Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold34
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: 1758877
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
File 11 of 12
Found at i:1552383 original size:17 final size:17
Alignment explanation
Indices: 1552361--1552428 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
1552351 TTATCCGTGG
1552361 ATTTTATCTAAAAAAGC
1 ATTTTATCTAAAAAAGC
1552378 ATTTTATCTAAACAAA--
1 ATTTTATCTAAA-AAAGC
**
1552394 ATTCGA-CTTAACAAAAAGC
1 ATTTTATC-T-A-AAAAAGC
1552413 ATTTTATCTAAAAAAG
1 ATTTTATCTAAAAAAG
1552429 TCATAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
15 1 0.03
16 5 0.12
17 22 0.55
18 6 0.15
19 5 0.12
20 1 0.03
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (17 bp):
ATTTTATCTAAAAAAGC
Found at i:1553276 original size:26 final size:26
Alignment explanation
Indices: 1553247--1553334 Score: 81
Period size: 26 Copynumber: 3.3 Consensus size: 26
1553237 GTGGGCTTTA
1553247 AAAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
** *
1553273 AAAGGTG-CCACCAACTTGTGTGGG-CTTTG
1 AAAGGTGTCCTGC-TCTT-TG-GGGAC--TG
*
1553302 AAAGGGGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
1553328 AAAGGTG
1 AAAGGTG
1553335 CCACCAACTT
Statistics
Matches: 47, Mismatches: 8, Indels: 14
0.68 0.12 0.20
Matches are distributed among these distances:
25 3 0.06
26 18 0.38
27 6 0.13
28 6 0.13
29 11 0.23
30 3 0.06
ACGTcount: A:0.19, C:0.18, G:0.35, T:0.27
Consensus pattern (26 bp):
AAAGGTGTCCTGCTCTTTGGGGACTG
Found at i:1553482 original size:59 final size:59
Alignment explanation
Indices: 1553089--1553801 Score: 832
Period size: 55 Copynumber: 12.3 Consensus size: 59
1553079 ATAAAGTGTA
* * *
1553089 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT----G-AAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
1553144 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
** * *
1553199 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACATGTGTGGGCTTT-----AAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
1553254 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGGG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
1553309 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
** *
1553370 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTT-TAGGAGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGT--GTGGGCTTTAAAAGAAAAGGCG
* *
1553430 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
1553489 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
1553548 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
1553608 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAG----GG-G
1 TCCTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * * *
1553663 TCCTACTCTTTGGGGACGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* ** *
1553723 TCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
1553784 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
1553802 AAAAAGCGGA
Statistics
Matches: 584, Mismatches: 44, Indels: 54
0.86 0.06 0.08
Matches are distributed among these distances:
53 1 0.00
54 3 0.01
55 232 0.40
56 3 0.01
57 1 0.00
59 129 0.22
60 126 0.22
61 86 0.15
62 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (59 bp):
TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
Found at i:1567462 original size:52 final size:51
Alignment explanation
Indices: 1567356--1567534 Score: 177
Period size: 52 Copynumber: 3.5 Consensus size: 51
1567346 ATATTTTGGG
* * * * *
1567356 AATAAAGCCGGGGTTGGAGTATCCCC--TCG-GAGGAAAATTGGTGTTTTGAA
1 AATAAAACCGGGGTTAGAGTATCCCCGATTGTG-GAAAAATTAGTGTTTTG-A
*
1567406 AATAAAACCGGGGTTAGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGC
1 AATAAAACCGGGGTTAGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-GA
* * * * *
1567458 AATAAAACCGGGGTTGGAGTATCCCCGATTAT-GAAAAATCAATATTTTGGA
1 AATAAAACCGGGGTTAGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-GA
**
1567509 AATAAAGTCGGGGTTAGAGTATCCCC
1 AATAAAACCGGGGTTAGAGTATCCCC
1567535 TCGAAAATAA
Statistics
Matches: 109, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
50 24 0.22
51 37 0.34
52 46 0.42
53 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (51 bp):
AATAAAACCGGGGTTAGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTGA
Found at i:1567521 original size:51 final size:51
Alignment explanation
Indices: 1567313--1567534 Score: 194
Period size: 51 Copynumber: 4.4 Consensus size: 51
1567303 TCGGAAATAA
** * * * *
1567313 CGGGGTTGGAGTATCCCTAATTATGAGAAATCGATATTTTGGGAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAAC
**** * *** * *
1567364 CGGGGTTGGAGTATCCCCTCGGA-GGAAAATTGGTGTTTTGAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAAC
* * * * * * *
1567414 CGGGGTTAGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAAATCAATATTTTGGAAATAAAAC
**
1567466 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAAC
*
1567517 CGGGGTTAGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
1567535 TCGAAAATAA
Statistics
Matches: 135, Mismatches: 34, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
50 36 0.27
51 55 0.41
52 44 0.33
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAAC
Found at i:1567643 original size:54 final size:51
Alignment explanation
Indices: 1567576--1567706 Score: 158
Period size: 51 Copynumber: 2.5 Consensus size: 51
1567566 GATTAACAGG
* *
1567576 GTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTAGAA-ATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAGTG--TTTT-GAAGATAAAATCGGA
*
1567630 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAGATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTTTTGAAGATAAAATCGGA
*
1567681 GTTGGAATATCCCCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
1567707 TTGAGAAACT
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
50 3 0.04
51 33 0.49
52 4 0.06
53 10 0.15
54 18 0.26
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTGAAGATAAAATCGGA
Found at i:1570014 original size:13 final size:13
Alignment explanation
Indices: 1569996--1570022 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1569986 AAAATGCCTG
1569996 AATGTATCGATAC
1 AATGTATCGATAC
1570009 AATGTATCGATAC
1 AATGTATCGATAC
1570022 A
1 A
1570023 TAGAAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1570121 original size:33 final size:32
Alignment explanation
Indices: 1570065--1570128 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1570055 TAGCTAATTA
* *
1570065 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATAAAAAACTTATGTATCGATACAT
1570097 TGTATCGATAAAAAAACTTATGTATCGATACA
1 TGTATCGAT-AAAAAACTTATGTATCGATACA
1570129 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 9 0.31
33 20 0.69
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (32 bp):
TGTATCGATAAAAAACTTATGTATCGATACAT
Found at i:1570192 original size:21 final size:21
Alignment explanation
Indices: 1570166--1570242 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
1570156 GTTGGGACCC
* *
1570166 TGTATCGATACATTTTACGAA
1 TGTATCGATACATTCTACAAA
*
1570187 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCTACAAA
1570208 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
*
1570229 TGTATTGATACATT
1 TGTATCGATACATT
1570243 TGATTTTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTCTACAAA
Found at i:1571358 original size:21 final size:20
Alignment explanation
Indices: 1571329--1571386 Score: 93
Period size: 19 Copynumber: 3.0 Consensus size: 20
1571319 TTGTTAAATT
1571329 ATTTT-ATTAAGGGGGAGAA
1 ATTTTGATTAAGGGGGAGAA
1571348 ACTTTTGATTAAGGGGGAG-A
1 A-TTTTGATTAAGGGGGAGAA
1571368 ATTTTGATTAAGGGGGAGA
1 ATTTTGATTAAGGGGGAGA
1571387 GAAAAGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
19 18 0.50
20 6 0.17
21 12 0.33
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.31
Consensus pattern (20 bp):
ATTTTGATTAAGGGGGAGAA
Found at i:1571388 original size:21 final size:21
Alignment explanation
Indices: 1571329--1571389 Score: 85
Period size: 20 Copynumber: 3.0 Consensus size: 21
1571319 TTGTTAAATT
1571329 ATTTT-ATTAAGGGGGAGA-A
1 ATTTTGATTAAGGGGGAGAGA
1571348 ACTTTTGATTAA-GGGG-GAGA
1 A-TTTTGATTAAGGGGGAGAGA
1571368 ATTTTGATTAAGGGGGAGAGA
1 ATTTTGATTAAGGGGGAGAGA
1571389 A
1 A
1571390 AAGAAAAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
19 13 0.35
20 14 0.38
21 10 0.27
ACGTcount: A:0.34, C:0.02, G:0.34, T:0.30
Consensus pattern (21 bp):
ATTTTGATTAAGGGGGAGAGA
Found at i:1571964 original size:20 final size:19
Alignment explanation
Indices: 1571897--1571970 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 19
1571887 CAAAACCCTG
*
1571897 AAATGTATCGATACACCT-TC
1 AAATGTATCGATACA--TACC
*
1571917 AAATGTATCGATACATATTGC
1 AAATGTATCGATACATA--CC
*
1571938 ACA-GTATCGATACATGACC
1 AAATGTATCGATACAT-ACC
1571957 AAATGTATCGATAC
1 AAATGTATCGATAC
1571971 TTGTTAAGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
18 1 0.02
19 3 0.07
20 37 0.82
21 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (19 bp):
AAATGTATCGATACATACC
Found at i:1572094 original size:33 final size:32
Alignment explanation
Indices: 1572033--1572100 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
1572023 CCTTAACTGT
*
1572033 TTGTATCGATACACACAATATGTATCGATAAA
1 TTGTATCGATACACACAAAATGTATCGATAAA
* *
1572065 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATAAA
1572098 TTG
1 TTG
1572101 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATAAA
Found at i:1575046 original size:3 final size:3
Alignment explanation
Indices: 1575038--1575073 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1575028 AGACGTTGAA
*
1575038 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GGT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1575074 TCGGATGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:1576310 original size:344 final size:344
Alignment explanation
Indices: 1575677--1576339 Score: 979
Period size: 344 Copynumber: 1.9 Consensus size: 344
1575667 AAAGTTGGCT
* * * **
1575677 AATGAAAATAATGAATTAGCTAAGAAAAATAAGAACTTGCATGATTCATTTTCTATGTTTTAGAT
1 AATGAAAATAATGAATTAGCTAAGAAAAACAAAAACTTGCATGAATCATTCACTATGTTTTAGAT
* * *
1575742 GGCGCATCAAAAATTGAATGATATGCTTGAAACTCAAAGAGCATTCTTTGATAAAAATGGTTTAG
66 GGCACATCAAAAATTGAATGATATGCTAGAAACTCAAAAAGCATTCTTTGATAAAAATGGTTTAG
*
1575807 GATACAATGCCTTTGAGAAAGAAACAAAATTTAACAATTTCTTTGTTAAGCATAATCCACAATAT
131 GATACAATGCCTTTGAGAAAGAAACAAAATTTAACAATTTCTTTGTCAAGCATAATCCACAATAT
* * *
1575872 AATACTTCATATATGTGTTCATTATACCATAAACATGGTCACACATTTCACACATGTAATTCTAA
196 AATACCTCATACATGTATTCATTATACCATAAACATGGTCACACATTTCACACATGTAATTCTAA
* *
1575937 AATAAATAAATTTAGAGGCAAAGTTATTAAGAAAATAT-GAGTGCCTAAAGGAATCGGAAGTGAG
261 AATAAATAAATTTAGAGGCAAAATTATTAAGAAAATATGGA-TGCCTAAAAGAATCGGAAGTGAG
1576001 ATATTAATAAAATCCTAACC
325 ATATTAATAAAATCCTAACC
* *
1576021 AATGAAAATAATGAATTAG-TAAGGAAAAACAAAAATTTGCATGAATCATTCACTATGTTTTATA
1 AATGAAAATAATGAATTAGCTAA-GAAAAACAAAAACTTGCATGAATCATTCACTATGTTTTAGA
* * * * *
1576085 TGTCACATCAAAAGTTTAATGATATGCTAGAAACTCAAAAAGCATTTTTTGATAAAGATGGTTTA
65 TGGCACATCAAAAATTGAATGATATGCTAGAAACTCAAAAAGCATTCTTTGATAAAAATGGTTTA
* * **
1576150 GGATACAATGCCTTTGAGAAAGAAACAAAATTTAAGAATTTCTTTGTCAAGCATAATCTATGATA
130 GGATACAATGCCTTTGAGAAAGAAACAAAATTTAACAATTTCTTTGTCAAGCATAATCCACAATA
* * * ** * *
1576215 TGATGCCTCGTACATGTATTCATTATGTCATAAACGTGGTCACATATTTCACACATGTAATTCTA
195 TAATACCTCATACATGTATTCATTATACCATAAACATGGTCACACATTTCACACATGTAATTCTA
* * *
1576280 GAATAAATAAATTTAGAGGCAAAATTATTAAGAAAATGTGGATGCCTAAAATAATCGGAA
260 AAATAAATAAATTTAGAGGCAAAATTATTAAGAAAATATGGATGCCTAAAAGAATCGGAA
1576340 CTTTTAATGA
Statistics
Matches: 282, Mismatches: 35, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
343 3 0.01
344 277 0.98
345 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (344 bp):
AATGAAAATAATGAATTAGCTAAGAAAAACAAAAACTTGCATGAATCATTCACTATGTTTTAGAT
GGCACATCAAAAATTGAATGATATGCTAGAAACTCAAAAAGCATTCTTTGATAAAAATGGTTTAG
GATACAATGCCTTTGAGAAAGAAACAAAATTTAACAATTTCTTTGTCAAGCATAATCCACAATAT
AATACCTCATACATGTATTCATTATACCATAAACATGGTCACACATTTCACACATGTAATTCTAA
AATAAATAAATTTAGAGGCAAAATTATTAAGAAAATATGGATGCCTAAAAGAATCGGAAGTGAGA
TATTAATAAAATCCTAACC
Found at i:1579985 original size:13 final size:13
Alignment explanation
Indices: 1579967--1580024 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
1579957 AAAACCCAGA
1579967 TGTATCGATACAT
1 TGTATCGATACAT
1579980 TGTATCGATACA-
1 TGTATCGATACAT
* *
1579992 ---AT--ATTCTT
1 TGTATCGATACAT
1580000 TGTATCGATACAT
1 TGTATCGATACAT
1580013 TGTATCGATACA
1 TGTATCGATACA
1580025 ATATTCTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
7 3 0.09
9 2 0.06
11 2 0.06
13 28 0.80
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1580004 original size:20 final size:20
Alignment explanation
Indices: 1579979--1580044 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1579969 TATCGATACA
1579979 TTGTATCGATACAATATTCT
1 TTGTATCGATACAATATTCT
1579999 TTGTATCGATAC---A----
1 TTGTATCGATACAATATTCT
1580012 TTGTATCGATACAATATTCT
1 TTGTATCGATACAATATTCT
*
1580032 TTATATCGATACA
1 TTGTATCGATACA
1580045 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
13 12 0.32
16 1 0.03
17 1 0.03
20 24 0.63
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACAATATTCT
Found at i:1580009 original size:33 final size:33
Alignment explanation
Indices: 1579967--1580058 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
1579957 AAAACCCAGA
1579967 TGTATCGATACATTGTATCGATACAATATTCTT
1 TGTATCGATACATTGTATCGATACAATATTCTT
1580000 TGTATCGATACATTGTATCGATACAATATTCTT
1 TGTATCGATACATTGTATCGATACAATATTCTT
*
1580033 TATATCGATACATTGTATCGATACAA
1 TGTATCGATACATTGTATCGATACAA
1580059 GGATTACTAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATTGTATCGATACAATATTCTT
Found at i:1581610 original size:20 final size:20
Alignment explanation
Indices: 1581585--1581636 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1581575 ATACTTCAAA
1581585 GTATCGATACATAGGTATTT
1 GTATCGATACATAGGTATTT
1581605 GTATCGATACATAGGTATTT
1 GTATCGATACATAGGTATTT
1581625 GTATCGATACAT
1 GTATCGATACAT
1581637 TATGGTTGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (20 bp):
GTATCGATACATAGGTATTT
Found at i:1582748 original size:52 final size:52
Alignment explanation
Indices: 1582690--1582861 Score: 141
Period size: 52 Copynumber: 3.1 Consensus size: 52
1582680 ACTATTGAGT
1582690 ATGTATCGATACAATAAGCATATATCGATACAATGTATCGATACAAAGCATA
1 ATGTATCGATACAATAAGCATATATCGATACAATGTATCGATACAAAGCATA
* ** * * * *
1582742 ATGTATCGATACATTTCACTTAGGGTAGCTACTGCTAGTTTC-ATGTATCGATACAATTGAAT-
1 ATGTATCGATACA----A-TAAGCATA--TA-T-C--GATACAATGTATCGATACAA-AGCATA
* *
1582804 ATGTATTGATACAATAAGCATATATCGATATAATGTATCGATACAAAGCATA
1 ATGTATCGATACAATAAGCATATATCGATACAATGTATCGATACAAAGCATA
1582856 ATGTAT
1 ATGTAT
1582862 AAATATATCT
Statistics
Matches: 90, Mismatches: 16, Indels: 28
0.67 0.12 0.21
Matches are distributed among these distances:
51 5 0.06
52 33 0.37
53 1 0.01
54 1 0.01
55 2 0.02
56 1 0.01
57 10 0.11
58 1 0.01
59 2 0.02
60 1 0.01
61 1 0.01
62 26 0.29
63 6 0.07
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (52 bp):
ATGTATCGATACAATAAGCATATATCGATACAATGTATCGATACAAAGCATA
Found at i:1582831 original size:114 final size:114
Alignment explanation
Indices: 1582631--1582861 Score: 408
Period size: 114 Copynumber: 2.0 Consensus size: 114
1582621 ATGTCCCATA
* * *
1582631 TATCGCTACATTTCACTCAGGGTAGCTACTGCTAGTTTCATGTATCGATACTATTGAGTATGTAT
1 TATCGATACATTTCACTCAGGGTAGCTACTGCTAGTTTCATGTATCGATACAATTGAATATGTAT
1582696 CGATACAATAAGCATATATCGATACAATGTATCGATACAAAGCATAATG
66 CGATACAATAAGCATATATCGATACAATGTATCGATACAAAGCATAATG
*
1582745 TATCGATACATTTCACTTAGGGTAGCTACTGCTAGTTTCATGTATCGATACAATTGAATATGTAT
1 TATCGATACATTTCACTCAGGGTAGCTACTGCTAGTTTCATGTATCGATACAATTGAATATGTAT
* *
1582810 TGATACAATAAGCATATATCGATATAATGTATCGATACAAAGCATAATG
66 CGATACAATAAGCATATATCGATACAATGTATCGATACAAAGCATAATG
1582859 TAT
1 TAT
1582862 AAATATATCT
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 111 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (114 bp):
TATCGATACATTTCACTCAGGGTAGCTACTGCTAGTTTCATGTATCGATACAATTGAATATGTAT
CGATACAATAAGCATATATCGATACAATGTATCGATACAAAGCATAATG
Found at i:1583615 original size:21 final size:19
Alignment explanation
Indices: 1583590--1583635 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1583580 TCCCCCTTTG
*
1583590 TCAAATGCCAAAATTTATTT
1 TCAAAAGCC-AAATTTATTT
*
1583610 ATCAAAAGTCAAATTTATTT
1 -TCAAAAGCCAAATTTATTT
1583630 TCAAAA
1 TCAAAA
1583636 ATTTCTTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 10 0.43
21 7 0.30
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (19 bp):
TCAAAAGCCAAATTTATTT
Found at i:1585495 original size:13 final size:13
Alignment explanation
Indices: 1585477--1585514 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1585467 ATAATAACCC
*
1585477 TGTATCGATATAA
1 TGTATCGATACAA
1585490 TGTATCGATACAA
1 TGTATCGATACAA
*
1585503 TATATCGATACA
1 TGTATCGATACA
1585515 TTTGGGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1586249 original size:20 final size:19
Alignment explanation
Indices: 1586199--1586276 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
1586189 TTTTACCCAG
* *
1586199 ATGTATCGATACATTTTTCA
1 ATGTATCGATACA-TTATGA
* *
1586219 ATATATTGATACATGTATGA
1 ATGTATCGATACAT-TATGA
* *
1586239 ATGTATCGATATATTCTGCA
1 ATGTATCGATACATTATG-A
1586259 ATGTATCGATACATTATG
1 ATGTATCGATACATTATG
1586277 TCTTTTTACC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
19 4 0.09
20 42 0.91
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (19 bp):
ATGTATCGATACATTATGA
Found at i:1586270 original size:40 final size:39
Alignment explanation
Indices: 1586199--1586276 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1586189 TTTTACCCAG
* * *
1586199 ATGTATCGATACATTTTTCAATATATTGATACATGTATGA
1 ATGTATCGATACATTCTGCAATATATCGATACAT-TATGA
* *
1586239 ATGTATCGATATATTCTGCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTGCAATATATCGATACATTATG
1586277 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTGCAATATATCGATACATTATGA
Found at i:1598211 original size:41 final size:41
Alignment explanation
Indices: 1598153--1598233 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
1598143 ATTGTGTTAG
1598153 ATATTTTCGTATATAATGTGTAAGGACTCAGTTTGCTGTCA
1 ATATTTTCGTATATAATGTGTAAGGACTCAGTTTGCTGTCA
*
1598194 ATATTTTCGTATTTAATGTGTAAGGACTCAGTTTGCTGTC
1 ATATTTTCGTATATAATGTGTAAGGACTCAGTTTGCTGTC
1598234 CTAAATGTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (41 bp):
ATATTTTCGTATATAATGTGTAAGGACTCAGTTTGCTGTCA
Found at i:1603075 original size:13 final size:13
Alignment explanation
Indices: 1603057--1603082 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1603047 CAATTTTTTG
1603057 TGTATCGATACAT
1 TGTATCGATACAT
1603070 TGTATCGATACAT
1 TGTATCGATACAT
1603083 ACTTGCTATA
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:1606813 original size:5 final size:5
Alignment explanation
Indices: 1606799--1606845 Score: 69
Period size: 5 Copynumber: 9.6 Consensus size: 5
1606789 CCTTTACACC
* *
1606799 CAAAA AAAAA CAAAA CAAAA CAAAA CAAAA -AAAA CAAAA AAAAA CAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAA
1606846 GAAAAAATAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
4 4 0.11
5 33 0.89
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:1606850 original size:10 final size:10
Alignment explanation
Indices: 1606810--1606870 Score: 58
Period size: 10 Copynumber: 6.3 Consensus size: 10
1606800 AAAAAAAAAC
1606810 AAAACAA-AA
1 AAAACAAGAA
1606819 CAAAACAA-AA
1 -AAAACAAGAA
*
1606829 AAAACAAAAA
1 AAAACAAGAA
1606839 AAAACAAGAA
1 AAAACAAGAA
*
1606849 AAAA-TAGCAA
1 AAAACAAG-AA
1606859 AAAA-AAGAA
1 AAAACAAGAA
1606868 AAA
1 AAA
1606871 GGTCTAGATG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
9 14 0.30
10 32 0.70
ACGTcount: A:0.84, C:0.10, G:0.05, T:0.02
Consensus pattern (10 bp):
AAAACAAGAA
Found at i:1606852 original size:24 final size:23
Alignment explanation
Indices: 1606800--1606864 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 23
1606790 CTTTACACCC
*
1606800 AAAAAAAAACAAAACAAAACAAA
1 AAAAAAAAACAAAAAAAAACAAA
*
1606823 ACAAAAAAAACAAAAAAAAACAAG
1 A-AAAAAAAACAAAAAAAAACAAA
* *
1606847 AAAAAATAGCAAAAAAAA
1 AAAAAAAAACAAAAAAAA
1606865 GAAAAAGGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
23 16 0.43
24 21 0.57
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.02
Consensus pattern (23 bp):
AAAAAAAAACAAAAAAAAACAAA
Found at i:1606863 original size:13 final size:11
Alignment explanation
Indices: 1606800--1606864 Score: 62
Period size: 12 Copynumber: 5.6 Consensus size: 11
1606790 CTTTACACCC
1606800 AAAAAAAAACA
1 AAAAAAAAACA
1606811 AAACAAAACAA-A
1 AAA-AAAA-AACA
1606823 ACAAAAAAAAC-
1 A-AAAAAAAACA
1606834 AAAAAAAAACA
1 AAAAAAAAACA
*
1606845 AGAAAAAATAGCA
1 A-AAAAAA-AACA
1606858 AAAAAAA
1 AAAAAAA
1606865 GAAAAAGGTC
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
10 9 0.20
11 7 0.15
12 22 0.48
13 8 0.17
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.02
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:1608196 original size:28 final size:28
Alignment explanation
Indices: 1608070--1609381 Score: 1430
Period size: 28 Copynumber: 45.7 Consensus size: 28
1608060 GTTCATCCCC
* *
1608070 TTCAAAGCCCATGAA-TCAGTGGCACTCTT
1 TTCAAAGCCCA-CAAGTCAGTGGCAC-CCT
**
1608099 TTCAAAGCCCATGAGTCAGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCC-T
* *
1608128 TTCAAAGCCCATAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
*
1608157 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1608185 TTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
1608213 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
1608241 TTCAGAGCCCACAAGTCAGTGGCACCAT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1608269 TTCGAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
1608297 TTCGAAGCCCACAATTCAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1608325 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1608353 TTCAAAGCCCATACAAGTCATTGGCACCCCT
1 TTCAAAGCCC--ACAAGTCAGTGGCA-CCCT
*
1608384 TTCAAAGCCCACACAAGTCGGTGGCAACTCCT
1 TTCAAAG-CC-CACAAGTCAGTGGC-AC-CCT
* * *
1608416 TTTAAAGCCCATAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
1608445 TTCAAAACCCACAAGTCAATGGCACCCG
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
1608473 TTC-AAGCCCACGAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
**
1608500 TTC-AAGCCCACAAGTCAGTGGCACATT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
** *
1608527 TTCAAAGCCCATGAGTCAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1608555 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
1608583 TTCAAAGCCCACACAAGTCAGTGGCACCCT
1 TTCAAAG-CC-CACAAGTCAGTGGCACCCT
* ** *
1608613 TTTAAAGCCCACGCAAGTCAGTAACACCTT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCT
* *
1608643 TTCAAAGCCCACGAGTCAGTGGCACCTTT
1 TTCAAAGCCCACAAGTCAGTGGCACC-CT
* *
1608672 TTCAAAGCCCACGAGTCAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1608700 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
1608728 TTCAAAGCCCACACAAGTTAATGACACCCT
1 TTCAAAG-CC-CACAAGTCAGTGGCACCCT
* *
1608758 TTTAAAGCCCACGCAAGTCAGTGGCACCTTT
1 TTCAAAGCCCA--CAAGTCAGTGGCACC-CT
* *
1608789 TTCAAAGCCCACGAGTCAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1608817 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
1608845 TTCAAAGCCCACGCAAGTTAGTGACACCCT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCT
* *
1608875 TTTAAAGCCCACGCAAGTCAGTGGCACCTT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCT
*
1608905 TTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
1608933 TTCAAAGCCCACAAGTCAGTAGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1608961 TTCAAAGCCCACGCAAGTTAGTGGCACCCT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCT
* **
1608991 TTTAAAGCCCACGCAAGTCAGTGGCACATT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCT
* * *
1609021 TTC-AAGCCCACGAGTTAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1609048 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1609076 TTCAAAGCCTACGCAAGTCAGTGGCACCCT
1 TTCAAAGCC--CACAAGTCAGTGGCACCCT
* * *
1609106 TTTAAAGCCCACGCAAGTCAGTAGCACTCTT
1 TTCAAAGCCCA--CAAGTCAGTGGCAC-CCT
*
1609137 TTCAAAGCCCACGTAAGTCAGTGGCACTCT
1 TTCAAAGCCCAC--AAGTCAGTGGCACCCT
**
1609167 TGTCAAAGCCCATGAGTCAGTGGCACCCT
1 T-TCAAAGCCCACAAGTCAGTGGCACCCT
** * **
1609196 TTCAAAGCCCATGAGTAAGTGGCACATT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * **
1609224 TTC-AAGCTCACAAGTCAGTGGTACTTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* **
1609251 TTC-AAGCCCACAAGTTAGTGGCACTTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* **
1609278 TTCAAAGCCCACAAGTCAGTGGTACTTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
1609306 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
**
1609334 TTCAAAGCCCACAAGTCAGTGGCACATT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1609362 TTCAAAGCCCACAAGCCAGT
1 TTCAAAGCCCACAAGTCAGT
1609382 AAGTAACTCT
Statistics
Matches: 1099, Mismatches: 149, Indels: 71
0.83 0.11 0.05
Matches are distributed among these distances:
27 106 0.10
28 505 0.46
29 167 0.15
30 239 0.22
31 69 0.06
32 12 0.01
33 1 0.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:1610037 original size:20 final size:20
Alignment explanation
Indices: 1610012--1610083 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
1610002 TACCCAGATG
1610012 TATCGATACATTTTTCAATA
1 TATCGATACATTTTTCAATA
* * *
1610032 TATCGATACATGTATGAATA
1 TATCGATACATTTTTCAATA
* * * *
1610052 TATCGATATATTCTGCAATG
1 TATCGATACATTTTTCAATA
1610072 TATCGATACATT
1 TATCGATACATT
1610084 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (20 bp):
TATCGATACATTTTTCAATA
Found at i:1611025 original size:20 final size:21
Alignment explanation
Indices: 1610988--1611026 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1610978 AGCCTTTGAC
**
1610988 CATGCATTTTTTTTTATGTTT
1 CATGCATTTTTTAATATGTTT
1611009 CATGCA-TTTTTAATATGT
1 CATGCATTTTTTAATATGT
1611027 CGAGCATCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (21 bp):
CATGCATTTTTTAATATGTTT
Found at i:1618778 original size:35 final size:35
Alignment explanation
Indices: 1618733--1618800 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
1618723 CCCAAAGTTT
1618733 ATACATACTAATTTAAAAAATCAAAAACCTTAATC
1 ATACATACTAATTTAAAAAATCAAAAACCTTAATC
*
1618768 ATACATACTAATTTAGAAAATCAAAAACCTTAA
1 ATACATACTAATTTAAAAAATCAAAAACCTTAA
1618801 GATAAAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.54, C:0.16, G:0.01, T:0.28
Consensus pattern (35 bp):
ATACATACTAATTTAAAAAATCAAAAACCTTAATC
Found at i:1619374 original size:24 final size:24
Alignment explanation
Indices: 1619347--1619397 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1619337 TACCCATGTA
*
1619347 CAACGAATTTCAACCTTATTTATG
1 CAACGAATTTCAACCTAATTTATG
1619371 CAACGAATTTCAACCTAATTTATG
1 CAACGAATTTCAACCTAATTTATG
1619395 CAA
1 CAA
1619398 TTGTAGTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (24 bp):
CAACGAATTTCAACCTAATTTATG
Found at i:1619707 original size:13 final size:13
Alignment explanation
Indices: 1619686--1619722 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1619676 ATTGAAAATG
1619686 TAATGAATAAATAT
1 TAAT-AATAAATAT
1619700 TAATAATAAATAT
1 TAATAATAAATAT
*
1619713 TGATAATAAA
1 TAATAATAAA
1619723 AAAATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (13 bp):
TAATAATAAATAT
Found at i:1620276 original size:2 final size:2
Alignment explanation
Indices: 1620269--1620304 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1620259 TCCCTTTTGC
*
1620269 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1620305 TCTAATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1620759 original size:3 final size:3
Alignment explanation
Indices: 1620746--1620830 Score: 75
Period size: 3 Copynumber: 26.7 Consensus size: 3
1620736 TAGATAGATA
1620746 AAT AAT AAAT AAT AAT AAT AAT AAT AA- ATAT AA- ATAT AAAT AAAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT A-AT AAT A-AT -AAT -AAT
* *
1620791 AGAT AAT AAAG AAC AAT AAT AAT AAT AAT AAT AAT AAT AA
1 A-AT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1620831 GAAGGTGGGC
Statistics
Matches: 71, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
2 2 0.03
3 53 0.75
4 15 0.21
5 1 0.01
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:1624735 original size:50 final size:50
Alignment explanation
Indices: 1624674--1624783 Score: 132
Period size: 50 Copynumber: 2.2 Consensus size: 50
1624664 AGTTGCTTAG
* * * * * * *
1624674 AGTCAATAATTATGGCCACCTCTTTTGATTGTCAAAAG-TTGGTGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTGTC-AAAGTTTAGTGAAAAAT
*
1624724 AGTCAACAATTACGATCACCTCTCTCGATTGTCAAAGTTTAGTGAAAAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAGTTTAGTGAAAAAT
1624774 AGTCAACAAT
1 AGTCAACAAT
1624784 GACAACACCT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 4 0.08
50 47 0.92
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (50 bp):
AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAGTTTAGTGAAAAAT
Found at i:1626005 original size:15 final size:15
Alignment explanation
Indices: 1625970--1626012 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
1625960 ATAAATAAAT
*
1625970 AATTATTTATTTTTAT
1 AATT-TTTATTTTTAA
*
1625986 CATTTTTATTTTTAA
1 AATTTTTATTTTTAA
1626001 AATTTTATATTT
1 AATTTT-TATTT
1626013 AATTAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
AATTTTTATTTTTAA
Found at i:1626853 original size:2 final size:2
Alignment explanation
Indices: 1626841--1626883 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1626831 AAAGTTCTTT
1626841 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1626882 TA
1 TA
1626884 CTATCGAGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1627584 original size:8 final size:8
Alignment explanation
Indices: 1627571--1627605 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
1627561 TTTTTAAAAT
1627571 AAAATATA
1 AAAATATA
1627579 AAAATATAA
1 AAAATAT-A
1627588 AAAATATA
1 AAAATATA
*
1627596 AACATATA
1 AAAATATA
1627604 AA
1 AA
1627606 TTTAATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAATATA
Found at i:1627593 original size:17 final size:17
Alignment explanation
Indices: 1627571--1627605 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1627561 TTTTTAAAAT
1627571 AAAATATAAAAATATAA
1 AAAATATAAAAATATAA
*
1627588 AAAATATAAACATATAA
1 AAAATATAAAAATATAA
1627605 A
1 A
1627606 TTTAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAATATAAAAATATAA
Found at i:1627802 original size:24 final size:23
Alignment explanation
Indices: 1627771--1627819 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
1627761 CTAACACTAT
*
1627771 TAATATAAT-TTTTTATTATTTAA
1 TAATATAATATTTTT-TTATTGAA
1627794 TAATCATAATATTTTTTTATTGAA
1 TAAT-ATAATATTTTTTTATTGAA
1627818 TA
1 TA
1627820 CTCCAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TAATATAATATTTTTTTATTGAA
Found at i:1631485 original size:30 final size:30
Alignment explanation
Indices: 1631425--1631485 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
1631415 TTTAATTTTA
**
1631425 AAAAAATAAAATATTAAAATATTTATTATT
1 AAAAAATAAAATATTAAAATAAATATTATT
*
1631455 AAAAAATAAAAT-TTAATATAAATATGTATT
1 AAAAAATAAAATATTAAAATAAATAT-TATT
1631485 A
1 A
1631486 GTATGTTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAAAATAAAATATTAAAATAAATATTATT
Found at i:1632113 original size:17 final size:17
Alignment explanation
Indices: 1632084--1632142 Score: 91
Period size: 17 Copynumber: 3.4 Consensus size: 17
1632074 TGTTTGTATA
1632084 TTTATATTTATATTATTT
1 TTTATA-TTATATTATTT
* *
1632102 TTTATATTATATCATAT
1 TTTATATTATATTATTT
1632119 TTTATATTATATTATTT
1 TTTATATTATATTATTT
1632136 TTTATAT
1 TTTATAT
1632143 CGTGTAATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
17 31 0.84
18 6 0.16
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATATTATATTATTT
Found at i:1632723 original size:16 final size:16
Alignment explanation
Indices: 1632691--1632737 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1632681 AATATTTGAA
*
1632691 ATATA-ACATGAAAATG
1 ATATACACAT-AATATG
1632707 ATATACACATAATATG
1 ATATACACATAATATG
1632723 A-ATACACATACATAT
1 ATATACACATA-ATAT
1632738 AAAAATATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 9 0.32
16 15 0.54
17 4 0.14
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.28
Consensus pattern (16 bp):
ATATACACATAATATG
Found at i:1632729 original size:15 final size:17
Alignment explanation
Indices: 1632704--1632737 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1632694 TAACATGAAA
1632704 ATGATATACACATA-AT
1 ATGATATACACATACAT
1632720 ATGA-ATACACATACAT
1 ATGATATACACATACAT
1632736 AT
1 AT
1632738 AAAAATATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (17 bp):
ATGATATACACATACAT
Found at i:1632801 original size:24 final size:25
Alignment explanation
Indices: 1632749--1632803 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
1632739 AAAATATACA
*
1632749 TAAAATAAAATAAATTATTAATATG
1 TAAAATAAAATAAAATATTAATATG
*
1632774 TAAAA-AAATATAAAATA-TAATATT
1 TAAAATAAA-ATAAAATATTAATATG
1632798 TAAAAT
1 TAAAAT
1632804 GCAAAAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
TAAAATAAAATAAAATATTAATATG
Found at i:1633257 original size:13 final size:13
Alignment explanation
Indices: 1633239--1633269 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1633229 ATTTTGAATA
1633239 ATATTAGATACAT
1 ATATTAGATACAT
1633252 ATATTAGATACAT
1 ATATTAGATACAT
1633265 ATATT
1 ATATT
1633270 GAAATAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (13 bp):
ATATTAGATACAT
Found at i:1633279 original size:13 final size:13
Alignment explanation
Indices: 1633239--1633281 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1633229 ATTTTGAATA
*
1633239 ATATTAGATACAT
1 ATATTAAATACAT
*
1633252 ATATTAGATACAT
1 ATATTAAATACAT
1633265 ATATTGAAATA-AT
1 ATATT-AAATACAT
1633278 ATAT
1 ATAT
1633282 GCTTTTTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
13 24 0.86
14 4 0.14
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (13 bp):
ATATTAAATACAT
Found at i:1634005 original size:18 final size:19
Alignment explanation
Indices: 1633967--1634008 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1633957 AATTTGTATG
* *
1633967 TTTATAAAATAATTTATTT
1 TTTAAAAAAAAATTTATTT
1633986 TTTAAAAAAAAATTTATTT
1 TTTAAAAAAAAATTTATTT
1634005 TTTA
1 TTTA
1634009 TCGTAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAAAAAAAATTTATTT
Found at i:1634748 original size:21 final size:21
Alignment explanation
Indices: 1634724--1634763 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1634714 TCTCTTCTAA
1634724 TCTTTCGAAATTCAAACCTCC
1 TCTTTCGAAATTCAAACCTCC
* *
1634745 TCTTTCTAAGTTCAAACCT
1 TCTTTCGAAATTCAAACCT
1634764 TAAAAAGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.30, G:0.05, T:0.38
Consensus pattern (21 bp):
TCTTTCGAAATTCAAACCTCC
Found at i:1640635 original size:138 final size:138
Alignment explanation
Indices: 1640382--1640636 Score: 334
Period size: 138 Copynumber: 1.8 Consensus size: 138
1640372 CTGCATGGCA
* *
1640382 AATGAAGCAAAGCAACATCTTGAGTCTCAACTCAGTAGCATGGCAACAGATACAGAGACAATGTC
1 AATGAAGCAAAGCAACATCTTGAGTCTCAACTCAGTAGCATAGCAACAGAGACAGAGACAATGTC
* * * *
1640447 CGCTAAGATTGACTCATTAGAAGCAGAAATTGAAAAGGAAAGGACCTTGTCAGAGCAAGTTTCAG
66 AGCAAAGATTGACTCATTAGAAACAGAAATTGAAAAGGAAAGGACATTGTCAGAGCAAGTTTCAG
1640512 TTAACTCG
131 TTAACTCG
* * * * * * *
1640520 AATGAATCAAAGCAACTTCTTGAGTCTCAACTCATTAGCCTAG-AAGCAGAGGCTCG-GACGATG
1 AATGAAGCAAAGCAACATCTTGAGTCTCAACTCAGTAGCATAGCAA-CAGAGAC-AGAGACAATG
* * *
1640583 TCAGCAAAGATTGATTCATTAGAAACAGAAGTTGAAAAGGAAAGGGCATTGTCA
64 TCAGCAAAGATTGACTCATTAGAAACAGAAATTGAAAAGGAAAGGACATTGTCA
1640637 TCAAAAATTT
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
137 2 0.02
138 96 0.97
139 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (138 bp):
AATGAAGCAAAGCAACATCTTGAGTCTCAACTCAGTAGCATAGCAACAGAGACAGAGACAATGTC
AGCAAAGATTGACTCATTAGAAACAGAAATTGAAAAGGAAAGGACATTGTCAGAGCAAGTTTCAG
TTAACTCG
Found at i:1642124 original size:20 final size:20
Alignment explanation
Indices: 1642088--1642125 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1642078 TGATTATATT
*
1642088 AAATTTTTTATATATTTAAA
1 AAATTTTTTATACATTTAAA
1642108 AAATTATTTT-TACATTTA
1 AAATT-TTTTATACATTTA
1642126 TATTCGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
AAATTTTTTATACATTTAAA
Found at i:1647085 original size:18 final size:17
Alignment explanation
Indices: 1647036--1647103 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 17
1647026 ATATATATTT
*
1647036 TAAAATTTTTAT-AATA
1 TAAAATTTATATAAATA
1647052 T-AAA-TTAT-TAACATA
1 TAAAATTTATATAA-ATA
1647067 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
1647085 TAAAATATT-T-TAAATA
1 TAAAAT-TTATATAAATA
1647101 TAA
1 TAA
1647104 TAAAATGTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
13 1 0.02
14 4 0.09
15 6 0.14
16 11 0.25
17 10 0.23
18 9 0.20
19 3 0.07
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:1647121 original size:20 final size:17
Alignment explanation
Indices: 1647096--1647134 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 17
1647086 AAAATATTTT
1647096 AAATATAATAAAATGTAATA
1 AAATAT-AT-AAAT-TAATA
1647116 AAATATATAAATTAATA
1 AAATATATAAATTAATA
1647133 AA
1 AA
1647135 TTAAAGCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 2 0.11
20 6 0.32
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
AAATATATAAATTAATA
Found at i:1647135 original size:36 final size:34
Alignment explanation
Indices: 1647049--1647135 Score: 88
Period size: 36 Copynumber: 2.5 Consensus size: 34
1647039 AATTTTTATA
*
1647049 ATATAAATTATTAACATATTAAAATTTATATAAAT
1 ATATAAATTATTAA-ATATTAAAATTAATATAAAT
*
1647084 ATA-AAATATTTTAAATATAATAAAATGTAATA-AAAT
1 ATATAAAT-TATTAAATAT--TAAAAT-TAATATAAAT
*
1647120 ATATAAATTAATAAAT
1 ATATAAATTATTAAAT
1647136 TAAAGCAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
34 8 0.19
35 8 0.19
36 19 0.44
37 8 0.19
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (34 bp):
ATATAAATTATTAAATATTAAAATTAATATAAAT
Found at i:1647555 original size:25 final size:25
Alignment explanation
Indices: 1647505--1647564 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
1647495 AATTTTTAGT
* *
1647505 AAATAAAATTTTTAAAATATCGAATA
1 AAATTAAATTTTTAAAAAATC-AATA
1647531 AAATTAAATTATTTAAAAAAT-AATA
1 AAATTAAATT-TTTAAAAAATCAATA
1647556 AAATTAAAT
1 AAATTAAAT
1647565 ATTCTTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 13 0.42
26 9 0.29
27 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
AAATTAAATTTTTAAAAAATCAATA
Found at i:1647745 original size:21 final size:21
Alignment explanation
Indices: 1647721--1647761 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1647711 TATTATCACA
* *
1647721 ATAATATTTAATTTTATTATT
1 ATAATAATTAATCTTATTATT
1647742 ATAATAATTAATCTTATTAT
1 ATAATAATTAATCTTATTAT
1647762 AATTACTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
ATAATAATTAATCTTATTATT
Found at i:1650215 original size:18 final size:18
Alignment explanation
Indices: 1650189--1650230 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1650179 TTATAATAAA
* *
1650189 TTATTTAACAAATTGATT
1 TTATATAACAAATTAATT
*
1650207 TTATATAACAAGTTAATT
1 TTATATAACAAATTAATT
1650225 TTATAT
1 TTATAT
1650231 CTTTTTATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (18 bp):
TTATATAACAAATTAATT
Found at i:1656350 original size:28 final size:28
Alignment explanation
Indices: 1656307--1656365 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
1656297 AATGCATGAC
1656307 AAAATTTATAGATAAAT-TATTAATATATAA
1 AAAATTTATA-ATAAATATA-TAATAT-TAA
1656337 AAAATTTAT-ATAAATATATAATATTAA
1 AAAATTTATAATAAATATATAATATTAA
1656364 AA
1 AA
1656366 TTTAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 5 0.18
28 12 0.43
29 2 0.07
30 9 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (28 bp):
AAAATTTATAATAAATATATAATATTAA
Found at i:1656500 original size:36 final size:36
Alignment explanation
Indices: 1656451--1656519 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
1656441 TTTATCCTTT
* *
1656451 AAAGGTGGCAAGATAGTGAATT-GGATACTCTTTTTG
1 AAAGGTAGCAAGATAGTAAATTGGGA-ACTCTTTTTG
* *
1656487 AAAGGTAGTAAGATATTAAATTGGGAACTCTTT
1 AAAGGTAGCAAGATAGTAAATTGGGAACTCTTT
1656520 AGCAAGTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 25 0.89
37 3 0.11
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (36 bp):
AAAGGTAGCAAGATAGTAAATTGGGAACTCTTTTTG
Found at i:1658975 original size:15 final size:15
Alignment explanation
Indices: 1658934--1658975 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1658924 TTTGCATGAA
*
1658934 TAAATATATTTTTAG
1 TAAATATATTTTAAG
1658949 TAAAT-TACTTTTAAG
1 TAAATATA-TTTTAAG
*
1658964 TCAATATATTTT
1 TAAATATATTTT
1658976 TGAAAACGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.09
15 19 0.83
16 2 0.09
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (15 bp):
TAAATATATTTTAAG
Found at i:1660292 original size:18 final size:18
Alignment explanation
Indices: 1660253--1660293 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
1660243 TGTTTGTATT
*
1660253 ATATTTTTATAATTTTTG
1 ATATTTTTATAAATTTTG
1660271 -TATTTTT-TAAGATTTTG
1 ATATTTTTATAA-ATTTTG
1660288 ATATTT
1 ATATTT
1660294 GTATCTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.15
17 12 0.60
18 5 0.25
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (18 bp):
ATATTTTTATAAATTTTG
Found at i:1662860 original size:18 final size:19
Alignment explanation
Indices: 1662826--1662862 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1662816 ATTATAATAT
1662826 AATATAAAAATATGAATTA
1 AATATAAAAATATGAATTA
*
1662845 AATATGAAAA-ATGAATTA
1 AATATAAAAATATGAATTA
1662863 TTTGATCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (19 bp):
AATATAAAAATATGAATTA
Found at i:1664154 original size:97 final size:97
Alignment explanation
Indices: 1664053--1664231 Score: 322
Period size: 97 Copynumber: 1.8 Consensus size: 97
1664043 AGAAAATGAA
*
1664053 GATCGGAAGGTTTTGGTGCGTGCTTCTTCATTCAGGCATAGTCTAAAAGGAAAAAGTGAGACTAA
1 GATCGGAAGGTTTGGGTGCGTGCTTCTTCATTCAGGCATAGTCTAAAAGGAAAAAGTGAGACTAA
*
1664118 TTTAATGAAAATCTTTAGACCTAAGAAAAAAC
66 TTTAATAAAAATCTTTAGACCTAAGAAAAAAC
* *
1664150 GATCGGAAGGTTTGGGTGCGTGCTTTTTCATTCATGCATAGTCTAAAAGGAAAAAGTGAGACTAA
1 GATCGGAAGGTTTGGGTGCGTGCTTCTTCATTCAGGCATAGTCTAAAAGGAAAAAGTGAGACTAA
1664215 TTTAATAAAAATCTTTA
66 TTTAATAAAAATCTTTA
1664232 ATTTAAAACT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
97 78 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (97 bp):
GATCGGAAGGTTTGGGTGCGTGCTTCTTCATTCAGGCATAGTCTAAAAGGAAAAAGTGAGACTAA
TTTAATAAAAATCTTTAGACCTAAGAAAAAAC
Found at i:1665779 original size:12 final size:13
Alignment explanation
Indices: 1665764--1665795 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1665754 GAAAAAATGG
1665764 AGAAAAAAG-AGA
1 AGAAAAAAGAAGA
1665776 AGAAAAAAGAAGA
1 AGAAAAAAGAAGA
1665789 A-AAAAAA
1 AGAAAAAA
1665796 CTAGTTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AGAAAAAAGAAGA
Found at i:1665794 original size:11 final size:11
Alignment explanation
Indices: 1665753--1665794 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
1665743 CGGGCACGTG
* *
1665753 AGAAAAAATGG
1 AGAAAAAAAGA
1665764 AGAAAAAAGAGA
1 AGAAAAAA-AGA
1665776 AG-AAAAAAGA
1 AGAAAAAAAGA
1665786 AGAAAAAAA
1 AGAAAAAAA
1665795 ACTAGTTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 5 0.19
11 19 0.70
12 3 0.11
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (11 bp):
AGAAAAAAAGA
Found at i:1667195 original size:155 final size:155
Alignment explanation
Indices: 1666926--1667219 Score: 376
Period size: 155 Copynumber: 1.9 Consensus size: 155
1666916 TTTTGAGCAT
** * * *
1666926 TTTAGGAGTGTCAGTTACTTTTACGTCGAAGGTATCCCTTAGAGGTATTTTCGTAATTTTTTAGA
1 TTTAGGAGTGTCAGGCACTTTTACATCGAAAGTATCCCTTAGAGGTATTTTCGTAATTTTTCAGA
* * * * * * * *
1666991 ACCGAGTCATAGGTTGTCACCGGGTCTGCTTTTATGCTGATGGTTGGTATTTAGGATAGGTTCAT
66 ACCAAGTCATAAGTTATCACCGGATCCGCTTTTATGCTGAAGGTGGGTATTTAGGAAAGGTTCAT
1667056 CCCATCTATAATCCTTTTCAAACCC
131 CCCATCTATAATCCTTTTCAAACCC
* *
1667081 TTTAGGGGTGTCAGGCATTTTTACATCGAAAGTATCCC-TAG-GAGTATTTTCGTAATTTTTCAG
1 TTTAGGAGTGTCAGGCACTTTTACATCGAAAGTATCCCTTAGAG-GTATTTTCGTAATTTTTCAG
* * * * *
1667144 AATCAAGTCTTAAGTTATCACTGGATCCGCTTTTATGTTGAAGGTGGGGTATTTAGGAAATGTTC
65 AACCAAGTCATAAGTTATCACCGGATCCGCTTTTATGCTGAAGGT-GGGTATTTAGGAAAGGTTC
1667209 ATCCCATCTAT
129 ATCCCATCTAT
1667220 TATTTTTTAA
Statistics
Matches: 117, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
153 1 0.01
154 57 0.49
155 59 0.50
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (155 bp):
TTTAGGAGTGTCAGGCACTTTTACATCGAAAGTATCCCTTAGAGGTATTTTCGTAATTTTTCAGA
ACCAAGTCATAAGTTATCACCGGATCCGCTTTTATGCTGAAGGTGGGTATTTAGGAAAGGTTCAT
CCCATCTATAATCCTTTTCAAACCC
Found at i:1668064 original size:13 final size:13
Alignment explanation
Indices: 1668046--1668070 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1668036 TTTATCCAAA
1668046 TGTATCGATACAT
1 TGTATCGATACAT
1668059 TGTATCGATACA
1 TGTATCGATACA
1668071 AAGCTACCCT
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:1672296 original size:20 final size:19
Alignment explanation
Indices: 1672271--1672364 Score: 84
Period size: 20 Copynumber: 4.8 Consensus size: 19
1672261 TTTTTACCCA
*
1672271 AATGTATCGATACATGTATG
1 AATGTATCGATACAT-TATC
*
1672291 AATGTATCGATACATTCTTC
1 AATGTATCGATACATT-ATC
* *
1672311 AATGTACCGATACATTTACCC
1 AATGTATCGATACA-TTA-TC
*
1672332 AGATGTATCGATACA-T-TG
1 A-ATGTATCGATACATTATC
1672350 AATGTATCGATACAT
1 AATGTATCGATACAT
1672365 CTAGTTAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
17 13 0.21
18 1 0.02
19 1 0.02
20 30 0.49
21 4 0.07
22 12 0.20
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (19 bp):
AATGTATCGATACATTATC
Found at i:1676955 original size:33 final size:33
Alignment explanation
Indices: 1676918--1676984 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1676908 TTCAACGATT
1676918 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1676951 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1676984 T
1 T
1676985 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1676956 original size:13 final size:13
Alignment explanation
Indices: 1676938--1676962 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1676928 CATAAAATGT
1676938 TGTATCGATACAA
1 TGTATCGATACAA
1676951 TGTATCGATACA
1 TGTATCGATACA
1676963 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:1677045 original size:13 final size:13
Alignment explanation
Indices: 1677027--1677051 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1677017 ATTACTCACA
1677027 TGTATCGATACAT
1 TGTATCGATACAT
1677040 TGTATCGATACA
1 TGTATCGATACA
1677052 CTGATCTTTG
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:1677188 original size:52 final size:52
Alignment explanation
Indices: 1677060--1677180 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1677050 CACTGATCTT
*
1677060 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1677112 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1677164 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1677181 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1680438 original size:1 final size:1
Alignment explanation
Indices: 1680432--1680531 Score: 65
Period size: 1 Copynumber: 100.0 Consensus size: 1
1680422 AAGAAGTGAT
* * * * * * * * * *
1680432 AAAAAAAAAAACAAACAAACAAAAAAAAAACACACAAAAAAAAAAAACAACAAAAAACACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
1680497 ACAAAAAACAAAAAAAAACAAACACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1680532 GTGCAAAGGT
Statistics
Matches: 69, Mismatches: 30, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1680455 original size:15 final size:14
Alignment explanation
Indices: 1680437--1680529 Score: 104
Period size: 14 Copynumber: 6.6 Consensus size: 14
1680427 GTGATAAAAA
1680437 AAAAAACAAACAAAC
1 AAAAAA-AAACAAAC
*
1680452 AAAAAAAAAACACAC
1 -AAAAAAAAACAAAC
1680467 AAAAAAAAA-AAAC
1 AAAAAAAAACAAAC
*
1680480 AACAAAAAAC--AC
1 AAAAAAAAACAAAC
1680492 AAAAAACAAA-AAAC
1 AAAAAA-AAACAAAC
1680506 AAAAAAAAACAAAC
1 AAAAAAAAACAAAC
1680520 ACAAAAAAAA
1 A-AAAAAAAA
1680530 AAGTGCAAAG
Statistics
Matches: 67, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
12 7 0.10
13 17 0.25
14 22 0.33
15 15 0.22
16 6 0.09
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAACAAAC
Found at i:1680455 original size:16 final size:16
Alignment explanation
Indices: 1680436--1680531 Score: 84
Period size: 15 Copynumber: 6.4 Consensus size: 16
1680426 AGTGATAAAA
1680436 AAAAAAACAAACAAAC
1 AAAAAAACAAACAAAC
*
1680452 AAAAAAA-AAACACAC
1 AAAAAAACAAACAAAC
*
1680467 AAAAAAA-AAAAACAAC
1 AAAAAAACAAACA-AAC
1680483 AAAAAACACAAA-AAAC
1 AAAAAA-ACAAACAAAC
1680499 -AAAAAACAAA-AAA-
1 AAAAAAACAAACAAAC
*
1680512 AAACAAAC--ACAAA-
1 AAAAAAACAAACAAAC
1680525 AAAAAAA
1 AAAAAAA
1680532 GTGCAAAGGT
Statistics
Matches: 70, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
12 1 0.01
13 9 0.13
14 14 0.20
15 23 0.33
16 18 0.26
17 2 0.03
18 3 0.04
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAACAAAC
Found at i:1680455 original size:17 final size:17
Alignment explanation
Indices: 1680435--1680531 Score: 90
Period size: 17 Copynumber: 5.5 Consensus size: 17
1680425 AAGTGATAAA
1680435 AAAAAAAACAAACAAAC
1 AAAAAAAACAAACAAAC
* *
1680452 AAAAAAAAAACACACAAAA
1 --AAAAAAAACAAACAAAC
*
1680471 AAAAAAAACAACAAAAAAC
1 AAAAAAAAC-A-AACAAAC
*
1680490 ACAAAAAACAAA-AAAC
1 AAAAAAAACAAACAAAC
1680506 AAAAAAAAACAAACACAA-
1 -AAAAAAAACAAACA-AAC
1680524 AAAAAAAA
1 AAAAAAAA
1680532 GTGCAAAGGT
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
16 4 0.06
17 30 0.45
18 3 0.05
19 29 0.44
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAACAAACAAAC
Found at i:1680496 original size:39 final size:38
Alignment explanation
Indices: 1680432--1680531 Score: 127
Period size: 39 Copynumber: 2.6 Consensus size: 38
1680422 AAGAAGTGAT
*
1680432 AAAAAAAAA-AACAAACAAACAAAAAAA-AAACACACAAA
1 AAAAAAAAACAACAAA-AAACAAAAAAACAAA-AAACAAA
1680470 AAAAAAAAACAACAAAAAACACAAAAAACAAAAAACAAA
1 AAAAAAAAACAACAAAAAACA-AAAAAACAAAAAACAAA
1680509 AAAAAACAAAC-ACAAAAAA-AAAA
1 AAAAAA-AAACAACAAAAAACAAAA
1680532 GTGCAAAGGT
Statistics
Matches: 57, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
37 3 0.05
38 15 0.26
39 32 0.56
40 7 0.12
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (38 bp):
AAAAAAAAACAACAAAAAACAAAAAAACAAAAAACAAA
Found at i:1680786 original size:1 final size:1
Alignment explanation
Indices: 1680776--1680811 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
1680766 TTCCAAACAC
*
1680776 AAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1680812 CCCCTTTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:1681831 original size:32 final size:32
Alignment explanation
Indices: 1681780--1681998 Score: 160
Period size: 32 Copynumber: 6.7 Consensus size: 32
1681770 ATCTCTTCTC
* * * *
1681780 AAAGTCCACGACTCAGTGGCATTTTTTTCTTC
1 AAAGCCCACAACTCCGTGGCATTTTTTTCTTT
* ** *
1681812 AAAGCCCACAACTTCGTGGCACCTTTTCCTTT
1 AAAGCCCACAACTCCGTGGCATTTTTTTCTTT
***
1681844 AAAGCCCACAACTCCGTGGCA---CCCT-TTT
1 AAAGCCCACAACTCCGTGGCATTTTTTTCTTT
* *
1681872 AAAGCCCACAATTCTGTGGCACTTTTTTTCATTTTT
1 AAAGCCCACAACTCCGTGGCA-TTTTTTTC---TTT
*
1681908 AAAGCCCACAACTCCGTGGCACCTTCTTCTT-TTT
1 AAAGCCCACAACTCCGTGGCA--TT-TTTTTCTTT
*
1681942 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
1 AAAGCCCACAACTCCGTGGCA-T-TTTTT-TCTTT
* *
1681977 TAAGTCCACAACTCCGTGGCAT
1 AAAGCCCACAACTCCGTGGCAT
1681999 CTTTCTCCCT
Statistics
Matches: 149, Mismatches: 25, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
28 22 0.15
32 45 0.30
33 5 0.03
34 26 0.17
35 22 0.15
36 22 0.15
37 3 0.02
38 4 0.03
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.32
Consensus pattern (32 bp):
AAAGCCCACAACTCCGTGGCATTTTTTTCTTT
Found at i:1681946 original size:34 final size:33
Alignment explanation
Indices: 1681812--1681997 Score: 188
Period size: 35 Copynumber: 5.6 Consensus size: 33
1681802 TTTTTTCTTC
* *
1681812 AAAGCCCACAACTTCGTGGCACCTT-TTCCTTT
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
1681844 AAAGCCCACAACTCCGTGGCA-C--C--CTTTT
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
* * * *
1681872 AAAGCCCACAATTCTGTGGCACTTTTTTTCATTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTCTTC--TTTT
1681908 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTCTTC-TTTT
*
1681942 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTCTT--CTTTT
*
1681978 -AAGTCCACAACTCCGTGGCA
1 AAAGCCCACAACTCCGTGGCA
1681998 TCTTTCTCCC
Statistics
Matches: 130, Mismatches: 12, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
28 23 0.18
31 1 0.01
32 20 0.15
34 28 0.22
35 29 0.22
36 28 0.22
37 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.13, T:0.31
Consensus pattern (33 bp):
AAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
Found at i:1681970 original size:70 final size:62
Alignment explanation
Indices: 1681812--1681997 Score: 207
Period size: 70 Copynumber: 2.9 Consensus size: 62
1681802 TTTTTTCTTC
* *
1681812 AAAGCCCACAACTTCGTGGCAC-C-TTTTCCTTTAAAGCCCACAACTCCGTGGCACCCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCCTTTT
* * *
1681872 AAAGCCCACAATTCTGTGGCACTTTTTTTCATTTTTAAAGCCCACAACTCCGTGGCACCTTCTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC--TTTTAAAGCCCACAACTCCGTGGCA-C--C--C
1681937 TTTTT
59 -TTTT
*
1681942 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT-AAGTCCACAACTCCGTGGCA
1 AAAGCCCACAACTCCGTGGCACTCTTTTT--CTTTTAAAGCCCACAACTCCGTGGCA
1681998 TCTTTCTCCC
Statistics
Matches: 105, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
60 19 0.18
62 5 0.05
64 24 0.23
65 1 0.01
67 1 0.01
69 20 0.19
70 34 0.32
72 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.13, T:0.31
Consensus pattern (62 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCCTTTT
Found at i:1681993 original size:35 final size:36
Alignment explanation
Indices: 1681865--1682022 Score: 189
Period size: 34 Copynumber: 4.5 Consensus size: 36
1681855 CTCCGTGGCA
* * *
1681865 CCCTTTTAAAGCCCACAATTCTGTGGCACTTTTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
** *
1681901 CATTTTTAAAGCCCACAACTCCGTGGCAC-CTTCTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
*
1681936 -CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
* *
1681971 CCCTTTT-AAGTCCACAACTCCGTGGCA-TCTTTCT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
*
1682005 CCCTTCCTAAAGCCCACA
1 CCCTT-TTAAAGCCCACA
1682023 CAAGTCGGTG
Statistics
Matches: 105, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
34 38 0.36
35 29 0.28
36 38 0.36
ACGTcount: A:0.21, C:0.34, G:0.11, T:0.34
Consensus pattern (36 bp):
CCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
Found at i:1682008 original size:34 final size:35
Alignment explanation
Indices: 1681865--1682022 Score: 167
Period size: 36 Copynumber: 4.5 Consensus size: 35
1681855 CTCCGTGGCA
* * * *
1681865 CCCTTTTAAAGCCCACAATTCTGTGGCACTTTTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCA-TCTTTCT
** *
1681901 CATTTTTAAAGCCCACAACTCCGTGGCA-CCTTCT
1 CCCTTTTAAAGCCCACAACTCCGTGGCATCTTTCT
* * *
1681935 TCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCA-TCTTTCT
*
1681971 CCCTTTT-AAGTCCACAACTCCGTGGCATCTTTCT
1 CCCTTTTAAAGCCCACAACTCCGTGGCATCTTTCT
*
1682005 CCCTTCCTAAAGCCCACA
1 CCCTT-TTAAAGCCCACA
1682023 CAAGTCGGTG
Statistics
Matches: 101, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
34 40 0.40
35 20 0.20
36 41 0.41
ACGTcount: A:0.21, C:0.34, G:0.11, T:0.34
Consensus pattern (35 bp):
CCCTTTTAAAGCCCACAACTCCGTGGCATCTTTCT
Found at i:1682050 original size:33 final size:34
Alignment explanation
Indices: 1682007--1682071 Score: 123
Period size: 33 Copynumber: 1.9 Consensus size: 34
1681997 ATCTTTCTCC
1682007 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTT
1682041 CTTCC-AAAGCCCACACAAGTCGGTGGCAACC
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACC
1682072 CCTCTAAGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.28, C:0.37, G:0.18, T:0.17
Consensus pattern (34 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTT
Found at i:1682158 original size:49 final size:49
Alignment explanation
Indices: 1682101--1682777 Score: 976
Period size: 49 Copynumber: 13.9 Consensus size: 49
1682091 TGGCCTTTTC
* *
1682101 CATCTTTAAGTCCAATGTAGCTGGCCTTGATTCAGCACATTGGCACCTT
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* *
1682150 CATCTTTAAGTCCAATATCA-CTGGCCTTGAATCAGCATATTGGCATCTT
1 CATCTTTAAGTCCAATAT-AGCTGGCCTTGAATCAGCACATTGGCACCTT
* *
1682199 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTT
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* *
1682248 CATCTTTAAGTCCAATATCA-CTGGCCTTGAATCAGCATATTGGCATCTT
1 CATCTTTAAGTCCAATAT-AGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
1682297 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTTAGCACATTGGCACCTT
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* *
1682346 CATCTTTAAGTCCAATATCA-CTGGCCTTGAATCAGCATATTGGCATCTT
1 CATCTTTAAGTCCAATAT-AGCTGGCCTTGAATCAGCACATTGGCACCTT
* *
1682395 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTT
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
1682444 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* *
1682493 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTT
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
1682542 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* *
1682591 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTT
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* * * *
1682640 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* *
1682689 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATTAGCACATTGGCA----
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
*
1682734 C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
1682778 ATTTTCCATC
Statistics
Matches: 561, Mismatches: 60, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
43 39 0.07
45 1 0.00
48 3 0.01
49 515 0.92
50 3 0.01
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.32
Consensus pattern (49 bp):
CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
Found at i:1682270 original size:98 final size:98
Alignment explanation
Indices: 1682101--1682776 Score: 1222
Period size: 98 Copynumber: 7.0 Consensus size: 98
1682091 TGGCCTTTTC
*
1682101 CATCTTTAAGTCCAATGTAGCTGGCCTTGATTCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
1682166 ATCACTGGCCTTGAATCAGCATATTGGCATCTT
66 ATCACTGGCCTTGAATCAGCATATTGGCATCTT
1682199 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
1682264 ATCACTGGCCTTGAATCAGCATATTGGCATCTT
66 ATCACTGGCCTTGAATCAGCATATTGGCATCTT
*
1682297 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTTAGCACATTGGCACCTTCATCTTTAAGTCCAAT
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
1682362 ATCACTGGCCTTGAATCAGCATATTGGCATCTT
66 ATCACTGGCCTTGAATCAGCATATTGGCATCTT
1682395 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
*
1682460 ATCGCTGGCCTTGAATCAGCATATTGGCATCTT
66 ATCACTGGCCTTGAATCAGCATATTGGCATCTT
1682493 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
*
1682558 ATCGCTGGCCTTGAATCAGCATATTGGCATCTT
66 ATCACTGGCCTTGAATCAGCATATTGGCATCTT
*
1682591 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTTTAAGTCCAAT
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
*
1682656 ATCGCTGGCCTTGAATCAGCATATTGGCATCTT
66 ATCACTGGCCTTGAATCAGCATATTGGCATCTT
* *
1682689 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATTAGCACATTGGCA----C--CTTTAAGTCCAAT
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
1682748 AT-AGCTGGCCTTGAATCAGCATATTGGCA
66 ATCA-CTGGCCTTGAATCAGCATATTGGCA
1682777 CATTTTCCAT
Statistics
Matches: 569, Mismatches: 8, Indels: 8
0.97 0.01 0.01
Matches are distributed among these distances:
92 40 0.07
94 1 0.00
98 528 0.93
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (98 bp):
CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
ATCACTGGCCTTGAATCAGCATATTGGCATCTT
Found at i:1682753 original size:43 final size:43
Alignment explanation
Indices: 1682692--1682810 Score: 145
Period size: 43 Copynumber: 2.8 Consensus size: 43
1682682 GCATCTTCAT
* * *
1682692 CTTTAAGTCCAATGTAGCTGGCCTTGAATTAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1682735 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
* * *
1682778 ATTT---TCCATCTTTAAGCTGGCCTTGAATCAGCA
1 CTTTAAGTCCA-ATAT-AGCTGGCCTTGAATCAGCA
1682811 CGTTGACATC
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
40 4 0.06
41 2 0.03
42 19 0.28
43 43 0.63
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
Found at i:1682806 original size:42 final size:41
Alignment explanation
Indices: 1682650--1682811 Score: 137
Period size: 43 Copynumber: 3.7 Consensus size: 41
1682640 CACCTTTAAG
* *
1682650 TCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAA
1 TCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----CA--TTT-A
* * *
1682698 GTCCAATGTAGCTGGCCTTGAATTAGCACATTGGCACCTTTAA
1 -TCCAATATAGCTGGCCTTGAATCAGCACATTGGCACATTT-A
*
1682741 GTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTT-
1 -TCCAATATAGCTGGCCTTGAATCAGCACATTGGCACATTTA
* *
1682782 TCCATCTTTAAGCTGGCCTTGAATCAGCAC
1 TCCA-ATAT-AGCTGGCCTTGAATCAGCAC
1682812 GTTGACATCC
Statistics
Matches: 99, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
40 4 0.04
41 2 0.02
42 19 0.19
43 42 0.42
45 1 0.01
49 31 0.31
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (41 bp):
TCCAATATAGCTGGCCTTGAATCAGCACATTGGCACATTTA
Found at i:1683070 original size:164 final size:164
Alignment explanation
Indices: 1682735--1683112 Score: 558
Period size: 171 Copynumber: 2.3 Consensus size: 164
1682725 ACATTGGCAC
* *
1682735 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA---CAT-TTTCCATCTTTAAGCT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTCATCTTTCAATCTGTAAGCT
1682796 GGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATGAAT
66 GGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATGAAT
1682861 CAACATATTGGCATCTTTATCACTTTTCTCATCAT
131 CAACATATTGGCATCTTTATCACTTTTCT-ATCAT
*
1682896 CATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTT-AAGTTCAA
1 C---TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTTCATCTTTCAA--TC--
*
1682960 TGT-AGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGG
58 TGTAAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGG
1683024 CCATGAATCAACATATTGGCATCTTTATCAC-TTT-T-TCAT
123 CCATGAATCAACATATTGGCATCTTTATCACTTTTCTATCAT
*
1683063 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTTCATC
1683113 ATCTCTAAAA
Statistics
Matches: 199, Mismatches: 6, Indels: 21
0.88 0.03 0.09
Matches are distributed among these distances:
161 1 0.01
164 87 0.44
167 5 0.03
168 4 0.02
169 4 0.02
170 5 0.03
171 91 0.46
172 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (164 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTCATCTTTCAATCTGTAAGCT
GGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATGAAT
CAACATATTGGCATCTTTATCACTTTTCTATCAT
Found at i:1683075 original size:60 final size:61
Alignment explanation
Indices: 1682994--1683113 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 61
1682984 TTGACATCCT
* * * *
1682994 TTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCAC
1 TTTTCTCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCAC
* * * *
1683055 TTTT-TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCA
1 TTTTCTCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCA
1683114 TCTCTAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
60 47 0.92
61 4 0.08
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.38
Consensus pattern (61 bp):
TTTTCTCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCAC
Found at i:1683948 original size:33 final size:33
Alignment explanation
Indices: 1683911--1683977 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1683901 TTCAACGATT
1683911 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1683944 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1683977 T
1 T
1683978 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1683949 original size:13 final size:13
Alignment explanation
Indices: 1683931--1683955 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1683921 CATAAAATGT
1683931 TGTATCGATACAA
1 TGTATCGATACAA
1683944 TGTATCGATACA
1 TGTATCGATACA
1683956 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:1684038 original size:13 final size:13
Alignment explanation
Indices: 1684020--1684044 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1684010 ATTACTCACA
1684020 TGTATCGATACAT
1 TGTATCGATACAT
1684033 TGTATCGATACA
1 TGTATCGATACA
1684045 CTGATCTTTG
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:1684181 original size:52 final size:52
Alignment explanation
Indices: 1684053--1684173 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1684043 CACTGATCTT
*
1684053 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1684105 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1684157 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1684174 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1691226 original size:28 final size:28
Alignment explanation
Indices: 1691128--1691646 Score: 508
Period size: 27 Copynumber: 18.8 Consensus size: 28
1691118 TGACCTCTTC
* * *
1691128 AAAGTCCACAATTCAGTGGCATTTCTTTT
1 AAAGTCCACAACTCCGTGGCA-TCCTTTT
*
1691157 CAAAGTCCACAACTCCATGGCATCCTTTT
1 -AAAGTCCACAACTCCGTGGCATCCTTTT
* *
1691186 -AAGTCCACAACTCCGTGGTATTCTTTT
1 AAAGTCCACAACTCCGTGGCATCCTTTT
* *
1691213 AAAGTTCACAACTCCGTGGCACCCTTTT
1 AAAGTCCACAACTCCGTGGCATCCTTTT
* * *
1691241 AAAGTCCATAATTCCGTGGCACCCTTTT
1 AAAGTCCACAACTCCGTGGCATCCTTTT
* *
1691269 AAAGTCCACAACTCCATGACATCCTTTT
1 AAAGTCCACAACTCCGTGGCATCCTTTT
*
1691297 -AAGTCCACAACTCCAT-G-ATACCTTTT
1 AAAGTCCACAACTCCGTGGCAT-CCTTTT
* *
1691323 AAAGTCCACAACTCCGTGACACCCTTTT
1 AAAGTCCACAACTCCGTGGCATCCTTTT
* *
1691351 AAAGTCAACAACTTCGTGGCATCCTTTT
1 AAAGTCCACAACTCCGTGGCATCCTTTT
* *
1691379 -AAGTCCACAACTCTGTGGCA-CCCTTT
1 AAAGTCCACAACTCCGTGGCATCCTTTT
*
1691405 AAAGTCCACAACTTCGTGGCATCC-TTT
1 AAAGTCCACAACTCCGTGGCATCCTTTT
* *
1691432 AAAGTCCACAACTCTGTGGCA-CCCTTT
1 AAAGTCCACAACTCCGTGGCATCCTTTT
* * * *
1691459 AAAGTCCACAACTCTGCGG--TACTCTTC
1 AAAGTCCACAACTCCGTGGCATCCT-TTT
* * *
1691486 AAAGTCCACCATTCCGTGGCACCCTTTT
1 AAAGTCCACAACTCCGTGGCATCCTTTT
* *
1691514 AAAGTCCATC-ATTCCGTGGCACCCTTTT
1 AAAGTCCA-CAACTCCGTGGCATCCTTTT
*
1691542 -AAGTCCACAACTCTGTGGCATCCTTTT
1 AAAGTCCACAACTCCGTGGCATCCTTTT
* * *
1691569 -AAGTCCATAACCCCGTAGCATCCTTTT
1 AAAGTCCACAACTCCGTGGCATCCTTTT
*
1691596 -AAGTCCACAACTTCGTGGCAGTACCCTTTT
1 AAAGTCCACAACTCCGTGGCA-T--CCTTTT
* * *
1691626 AAAGCCCACAAGTCGGTGGCA
1 AAAGTCCACAACTCCGTGGCA
1691647 ACTCATTTCA
Statistics
Matches: 410, Mismatches: 61, Indels: 35
0.81 0.12 0.07
Matches are distributed among these distances:
25 2 0.00
26 15 0.04
27 211 0.51
28 132 0.32
29 10 0.02
30 24 0.06
31 16 0.04
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (28 bp):
AAAGTCCACAACTCCGTGGCATCCTTTT
Found at i:1691346 original size:82 final size:82
Alignment explanation
Indices: 1691152--1691615 Score: 508
Period size: 82 Copynumber: 5.7 Consensus size: 82
1691142 AGTGGCATTT
* * * *
1691152 CTTTTCAAAGTCCACAACTCCATGGCATCCTTTT-AAGTCCACAACTCCGTGGTATTCTTTTAAA
1 CTTTT-AAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTT-AA
* * *
1691216 GTTCACAACTCCGTGGCACC
64 GTCCACAACTCTGTGGTA-C
* * * *
1691236 CTTTTAAAGTCCATAATTCCGTGGCACCCTTTTAAAGTCCACAACTCCATGACATCCTTTTAAGT
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGT
** *
1691301 CCACAACTCCATGATAC
66 CCACAACTCTGTGGTAC
* * *
1691318 CTTTTAAAGTCCACAACTCCGTGACACCCTTTTAAAGTCAACAACTTCGTGGCATCCTTTTAAGT
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGT
*
1691383 CCACAACTCTGTGGCAC
66 CCACAACTCTGTGGTAC
* * * * * *
1691400 CCTTTAAAGTCCACAACTTCGTGGCATCC-TTTAAAGTCCACAACTCTGTGGCACCCTTTAAAGT
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGT
*
1691464 CCACAACTCTGCGGTA-
66 CCACAACTCTGTGGTAC
* * * * *
1691480 CTCTTCAAAGTCCACCATTCCGTGGCACCCTTTTAAAGTCCATC-ATTCCGTGGCACCCTTTTAA
1 CT-TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCA-CAACTCCGTGGCATCCTTTTAA
*
1691544 GTCCACAACTCTGTGGCATC
64 GTCCACAACTCTGTGGTA-C
* * * * *
1691564 CTTTT-AAGTCCATAACCCCGTAGCATCCTTTT-AAGTCCACAACTTCGTGGCA
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCA
1691616 GTACCCTTTT
Statistics
Matches: 319, Mismatches: 54, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
80 2 0.01
81 82 0.26
82 162 0.51
83 43 0.13
84 30 0.09
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30
Consensus pattern (82 bp):
CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGT
CCACAACTCTGTGGTAC
Found at i:1691662 original size:30 final size:29
Alignment explanation
Indices: 1691620--1692364 Score: 626
Period size: 28 Copynumber: 25.3 Consensus size: 29
1691610 GTGGCAGTAC
* *
1691620 CCTTTTAAAGCCCACAAGTCGGTGGCAACT
1 CCTTTCAAAGCCCACAAGTCAGTGGC-ACT
* * *
1691650 CATTTCAAAGCCCACACAAGTCGGTGACAACT
1 CCTTTCAAAG-CC-CACAAGTCAGTGGC-ACT
* * **
1691682 CATTTGAAAGCCCACACAAGTTGGTGGCAAC-
1 CCTTTCAAAG-CC-CACAAGTCAGTGGC-ACT
*
1691713 CCATTTCAAAGTCCACACAAGTCGGTGGCAAC-
1 CC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACT
*
1691745 CTATTTCAAAGCCCACAAGTCAGTGGCA-T
1 C-CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1691774 CTTTTCAAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTC-AAAGCCCACAAGTCAGTGGCACT
*
1691803 CCTTTCAAAGCCCATAAAAGTCAGTGGCAACT
1 CCTTTCAAAGCCC--ACAAGTCAGTGGC-ACT
*
1691835 CTTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * ** **
1691863 CTTTTCAAAAGACCACAAGTTGGTAACAC-
1 CCTTTC-AAAGCCCACAAGTCAGTGGCACT
* ** *
1691892 CCTTTCAAAACCCACACAAGTTGGTGGTAACT
1 CCTTTC-AAAGCC-CACAAGTCAGTGG-CACT
*
1691924 CTTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1691952 -CTCTTCAAAAGCCCACAAGTCAGTGGCAC-
1 CCT-TTC-AAAGCCCACAAGTCAGTGGCACT
* *
1691981 CCTTTCAAAGCCCACACAAGTCGGTGGCAACC
1 CCTTTCAAAG-CC-CACAAGTCAGTGGC-ACT
*
1692013 CCTTTCAAAGCCCACACAAGTCAATGGCAC-
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCACT
* *
1692043 CCTTTCAAAGCCAACAAATCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1692071 CCTTTCAAAGCACAAAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1692100 CTTTTTAAAGCCCACAAGTTAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1692128 CCTTTCAAAGCCCACAAGCCAATAGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1692156 CCTTTCAAAGCCCACGCAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
*
1692186 CCTTTCAAAGACCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1692215 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1692243 CCTTTCAAAGCCTACAA-TCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1692271 CTTTTCAAAGCCCAAAAGTTAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* ** *
1692299 CCCTTCAAAGCCCTTAAGTCAATGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
1692327 CCTTTTAAAGCACACAAATCAGTGGCAAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1692356 CTTTTCAAA
1 CCTTTCAAA
1692365 TCAGAATGCG
Statistics
Matches: 600, Mismatches: 82, Indels: 67
0.80 0.11 0.09
Matches are distributed among these distances:
27 11 0.02
28 183 0.31
29 149 0.25
30 116 0.19
31 18 0.03
32 123 0.20
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.22
Consensus pattern (29 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:1691794 original size:29 final size:28
Alignment explanation
Indices: 1691125--1692364 Score: 598
Period size: 28 Copynumber: 43.2 Consensus size: 28
1691115 CTGTGACCTC
* * *
1691125 TTCAAAGTCCACAATTCAGTGGCATTTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA--TCCT
* *
1691155 TTCAAAGTCCACAACTCCA-TGGCATCCT
1 TTCAAAGCCCACAAGT-CAGTGGCATCCT
* * * * * *
1691183 TT-TAAGTCCACAACTCCGTGGTATTCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* ** * * *
1691210 TTTAAAGTTCACAACTCCGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * * *
1691238 TTTAAAGTCCATAATTCCGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
1691266 TTTAAAGTCCACAACTCCA-TGACATCCT
1 TTCAAAGCCCACAAGT-CAGTGGCATCCT
* * *
1691294 TT-TAAGTCCACAACTCCA-T-G-ATACCT
1 TTCAAAGCCCACAAGT-CAGTGGCAT-CCT
* * * * * *
1691320 TTTAAAGTCCACAACTCCGTGACACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
1691348 TTTAAAGTCAACAACTTC-GTGGCATCCT
1 TTCAAAGCCCACAA-GTCAGTGGCATCCT
* * * * *
1691376 TT-TAAGTCCACAACTCTGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1691403 TT-AAAGTCCACAACTTC-GTGGCATCCT
1 TTCAAAGCCCACAA-GTCAGTGGCATCCT
* * * *
1691430 TT-AAAGTCCACAACTCTGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * *
1691457 TT-AAAGTCCACAACTCTGCGG--TACT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * *
1691482 CTTCAAAGTCCACCATTCCGTGGCACCCT
1 -TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * *
1691511 TTTAAAGTCCATC-ATTCCGTGGCACCCT
1 TTCAAAGCCCA-CAAGTCAGTGGCATCCT
* * * *
1691539 TT-TAAGTCCACAACTCTGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * ** * *
1691566 TT-TAAGTCCATAACCCCGTAGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1691593 TT-TAAGTCCACAACTTC-GTGGCAGTACCCT
1 TTCAAAGCCCACAA-GTCAGTGGCA-T--CCT
* * *
1691623 TTTAAAGCCCACAAGTCGGTGGCAACTCAT
1 TTCAAAGCCCACAAGTCAGTGGC-A-TCCT
* * *
1691653 TTCAAAGCCCACACAAGTCGGTGACAACTCAT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCCT
* ** *
1691685 TTGAAAGCCCACACAAGTTGGTGGCAACCCAT
1 TTCAAAG-CC-CACAAGTCAGTGGC-ATCC-T
* *
1691717 TTCAAAGTCCACACAAGTCGGTGGCAACCTAT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCC--T
*
1691749 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1691777 TTCAAAAGCCCACAAGTCAGTGGCACCCT
1 TTC-AAAGCCCACAAGTCAGTGGCATCCT
* *
1691806 TTCAAAGCCCATAAAAGTCAGTGGCAACTCTT
1 TTCAAAGCCC--ACAAGTCAGTGGC-A-TCCT
*
1691838 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* ** ** *
1691866 TTCAAAAGACCACAAGTTGGTAACACCCT
1 TTC-AAAGCCCACAAGTCAGTGGCATCCT
* ** * *
1691895 TTCAAAACCCACACAAGTTGGTGGTAACTCTT
1 TTC-AAAGCC-CACAAGTCAGTGG-CA-TCCT
1691927 TTCAAAGCCCACAAGTCAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1691954 CTTCAAAAGCCCACAAGTCAGTGGCACCCT
1 -TTC-AAAGCCCACAAGTCAGTGGCATCCT
* *
1691984 TTCAAAGCCCACACAAGTCGGTGGCAACCCCT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCCT
* *
1692016 TTCAAAGCCCACACAAGTCAATGGCACCCT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCT
* *
1692046 TTCAAAGCCAACAAATCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1692074 TTCAAAGCACAAAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* *
1692103 TTTAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
1692131 TTCAAAGCCCACAAGCCAATAGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1692159 TTCAAAGCCCACGCAAGTCAGTGGCACCCT
1 TTCAAAGCCCA--CAAGTCAGTGGCATCCT
* *
1692189 TTCAAAGACCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
*
1692218 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1692246 TTCAAAGCCTACAA-TCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* * *
1692274 TTCAAAGCCCAAAAGTTAGTGGCATCCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
** *
1692302 TTCAAAGCCCTTAAGTCAATGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
1692330 TTTAAAGCACACAAATCAGTGGCAATCTT
1 TTCAAAGCCCACAAGTCAGTGGC-ATCCT
1692359 TTCAAA
1 TTCAAA
1692365 TCAGAATGCG
Statistics
Matches: 999, Mismatches: 158, Indels: 107
0.79 0.12 0.08
Matches are distributed among these distances:
25 4 0.00
26 14 0.01
27 215 0.22
28 311 0.31
29 154 0.15
30 146 0.15
31 33 0.03
32 122 0.12
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:1691824 original size:89 final size:88
Alignment explanation
Indices: 1691618--1692364 Score: 777
Period size: 89 Copynumber: 8.5 Consensus size: 88
1691608 TCGTGGCAGT
* * * * *
1691618 ACCCTTTTAAAG-CC-CACAAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTCGGTGACAAC
1 ACCCTTTCAAAGCCCACACAAGTCAGTGGCAACTCTTTTCAAAG-CC-CACAAGTCAGTGGC-A-
* * **
1691681 TCATTTGAAAGCCCACACAAGTTGGTGGC
62 TCTTTTCAAAG-CC-CACAAGTCAGTGGC
* *
1691710 AACCCATTTCAAAGTCCACACAAGTCGGTGGCAAC-CTATTTCAAAGCCCACAAGTCAGTGGCAT
1 -ACCC-TTTCAAAGCCCACACAAGTCAGTGGCAACTCT-TTTCAAAGCCCACAAGTCAGTGGCAT
1691774 CTTTTCAAAAGCCCACAAGTCAGTGGC
63 CTTTTC-AAAGCCCACAAGTCAGTGGC
* *
1691801 ACCCTTTCAAAGCCCATAAAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTT
1 ACCCTTTCAAAGCCCACACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTT
* ** **
1691866 TTCAAAAGACCACAAGTTGGTAAC
66 TTC-AAAGCCCACAAGTCAGTGGC
* ** * *
1691890 ACCCTTTCAAAACCCACACAAGTTGGTGGTAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTC
1 ACCCTTTCAAAGCCCACACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTT
1691955 TTCAAAAGCCCACAAGTCAGTGGC
66 TTC-AAAGCCCACAAGTCAGTGGC
* * * * *
1691979 ACCCTTTCAAAGCCCACACAAGTCGGTGGCAACCCCTTTCAAAGCCCACACAAGTCAATGGCACC
1 ACCCTTTCAAAGCCCACACAAGTCAGTGGCAACTCTTTTCAAAG-CC-CACAAGTCAGTGGCATC
* * *
1692044 CTTTCAAAGCCAACAAATCAGTGGC
64 TTTTCAAAGCCCACAAGTCAGTGGC
* * * * *
1692069 ATCCTTTCAAAG--CACAAAAGTCAGTGGC-ACTCTTTTTAAAGCCCACAAGTTAGTGGCATCCT
1 ACCCTTTCAAAGCCCACACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTT
* * *
1692131 TTCAAAGCCCACAAGCCAATAGC
66 TTCAAAGCCCACAAGTCAGTGGC
* * *
1692154 ACCCTTTCAAAGCCCACGCAAGTCAGTGGC-AC-CCTTTCAAAGACCACAAGTCAGTGGCACTCT
1 ACCCTTTCAAAGCCCACACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCA-TCT
1692217 TTTCAAAGCCCACAAGTCAGTGGC
65 TTTCAAAGCCCACAAGTCAGTGGC
* * * **
1692241 ACCCTTTCAAAG-CC-TACAA-TCAGTGGC-ACTCTTTTCAAAGCCCAAAAGTTAGTGGCATCCC
1 ACCCTTTCAAAGCCCACACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTT
** *
1692302 TTCAAAGCCCTTAAGTCAATGGC
66 TTCAAAGCCCACAAGTCAGTGGC
* * *
1692325 ATCCTTTTAAAG--CACACAAATCAGTGGCAA-TCTTTTCAAA
1 ACCCTTTCAAAGCCCACACAAGTCAGTGGCAACTCTTTTCAAA
1692365 TCAGAATGCG
Statistics
Matches: 560, Mismatches: 79, Indels: 38
0.83 0.12 0.06
Matches are distributed among these distances:
83 1 0.00
84 46 0.08
85 89 0.16
86 28 0.05
87 61 0.11
88 14 0.03
89 189 0.34
90 37 0.07
91 30 0.05
92 7 0.01
93 9 0.02
94 19 0.03
95 5 0.01
96 25 0.04
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (88 bp):
ACCCTTTCAAAGCCCACACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTT
TTCAAAGCCCACAAGTCAGTGGC
Found at i:1694034 original size:20 final size:21
Alignment explanation
Indices: 1694009--1694065 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
1693999 GTAAAAAGAC
*
1694009 AGAATGTATCGATACATTGA-
1 AGAATGTATCGATACATTCAT
1694029 AGAATGTATCGATACATTCAT
1 AGAATGTATCGATACATTCAT
*
1694050 A-CATGTATCGATACAT
1 AGAATGTATCGATACAT
1694066 CTGGGTACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 33 0.97
21 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (21 bp):
AGAATGTATCGATACATTCAT
Found at i:1694688 original size:45 final size:49
Alignment explanation
Indices: 1694635--1694732 Score: 123
Period size: 49 Copynumber: 2.1 Consensus size: 49
1694625 CGCTAGCATT
* * *
1694635 GAATCAGCATATTGG-C-AC-CTTT-ATTAGCCCAATGTCGCTGGCCTC
1 GAATCAGCAAATTGGTCTACTCTTTCATTAGCCCAATGTCGCTGACCTA
* *
1694680 GAATCAGCAAATTGGTCTACTTTTTCCTTAGCCCAATGTCGCTGACCTA
1 GAATCAGCAAATTGGTCTACTCTTTCATTAGCCCAATGTCGCTGACCTA
1694729 GAAT
1 GAAT
1694733 TGGCACATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
45 14 0.32
46 1 0.02
47 2 0.05
48 3 0.07
49 24 0.55
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (49 bp):
GAATCAGCAAATTGGTCTACTCTTTCATTAGCCCAATGTCGCTGACCTA
Found at i:1695484 original size:20 final size:20
Alignment explanation
Indices: 1695455--1695510 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1695445 TTTTACCCAG
* *
1695455 ATGTACCGATACATGT-ATGA
1 ATGTATCGATACAT-TCATCA
*
1695475 ATGTATCGATACATTCCTCA
1 ATGTATCGATACATTCATCA
1695495 ATGTATCGATACATTC
1 ATGTATCGATACATTC
1695511 TGTCTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTCATCA
Found at i:1696454 original size:20 final size:21
Alignment explanation
Indices: 1696417--1696455 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1696407 AGCCTTTGAC
*
1696417 CATGCATTTTTGATTATGTTT
1 CATGCATTTTTGAATATGTTT
1696438 CATGCATTTTT-AATATGT
1 CATGCATTTTTGAATATGT
1696456 CTAGCATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.54
Consensus pattern (21 bp):
CATGCATTTTTGAATATGTTT
Found at i:1699126 original size:22 final size:23
Alignment explanation
Indices: 1699101--1699162 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 23
1699091 ATTTATTTTT
* *
1699101 TATATGATATAAATTATATA-AA
1 TATATAATATAAATTAAATATAA
*
1699123 TATA-AATATAAAAATAAATATAA
1 TATATAATAT-AAATTAAATATAA
*
1699146 TATATTATA-AAATTAAA
1 TATATAATATAAATTAAA
1699163 AATGGGCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 4 0.12
22 19 0.59
23 6 0.19
24 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
TATATAATATAAATTAAATATAA
Found at i:1699127 original size:6 final size:6
Alignment explanation
Indices: 1699116--1699149 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1699106 GATATAAATT
*
1699116 ATATAA ATATAA ATATAA AAATAA ATAT-A ATATA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATA
1699150 TTATAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:1699132 original size:14 final size:13
Alignment explanation
Indices: 1699107--1699150 Score: 54
Period size: 12 Copynumber: 3.3 Consensus size: 13
1699097 TTTTTATATG
1699107 ATATAAATTATATAA
1 ATATAAA-TATA-AA
1699122 ATATAAATATAAA
1 ATATAAATATAAA
*
1699135 A-ATAAATATAAT
1 ATATAAATATAAA
1699147 ATAT
1 ATAT
1699151 TATAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 11 0.41
13 5 0.19
14 4 0.15
15 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATATAAATATAAA
Found at i:1700966 original size:18 final size:19
Alignment explanation
Indices: 1700925--1700964 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1700915 AAATGTAGAT
*
1700925 TTTAAATAAAAACTAATAA
1 TTTAAATAAAAAATAATAA
1700944 TTTAAATAAAAAGATAA-AA
1 TTTAAATAAAAA-ATAATAA
1700963 TT
1 TT
1700965 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
TTTAAATAAAAAATAATAA
Found at i:1705386 original size:19 final size:20
Alignment explanation
Indices: 1705362--1705412 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
1705352 CGATACATTA
1705362 TATCGATACAATACT-TATG
1 TATCGATACAATACTGTATG
* *
1705381 TATCGATACATTTACTGTTTG
1 TATCGATACA-ATACTGTATG
1705402 TATCGATACAA
1 TATCGATACAA
1705413 ATTGTTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 10 0.37
20 4 0.15
21 13 0.48
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (20 bp):
TATCGATACAATACTGTATG
Found at i:1705504 original size:21 final size:21
Alignment explanation
Indices: 1705448--1705504 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1705438 TTTAGGACCT
*
1705448 TGTATCGATACATTCTAGCAA
1 TGTATCGATACATTTTAGCAA
1705469 TGTATCGATACATTTTAGCAA
1 TGTATCGATACATTTTAGCAA
*
1705490 TGTATCGATATATTT
1 TGTATCGATACATTT
1705505 GGATAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTTTAGCAA
Found at i:1706602 original size:2 final size:2
Alignment explanation
Indices: 1706595--1706631 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1706585 AATTTTTAAA
1706595 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1706632 AACTTTACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1706836 original size:14 final size:14
Alignment explanation
Indices: 1706795--1706836 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1706785 TACATAGATG
1706795 ATAATTTAAATATAT
1 ATAATTTAAA-ATAT
*
1706810 ATAA-TTATCAATAT
1 ATAATTTA-AAATAT
1706824 ATAATTTAAAATA
1 ATAATTTAAAATA
1706837 AAATTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAATTTAAAATAT
Found at i:1708614 original size:2 final size:2
Alignment explanation
Indices: 1708607--1708654 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1708597 TTGTTAAGGC
1708607 AT AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT
1708649 AT AT AT
1 AT AT AT
1708655 TTGCTAATTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1715997 original size:21 final size:21
Alignment explanation
Indices: 1715930--1715998 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
1715920 AGCAACATGC
*
1715930 ATTGTATCGATACAAAGCCAT
1 ATTGTATCAATACAAAGCCAT
* * * * *
1715951 ATAGTATCATTATAATGCC-C
1 ATTGTATCAATACAAAGCCAT
*
1715971 ATTGTATCAATACAAGGCCAT
1 ATTGTATCAATACAAAGCCAT
1715992 ATTGTAT
1 ATTGTAT
1715999 TGATACGATA
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (21 bp):
ATTGTATCAATACAAAGCCAT
Found at i:1719166 original size:21 final size:21
Alignment explanation
Indices: 1719141--1719193 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1719131 TTTTATAATT
1719141 TGTATCGATACAAATAA-TAAA
1 TGTATCGATAC-AATAAGTAAA
* *
1719162 TGTATTGATAC-ATAAGTGAA
1 TGTATCGATACAATAAGTAAA
1719182 TGTATCGATACA
1 TGTATCGATACA
1719194 TGCCTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 4 0.15
20 13 0.48
21 10 0.37
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.32
Consensus pattern (21 bp):
TGTATCGATACAATAAGTAAA
Found at i:1724719 original size:52 final size:52
Alignment explanation
Indices: 1724675--1724800 Score: 234
Period size: 52 Copynumber: 2.4 Consensus size: 52
1724665 CACTGATCTT
1724675 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
1724727 TGTATCGATACATGCAAGCAAATTTTCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1724779 TGTATCGATACATGCAGGCAAA
1 TGTATCGATACATGCAGGCAAA
1724801 ATTTCATATT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Done.