA-AATTA
1 AAATATAAAATTATTT
*
1566315 AAATTTAAAATTATTT
1 AAATATAAAATTATTT
* * * *
1566331 AAATTTTAAA-TAATA
1 AAATATAAAATTATTT
* *
1566346 AAAAATTAAAA--ATTC
1 AAATA-TAAAATTATTT
* *
1566361 AAATTTAATATTATTT
1 AAATATAAAATTATTT
*
1566377 -AATATCAAAATAATTT
1 AAATAT-AAAATTATTT
*
1566393 AAATATAAAATAATTT
1 AAATATAAAATTATTT
* *
1566409 AAATTTAAAATAATTT
1 AAATATAAAATTATTT
1566425 AAA
1 AAA
1566428 CTCAATCTCA
Statistics
Matches: 99, Mismatches: 21, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
14 11 0.11
15 23 0.23
16 60 0.61
17 5 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATATAAAATTATTT
Found at i:1570480 original size:22 final size:22
Alignment explanation
Indices: 1570438--1570480 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1570428 AAAGTTGTAC
*
1570438 GTAGTTAAATTTATTTTTTTAA
1 GTAGTTAAATTTATATTTTTAA
1570460 GTAGTTAAA-TTATGATTTTTA
1 GTAGTTAAATTTAT-ATTTTTA
1570481 GATACATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (22 bp):
GTAGTTAAATTTATATTTTTAA
Found at i:1571048 original size:38 final size:37
Alignment explanation
Indices: 1570994--1571102 Score: 137
Period size: 38 Copynumber: 2.9 Consensus size: 37
1570984 TCAAACTATG
* * *
1570994 CCACCGGTTAAAAATAGTGATTTTTGTACTGAACCGTA
1 CCACCGGATAAAAATAGT-ATTTTTGTAATGAACCATA
* *
1571032 CCACCGGATAAGAATAGTATTTTTTGTAATGGACCATA
1 CCACCGGATAAAAATAGTA-TTTTTGTAATGAACCATA
* *
1571070 CCACCGAATAAAAATAGTAATTTTGTAATGAAC
1 CCACCGGATAAAAATAGTATTTTTGTAATGAAC
1571103 TGTGCTATCA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
37 13 0.21
38 48 0.79
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (37 bp):
CCACCGGATAAAAATAGTATTTTTGTAATGAACCATA
Found at i:1572488 original size:38 final size:38
Alignment explanation
Indices: 1572371--1572491 Score: 154
Period size: 38 Copynumber: 3.2 Consensus size: 38
1572361 ATCGATTTCA
* * * *
1572371 AACCATGCCACTAGTTAAGAATAGT-AGTTTTTGTATTG
1 AACCGTGCCACCAGATAAGAATAGTGA-TTTTTGTAATG
**
1572409 AACTATGCCACCAGATAAGAATAGTGATTTTTGTAATG
1 AACCGTGCCACCAGATAAGAATAGTGATTTTTGTAATG
* *
1572447 AACCGTGCCACCGGATAAGAGTAGTGATTTTTGTAATG
1 AACCGTGCCACCAGATAAGAATAGTGATTTTTGTAATG
1572485 AACCGTG
1 AACCGTG
1572492 TCATCGGTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 73 0.99
39 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (38 bp):
AACCGTGCCACCAGATAAGAATAGTGATTTTTGTAATG
Found at i:1572515 original size:38 final size:38
Alignment explanation
Indices: 1572386--1572534 Score: 151
Period size: 38 Copynumber: 3.9 Consensus size: 38
1572376 TGCCACTAGT
* ** *
1572386 TAAGAATAGT-AGTTTTTGTATTGAACTATGCCACCAGA
1 TAAGAATAGTGA-TTTTTGTAATGAACCGTGCCACCGGA
1572424 TAAGAATAGTGATTTTTGTAATGAACCGTGCCACCGGA
1 TAAGAATAGTGATTTTTGTAATGAACCGTGCCACCGGA
* * * *
1572462 TAAGAGTAGTGATTTTTGTAATGAACCGTGTCATCGGTT
1 TAAGAATAGTGATTTTTGTAATGAACCGTGCCACCGG-A
* * *
1572501 TAA-AATAGTAATTTTTAT-TTCGAACCGTGCCACC
1 TAAGAATAGTGATTTTTGTAAT-GAACCGTGCCACC
1572535 AGTTTAGAAT
Statistics
Matches: 94, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
37 1 0.01
38 89 0.95
39 4 0.04
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (38 bp):
TAAGAATAGTGATTTTTGTAATGAACCGTGCCACCGGA
Found at i:1572540 original size:38 final size:38
Alignment explanation
Indices: 1572484--1572592 Score: 128
Period size: 38 Copynumber: 2.9 Consensus size: 38
1572474 TTTTTGTAAT
* *
1572484 GAACCGTGTCATCGGTTTAAAATAGTAATTTTTATTTC
1 GAACCGTGCCACCGGTTTAAAATAGTAATTTTTATTTC
* * * *
1572522 GAACCGTGCCACCAGTTTAGAATAGTAGTTTTCATTTC
1 GAACCGTGCCACCGGTTTAAAATAGTAATTTTTATTTC
** * *
1572560 GAACTATGCTACCGGTTTAAAATAGTGATTTTT
1 GAACCGTGCCACCGGTTTAAAATAGTAATTTTT
1572593 GTTCATAGCT
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (38 bp):
GAACCGTGCCACCGGTTTAAAATAGTAATTTTTATTTC
Found at i:1575078 original size:13 final size:13
Alignment explanation
Indices: 1575060--1575085 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1575050 CAATTTTTTG
1575060 TGTATCGATACAT
1 TGTATCGATACAT
1575073 TGTATCGATACAT
1 TGTATCGATACAT
1575086 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1575825 original size:21 final size:21
Alignment explanation
Indices: 1575784--1575827 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1575774 CTCTCCTTTA
* *
1575784 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1575805 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1575826 TC
1 TC
1575828 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1577649 original size:13 final size:13
Alignment explanation
Indices: 1577631--1577669 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1577621 ATAATCACCC
1577631 TGTATCGATACAA
1 TGTATCGATACAA
1577644 TGTATCGATACAA
1 TGTATCGATACAA
1577657 TGTATCGATACAA
1 TGTATCGATACAA
1577670 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1579745 original size:15 final size:15
Alignment explanation
Indices: 1579725--1579755 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1579715 ATTTCGTTTG
*
1579725 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1579740 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1579755 G
1 G
1579756 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1581588 original size:21 final size:20
Alignment explanation
Indices: 1581559--1581602 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1581549 AAGTTTTCAT
*
1581559 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTC-TTA
1581579 TTTTCATTAGCCAACTTCTTA
1 TTTTC-TTAGCCAACTTCTTA
1581600 TTT
1 TTT
1581603 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 14 0.67
22 2 0.10
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.52
Consensus pattern (20 bp):
TTTTCTTAGCCAACTTCTTA
Found at i:1583838 original size:13 final size:13
Alignment explanation
Indices: 1583820--1583845 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1583810 CAATTTTTTG
1583820 TGTATCGATACAT
1 TGTATCGATACAT
1583833 TGTATCGATACAT
1 TGTATCGATACAT
1583846 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1584312 original size:21 final size:20
Alignment explanation
Indices: 1584262--1584320 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
1584252 CAATATAATA
1584262 AGGT-AATGTATCGATACAT
1 AGGTGAATGTATCGATACAT
*
1584281 AGGTGAATGTATTGATACAT
1 AGGTGAATGTATCGATACAT
**
1584301 ATTTGAAATGTATCGATACA
1 AGGTG-AATGTATCGATACA
1584321 GAACCATGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.12
20 17 0.50
21 13 0.38
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.34
Consensus pattern (20 bp):
AGGTGAATGTATCGATACAT
Found at i:1584448 original size:51 final size:52
Alignment explanation
Indices: 1584356--1584494 Score: 183
Period size: 53 Copynumber: 2.7 Consensus size: 52
1584346 TCTAGAATGA
* *
1584356 AAATGTATTGATACATT-TTCATTGTATCGATACATTCTAGG-TTTTAACCC
1 AAATGTATCGATACATTCTTCAATGTATCGATACATTCTAGGTTTTTAACCC
* * * *
1584406 AAATGTATCGATACATTCTTCACTATATCGATACATTTTAGGTTTTTTTACCC
1 AAATGTATCGATACATTCTTCAATGTATCGATACATTCTAGG-TTTTTAACCC
* *
1584459 AAATTTATCGATACATTCTTCAATGTATCAATACAT
1 AAATGTATCGATACATTCTTCAATGTATCGATACAT
1584495 ACAAGCAAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
50 16 0.21
51 21 0.27
53 40 0.52
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (52 bp):
AAATGTATCGATACATTCTTCAATGTATCGATACATTCTAGGTTTTTAACCC
Found at i:1588009 original size:15 final size:16
Alignment explanation
Indices: 1587975--1588008 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1587965 TCAAGTCAAA
*
1587975 TTTGTTTTGATCATTT
1 TTTGTTTAGATCATTT
*
1587991 TTTGTTTAGATTATTT
1 TTTGTTTAGATCATTT
1588007 TT
1 TT
1588009 GATTTTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.03, G:0.12, T:0.71
Consensus pattern (16 bp):
TTTGTTTAGATCATTT
Found at i:1590589 original size:14 final size:15
Alignment explanation
Indices: 1590559--1590598 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
1590549 TAAAATTATT
1590559 ATTTTATATTATTTAC
1 ATTTTA-ATTATTTAC
1590575 ATTTTAATT-TTTAC
1 ATTTTAATTATTTAC
1590589 ATTTTAATTA
1 ATTTTAATTA
1590599 AAAATTAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.61
15 3 0.13
16 6 0.26
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTAATTATTTAC
Found at i:1590767 original size:16 final size:15
Alignment explanation
Indices: 1590732--1590794 Score: 56
Period size: 16 Copynumber: 4.0 Consensus size: 15
1590722 GTTCAAGTTA
* *
1590732 TTTTAGACTTAGATT
1 TTTTAGATTTAAATT
1590747 ATTTTAGATTTAAATCT
1 -TTTTAGATTTAAAT-T
1590764 TTTT-GAATTTAAAGTT
1 TTTTAG-ATTTAAA-TT
*
1590780 TTTTAAATTTAAATT
1 TTTTAGATTTAAATT
1590795 ATCTTTTAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
15 3 0.08
16 35 0.88
17 2 0.05
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (15 bp):
TTTTAGATTTAAATT
Found at i:1590842 original size:17 final size:16
Alignment explanation
Indices: 1590805--1590839 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1590795 ATCTTTTAAG
*
1590805 TTTAAACTATTTTGAT
1 TTTAAAATATTTTGAT
*
1590821 TTTAAAATATTTTTAT
1 TTTAAAATATTTTGAT
1590837 TTT
1 TTT
1590840 TAATCAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (16 bp):
TTTAAAATATTTTGAT
Found at i:1591782 original size:23 final size:22
Alignment explanation
Indices: 1591756--1591807 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1591746 TAGGTTATAT
*
1591756 ATATGTTTAAAAATAAATATTAA
1 ATATATTT-AAAATAAATATTAA
*
1591779 ATATATTTAAAATTAATATT--
1 ATATATTTAAAATAAATATTAA
1591799 ATATATTTA
1 ATATATTTA
1591808 CATTTATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 9 0.33
22 11 0.41
23 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
ATATATTTAAAATAAATATTAA
Found at i:1591899 original size:12 final size:12
Alignment explanation
Indices: 1591878--1591928 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
1591868 CTTAATCATA
1591878 TTTT-ATATTAT
1 TTTTAATATTAT
1591889 TTTTAATATTAT
1 TTTTAATATTAT
* *
1591901 TCTAAATATTAT
1 TTTTAATATTAT
*
1591913 TTTTAAATATAAT
1 TTTT-AATATTAT
1591926 TTT
1 TTT
1591929 ATTTTAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
11 4 0.12
12 19 0.58
13 10 0.30
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTTAATATTAT
Found at i:1592400 original size:15 final size:15
Alignment explanation
Indices: 1592361--1592435 Score: 69
Period size: 15 Copynumber: 4.8 Consensus size: 15
1592351 TTTGGATAGA
* *
1592361 TTTAAATTTGAATTT
1 TTTAGATTTAAATTT
*
1592376 ATTCAGATTTAAATTT
1 -TTTAGATTTAAATTT
*
1592392 TTTAGATTTAATTTT
1 TTTAGATTTAAATTT
* *
1592407 TTTTGAGTTTGAAGTTT
1 TTTAGA-TTT-AAATTT
1592424 TTTAGATTTAAA
1 TTTAGATTTAAA
1592436 CTTATTGGGG
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
15 20 0.42
16 18 0.38
17 10 0.21
ACGTcount: A:0.31, C:0.01, G:0.11, T:0.57
Consensus pattern (15 bp):
TTTAGATTTAAATTT
Found at i:1592689 original size:20 final size:18
Alignment explanation
Indices: 1592662--1592700 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1592652 TGAAATCTAT
1592662 ATTTA-TATATAAAATTA
1 ATTTATTATATAAAATTA
1592679 ATTTATTATATAAAATTA
1 ATTTATTATATAAAATTA
1592697 ATTT
1 ATTT
1592701 TTTAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTATTATATAAAATTA
Found at i:1592709 original size:18 final size:18
Alignment explanation
Indices: 1592670--1592709 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1592660 ATATTTATAT
*
1592670 ATAAAATTAATTTATTAT
1 ATAAAATTAATTTATTAA
*
1592688 ATAAAATTAATTTTTTAA
1 ATAAAATTAATTTATTAA
1592706 ATAA
1 ATAA
1592710 TTTATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAAAATTAATTTATTAA
Found at i:1593929 original size:16 final size:15
Alignment explanation
Indices: 1593902--1593931 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1593892 ATGTTAACTT
1593902 TATATTCTATTCTAC
1 TATATTCTATTCTAC
1593917 TATATTGCTATTCTA
1 TATATT-CTATTCTA
1593932 AGTATAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.17, G:0.03, T:0.53
Consensus pattern (15 bp):
TATATTCTATTCTAC
Found at i:1594474 original size:16 final size:16
Alignment explanation
Indices: 1594404--1594477 Score: 103
Period size: 16 Copynumber: 4.6 Consensus size: 16
1594394 GTCAGTCTCG
*
1594404 AATTTAAATTCTTTCA
1 AATTCAAATTCTTTCA
*
1594420 AATTCAGATTCTTTCA
1 AATTCAAATTCTTTCA
*
1594436 AATTCGAATTCTTTCA
1 AATTCAAATTCTTTCA
* *
1594452 AATTCAAATTTTTTTA
1 AATTCAAATTCTTTCA
1594468 AATTCAAATT
1 AATTCAAATT
1594478 ATCTTAAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (16 bp):
AATTCAAATTCTTTCA
Found at i:1594484 original size:16 final size:16
Alignment explanation
Indices: 1594451--1594487 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1594441 GAATTCTTTC
* *
1594451 AAATTCAAATTTTTTT
1 AAATTCAAATTATCTT
1594467 AAATTCAAATTATCTT
1 AAATTCAAATTATCTT
1594483 AAATT
1 AAATT
1594488 TTTAACTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATTCAAATTATCTT
Found at i:1594487 original size:32 final size:32
Alignment explanation
Indices: 1594417--1594487 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
1594407 TTAAATTCTT
* * * *
1594417 TCAAATTCAGATTCTTTCAAATTCGAATTCTT
1 TCAAATTCAAATTCTTTCAAATTCAAATTATC
* *
1594449 TCAAATTCAAATTTTTTTAAATTCAAATTATC
1 TCAAATTCAAATTCTTTCAAATTCAAATTATC
*
1594481 TTAAATT
1 TCAAATT
1594488 TTTAACTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (32 bp):
TCAAATTCAAATTCTTTCAAATTCAAATTATC
Found at i:1594523 original size:6 final size:6
Alignment explanation
Indices: 1594501--1594542 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
1594491 AACTTTTTAA
* *
1594501 TTAAA- TTAAAT TT-AAT TCAAAT TTAAAT GTAAAT TTAAAT TT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT
1594543 TTTTAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
5 9 0.29
6 22 0.71
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:1595111 original size:15 final size:16
Alignment explanation
Indices: 1595078--1595115 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1595068 AATATTTAGT
1595078 TTATAATTTTATTTGA
1 TTATAATTTTATTTGA
*
1595094 TTATATTTTTATTT-A
1 TTATAATTTTATTTGA
1595109 TTA-AATT
1 TTATAATT
1595116 AATATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 3 0.15
15 4 0.20
16 13 0.65
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
TTATAATTTTATTTGA
Found at i:1598386 original size:16 final size:16
Alignment explanation
Indices: 1598348--1598386 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1598338 CAAATAGGAT
*
1598348 TATTTTTAGATTTGGA
1 TATTTTTAGATTTAGA
* *
1598364 TAATTTTAGGTTTAGA
1 TATTTTTAGATTTAGA
1598380 TATTTTT
1 TATTTTT
1598387 GAATTCAGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (16 bp):
TATTTTTAGATTTAGA
Found at i:1599622 original size:103 final size:104
Alignment explanation
Indices: 1599513--1599708 Score: 304
Period size: 104 Copynumber: 1.9 Consensus size: 104
1599503 ATTTTTTTGA
*
1599513 AAGGATTTCTCTAAATTTATAATTTTCAAAA-TTCTTCAAATATTATTGTTTAATTCATATTAAA
1 AAGGATTTCTCTAAATTTATAATTTTCAAAATTTCTTCAAATATTACTGTTTAATTCATATTAAA
* * *
1599577 TCAGTTTTGAAAATTTTAATTCATTTTAAATTTTCCAAT
66 TCAGTATTAAAAAATTTAATTCATTTTAAATTTTCCAAT
* * * *
1599616 AAGGATTTTTCTAAATTTATAATTTTTAAAATTTTTTTAAATATTACTGTTTAATTCATATTAAA
1 AAGGATTTCTCTAAATTTATAATTTTCAAAATTTCTTCAAATATTACTGTTTAATTCATATTAAA
*
1599681 TTAGTATTAAAAAATTTAATTCATTTTA
66 TCAGTATTAAAAAATTTAATTCATTTTA
1599709 TAAGTTTTAG
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
103 29 0.35
104 54 0.65
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (104 bp):
AAGGATTTCTCTAAATTTATAATTTTCAAAATTTCTTCAAATATTACTGTTTAATTCATATTAAA
TCAGTATTAAAAAATTTAATTCATTTTAAATTTTCCAAT
Found at i:1599802 original size:257 final size:257
Alignment explanation
Indices: 1599362--1599846 Score: 679
Period size: 257 Copynumber: 1.9 Consensus size: 257
1599352 TCTTTGAGAA
* * *
1599362 GATTTTTCTAAATTTATAATTTTCAAAATTTATCAAATATTATTATTTAATTTATGTTAAATCAG
1 GATTTTTCTAAATTTATAATTTTCAAAATTTATCAAATATTACTATTTAATTCATATTAAATCAG
* * *
1599427 TTTGAAAAAATTCAATTCATTTTATGAGTTTTAAAATTTTTTCTATTACCGAAATATGAAGTTTT
66 TTTGAAAAAATTCAATTCATTTTATAAGTTTTAAAATTTTTTCTATTACCAAAATACGAAGTTTT
* * ** *
1599492 TTACTCCGTAAATTTTTTTGAAAGGATTTCTCTAAATTTATAATTTTCAAAATTCT-TCAAATAT
131 CTACTCCATAAATTTTTCCGAAAGGATTTCTCTAAATTTATAATTTCCAAAATT-TATCAAATAT
*
1599556 TATTGTTTAATTCATATTAAATCAGTTTTGAAAATTTTAATTCATTTTAAATTTTCCAATAAG
195 TATTGTCTAATTCATATTAAATCAGTTTTGAAAATTTTAATTCATTTTAAATTTTCCAATAAG
* * * * *
1599619 GATTTTTCTAAATTTATAATTTTTAAAATTTTTTTAAATATTACTGTTTAATTCATATTAAATTA
1 GATTTTTCTAAATTTATAATTTTCAAAA-TTTATCAAATATTACTATTTAATTCATATTAAATCA
* * * * *
1599684 GTATT-AAAAAATTTAATTCATTTTATAAGTTTTAGAA-TTTTTCTGTTACCAAAATGCGGAGTT
65 GT-TTGAAAAAATTCAATTCATTTTATAAGTTTTAAAATTTTTTCTATTACCAAAATACGAAGTT
* * *
1599747 TTCTACTTCATAAATTTTTCCGGAAGGATTTTTCTAAATTTATAATTTCCAAAATTTATCAAATA
129 TTCTACTCCATAAATTTTTCCGAAAGGATTTCTCTAAATTTATAATTTCCAAAATTTATCAAATA
* *
1599812 TTATTGTCTAATTCGTATTAAATTAGTTTTGAAAA
194 TTATTGTCTAATTCATATTAAATCAGTTTTGAAAA
1599847 AAATCAATTT
Statistics
Matches: 198, Mismatches: 27, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
256 1 0.01
257 135 0.68
258 60 0.30
259 2 0.01
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.48
Consensus pattern (257 bp):
GATTTTTCTAAATTTATAATTTTCAAAATTTATCAAATATTACTATTTAATTCATATTAAATCAG
TTTGAAAAAATTCAATTCATTTTATAAGTTTTAAAATTTTTTCTATTACCAAAATACGAAGTTTT
CTACTCCATAAATTTTTCCGAAAGGATTTCTCTAAATTTATAATTTCCAAAATTTATCAAATATT
ATTGTCTAATTCATATTAAATCAGTTTTGAAAATTTTAATTCATTTTAAATTTTCCAATAAG
Found at i:1600034 original size:155 final size:155
Alignment explanation
Indices: 1599743--1600021 Score: 350
Period size: 155 Copynumber: 1.8 Consensus size: 155
1599733 CAAAATGCGG
* * *
1599743 AGTTTTCTACTTCATAAATTTTTCCGGAAGGATTTTTCTAAATTTATAATTTCCAAAATTTATCA
1 AGTTTTCTACTACATAAATTTTTCCGGAAGGATTTTTCTAAATTTACAATTTCCAAAATTCATCA
* * *
1599808 AATATTATTGTCTAATTCGTATTAAATTAGTTTTGAAAAAAATCAATTTACTTTATGAGTTCTAA
66 AATATTATTATCTAATTCATAGTAAATTAGTTTTGAAAAAAATCAATTTACTTTATGAGTTCTAA
1599873 AATTTTTTCAATTTTTAAGATACGA
131 AATTTTTTCAATTTTTAAGATACGA
* ** * * * **
1599898 AGTTTTCTACTACATAAATTTCTT-TGGTTGTATTTTTCTTAGTTTACAATTTTTAAAATTCATC
1 AGTTTTCTACTACATAAATTT-TTCCGGAAGGATTTTTCTAAATTTACAATTTCCAAAATTCATC
* * * *
1599962 AAATATTTTTAT-TAAATTCATAGT-AATTAG-TTTGTAAAAATTCAATTTATTTTATGAGTT
65 AAATATTATTATCT-AATTCATAGTAAATTAGTTTTGAAAAAAATCAATTTACTTTATGAGTT
1600022 TTGCAGTTTT
Statistics
Matches: 104, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
153 27 0.26
154 7 0.07
155 68 0.65
156 2 0.02
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.48
Consensus pattern (155 bp):
AGTTTTCTACTACATAAATTTTTCCGGAAGGATTTTTCTAAATTTACAATTTCCAAAATTCATCA
AATATTATTATCTAATTCATAGTAAATTAGTTTTGAAAAAAATCAATTTACTTTATGAGTTCTAA
AATTTTTTCAATTTTTAAGATACGA
Found at i:1603833 original size:20 final size:19
Alignment explanation
Indices: 1603799--1603837 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1603789 AATTGTATCG
1603799 ATACAAATATATCAATACA
1 ATACAAATATATCAATACA
*
1603818 ATACACAATGTATCAATACA
1 ATACA-AATATATCAATACA
1603838 TCTAAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.54, C:0.18, G:0.03, T:0.26
Consensus pattern (19 bp):
ATACAAATATATCAATACA
Found at i:1603847 original size:20 final size:19
Alignment explanation
Indices: 1603824--1603861 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1603814 TACAATACAC
1603824 AATGTATCAATACATCTAAA
1 AATGTATCAATAC-TCTAAA
*
1603844 AATGTTTCAATACTCTAA
1 AATGTATCAATACTCTAA
1603862 GCTATAACGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (19 bp):
AATGTATCAATACTCTAAA
Found at i:1606497 original size:2 final size:2
Alignment explanation
Indices: 1606485--1606515 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1606475 CAAGTTATCT
*
1606485 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1606516 GAATATCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1607316 original size:24 final size:24
Alignment explanation
Indices: 1607282--1607340 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
1607272 GTTATATGAA
*
1607282 TAAAA-ATAATATTAAAAA-ATAAT
1 TAAAATATAATA-TAAAAATAAAAT
1607305 TAAAATATAATATAAAAATAAAAT
1 TAAAATATAATATAAAAATAAAAT
* *
1607329 AAAAATAAAATA
1 TAAAATATAATA
1607341 AATATATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 11 0.35
24 20 0.65
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (24 bp):
TAAAATATAATATAAAAATAAAAT
Found at i:1607321 original size:22 final size:22
Alignment explanation
Indices: 1607280--1607352 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
1607270 TAGTTATATG
1607280 AATAAAAATAATATTAAAAA-ATA
1 AATAAAAATAATA-TAAAAATA-A
*
1607303 ATTAAAATATAATATAAAAATAA
1 AATAAAA-ATAATATAAAAATAA
* *
1607326 AATAAAAATAAAATAAATATATA
1 AATAAAAATAATATAAAAATA-A
1607349 AATA
1 AATA
1607353 TATTAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
22 12 0.28
23 24 0.56
24 7 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
AATAAAAATAATATAAAAATAA
Found at i:1607325 original size:11 final size:11
Alignment explanation
Indices: 1607281--1607342 Score: 72
Period size: 11 Copynumber: 5.5 Consensus size: 11
1607271 AGTTATATGA
1607281 ATAAAAATAAT
1 ATAAAAATAAT
1607292 ATTAAAAAATAAT
1 A-T-AAAAATAAT
1607305 -TAAAATATAAT
1 ATAAAA-ATAAT
*
1607316 ATAAAAATAAA
1 ATAAAAATAAT
*
1607327 ATAAAAATAAA
1 ATAAAAATAAT
1607338 ATAAA
1 ATAAA
1607343 TATATAAATA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
10 4 0.09
11 27 0.59
12 6 0.13
13 9 0.20
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:1607530 original size:20 final size:20
Alignment explanation
Indices: 1607484--1607547 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 20
1607474 TAATATTATT
1607484 ATAATATAA-AAATAT-AAA
1 ATAATATAATAAATATAAAA
*
1607502 AT-ATTTAATAAATATAAAA
1 ATAATATAATAAATATAAAA
1607521 ATAATATAAT--A-ATAAAA
1 ATAATATAATAAATATAAAA
1607538 ATAAT-TAATA
1 ATAATATAATA
1607548 CAGTAAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 4 0.10
17 16 0.40
18 9 0.22
19 5 0.12
20 6 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATATAATAAATATAAAA
Found at i:1607554 original size:18 final size:16
Alignment explanation
Indices: 1607515--1607562 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 16
1607505 TTTAATAAAT
1607515 ATAAAAATAATATAATA
1 ATAAAAATAAT-TAATA
1607532 ATAAAAATAATTAATA
1 ATAAAAATAATTAATA
*
1607548 CAGTAAATATAATTA
1 -A-TAAAAATAATTA
1607563 TGTTCACATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 5 0.18
17 12 0.43
18 11 0.39
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (16 bp):
ATAAAAATAATTAATA
Found at i:1607893 original size:6 final size:6
Alignment explanation
Indices: 1607882--1607928 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
1607872 GGGATCGGTA
* *
1607882 TCATCG TCATCG TCATCT TCATCT TCATCT TCATCT TCATCT TCATC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATC
1607929 GTCTTTCTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.17, C:0.34, G:0.04, T:0.45
Consensus pattern (6 bp):
TCATCT
Found at i:1615292 original size:2 final size:2
Alignment explanation
Indices: 1615285--1615314 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1615275 TAAGTACATG
1615285 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
1615315 CAATACAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1617499 original size:26 final size:22
Alignment explanation
Indices: 1617435--1617489 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1617425 TGTTTTCTTC
***
1617435 AGTGTTGTTAATGCATGCGCTT
1 AGTGTTGTTAATGCACATGCTT
1617457 AGTGTTGTTAATGCACATGCTT
1 AGTGTTGTTAATGCACATGCTT
1617479 AGTGTTGTTAA
1 AGTGTTGTTAA
1617490 GGGATGCACA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (22 bp):
AGTGTTGTTAATGCACATGCTT
Found at i:1636865 original size:23 final size:24
Alignment explanation
Indices: 1636820--1636876 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
1636810 ATAATAATTG
1636820 TATATTATA-AAAATATTTATATT
1 TATATTATATAAAATATTTATATT
* *
1636843 TATATTATATAATAT-TTTTTATT
1 TATATTATATAAAATATTTATATT
*
1636866 TTTATT-TATAA
1 TATATTATATAA
1636877 GTTAGATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.17
23 21 0.70
24 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATATTATATAAAATATTTATATT
Found at i:1636915 original size:18 final size:17
Alignment explanation
Indices: 1636886--1636920 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1636876 AGTTAGATAA
*
1636886 AAATTTATTAATTAAAT
1 AAATTTATTAATAAAAT
1636903 AAATTTAATTAATAAAAT
1 AAATTT-ATTAATAAAAT
1636921 TTTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTTATTAATAAAAT
Found at i:1637330 original size:16 final size:16
Alignment explanation
Indices: 1637311--1637362 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
1637301 ATTGTACTGT
1637311 TTTTAAATTTTAATTA
1 TTTTAAATTTTAATTA
*
1637327 TTTTATATTTTAATTA
1 TTTTAAATTTTAATTA
1637343 ---TAAATTTT--TTA
1 TTTTAAATTTTAATTA
1637354 TTTTAAATT
1 TTTTAAATT
1637363 ATTTTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
11 3 0.10
13 7 0.23
14 6 0.19
16 15 0.48
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAAATTTTAATTA
Found at i:1637355 original size:20 final size:21
Alignment explanation
Indices: 1637311--1637364 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
1637301 ATTGTACTGT
*
1637311 TTTTAAATTTTAATTATTTTATA
1 TTTTAAATTATAA--ATTTTATA
*
1637334 TTTT-AATTATAAATTTTTTA
1 TTTTAAATTATAAATTTTATA
1637354 TTTTAAATTAT
1 TTTTAAATTAT
1637365 TTTATATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 11 0.39
21 6 0.21
22 7 0.25
23 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTAAATTATAAATTTTATA
Found at i:1637367 original size:15 final size:15
Alignment explanation
Indices: 1637332--1637374 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
1637322 AATTATTTTA
*
1637332 TATTTTAATTATAAAT
1 TATTTT-ATTTTAAAT
1637348 T-TTTTATTTTAAAT
1 TATTTTATTTTAAAT
1637362 TATTTTATATTTA
1 TATTTTAT-TTTA
1637375 TATCAGTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 9 0.38
15 10 0.42
16 5 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTTATTTTAAAT
Found at i:1637590 original size:24 final size:24
Alignment explanation
Indices: 1637553--1637599 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1637543 TATTAATACA
1637553 TTATATTTAATATTATTTATAATTT
1 TTATATTTAATATTATTTA-AATTT
1637578 TTAT-TTTAATATTATTTAAATT
1 TTATATTTAATATTATTTAAATT
1637600 CAAATAAGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 4 0.18
24 14 0.64
25 4 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTATATTTAATATTATTTAAATTT
Found at i:1637786 original size:5 final size:5
Alignment explanation
Indices: 1637770--1637812 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
1637760 ATTTTTTAAT
*
1637770 AAATA AACTA AAATA AATATA AAATA ATAAT- AAATA AAATA AA
1 AAATA AAATA AAATA AA-ATA AAATA A-AATA AAATA AAATA AA
1637813 TATTAATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.09
5 22 0.67
6 8 0.24
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:1637795 original size:21 final size:20
Alignment explanation
Indices: 1637780--1637821 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1637770 AAATAAACTA
1637780 AAATAAATATAAAATAATAAT
1 AAATAAA-ATAAAATAATAAT
*
1637801 AAATAAAAT-AAATATTAAT
1 AAATAAAATAAAATAATAAT
1637820 AA
1 AA
1637822 TTATTAGGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 2 0.10
21 7 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATAAAATAAAATAATAAT
Found at i:1637803 original size:17 final size:16
Alignment explanation
Indices: 1637772--1637805 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1637762 TTTTTAATAA
*
1637772 ATAAACTAAAATAAAT
1 ATAAAATAAAATAAAT
1637788 ATAAAATAATAATAAAT
1 ATAAAATAA-AATAAAT
1637805 A
1 A
1637806 AAATAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAATAAAATAAAT
Found at i:1637820 original size:15 final size:14
Alignment explanation
Indices: 1637767--1637821 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 14
1637757 TGAATTTTTT
1637767 AATAAATA-AACTAA
1 AATAAATATAA-TAA
1637781 AATAAATATAA-AA
1 AATAAATATAATAA
1637794 TAAT-AATA-AATAA
1 -AATAAATATAATAA
1637807 AATAAATATTAATAA
1 AATAAATA-TAATAA
1637822 TTATTAGGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
12 5 0.14
13 12 0.34
14 11 0.31
15 7 0.20
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAAATATAATAA
Found at i:1639465 original size:19 final size:19
Alignment explanation
Indices: 1639443--1639492 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1639433 ATCATGTCAT
1639443 TTTTTTTTTTCAATTTGGA
1 TTTTTTTTTTCAATTTGGA
* ** *
1639462 TTTTTTCTTAAAATTTTGA
1 TTTTTTTTTTCAATTTGGA
1639481 TTTTTTTTTTCA
1 TTTTTTTTTTCA
1639493 GAATTTAAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (19 bp):
TTTTTTTTTTCAATTTGGA
Found at i:1639728 original size:25 final size:25
Alignment explanation
Indices: 1639680--1639728 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1639670 AAAATAATTA
* * *
1639680 AAATATAATATATACGTAATAATAC
1 AAATATAATATAGACATAAAAATAC
1639705 AAATATAATATAGACATAAAAATA
1 AAATATAATATAGACATAAAAATA
1639729 TGTAAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.29
Consensus pattern (25 bp):
AAATATAATATAGACATAAAAATAC
Found at i:1641430 original size:18 final size:18
Alignment explanation
Indices: 1641398--1641433 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1641388 ATTGACACAA
**
1641398 ATTTAAATTTTTTTTAAT
1 ATTTAAATTACTTTTAAT
1641416 ATTTAAATTACTTTTAAT
1 ATTTAAATTACTTTTAAT
1641434 GAATTATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTAAATTACTTTTAAT
Found at i:1641974 original size:2 final size:2
Alignment explanation
Indices: 1641961--1641990 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1641951 GTACGACAGA
*
1641961 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1641991 CAATAAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1644605 original size:12 final size:13
Alignment explanation
Indices: 1644588--1644627 Score: 64
Period size: 12 Copynumber: 3.1 Consensus size: 13
1644578 AATAAATTTT
1644588 TTAAAATTAAA-A
1 TTAAAATTAAATA
1644600 TTAAAATTAAATA
1 TTAAAATTAAATA
1644613 TTAAATATTAAATA
1 TTAAA-ATTAAATA
1644627 T
1 T
1644628 ATCATTATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 11 0.42
13 6 0.23
14 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TTAAAATTAAATA
Found at i:1644627 original size:7 final size:6
Alignment explanation
Indices: 1644588--1644624 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
1644578 AATAAATTTT
1644588 TTAAAA TTAAAA TTAAAA TTAAATA TTAAATA TTAAA
1 TTAAAA TTAAAA TTAAAA TTAAA-A TTAAA-A TTAAA
1644625 TATATCATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 17 0.57
7 13 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TTAAAA
Found at i:1646180 original size:18 final size:17
Alignment explanation
Indices: 1646148--1646195 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1646138 AATAAATTCT
*
1646148 TTTTAGAAAAATAATAATA
1 TTTTA-AAAATTAATAA-A
1646167 TTTTAAAAATTAATAAA
1 TTTTAAAAATTAATAAA
**
1646184 TTAAAAAAATTA
1 TTTTAAAAATTA
1646196 TATGTGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 11 0.42
18 10 0.38
19 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
TTTTAAAAATTAATAAA
Found at i:1648589 original size:6 final size:6
Alignment explanation
Indices: 1648553--1648587 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1648543 TTTTCCCTCT
* *
1648553 TATTAA TATTAA TATTAA TATTGA TATTAT TATTA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTA
1648588 TTTAATCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
TATTAA
Found at i:1649449 original size:16 final size:16
Alignment explanation
Indices: 1649428--1649462 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1649418 ATATCTTCGA
1649428 TTTAATTATCTTTTAT
1 TTTAATTATCTTTTAT
1649444 TTTAATTATCTTTTAT
1 TTTAATTATCTTTTAT
1649460 TTT
1 TTT
1649463 CGTTTTGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTAATTATCTTTTAT
Found at i:1650153 original size:32 final size:31
Alignment explanation
Indices: 1650117--1650188 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 31
1650107 CACGAACATG
1650117 TAAATATTTATATAAAATAAATTATTAATGTA
1 TAAATATTTATATAAAAT-AATTATTAATGTA
1650149 TAAATA--T-T-T---ATAATTATTAATGTA
1 TAAATATTTATATAAAATAATTATTAATGTA
1650173 TAAATATTTATATAAA
1 TAAATATTTATATAAA
1650189 TTTATAATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 15
0.69 0.00 0.31
Matches are distributed among these distances:
24 19 0.58
25 2 0.06
26 1 0.03
27 1 0.03
28 2 0.06
29 1 0.03
30 1 0.03
32 6 0.18
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (31 bp):
TAAATATTTATATAAAATAATTATTAATGTA
Found at i:1650156 original size:14 final size:14
Alignment explanation
Indices: 1650133--1650180 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1650123 TTTATATAAA
1650133 ATAAATTATTAATGT
1 ATAAA-TATTAATGT
1650148 ATAAATA-T--T-T
1 ATAAATATTAATGT
*
1650158 ATAATTATTAATGT
1 ATAAATATTAATGT
1650172 ATAAATATT
1 ATAAATATT
1650181 TATATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
10 7 0.26
11 2 0.07
13 2 0.07
14 11 0.41
15 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (14 bp):
ATAAATATTAATGT
Found at i:1650163 original size:24 final size:24
Alignment explanation
Indices: 1650136--1650184 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1650126 ATATAAAATA
1650136 AATTATTAATGTATAAATATTTAT
1 AATTATTAATGTATAAATATTTAT
1650160 AATTATTAATGTATAAATATTTAT
1 AATTATTAATGTATAAATATTTAT
1650184 A
1 A
1650185 TAAATTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
AATTATTAATGTATAAATATTTAT
Found at i:1651132 original size:22 final size:22
Alignment explanation
Indices: 1651100--1651148 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1651090 AATTTTTTTC
*
1651100 TTTTTCTTTCTTTCCT-TTCTTT
1 TTTTTCCTTCTTT-CTGTTCTTT
*
1651122 TTTTTCCTTCTTTCTGTTTTTT
1 TTTTTCCTTCTTTCTGTTCTTT
1651144 TTTTT
1 TTTTT
1651149 AATCTTTGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTTTCCTTCTTTCTGTTCTTT
Found at i:1651267 original size:2 final size:2
Alignment explanation
Indices: 1651222--1651254 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1651212 TAATTGATTT
1651222 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1651255 GCATAGATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1651848 original size:3 final size:3
Alignment explanation
Indices: 1651840--1651869 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1651830 TTGAAAAAGA
1651840 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1651870 GTTTTTAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1658037 original size:20 final size:20
Alignment explanation
Indices: 1657988--1658038 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1657978 TTCATACATG
*
1657988 TATCGATACATTAAAAAATT
1 TATCGATACCTTAAAAAATT
1658008 TATCGATACCTTAAAAAATT
1 TATCGATACCTTAAAAAATT
1658028 TATCGATACCT
1 TATCGATACCT
1658039 CTGGGTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (20 bp):
TATCGATACCTTAAAAAATT
Found at i:1658746 original size:21 final size:20
Alignment explanation
Indices: 1658716--1658770 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
1658706 GGTGTCTATA
*
1658716 GTATCAATACAAACAGTAAAT
1 GTATCGATACAAA-AGTAAAT
* *
1658737 GTATCGATACATAAGTGAAT
1 GTATCGATACAAAAGTAAAT
* *
1658757 GTATTGATATAAAA
1 GTATCGATACAAAA
1658771 CTACCGTGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (20 bp):
GTATCGATACAAAAGTAAAT
Found at i:1658820 original size:20 final size:19
Alignment explanation
Indices: 1658792--1658873 Score: 74
Period size: 20 Copynumber: 4.1 Consensus size: 19
1658782 ACTGCCAAGA
* *
1658792 AAATATATCGATACATTAGT
1 AAATGTATCGATACATT-CT
*
1658812 AAATGTATCGATACATGTTT
1 AAATGTATCGATACAT-TCT
1658832 ACAATTGTATCGATACATTTCT
1 A-AA-TGTATCGATACA-TTCT
* *
1658854 CATTGTATCGATACATTCT
1 AAATGTATCGATACATTCT
1658873 A
1 A
1658874 GGTTTTTGAC
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
19 4 0.08
20 29 0.56
21 4 0.08
22 14 0.27
23 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (19 bp):
AAATGTATCGATACATTCT
Found at i:1658843 original size:22 final size:20
Alignment explanation
Indices: 1658815--1658870 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 20
1658805 CATTAGTAAA
1658815 TGTATCGATACATGTT-TACAAT
1 TGTATCGATACAT-TTCT-C-AT
1658837 TGTATCGATACATTTCTCAT
1 TGTATCGATACATTTCTCAT
1658857 TGTATCGATACATT
1 TGTATCGATACATT
1658871 CTAGGTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.48
21 3 0.09
22 14 0.42
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTTCTCAT
Found at i:1661264 original size:27 final size:27
Alignment explanation
Indices: 1661234--1661285 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1661224 AAATACCAAA
* *
1661234 ATTTATTTATCGGGATACTCTAACCCT
1 ATTTATTTAACGGGATACTCGAACCCT
* *
1661261 ATTTTTTTAAGGGGATACTCGAACC
1 ATTTATTTAACGGGATACTCGAACC
1661286 TTTCTTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (27 bp):
ATTTATTTAACGGGATACTCGAACCCT
Found at i:1661856 original size:13 final size:13
Alignment explanation
Indices: 1661838--1661862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1661828 CATAAAATGT
1661838 TGTATCGATACAA
1 TGTATCGATACAA
1661851 TGTATCGATACA
1 TGTATCGATACA
1661863 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1661860 original size:33 final size:33
Alignment explanation
Indices: 1661818--1661887 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1661808 TTCAACGATT
1661818 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1661851 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1661884 TGTA
1 TGTA
1661888 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1661945 original size:13 final size:13
Alignment explanation
Indices: 1661927--1661951 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1661917 ATTACTCACA
1661927 TGTATCGATACAT
1 TGTATCGATACAT
1661940 TGTATCGATACA
1 TGTATCGATACA
1661952 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1662088 original size:52 final size:52
Alignment explanation
Indices: 1661940--1662080 Score: 228
Period size: 52 Copynumber: 2.7 Consensus size: 52
1661930 ATCGATACAT
* ***
1661940 TGTATCGATACACTAATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
1661992 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1662044 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1662081 ATAAATTTTC
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 81 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:1667075 original size:1 final size:1
Alignment explanation
Indices: 1667069--1667149 Score: 63
Period size: 1 Copynumber: 81.0 Consensus size: 1
1667059 AAATCTTCAC
* * ** * * * ** *
1667069 TTTTTTTTTTGTTTTTTTTTTCTTTTTCCTTTTGTTTGTTTTTTTTTTCTTTTTCCTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
1667134 TTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTT
1667150 CCAATTGCCA
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.00, C:0.07, G:0.06, T:0.86
Consensus pattern (1 bp):
T
Found at i:1667150 original size:27 final size:27
Alignment explanation
Indices: 1667071--1667151 Score: 137
Period size: 27 Copynumber: 3.0 Consensus size: 27
1667061 ATCTTCACTT
1667071 TTTTTTTTGTTTTTTTTTTCTTTTTCC
1 TTTTTTTTGTTTTTTTTTTCTTTTTCC
*
1667098 TTTTGTTTGTTTTTTTTTTCTTTTTCC
1 TTTTTTTTGTTTTTTTTTTCTTTTTCC
1667125 TTTTTTTTGTTTTGTTTTTT-TTTTTCC
1 TTTTTTTTGTTTT-TTTTTTCTTTTTCC
1667152 AATTGCCATG
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
27 45 0.88
28 6 0.12
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (27 bp):
TTTTTTTTGTTTTTTTTTTCTTTTTCC
Found at i:1678781 original size:25 final size:25
Alignment explanation
Indices: 1678719--1678785 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
1678709 TTCAAATTAG
*
1678719 TACTC-CCTCTTAACAAAATATTTAA
1 TACTCTCC-CTTAACAAAAAATTTAA
** * *
1678744 CGCTTTCCTTTAACAAAAAATTTAA
1 TACTCTCCCTTAACAAAAAATTTAA
1678769 TACTCTCCCTTAACAAA
1 TACTCTCCCTTAACAAA
1678786 TTATCCCCCT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
25 30 0.94
26 2 0.06
ACGTcount: A:0.39, C:0.25, G:0.01, T:0.34
Consensus pattern (25 bp):
TACTCTCCCTTAACAAAAAATTTAA
Found at i:1690114 original size:15 final size:16
Alignment explanation
Indices: 1690094--1690132 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
1690084 AAGCAAAAGC
1690094 ACAAAAAAAAAAGAAA
1 ACAAAAAAAAAAGAAA
*
1690110 A-AAAAGAAAAAGAAA
1 ACAAAAAAAAAAGAAA
1690125 ACAAAAAA
1 ACAAAAAA
1690133 GTGCAAAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (16 bp):
ACAAAAAAAAAAGAAA
Found at i:1694890 original size:61 final size:60
Alignment explanation
Indices: 1694825--1694962 Score: 177
Period size: 61 Copynumber: 2.2 Consensus size: 60
1694815 GTTAGTGACG
** * *
1694825 TTGGGCTTAAGGATGTGAAGAATGATAAAGGTGCCAATATGCTAATTCATGGCCAGCAATA
1 TTGGGCTTAA-GATGAAAAGAATGATAAAGGTGCCAATATGCTAATTCAAGGCCAACAATA
** * *
1694886 TTGGGCTTGAAGATGAAAAGAATGATAGGGGTGCCAATATGCTAATTGAAGGCCAACGATA
1 TTGGGCTT-AAGATGAAAAGAATGATAAAGGTGCCAATATGCTAATTCAAGGCCAACAATA
1694947 TTGGGCTTAAAGATGA
1 TTGGGCTT-AAGATGA
1694963 CAAAAGGTGC
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
61 65 0.97
62 2 0.03
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (60 bp):
TTGGGCTTAAGATGAAAAGAATGATAAAGGTGCCAATATGCTAATTCAAGGCCAACAATA
Found at i:1695038 original size:52 final size:51
Alignment explanation
Indices: 1694970--1695103 Score: 171
Period size: 52 Copynumber: 2.6 Consensus size: 51
1694960 TGACAAAAGG
*
1694970 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACATAAATAT-ACGAAGAA
1 TGCCAATGTGCTGATTCAA-GCCAGCGACATTAGACATAAAGATGA-GAAGAA
* * * * *
1695022 TGTCAATATGCTGATTCACAGCCAGTGACATTAGACTTGAAGATGAGAAGAA
1 TGCCAATGTGCTGATTCA-AGCCAGCGACATTAGACATAAAGATGAGAAGAA
1695074 TGCCAATGTGCTGATTCAAAGCCAGCGACA
1 TGCCAATGTGCTGATTC-AAGCCAGCGACA
1695104 GTGGGCTTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
52 67 0.96
53 3 0.04
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (51 bp):
TGCCAATGTGCTGATTCAAGCCAGCGACATTAGACATAAAGATGAGAAGAA
Found at i:1695312 original size:43 final size:43
Alignment explanation
Indices: 1695230--1695322 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 43
1695220 AGAAGGATGA
* * ** *
1695230 TAAAGGTGCCAATTTGCTGATTCAAGGCCGGCGATATTGGACT
1 TAAAGGTGCCAATGTGCTGATTCAAGCCCAACGACATTGGACT
* *
1695273 TAAAGGTGCCAATGTGCTGATTCAAGCCCAATGACATTGGGCT
1 TAAAGGTGCCAATGTGCTGATTCAAGCCCAACGACATTGGACT
1695316 TAGAAGG
1 TA-AAGG
1695323 AGATGCCACC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 38 0.90
44 4 0.10
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (43 bp):
TAAAGGTGCCAATGTGCTGATTCAAGCCCAACGACATTGGACT
Found at i:1695370 original size:32 final size:32
Alignment explanation
Indices: 1695326--1695517 Score: 166
Period size: 32 Copynumber: 6.0 Consensus size: 32
1695316 TAGAAGGAGA
*
1695326 TGCCACCA-ACTTGTGTGGGCTTTTGAAAGGGT
1 TGCCA-CAGACTTGTGTGGGCTTTTGAAAAGGT
*
1695358 TGCCACAGACTTGTGTAGGC-TTTGAAAAAGGT
1 TGCCACAGACTTGTGTGGGCTTTTG-AAAAGGT
* * *
1695390 TGCTACCAG-CTTATGTGGGC-TTTGGAAAGGT
1 TGCCA-CAGACTTGTGTGGGCTTTTGAAAAGGT
* *
1695421 TGCCACCGACTTGTGTGGGC-TTTAAAAAGGGT
1 TGCCACAGACTTGTGTGGGCTTTTGAAAA-GGT
* *
1695453 CGCCACTA-ACTTGTATGGGC-TTTGAAGAAGGT
1 TGCCAC-AGACTTGTGTGGGCTTTTGAA-AAGGT
* *
1695485 TGCCACTAG-CTTGTGTGGGCTTTAGAGAAGGT
1 TGCCAC-AGACTTGTGTGGGCTTTTGAAAAGGT
1695517 T
1 T
1695518 CCTCCACTAG
Statistics
Matches: 132, Mismatches: 19, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
30 2 0.02
31 32 0.24
32 89 0.67
33 9 0.07
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (32 bp):
TGCCACAGACTTGTGTGGGCTTTTGAAAAGGT
Found at i:1695419 original size:64 final size:62
Alignment explanation
Indices: 1695327--1695508 Score: 215
Period size: 63 Copynumber: 2.9 Consensus size: 62
1695317 AGAAGGAGAT
* *
1695327 GCCACCAACTTGTGTGGGCTTTTGAAAGGGTTGCCACAGACTTGTGTAGGCTTTGAAAAA-GGTT
1 GCCACCAACTTGTGTGGGC-TTTGAAA-GGTTGCCACAGACTTGTGTGGGCTTT-AAAAAGGGTC
* * * *
1695391 GCTACCAGCTTATGTGGGCTTTGGAAAGGTTGCCACCGACTTGTGTGGGCTTTAAAAAGGGTC
1 GCCACCAACTTGTGTGGGCTTT-GAAAGGTTGCCACAGACTTGTGTGGGCTTTAAAAAGGGTC
* *
1695454 GCCACTAACTTGTATGGGCTTTGAAGAAGGTTGCCACTAG-CTTGTGTGGGCTTTA
1 GCCACCAACTTGTGTGGGCTTTG-A-AAGGTTGCCAC-AGACTTGTGTGGGCTTTA
1695509 GAGAAGGTTC
Statistics
Matches: 101, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
62 6 0.06
63 48 0.48
64 46 0.46
65 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.30
Consensus pattern (62 bp):
GCCACCAACTTGTGTGGGCTTTGAAAGGTTGCCACAGACTTGTGTGGGCTTTAAAAAGGGTC
Found at i:1695432 original size:63 final size:63
Alignment explanation
Indices: 1695330--1695517 Score: 193
Period size: 64 Copynumber: 3.0 Consensus size: 63
1695320 AGGAGATGCC
* *
1695330 ACCAACTTGTGTGGGCTTTTGAAAGGGTTGCCACAGACTTGTGTAGGCTTTGAAAAAGGTTGCT
1 ACCAACTTATGTGGGCTTTGGAAAGGGTTGCCACAGACTTGTGTAGGCTTT-AAAAAGGTTGCT
* * * * *
1695394 ACCAGCTTATGTGGGCTTTGGAAA-GGTTGCCACCGACTTGTGTGGGCTTTAAAAAGGGTCGCC
1 ACCAACTTATGTGGGCTTTGGAAAGGGTTGCCACAGACTTGTGTAGGCTTTAAAAA-GGTTGCT
* * * * * *
1695457 ACTAACTTGTATGGGCTTT-GAAGAAGGTTGCCACTAG-CTTGTGTGGGCTTTAGAGAAGGTT
1 ACCAACTTATGTGGGCTTTGGAA-AGGGTTGCCAC-AGACTTGTGTAGGCTTTA-AAAAGGTT
1695518 CCTCCACTAG
Statistics
Matches: 105, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
62 8 0.08
63 45 0.43
64 48 0.46
65 4 0.04
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.30
Consensus pattern (63 bp):
ACCAACTTATGTGGGCTTTGGAAAGGGTTGCCACAGACTTGTGTAGGCTTTAAAAAGGTTGCT
Found at i:1695474 original size:95 final size:96
Alignment explanation
Indices: 1695326--1695517 Score: 262
Period size: 95 Copynumber: 2.0 Consensus size: 96
1695316 TAGAAGGAGA
** * *
1695326 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGTTGCCACAGACTTGTGTAGGCTTTGAAAAAGGTT
1 TGCCACCAACTTGTGTGGGCTTTAAAAAGGGTCGCCACAGACTTGTATAGGCTTTGAAAAAGGTT
* *
1695391 GCTACCAGCTTATGTGGGCTTTGGA-AAGGT
66 GCCACCAGCTTATGTGGGCTTTAGAGAAGGT
* * *
1695421 TGCCACCGACTTGTGTGGGCTTTAAAAAGGGTCGCCACTA-ACTTGTATGGGCTTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTAAAAAGGGTCGCCAC-AGACTTGTATAGGCTTTGAAAAAGGT
* *
1695485 TGCCACTAGCTTGTGTGGGCTTTAGAGAAGGT
65 TGCCACCAGCTTATGTGGGCTTTAGAGAAGGT
1695517 T
1 T
1695518 CCTCCACTAG
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
95 77 0.92
96 7 0.08
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (96 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAAGGGTCGCCACAGACTTGTATAGGCTTTGAAAAAGGTT
GCCACCAGCTTATGTGGGCTTTAGAGAAGGT
Found at i:1695733 original size:28 final size:27
Alignment explanation
Indices: 1695690--1695751 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 27
1695680 ATACAGCAAG
*
1695690 TGCCACTGATTGTGGACTTCAAAAAGA
1 TGCCACTAATTGTGGACTTCAAAAAGA
* *
1695717 TGCCACTAACTTGTGGACTTCAAAGAGG
1 TGCCACTAA-TTGTGGACTTCAAAAAGA
1695745 TGCCACT
1 TGCCACT
1695752 GACTGGTGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 8 0.26
28 23 0.74
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (27 bp):
TGCCACTAATTGTGGACTTCAAAAAGA
Found at i:1695825 original size:13 final size:13
Alignment explanation
Indices: 1695801--1695841 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
1695791 TTTCTTAACG
* *
1695801 AAGTTTTTGACAC
1 AAGTTCTTGACAA
*
1695814 ACGTTCTTGACAA
1 AAGTTCTTGACAA
1695827 AAGTTCTTGACAA
1 AAGTTCTTGACAA
1695840 AA
1 AA
1695842 ATTTCTTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (13 bp):
AAGTTCTTGACAA
Found at i:1695847 original size:14 final size:14
Alignment explanation
Indices: 1695817--1695859 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1695807 TTGACACACG
*
1695817 TTCTTGAC-AAAAG
1 TTCTTGACAAAAAT
1695830 TTCTTGACAAAAAT
1 TTCTTGACAAAAAT
* *
1695844 TTCTTAACAATAAT
1 TTCTTGACAAAAAT
1695858 TT
1 TT
1695860 TGTTGACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 8 0.31
14 18 0.69
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (14 bp):
TTCTTGACAAAAAT
Found at i:1697133 original size:16 final size:15
Alignment explanation
Indices: 1697108--1697182 Score: 61
Period size: 16 Copynumber: 5.2 Consensus size: 15
1697098 TTTCTTCCCC
*
1697108 TTTTTCTTGTTTGTT
1 TTTTTTTTGTTTGTT
1697123 GTTTTTTTTG--TGTT
1 -TTTTTTTTGTTTGTT
*
1697137 TTTTTTAT-TTTG-T
1 TTTTTTTTGTTTGTT
*
1697150 GTTTTTTTGTTTGCTT
1 TTTTTTTTGTTTG-TT
*
1697166 TTTTGTTTGTTT-TT
1 TTTTTTTTGTTTGTT
1697180 TTT
1 TTT
1697183 GTAGTGGACT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
13 14 0.29
14 15 0.31
16 19 0.40
ACGTcount: A:0.01, C:0.03, G:0.15, T:0.81
Consensus pattern (15 bp):
TTTTTTTTGTTTGTT
Found at i:1697138 original size:11 final size:12
Alignment explanation
Indices: 1697117--1697184 Score: 59
Period size: 12 Copynumber: 5.4 Consensus size: 12
1697107 CTTTTTCTTG
1697117 TTTGTTGTTTTT
1 TTTGTTGTTTTT
1697129 TTTG-TGTTTTTT
1 TTTGTTG-TTTTT
*
1697141 TTATTTTGTGTTTT
1 TT-TGTTGT-TTTT
*
1697155 TTTGTT-TGCTTT
1 TTTGTTGT-TTTT
1697167 TTTGTTTGTTTTT
1 TTTG-TTGTTTTT
1697180 TTTGT
1 TTTGT
1697185 AGTGGACTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
11 2 0.04
12 21 0.46
13 14 0.30
14 9 0.20
ACGTcount: A:0.01, C:0.01, G:0.16, T:0.81
Consensus pattern (12 bp):
TTTGTTGTTTTT
Found at i:1697138 original size:27 final size:27
Alignment explanation
Indices: 1697108--1697182 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
1697098 TTTCTTCCCC
1697108 TTTTTCTTGTTTGTTGTTTTTTT-TGTG
1 TTTTT-TTGTTTGTTGTTTTTTTGTGTG
* *
1697135 TTTTTTT-TATTTTGTGTTTTTTTGTTTG
1 TTTTTTTGT-TTGT-TGTTTTTTTGTGTG
*
1697163 CTTTTTTGTTTGTT-TTTTTT
1 TTTTTTTGTTTGTTGTTTTTT
1697183 GTAGTGGACT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
25 1 0.03
26 11 0.28
27 15 0.38
28 12 0.30
29 1 0.03
ACGTcount: A:0.01, C:0.03, G:0.15, T:0.81
Consensus pattern (27 bp):
TTTTTTTGTTTGTTGTTTTTTTGTGTG
Found at i:1697141 original size:14 final size:13
Alignment explanation
Indices: 1697117--1697182 Score: 62
Period size: 14 Copynumber: 4.9 Consensus size: 13
1697107 CTTTTTCTTG
1697117 TTTGTTGTTTTTTT
1 TTTGTT-TTTTTTT
*
1697131 TGTGTTTTTTTTAT
1 TTTGTTTTTTTT-T
*
1697145 TTTGTGTTTTTTTG
1 TTTGT-TTTTTTTT
* *
1697159 TTTG-CTTTTTTG
1 TTTGTTTTTTTTT
1697171 TTTGTTTTTTTT
1 TTTGTTTTTTTT
1697183 GTAGTGGACT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
12 11 0.25
13 12 0.27
14 14 0.32
15 7 0.16
ACGTcount: A:0.02, C:0.02, G:0.15, T:0.82
Consensus pattern (13 bp):
TTTGTTTTTTTTT
Found at i:1697154 original size:26 final size:24
Alignment explanation
Indices: 1697110--1697184 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 24
1697100 TCTTCCCCTT
*
1697110 TTTCTTGTTTG-TTGTTTTTTTTG
1 TTTCTTTTTTGTTTGTTTTTTTTG
*
1697133 TGTT-TTTTTTATTTTGTGTTTTTTTG
1 T-TTCTTTTTT-GTTTGT-TTTTTTTG
1697159 TTTGCTTTTTTGTTTGTTTTTTTTG
1 TTT-CTTTTTTGTTTGTTTTTTTTG
1697184 T
1 T
1697185 AGTGGACTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
23 6 0.14
24 2 0.05
25 15 0.35
26 14 0.33
27 6 0.14
ACGTcount: A:0.01, C:0.03, G:0.16, T:0.80
Consensus pattern (24 bp):
TTTCTTTTTTGTTTGTTTTTTTTG
Found at i:1706693 original size:19 final size:19
Alignment explanation
Indices: 1706669--1706731 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
1706659 ATCGATATAA
1706669 TGTATCGATACATAAGTAT
1 TGTATCGATACATAAGTAT
1706688 TGTATCGATAC--AA-TA-
1 TGTATCGATACATAAGTAT
*
1706703 --TATCGATACATAAGTTT
1 TGTATCGATACATAAGTAT
*
1706720 TATATCGATACA
1 TGTATCGATACA
1706732 ATGTATCAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 9 0.24
15 2 0.05
16 3 0.08
17 2 0.05
19 21 0.57
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATAAGTAT
Found at i:1706696 original size:32 final size:32
Alignment explanation
Indices: 1706658--1706771 Score: 183
Period size: 32 Copynumber: 3.6 Consensus size: 32
1706648 CAACGATTTG
* * *
1706658 TATCGATATAATGTATCGATACATAAGTATTG
1 TATCGATACAATGTATCGATACATAAGTTTTA
*
1706690 TATCGATACAATATATCGATACATAAGTTTTA
1 TATCGATACAATGTATCGATACATAAGTTTTA
*
1706722 TATCGATACAATGTATCAATACATAAGTTTTA
1 TATCGATACAATGTATCGATACATAAGTTTTA
1706754 TATCGATACAATGTATCG
1 TATCGATACAATGTATCG
1706772 CTATGAAGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 75 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (32 bp):
TATCGATACAATGTATCGATACATAAGTTTTA
Found at i:1706762 original size:19 final size:19
Alignment explanation
Indices: 1706701--1706763 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
1706691 ATCGATACAA
1706701 TATATCGATACATAAGTTT
1 TATATCGATACATAAGTTT
1706720 TATATCGATAC--AA----
1 TATATCGATACATAAGTTT
* *
1706733 TGTATCAATACATAAGTTT
1 TATATCGATACATAAGTTT
1706752 TATATCGATACA
1 TATATCGATACA
1706764 ATGTATCGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
13 9 0.26
15 2 0.06
17 2 0.06
19 21 0.62
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.38
Consensus pattern (19 bp):
TATATCGATACATAAGTTT
Found at i:1706834 original size:13 final size:13
Alignment explanation
Indices: 1706816--1706843 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1706806 ATTACTCAAA
1706816 TGTATCGATACAT
1 TGTATCGATACAT
1706829 TGTATCGATACAT
1 TGTATCGATACAT
1706842 TG
1 TG
1706844 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1713019 original size:33 final size:33
Alignment explanation
Indices: 1712982--1713048 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1712972 TTCAATGATT
1712982 TGTATCAATACATAAAATGTTGTATCGATACAA
1 TGTATCAATACATAAAATGTTGTATCGATACAA
* *** *
1713015 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCAATACATAAAATGTTGTATCGATACAA
1713048 T
1 T
1713049 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (33 bp):
TGTATCAATACATAAAATGTTGTATCGATACAA
Found at i:1713020 original size:13 final size:13
Alignment explanation
Indices: 1713002--1713026 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1712992 CATAAAATGT
1713002 TGTATCGATACAA
1 TGTATCGATACAA
1713015 TGTATCGATACA
1 TGTATCGATACA
1713027 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1713109 original size:13 final size:13
Alignment explanation
Indices: 1713091--1713115 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1713081 ATTACTCACA
1713091 TGTATCGATACAT
1 TGTATCGATACAT
1713104 TGTATCGATACA
1 TGTATCGATACA
1713116 CTGATTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1713187 original size:51 final size:52
Alignment explanation
Indices: 1713104--1713243 Score: 230
Period size: 51 Copynumber: 2.7 Consensus size: 52
1713094 ATCGATACAT
**
1713104 TGTATCGATACACTGATT-TTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
1713156 TGTATCGATACATTA-TAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1713207 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1713244 TAACTTTTCA
Statistics
Matches: 82, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
50 1 0.01
51 47 0.57
52 34 0.41
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:1724377 original size:9 final size:9
Alignment explanation
Indices: 1724365--1724439 Score: 53
Period size: 10 Copynumber: 7.6 Consensus size: 9
1724355 AAAAAGAAGA
1724365 AAAAAAAAC
1 AAAAAAAAC
1724374 AAAACAAAA-
1 AAAA-AAAAC
*
1724383 AAAAAGAGAAG
1 AAAAA-A-AAC
1724394 AAAAAAAAC
1 AAAAAAAAC
*
1724403 AAAAAAAAAGA
1 -AAAAAAAA-C
1724414 AAAAAAAAC
1 AAAAAAAAC
1724423 AACAACAACAAC
1 AA-AA-AA-AAC
1724435 AAAAA
1 AAAAA
1724440 GGGTCCGGAT
Statistics
Matches: 54, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
8 1 0.02
9 13 0.24
10 26 0.48
11 9 0.17
12 5 0.09
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:1724386 original size:29 final size:29
Alignment explanation
Indices: 1724353--1724439 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 29
1724343 CGTCCTCCAC
1724353 AAAAAAAGAAGAAAAAAAAACAAAACAAA
1 AAAAAAAGAAGAAAAAAAAACAAAACAAA
1724382 AAAAAAGAGAAG-AAAAAAAACAAAA-AAA
1 AAAAAA-AGAAGAAAAAAAAACAAAACAAA
* * *
1724410 AAGAAAA-AA-AAACAACAACAACAACAAA
1 AAAAAAAGAAGAAAAAAAAACAA-AACAAA
1724438 AA
1 AA
1724440 GGGTCCGGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
26 11 0.22
27 3 0.06
28 13 0.25
29 19 0.37
30 5 0.10
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (29 bp):
AAAAAAAGAAGAAAAAAAAACAAAACAAA
Found at i:1724401 original size:33 final size:34
Alignment explanation
Indices: 1724358--1724421 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
1724348 TCCACAAAAA
* *
1724358 AAGAAGAAAAA-AAAACAAAACAAAAAAAAAGAG
1 AAGAAAAAAAACAAAAAAAAACAAAAAAAAAGAG
*
1724391 AAGAAAAAAAACAAAAAAAAAGAAAAAAAAA
1 AAGAAAAAAAACAAAAAAAAACAAAAAAAAA
1724422 CAACAACAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 10 0.37
34 17 0.63
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (34 bp):
AAGAAAAAAAACAAAAAAAAACAAAAAAAAAGAG
Found at i:1724406 original size:22 final size:23
Alignment explanation
Indices: 1724351--1724427 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 23
1724341 GGCGTCCTCC
1724351 ACAAAAAAAGAAGAAAAAAAAACAAA
1 ACAAAAAAA-AAGAAAAAAAAAC--A
1724377 ACAAAAAAAAAGAGAAGAAAAAA-A
1 ACAAAAAAAAAGA-AA-AAAAAACA
1724401 ACAAAAAAAAAGAAAAAAAAACA
1 ACAAAAAAAAAGAAAAAAAAACA
1724424 ACAA
1 ACAA
1724428 CAACAACAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
22 6 0.12
23 7 0.15
24 14 0.29
25 4 0.08
26 11 0.23
27 6 0.12
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (23 bp):
ACAAAAAAAAAGAAAAAAAAACA
Found at i:1724439 original size:1 final size:1
Alignment explanation
Indices: 1724353--1724421 Score: 57
Period size: 1 Copynumber: 69.0 Consensus size: 1
1724343 CGTCCTCCAC
* * * * * * * * *
1724353 AAAAAAAGAAGAAAAAAAAACAAAACAAAAAAAAAGAGAAGAAAAAAAACAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1724418 AAAA
1 AAAA
1724422 CAACAACAAC
Statistics
Matches: 50, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:1725950 original size:28 final size:28
Alignment explanation
Indices: 1725868--1725952 Score: 109
Period size: 30 Copynumber: 3.0 Consensus size: 28
1725858 CATTCCTCAC
*
1725868 CCTTCAAAAGCCCACAAGTCAGTGGCAC
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
1725896 CCTTTTTC-AAAGCCCACAAATCAGTGGCAA
1 CC---TTCAAAAGCCCACAAGTCAGTGGCAA
*
1725926 CCTTCAAAAGCCCACAAGTCCGTGGCA
1 CCTTCAAAAGCCCACAAGTCAGTGGCA
1725953 TTTTTTCCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
27 3 0.06
28 21 0.43
30 22 0.45
31 3 0.06
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (28 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAA
Done.