Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008694.1 Hibiscus syriacus cultivar Beakdansim tig00111723_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: 1352611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1123045 original size:45 final size:46
Alignment explanation
Indices: 1122946--1123053 Score: 121
Period size: 45 Copynumber: 2.3 Consensus size: 46
1122936 ATATGCTATG
* * * *
1122946 TGATCATAATCTATGTGTTTTATGATCTATGTGATTACATGATAATA
1 TGAT-ATAAGCTATGTGTTATATGACCTAAGTGATTACATGATAATA
* *
1122993 TGATATAAGCTATGTGTTAT-TGACCTAAGTGATTATATGA-ACATG
1 TGATATAAGCTATGTGTTATATGACCTAAGTGATTACATGATA-ATA
*
1123038 TGCTATAAGCTATGTG
1 TGATATAAGCTATGTG
1123054 ATAAGTATCT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 1 0.02
45 34 0.64
46 14 0.26
47 4 0.08
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (46 bp):
TGATATAAGCTATGTGTTATATGACCTAAGTGATTACATGATAATA
Found at i:1123277 original size:23 final size:23
Alignment explanation
Indices: 1123251--1123352 Score: 96
Period size: 23 Copynumber: 4.4 Consensus size: 23
1123241 GGTTCTACAC
*
1123251 GGTCCTTTGGGACAATTCTACGT
1 GGTCCTTCGGGACAATTCTACGT
* * **
1123274 GGTCCTACGGGACATTTCTACAC
1 GGTCCTTCGGGACAATTCTACGT
* * *
1123297 GGTCCTTCGGGATAATACTATGT
1 GGTCCTTCGGGACAATTCTACGT
* * *
1123320 GGTCATTCGGGACATTTCTATGT
1 GGTCCTTCGGGACAATTCTACGT
*
1123343 GGTACTTCGG
1 GGTCCTTCGG
1123353 TGCAAATTTC
Statistics
Matches: 61, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTACGT
Found at i:1123322 original size:46 final size:46
Alignment explanation
Indices: 1123243--1123339 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 46
1123233 GAGTCGAGGG
* * *
1123243 TTCTACACGGTCCTTTGGGACAATTCTACGTGGTCCTACGGGACAT
1 TTCTACACGGTCCTTCGGGACAATACTACGTGGTCATACGGGACAT
* * *
1123289 TTCTACACGGTCCTTCGGGATAATACTATGTGGTCATTCGGGACAT
1 TTCTACACGGTCCTTCGGGACAATACTACGTGGTCATACGGGACAT
1123335 TTCTA
1 TTCTA
1123340 TGTGGTACTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.33
Consensus pattern (46 bp):
TTCTACACGGTCCTTCGGGACAATACTACGTGGTCATACGGGACAT
Found at i:1123390 original size:24 final size:25
Alignment explanation
Indices: 1123333--1123390 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
1123323 CATTCGGGAC
*
1123333 ATTTCTATGTGGTACTTCGGTGCAA
1 ATTTCTATGTAGTACTTCGGTGCAA
1123358 ATTTCTATGTAGTACTTCGGTGC-A
1 ATTTCTATGTAGTACTTCGGTGCAA
*
1123382 ATTTATATG
1 ATTTCTATG
1123391 AGTTGTGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 9 0.29
25 22 0.71
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.43
Consensus pattern (25 bp):
ATTTCTATGTAGTACTTCGGTGCAA
Found at i:1123565 original size:6 final size:6
Alignment explanation
Indices: 1123498--1123562 Score: 85
Period size: 6 Copynumber: 10.8 Consensus size: 6
1123488 TGAACAGTGC
* *
1123498 ATGATA ATGATA ATGATG ATGATA ATGATA ATGATA ATGGTA ATGATA
1 ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA
* * *
1123546 GTGATA GTGATG ATGAT
1 ATGATA ATGATA ATGAT
1123563 GATATGTATA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.34
Consensus pattern (6 bp):
ATGATA
Found at i:1135817 original size:43 final size:43
Alignment explanation
Indices: 1135751--1135834 Score: 150
Period size: 43 Copynumber: 2.0 Consensus size: 43
1135741 TGCCAAAATG
*
1135751 AATCATCACAAGACCATTAGGCCAAGGGAGATGTTTATCCAAT
1 AATCATCACAAGACCATTAGGCCAAGGGAGATGTTCATCCAAT
*
1135794 AATCATCACAAGACCATTCGGCCAAGGGAGATGTTCATCCA
1 AATCATCACAAGACCATTAGGCCAAGGGAGATGTTCATCCA
1135835 TTCTAGCCGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (43 bp):
AATCATCACAAGACCATTAGGCCAAGGGAGATGTTCATCCAAT
Found at i:1146299 original size:2 final size:2
Alignment explanation
Indices: 1146292--1146330 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1146282 TAAACATAAC
*
1146292 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1146331 GTTAAAGTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1152489 original size:12 final size:13
Alignment explanation
Indices: 1152473--1152520 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
1152463 GCTACAATAA
1152473 AAGAAACAA-AAAG
1 AAGAAA-AAGAAAG
1152486 -AGAAAAAGAAAG
1 AAGAAAAAGAAAG
*
1152498 AAGAAAAACAAA-
1 AAGAAAAAGAAAG
1152510 AA-AAAAAGAAA
1 AAGAAAAAGAAA
1152521 AAAACTCCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
11 10 0.32
12 11 0.35
13 10 0.32
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAG
Found at i:1152511 original size:20 final size:19
Alignment explanation
Indices: 1152488--1152525 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1152478 ACAAAAAGAG
*
1152488 AAAAAGAAAGAAGAAAAACA
1 AAAAAAAAAGAA-AAAAACA
1152508 AAAAAAAAAGAAAAAAAC
1 AAAAAAAAAGAAAAAAAC
1152526 TCCTACATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAGAAAAAAACA
Found at i:1158988 original size:19 final size:20
Alignment explanation
Indices: 1158947--1158997 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1158937 GAAACCCCTT
*
1158947 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
1158967 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1158986 TGAAGATACATG
1 TGAAAATACATG
1158998 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1159940 original size:30 final size:31
Alignment explanation
Indices: 1159900--1159959 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
1159890 ACATGCTGCC
**
1159900 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
1159931 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
1159960 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:1165570 original size:18 final size:18
Alignment explanation
Indices: 1165547--1165591 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1165537 TCACATGTTA
1165547 CTGAAGCATATTGAAATG
1 CTGAAGCATATTGAAATG
1165565 CTGAAGCATATTGAAATG
1 CTGAAGCATATTGAAATG
*
1165583 ATGAAGCAT
1 CTGAAGCAT
1165592 TTCTGGCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.27
Consensus pattern (18 bp):
CTGAAGCATATTGAAATG
Found at i:1168171 original size:20 final size:20
Alignment explanation
Indices: 1168142--1168180 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1168132 AGAGCCCATA
*
1168142 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1168162 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1168181 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1172468 original size:12 final size:12
Alignment explanation
Indices: 1172448--1172477 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1172438 AAGAAAAATA
*
1172448 CAAAATGAAGTG
1 CAAAGTGAAGTG
1172460 CAAAGTGAAGTG
1 CAAAGTGAAGTG
1172472 CAAAGT
1 CAAAGT
1172478 TAAAGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.27, T:0.17
Consensus pattern (12 bp):
CAAAGTGAAGTG
Found at i:1172531 original size:27 final size:27
Alignment explanation
Indices: 1172501--1172590 Score: 126
Period size: 27 Copynumber: 3.3 Consensus size: 27
1172491 AAAAATCAGA
**
1172501 AAAGAAAATGAAGCACTCAAAAGAAAG
1 AAAGAAAATCCAGCACTCAAAAGAAAG
*
1172528 AAAGAAAATCCATCACTCAAAAGAAAG
1 AAAGAAAATCCAGCACTCAAAAGAAAG
* *
1172555 AAAAAAAATCCAGCACTCAAAAGAAGAA
1 AAAGAAAATCCAGCACTCAAAAGAA-AG
1172583 AAAGAAAA
1 AAAGAAAA
1172591 GAAAAGAAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 47 0.85
28 8 0.15
ACGTcount: A:0.64, C:0.14, G:0.13, T:0.08
Consensus pattern (27 bp):
AAAGAAAATCCAGCACTCAAAAGAAAG
Found at i:1172603 original size:20 final size:19
Alignment explanation
Indices: 1172573--1172611 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1172563 TCCAGCACTC
*
1172573 AAAAGAAGAAAAAGAAAAG
1 AAAAGAAGAAAAAAAAAAG
1172592 AAAAGAAAGAAAAAAAAAAG
1 AAAAG-AAGAAAAAAAAAAG
1172612 TTGAAGCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAGAAGAAAAAAAAAAG
Found at i:1175749 original size:35 final size:35
Alignment explanation
Indices: 1175710--1175789 Score: 151
Period size: 35 Copynumber: 2.3 Consensus size: 35
1175700 CATAGAATGA
1175710 ATGCACATGTTATGATAATTCAAGTATAGTATAAT
1 ATGCACATGTTATGATAATTCAAGTATAGTATAAT
1175745 ATGCACATGTTATGATAATTCAAGTATAGTATAAT
1 ATGCACATGTTATGATAATTCAAGTATAGTATAAT
*
1175780 ATGCAAATGT
1 ATGCACATGT
1175790 ATGCTCATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (35 bp):
ATGCACATGTTATGATAATTCAAGTATAGTATAAT
Found at i:1180206 original size:15 final size:15
Alignment explanation
Indices: 1180186--1180216 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1180176 TAGAGTTTTG
1180186 TAGGATAACAAATGT
1 TAGGATAACAAATGT
1180201 TAGGATAACAAATGT
1 TAGGATAACAAATGT
1180216 T
1 T
1180217 TCCTAATGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.29
Consensus pattern (15 bp):
TAGGATAACAAATGT
Found at i:1181339 original size:22 final size:22
Alignment explanation
Indices: 1181284--1181341 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1181274 CTTGGTTTTG
*
1181284 CTTTTCTCTTTTTGTTTGAAATT
1 CTTTT-TCTTTTTGTTTGAAATC
* *
1181307 CTTTTTCTTTTTTTTTGAACTC
1 CTTTTTCTTTTTGTTTGAAATC
*
1181329 CTTTGT-TTTTTGT
1 CTTTTTCTTTTTGT
1181342 AGGATTTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 5 0.17
ACGTcount: A:0.09, C:0.14, G:0.09, T:0.69
Consensus pattern (22 bp):
CTTTTTCTTTTTGTTTGAAATC
Found at i:1181689 original size:22 final size:22
Alignment explanation
Indices: 1181661--1181703 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1181651 AGAATTATGT
1181661 AGATGTTGATGGTCTTGATGGA
1 AGATGTTGATGGTCTTGATGGA
*
1181683 AGATGTTGATGGTGTTGATGG
1 AGATGTTGATGGTCTTGATGG
1181704 TGAAATAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.02, G:0.40, T:0.37
Consensus pattern (22 bp):
AGATGTTGATGGTCTTGATGGA
Found at i:1197814 original size:24 final size:24
Alignment explanation
Indices: 1197775--1197828 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
1197765 TTCTTTTCTT
1197775 TTTCTTCCTTTTTGAGTGCTTACAA
1 TTTCTTCCTTTTTGAGTGCTT-CAA
*
1197800 CTTTCTT-C-TTTTGAGTTCTTCAA
1 -TTTCTTCCTTTTTGAGTGCTTCAA
1197823 TTTCTT
1 TTTCTT
1197829 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 6 0.22
23 3 0.11
24 11 0.41
25 1 0.04
26 6 0.22
ACGTcount: A:0.13, C:0.20, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTCTTCCTTTTTGAGTGCTTCAA
Found at i:1203586 original size:24 final size:24
Alignment explanation
Indices: 1203547--1203600 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
1203537 TTCTTTTCTT
1203547 TTTCTTCCTTTTTGAGTGCTTACAA
1 TTTCTTCCTTTTTGAGTGCTT-CAA
*
1203572 CTTTCTT-C-TTTTGAGTTCTTCAA
1 -TTTCTTCCTTTTTGAGTGCTTCAA
1203595 TTTCTT
1 TTTCTT
1203601 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 6 0.22
23 3 0.11
24 11 0.41
25 1 0.04
26 6 0.22
ACGTcount: A:0.13, C:0.20, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTCTTCCTTTTTGAGTGCTTCAA
Found at i:1213562 original size:24 final size:24
Alignment explanation
Indices: 1213535--1213597 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
1213525 ATGATCACAA
**
1213535 CTTTTGGCTCTTCAATTGATATTT
1 CTTTTGGAACTTCAATTGATATTT
*
1213559 CTTTTGGAACTTCAATTGATGTTT
1 CTTTTGGAACTTCAATTGATATTT
*
1213583 CTTTTGGAATTTCAA
1 CTTTTGGAACTTCAA
1213598 GTGGCATAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.51
Consensus pattern (24 bp):
CTTTTGGAACTTCAATTGATATTT
Found at i:1220778 original size:25 final size:25
Alignment explanation
Indices: 1220749--1220805 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
1220739 TGTTCACCAC
1220749 GAAATTCCACCTATAGAATTTTCAA
1 GAAATTCCACCTATAGAATTTTCAA
* *
1220774 GAAATTCCTCCTATAGAATTTTTAA
1 GAAATTCCACCTATAGAATTTTCAA
1220799 GAAATTC
1 GAAATTC
1220806 GAAAAGATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.35
Consensus pattern (25 bp):
GAAATTCCACCTATAGAATTTTCAA
Found at i:1225121 original size:15 final size:17
Alignment explanation
Indices: 1225098--1225132 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1225088 TTAAGACATG
1225098 TTTAGTTTATTA-TTAT
1 TTTAGTTTATTAGTTAT
1225114 TTTA-TTTATTAGTTAT
1 TTTAGTTTATTAGTTAT
1225130 TTT
1 TTT
1225133 GGACCTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTAGTTTATTAGTTAT
Found at i:1225915 original size:18 final size:18
Alignment explanation
Indices: 1225875--1225916 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1225865 GTTTGCTTTT
*
1225875 AAAAAAAATAAAAAAGGC
1 AAAAAAAATAAAAAAGAC
* *
1225893 CAAAAAAATCAAAAAGAC
1 AAAAAAAATAAAAAAGAC
1225911 AAAAAA
1 AAAAAA
1225917 GTCACAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.79, C:0.10, G:0.07, T:0.05
Consensus pattern (18 bp):
AAAAAAAATAAAAAAGAC
Found at i:1231035 original size:12 final size:12
Alignment explanation
Indices: 1231018--1231065 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
1231008 CAACAAAAAG
1231018 AAAAAAAAGAGA
1 AAAAAAAAGAGA
1231030 AAAAAAGAA-AGA
1 AAAAAA-AAGAGA
*
1231042 AAAAACAAAAAGA
1 AAAAA-AAAGAGA
1231055 AAAGAAAAAGA
1 AAA-AAAAAGA
1231066 CTCCTAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 16 0.52
13 13 0.42
14 2 0.06
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAGA
Found at i:1231051 original size:18 final size:19
Alignment explanation
Indices: 1231012--1231065 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1231002 GTGCTGCAAC
1231012 AAAAAGAAA-AAAAAGAGAA
1 AAAAAGAAAGAAAAAGAG-A
*
1231031 AAAAAGAAAGAAAAA-A-C
1 AAAAAGAAAGAAAAAGAGA
1231048 AAAAAGAAAAGAAAAAGA
1 AAAAAG-AAAGAAAAAGA
1231066 CTCCTAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 6 0.19
18 9 0.29
19 11 0.35
20 5 0.16
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAGAAAAAGAGA
Found at i:1231065 original size:11 final size:10
Alignment explanation
Indices: 1231012--1231063 Score: 61
Period size: 11 Copynumber: 5.1 Consensus size: 10
1231002 GTGCTGCAAC
1231012 AAAAAG-AAA
1 AAAAAGAAAA
*
1231021 AAAAAGAGAA
1 AAAAAGAAAA
1231031 AAAAAGAAAGA
1 AAAAAGAAA-A
*
1231042 AAAAACAAAA
1 AAAAAGAAAA
1231052 AGAAAAGAAAA
1 A-AAAAGAAAA
1231063 A
1 A
1231064 GACTCCTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
9 6 0.17
10 12 0.33
11 18 0.50
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:1239353 original size:19 final size:20
Alignment explanation
Indices: 1239315--1239357 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1239305 GAAAACCCTT
*
1239315 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
1239335 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
1239354 TGAA
1 TGAA
1239358 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:1242585 original size:6 final size:6
Alignment explanation
Indices: 1242562--1242605 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
1242552 GTTGTAGGAG
* *
1242562 TCTTTT TCTTTC TCTTTT TGTTTT TCTTCTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT T
1242606 GTTGCTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:1242595 original size:25 final size:24
Alignment explanation
Indices: 1242562--1242608 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
1242552 GTTGTAGGAG
1242562 TCTTTTTCTTTCTCTTTTTGTTTT
1 TCTTTTTCTTTCTCTTTTTGTTTT
*
1242586 TCTTCTTTCTTTTTCTTTTTGTT
1 TCTT-TTTCTTTCTCTTTTTGTT
1242609 GCTTTTGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (24 bp):
TCTTTTTCTTTCTCTTTTTGTTTT
Found at i:1242596 original size:19 final size:18
Alignment explanation
Indices: 1242562--1242605 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
1242552 GTTGTAGGAG
1242562 TCTTTTTCTTTCTCTTTT
1 TCTTTTTCTTTCTCTTTT
* *
1242580 TGTTTTTCTTCTTTCTTTT
1 TCTTTTTCTT-TCTCTTTT
1242599 TCTTTTT
1 TCTTTTT
1242606 GTTGCTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (18 bp):
TCTTTTTCTTTCTCTTTT
Found at i:1245877 original size:12 final size:13
Alignment explanation
Indices: 1245854--1245895 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
1245844 AAAGTGCTAC
1245854 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
* *
1245867 AAAGAATAAAAAG
1 AAAAAAGAAAAAG
1245880 AAAAAAG-AAAAG
1 AAAAAAGAAAAAG
1245892 AAAA
1 AAAA
1245896 TAACTCCTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:1257303 original size:20 final size:21
Alignment explanation
Indices: 1257258--1257303 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1257248 ATAACATTTC
* *
1257258 TATCACTTTCATTTCTTCCAT
1 TATCAATTTCATTTCTTCAAT
1257279 T-TCAATTTCATTTCTT-AAT
1 TATCAATTTCATTTCTTCAAT
1257298 TATCAA
1 TATCAA
1257304 ATTACTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 3 0.14
20 18 0.82
21 1 0.05
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (21 bp):
TATCAATTTCATTTCTTCAAT
Found at i:1257511 original size:21 final size:21
Alignment explanation
Indices: 1257487--1257526 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1257477 GTGCTGCAAC
*
1257487 AAAAGAGAAAAAGGAAGAAGA
1 AAAAGAGAAAAAGAAAGAAGA
*
1257508 AAAAGAGAAAGAGAAAGAA
1 AAAAGAGAAAAAGAAAGAA
1257527 AAAGACTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (21 bp):
AAAAGAGAAAAAGAAAGAAGA
Found at i:1260957 original size:14 final size:14
Alignment explanation
Indices: 1260938--1260965 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1260928 TAAGATACTA
1260938 TTTCCATCACCATC
1 TTTCCATCACCATC
1260952 TTTCCATCACCATC
1 TTTCCATCACCATC
1260966 AATCCTTAAC
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:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:1266385 original size:19 final size:18
Alignment explanation
Indices: 1266358--1266393 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1266348 ATGTAGGAGT
*
1266358 TTTTTTTCTTTCTCTTTTG
1 TTTTCTTCTTTCT-TTTTG
1266377 TTTTCTTCTTTCTTTTT
1 TTTTCTTCTTTCTTTTT
1266394 CACTTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.81
Consensus pattern (18 bp):
TTTTCTTCTTTCTTTTTG
Found at i:1273142 original size:16 final size:15
Alignment explanation
Indices: 1273108--1273150 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1273098 AAATAAGAAT
*
1273108 AAATGAAAGATAAGG
1 AAATGAAAGATAAGA
*
1273123 AAATGAAATAGTAAGA
1 AAATGAAAGA-TAAGA
1273139 AAATG-AAGATAA
1 AAATGAAAGATAA
1273151 CTTACAACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 3 0.12
15 12 0.50
16 9 0.38
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (15 bp):
AAATGAAAGATAAGA
Found at i:1273355 original size:13 final size:13
Alignment explanation
Indices: 1273337--1273376 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1273327 AGTTATTTTC
1273337 TTTTCTCTTTTGT
1 TTTTCTCTTTTGT
*
1273350 TTTTCT-TCTTTCT
1 TTTTCTCT-TTTGT
1273363 TTTTCTCTTTTGT
1 TTTTCTCTTTTGT
1273376 T
1 T
1273377 ACTTTTGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 1 0.04
13 21 0.91
14 1 0.04
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (13 bp):
TTTTCTCTTTTGT
Found at i:1273783 original size:14 final size:14
Alignment explanation
Indices: 1273764--1273791 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1273754 GATGATGGAG
1273764 GATGGTGATGGAAA
1 GATGGTGATGGAAA
1273778 GATGGTGATGGAAA
1 GATGGTGATGGAAA
1273792 TAGATAGTAT
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):
GATGGTGATGGAAA
Found at i:1282481 original size:13 final size:13
Alignment explanation
Indices: 1282463--1282506 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
1282453 TTGTAGGAGT
1282463 TTTTTCTTTTCTC
1 TTTTTCTTTTCTC
1282476 TTTTTCTTTTCT-
1 TTTTTCTTTTCTC
*
1282488 TCTTTCTTTTCATC
1 TTTTTCTTTTC-TC
1282502 TTTTT
1 TTTTT
1282507 GTTGCAGCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 10 0.37
13 13 0.48
14 4 0.15
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTCTTTTCTC
Found at i:1282493 original size:12 final size:12
Alignment explanation
Indices: 1282465--1282504 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1282455 GTAGGAGTTT
*
1282465 TTTCTTTTCTCTT
1 TTTCTTTTCT-TC
1282478 TTTCTTTTCTTC
1 TTTCTTTTCTTC
*
1282490 TTTCTTTTCATC
1 TTTCTTTTCTTC
1282502 TTT
1 TTT
1282505 TTGTTGCAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTCTTTTCTTC
Found at i:1286779 original size:11 final size:11
Alignment explanation
Indices: 1286763--1286829 Score: 62
Period size: 11 Copynumber: 5.5 Consensus size: 11
1286753 AACTTGCAGC
1286763 TCTTTTTTTTT
1 TCTTTTTTTTT
1286774 TCTTTTCTTTTTCT
1 TC-TTT-TTTTT-T
*
1286788 TCTTTTTCTTT
1 TCTTTTTTTTT
*
1286799 TCTTTTCTTTT
1 TCTTTTTTTTT
1286810 TCTTCTTTTTCTT
1 TCTT-TTTTT-TT
1286823 TACTTTT
1 T-CTTTT
1286830 GCACTCCAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
11 16 0.35
12 11 0.24
13 13 0.28
14 6 0.13
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:1286790 original size:9 final size:9
Alignment explanation
Indices: 1286778--1286822 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
1286768 TTTTTTTCTT
1286778 TTCTTTTTC
1 TTCTTTTTC
1286787 TTCTTTTTC
1 TTCTTTTTC
*
1286796 TT-TTCTT-
1 TTCTTTTTC
1286803 TTCTTTTTC
1 TTCTTTTTC
1286812 TTCTTTTTC
1 TTCTTTTTC
1286821 TT
1 TT
1286823 TACTTTTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 2 0.06
8 8 0.25
9 22 0.69
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:1286799 original size:25 final size:25
Alignment explanation
Indices: 1286763--1286829 Score: 116
Period size: 25 Copynumber: 2.7 Consensus size: 25
1286753 AACTTGCAGC
*
1286763 TCTTTTTTTTTTCTTTTCTTTTTCT
1 TCTTTTTCTTTTCTTTTCTTTTTCT
1286788 TCTTTTTCTTTTCTTTTCTTTTTCT
1 TCTTTTTCTTTTCTTTTCTTTTTCT
*
1286813 TCTTTTTCTTTACTTTT
1 TCTTTTTCTTTTCTTTT
1286830 GCACTCCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (25 bp):
TCTTTTTCTTTTCTTTTCTTTTTCT
Found at i:1286828 original size:20 final size:18
Alignment explanation
Indices: 1286768--1286829 Score: 79
Period size: 20 Copynumber: 3.2 Consensus size: 18
1286758 GCAGCTCTTT
1286768 TTTTTTTCTTTTCTTTTTC
1 TTTTTTTCTTTTC-TTTTC
1286787 TTCTTTTTCTTTTCTTTTC
1 TT-TTTTTCTTTTCTTTTC
*
1286806 TTTTTCTTCTTTTTCTTTAC
1 TTTTT-TTC-TTTTCTTTTC
1286826 TTTT
1 TTTT
1286830 GCACTCCAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
18 3 0.08
19 12 0.31
20 24 0.62
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTTTCTTTTCTTTTC
Found at i:1286871 original size:13 final size:13
Alignment explanation
Indices: 1286853--1286896 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
1286843 TTGTAGGAGT
1286853 TTTTTCTTTTCTC
1 TTTTTCTTTTCTC
1286866 TTTTTCTTTTCT-
1 TTTTTCTTTTCTC
*
1286878 TCTTTCTTTTTCTC
1 TTTTTC-TTTTCTC
1286892 TTTTT
1 TTTTT
1286897 GTTGCAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 5 0.19
13 18 0.67
14 4 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTCTC
Found at i:1286877 original size:18 final size:18
Alignment explanation
Indices: 1286854--1286890 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1286844 TGTAGGAGTT
1286854 TTTTCTT-TTCTCTTTTTC
1 TTTTCTTCTT-TCTTTTTC
1286872 TTTTCTTCTTTCTTTTTC
1 TTTTCTTCTTTCTTTTTC
1286890 T
1 T
1286891 CTTTTTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTTCTTTCTTTTTC
Found at i:1287282 original size:14 final size:14
Alignment explanation
Indices: 1287263--1287290 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1287253 GATGATAGAG
1287263 GATGGTGATGGAAA
1 GATGGTGATGGAAA
1287277 GATGGTGATGGAAA
1 GATGGTGATGGAAA
1287291 TAGATAGTAT
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):
GATGGTGATGGAAA
Found at i:1291525 original size:5 final size:5
Alignment explanation
Indices: 1291503--1291552 Score: 79
Period size: 5 Copynumber: 10.6 Consensus size: 5
1291493 GTGCTTTCAA
1291503 CTTTT C-TTT C-TTT C-TTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
1291550 CTT
1 CTT
1291553 CTTTTTGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
4 12 0.27
5 32 0.73
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
CTTTT
Found at i:1298912 original size:24 final size:24
Alignment explanation
Indices: 1298878--1298933 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
1298868 AAAAATCAGC
*
1298878 AAAA-AAAAGTCAAGCACTCTAAA
1 AAAAGAAAAGTCAAGCACTCCAAA
1298901 AAAAGAAAAGTCAAGCACTCCAAA
1 AAAAGAAAAGTCAAGCACTCCAAA
*
1298925 AGAAGAAAA
1 AAAAGAAAA
1298934 AACAAAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 4 0.13
24 26 0.87
ACGTcount: A:0.62, C:0.16, G:0.12, T:0.09
Consensus pattern (24 bp):
AAAAGAAAAGTCAAGCACTCCAAA
Found at i:1303601 original size:24 final size:25
Alignment explanation
Indices: 1303566--1303620 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
1303556 ACTTGGAGCC
*
1303566 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
1303590 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
1303614 TCAAGTG
1 TCAAGTG
1303621 GCATAACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:1309569 original size:14 final size:14
Alignment explanation
Indices: 1309550--1309592 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1309540 ATAAGATACT
* *
1309550 ATCTATTCATCATC
1 ATCTATCCATCACC
1309564 ATCTATCCATCACC
1 ATCTATCCATCACC
*
1309578 ATC-CTCCATCACC
1 ATCTATCCATCACC
1309591 AT
1 AT
1309593 TCACGCCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.33
Consensus pattern (14 bp):
ATCTATCCATCACC
Found at i:1311220 original size:21 final size:20
Alignment explanation
Indices: 1311178--1311217 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1311168 ATCCATTGAA
1311178 CAACAAAGGAGACAAATTTT
1 CAACAAAGGAGACAAATTTT
*
1311198 CAACAAATG-GACATAATTTT
1 CAACAAAGGAGACA-AATTTT
1311218 TCATTCAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.25
Consensus pattern (20 bp):
CAACAAAGGAGACAAATTTT
Found at i:1311687 original size:22 final size:22
Alignment explanation
Indices: 1311661--1311702 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1311651 TATTTATAGT
1311661 TATGAAGATGA-TATTATGAATG
1 TATGAAG-TGATTATTATGAATG
*
1311683 TATGAAGTTATTATTATGAA
1 TATGAAGTGATTATTATGAA
1311703 CCACATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (22 bp):
TATGAAGTGATTATTATGAATG
Found at i:1317027 original size:33 final size:33
Alignment explanation
Indices: 1316963--1317063 Score: 82
Period size: 33 Copynumber: 3.0 Consensus size: 33
1316953 CTTGTTGATG
* * *
1316963 AATG-AAGGATGAT-TTAATGGTGATGAAATGGT
1 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
1316995 AATGAAAGGATGATGTTATTGGCGTGATATGGT
1 AATGAAAGGATGATGTTATTGGCGTGATATGGT
* * *
1317028 GATGGAATATGG-TGATGATATAGGCGTGATAATGGT
1 AAT-GAA-A-GGATGATGTTATTGGCGTGAT-ATGGT
1317064 GATGGACAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
32 4 0.07
33 19 0.33
34 10 0.18
35 17 0.30
36 7 0.12
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.32
Consensus pattern (33 bp):
AATGAAAGGATGATGTTATTGGCGTGATATGGT
Found at i:1321459 original size:33 final size:33
Alignment explanation
Indices: 1321395--1321495 Score: 82
Period size: 33 Copynumber: 3.0 Consensus size: 33
1321385 CTTGTTGATG
* * *
1321395 AATG-AAGGATGAT-TTAATGGTGATGAAATGGT
1 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
1321427 AATGAAAGGATGATGTTATTGGCGTGATATGGT
1 AATGAAAGGATGATGTTATTGGCGTGATATGGT
* * *
1321460 GATGGAATATGG-TGATGATATAGGCGTGATAATGGT
1 AAT-GAA-A-GGATGATGTTATTGGCGTGAT-ATGGT
1321496 GATGGACAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
32 4 0.07
33 19 0.33
34 10 0.18
35 17 0.30
36 7 0.12
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.32
Consensus pattern (33 bp):
AATGAAAGGATGATGTTATTGGCGTGATATGGT
Found at i:1329825 original size:36 final size:34
Alignment explanation
Indices: 1329733--1329842 Score: 132
Period size: 35 Copynumber: 3.2 Consensus size: 34
1329723 TTGGTGGTTA
* * *
1329733 TATAGGCGTGAATGGTGATAGAAGATGGTAAGGA
1 TATAGGCGTGAATGGTGATGGAAGATGGTAATGT
* * *
1329767 TATAGGCTTGCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTG-AATGGTGATGGAAGATGGTAATGT
1329802 TATAGGCGTGAAAATGGTGATGGAAGATGGTAATGT
1 TATAGGCGTG--AATGGTGATGGAAGATGGTAATGT
1329838 T-TAGG
1 TATAGG
1329843 TAGTCTTATA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 9 0.14
35 32 0.50
36 23 0.36
ACGTcount: A:0.32, C:0.04, G:0.36, T:0.28
Consensus pattern (34 bp):
TATAGGCGTGAATGGTGATGGAAGATGGTAATGT
Found at i:1333863 original size:8 final size:8
Alignment explanation
Indices: 1333852--1333882 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1333842 GAGAAAAATC
1333852 AGAAAAGA
1 AGAAAAGA
1333860 AGAAAAGA
1 AGAAAAGA
1333868 AGAAAAGAA
1 AGAAAAG-A
1333877 AGAAAA
1 AGAAAA
1333883 AGAGAAGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.68
9 7 0.32
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:1333865 original size:17 final size:16
Alignment explanation
Indices: 1333835--1333888 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 16
1333825 TTGGAGTGCA
1333835 AAAAGAAGAGAAAAATCAG
1 AAAAGAA-AGAAAAA--AG
1333854 AAAAG-AAGAAAAGAAG
1 AAAAGAAAGAAAA-AAG
1333870 AAAAGAAAGAAAAAGAG
1 AAAAGAAAGAAAAA-AG
1333887 AA
1 AA
1333889 GTTCAAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 8 0.25
17 17 0.53
18 2 0.06
19 5 0.16
ACGTcount: A:0.74, C:0.02, G:0.22, T:0.02
Consensus pattern (16 bp):
AAAAGAAAGAAAAAAG
Found at i:1342127 original size:19 final size:21
Alignment explanation
Indices: 1342103--1342154 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1342093 CGGCCAAGAG
*
1342103 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
*
1342122 CATGTATTTTAATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
1342143 CATGTATTTTCA
1 CATGTATTTTCA
1342155 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 2 0.07
21 16 0.57
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:1349630 original size:21 final size:21
Alignment explanation
Indices: 1349606--1349645 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1349596 GAATGAAGAA
1349606 GAAAGGAAAT-GATAAGAAAAG
1 GAAAGGAAATGGAT-AGAAAAG
*
1349627 GAAATGAAATGGATAGAAA
1 GAAAGGAAATGGATAGAAA
1349646 TGTTATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (21 bp):
GAAAGGAAATGGATAGAAAAG
Done.