Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000520.1 Hibiscus syriacus cultivar Beakdansim tig00000991_pilon, whole genome shotgun sequence
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: 1956684
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1550868 original size:3 final size:3
Alignment explanation
Indices: 1550860--1550933 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
1550850 TTTTTATCCA
1550860 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1550908 TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1550934 AATATATATT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1551418 original size:27 final size:25
Alignment explanation
Indices: 1551395--1551446 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1551385 GATATAGAAC
1551395 GAGACAGAGAGACAAAAAAAATAGAGA
1 GAGACAGAGA-A-AAAAAAAATAGAGA
* *
1551422 GAGACATAGAAAAAAAAAACAGAGA
1 GAGACAGAGAAAAAAAAAATAGAGA
1551447 AAATACAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 13 0.57
26 1 0.04
27 9 0.39
ACGTcount: A:0.65, C:0.08, G:0.23, T:0.04
Consensus pattern (25 bp):
GAGACAGAGAAAAAAAAAATAGAGA
Found at i:1552271 original size:19 final size:18
Alignment explanation
Indices: 1552235--1552283 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
1552225 TAGATTTTTA
*
1552235 ATTTTATT-TTTTCGTTT
1 ATTTTATTGTTTTCATTT
1552252 ATTTTATATGTTTTCATTT
1 ATTTTAT-TGTTTTCATTT
1552271 ATTTTATTGTTTT
1 ATTTTATTGTTTT
1552284 TAAATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (18 bp):
ATTTTATTGTTTTCATTT
Found at i:1552338 original size:12 final size:12
Alignment explanation
Indices: 1552323--1552385 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
1552313 TTTTATTATA
1552323 TTATTAAATATT
1 TTATTAAATATT
1552335 TTATTAAATATT
1 TTATTAAATATT
*
1552347 TT-TATAAATATA
1 TTAT-TAAATATT
* *
1552359 TAATAAATAGTATT
1 TTATTAA-A-TATT
*
1552373 TTTTTAAATATT
1 TTATTAAATATT
1552385 T
1 T
1552386 ATTTTTAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 1 0.03
12 29 0.73
13 3 0.08
14 7 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
TTATTAAATATT
Found at i:1552395 original size:13 final size:12
Alignment explanation
Indices: 1552326--1552396 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
1552316 TATTATATTA
*
1552326 TTAAATATTTTA
1 TTAAATATTTTT
1552338 TTAAATATTTTT
1 TTAAATATTTTT
* * **
1552350 ATAAATATATAA
1 TTAAATATTTTT
*
1552362 TAAATAGTATTTTT
1 TTAA-A-TATTTTT
1552376 TTAAATATTTATT
1 TTAAATATTT-TT
*
1552389 TTTAATAT
1 TTAAATAT
1552397 CGAAGAAAAG
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
12 26 0.59
13 11 0.25
14 7 0.16
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (12 bp):
TTAAATATTTTT
Found at i:1554653 original size:130 final size:130
Alignment explanation
Indices: 1554508--1554755 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
1554498 TATTTATATA
*
1554508 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* *
1554573 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
1554638 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
1554703 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
1554756 GAAGAAAATT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1554786 original size:130 final size:129
Alignment explanation
Indices: 1554522--1554786 Score: 318
Period size: 130 Copynumber: 2.0 Consensus size: 129
1554512 ATTTGGTCCT
* *
1554522 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
1554587 TGACACGTGTCATTGGTGACACATGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
1554652 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
1554717 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
1554781 -A
128 CA
1554782 AAATT
1 AAATT
1554787 TGGGTCTTGG
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
130 101 0.89
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:1555245 original size:16 final size:18
Alignment explanation
Indices: 1555224--1555257 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1555214 ATTTCTTATT
1555224 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1555240 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1555258 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1555404 original size:21 final size:21
Alignment explanation
Indices: 1555380--1555422 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1555370 TATTACCTTA
1555380 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
1555401 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
1555422 A
1 A
1555423 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:1555440 original size:35 final size:35
Alignment explanation
Indices: 1555391--1555476 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
1555381 ATTGAAGTAT
** * *
1555391 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
1555426 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
1555461 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
1555477 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:1557110 original size:16 final size:16
Alignment explanation
Indices: 1557067--1557116 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1557057 AAAATATTTA
*
1557067 TTTATATTTTATTATAG
1 TTTATATTTTA-TATAT
1557084 TTTA-ATTTTATATAT
1 TTTATATTTTATATAT
*
1557099 TTTATATATTATAGTAT
1 TTTATATTTTATA-TAT
1557116 T
1 T
1557117 GTAAATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 8 0.28
16 13 0.45
17 8 0.28
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (16 bp):
TTTATATTTTATATAT
Found at i:1557377 original size:16 final size:16
Alignment explanation
Indices: 1557356--1557388 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1557346 TAATAAATAA
1557356 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1557372 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1557388 A
1 A
1557389 AAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1557478 original size:16 final size:16
Alignment explanation
Indices: 1557457--1557501 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
1557447 TAATAAATAA
1557457 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1557473 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1557489 ACGAACATAAACG
1 ACGAACATAAACG
1557502 TTGGAGACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.56, C:0.22, G:0.13, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1557978 original size:14 final size:14
Alignment explanation
Indices: 1557959--1557990 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1557949 GTTAAACATA
1557959 AACGAACATAACCG
1 AACGAACATAACCG
*
1557973 AACGAACATAACGG
1 AACGAACATAACCG
1557987 AACG
1 AACG
1557991 TTCACAAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.25, G:0.19, T:0.06
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1561936 original size:25 final size:25
Alignment explanation
Indices: 1561839--1561932 Score: 179
Period size: 25 Copynumber: 3.8 Consensus size: 25
1561829 CAGTTGGGGA
1561839 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
1561864 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
1561889 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
1561914 TTAGGGTTTGAAACCCTAA
1 TTAGGGTTTGAAACCCTAA
1561933 TCTGGTGGGT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
25 68 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:1562033 original size:13 final size:13
Alignment explanation
Indices: 1562015--1562045 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1562005 TAATATGTAA
1562015 AATAATTAATAAT
1 AATAATTAATAAT
1562028 AATAATTAATAAT
1 AATAATTAATAAT
1562041 AATAA
1 AATAA
1562046 AATAAAATAA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATAATTAATAAT
Found at i:1562054 original size:10 final size:10
Alignment explanation
Indices: 1562012--1562090 Score: 74
Period size: 9 Copynumber: 7.5 Consensus size: 10
1562002 ATGTAATATG
1562012 TAAAATAATTAA
1 TAAAATAA--AA
1562024 TAATAATAATTAA
1 TAA-AATAA--AA
1562037 TAATAATAAAA
1 TAA-AATAAAA
1562048 TAAAAT-AAA
1 TAAAATAAAA
1562057 TAAAA-AAAA
1 TAAAATAAAA
1562066 TAAAATAAAA
1 TAAAATAAAA
1562076 -AAAATAAATA
1 TAAAATAAA-A
1562086 TAAAA
1 TAAAA
1562091 GACCCGGACA
Statistics
Matches: 62, Mismatches: 0, Indels: 11
0.85 0.00 0.15
Matches are distributed among these distances:
9 24 0.39
10 8 0.13
11 9 0.15
12 3 0.05
13 18 0.29
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
TAAAATAAAA
Found at i:1562054 original size:13 final size:13
Alignment explanation
Indices: 1562012--1562090 Score: 58
Period size: 13 Copynumber: 5.8 Consensus size: 13
1562002 ATGTAATATG
1562012 TAAAATAATTAATAA
1 TAAAATAA--AATAA
1562027 TAATAATTAATAATAA
1 TAA-AA-TAA-AATAA
1562043 TAAAATAAAATAAA
1 TAAAATAAAAT-AA
1562057 TAAAA-AAAATAA
1 TAAAATAAAATAA
1562069 -AATAA-AAAA-AA
1 TAA-AATAAAATAA
1562080 TAAATATAAAA
1 TAAA-ATAAAA
1562091 GACCCGGACA
Statistics
Matches: 57, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
11 5 0.09
12 11 0.19
13 12 0.21
14 10 0.18
15 5 0.09
16 11 0.19
17 3 0.05
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAAATAAAATAA
Found at i:1562060 original size:14 final size:13
Alignment explanation
Indices: 1562041--1562090 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 13
1562031 AATTAATAAT
1562041 AATAAAATAAAATA
1 AATAAAA-AAAATA
1562055 AATAAAAAAAATAA
1 AATAAAAAAAAT-A
1562069 AATAAAAAAAATA
1 AATAAAAAAAATA
1562082 AATATAAAA
1 AATA-AAAA
1562091 GACCCGGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 10 0.29
14 24 0.71
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
AATAAAAAAAATA
Found at i:1562067 original size:23 final size:23
Alignment explanation
Indices: 1562013--1562083 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
1562003 TGTAATATGT
* *
1562013 AAAATAATTAATAATAATAATTAATA
1 AAAATAA--AATAA-AATAAATAAAA
*
1562039 ATAATAAAATAAAATAAATAAAA
1 AAAATAAAATAAAATAAATAAAA
*
1562062 AAAATAAAATAAAAAAAATAAA
1 AAAATAAAATAAAATAAATAAA
1562084 TATAAAAGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
23 29 0.73
24 5 0.12
26 6 0.15
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAATAAAATAAAATAAATAAAA
Found at i:1562579 original size:94 final size:91
Alignment explanation
Indices: 1562319--1562625 Score: 376
Period size: 94 Copynumber: 3.3 Consensus size: 91
1562309 GGTCAAGGGA
* * * *
1562319 TGACACGACTCATACGCGATGAAGAGTTCTGGTCATCTTTAAGAAGGGTGATAACTCGGTTCCTA
1 TGACACGGCTCATACGTGATGAAGA-ATCTGGCCATC-TT-AGAAGGGTGATAACTCGGTTCCTA
*
1562384 CGTGATGAGGACGGCTGATTATC-A-GGT
63 CGTGATGAGGACGGCTGGTTATCTATGGT
* *
1562411 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATC-TA-AA-GGTGATAACACGGTTCCTACG
1 TGACACGGCTCATACGTGATGAAGA-ATCTGGCCATCTTAGAAGGGTGATAACTCGGTTCCTACG
1562473 TGATGAGGACGGCTGGTTATCTATGGT
65 TGATGAGGACGGCTGGTTATCTATGGT
*
1562500 TGACACGGCTCATACATGATGAAGAACTCTGGCCATCGTTAGGAAGGGTGATAACTCGGTTCCTA
1 TGACACGGCTCATACGTGATGAAGAA-TCTGGCCATC-TTA-GAAGGGTGATAACTCGGTTCCTA
1562565 CGTGATGAGGACGGCTGGTTATCCTAAT-GT
63 CGTGATGAGGACGGCTGGTTAT-CT-ATGGT
* * *
1562595 TGACAC-TCTCCTACGTGATGAGGAGATCTGG
1 TGACACGGCTCATACGTGATGAAGA-ATCTGG
1562626 TCAGTTGATG
Statistics
Matches: 190, Mismatches: 14, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
87 40 0.21
88 4 0.02
89 37 0.19
90 1 0.01
91 2 0.01
92 32 0.17
93 2 0.01
94 59 0.31
95 11 0.06
96 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.27
Consensus pattern (91 bp):
TGACACGGCTCATACGTGATGAAGAATCTGGCCATCTTAGAAGGGTGATAACTCGGTTCCTACGT
GATGAGGACGGCTGGTTATCTATGGT
Found at i:1563599 original size:16 final size:16
Alignment explanation
Indices: 1563578--1563622 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1563568 CTTTATTTAT
1563578 TTTTTCTTCTTTTTCA
1 TTTTTCTTCTTTTTCA
1563594 TTTTTCATT-TTTTTCA
1 TTTTTC-TTCTTTTTCA
*
1563610 -TTTCCTTCTTTTT
1 TTTTTCTTCTTTTT
1563623 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 2 0.08
15 9 0.35
16 13 0.50
17 2 0.08
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCTTCTTTTTCA
Found at i:1577148 original size:76 final size:75
Alignment explanation
Indices: 1577022--1577191 Score: 313
Period size: 76 Copynumber: 2.3 Consensus size: 75
1577012 CAGTTGGGGA
1577022 TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACC
1 TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACC
1577087 CTAAACTGATT
66 CTAAACTGA-T
*
1577098 TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAATCTGATTTAGGGTTTGAAACC
1 TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACC
*
1577163 CTAATCTGAT
66 CTAAACTGAT
1577173 TTAGGGTTTGAAACCCTAA
1 TTAGGGTTTGAAACCCTAA
1577192 TCTGGTGGGT
Statistics
Matches: 92, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
75 20 0.22
76 72 0.78
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (75 bp):
TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACC
CTAAACTGAT
Found at i:1577195 original size:25 final size:25
Alignment explanation
Indices: 1577022--1577191 Score: 313
Period size: 25 Copynumber: 6.8 Consensus size: 25
1577012 CAGTTGGGGA
1577022 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
1577047 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
1577072 TTAGGGTTTGAAACCCTAAACTGATT
1 TTAGGGTTTGAAACCCTAAACTGA-T
1577098 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
1577123 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
1577148 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
1577173 TTAGGGTTTGAAACCCTAA
1 TTAGGGTTTGAAACCCTAA
1577192 TCTGGTGGGT
Statistics
Matches: 143, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
25 118 0.83
26 25 0.17
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:1577292 original size:13 final size:13
Alignment explanation
Indices: 1577274--1577304 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1577264 TAATATGTAA
1577274 AATAATTAATAAT
1 AATAATTAATAAT
1577287 AATAATTAATAAT
1 AATAATTAATAAT
1577300 AATAA
1 AATAA
1577305 AATAAAATAA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATAATTAATAAT
Found at i:1577313 original size:10 final size:10
Alignment explanation
Indices: 1577271--1577349 Score: 74
Period size: 9 Copynumber: 7.5 Consensus size: 10
1577261 ATGTAATATG
1577271 TAAAATAATTAA
1 TAAAATAA--AA
1577283 TAATAATAATTAA
1 TAA-AATAA--AA
1577296 TAATAATAAAA
1 TAA-AATAAAA
1577307 TAAAAT-AAA
1 TAAAATAAAA
1577316 TAAAA-AAAA
1 TAAAATAAAA
1577325 TAAAATAAAA
1 TAAAATAAAA
1577335 -AAAATAAATA
1 TAAAATAAA-A
1577345 TAAAA
1 TAAAA
1577350 GACCCGGACA
Statistics
Matches: 62, Mismatches: 0, Indels: 11
0.85 0.00 0.15
Matches are distributed among these distances:
9 24 0.39
10 8 0.13
11 9 0.15
12 3 0.05
13 18 0.29
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
TAAAATAAAA
Found at i:1577313 original size:13 final size:13
Alignment explanation
Indices: 1577271--1577349 Score: 58
Period size: 13 Copynumber: 5.8 Consensus size: 13
1577261 ATGTAATATG
1577271 TAAAATAATTAATAA
1 TAAAATAA--AATAA
1577286 TAATAATTAATAATAA
1 TAA-AA-TAA-AATAA
1577302 TAAAATAAAATAAA
1 TAAAATAAAAT-AA
1577316 TAAAA-AAAATAA
1 TAAAATAAAATAA
1577328 -AATAA-AAAA-AA
1 TAA-AATAAAATAA
1577339 TAAATATAAAA
1 TAAA-ATAAAA
1577350 GACCCGGACA
Statistics
Matches: 57, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
11 5 0.09
12 11 0.19
13 12 0.21
14 10 0.18
15 5 0.09
16 11 0.19
17 3 0.05
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAAATAAAATAA
Found at i:1577319 original size:14 final size:13
Alignment explanation
Indices: 1577300--1577349 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 13
1577290 AATTAATAAT
1577300 AATAAAATAAAATA
1 AATAAAA-AAAATA
1577314 AATAAAAAAAATAA
1 AATAAAAAAAAT-A
1577328 AATAAAAAAAATA
1 AATAAAAAAAATA
1577341 AATATAAAA
1 AATA-AAAA
1577350 GACCCGGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 10 0.29
14 24 0.71
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
AATAAAAAAAATA
Found at i:1577326 original size:23 final size:23
Alignment explanation
Indices: 1577272--1577342 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
1577262 TGTAATATGT
* *
1577272 AAAATAATTAATAATAATAATTAATA
1 AAAATAA--AATAA-AATAAATAAAA
*
1577298 ATAATAAAATAAAATAAATAAAA
1 AAAATAAAATAAAATAAATAAAA
*
1577321 AAAATAAAATAAAAAAAATAAA
1 AAAATAAAATAAAATAAATAAA
1577343 TATAAAAGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
23 29 0.73
24 5 0.12
26 6 0.15
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAATAAAATAAAATAAATAAAA
Found at i:1584021 original size:18 final size:18
Alignment explanation
Indices: 1583988--1584039 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
1583978 CCTTTTACGA
*
1583988 TTATTTT-TTATTATTGT
1 TTATTTTATTTTTATTGT
1584005 TTATTTTATTTTTATTGT
1 TTATTTTATTTTTATTGT
1584023 TTATTTTATTTCTTATT
1 TTATTTTATTT-TTATT
1584040 TTTTTCTCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 7 0.22
18 20 0.62
19 5 0.16
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (18 bp):
TTATTTTATTTTTATTGT
Found at i:1584137 original size:23 final size:21
Alignment explanation
Indices: 1584111--1584162 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
1584101 TTACCTAGTA
1584111 TTTTATATATATATTTATTA-TTG
1 TTTTAT-TAT-TATTT-TTACTTG
1584134 TTTTATTATTATTTTTACTTG
1 TTTTATTATTATTTTTACTTG
1584155 TTTTATTA
1 TTTTATTA
1584163 GACATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 3 0.11
23 6 0.21
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTTATTATTATTTTTACTTG
Found at i:1584155 original size:21 final size:22
Alignment explanation
Indices: 1583994--1584162 Score: 76
Period size: 24 Copynumber: 7.8 Consensus size: 22
1583984 ACGATTATTT
1583994 TTTATTATTG-TTTATT-T-TA
1 TTTATTATTGTTTTATTATATA
1584013 TTT-TTATTG-TTTATT-T-TA
1 TTTATTATTGTTTTATTATATA
* * *
1584031 TTTCTTATTTTTTTCTCTA-ATA
1 TTTATTATTGTTTTAT-TATATA
1584053 TTTTATTTATATG-TTTATATATATA
1 -TTTA-TTAT-TGTTTTAT-TATATA
* * *
1584078 TATATTACTT-TTCTTATT-TGTT
1 TTTATTA-TTGTT-TTATTATATA
* * *
1584100 TTTACCTAGTATTTTATATATATA
1 TTTA-TTATTGTTTTAT-TATATA
1584124 TTTATTATTGTTTTATTAT-TA
1 TTTATTATTGTTTTATTATATA
1584145 TTT-TTACTTGTTTTATTA
1 TTTATTA-TTGTTTTATTA
1584163 GACATTAAAT
Statistics
Matches: 116, Mismatches: 17, Indels: 32
0.70 0.10 0.19
Matches are distributed among these distances:
18 18 0.16
19 8 0.07
20 7 0.06
21 17 0.15
22 15 0.13
23 23 0.20
24 24 0.21
25 4 0.03
ACGTcount: A:0.23, C:0.05, G:0.04, T:0.68
Consensus pattern (22 bp):
TTTATTATTGTTTTATTATATA
Found at i:1584353 original size:17 final size:18
Alignment explanation
Indices: 1584331--1584368 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1584321 TTATTCTTAG
*
1584331 TTATTTTATT-ATTTTTT
1 TTATTTTATTCATTATTT
*
1584348 TTATTTTGTTCATTATTT
1 TTATTTTATTCATTATTT
1584366 TTA
1 TTA
1584369 ATATTTACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (18 bp):
TTATTTTATTCATTATTT
Found at i:1590797 original size:65 final size:63
Alignment explanation
Indices: 1590693--1590816 Score: 171
Period size: 65 Copynumber: 1.9 Consensus size: 63
1590683 AATATTTCAC
*
1590693 TTAGGATGAAAACCCGAGAAGGCGTCCTAAGTTGAAAAAAAAGAAAGAAGGAAAAAGAAAAACGT
1 TTAGGATGAAAACCCGAGAAGGCGTCCTAAATTGAAAAAAAAGAAA-AA-GAAAAAGAAAAACGT
* *
1590758 TTAGGGTGAAAACCCGA-AAGG-GTGCCCTAAATTGAAAAAAGAGAAAAAGAAAAAGAAAA
1 TTAGGATGAAAACCCGAGAAGGCGT--CCTAAATTGAAAAAAAAGAAAAAGAAAAAGAAAA
1590817 GAAAATAAGG
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
63 13 0.24
64 6 0.11
65 35 0.65
ACGTcount: A:0.53, C:0.10, G:0.24, T:0.12
Consensus pattern (63 bp):
TTAGGATGAAAACCCGAGAAGGCGTCCTAAATTGAAAAAAAAGAAAAAGAAAAAGAAAAACGT
Found at i:1591729 original size:61 final size:59
Alignment explanation
Indices: 1591656--1591810 Score: 226
Period size: 56 Copynumber: 2.6 Consensus size: 59
1591646 CTCAAGATTT
1591656 GATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACAAAAAATTG
1 GATTTCAACTTCACAACGAAGGATATCCAA-TCAAAGCCAATTTGGTGAAAC-AAAAATTG
***
1591717 GATTTCAACTTCACAACGAAGGATATCCAA-C-AA-CCAATTTGGTGAAACAACCCTTG
1 GATTTCAACTTCACAACGAAGGATATCCAATCAAAGCCAATTTGGTGAAACAAAAATTG
*
1591773 GATTTCAACTTCACAACGAAGGATATCAAATTCAAAGC
1 GATTTCAACTTCACAACGAAGGATATCCAA-TCAAAGC
1591811 TCAACTTCAC
Statistics
Matches: 86, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
56 34 0.40
57 15 0.17
58 3 0.03
59 3 0.03
60 1 0.01
61 30 0.35
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.23
Consensus pattern (59 bp):
GATTTCAACTTCACAACGAAGGATATCCAATCAAAGCCAATTTGGTGAAACAAAAATTG
Found at i:1593613 original size:17 final size:18
Alignment explanation
Indices: 1593591--1593628 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
1593581 TTACGATTAT
1593591 TTTTTATTGTTTA-TTTA
1 TTTTTATTGTTTATTTTA
1593608 TTTTTATTGTTTATTTTA
1 TTTTTATTGTTTATTTTA
1593626 TTT
1 TTT
1593629 CTTTATGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (18 bp):
TTTTTATTGTTTATTTTA
Found at i:1594665 original size:28 final size:28
Alignment explanation
Indices: 1594625--1594682 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
1594615 CGAACCTGAG
1594625 ACCTTACTTAAACGATATCAAGTTGCTT
1 ACCTTACTTAAACGATATCAAGTTGCTT
1594653 ACCTTACTTAAACGATATCAAGTTGCTT
1 ACCTTACTTAAACGATATCAAGTTGCTT
1594681 AC
1 AC
1594683 GATTTGAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.34
Consensus pattern (28 bp):
ACCTTACTTAAACGATATCAAGTTGCTT
Found at i:1595943 original size:41 final size:41
Alignment explanation
Indices: 1595898--1595979 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
1595888 ATAAGGTTGT
* * *
1595898 GTTCGTGCTCGTTTGTTTATTTTTGAAGGTGTTCATGTTCG
1 GTTCGTGCTCGTTTATTTACTTTCGAAGGTGTTCATGTTCG
* *
1595939 GTTCGTGTTTGTTTATTTACTTTCGAAGGTGTTCATGTTCG
1 GTTCGTGCTCGTTTATTTACTTTCGAAGGTGTTCATGTTCG
1595980 TTTATTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.11, C:0.12, G:0.26, T:0.51
Consensus pattern (41 bp):
GTTCGTGCTCGTTTATTTACTTTCGAAGGTGTTCATGTTCG
Found at i:1596085 original size:34 final size:34
Alignment explanation
Indices: 1596037--1596102 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
1596027 TCGATTACAT
1596037 GTTCGTTTAACGTTC-CAGAACATATTTGTTTAAC
1 GTTCGTTTAACGTTCAC-GAACATATTTGTTTAAC
* *
1596071 GTTCGTTTATCGTTCACGAACATGTTTGTTTA
1 GTTCGTTTAACGTTCACGAACATATTTGTTTA
1596103 GAATAAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.97
35 1 0.03
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.44
Consensus pattern (34 bp):
GTTCGTTTAACGTTCACGAACATATTTGTTTAAC
Found at i:1596163 original size:24 final size:25
Alignment explanation
Indices: 1596128--1596182 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 25
1596118 GAGAGTGAAC
1596128 GAAAAAGTTTTTTTTCTG-T-TAATAG
1 GAAAAAG--TTTTTTCTGTTATAATAG
1596153 GAAAAAG-TTTTTCTGTTATAATAG
1 GAAAAAGTTTTTTCTGTTATAATAG
1596177 GAAAAA
1 GAAAAA
1596183 TGGTAAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.29
23 1 0.04
24 12 0.43
25 7 0.25
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (25 bp):
GAAAAAGTTTTTTCTGTTATAATAG
Found at i:1596166 original size:22 final size:24
Alignment explanation
Indices: 1596138--1596182 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1596128 GAAAAAGTTT
1596138 TTTTTCTG-T-TAATAGGAAAAAG
1 TTTTTCTGTTATAATAGGAAAAAG
1596160 TTTTTCTGTTATAATAGGAAAAA
1 TTTTTCTGTTATAATAGGAAAAA
1596183 TGGTAAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.38
23 1 0.05
24 12 0.57
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (24 bp):
TTTTTCTGTTATAATAGGAAAAAG
Found at i:1602808 original size:22 final size:23
Alignment explanation
Indices: 1602782--1602824 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1602772 TTTTCTAAAG
1602782 TGATTTAAATTGTT-TGAATTAT
1 TGATTTAAATTGTTATGAATTAT
* *
1602804 TGATTTATATTTTTATGAATT
1 TGATTTAAATTGTTATGAATT
1602825 TATAATTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (23 bp):
TGATTTAAATTGTTATGAATTAT
Found at i:1606941 original size:10 final size:11
Alignment explanation
Indices: 1606921--1606950 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
1606911 CATGTATGAA
1606921 TTAAGTATGTT
1 TTAAGTATGTT
1606932 TTAA-TATGTT
1 TTAAGTATGTT
1606942 TTAAGTATG
1 TTAAGTATG
1606951 ATCAGTAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (11 bp):
TTAAGTATGTT
Found at i:1620193 original size:45 final size:44
Alignment explanation
Indices: 1620117--1620215 Score: 112
Period size: 45 Copynumber: 2.2 Consensus size: 44
1620107 TTTGTGCATA
* *
1620117 GTGCATCGATACACTAAGAAGGTGCATCGATGCATCCCTATAAAT
1 GTGCATCGATACACTAAGAAGATGCACCGATGCATCCCT-TAAAT
* *
1620162 GTGCATCGATACA-TCATA-AAGATGCACCGATGCATGCCTTGAAT
1 GTGCATCGATACACT-A-AGAAGATGCACCGATGCATCCCTTAAAT
*
1620206 GTGTATCGAT
1 GTGCATCGAT
1620216 GCACAGAGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
44 14 0.30
45 32 0.68
46 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (44 bp):
GTGCATCGATACACTAAGAAGATGCACCGATGCATCCCTTAAAT
Found at i:1622417 original size:14 final size:14
Alignment explanation
Indices: 1622398--1622425 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1622388 ACAAAAAGGG
1622398 GGGAGAAGTGTTAA
1 GGGAGAAGTGTTAA
1622412 GGGAGAAGTGTTAA
1 GGGAGAAGTGTTAA
1622426 AGTAAGAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (14 bp):
GGGAGAAGTGTTAA
Found at i:1624374 original size:81 final size:81
Alignment explanation
Indices: 1624238--1624554 Score: 397
Period size: 81 Copynumber: 3.9 Consensus size: 81
1624228 TAACTTTTCA
** * * **
1624238 TCTTTTACTCAACGGTA-TCTAATTGTTCATCTAACTGGAATAATTGGTACATTTCTACCAATTG
1 TCTTTTACTCAACGGTACT-TAATCATTCATCTAACTGGCATAAATGACACATTTCTACCAATTG
*
1624302 CACAATTAGGCCATTAT
65 CACAATTAGGCTATTAT
* *
1624319 TCTTTTACTCAACGGCACTTAATCATTCATCTAACTGGCATAAATGACACCTTTCTACCAATTGC
1 TCTTTTACTCAACGGTACTTAATCATTCATCTAACTGGCATAAATGACACATTTCTACCAATTGC
* *
1624384 ACAGTTAGACTATTAT
66 ACAATTAGGCTATTAT
* * * * **
1624400 TCTTTTACTCAACGATATTTAACCATTCATCTAACTGTCATAAATGACACATTTCTGTCAATTGC
1 TCTTTTACTCAACGGTACTTAATCATTCATCTAACTGGCATAAATGACACATTTCTACCAATTGC
*
1624465 ACAGTTAGGCTATTAT
66 ACAATTAGGCTATTAT
* * *
1624481 TCTTTTACTCAACGGTACTTAATCGTTCATCAAACTGGCATAATTTGTAC-C-TTTCTACCAATT
1 TCTTTTACTCAACGGTACTTAATCATTCATCTAACTGGCATAA-ATG-ACACATTTCTACCAATT
1624544 GCACAATTAGG
64 GCACAATTAGG
1624555 TCTCAAAGGC
Statistics
Matches: 203, Mismatches: 30, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
81 197 0.97
82 4 0.02
83 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (81 bp):
TCTTTTACTCAACGGTACTTAATCATTCATCTAACTGGCATAAATGACACATTTCTACCAATTGC
ACAATTAGGCTATTAT
Found at i:1624601 original size:68 final size:68
Alignment explanation
Indices: 1624506--1624697 Score: 235
Period size: 68 Copynumber: 2.8 Consensus size: 68
1624496 TACTTAATCG
* * * *
1624506 TTCATCAAACTGGCATAATTTG-TACCTTTCTACCA-ATTGCACAATTAGGTCTCAAAGGCACTT
1 TTCATCTAACTGGCATAA-ATGACACCTTTCTACCATA-TGCACAATTAGGCCTCAAAGGCACTT
1624569 AGCCT
64 AGCCT
** *
1624574 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTACCATATGCACAATTAGGCCTCAAAGGCACTTAG
1624639 CCT
66 CCT
* * ** * *
1624642 TTCATCTAATTGGCATAAATGACACTTTTCTGTCATATGCACAGTTAGTCCTCAAA
1 TTCATCTAACTGGCATAAATGACACCTTTCTACCATATGCACAATTAGGCCTCAAA
1624698 TCTTTTAACT
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
67 2 0.02
68 109 0.97
69 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.32
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTACCATATGCACAATTAGGCCTCAAAGGCACTTAG
CCT
Found at i:1625128 original size:58 final size:58
Alignment explanation
Indices: 1624917--1625133 Score: 262
Period size: 59 Copynumber: 3.7 Consensus size: 58
1624907 TCCCATACAA
* * * *
1624917 AAATTCTTACACCTTA-TATGAATTTCTTATCATTTTAGCACACTAAGTGCCCTATACG
1 AAATTCATACA-CTTAGTATAAATTTCTCATCATTTTAGCACACCAAGTGCCCTATACG
* *
1624975 AAAATTCATACACTTAGTATAAATTTCTCATCACTTTAGCACACCAAGTGCCCTATAAGG
1 -AAATTCATACACTTAGTATAAATTTCTCATCATTTTAGCACACCAAGTGCCCTAT-ACG
* * *
1625035 AAATTCACACAC--AGTATAAATTTCTCAACATTTTAGCACA-GAAGTGCCCTATACTG
1 AAATTCATACACTTAGTATAAATTTCTCATCATTTTAGCACACCAAGTGCCCTATAC-G
* * *
1625091 AAATTCATACTCTTAGTATGAATTTCTTATCATTTTAGCACAC
1 AAATTCATACACTTAGTATAAATTTCTCATCATTTTAGCACAC
1625134 TTAGTGCCAT
Statistics
Matches: 136, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
55 1 0.01
56 22 0.16
57 26 0.19
58 29 0.21
59 56 0.41
60 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (58 bp):
AAATTCATACACTTAGTATAAATTTCTCATCATTTTAGCACACCAAGTGCCCTATACG
Found at i:1625653 original size:13 final size:13
Alignment explanation
Indices: 1625635--1625659 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1625625 CGATGTTTCT
1625635 GGGTATCGATACC
1 GGGTATCGATACC
1625648 GGGTATCGATAC
1 GGGTATCGATAC
1625660 TGATTAAATC
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:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (13 bp):
GGGTATCGATACC
Found at i:1632935 original size:21 final size:21
Alignment explanation
Indices: 1632883--1632932 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1632873 TCATTTTTCA
* *
1632883 TGAAAATGGATCGATCCCTTC
1 TGAAAAAGGATCGATACCTTC
*
1632904 TGAAAAAGGATTGATACCTT-
1 TGAAAAAGGATCGATACCTTC
1632924 TGAAAAAGG
1 TGAAAAAGG
1632933 GATCCATCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (21 bp):
TGAAAAAGGATCGATACCTTC
Found at i:1642136 original size:30 final size:30
Alignment explanation
Indices: 1642025--1642311 Score: 209
Period size: 30 Copynumber: 9.7 Consensus size: 30
1642015 TTAAAATCAC
*
1642025 ATCTTAACATTAAAAAATATATTTTA-TCTT
1 ATCTTAAC-TTATAAAATATATTTTATTCTT
* ** * *
1642055 TTACTTAACTTATTGACTATGTTTTATTCTT
1 AT-CTTAACTTATAAAATATATTTTATTCTT
*
1642086 ATCTTAAC-TA-AAATATATATTTTAATCTT
1 ATCTTAACTTATAAA-ATATATTTTATTCTT
* *
1642115 ATCTCAACTTATAAAATATATTTTATTCCT
1 ATCTTAACTTATAAAATATATTTTATTCTT
* *
1642145 ACCTTAACTTA-AAAATATATATT-TT-TT
1 ATCTTAACTTATAAAATATATTTTATTCTT
* * * * *
1642172 ATCTTAACATGTTACATATATTATATTCTT
1 ATCTTAACTTATAAAATATATTTTATTCTT
* *
1642202 AACTTCAA-TTATTAAAA-ATATTATATTCTT
1 ATCTT-AACTTA-TAAAATATATTTTATTCTT
* * * *
1642232 AGCTTAAATTATTATAT-TA-TTTATTCTT
1 ATCTTAACTTATAAAATATATTTTATTCTT
*
1642260 ATCTTAACTTAAAAATATATATTTTATTCTT
1 ATCTTAACTTATAAA-ATATATTTTATTCTT
* *
1642291 ATGTTAATTTA-AGAAATATAT
1 ATCTTAACTTATA-AAATATAT
1642312 ATATTTTAAT
Statistics
Matches: 199, Mismatches: 42, Indels: 32
0.73 0.15 0.12
Matches are distributed among these distances:
27 9 0.05
28 29 0.15
29 43 0.22
30 79 0.40
31 39 0.20
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (30 bp):
ATCTTAACTTATAAAATATATTTTATTCTT
Found at i:1642278 original size:87 final size:87
Alignment explanation
Indices: 1642077--1642279 Score: 195
Period size: 87 Copynumber: 2.3 Consensus size: 87
1642067 TTGACTATGT
* * *
1642077 TTTATTCTTATCTTAAC-TAAAATATATATTTTAATCTTATCTCAACTTATAAAATATATTTTAT
1 TTTATTCTTATCTTAACTTAAAA-ATATATTATAATCTTAACTCAACTTATAAAATATATTATAT
*
1642141 TCCTACCTTAACTTAAAAATATA
65 TCCTACCTTAAATTAAAAATATA
* * *
1642164 TATT-TT-TTATCTTAACATGT-TACATATATTATATTCTTAACTTCAA-TTATTAAAA-ATATT
1 T-TTATTCTTATCTTAAC-T-TAAAAATATATTATAATCTTAAC-TCAACTTA-TAAAATATATT
* * **
1642224 ATATTCTTAGCTTAAATT-ATTATATTA
61 ATATTCCTACCTTAAATTAAAAATA-TA
1642251 TTTATTCTTATCTTAACTTAAAAATATAT
1 TTTATTCTTATCTTAACTTAAAAATATAT
1642280 ATTTTATTCT
Statistics
Matches: 93, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
86 17 0.18
87 53 0.57
88 22 0.24
89 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (87 bp):
TTTATTCTTATCTTAACTTAAAAATATATTATAATCTTAACTCAACTTATAAAATATATTATATT
CCTACCTTAAATTAAAAATATA
Found at i:1642286 original size:31 final size:32
Alignment explanation
Indices: 1642251--1642313 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 32
1642241 TATTATATTA
1642251 TTTATTCTTATCTTAACTTAA-AAATATATAT
1 TTTATTCTTATCTTAACTTAAGAAATATATAT
* *
1642282 TTTATTCTTATGTTAATTTAAGAAATATATAT
1 TTTATTCTTATCTTAACTTAAGAAATATATAT
1642314 ATTTTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 19 0.66
32 10 0.34
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.52
Consensus pattern (32 bp):
TTTATTCTTATCTTAACTTAAGAAATATATAT
Found at i:1642290 original size:59 final size:60
Alignment explanation
Indices: 1642025--1642366 Score: 214
Period size: 59 Copynumber: 5.8 Consensus size: 60
1642015 TTAAAATCAC
* * *
1642025 ATCTTAACATTAAAAA-ATATATTTTA-TCTTTTACTTAACTTATTGACTATGT-TTTATTCTT
1 ATCTTAAC-TTAAAAATATATATTTTATTCTTAT-CTTAAATTATT-A-TATATATTTATTCTT
* * * * * *
1642086 ATCTTAAC-T-AAAATATATATTTTAATCTTATCTCAACTTATAAAATATATTTTATTCCT
1 ATCTTAACTTAAAAATATATATTTTATTCTTATCTTAAATTATTATATATA-TTTATTCTT
* * *
1642145 ACCTTAACTTAAAAATATATA--TT-TT-TTATCTTAACA-TGTTACATATATTATATTCTT
1 ATCTTAACTTAAAAATATATATTTTATTCTTATCTTAA-ATTATTATATATATT-TATTCTT
* * * *
1642202 AACTTCAA-TTATTAAA-A-ATATTATATTCTTAGCTTAAATTATTATAT-TATTTATTCTT
1 ATCTT-AACTTA-AAAATATATATTTTATTCTTATCTTAAATTATTATATATATTTATTCTT
* * ** * *
1642260 ATCTTAACTTAAAAATATATATTTTATTCTTATGTTAATTTAAGAAATATATATATT-TT
1 ATCTTAACTTAAAAATATATATTTTATTCTTATCTTAAATTATTATATATATTTATTCTT
* * * * *
1642319 AATATTAATTATAAAAATA-ATTTTTTA-TCTTAGTTTTAAAATATTATA
1 -ATCTTAACT-TAAAAATATATATTTTATTCTTA-TCTTAAATTATTATA
1642367 AAAATAAAAT
Statistics
Matches: 220, Mismatches: 39, Indels: 45
0.72 0.13 0.15
Matches are distributed among these distances:
56 5 0.02
57 38 0.17
58 27 0.12
59 74 0.34
60 50 0.23
61 26 0.12
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (60 bp):
ATCTTAACTTAAAAATATATATTTTATTCTTATCTTAAATTATTATATATATTTATTCTT
Found at i:1642317 original size:34 final size:32
Alignment explanation
Indices: 1642228--1642319 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 32
1642218 AATATTATAT
* *
1642228 TCTTAGCTTAAATTAT-TATATTATTTATTCTTA
1 TCTTAACTTAAAATATATATA-T-TTTATTCTTA
1642261 TCTTAACTTAAAA-ATATATATTTTATTCTTA
1 TCTTAACTTAAAATATATATATTTTATTCTTA
* *
1642292 TGTTAATTTAAGAAATATATATATTTTA
1 TCTTAACTT-A-AAATATATATATTTTA
1642320 ATATTAATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
31 17 0.33
32 4 0.08
33 18 0.35
34 12 0.24
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (32 bp):
TCTTAACTTAAAATATATATATTTTATTCTTA
Found at i:1648324 original size:19 final size:19
Alignment explanation
Indices: 1648287--1648325 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1648277 CGAATATAAA
* *
1648287 ATTAAAATATGATCCATTT
1 ATTAAAATATAATCAATTT
*
1648306 ATTAAAATATAATTAATTT
1 ATTAAAATATAATCAATTT
1648325 A
1 A
1648326 CTTCGAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (19 bp):
ATTAAAATATAATCAATTT
Found at i:1651149 original size:23 final size:23
Alignment explanation
Indices: 1651123--1651170 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1651113 TATCTAAATG
1651123 AACATATTCACGAACATTAAACA
1 AACATATTCACGAACATTAAACA
* ** *
1651146 AACATGTTCGTGAACGTTAAACA
1 AACATATTCACGAACATTAAACA
1651169 AA
1 AA
1651171 GAACACATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (23 bp):
AACATATTCACGAACATTAAACA
Found at i:1651190 original size:26 final size:27
Alignment explanation
Indices: 1651152--1651202 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
1651142 AACAAACATG
*
1651152 TTCGTGAACGTTAAA-CAAAGAACACA
1 TTCGCGAACGTTAAATCAAAGAACACA
* *
1651178 TTCGCGAATGTTAAATGAAAGAACA
1 TTCGCGAACGTTAAATCAAAGAACA
1651203 AAATACCTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.22
Consensus pattern (27 bp):
TTCGCGAACGTTAAATCAAAGAACACA
Found at i:1651827 original size:21 final size:20
Alignment explanation
Indices: 1651803--1651842 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1651793 ATGGTACCGA
1651803 TACTGAGCCTATCGGTATCGG
1 TACTGA-CCTATCGGTATCGG
* *
1651824 TACTGACTTATGGGTATCG
1 TACTGACCTATCGGTATCG
1651843 ATACCAGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (20 bp):
TACTGACCTATCGGTATCGG
Found at i:1653849 original size:6 final size:6
Alignment explanation
Indices: 1653839--1654129 Score: 485
Period size: 6 Copynumber: 48.5 Consensus size: 6
1653829 TGTCACATAT
*
1653839 GTGTGT GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
*
1653887 GTGTGA GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
1653935 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
* *
1653983 GTGTGC GTGTGC GTGTGC GTGTGC GCGTGC GTGTGC GTGTGC GCGTGC
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
* *
1654031 GTGTGC GTGTGC GCGTGC GTGTGC GTGTGC GTGTGC GCGTGC GTGTGC
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
* * *
1654079 GTGTGC GTGTGC GTGTGC GCGTGC -TCGTGC GCGTGC GTGTGC GCGTGC
1 GTGTGC GTGTGC GTGTGC GTGTGC GT-GTGC GTGTGC GTGTGC GTGTGC
1654127 GTG
1 GTG
1654130 CGTGCGTGCG
Statistics
Matches: 266, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
6 266 1.00
ACGTcount: A:0.00, C:0.19, G:0.50, T:0.31
Consensus pattern (6 bp):
GTGTGC
Found at i:1654136 original size:12 final size:12
Alignment explanation
Indices: 1653997--1654279 Score: 284
Period size: 12 Copynumber: 24.6 Consensus size: 12
1653987 GCGTGTGCGT
* *
1653997 GTGCGTGTGCGC
1 GTGCGTGCGTGC
1654009 GTGCGT--GTGC
1 GTGCGTGCGTGC
* *
1654019 GTGTGCGCGTGC
1 GTGCGTGCGTGC
*
1654031 GT--GTGCGTGT
1 GTGCGTGCGTGC
* *
1654041 GCGCGTGCGTGT
1 GTGCGTGCGTGC
* * *
1654053 GCGTGTGCGTGT
1 GTGCGTGCGTGC
*
1654065 GCGCGTGCGT--
1 GTGCGTGCGTGC
* * *
1654075 GTGCGTGTGCGT
1 GTGCGTGCGTGC
* *
1654087 GTGCGTGTGCGC
1 GTGCGTGCGTGC
1654099 GTGC-T-CGTGC
1 GTGCGTGCGTGC
*
1654109 --GCGTGCGTGT
1 GTGCGTGCGTGC
*
1654119 GCGCGTGCGTGC
1 GTGCGTGCGTGC
1654131 GTGCGTGCGTGC
1 GTGCGTGCGTGC
* *
1654143 --GCGCGCGCGC
1 GTGCGTGCGTGC
*
1654153 GCGCGTGCGTGC
1 GTGCGTGCGTGC
*
1654165 GTGCGCGCGTGC
1 GTGCGTGCGTGC
1654177 GTGCGTGCGTGC
1 GTGCGTGCGTGC
1654189 GTGCGTGCGTGC
1 GTGCGTGCGTGC
1654201 GTGCGTGCGTGC
1 GTGCGTGCGTGC
1654213 GTGCGTGCGTGC
1 GTGCGTGCGTGC
1654225 GTGCGTGCGTGC
1 GTGCGTGCGTGC
1654237 GTGCGTGCGTGC
1 GTGCGTGCGTGC
1654249 GTGCGTGCGTGC
1 GTGCGTGCGTGC
1654261 GTGCGTGCGTGC
1 GTGCGTGCGTGC
1654273 GTGCGTG
1 GTGCGTG
1654280 TGTGTGTTAA
Statistics
Matches: 235, Mismatches: 24, Indels: 24
0.83 0.08 0.08
Matches are distributed among these distances:
8 2 0.01
9 1 0.00
10 36 0.15
11 1 0.00
12 195 0.83
ACGTcount: A:0.00, C:0.25, G:0.50, T:0.25
Consensus pattern (12 bp):
GTGCGTGCGTGC
Found at i:1654136 original size:24 final size:24
Alignment explanation
Indices: 1653840--1654286 Score: 401
Period size: 24 Copynumber: 18.4 Consensus size: 24
1653830 GTCACATATG
* * *
1653840 TGTGTGTGTGCGTGTGCGTGTGCG
1 TGTGCGTGTGCGTGCGCGCGTGCG
* *
1653864 TGTGCGTGTGCGTGTGCGTGTGCG
1 TGTGCGTGTGCGTGCGCGCGTGCG
* * *
1653888 TGTGAGTGTGCGTGTGCGTGTGCG
1 TGTGCGTGTGCGTGCGCGCGTGCG
* *
1653912 TGTGCGTGTGCGTGTGCGTGTGCG
1 TGTGCGTGTGCGTGCGCGCGTGCG
* *
1653936 TGTGCGTGTGCGTGTGCGTGTGCG
1 TGTGCGTGTGCGTGCGCGCGTGCG
* *
1653960 TGTGCGTGTGCGTGTGCGTGTGCG
1 TGTGCGTGTGCGTGCGCGCGTGCG
* *
1653984 TGTGCGTGTGCGTGTGCGTGTGCG
1 TGTGCGTGTGCGTGCGCGCGTGCG
* *
1654008 CGTGCGTGTGCGTGTGCGCGTGCG
1 TGTGCGTGTGCGTGCGCGCGTGCG
* * *
1654032 TGTGCGTGTGCGCGTGCGTGTGCG
1 TGTGCGTGTGCGTGCGCGCGTGCG
* * *
1654056 TGTGCGTGTGCGCGTGCGTGTGCG
1 TGTGCGTGTGCGTGCGCGCGTGCG
*
1654080 TGTGCGTGTGCGTGTGCGCGTGC-
1 TGTGCGTGTGCGTGCGCGCGTGCG
* *
1654103 TCGTGCGCGTGCGTGTGCGCGTGCG
1 T-GTGCGTGTGCGTGCGCGCGTGCG
* * * *
1654128 TGCGTGCGTGCGTGCGCGCGCGCG
1 TGTGCGTGTGCGTGCGCGCGTGCG
* *
1654152 CGCGCGTGCGTGCGTGCGCGCGTGCG
1 TGTGCGT--GTGCGTGCGCGCGTGCG
*
1654178 TGCGTGCGTGCGTGCGTGCGTGCGTGCG
1 T--GTGCGT--GTGCGTGCGCGCGTGCG
* * * *
1654206 TGCGTGCGTGCGTGCGTGCGTGCG
1 TGTGCGTGTGCGTGCGCGCGTGCG
* * * *
1654230 TGCGTGCGTGCGTGCGTGCGTGCG
1 TGTGCGTGTGCGTGCGCGCGTGCG
* * * *
1654254 TGCGTGCGTGCGTGCGTGCGTGCG
1 TGTGCGTGTGCGTGCGCGCGTGCG
*
1654278 TGTGTGTGT
1 TGTGCGTGT
1654287 TAAATGAGTT
Statistics
Matches: 390, Mismatches: 27, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
23 1 0.00
24 345 0.88
25 1 0.00
26 19 0.05
28 24 0.06
ACGTcount: A:0.00, C:0.21, G:0.50, T:0.29
Consensus pattern (24 bp):
TGTGCGTGTGCGTGCGCGCGTGCG
Found at i:1654137 original size:36 final size:36
Alignment explanation
Indices: 1653865--1654279 Score: 255
Period size: 36 Copynumber: 11.9 Consensus size: 36
1653855 GCGTGTGCGT
* * * * *
1653865 GTGCGTGTGCGTGTGCGTGTGCGTGTGAGTGTGCGT-
1 GTGCGCGTGCGTGTGCGCGTGCGTGCGTGCGTGC-TC
* * * * *
1653901 GTGCGTGTGCGTGTGCGTGTGCGTGTGCGTGTGCGT-
1 GTGCGCGTGCGTGTGCGCGTGCGTGCGTGCGTGC-TC
* * * * *
1653937 GTGCGTGTGCGTGTGCGTGTGCGTGTGCGTGTGCGT-
1 GTGCGCGTGCGTGTGCGCGTGCGTGCGTGCGTGC-TC
* * * * * *
1653973 GTGCGTGTGCGTGTGCGTGTGCGTGTGCGTGTGCGC
1 GTGCGCGTGCGTGTGCGCGTGCGTGCGTGCGTGCTC
*
1654009 GTGCGTGTGCGTGTGCGCGTGCGT--GTGC--G-T-
1 GTGCGCGTGCGTGTGCGCGTGCGTGCGTGCGTGCTC
*
1654039 GTGCGCGTGCGTGT--GCGT--GTGCGT--GTGCGC
1 GTGCGCGTGCGTGTGCGCGTGCGTGCGTGCGTGCTC
* * * *
1654069 GTGCGTGTGCGTGTGCGTGTGCGTGTGCGCGTGCTC
1 GTGCGCGTGCGTGTGCGCGTGCGTGCGTGCGTGCTC
1654105 GTGCGCGTGCGTGTGCGCGTGCGTGCGTGCGTG--C
1 GTGCGCGTGCGTGTGCGCGTGCGTGCGTGCGTGCTC
* * * *
1654139 GTGCGCGCGCGCGCGCGCGTGCGTGCGTGC--GCGC
1 GTGCGCGTGCGTGTGCGCGTGCGTGCGTGCGTGCTC
* *
1654173 GT--GCGTGCGTGCGTGCGTGCGTGCGTGCGTG--C
1 GTGCGCGTGCGTGTGCGCGTGCGTGCGTGCGTGCTC
* *
1654205 GTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGC
1 GTGC--GCGTGCGTGTGCGCGTGCGTGCGTGCGTGC-T-C
* *
1654245 GTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTG
1 GTGC--GCGTGCGTGTGCGCGTGCGTGCGTGCGTG
1654280 TGTGTGTTAA
Statistics
Matches: 331, Mismatches: 23, Indels: 46
0.83 0.06 0.12
Matches are distributed among these distances:
26 2 0.01
28 7 0.02
30 26 0.08
32 31 0.09
34 38 0.11
36 191 0.58
40 36 0.11
ACGTcount: A:0.00, C:0.22, G:0.50, T:0.27
Consensus pattern (36 bp):
GTGCGCGTGCGTGTGCGCGTGCGTGCGTGCGTGCTC
Found at i:1655552 original size:2 final size:2
Alignment explanation
Indices: 1655545--1655586 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1655535 AAAAGAAATA
1655545 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1655586 A
1 A
1655587 ACATATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1655598 original size:16 final size:17
Alignment explanation
Indices: 1655540--1655598 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 17
1655530 ATATAAAAAG
1655540 AAATAATATATATATAT
1 AAATAATATATATATAT
1655557 ATATATATATATATATATAT
1 A-A-ATA-ATATATATATAT
* *
1655577 ATATAATATA-ACATAT
1 AAATAATATATATATAT
1655593 AAATAA
1 AAATAA
1655599 AATAAGTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 10 0.28
17 6 0.17
18 4 0.11
19 3 0.08
20 13 0.36
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATAATATATATATAT
Found at i:1657784 original size:110 final size:110
Alignment explanation
Indices: 1657630--1657833 Score: 318
Period size: 110 Copynumber: 1.9 Consensus size: 110
1657620 TGGGAAATTA
* * **
1657630 TTTGTTGACAATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTATCTTGAGTCCAATATCC
1 TTTGTTGACAATCAGCCACCCCTTCATCATGAAGTTGAGCTTGTGTTATCTTGAGTCCAATATCC
*
1657695 TTCGTTGTGAAGTTGAAATTGACTCTGAATAAAATTGAAAAGTTG
66 TTCGTTGTGAAGTTAAAATTGACTCTGAATAAAATTGAAAAGTTG
* * *
1657740 TTTGTTGGCAATCAGCCACCCCTTCATCATGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCC
1 TTTGTTGACAATCAGCCACCCCTTCATCATGAAGTTGAGCTTGTGTTATCTTGAGTCCAATATCC
* *
1657805 TTCGTTGTGATGTTAAAATTGGCTCTGAA
66 TTCGTTGTGAAGTTAAAATTGACTCTGAA
1657834 ATTGGGAAGC
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
110 84 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (110 bp):
TTTGTTGACAATCAGCCACCCCTTCATCATGAAGTTGAGCTTGTGTTATCTTGAGTCCAATATCC
TTCGTTGTGAAGTTAAAATTGACTCTGAATAAAATTGAAAAGTTG
Found at i:1658869 original size:16 final size:15
Alignment explanation
Indices: 1658833--1658880 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
1658823 ACCCTCCTTA
1658833 TTTTC-TTTTTC--T
1 TTTTCTTTTTTCATT
1658845 TTTTCTTTTGTT-ATT
1 TTTTCTTTT-TTCATT
1658860 TTTCTCTTTTTTCATT
1 TTT-TCTTTTTTCATT
1658876 TTTTC
1 TTTTC
1658881 AATTTAGGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
12 5 0.17
13 3 0.10
14 2 0.07
15 8 0.27
16 12 0.40
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTTTCATT
Found at i:1658937 original size:17 final size:17
Alignment explanation
Indices: 1658917--1658957 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1658907 ACCCTAAACA
1658917 TTTTTTTATCTTTTTTG
1 TTTTTTTATCTTTTTTG
* *
1658934 TTTTTTTGTTTTTTTTG
1 TTTTTTTATCTTTTTTG
1658951 TTTTTTT
1 TTTTTTT
1658958 CTGACTTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.02, C:0.02, G:0.07, T:0.88
Consensus pattern (17 bp):
TTTTTTTATCTTTTTTG
Found at i:1658938 original size:8 final size:8
Alignment explanation
Indices: 1658917--1658957 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
1658907 ACCCTAAACA
*
1658917 TTTTTTTA
1 TTTTTTTG
1658925 TCTTTTTTG
1 T-TTTTTTG
1658934 TTTTTTTG
1 TTTTTTTG
1658942 TTTTTTTTG
1 -TTTTTTTG
1658951 TTTTTTT
1 TTTTTTT
1658958 CTGACTTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 15 0.50
9 15 0.50
ACGTcount: A:0.02, C:0.02, G:0.07, T:0.88
Consensus pattern (8 bp):
TTTTTTTG
Found at i:1658939 original size:9 final size:9
Alignment explanation
Indices: 1658917--1658957 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
1658907 ACCCTAAACA
*
1658917 TTTTTTTAT
1 TTTTTTTGT
*
1658926 CTTTTTTG-
1 TTTTTTTGT
1658934 TTTTTTTGT
1 TTTTTTTGT
1658943 TTTTTTTGT
1 TTTTTTTGT
1658952 TTTTTT
1 TTTTTT
1658958 CTGACTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 7 0.25
9 21 0.75
ACGTcount: A:0.02, C:0.02, G:0.07, T:0.88
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:1669196 original size:18 final size:18
Alignment explanation
Indices: 1669173--1669214 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1669163 GATCAATTGA
*
1669173 AAATAAGGA-AAATGAAAT
1 AAATAAGAATAAAT-AAAT
1669191 AAATAAGAATAAATAAAT
1 AAATAAGAATAAATAAAT
1669209 AAATAA
1 AAATAA
1669215 TAACATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (18 bp):
AAATAAGAATAAATAAAT
Found at i:1669224 original size:18 final size:18
Alignment explanation
Indices: 1669173--1669225 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1669163 GATCAATTGA
*
1669173 AAATAAGGA-AAATGAAAT
1 AAATAAGAACAAAT-AAAT
*
1669191 AAATAAGAATAAATAAAT
1 AAATAAGAACAAATAAAT
* *
1669209 AAATAATAACATATAAA
1 AAATAAGAACAAATAAA
1669226 ACAAAGACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.21
Consensus pattern (18 bp):
AAATAAGAACAAATAAAT
Found at i:1672192 original size:21 final size:21
Alignment explanation
Indices: 1672163--1672207 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1672153 ATTCTGACCA
1672163 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1672184 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
1672205 TCG
1 TCG
1672208 AAAATCGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1672276 original size:20 final size:20
Alignment explanation
Indices: 1672213--1672329 Score: 153
Period size: 20 Copynumber: 5.8 Consensus size: 20
1672203 ATTCGAAAAT
1672213 CGAATACGTAAATCGCAACG
1 CGAATACGTAAATCGCAACG
** * *
1672233 CGAATTTGGAAAATCGCAATG
1 CGAA-TACGTAAATCGCAACG
* *
1672254 CGATTACGTAAATCACAACG
1 CGAATACGTAAATCGCAACG
1672274 CGAATACGTAAATCGCAACG
1 CGAATACGTAAATCGCAACG
*
1672294 CGAATACGTAAATCGCAATG
1 CGAATACGTAAATCGCAACG
*
1672314 CAAATACGTAAATCGC
1 CGAATACGTAAATCGC
1672330 GTTGCGATTT
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 67 0.82
21 15 0.18
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
CGAATACGTAAATCGCAACG
Found at i:1672345 original size:40 final size:40
Alignment explanation
Indices: 1672217--1672353 Score: 150
Period size: 40 Copynumber: 3.4 Consensus size: 40
1672207 GAAAATCGAA
* ** *
1672217 TACGTAAATCGCAACGCGAATTTGGAAAATCGCAATGCGAT
1 TACGTAAATCGCAACGC-AAATACGTAAATCGCAATGCGAT
* * * *
1672258 TACGTAAATCACAACGCGAATACGTAAATCGCAACGCGAA
1 TACGTAAATCGCAACGCAAATACGTAAATCGCAATGCGAT
* **
1672298 TACGTAAATCGCAATGCAAATACGTAAATCGCGTTGCGATT
1 TACGTAAATCGCAACGCAAATACGTAAATCGCAATGCGA-T
1672339 TA-GTAAATCGCAACG
1 TACGTAAATCGCAACG
1672354 AGATTCTGAC
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
40 61 0.77
41 18 0.23
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (40 bp):
TACGTAAATCGCAACGCAAATACGTAAATCGCAATGCGAT
Found at i:1672353 original size:60 final size:61
Alignment explanation
Indices: 1672213--1672327 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 61
1672203 ATTCGAAAAT
** * *
1672213 CGAATACGTAAATCGCAACGCGAATTTGGAAAATCGCAATGCGATTACGTAAATCACAACG
1 CGAATACGTAAATCGCAACGCGAATTACGAAAATCGCAATGCAAATACGTAAATCACAACG
*
1672274 CGAATACGTAAATCGCAACGCGAA-TACGTAAATCGCAATGCAAATACGTAAATC
1 CGAATACGTAAATCGCAACGCGAATTACGAAAATCGCAATGCAAATACGTAAATC
1672328 GCGTTGCGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 25 0.51
61 24 0.49
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (61 bp):
CGAATACGTAAATCGCAACGCGAATTACGAAAATCGCAATGCAAATACGTAAATCACAACG
Found at i:1673264 original size:24 final size:24
Alignment explanation
Indices: 1673213--1673266 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1673203 GTATTCGAAA
*
1673213 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1673237 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1673261 TTTGAT
1 TTTGAT
1673267 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1675853 original size:52 final size:52
Alignment explanation
Indices: 1675774--1676066 Score: 230
Period size: 52 Copynumber: 5.5 Consensus size: 52
1675764 CTTAATGTCT
*
1675774 ATCGCAACGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCAAAATGAAA
1 ATCGCAACGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
*
1675827 ATCGCAACGCGAAACT-AAAATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAA-TGAAAATCGCAACG-AG-AA--A--ATCGCAATGCGAAATGAAA
* * **
1675885 ATCGCAACGAGAGAATCG-CAAT-GCGAA--ATGAAAATCGCAA--CG--A-GGGA
1 ATCGCAACGCGA-AAT-GAAAATCGC-AACGA-GAAAATCGCAATGCGAAATGAAA
* * * * *
1675932 ATCGCAAAGCGAAATGAAAATTGCAACGAAACTAAAATCGCAACGCGAAATGACA
1 ATCGCAACGCGAAATGAAAATCGCAACG--A-GAAAATCGCAATGCGAAATGAAA
* ** *
1675987 ATCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAAAGCGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
1676039 ATCGCAACGCGAAACT-AAAATCGCAACG
1 ATCGCAACGCGAAA-TGAAAATCGCAACG
1676067 CGAATTTAGT
Statistics
Matches: 194, Mismatches: 22, Indels: 49
0.73 0.08 0.18
Matches are distributed among these distances:
45 1 0.01
46 8 0.04
47 14 0.07
48 1 0.01
50 13 0.07
52 68 0.35
53 14 0.07
54 4 0.02
55 28 0.14
56 3 0.02
57 1 0.01
58 32 0.16
59 7 0.04
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (52 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
Found at i:1675870 original size:39 final size:37
Alignment explanation
Indices: 1675774--1676068 Score: 172
Period size: 33 Copynumber: 8.3 Consensus size: 37
1675764 CTTAATGTCT
*
1675774 ATCGCAACGCGGAAATGAAAATCGCAA-CG--AGAAA
1 ATCGCAACGCGGAAATGAAAATCGCAAGCGAAATAAA
* *
1675808 ATCGCAATGC-AAAATGAAAATCGCAACGCGAAACTAAA
1 ATCGCAACGCGGAAATGAAAATCGCAA-GCGAAA-TAAA
**
1675846 ATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAATGAAAATCGCAA-GCGAAAT-AAA
*
1675885 ATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAATGAAAATCGCAA-GCGAAAT-AAA
*
1675918 ATCGCAACGAGG----G--AATCGCAAAGCGAAATGAAA
1 ATCGCAACGCGGAAATGAAAATCGC-AAGCGAAAT-AAA
* *
1675951 ATTGCAA--C-GAAACT-AAAATCGCAACGCGAAATGACA
1 ATCGCAACGCGGAAA-TGAAAATCGCAA-GCGAAAT-AAA
* ***
1675987 ATCGCAATGC-GAAATGAAAATCGCAA-CG--AGGGA
1 ATCGCAACGCGGAAATGAAAATCGCAAGCGAAATAAA
*
1676020 ATCGCAAAGC-GAAATGAAAATCGCAACGCGAAACTAAA
1 ATCGCAACGCGGAAATGAAAATCGCAA-GCGAAA-TAAA
1676058 ATCGCAACGCG
1 ATCGCAACGCG
1676069 AATTTAGTTT
Statistics
Matches: 210, Mismatches: 23, Indels: 51
0.74 0.08 0.18
Matches are distributed among these distances:
30 1 0.00
33 92 0.44
34 13 0.06
35 7 0.03
36 26 0.12
37 4 0.02
38 38 0.18
39 29 0.14
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (37 bp):
ATCGCAACGCGGAAATGAAAATCGCAAGCGAAATAAA
Found at i:1676002 original size:88 final size:89
Alignment explanation
Indices: 1675898--1676070 Score: 321
Period size: 88 Copynumber: 1.9 Consensus size: 89
1675888 GCAACGAGAG
*
1675898 AATCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATTGCAA-CGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACCGAA
1675962 ACTAAAATCGCAACGCGAAATGAC
66 ACTAAAATCGCAACGCGAAATGAC
1675986 AATCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATCGCAAC-CGA
1676051 AACTAAAATCGCAACGCGAA
65 AACTAAAATCGCAACGCGAA
1676071 TTTAGTTTCG
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
88 59 0.72
90 23 0.28
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (89 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACCGAA
ACTAAAATCGCAACGCGAAATGAC
Found at i:1676023 original size:121 final size:123
Alignment explanation
Indices: 1675774--1676052 Score: 436
Period size: 121 Copynumber: 2.3 Consensus size: 123
1675764 CTTAATGTCT
* *
1675774 ATCGCAACGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCAAAATGAAAATCGCAACGCGA
1 ATCGCAAAGC-GAAATGAAAATCGCAACGAGAAAATCGCAAAGCAAAATGAAAATCGCAAC-CGA
*
1675839 AACTAAAATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAAATCGCAACGAGAGA
64 AACTAAAATCGCAACGCGGAAATGACAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* ** * *
1675899 ATCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATTGCAA-CGAAA
1 ATCGCAAAGCGAAATGAAAATCGCAACGAGAAAATCGCAAAGCAAAATGAAAATCGCAACCGAAA
*
1675963 CTAAAATCGCAACGC-GAAATGACAATCGCAATGCGAAATGAAAATCGCAACGAGGGA
66 CTAAAATCGCAACGCGGAAATGACAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1676020 ATCGCAAAGCGAAATGAAAATCGCAACGCGAAA
1 ATCGCAAAGCGAAATGAAAATCGCAACGAGAAA
1676053 CTAAAATCGC
Statistics
Matches: 142, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
121 69 0.49
122 20 0.14
124 44 0.31
125 9 0.06
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (123 bp):
ATCGCAAAGCGAAATGAAAATCGCAACGAGAAAATCGCAAAGCAAAATGAAAATCGCAACCGAAA
CTAAAATCGCAACGCGGAAATGACAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1676043 original size:19 final size:19
Alignment explanation
Indices: 1675774--1676070 Score: 194
Period size: 19 Copynumber: 16.7 Consensus size: 19
1675764 CTTAATGTCT
*
1675774 ATCGCAACGCGGAAATGAAA
1 ATCGCAAAGC-GAAATGAAA
1675794 ATCGC-AA-CG--A-GAAA
1 ATCGCAAAGCGAAATGAAA
* *
1675808 ATCGCAATGCAAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
1675827 ATCGCAACGCGAAACT-AAA
1 ATCGCAAAGCGAAA-TGAAA
* **
1675846 ATCGCAACGCGGAAATGACT
1 ATCGCAAAGC-GAAATGAAA
*
1675866 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
1675885 ATCGC-AA-CG--A-GAGA
1 ATCGCAAAGCGAAATGAAA
*
1675899 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
**
1675918 ATCGC-AA-CG--A-GGGA
1 ATCGCAAAGCGAAATGAAA
1675932 ATCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
1675951 ATTGC-AA-CGAAACT-AAA
1 ATCGCAAAGCGAAA-TGAAA
* *
1675968 ATCGCAACGCGAAATGACA
1 ATCGCAAAGCGAAATGAAA
*
1675987 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
**
1676006 ATCGC-AA-CG--A-GGGA
1 ATCGCAAAGCGAAATGAAA
1676020 ATCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
1676039 ATCGCAACGCGAAACT-AAA
1 ATCGCAAAGCGAAA-TGAAA
*
1676058 ATCGCAACGCGAA
1 ATCGCAAAGCGAA
1676071 TTTAGTTTCG
Statistics
Matches: 218, Mismatches: 31, Indels: 57
0.71 0.10 0.19
Matches are distributed among these distances:
14 31 0.14
15 10 0.05
16 7 0.03
17 19 0.09
18 13 0.06
19 117 0.54
20 21 0.10
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAAAGCGAAATGAAA
Found at i:1676108 original size:19 final size:19
Alignment explanation
Indices: 1676066--1676142 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 19
1676056 AAATCGCAAC
*
1676066 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
* *
1676085 GCGATTTTATTTTCGTGTT
1 GCGATTTTAGTTTCGCGTT
1676104 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
*
1676118 GCGATTTTCA-TTTCGCATT
1 GCGATTTT-AGTTTCGCGTT
1676137 GCGATT
1 GCGATT
1676143 CTCTCGTTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
14 11 0.24
16 1 0.02
17 1 0.02
19 33 0.72
ACGTcount: A:0.13, C:0.16, G:0.23, T:0.48
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:1676123 original size:33 final size:34
Alignment explanation
Indices: 1676081--1676174 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
1676071 TTTAGTTTCG
** * *
1676081 CGTTGCGATTTT-ATTTTCGTGTTGCGATTTTGT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1676114 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1676147 CGTTGCGATTTTCA-TTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
1676175 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 55 0.98
34 1 0.02
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:1676173 original size:19 final size:19
Alignment explanation
Indices: 1676116--1676174 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1676106 GATTTTGTCG
1676116 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1676135 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1676149 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1676168 TTGCGAT
1 TTGCGAT
1676175 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1676182 original size:19 final size:17
Alignment explanation
Indices: 1676124--1676174 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1676114 CGTTGCGATT
1676124 TTCATTTCGCATTGCGA
1 TTCATTTCGCATTGCGA
*
1676141 TTC-TCTCG--TTGCGA
1 TTCATTTCGCATTGCGA
1676155 TTTTCATTTCGCATTGCGA
1 --TTCATTTCGCATTGCGA
1676174 T
1 T
1676175 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
14 6 0.22
16 7 0.26
17 8 0.30
19 6 0.22
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (17 bp):
TTCATTTCGCATTGCGA
Found at i:1676300 original size:14 final size:14
Alignment explanation
Indices: 1676281--1676317 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1676271 CATCAATTAA
1676281 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1676295 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1676309 ACAAATCAA
1 ACAAATCAA
1676318 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1679661 original size:20 final size:20
Alignment explanation
Indices: 1679638--1679693 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1679628 TGAAATGAAA
*
1679638 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATAACT
*
1679658 ATCGCAACGTG-GAAATAACT
1 ATCGCAACGAGAG-AATAACT
1679678 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
1679694 CGCAACGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGAGAATAACT
Found at i:1679697 original size:14 final size:14
Alignment explanation
Indices: 1679678--1679738 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
1679668 GGAAATAACT
*
1679678 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
1679692 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
*
1679711 ATCGCAACGAGATA
1 ATCGCAACGAGAAA
*
1679725 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
1679739 TTAAAATCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1679715 original size:19 final size:19
Alignment explanation
Indices: 1679629--1679774 Score: 107
Period size: 19 Copynumber: 8.1 Consensus size: 19
1679619 TCTTTTGGTT
*
1679629 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
** *
1679648 GAGAATGACTATCGCAACGTG
1 GA-AATGAAAATCGCAACG-C
*
1679669 GAAAT-AACTATCGCAA--C
1 GAAATGAA-AATCGCAACGC
*
1679686 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1679702 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1679719 G--A-GATAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1679735 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1679754 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1679773 GA
1 GA
1679775 TTTTGGTTTC
Statistics
Matches: 100, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
14 17 0.17
15 3 0.03
16 4 0.04
17 3 0.03
18 2 0.02
19 44 0.44
20 25 0.25
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1679715 original size:33 final size:33
Alignment explanation
Indices: 1679629--1679752 Score: 133
Period size: 33 Copynumber: 3.5 Consensus size: 33
1679619 TCTTTTGGTT
*
1679629 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGTG
1 GAAATGAAAATCGCAAC--GAG-A-GA--ATCGCAACG-C
*
1679669 GAAAT-AACTATCGCAACGAGAGAATCGCAACGC
1 GAAATGAA-AATCGCAACGAGAGAATCGCAACGC
*
1679702 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1679735 GAAATTAAAATCGCAACG
1 GAAATGAAAATCGCAACG
1679753 CGAAATGAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
33 45 0.58
34 11 0.14
36 2 0.03
37 1 0.01
38 3 0.04
39 2 0.03
40 13 0.17
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1679803 original size:19 final size:20
Alignment explanation
Indices: 1679781--1679856 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 20
1679771 GCGATTTTGG
1679781 TTTCGCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
* **
1679800 TTTCTCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATTTTCAT
*
1679820 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
**
1679840 TTTCATGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
1679857 AAGTTTAGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 16 0.33
20 32 0.67
ACGTcount: A:0.12, C:0.17, G:0.20, T:0.51
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:1680443 original size:20 final size:20
Alignment explanation
Indices: 1680417--1680600 Score: 148
Period size: 20 Copynumber: 9.4 Consensus size: 20
1680407 TAAAAATCAT
1680417 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1680437 ATTGCGATTTTAC-G-TA---
1 GTTGCGA-TTTACGGATACGC
1680453 -TTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * * *
1680472 ATTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGC
* *
1680492 GTTGAGATTTACAGATACGC
1 GTTGCGATTTACGGATACGC
* * **
1680512 GTTGCGATTTACGTATTCTT
1 GTTGCGATTTACGGATACGC
1680532 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
1680552 GTTACGATTTTACGTAT-TGTC
1 GTTGCGA-TTTACGGATACG-C
* *
1680573 ATTGCGATTTACGGATACTC
1 GTTGCGATTTACGGATACGC
1680593 GTTGCGAT
1 GTTGCGAT
1680601 AGTCAGAATC
Statistics
Matches: 125, Mismatches: 29, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
14 5 0.04
15 7 0.06
16 2 0.02
19 2 0.02
20 90 0.72
21 19 0.15
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1680464 original size:14 final size:15
Alignment explanation
Indices: 1680432--1680461 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1680422 GATTTACGGA
1680432 TACGCATTGCGATTT
1 TACGCATTGCGATTT
*
1680447 TACGTATTGCGATTT
1 TACGCATTGCGATTT
1680462 ACGGATACGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (15 bp):
TACGCATTGCGATTT
Found at i:1680517 original size:40 final size:40
Alignment explanation
Indices: 1680417--1680600 Score: 227
Period size: 40 Copynumber: 4.7 Consensus size: 40
1680407 TAAAAATCAT
*
1680417 GTTGCGATTTACGGATACGCATTGCGATTTTACGTA-----
1 GTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCTC
*
1680453 -TTGCGATTTACGGATACGCATTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTC
* * *
1680492 GTTGAGATTTACAGATACGCGTTGCGATTTACGTATTCTT
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTC
* *
1680532 GTTGCGATTTACGGATACGCGTTACGATTTTACGTATTGTC
1 GTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCTC
* *
1680573 ATTGCGATTTACGGATACTCGTTGCGAT
1 GTTGCGATTTACGGATACGCGTTGCGAT
1680601 AGTCAGAATC
Statistics
Matches: 129, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
34 8 0.06
35 26 0.20
40 60 0.47
41 35 0.27
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (40 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTC
Found at i:1680633 original size:20 final size:19
Alignment explanation
Indices: 1680609--1680661 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
1680599 ATAGTCAGAA
1680609 TCGCGTTGCGATTT-ATAT
1 TCGCGTTGCGATTTCATAT
1680627 GTCCGCGTTGCGATTTTCATAT
1 -T-CGCGTTGCGA-TTTCATAT
1680649 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1680662 ATGGAAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
19 3 0.10
20 20 0.65
21 4 0.13
22 4 0.13
ACGTcount: A:0.13, C:0.21, G:0.25, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTCATAT
Found at i:1680654 original size:101 final size:100
Alignment explanation
Indices: 1680471--1680661 Score: 217
Period size: 101 Copynumber: 1.9 Consensus size: 100
1680461 TACGGATACG
* * * **
1680471 CATTGCGATTTACGTATTCTCGTTGAGATTTACAGATACGCGTTGCGATTTACGTATTCTTGTTG
1 CATTGCGATTTACGGATACTCGTTGAGATGTACAGATACGCGTTGCGATTTAC-TATTCGCGTTG
*
1680536 CGATTTACGGATACGCGTTACGATTTTACGTATTGT
65 CGATTTACAGATACGCGTTACGATTTTACGTATTGT
*
1680572 CATTGCGATTTACGGATACTCGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTA-TATGTCCGCG
1 CATTGCGATTTACGGATACTCGTTGAGAT-GTACAGATA-CGCGTTGCGATTTACTAT-T-CGCG
* * * *
1680634 TTGCGATTTTCATATTCGCGTTGCGATT
62 TTGCGATTTACAGATACGCGTTACGATT
1680662 ATGGAAAATC
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
99 3 0.04
100 2 0.03
101 69 0.92
102 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (100 bp):
CATTGCGATTTACGGATACTCGTTGAGATGTACAGATACGCGTTGCGATTTACTATTCGCGTTGC
GATTTACAGATACGCGTTACGATTTTACGTATTGT
Found at i:1680962 original size:20 final size:20
Alignment explanation
Indices: 1680937--1681119 Score: 155
Period size: 20 Copynumber: 9.3 Consensus size: 20
1680927 AAAAATCGCA
1680937 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
1680957 TTGCGATTTTAC-G-TA----
1 TTGCGA-TTTACGGATACGCG
* *
1680972 TTGCAATTTACGGATACGCA
1 TTGCGATTTACGGATACGCG
* * * *
1680992 TTGCAATTTACGTATTCTCG
1 TTGCGATTTACGGATACGCG
* *
1681012 TTGCGATTTACAGATACGCT
1 TTGCGATTTACGGATACGCG
* * *
1681032 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACGCG
1681052 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* *
1681072 TTGCGATTTTACGTAT-TGTCG
1 TTGCGA-TTTACGGATACG-CG
* *
1681093 TTGCGATTTACAGATACTCG
1 TTGCGATTTACGGATACGCG
1681113 TTGCGAT
1 TTGCGAT
1681120 AGTCAGAATC
Statistics
Matches: 128, Mismatches: 25, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
14 5 0.04
15 6 0.05
16 2 0.02
19 2 0.02
20 92 0.72
21 21 0.16
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGGATACGCG
Found at i:1681041 original size:40 final size:40
Alignment explanation
Indices: 1680937--1681180 Score: 234
Period size: 40 Copynumber: 6.2 Consensus size: 40
1680927 AAAAATCGCA
*
1680937 TTGCGATTTACGGATACGCGTTGCGATTTTACGTA------
1 TTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCG
* * * *
1680972 TTGCAATTTACGGATACGCATTGCAATTTACGTATTCTCG
1 TTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCG
*
1681012 TTGCGATTTACAGATACGCTTTGCGATTTACGTATTCTCG
1 TTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCG
* *
1681052 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCG
1 TTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCG
* * * *
1681093 TTGCGATTTACAGATACTCGTTGCGATAGT-CAG-AATCGCG
1 TTGCGATTTACAGATACGCGTTGCGAT-TTAC-GTATTCTCG
* * * * * *
1681133 TTGCGATTTATATATTCGCGTTGCGATTTTCATATTCGCG
1 TTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCG
1681173 TTGCGATT
1 TTGCGATT
1681181 ATGGAAAATC
Statistics
Matches: 175, Mismatches: 23, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
34 8 0.05
35 23 0.13
39 1 0.01
40 104 0.59
41 39 0.22
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (40 bp):
TTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCG
Found at i:1681151 original size:20 final size:20
Alignment explanation
Indices: 1680992--1681180 Score: 157
Period size: 20 Copynumber: 9.4 Consensus size: 20
1680982 CGGATACGCA
* * *
1680992 TTGCAATTTACGTATTCTCG
1 TTGCGATTTACATATTCGCG
* * *
1681012 TTGCGATTTACAGATACGCT
1 TTGCGATTTACATATTCGCG
* *
1681032 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACATATTCGCG
** *
1681052 TTGCGATTTACGGATACGCG
1 TTGCGATTTACATATTCGCG
*
1681072 TTGCGATTTTACGTATT-GTCG
1 TTGCGA-TTTACATATTCG-CG
* * *
1681093 TTGCGATTTACAGATACTCG
1 TTGCGATTTACATATTCGCG
* * *
1681113 TTGCGATAGT-CAGAATCGCG
1 TTGCGAT-TTACATATTCGCG
*
1681133 TTGCGATTTATATATTCGCG
1 TTGCGATTTACATATTCGCG
*
1681153 TTGCGATTTTCATATTCGCG
1 TTGCGATTTACATATTCGCG
1681173 TTGCGATT
1 TTGCGATT
1681181 ATGGAAAATC
Statistics
Matches: 134, Mismatches: 30, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
19 1 0.01
20 116 0.87
21 17 0.13
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACATATTCGCG
Found at i:1681279 original size:20 final size:20
Alignment explanation
Indices: 1681126--1681283 Score: 67
Period size: 20 Copynumber: 7.8 Consensus size: 20
1681116 CGATAGTCAG
*
1681126 AATCGCGTTGCGATT-T-AT
1 AATCGCGTTGCGATTCTGGT
* **
1681144 ATATTCGCGTTGCGATTTTCAT
1 A-A-TCGCGTTGCGATTCTGGT
* * *
1681166 ATTCGCGTTGCGATTATGGAA
1 AATCGCGTTGCGATTCTGG-T
**
1681187 AATCGCAATGCGAATT-T-GT
1 AATCGCGTTGCG-ATTCTGGT
* **
1681206 ACTATCGCATTGCGATTCTTAAT
1 A--ATCGCGTTGCGATTC-TGGT
1681229 AATCGCGTTGCGATTCTGGT
1 AATCGCGTTGCGATTCTGGT
**
1681249 AA-CTGATTTGCGATTCTGG-
1 AATC-GCGTTGCGATTCTGGT
1681268 AGATCGCGTTGCGATT
1 A-ATCGCGTTGCGATT
1681284 TGTATTTCGC
Statistics
Matches: 108, Mismatches: 18, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
18 1 0.01
19 4 0.04
20 58 0.54
21 36 0.33
22 7 0.06
23 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
AATCGCGTTGCGATTCTGGT
Found at i:1681328 original size:519 final size:515
Alignment explanation
Indices: 1680349--1681384 Score: 1847
Period size: 519 Copynumber: 2.0 Consensus size: 515
1680339 GTTCCGATAA
*
1680349 TTAATATTCGTGTTTGGAATTTGAAAATAAAATACGTGTCGCGATTGTAATGGCGCTTTAAAAAT
1 TTAATATTCGTGTTTGGAATTTGAAAATAAAATACGCGTCGCGATTGTAATGGCGCTTTAAAAAT
** * *
1680414 CATGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTGCGATTTACGGATACGCATTGCGA
66 CACATTGCGATTTACGGATACGCATTGCGATTTTACGTATTGCAATTTACGGATACGCATTGCAA
*
1680479 TTTACGTATTCTCGTTGAGATTTACAGATACGCGTTGCGATTTACGTATTCTTGTTGCGATTTAC
131 TTTACGTATTCTCGTTGAGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTAC
*
1680544 GGATACGCGTTACGATTTTACGTATTGTCATTGCGATTTACGGATACTCGTTGCGATAGTCAGAA
196 GGATACGCGTTACGATTTTACGTATTGTCATTGCGATTTACAGATACTCGTTGCGATAGTCAGAA
*
1680609 TCGCGTTGCGATTTATATGTCCGCGTTGCGATTTTCATATTCGCGTTGCGATTATGGAAAATCGC
261 TCGCGTTGCGATTTATATATCCGCGTTGCGATTTTCATATTCGCGTTGCGATTATGGAAAATCGC
1680674 AATGCGAATTTGTACTATCGCATTGCGATTCTTAATAATCGCGTTGCGATTCTGGTAACTGATTT
326 AATGCGAATTTGTACTATCGCATTGCGATTCTTAATAATCGCGTTGCGATTCTGGTAACTGATTT
*
1680739 GCAATTCTGGAGATCGCGTTGCGATTTGTATTTCGCATTGCGATTTTGTTGGTCATTTTGGTAAA
391 GCAATTCTGGAGATCGCGTTGCGATTTGTATTTCGCATTGCGATTTTGTTGGTCATTTTGGCAAA
* *
1680804 TCCAAAAAAAGTTGGTTAAAATCGTATATTATAAGGCATTTTTGGTCACTGAGGTTATTTTCTC
456 TCCAAAAAAA----ATTAAAATCGTATATTATAAGGCATTTTTGGTCACTGAGATTATTTTCTC
1680868 TTAATATTCGTGTTTGGAATTTGAAAATAAAATACGCGTCGCGATTGTAATGGCGCTTTAAAAAT
1 TTAATATTCGTGTTTGGAATTTGAAAATAAAATACGCGTCGCGATTGTAATGGCGCTTTAAAAAT
* *
1680933 CGCATTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGCAATTTACGGATACGCATTGCAA
66 CACATTGCGATTTACGGATACGCATTGCGATTTTACGTATTGCAATTTACGGATACGCATTGCAA
* *
1680998 TTTACGTATTCTCGTTGCGATTTACAGATACGCTTTGCGATTTACGTATTCTCGTTGCGATTTAC
131 TTTACGTATTCTCGTTGAGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTAC
* *
1681063 GGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACAGATACTCGTTGCGATAGTCAGAA
196 GGATACGCGTTACGATTTTACGTATTGTCATTGCGATTTACAGATACTCGTTGCGATAGTCAGAA
*
1681128 TCGCGTTGCGATTTATATATTCGCGTTGCGATTTTCATATTCGCGTTGCGATTATGGAAAATCGC
261 TCGCGTTGCGATTTATATATCCGCGTTGCGATTTTCATATTCGCGTTGCGATTATGGAAAATCGC
1681193 AATGCGAATTTGTACTATCGCATTGCGATTCTTAATAATCGCGTTGCGATTCTGGTAACTGATTT
326 AATGCGAATTTGTACTATCGCATTGCGATTCTTAATAATCGCGTTGCGATTCTGGTAACTGATTT
*
1681258 GCGATTCTGGAGATCGCGTTGCGATTTGTATTTCGCATTGCGATTTTGTTGGTCATTTTGGCAAA
391 GCAATTCTGGAGATCGCGTTGCGATTTGTATTTCGCATTGCGATTTTGTTGGTCATTTTGGCAAA
* *
1681323 TCCAAAAAAAATTAAAATCGTATATTATAAGGTATTTTTTGTCACTGAGATTATTTTCTC
456 TCCAAAAAAAATTAAAATCGTATATTATAAGGCATTTTTGGTCACTGAGATTATTTTCTC
1681383 TT
1 TT
1681385 TCTTAAAAAA
Statistics
Matches: 496, Mismatches: 21, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
515 48 0.10
519 448 0.90
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (515 bp):
TTAATATTCGTGTTTGGAATTTGAAAATAAAATACGCGTCGCGATTGTAATGGCGCTTTAAAAAT
CACATTGCGATTTACGGATACGCATTGCGATTTTACGTATTGCAATTTACGGATACGCATTGCAA
TTTACGTATTCTCGTTGAGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTAC
GGATACGCGTTACGATTTTACGTATTGTCATTGCGATTTACAGATACTCGTTGCGATAGTCAGAA
TCGCGTTGCGATTTATATATCCGCGTTGCGATTTTCATATTCGCGTTGCGATTATGGAAAATCGC
AATGCGAATTTGTACTATCGCATTGCGATTCTTAATAATCGCGTTGCGATTCTGGTAACTGATTT
GCAATTCTGGAGATCGCGTTGCGATTTGTATTTCGCATTGCGATTTTGTTGGTCATTTTGGCAAA
TCCAAAAAAAATTAAAATCGTATATTATAAGGCATTTTTGGTCACTGAGATTATTTTCTC
Found at i:1682176 original size:15 final size:14
Alignment explanation
Indices: 1682151--1682184 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1682141 TTGAAAATTG
1682151 ATTTTTATAATTTA
1 ATTTTTATAATTTA
*
1682165 ATTTTATATAATTTG
1 ATTTT-TATAATTTA
1682180 ATTTT
1 ATTTT
1682185 CTTCCTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
ATTTTTATAATTTA
Found at i:1687715 original size:21 final size:21
Alignment explanation
Indices: 1687674--1687715 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1687664 TTGGCATCAG
* *
1687674 GTTCAGTTCGAGTTAATTTCA
1 GTTCAGATCGAGTTAAGTTCA
1687695 GTTCAGATCGATGTT-AGTTCA
1 GTTCAGATCGA-GTTAAGTTCA
1687716 CGTCAAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (21 bp):
GTTCAGATCGAGTTAAGTTCA
Found at i:1687730 original size:15 final size:16
Alignment explanation
Indices: 1687710--1687744 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1687700 GATCGATGTT
1687710 AGTTCACGT-CAAAAC
1 AGTTCACGTCCAAAAC
*
1687725 AGTTCATGTCCAAAAC
1 AGTTCACGTCCAAAAC
1687741 AGTT
1 AGTT
1687745 AAATACCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (16 bp):
AGTTCACGTCCAAAAC
Found at i:1687906 original size:2 final size:2
Alignment explanation
Indices: 1687889--1688053 Score: 53
Period size: 2 Copynumber: 83.0 Consensus size: 2
1687879 ATACTTATTG
* ** *
1687889 AT AT GT AT ACT AT AT AT AT AT GC AT A- AGT AT AT AT AT AA AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
** * * *
1687932 AT AT -T AT GC AT -T AGT TT AT -T AT AT AT AT A- AGT AT AT AG AA
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * *
1687972 AT AT AT AT AA AGT AT AT AT AT A- AT AGT AC AT AC AT A- AGT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT
* *
1688013 AA AT AT AT A- AGT AT AT AT AT A- AGT AT A- AT AT AT AT GT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
1688054 GTAAGTATAT
Statistics
Matches: 117, Mismatches: 27, Indels: 38
0.64 0.15 0.21
Matches are distributed among these distances:
1 10 0.09
2 96 0.82
3 11 0.09
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1687927 original size:12 final size:12
Alignment explanation
Indices: 1687912--1688053 Score: 107
Period size: 12 Copynumber: 11.8 Consensus size: 12
1687902 ATATATATGC
1687912 ATAAGTATATAT
1 ATAAGTATATAT
*
1687924 ATAAATATATAT
1 ATAAGTATATAT
* *
1687936 -TATGCAT-TAGT
1 ATAAGTATATA-T
* *
1687947 -TTATTATATAT
1 ATAAGTATATAT
*
1687958 ATAAGTATATAG
1 ATAAGTATATAT
1687970 A-AA-TATATAT
1 ATAAGTATATAT
1687980 A-AAGTATATAT
1 ATAAGTATATAT
* *
1687991 ATAATAGTACATAC
1 AT-A-AGTATATAT
1688005 ATAAGTATAAATAT
1 ATAAGTAT--ATAT
1688019 ATAAGTATATAT
1 ATAAGTATATAT
1688031 ATAAGTATAATAT
1 ATAAGTAT-ATAT
*
1688044 ATATGTATAT
1 ATAAGTATAT
1688054 GTAAGTATAT
Statistics
Matches: 103, Mismatches: 17, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
10 11 0.11
11 19 0.18
12 40 0.39
13 13 0.13
14 20 0.19
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (12 bp):
ATAAGTATATAT
Found at i:1687968 original size:10 final size:10
Alignment explanation
Indices: 1687953--1688063 Score: 59
Period size: 10 Copynumber: 10.5 Consensus size: 10
1687943 TAGTTTATTA
1687953 TATATATAAG
1 TATATATAAG
* *
1687963 TATATAGAAA
1 TATATATAAG
1687973 TATATATAAAG
1 TATATAT-AAG
*
1687984 TATATATATAA
1 TATATATA-AG
*
1687995 TAGTACATACA-
1 TA-TATATA-AG
1688006 TA-AGTATAA-
1 TATA-TATAAG
1688015 -ATATATAAG
1 TATATATAAG
1688024 TATATATATAAG
1 --TATATATAAG
1688036 TATAATATATATG
1 TAT-ATATA-A-G
*
1688049 TATATGTAAG
1 TATATATAAG
1688059 TATAT
1 TATAT
1688064 GTATGTGATG
Statistics
Matches: 80, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
8 6 0.08
9 3 0.04
10 27 0.34
11 20 0.25
12 20 0.25
13 4 0.05
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (10 bp):
TATATATAAG
Found at i:1688018 original size:26 final size:27
Alignment explanation
Indices: 1687981--1688046 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 27
1687971 AATATATATA
*
1687981 AAGTATATATATAAT-AGTACATACAT
1 AAGTATAAATATAATAAGTACATACAT
* *
1688007 AAGTATAAATAT-ATAAGTATATATAT
1 AAGTATAAATATAATAAGTACATACAT
1688033 AAGTATAATATATA
1 AAGTATAA-ATATA
1688047 TGTATATGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.06
26 28 0.82
27 4 0.12
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (27 bp):
AAGTATAAATATAATAAGTACATACAT
Found at i:1688432 original size:27 final size:27
Alignment explanation
Indices: 1688402--1688476 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
1688392 TATTCTCTCT
1688402 AAATTTTTCAATTTTCCTCTAGTCCT-A
1 AAATTTTTCAATTTTCCTCTA-TCCTCA
*** * *
1688429 AAATTCCCCAATTTCCCTCTATTCTCA
1 AAATTTTTCAATTTTCCTCTATCCTCA
1688456 AAATTTTTCAATTTTCCTCTA
1 AAATTTTTCAATTTTCCTCTA
1688477 AATTCCCAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 3 0.08
27 35 0.92
ACGTcount: A:0.27, C:0.27, G:0.01, T:0.45
Consensus pattern (27 bp):
AAATTTTTCAATTTTCCTCTATCCTCA
Found at i:1688589 original size:19 final size:19
Alignment explanation
Indices: 1688565--1688604 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1688555 TATTATATAT
1688565 ATATATATATGAATTTTTA
1 ATATATATATGAATTTTTA
1688584 ATATATATATGAATTTTTA
1 ATATATATATGAATTTTTA
1688603 AT
1 AT
1688605 CTCAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
ATATATATATGAATTTTTA
Found at i:1688975 original size:16 final size:16
Alignment explanation
Indices: 1688951--1689005 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1688941 TATAACTTAT
* *
1688951 AAGTAAGGTAAATACC
1 AAGTCAGGTAAATAAC
*
1688967 AAGTCAGGTAAATATC
1 AAGTCAGGTAAATAAC
* * *
1688983 AAATTAGGTCAATAAC
1 AAGTCAGGTAAATAAC
1688999 AAGTCAG
1 AAGTCAG
1689006 ATTATTTACA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (16 bp):
AAGTCAGGTAAATAAC
Found at i:1689574 original size:21 final size:21
Alignment explanation
Indices: 1689545--1689703 Score: 85
Period size: 21 Copynumber: 7.7 Consensus size: 21
1689535 GCGCTGCATT
1689545 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
1689566 TCGCATTGCGAT-TTTCTATT
1 TCGCGTTGCGATAGTTGAAAA
1689586 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * *****
1689607 TCGCGTTACGAT-TTTCCTTT
1 TCGCGTTGCGATAGTTGAAAA
* *
1689627 TCGCGTTGCGATAGTCT-ACAG
1 TCGCGTTGCGATAGT-TGAAAA
* ** **
1689648 T-GTCGTTGCGAT-TTTCCATT
1 TCG-CGTTGCGATAGTTGAAAA
1689668 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
1689689 TCGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
1689704 GTACAGTGTC
Statistics
Matches: 96, Mismatches: 35, Indels: 14
0.66 0.24 0.10
Matches are distributed among these distances:
19 1 0.01
20 39 0.41
21 55 0.57
22 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:1689587 original size:41 final size:41
Alignment explanation
Indices: 1689542--1689700 Score: 225
Period size: 41 Copynumber: 3.9 Consensus size: 41
1689532 TTCGCGCTGC
*
1689542 ATTTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTCT
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCT
*
1689583 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCT
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTT-CT
* * *
1689625 -TTTCGCGTTGCGATAGTCT-ACAGT-GTCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCT
1689665 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1689701 AGTGTACAGT
Statistics
Matches: 104, Mismatches: 8, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
40 3 0.03
41 97 0.93
42 4 0.04
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (41 bp):
ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCT
Found at i:1689594 original size:20 final size:20
Alignment explanation
Indices: 1689566--1689679 Score: 70
Period size: 20 Copynumber: 5.6 Consensus size: 20
1689556 TAGTTGAAAA
*
1689566 TCGCATTGCGATTTTCTATT
1 TCGCGTTGCGATTTTCTATT
* ** **
1689586 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCTATT
*
1689607 TCGCGTTACGATTTTCCT-TT
1 TCGCGTTGCGATTTT-CTATT
** **
1689627 TCGCGTTGCGATAGTCTACAG
1 TCGCGTTGCGATTTTCTA-TT
*
1689648 T-GTCGTTGCGATTTTCCATT
1 TCG-CGTTGCGATTTTCTATT
1689668 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1689680 AGTTGAAAAT
Statistics
Matches: 66, Mismatches: 22, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
19 2 0.03
20 36 0.55
21 28 0.42
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCTATT
Found at i:1690362 original size:6 final size:6
Alignment explanation
Indices: 1690288--1690439 Score: 154
Period size: 5 Copynumber: 27.7 Consensus size: 6
1690278 CGCCGCCGTC
1690288 TCGT-G TCGT-G TCG-GG TCG-GG TCG-GG TCG-GG TCGT-G TCGT-G
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
* *
1690328 TCG-AG TCG-GG TCG-GG TCG-GG TCG-GG TCGTGG TCGTGG TCTTGGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGT-GG
* *
1690372 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T-GTCG T-GTCG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1690418 TCGTGG TCGTGG TCGTGG TCGT
1 TCGTGG TCGTGG TCGTGG TCGT
1690440 CGTGTAATAC
Statistics
Matches: 136, Mismatches: 5, Indels: 11
0.89 0.03 0.07
Matches are distributed among these distances:
5 68 0.50
6 63 0.46
7 5 0.04
ACGTcount: A:0.01, C:0.18, G:0.49, T:0.32
Consensus pattern (6 bp):
TCGTGG
Found at i:1690600 original size:41 final size:41
Alignment explanation
Indices: 1690530--1690662 Score: 189
Period size: 41 Copynumber: 3.3 Consensus size: 41
1690520 TTTACTATAG
* *
1690530 ACTATCGCAA--CGAATTTGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAA-ATGGAAAATCGCAACGACACTGTAC
*
1690570 ACTATCACAACGCGAAATGGAAAATCGCAACGACACTGTAC
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAC
* * *
1690611 ACTATCGCAATGCGAGATGGAAAATCGCAATGACACTGTAC
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAC
1690652 ACTATCGCAAC
1 ACTATCGCAAC
1690663 ACGATTTTCA
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
40 9 0.11
41 70 0.84
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAC
Found at i:1690618 original size:21 final size:21
Alignment explanation
Indices: 1690593--1690662 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
1690583 GAAATGGAAA
1690593 ATCGCAACGACACTGTACACT
1 ATCGCAACGACACTGTACACT
* * *
1690614 ATCGCAATGCGAGA-TGGA-A-A
1 ATCGCAA--CGACACTGTACACT
*
1690634 ATCGCAATGACACTGTACACT
1 ATCGCAACGACACTGTACACT
1690655 ATCGCAAC
1 ATCGCAAC
1690663 ACGATTTTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 8 0.22
21 15 0.42
22 3 0.08
23 4 0.11
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.19
Consensus pattern (21 bp):
ATCGCAACGACACTGTACACT
Found at i:1690700 original size:41 final size:42
Alignment explanation
Indices: 1690655--1690814 Score: 184
Period size: 41 Copynumber: 3.7 Consensus size: 42
1690645 ACTGTACACT
*
1690655 ATCGCAAC-ACGATT-TTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGACGATTGTAC-ACTATCGCAACGCGAAATGGAAA
1690696 ATCGCAACGATCGCAATGACTGTACACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGA-CG--AT---TGTACACTATCGCAACGCGAAATGGAAA
* *
1690744 ATCGCAACGAC-ACTGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGACGATTGTACACTATCGCAACGCGAAATGGAAA
* *
1690785 ATCGCAACGAC-ACTGTAGACTATCGCAACG
1 ATCGCAACGACGATTGTACACTATCGCAACG
1690815 ACACTGTAGA
Statistics
Matches: 108, Mismatches: 3, Indels: 16
0.85 0.02 0.13
Matches are distributed among these distances:
41 65 0.60
42 1 0.01
43 2 0.02
44 1 0.01
45 2 0.02
47 1 0.01
48 34 0.31
49 2 0.02
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.17
Consensus pattern (42 bp):
ATCGCAACGACGATTGTACACTATCGCAACGCGAAATGGAAA
Found at i:1690770 original size:21 final size:21
Alignment explanation
Indices: 1690744--1690835 Score: 118
Period size: 21 Copynumber: 4.4 Consensus size: 21
1690734 GAAATGGAAA
1690744 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* **
1690765 ATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGAC--ACTGTAGACT
1690785 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
1690806 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
1690827 ATCGCAACG
1 ATCGCAACG
1690836 CGAAATGCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
19 3 0.05
20 12 0.20
21 42 0.70
22 3 0.05
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACT
Done.