Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009576.1 Hibiscus syriacus cultivar Beakdansim tig00116944_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: 1684752
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1253075 original size:19 final size:19
Alignment explanation
Indices: 1253034--1253097 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
1253024 AAAGAAAAGA
*
1253034 AAAAGAAAAGGAAAATAAC
1 AAAAGAAAAGGAAAAAAAC
*
1253053 AAAAGAAAA-TAAAAAAAC
1 AAAAGAAAAGGAAAAAAAC
** *
1253071 TAAAA-ATTAGAAAAAAAAC
1 -AAAAGAAAAGGAAAAAAAC
1253090 AAAA-AAAA
1 AAAAGAAAA
1253098 TAATATGTAG
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
18 15 0.42
19 21 0.58
ACGTcount: A:0.80, C:0.05, G:0.08, T:0.08
Consensus pattern (19 bp):
AAAAGAAAAGGAAAAAAAC
Found at i:1266958 original size:14 final size:15
Alignment explanation
Indices: 1266920--1266960 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
1266910 AATTGAGATC
*
1266920 TCTA-ATTTTTGTAA
1 TCTATATTTTTTTAA
1266934 TCTCATATTTTTTTAA
1 TCT-ATATTTTTTTAA
1266950 TCT-TATTTTTT
1 TCTATATTTTTT
1266961 ACATTTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 11 0.46
15 1 0.04
16 12 0.50
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (15 bp):
TCTATATTTTTTTAA
Found at i:1266993 original size:42 final size:42
Alignment explanation
Indices: 1266942--1267031 Score: 137
Period size: 42 Copynumber: 2.1 Consensus size: 42
1266932 AATCTCATAT
* * *
1266942 TTTTTTAATCTTATTTTTTACATTTATAATTGA-GATCCTTAA
1 TTTTTTAATCTCACTTTTTACATTTATAATTGATG-TCCCTAA
1266984 TTTTTTAATCTCACTTTTTACATTTATAATTGATGTCCCTAA
1 TTTTTTAATCTCACTTTTTACATTTATAATTGATGTCCCTAA
1267026 TTTTTT
1 TTTTTT
1267032 TCAATATCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 43 0.98
43 1 0.02
ACGTcount: A:0.26, C:0.12, G:0.04, T:0.58
Consensus pattern (42 bp):
TTTTTTAATCTCACTTTTTACATTTATAATTGATGTCCCTAA
Found at i:1268604 original size:17 final size:17
Alignment explanation
Indices: 1268543--1268607 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 17
1268533 TTGTCTCTAT
*
1268543 TATTAAAAATTCAAAATA
1 TATTTAAAATT-AAAATA
*
1268561 TATTT-AATTTAAATTTATA
1 TATTTAAAATTAAA---ATA
1268580 TTATTTTAAAATTAAAATA
1 -TA-TTTAAAATTAAAATA
1268599 TATTTAAAA
1 TATTTAAAA
1268608 ATATCGGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
16 3 0.08
17 11 0.29
18 6 0.16
19 6 0.16
20 2 0.05
21 3 0.08
22 7 0.18
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTTAAAATTAAAATA
Found at i:1268695 original size:17 final size:18
Alignment explanation
Indices: 1268673--1268708 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1268663 AAATAAATAA
*
1268673 ATGACAAACATTT-TTTT
1 ATGACAAAAATTTATTTT
1268690 ATGACAAAAATTTATTTT
1 ATGACAAAAATTTATTTT
1268708 A
1 A
1268709 ATATAGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (18 bp):
ATGACAAAAATTTATTTT
Found at i:1268936 original size:15 final size:17
Alignment explanation
Indices: 1268916--1268947 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1268906 GAAAATAAAT
1268916 AAAAAT-TAT-TATTTA
1 AAAAATATATATATTTA
1268931 AAAAATATATATATTTA
1 AAAAATATATATATTTA
1268948 TATGACTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAAATATATATATTTA
Found at i:1270283 original size:3 final size:3
Alignment explanation
Indices: 1270275--1270362 Score: 122
Period size: 3 Copynumber: 28.7 Consensus size: 3
1270265 TTATTTATTA
*
1270275 AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
* **
1270322 AAT AAT ACT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1270363 CTTTAAATGA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
3 69 0.92
4 6 0.08
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1270652 original size:76 final size:76
Alignment explanation
Indices: 1270491--1271286 Score: 1502
Period size: 76 Copynumber: 10.5 Consensus size: 76
1270481 GATGGAAATG
* *
1270491 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
*
1270556 TTCCGAAGGCTT
65 TCCCGAAGGCTT
1270568 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1270633 CCCGAAGGCTT
66 CCCGAAGGCTT
1270644 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1270709 CCCGAAGGCTT
66 CCCGAAGGCTT
1270720 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1270785 CCCGAAGGCTT
66 CCCGAAGGCTT
1270796 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1270861 CCCGAAGGCTT
66 CCCGAAGGCTT
1270872 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1270937 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1270948 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1271013 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
1271024 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGGAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1271089 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1271100 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1271165 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1271176 TTTGGAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1271241 CCCGAAGGCTT
66 CCCGAAGGCTT
1271252 TTTGGAAACATCATGCACTGAAGGGCTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATG
1271287 TGAGAAATAG
Statistics
Matches: 708, Mismatches: 11, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
76 665 0.94
77 43 0.06
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:1271973 original size:22 final size:22
Alignment explanation
Indices: 1271948--1272002 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1271938 CATAAAGCTT
*
1271948 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAACCTA
*
1271970 TCATCTTTAAAAAGAGAACCTA
1 TCATCTTTGAAAAGAGAACCTA
1271992 TCATCTTTGAA
1 TCATCTTTGAA
1272003 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAACCTA
Found at i:1272449 original size:54 final size:54
Alignment explanation
Indices: 1272367--1272478 Score: 161
Period size: 54 Copynumber: 2.1 Consensus size: 54
1272357 CGAATAGCAA
***
1272367 GTTCGTAAAACATTTAACAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* ** *
1272421 GTTCGTAAAACATTTGACAACACATTCATCCTTTTTTGTGGCTTCTGCTCAGCT
1 GTTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1272475 GTTC
1 GTTC
1272479 TCAATCATTG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:1273872 original size:114 final size:114
Alignment explanation
Indices: 1273666--1273889 Score: 360
Period size: 114 Copynumber: 2.0 Consensus size: 114
1273656 GATCATGCAG
* * *
1273666 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCTTACCGAACAAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACAAGATCAGATAACTCAAAGA
* * *
1273731 ACATTTCTAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCAAA
*
1273780 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAA-ATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAA-CAAGATCAGATAACTCAAAG
*
1273844 AACACTTCCAGAAGATGCTATTATGTCTCCTTATTTCTACTATGAG
65 AACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAG
1273890 AACGTGGCAC
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
114 98 0.97
115 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACAAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:1281339 original size:17 final size:17
Alignment explanation
Indices: 1281278--1281342 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 17
1281268 TTGTCTCTAT
*
1281278 TATTAAAAATTCAAAATA
1 TATTTAAAATT-AAAATA
*
1281296 TATTT-AATTTAAATTTATA
1 TATTTAAAATTAAA---ATA
1281315 TTATTTTAAAATTAAAATA
1 -TA-TTTAAAATTAAAATA
1281334 TATTTAAAA
1 TATTTAAAA
1281343 ATATCGGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
16 3 0.08
17 11 0.29
18 6 0.16
19 6 0.16
20 2 0.05
21 3 0.08
22 7 0.18
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTTAAAATTAAAATA
Found at i:1281430 original size:17 final size:18
Alignment explanation
Indices: 1281408--1281443 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1281398 AAATAAATAA
*
1281408 ATGACAAACATTT-TTTT
1 ATGACAAAAATTTATTTT
1281425 ATGACAAAAATTTATTTT
1 ATGACAAAAATTTATTTT
1281443 A
1 A
1281444 ATATAGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (18 bp):
ATGACAAAAATTTATTTT
Found at i:1282301 original size:13 final size:13
Alignment explanation
Indices: 1282283--1282311 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1282273 CCACCGTACT
1282283 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
1282296 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
1282309 CCG
1 CCG
1282312 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:1283033 original size:3 final size:3
Alignment explanation
Indices: 1283025--1283133 Score: 128
Period size: 3 Copynumber: 35.7 Consensus size: 3
1283015 TTATTTATTA
*
1283025 AAT AAT AAT ATAT AAT AAT ATT AAT AAT AAT AAAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
* * * * *
1283072 TAT TAT TAT TAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
1283120 TTT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
1283134 CTTTAAATGA
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
3 88 0.94
4 6 0.06
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:1286227 original size:22 final size:23
Alignment explanation
Indices: 1286185--1286245 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
1286175 ACTAAAGTTG
1286185 ATAAATTATTTTAATTATTTG-AT
1 ATAAA-TATTTTAATTATTTGCAT
1286208 AATAAATATTTATAA-T-TTTGCAT
1 -ATAAATATTT-TAATTATTTGCAT
*
1286231 ATAAATATTTGAATT
1 ATAAATATTTTAATT
1286246 CAAGAATTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 2 0.06
22 15 0.45
23 8 0.24
24 8 0.24
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (23 bp):
ATAAATATTTTAATTATTTGCAT
Found at i:1286713 original size:10 final size:10
Alignment explanation
Indices: 1286698--1286737 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1286688 TTTGTCACAC
1286698 CAAATTCTCT
1 CAAATTCTCT
1286708 CAAATTCTCT
1 CAAATTCTCT
1286718 -AAATTTCTCT
1 CAAA-TTCTCT
*
1286728 CAAATACTCT
1 CAAATTCTCT
1286738 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1287058 original size:111 final size:111
Alignment explanation
Indices: 1286864--1287196 Score: 621
Period size: 111 Copynumber: 3.0 Consensus size: 111
1286854 TAAAAATCAT
*
1286864 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
1286929 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
1286975 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1287040 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
1287086 ATATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
1287151 TAATTAGTTGGTTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
1287197 TTTTTGTAAT
Statistics
Matches: 217, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 217 1.00
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:1289062 original size:9 final size:9
Alignment explanation
Indices: 1289050--1289085 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
1289040 ACCTGCTCAG
1289050 GACGACGAT
1 GACGACGAT
* *
1289059 GACGATGGT
1 GACGACGAT
1289068 GACGACGAT
1 GACGACGAT
1289077 GACGACGAT
1 GACGACGAT
1289086 AATGATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.31, C:0.19, G:0.36, T:0.14
Consensus pattern (9 bp):
GACGACGAT
Found at i:1292963 original size:50 final size:50
Alignment explanation
Indices: 1292909--1293018 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
1292899 TAGCGCAGAT
* * * * *
1292909 CAGGGGGCGCGCTATACCCACGTGGTGTCAGATCATCGTATATCGCGGGG
1 CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAACGTATAACGCGGGG
* * * **
1292959 CAGGGCGCACGTTATACCCACGTGGCGCCAAATCAACGTATAACGCGGTT
1 CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAACGTATAACGCGGGG
1293009 CAGGGGGCGC
1 CAGGGGGCGC
1293019 ACTTTACTGC
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.21, C:0.28, G:0.34, T:0.17
Consensus pattern (50 bp):
CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAACGTATAACGCGGGG
Found at i:1294174 original size:24 final size:24
Alignment explanation
Indices: 1294142--1294197 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
1294132 CTATTCTTTC
1294142 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
1294166 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
1294190 GCTTCAAT
1 GCTTCAAT
1294198 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:1294987 original size:26 final size:26
Alignment explanation
Indices: 1294956--1295012 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
1294946 AAAAGCAATG
1294956 ATGATGCCAATAGACATCATTAAAAT
1 ATGATGCCAATAGACATCATTAAAAT
1294982 ATGATGCCAATAGACATCATTAAAAT
1 ATGATGCCAATAGACATCATTAAAAT
1295008 ATGAT
1 ATGAT
1295013 TTTACAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (26 bp):
ATGATGCCAATAGACATCATTAAAAT
Found at i:1298191 original size:31 final size:30
Alignment explanation
Indices: 1298155--1298213 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
1298145 AAAATTAATG
1298155 TTTAAAAT-ATTAAGATTAATATAAAAATATT
1 TTTAAAATAATTAAGATT-ATA-AAAAATATT
*
1298186 TTTAAAATAATTAATATTATAAAAAATA
1 TTTAAAATAATTAAGATTATAAAAAATA
1298214 GTTCAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 7 0.27
31 11 0.42
32 8 0.31
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
TTTAAAATAATTAAGATTATAAAAAATATT
Found at i:1301284 original size:6 final size:6
Alignment explanation
Indices: 1301273--1301304 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1301263 CTGGTGAGAC
*
1301273 GAGAGG GAGAGG GAGAGG GAGAGG GAGGGG GA
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GA
1301305 ACTGGAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:1302937 original size:208 final size:214
Alignment explanation
Indices: 1302589--1303129 Score: 575
Period size: 208 Copynumber: 2.5 Consensus size: 214
1302579 TACTTGGATG
* * * * *
1302589 TAAATGGTG-TTTGCCATCTCTTTAGATTTGATTAGTTGGTTATCATCTTTGCTTTCACGAACTG
1 TAAACGGTGTTTTGCCATCTCTTTAGA-TTGATTAATTGGCTATCATC--AG-TTTCATGAAC--
* * ** * *
1302653 CTG-CTATATGTATATAGTTCGACATCGAAAATCCAGTCTTTTGGGCTAGAACGATAGCTTTCGT
60 C-GACTATATGTATGTAGTTCGACATCGAAAATTCAGTCTTTTGAACTAGAACGATAGATTTCAT
* ** *
1302717 GTGTTGAAGATCTATGGTGAATTCGA-GTTGTTG-A-T-CTG-GT-TTTCCC-TTCCTCCATGAT
124 ATGTCAAAGATCTAGGGTGAATTC-ATGTTGTTGAATTGCTGAGTGTTTCCCTTTCCTCCATGAT
*
1302775 TAATATATGCAGTCCTCTACTTAAATC
188 TAATATATGCAGCCCTCTACTTAAATC
*
1302802 TAAAGGGTGTTTTGCCATCTCTTTAGATATGATTAATTGGCTATCATCAGTTTCATGAACC-ACT
1 TAAACGGTGTTTTGCCATCTCTTTAGAT-TGATTAATTGGCTATCATCAGTTTCATGAACCGACT
* *
1302866 ATATGTATGTAGTTCAACATCGAAAATTCAGTCTTTTTAACTA-AACTGATAGATTTCATATGTC
65 ATATGTATGTAGTTCGACATCGAAAATTCAGTCTTTTGAACTAGAAC-GATAGATTTCATATGTC
*
1302930 AAAGATCTAGGGTGAATTCATGTTGTTGATCTAATTGGACTGATGTGGTTTCCCTTTTCTCCATG
129 AAAGATCTAGGGTGAATTCATGTTGTTG----AATT-G-CTGA-GT-GTTTCCCTTTCCTCCATG
1302995 ATTAATATATGCAGCCCTCTACTTAAATC
186 ATTAATATATGCAGCCCTCTACTTAAATC
* **
1303024 TAAACGGTGTTTTGGCATCTCTTTAGATTGATTAATTGGCTATCATTGGTTTCATGAACCGA-TA
1 TAAACGGTGTTTTGCCATCTCTTTAGATTGATTAATTGGCTATCATCAGTTTCATGAACCGACTA
** * * * *
1303088 TACATATGCAGTTCGACATAGAAAATTCAGTATTTTGGACTA
66 TATGTATGTAGTTCGACATCGAAAATTCAGTCTTTTGAACTA
1303130 ATTAGATCTA
Statistics
Matches: 277, Mismatches: 31, Indels: 32
0.81 0.09 0.09
Matches are distributed among these distances:
207 4 0.01
208 76 0.27
209 1 0.00
211 9 0.03
212 1 0.00
213 10 0.04
214 35 0.13
217 3 0.01
219 2 0.01
221 72 0.26
222 64 0.23
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (214 bp):
TAAACGGTGTTTTGCCATCTCTTTAGATTGATTAATTGGCTATCATCAGTTTCATGAACCGACTA
TATGTATGTAGTTCGACATCGAAAATTCAGTCTTTTGAACTAGAACGATAGATTTCATATGTCAA
AGATCTAGGGTGAATTCATGTTGTTGAATTGCTGAGTGTTTCCCTTTCCTCCATGATTAATATAT
GCAGCCCTCTACTTAAATC
Found at i:1310281 original size:18 final size:19
Alignment explanation
Indices: 1310228--1310283 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 19
1310218 GTGATTTAAC
1310228 CAATTTAAGATAAAACTCAAT
1 CAATTTAAGATAAAA--CAAT
*
1310249 CATATTTATA-TTAAAA-AAT
1 CA-ATTTA-AGATAAAACAAT
1310268 CAATTTAAGATAAAAC
1 CAATTTAAGATAAAAC
1310284 TCAATCAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
17 1 0.03
18 10 0.34
19 5 0.17
21 2 0.07
22 10 0.34
23 1 0.03
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.32
Consensus pattern (19 bp):
CAATTTAAGATAAAACAAT
Found at i:1310976 original size:156 final size:156
Alignment explanation
Indices: 1310809--1311128 Score: 640
Period size: 156 Copynumber: 2.1 Consensus size: 156
1310799 CCAAAAAAAT
1310809 GTTTTTTTTTCATGGTGCTCGAATTCGAGACCACAAGGAATAACAACGATTCTTTTACCATCGAA
1 GTTTTTTTTTCATGGTGCTCGAATTCGAGACCACAAGGAATAACAACGATTCTTTTACCATCGAA
1310874 ATCTATTAGTTCGTGCAAATTAAATTTAAATTCAGGAACTATCCTTAGGATCTTTATTAATGCAT
66 ATCTATTAGTTCGTGCAAATTAAATTTAAATTCAGGAACTATCCTTAGGATCTTTATTAATGCAT
1310939 ATAAAAAATTATCTTTGTTCATCCAA
131 ATAAAAAATTATCTTTGTTCATCCAA
1310965 GTTTTTTTTTCATGGTGCTCGAATTCGAGACCACAAGGAATAACAACGATTCTTTTACCATCGAA
1 GTTTTTTTTTCATGGTGCTCGAATTCGAGACCACAAGGAATAACAACGATTCTTTTACCATCGAA
1311030 ATCTATTAGTTCGTGCAAATTAAATTTAAATTCAGGAACTATCCTTAGGATCTTTATTAATGCAT
66 ATCTATTAGTTCGTGCAAATTAAATTTAAATTCAGGAACTATCCTTAGGATCTTTATTAATGCAT
1311095 ATAAAAAATTATCTTTGTTCATCCAA
131 ATAAAAAATTATCTTTGTTCATCCAA
1311121 GTTTTTTT
1 GTTTTTTT
1311129 GTTTTTTTTT
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 164 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (156 bp):
GTTTTTTTTTCATGGTGCTCGAATTCGAGACCACAAGGAATAACAACGATTCTTTTACCATCGAA
ATCTATTAGTTCGTGCAAATTAAATTTAAATTCAGGAACTATCCTTAGGATCTTTATTAATGCAT
ATAAAAAATTATCTTTGTTCATCCAA
Found at i:1311846 original size:24 final size:24
Alignment explanation
Indices: 1311819--1311866 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1311809 TTCGTAAACA
1311819 TTCGGTTATGTTCGTTTATGTTTG
1 TTCGGTTATGTTCGTTTATGTTTG
1311843 TTCGGTTATGTTCGTTTATGTTTG
1 TTCGGTTATGTTCGTTTATGTTTG
1311867 CTTATGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.08, G:0.25, T:0.58
Consensus pattern (24 bp):
TTCGGTTATGTTCGTTTATGTTTG
Found at i:1313085 original size:16 final size:16
Alignment explanation
Indices: 1313061--1313093 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1313051 AATTTTTGTT
*
1313061 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1313077 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1313093 T
1 T
1313094 TTATTTATTA
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:0.06, C:0.09, G:0.24, T:0.61
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1319531 original size:30 final size:31
Alignment explanation
Indices: 1319465--1319552 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 31
1319455 GAGTCGAGGG
* *
1319465 TTACCTATGTCATTCGGGATATATGGACAGT
1 TTACCTATGTCATTCGGAACATATGGACAGT
* *
1319496 TTACCTATGTCCTTCGGAACATATGGGCA-T
1 TTACCTATGTCATTCGGAACATATGGACAGT
** *
1319526 TTACCTATGTTTTTTGGAACATATGGA
1 TTACCTATGTCATTCGGAACATATGGA
1319553 TAGTGGTCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 24 0.49
31 25 0.51
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (31 bp):
TTACCTATGTCATTCGGAACATATGGACAGT
Found at i:1319585 original size:22 final size:22
Alignment explanation
Indices: 1319557--1319614 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1319547 TATGGATAGT
*
1319557 GGTCCTTTGGGACATATACAGA
1 GGTCCTTCGGGACATATACAGA
* * *
1319579 GGTCCTTCGGAACTTATACATA
1 GGTCCTTCGGGACATATACAGA
*
1319601 GGTCATTCGGGACA
1 GGTCCTTCGGGACA
1319615 CAAATTTCAC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (22 bp):
GGTCCTTCGGGACATATACAGA
Found at i:1321037 original size:23 final size:24
Alignment explanation
Indices: 1321011--1321067 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
1321001 TGTTTGTGTT
* *
1321011 TGTTTATTTAT-TTTTCGCAAACA
1 TGTTTATTTATATGTTCACAAACA
* *
1321034 TGTTTGTTTATATGTTCACGAACA
1 TGTTTATTTATATGTTCACAAACA
*
1321058 TGTTCATTTA
1 TGTTTATTTA
1321068 GAGTTTAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (24 bp):
TGTTTATTTATATGTTCACAAACA
Found at i:1321095 original size:22 final size:23
Alignment explanation
Indices: 1321030--1321095 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 23
1321020 ATTTTTCGCA
* *
1321030 AACATGTTTGTTTATATGTTCACG
1 AACATGTTCGTTTAT-TGTTTACG
* **
1321054 AACATGTTCATTTAGAGTTTA-G
1 AACATGTTCGTTTATTGTTTACG
*
1321076 AGCATGTTCGTTTATTGTTT
1 AACATGTTCGTTTATTGTTT
1321096 GTTTATATAT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 17 0.52
23 4 0.12
24 12 0.36
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (23 bp):
AACATGTTCGTTTATTGTTTACG
Found at i:1321377 original size:20 final size:20
Alignment explanation
Indices: 1321352--1321438 Score: 122
Period size: 20 Copynumber: 4.3 Consensus size: 20
1321342 AATATGTAAA
1321352 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
1321372 TCGCAACGC-GATAATCAAAT
1 TCGCAACACAGA-AGTCAAAT
1321392 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
1321412 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
1321432 TCACAAC
1 TCGCAAC
1321439 TAAATTTCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
19 2 0.03
20 55 0.93
21 2 0.03
ACGTcount: A:0.45, C:0.26, G:0.13, T:0.16
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:1321450 original size:19 final size:19
Alignment explanation
Indices: 1321426--1321476 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
1321416 AACACAAAAG
1321426 TCAAATTCACAACTAAATT
1 TCAAATTCACAACTAAATT
* * *
1321445 TCAAATTCGCAATTGAATT
1 TCAAATTCACAACTAAATT
1321464 TCAAATTCACAAC
1 TCAAATTCACAAC
1321477 ACGAATTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.43, C:0.22, G:0.04, T:0.31
Consensus pattern (19 bp):
TCAAATTCACAACTAAATT
Found at i:1321484 original size:20 final size:20
Alignment explanation
Indices: 1321352--1321484 Score: 89
Period size: 20 Copynumber: 6.8 Consensus size: 20
1321342 AATATGTAAA
*
1321352 TCGCAACACAGAA-GTCAAAT
1 TCGCAACAC-GAATTTCAAAT
* *
1321372 TCGCAACGCG-ATAATCAAAT
1 TCGCAACACGAAT-TTCAAAT
*
1321392 TCGCAACACAGAA-GTCAAAT
1 TCGCAACAC-GAATTTCAAAT
* **
1321412 TCGCAACACAAAAGTCAAAT
1 TCGCAACACGAATTTCAAAT
*
1321432 TCACAACTA--AATTTCAAAT
1 TCGCAAC-ACGAATTTCAAAT
**
1321451 TCGCAA-TTGAATTTCAAAT
1 TCGCAACACGAATTTCAAAT
*
1321470 TCACAACACGAATTT
1 TCGCAACACGAATTT
1321485 AATTTCGTAA
Statistics
Matches: 91, Mismatches: 13, Indels: 18
0.75 0.11 0.15
Matches are distributed among these distances:
18 1 0.01
19 31 0.34
20 56 0.62
21 2 0.02
22 1 0.01
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.23
Consensus pattern (20 bp):
TCGCAACACGAATTTCAAAT
Found at i:1321671 original size:14 final size:15
Alignment explanation
Indices: 1321652--1321689 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1321642 TCCCCATCTC
1321652 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1321666 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1321682 TAATTTTT
1 TAATTTTT
1321690 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1324996 original size:20 final size:20
Alignment explanation
Indices: 1324967--1325016 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1324957 ATGTTGCAAT
* *
1324967 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTAAAATTCA
*
1324987 CAACGTGAAAGTAAAATTCA
1 CAACGCGAAAGTAAAATTCA
1325007 CAACGCGAAA
1 CAACGCGAAA
1325017 TAAGCGCTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.14
Consensus pattern (20 bp):
CAACGCGAAAGTAAAATTCA
Found at i:1325075 original size:20 final size:20
Alignment explanation
Indices: 1325050--1325113 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
1325040 GCAACGCTTA
1325050 TTTCGCGTTGCAAATTTACC
1 TTTCGCGTTGCAAATTTACC
* *
1325070 TTTCGCGTTTCGAATTTGA-C
1 TTTCGCGTTGCAAATTT-ACC
*
1325090 TTTCGCGTTGTGAAAGTTTACC
1 TTTCGCGTTG-CAAA-TTTACC
1325112 TT
1 TT
1325114 CAACAGGTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 25 0.71
21 4 0.11
22 6 0.17
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCAAATTTACC
Found at i:1325215 original size:25 final size:25
Alignment explanation
Indices: 1325174--1325223 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1325164 AAATCAATTA
*
1325174 AACATTGTTGTGTGTACATTATTTG
1 AACATTGTTATGTGTACATTATTTG
1325199 AACATTGTTATAG-GTACATTATTTG
1 AACATTGTTAT-GTGTACATTATTTG
1325224 GAAAATAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (25 bp):
AACATTGTTATGTGTACATTATTTG
Found at i:1325630 original size:18 final size:18
Alignment explanation
Indices: 1325609--1325645 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1325599 GTAATTGGAG
1325609 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1325627 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1325645 T
1 T
1325646 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1325652 original size:24 final size:24
Alignment explanation
Indices: 1325601--1325653 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1325591 TTTCATATGT
* * *
1325601 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
1325625 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1325649 AATTT
1 AATTT
1325654 CGGTTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1326869 original size:13 final size:14
Alignment explanation
Indices: 1326844--1326876 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
1326834 ATCAAATTAA
1326844 ACAAATAAACTTTT
1 ACAAATAAACTTTT
1326858 ACAAAT-AACTTTT
1 ACAAATAAACTTTT
1326871 ACAAAT
1 ACAAAT
1326877 CAATTAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATAAACTTTT
Found at i:1326915 original size:78 final size:78
Alignment explanation
Indices: 1326779--1326933 Score: 260
Period size: 78 Copynumber: 2.0 Consensus size: 78
1326769 ATTTAAAACA
1326779 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTATACATCAAATTAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTATACATC-AATTAA
1326844 ACAAATAAACTTTT
65 ACAAATAAACTTTT
*
1326858 ACAAAT-AACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCT-CATCAATTAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTT-ATACATCAATTAA
*
1326921 ACAAATCAACTTT
65 ACAAATAAACTTT
1326934 CAATGTAAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
77 18 0.25
78 48 0.66
79 7 0.10
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.32
Consensus pattern (78 bp):
ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTATACATCAATTAAA
CAAATAAACTTTT
Found at i:1328330 original size:21 final size:21
Alignment explanation
Indices: 1328306--1328380 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
1328296 CGGGCGGGAT
*
1328306 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
1328327 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* * *
1328348 TTCTTCG-ACGATGAGATGGAC
1 CTCTT-GAACGATGAGAGGGGC
*
1328369 CTCTTAAACGAT
1 CTCTTGAACGAT
1328381 AGAAATCGCC
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 41 0.98
22 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:1331042 original size:22 final size:22
Alignment explanation
Indices: 1330997--1331049 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1330987 AGATAGATGA
* *
1330997 ATTTCGCCGGAGATGGGAATGG
1 ATTTCGTCGGAGATGGGAACGG
*
1331019 ATTTCGTCGGAGATGGGGACGG
1 ATTTCGTCGGAGATGGGAACGG
*
1331041 ATGTCGTCG
1 ATTTCGTCG
1331050 TAGAGAGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.42, T:0.25
Consensus pattern (22 bp):
ATTTCGTCGGAGATGGGAACGG
Found at i:1331181 original size:20 final size:20
Alignment explanation
Indices: 1331153--1331266 Score: 140
Period size: 20 Copynumber: 5.7 Consensus size: 20
1331143 GTTTTGCGCA
*
1331153 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTATCGTG
* * *
1331173 TTGCAAATTTGACTTTTGTG
1 TTGCGAATTTGACTATCGTG
1331193 TTGCGAATTTGACTATCGTG
1 TTGCGAATTTGACTATCGTG
*
1331213 TTGCAAATTTGACTTAT-GTG
1 TTGCGAATTTGAC-TATCGTG
* **
1331233 TTACGAATTTGACTATCGCA
1 TTGCGAATTTGACTATCGTG
1331253 TTGCGAATTTGACT
1 TTGCGAATTTGACT
1331267 TCTATGTTGC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.04
20 73 0.92
21 3 0.04
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGTG
Found at i:1331299 original size:40 final size:40
Alignment explanation
Indices: 1331153--1331278 Score: 189
Period size: 40 Copynumber: 3.1 Consensus size: 40
1331143 GTTTTGCGCA
*
1331153 TTGCGAATTTGACTATCGCGTTGCAAATTTGACTTTTGTG
1 TTGCGAATTTGACTATCGCGTTGCAAATTTGACTTATGTG
*
1331193 TTGCGAATTTGACTATCGTGTTGCAAATTTGACTTATGTG
1 TTGCGAATTTGACTATCGCGTTGCAAATTTGACTTATGTG
* * * * *
1331233 TTACGAATTTGACTATCGCATTGCGAATTTGACTTCTATG
1 TTGCGAATTTGACTATCGCGTTGCAAATTTGACTTATGTG
1331273 TTGCGA
1 TTGCGA
1331279 TTTACAAATT
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.41
Consensus pattern (40 bp):
TTGCGAATTTGACTATCGCGTTGCAAATTTGACTTATGTG
Found at i:1334011 original size:84 final size:83
Alignment explanation
Indices: 1333712--1334065 Score: 396
Period size: 85 Copynumber: 4.2 Consensus size: 83
1333702 TTGTTGATAG
* ** ** *
1333712 ATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTGGATACGCCTGAGAGCTGAATGTAATCGAAC
1 ATAACCCTTCTCGCCTTGAGTTATGTTGCAAA-T-GATGTGCCTTTGAGCTGAGTGTAATCGAAC
* * *
1333777 TCGAAGGAC-TTTGATGACAT
64 TCGAAGGTCTTTTGTTG-CAA
1333797 ATAACCCTTCTCGCCTTGAGTTATGCTT-CAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTCGCCTTGAGTTATG-TTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACT
1333861 CGAAGGTCTTTTTGTTGGCAGA
65 CGAAGGTC-TTTTGTT-GCA-A
* ** * * *
1333883 A-AACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTGCTTTTGAGCCGAGTGTAATCGAACTC
1 ATAACCCTTCTCGCCTTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1333947 GAAGGTCTTTTGTTAGCAA
66 GAAGGTCTTTTGTT-GCAA
* * *
1333966 ATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGTCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTCGCCTTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
1334031 GAAGGT-ATTTG--GCAA
66 GAAGGTCTTTTGTTGCAA
* * *
1334046 ATAGCCCTTCTTGTCTTGAG
1 ATAACCCTTCTCGCCTTGAG
1334066 CTTTGAATTG
Statistics
Matches: 235, Mismatches: 27, Indels: 19
0.84 0.10 0.07
Matches are distributed among these distances:
80 22 0.09
83 39 0.17
84 73 0.31
85 97 0.41
86 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (83 bp):
ATAACCCTTCTCGCCTTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
GAAGGTCTTTTGTTGCAA
Found at i:1334399 original size:112 final size:111
Alignment explanation
Indices: 1334251--1334499 Score: 365
Period size: 112 Copynumber: 2.2 Consensus size: 111
1334241 GTTACTTGTG
* * * *
1334251 GGCACGATATCCTTCGTTGTGAAGTTGAAATCGTGGATGACCTATTCGTTGTGAAGTTGAGCCTT
1 GGCACGAT-TCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCAATCGTTGTGAAGTTGAGCCTT
* *
1334316 GAATTGGATGTCCTTCGTCGTGAAGTTGAAATCCAATGTTGCTGGT-
65 GAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATGTTGCTGGTA
* * *
1334362 GAGCACGATTCACTTCGTCATGAAGTTGAAACCGTGGATGGCCCAATCGTTGTGTAGTTGAGCCT
1 G-GCACGATTC-CTTCGTCGTGAAGTTGAAACCGTGGATGACCCAATCGTTGTGAAGTTGAGCCT
*
1334427 TGAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATGTTGTTGGTA
64 TGAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATGTTGCTGGTA
1334475 GGCACGATTCCCTTCGTCGTGAAGT
1 GGCACGATT-CCTTCGTCGTGAAGT
1334500 CAAAATTGAC
Statistics
Matches: 123, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
111 3 0.02
112 118 0.96
113 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (111 bp):
GGCACGATTCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCAATCGTTGTGAAGTTGAGCCTTG
AATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATGTTGCTGGTA
Found at i:1334668 original size:43 final size:43
Alignment explanation
Indices: 1334621--1334731 Score: 159
Period size: 43 Copynumber: 2.6 Consensus size: 43
1334611 CGATTCCCTT
* * *
1334621 CGTCGTGAAGTTGAAACCGTGGATGTGTGGACACGATATCCTC
1 CGTCGTGGAGTTGAAATCGTGGATGCGTGGACACGATATCCTC
* * **
1334664 CGTCGTGGAGTTGAAATCATGGATCCGTGGTTACGATATCCTC
1 CGTCGTGGAGTTGAAATCGTGGATGCGTGGACACGATATCCTC
1334707 CGTCGTGGAGTTGAAATCGTGGATG
1 CGTCGTGGAGTTGAAATCGTGGATG
1334732 GCCCCTTCGT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.28
Consensus pattern (43 bp):
CGTCGTGGAGTTGAAATCGTGGATGCGTGGACACGATATCCTC
Found at i:1334882 original size:43 final size:43
Alignment explanation
Indices: 1334818--1334927 Score: 148
Period size: 43 Copynumber: 2.6 Consensus size: 43
1334808 CGATTCCCTT
* * * *
1334818 CGTCGTGAAGTTGAAACCGTGGTTGAGTGGGCACAATATCCTC
1 CGTCGTGGAGTTGAAATCGTGGATCAGTGGGCACAATATCCTC
* * *
1334861 CGTCGTGGAGTTGAAATCGTGGATCCGTGGGTACGATATCCTC
1 CGTCGTGGAGTTGAAATCGTGGATCAGTGGGCACAATATCCTC
*
1334904 TGTCGTGGAGTTGAAATCGTGGAT
1 CGTCGTGGAGTTGAAATCGTGGAT
1334928 GACCCATTCG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (43 bp):
CGTCGTGGAGTTGAAATCGTGGATCAGTGGGCACAATATCCTC
Found at i:1334947 original size:197 final size:197
Alignment explanation
Indices: 1334610--1334969 Score: 621
Period size: 197 Copynumber: 1.8 Consensus size: 197
1334600 GCTTGTGTGT
* *
1334610 ACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGTGTGGACACGATATCCTCCGTCGTGGAGT
1 ACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGAGTGGACACAATATCCTCCGTCGTGGAGT
* * *
1334675 TGAAATCATGGATCCGTGGTTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGGCCCCTTC
66 TGAAATCATGGATCCGTGGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGACCCATTC
1334740 GTCATGAAGTTGAGCCTTAACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGTTATGGGTGG
131 GTCATGAAGTTGAGCCTTAACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGTTATGGGTGG
1334805 AC
196 AC
* *
1334807 ACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGTTGAGTGGGCACAATATCCTCCGTCGTGGAGT
1 ACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGAGTGGACACAATATCCTCCGTCGTGGAGT
* *
1334872 TGAAATCGTGGATCCGTGGGTACGATATCCTCTGTCGTGGAGTTGAAATCGTGGATGACCCATTC
66 TGAAATCATGGATCCGTGGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGACCCATTC
* *
1334937 GTCGTGAAGTTGAGCCTTGACTTGAATATCCTT
131 GTCATGAAGTTGAGCCTTAACTTGAATATCCTT
1334970 TGTTCCTATT
Statistics
Matches: 152, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
197 152 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.30
Consensus pattern (197 bp):
ACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGAGTGGACACAATATCCTCCGTCGTGGAGT
TGAAATCATGGATCCGTGGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGACCCATTC
GTCATGAAGTTGAGCCTTAACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGTTATGGGTGG
AC
Found at i:1337217 original size:20 final size:20
Alignment explanation
Indices: 1337174--1337217 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1337164 AAATGTAAGA
* *
1337174 ATATCTATAATTTAATGATT
1 ATATATATAATTTAATGATG
1337194 ATATATATAATTTATATG-TG
1 ATATATATAATTTA-ATGATG
1337214 ATAT
1 ATAT
1337218 TAAATCTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (20 bp):
ATATATATAATTTAATGATG
Found at i:1340384 original size:7 final size:7
Alignment explanation
Indices: 1340372--1340419 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
1340362 TTGGTTTCTC
1340372 GGGTTTA
1 GGGTTTA
1340379 GGGTTTA
1 GGGTTTA
* *
1340386 TGATTTA
1 GGGTTTA
1340393 GGGTTTA
1 GGGTTTA
*
1340400 GAGTTTA
1 GGGTTTA
1340407 -GGTTTA
1 GGGTTTA
1340413 GGGTTTA
1 GGGTTTA
1340420 AGGTAATCCG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
6 5 0.15
7 29 0.85
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (7 bp):
GGGTTTA
Found at i:1340398 original size:21 final size:20
Alignment explanation
Indices: 1340372--1340419 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
1340362 TTGGTTTCTC
*
1340372 GGGTTTAGGGTTTATGATTTA
1 GGGTTTAGAGTTTA-GATTTA
*
1340393 GGGTTTAGAGTTTAGGTTTA
1 GGGTTTAGAGTTTAGATTTA
1340413 GGGTTTA
1 GGGTTTA
1340420 AGGTAATCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (20 bp):
GGGTTTAGAGTTTAGATTTA
Found at i:1340989 original size:24 final size:24
Alignment explanation
Indices: 1340962--1341008 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1340952 TTTTTACTAC
1340962 TAAATAATTATTAGTAATAATTAT
1 TAAATAATTATTAGTAATAATTAT
* * *
1340986 TAAATCATTATTATTAATTATTA
1 TAAATAATTATTAGTAATAATTA
1341009 CAATTTCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
TAAATAATTATTAGTAATAATTAT
Found at i:1341019 original size:21 final size:20
Alignment explanation
Indices: 1340979--1341021 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 20
1340969 TTATTAGTAA
1340979 TAATTATTAAATCATTATTAT
1 TAATTATTAAAT-ATTATTAT
1341000 TAATTATTACAAT-TTCATTAT
1 TAATTATTA-AATATT-ATTAT
1341021 T
1 T
1341022 TCAAATCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.10
21 15 0.75
22 3 0.15
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATTATTAAATATTATTAT
Found at i:1341128 original size:16 final size:16
Alignment explanation
Indices: 1341107--1341138 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1341097 ATCATTACTA
1341107 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
1341123 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
1341139 TAAATATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
ATCATTACTAAATCAT
Found at i:1341147 original size:26 final size:25
Alignment explanation
Indices: 1341096--1341155 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 25
1341086 ATTATTAGTT
1341096 AATCATTACTAATCATTACTAAATCA
1 AATCATTACTAATCATTAC-AAATCA
*
1341122 TATCATTACTAAATCATTA-AATATCA
1 AATCATTACT-AATCATTACAA-ATCA
1341148 AATCATTA
1 AATCATTA
1341156 AATTTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 2 0.07
26 20 0.67
27 8 0.27
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (25 bp):
AATCATTACTAATCATTACAAATCA
Found at i:1341208 original size:98 final size:93
Alignment explanation
Indices: 1341022--1341226 Score: 216
Period size: 98 Copynumber: 2.1 Consensus size: 93
1341012 TTTCATTATT
**
1341022 TCAAATCATTACTAAATCATTTGTATCAAATCATTAAATATTAATAATAAAAATTATTAGTATCA
1 TCAAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAAAATTATTAGTATCA
* *
1341087 TTATTAGTTAATCATTACTAATCATTACTAAA
66 TGA-TAGTTAATCAGTAC-AATCATT--TAAA
* * * *
1341119 TCATATCATTACTAAATCATTAAATATCAAATCATTAAATTTATAATTAGTAAATCATTATTAGT
1 TCAAATCATTACTAAATCATT-AATATCAAATCATTAAATAT-TAA-TAATAAA-AATTATTAGT
* * *
1341184 AATCATGA-ATTTAATTAGTA-AATCATTTATA
62 -ATCATGATAGTTAATCAGTACAATCATTTAAA
1341215 TCAAATCATTAC
1 TCAAATCATTAC
1341227 ATTATTATTA
Statistics
Matches: 91, Mismatches: 12, Indels: 11
0.80 0.11 0.10
Matches are distributed among these distances:
96 14 0.15
97 20 0.22
98 24 0.26
99 3 0.03
100 15 0.16
101 9 0.10
102 6 0.07
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.40
Consensus pattern (93 bp):
TCAAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAAAATTATTAGTATCA
TGATAGTTAATCAGTACAATCATTTAAA
Found at i:1341279 original size:23 final size:23
Alignment explanation
Indices: 1341236--1341281 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1341226 CATTATTATT
*
1341236 ATTAAATCATTAGTAGTTAAATC
1 ATTAAATCATAAGTAGTTAAATC
*
1341259 ATTAAATTCATAATTAG-TAAATC
1 ATTAAA-TCATAAGTAGTTAAATC
1341282 GTTATTAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (23 bp):
ATTAAATCATAAGTAGTTAAATC
Found at i:1341311 original size:26 final size:26
Alignment explanation
Indices: 1341282--1341344 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
1341272 TTAGTAAATC
1341282 GTTATTAGTAATTACTAAAATTGAGT
1 GTTATTAGTAATTACTAAAATTGAGT
1341308 GTTATTAGTAATTACTAAAATTGAGT
1 GTTATTAGTAATTACTAAAATTGAGT
*
1341334 ATTATTAGTAA
1 GTTATTAGTAA
1341345 ATTCATTTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (26 bp):
GTTATTAGTAATTACTAAAATTGAGT
Found at i:1341681 original size:10 final size:11
Alignment explanation
Indices: 1341662--1341691 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
1341652 TGATTAAATC
1341662 ATTATTATTAA
1 ATTATTATTAA
1341673 ATT-TTATTAA
1 ATTATTATTAA
1341683 ATTATTATT
1 ATTATTATT
1341692 TCATTTCAGT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTATTATTAA
Found at i:1343864 original size:30 final size:27
Alignment explanation
Indices: 1343831--1343882 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1343821 TTTAATTTGA
*
1343831 TGATGATAGAATTAGGGTTTTTTGGGG
1 TGATGATGGAATTAGGGTTTTTTGGGG
1343858 TGATGATGGAATTAGGGTTTTTTGG
1 TGATGATGGAATTAGGGTTTTTTGG
1343883 ATTTTGTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (27 bp):
TGATGATGGAATTAGGGTTTTTTGGGG
Found at i:1352314 original size:159 final size:159
Alignment explanation
Indices: 1352025--1352344 Score: 640
Period size: 159 Copynumber: 2.0 Consensus size: 159
1352015 TTTCGAAGGG
1352025 TTAAAGGAAAGGAGACTTTGAGGCCGACACGTGGCGAGGAGATCAAGACAACGGCCGTGGTAAAA
1 TTAAAGGAAAGGAGACTTTGAGGCCGACACGTGGCGAGGAGATCAAGACAACGGCCGTGGTAAAA
1352090 CTGGTAGATATCAGAATTCGTGGATGAGAGTGGGGATGAGATCCGATCAGTTTCTTTGATGTGAT
66 CTGGTAGATATCAGAATTCGTGGATGAGAGTGGGGATGAGATCCGATCAGTTTCTTTGATGTGAT
1352155 TGGTCCACGTGGGTTATGGCTTTTGGAAA
131 TGGTCCACGTGGGTTATGGCTTTTGGAAA
1352184 TTAAAGGAAAGGAGACTTTGAGGCCGACACGTGGCGAGGAGATCAAGACAACGGCCGTGGTAAAA
1 TTAAAGGAAAGGAGACTTTGAGGCCGACACGTGGCGAGGAGATCAAGACAACGGCCGTGGTAAAA
1352249 CTGGTAGATATCAGAATTCGTGGATGAGAGTGGGGATGAGATCCGATCAGTTTCTTTGATGTGAT
66 CTGGTAGATATCAGAATTCGTGGATGAGAGTGGGGATGAGATCCGATCAGTTTCTTTGATGTGAT
1352314 TGGTCCACGTGGGTTATGGCTTTTGGAAA
131 TGGTCCACGTGGGTTATGGCTTTTGGAAA
1352343 TT
1 TT
1352345 CGACACGTGT
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 161 1.00
ACGTcount: A:0.28, C:0.14, G:0.33, T:0.26
Consensus pattern (159 bp):
TTAAAGGAAAGGAGACTTTGAGGCCGACACGTGGCGAGGAGATCAAGACAACGGCCGTGGTAAAA
CTGGTAGATATCAGAATTCGTGGATGAGAGTGGGGATGAGATCCGATCAGTTTCTTTGATGTGAT
TGGTCCACGTGGGTTATGGCTTTTGGAAA
Found at i:1354721 original size:21 final size:21
Alignment explanation
Indices: 1354696--1354735 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1354686 TCAAAAATTA
*
1354696 TAAAATAATG-ATTAAATTTAT
1 TAAAA-AATGAATGAAATTTAT
1354717 TAAAAAATGAATGAAATTT
1 TAAAAAATGAATGAAATTT
1354736 TAAGCCTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
TAAAAAATGAATGAAATTTAT
Found at i:1358884 original size:21 final size:21
Alignment explanation
Indices: 1358832--1358892 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
1358822 CGTTGCGATT
*
1358832 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAATGCGAAC
*
1358851 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAATGCGAAC
*
1358874 TTGGACTATCGCATTGCGA
1 TTGGACTATCGCAATGCGA
1358893 TTTACATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 6 0.18
21 18 0.53
23 10 0.29
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:1358907 original size:20 final size:20
Alignment explanation
Indices: 1358882--1358954 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
1358872 ACTTGGACTA
1358882 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
1358902 TCGCATTGCGATAGT-CGAT-T
1 TCGCATTGCGAT-TTAC-ATAT
1358922 ATCGCATTGCGATTTACATAT
1 -TCGCATTGCGATTTACATAT
1358943 TCGCATTGCGAT
1 TCGCATTGCGAT
1358955 AGTCCAAGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
20 29 0.63
21 17 0.37
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1358925 original size:41 final size:42
Alignment explanation
Indices: 1358880--1358975 Score: 160
Period size: 41 Copynumber: 2.3 Consensus size: 42
1358870 GAACTTGGAC
* *
1358880 TATCGCATTGCGATTTACATATTCGCATTGCGATAGT-CGAT
1 TATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
1358921 TATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
1 TATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
1358963 T-TCGCATTGCGAT
1 TATCGCATTGCGAT
1358976 AGTCGAAGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
41 49 0.94
42 3 0.06
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (42 bp):
TATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
Found at i:1358926 original size:62 final size:62
Alignment explanation
Indices: 1358860--1358981 Score: 144
Period size: 62 Copynumber: 2.0 Consensus size: 62
1358850 TTTGGAATAA
*
1358860 ATCGCAATGCGAACTTGGAC-TA-TCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTCGAT
1 ATCGCAATGCG-A-TT-GACATATTCGCATTGCGATAGTACA-AGTTCGCATTGCGATAGTCGAT
1358921 T
62 T
* * *
1358922 ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGA
1 ATCGCAATGCGATTGACATATTCGCATTGCGATAGTACAAGTTCGCATTGCGATAGTCGA
1358982 AGTTCGCGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
59 2 0.04
60 4 0.08
61 14 0.27
62 32 0.62
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (62 bp):
ATCGCAATGCGATTGACATATTCGCATTGCGATAGTACAAGTTCGCATTGCGATAGTCGATT
Found at i:1358928 original size:21 final size:21
Alignment explanation
Indices: 1358880--1358978 Score: 84
Period size: 21 Copynumber: 4.8 Consensus size: 21
1358870 GAACTTGGAC
*
1358880 TATCGCATTGCGAT-TTAC-A
1 TATCGCATTGCGATAGTACGA
1358899 TATTCGCATTGCGATAGT-CGA
1 TA-TCGCATTGCGATAGTACGA
*
1358920 TTATCGCATTGCGAT-TTAC-A
1 -TATCGCATTGCGATAGTACGA
* *
1358940 TATTCGCATTGCGATAGTCCAA
1 TA-TCGCATTGCGATAGTACGA
1358962 GT-TCGCATTGCGATAGT
1 -TATCGCATTGCGATAGT
1358979 CGAAGTTCGC
Statistics
Matches: 67, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
19 4 0.06
20 27 0.40
21 32 0.48
22 3 0.04
23 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (21 bp):
TATCGCATTGCGATAGTACGA
Found at i:1358979 original size:21 final size:21
Alignment explanation
Indices: 1358901--1358995 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 21
1358891 GATTTACATA
* *
1358901 TTCGCATTGCGATAGT-CGAT
1 TTCGCATTGCGATAGTCCAAG
* *
1358921 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
1358942 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
1358963 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
1358984 TTCGCGTTGCGA
1 TTCGCATTGCGA
1358996 ATCTGGAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
20 15 0.23
21 48 0.75
22 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:1359164 original size:23 final size:23
Alignment explanation
Indices: 1359137--1359187 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1359127 TTATTTTCTC
1359137 ATAAATAT-AATATCAAATATATA
1 ATAAATATAAATA-CAAATATATA
* *
1359160 ATAAAAATAAATACAAATTTATA
1 ATAAATATAAATACAAATATATA
1359183 A-AAAT
1 ATAAAT
1359188 GATATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 3 0.12
23 17 0.71
24 4 0.17
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (23 bp):
ATAAATATAAATACAAATATATA
Found at i:1361332 original size:51 final size:50
Alignment explanation
Indices: 1361258--1361392 Score: 189
Period size: 51 Copynumber: 2.7 Consensus size: 50
1361248 ACCCTTTGCA
* *
1361258 GTAAGGCGCGCCCCTGCAACGCGCATTACGTTGATCTGGCGCCACGTGGG
1 GTAAGGCGCCCCCCTGCAACGCGCATTACGCTGATCTGGCGCCACGTGGG
1361308 GTAAGGCGCACCCCCTGCAACGCGCATTACGCTGATCTGGCGCCACGTGGG
1 GTAAGGCGC-CCCCCTGCAACGCGCATTACGCTGATCTGGCGCCACGTGGG
* * * * * *
1361359 GTAAGACGCGCCCCTACAGCGCGCCTTATGCTGA
1 GTAAGGCGCCCCCCTGCAACGCGCATTACGCTGA
1361393 CATGGACACA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
50 29 0.38
51 47 0.62
ACGTcount: A:0.18, C:0.34, G:0.31, T:0.17
Consensus pattern (50 bp):
GTAAGGCGCCCCCCTGCAACGCGCATTACGCTGATCTGGCGCCACGTGGG
Found at i:1365313 original size:23 final size:23
Alignment explanation
Indices: 1365287--1365352 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
1365277 ATTAAATGAT
*
1365287 AAATAATAAAAAATTACAATA-AA
1 AAATAATAAAAAACTA-AATACAA
*
1365310 AAATCAAATAAACAACTAAATACAA
1 AAAT--AATAAAAAACTAAATACAA
* *
1365335 ATATAATAAAAAAATAAA
1 AAATAATAAAAAACTAAA
1365353 ATCTATCGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 16 0.46
24 4 0.11
25 15 0.43
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.20
Consensus pattern (23 bp):
AAATAATAAAAAACTAAATACAA
Found at i:1367469 original size:9 final size:9
Alignment explanation
Indices: 1367455--1367504 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
1367445 CTGCAAAAAA
1367455 AAATTAAAT
1 AAATTAAAT
1367464 AAATTAAAT
1 AAATTAAAT
1367473 --ATTAAA-
1 AAATTAAAT
1367479 AAATTTAAAT
1 AAA-TTAAAT
*
1367489 -ACTTAAAT
1 AAATTAAAT
1367497 AAATTAAA
1 AAATTAAA
1367505 AACAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
7 6 0.18
8 7 0.21
9 21 0.62
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (9 bp):
AAATTAAAT
Found at i:1367478 original size:16 final size:16
Alignment explanation
Indices: 1367457--1367504 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 16
1367447 GCAAAAAAAA
1367457 ATTAAATAAATTAAAT
1 ATTAAATAAATTAAAT
1367473 ATTAAA-AAATTTAAAT
1 ATTAAATAAA-TTAAAT
1367489 ACTTAAATAAATTAAA
1 A-TTAAATAAATTAAA
1367505 AACAAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.10
16 13 0.45
17 10 0.34
18 3 0.10
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:1367494 original size:24 final size:26
Alignment explanation
Indices: 1367451--1367506 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
1367441 ATATCTGCAA
1367451 AAAAAAATTAAATAAATTAAAT-ATT
1 AAAAAAATTAAATAAATTAAATAATT
* *
1367476 AAAAAATTTAAAT-ACTTAAATAAATT
1 AAAAAAATTAAATAAATTAAAT-AATT
1367502 AAAAA
1 AAAAA
1367507 CAAAATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 7 0.26
25 12 0.44
26 8 0.30
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (26 bp):
AAAAAAATTAAATAAATTAAATAATT
Found at i:1372812 original size:160 final size:160
Alignment explanation
Indices: 1372638--1372964 Score: 627
Period size: 160 Copynumber: 2.0 Consensus size: 160
1372628 TATATGTAAT
1372638 TTTTTTGTATGTCACGTTGTATGCTATTTTTTTAAATTTTGTTTTTGTTTAATTAATTTTGACAT
1 TTTTTTGTATGTCACGTTGTATGCTATTTTTTTAAATTTTGTTTTTGTTTAATTAATTTTGACAT
1372703 GACATCCTTTTTTGCACGATTCGCATGGTAACCTCATTTGCATAACTCGACATATTACATAATTG
66 GACATCCTTTTTTGCACGATTCGCATGGTAACCTCATTTGCATAACTCGACATATTACATAATTG
1372768 AATTAAGGGTAATACACTTTTAATTTAAAA
131 AATTAAGGGTAATACACTTTTAATTTAAAA
*
1372798 TTTTTTGTATGTCACGTTGTATGCTATTTTTTTTAATTTTGTTTTTGTTTAATTAATTTTGACAT
1 TTTTTTGTATGTCACGTTGTATGCTATTTTTTTAAATTTTGTTTTTGTTTAATTAATTTTGACAT
*
1372863 GACATCCTTTTTTGCACGATTCGCATGGTAACCTCATTTGCATAACTCGACATATTATATAATTG
66 GACATCCTTTTTTGCACGATTCGCATGGTAACCTCATTTGCATAACTCGACATATTACATAATTG
1372928 AATTAAGGGTAATACACTTTTAATTTAAAA
131 AATTAAGGGTAATACACTTTTAATTTAAAA
1372958 TTATTTT
1 TT-TTTT
1372965 AAGTGAGTTG
Statistics
Matches: 164, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
160 160 0.98
161 4 0.02
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.48
Consensus pattern (160 bp):
TTTTTTGTATGTCACGTTGTATGCTATTTTTTTAAATTTTGTTTTTGTTTAATTAATTTTGACAT
GACATCCTTTTTTGCACGATTCGCATGGTAACCTCATTTGCATAACTCGACATATTACATAATTG
AATTAAGGGTAATACACTTTTAATTTAAAA
Found at i:1374533 original size:45 final size:47
Alignment explanation
Indices: 1374460--1374565 Score: 144
Period size: 45 Copynumber: 2.3 Consensus size: 47
1374450 TTATTTTTCG
*
1374460 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTA-GACTTA
1 TTTTTTGAAT-AATGCATGCGAACTAGATATCATGCGGTTAGGACTTA
* * *
1374507 TTTTTTGAATAA-GCATGCGAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTTGAATAATGCATGCGAACTAGATATCATGCGGTTAGGACTTA
1374553 TTTTTGTGAATAA
1 TTTTT-TGAATAA
1374566 CAAAGCATGG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
45 26 0.49
46 11 0.21
47 16 0.30
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (47 bp):
TTTTTTGAATAATGCATGCGAACTAGATATCATGCGGTTAGGACTTA
Found at i:1384211 original size:10 final size:9
Alignment explanation
Indices: 1384196--1384308 Score: 61
Period size: 10 Copynumber: 11.7 Consensus size: 9
1384186 ATTTCGCTTG
1384196 AAAAAGAAA
1 AAAAAGAAA
1384205 TAAAAAGAGAA
1 -AAAAAGA-AA
1384216 AAAAAGAAA
1 AAAAAGAAA
**
1384225 AAAGTGAAAA
1 AAAAAG-AAA
1384235 AAATAATGAAA
1 AAA-AA-GAAA
1384246 AAATAATGAAA
1 AAA-AA-GAAA
1384257 AAAAAG--A
1 AAAAAGAAA
*
1384264 GAAAAGAAA
1 AAAAAGAAA
*
1384273 AAATGATGAAA
1 AAA--AAGAAA
1384284 AAAGAA-AAA
1 AAA-AAGAAA
1384293 GAAAAAGAAA
1 -AAAAAGAAA
*
1384303 TAAAAG
1 AAAAAG
1384309 GGGGGTTCAA
Statistics
Matches: 84, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
7 6 0.07
9 20 0.24
10 30 0.36
11 27 0.32
12 1 0.01
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:1384244 original size:12 final size:12
Alignment explanation
Indices: 1384229--1384260 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
1384219 AAGAAAAAAG
1384229 TGAAAAAAATAA
1 TGAAAAAAATAA
1384241 TG-AAAAAATAA
1 TGAAAAAAATAA
1384252 TGAAAAAAA
1 TGAAAAAAA
1384261 AGAGAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (12 bp):
TGAAAAAAATAA
Found at i:1384261 original size:27 final size:25
Alignment explanation
Indices: 1384231--1384298 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 25
1384221 GAAAAAAGTG
* *
1384231 AAAAAAATAATGAAAAAATAATGAA
1 AAAAAAAAAAAGAAAAAATAATGAA
*
1384256 AAAAAAGAGAAAAGAAAAAATGATG-A
1 AAAAAA-A-AAAAGAAAAAATAATGAA
*
1384282 AAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAGAAAAA
1384299 GAAATAAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 10 0.27
25 7 0.19
26 7 0.19
27 13 0.35
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (25 bp):
AAAAAAAAAAAGAAAAAATAATGAA
Found at i:1384277 original size:24 final size:24
Alignment explanation
Indices: 1384217--1384298 Score: 82
Period size: 24 Copynumber: 3.4 Consensus size: 24
1384207 AAAAGAGAAA
1384217 AAAAGAAAAAAGTGAAAAAAATA-ATG
1 AAAAGAAAAAA-TGAAAAAAA-AGA-G
*
1384243 -AAA-AAATAATGAAAAAAAAGAG
1 AAAAGAAAAAATGAAAAAAAAGAG
*
1384265 AAAAGAAAAAATGATGAAAAAAGA-
1 AAAAGAAAAAATGA-AAAAAAAGAG
1384289 AAAAGAAAAA
1 AAAAGAAAAA
1384299 GAAATAAAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
22 2 0.04
23 13 0.27
24 23 0.47
25 11 0.22
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.09
Consensus pattern (24 bp):
AAAAGAAAAAATGAAAAAAAAGAG
Found at i:1385649 original size:37 final size:36
Alignment explanation
Indices: 1385585--1385659 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 36
1385575 AAACAAGTCA
*
1385585 ATCTTAAGCCTTCACGAAGAGTGGTGAAGCAAA-TC
1 ATCTTAAGCCTTCACGAAGAGTAGTGAAGCAAACTC
*
1385620 ATCTATAAGCCTTCATGGAAGAGTAGTGAAGCAAACTC
1 ATCT-TAAGCCTTCA-CGAAGAGTAGTGAAGCAAACTC
1385658 AT
1 AT
1385660 TTTATGAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
35 4 0.11
36 10 0.29
37 17 0.49
38 4 0.11
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (36 bp):
ATCTTAAGCCTTCACGAAGAGTAGTGAAGCAAACTC
Found at i:1385729 original size:51 final size:55
Alignment explanation
Indices: 1385670--1385976 Score: 317
Period size: 55 Copynumber: 5.7 Consensus size: 55
1385660 TTTATGAAGA
* *
1385670 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTG-A-A-T-A
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * *
1385721 TCGAGTCCTATACTCTCTGAGGGAATAGGGAACAGACCCGTTTGTTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * * * *
1385776 TCGAGT--TCTACTCCCTGAAGCAAGAGGGAGC-GAGCCCGTTTGTTGAAGACTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGA-CCCGTTTGTTGAAGATTGT
* * * * *
1385829 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACTCATTT-TATGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGT-TGAAGATTGT
* * * ** *
1385884 TCGAGTTCTATACTCCCTGAATGAATAGGGAGCGGACCCGTTTACTAAAGATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* *
1385939 TCGAGTCTTATACTC-CTTGAACGAATAGGGAGCGGACC
1 TCGAGTCCTATACTCTC-TGAAGGAATAGGGAGCGGACC
1385977 AGTCATTTGA
Statistics
Matches: 213, Mismatches: 32, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
51 43 0.20
52 3 0.01
53 44 0.21
54 3 0.01
55 119 0.56
56 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (55 bp):
TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
Found at i:1391917 original size:15 final size:15
Alignment explanation
Indices: 1391897--1391927 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1391887 CAACAAATAG
1391897 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1391912 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1391927 A
1 A
1391928 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1392401 original size:51 final size:50
Alignment explanation
Indices: 1392335--1392439 Score: 158
Period size: 51 Copynumber: 2.1 Consensus size: 50
1392325 AAAATTACAC
1392335 AAATGATATTACAATTATAAGATATTATTTTATCGAGTC-TCTTGATTATTA
1 AAATGATATTACAATTATAAGATATTATTTT-TCGAGTCTTCTT-ATTATTA
* * *
1392386 AAATGATCTTTCAATTATAAGATATTATTTTTCTAGTCTTCTTATTATTA
1 AAATGATATTACAATTATAAGATATTATTTTTCGAGTCTTCTTATTATTA
1392436 AAAT
1 AAAT
1392440 TTAAAAAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
50 17 0.34
51 33 0.66
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.48
Consensus pattern (50 bp):
AAATGATATTACAATTATAAGATATTATTTTTCGAGTCTTCTTATTATTA
Found at i:1396346 original size:3 final size:3
Alignment explanation
Indices: 1396338--1396362 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1396328 TGTAGATGAT
1396338 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1396363 CCGAAAGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1398500 original size:100 final size:97
Alignment explanation
Indices: 1398295--1398492 Score: 353
Period size: 100 Copynumber: 2.0 Consensus size: 97
1398285 ATAGAAGGGA
1398295 GAGAAATCCAGATGCTAGCATTTTGTTATTATCCGACGGTGCTTCCAATGAACGACATCATTCAA
1 GAGAAATCCAGATGCTAGCATTTTGTTATTATCCGACGGTGCTTCCAATGAACGACATCATTCAA
*
1398360 CCCGGGAGGGGGGGATTGCTGAAGCTAAAAGTTGG
66 CCC--G-GGGGGGGATTGCTGAAGCTAAAACTTGG
1398395 GAGAAATCCAGATGCTAGCATTTTGTTATTATCCGACGGTGCTTCCAATGAACGACATCATTCAA
1 GAGAAATCCAGATGCTAGCATTTTGTTATTATCCGACGGTGCTTCCAATGAACGACATCATTCAA
1398460 CCC-GGGGGGGATTGCTGAAGCTAAAACTTGG
66 CCCGGGGGGGGATTGCTGAAGCTAAAACTTGG
1398491 GA
1 GA
1398493 AGAAGAAAAC
Statistics
Matches: 97, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
96 29 0.30
100 68 0.70
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (97 bp):
GAGAAATCCAGATGCTAGCATTTTGTTATTATCCGACGGTGCTTCCAATGAACGACATCATTCAA
CCCGGGGGGGGATTGCTGAAGCTAAAACTTGG
Found at i:1402917 original size:29 final size:30
Alignment explanation
Indices: 1402880--1402940 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1402870 AAATTTGACC
*
1402880 AGTGACTAAAATAT-AAGTTT-AGAAAGTTT
1 AGTGACTAAAATATGAACTTTGA-AAAGTTT
*
1402909 AGTGGCTAAAATATGAACTTTGAAAAGTTT
1 AGTGACTAAAATATGAACTTTGAAAAGTTT
1402939 AG
1 AG
1402941 GACCCAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 13 0.46
30 14 0.50
31 1 0.04
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.33
Consensus pattern (30 bp):
AGTGACTAAAATATGAACTTTGAAAAGTTT
Found at i:1402938 original size:30 final size:29
Alignment explanation
Indices: 1402880--1402940 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
1402870 AAATTTGACC
*
1402880 AGTGACTAAAATATAAGTTTAGAAAGTTT
1 AGTGACTAAAATATAACTTTAGAAAGTTT
*
1402909 AGTGGCTAAAATATGAACTTT-GAAAAGTTT
1 AGTGACTAAAATAT-AACTTTAG-AAAGTTT
1402939 AG
1 AG
1402941 GACCCAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.33
Consensus pattern (29 bp):
AGTGACTAAAATATAACTTTAGAAAGTTT
Found at i:1405485 original size:18 final size:17
Alignment explanation
Indices: 1405462--1405495 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1405452 CAGTCTGTTT
1405462 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
1405480 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
1405496 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:1406133 original size:29 final size:30
Alignment explanation
Indices: 1406078--1406138 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
1406068 ATTTTGGGTC
*
1406078 CTAAACTTTTCAAAGTTCATACTTTAGCCA
1 CTAAACTTTTCAAACTTCATACTTTAGCCA
* *
1406108 CTAAAC-TTTCTAAACTT-ATATTTTAGTCA
1 CTAAACTTTTC-AAACTTCATACTTTAGCCA
1406137 CT
1 CT
1406139 GGTCAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (30 bp):
CTAAACTTTTCAAACTTCATACTTTAGCCA
Found at i:1407222 original size:16 final size:17
Alignment explanation
Indices: 1407196--1407229 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1407186 TATCGCCGAA
1407196 AAAATTTTACTACTCAC
1 AAAATTTTACTACTCAC
*
1407213 AAAA-TTTACTATTCAC
1 AAAATTTTACTACTCAC
1407229 A
1 A
1407230 TGAATAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATTTTACTACTCAC
Found at i:1410844 original size:21 final size:21
Alignment explanation
Indices: 1410820--1410863 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1410810 TAGAATCAAA
1410820 TATTGAAATAAATACATTATT
1 TATTGAAATAAATACATTATT
1410841 TATTGAAATAAATACATTATT
1 TATTGAAATAAATACATTATT
1410862 TA
1 TA
1410864 AGTTTATAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (21 bp):
TATTGAAATAAATACATTATT
Found at i:1412870 original size:2 final size:2
Alignment explanation
Indices: 1412863--1412917 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1412853 TATTTTTATC
1412863 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1412905 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1412918 GATAATGATG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1419439 original size:28 final size:28
Alignment explanation
Indices: 1419397--1419470 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
1419387 AAAATTCCCA
*
1419397 AAAAAACACCTTAAACTCCAAAAAATCTC
1 AAAAAACTCC-TAAACTCCAAAAAATCTC
* *
1419426 AAAAAACTCCTAAATTCCTAAAAATCTC
1 AAAAAACTCCTAAACTCCAAAAAATCTC
* *
1419454 AAAAAAATCATAAACTC
1 AAAAAACTCCTAAACTC
1419471 TAAATTATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 30 0.77
29 9 0.23
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.20
Consensus pattern (28 bp):
AAAAAACTCCTAAACTCCAAAAAATCTC
Found at i:1419460 original size:29 final size:30
Alignment explanation
Indices: 1419386--1419460 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 30
1419376 ATAAAATTAT
* *
1419386 TAAAATTCCCAAAAAAACACCTTAAACTCC
1 TAAAAATCTCAAAAAAACACCTTAAACTCC
* * *
1419416 AAAAAATCTC-AAAAAACTCC-TAAATTCC
1 TAAAAATCTCAAAAAAACACCTTAAACTCC
1419444 TAAAAATCTCAAAAAAA
1 TAAAAATCTCAAAAAAA
1419461 TCATAAACTC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 16 0.42
29 15 0.39
30 7 0.18
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (30 bp):
TAAAAATCTCAAAAAAACACCTTAAACTCC
Found at i:1420862 original size:2 final size:2
Alignment explanation
Indices: 1420855--1420880 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1420845 TATGTTTGAA
1420855 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1420881 TTGTTGCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1421109 original size:22 final size:22
Alignment explanation
Indices: 1421068--1421109 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1421058 CTTCTTGGTA
*
1421068 AATATTTAATTATTTGATAATT
1 AATATTTAATTATTTCATAATT
1421090 AATATTTAA-TATTTTCATAA
1 AATATTTAATTA-TTTCATAA
1421110 GTGAACTGCT
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:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
AATATTTAATTATTTCATAATT
Found at i:1422320 original size:33 final size:33
Alignment explanation
Indices: 1422278--1422582 Score: 355
Period size: 33 Copynumber: 9.2 Consensus size: 33
1422268 ACCTCCGTTG
* * *
1422278 ATTCAGGTTTTGGTAACTCAGGAGTTTTGGGTA
1 ATTCTGGTTTTGGTAACTCAGGAATTTTAGGTA
* *
1422311 ATTTTGGTTTTGGTATCTC-GAGAATTTTAGGTA
1 ATTCTGGTTTTGGTAACTCAG-GAATTTTAGGTA
* *
1422344 ATTCTGGTTTTGGTAATTCAGGAACTTTAGGTA
1 ATTCTGGTTTTGGTAACTCAGGAATTTTAGGTA
*
1422377 ATTCTGGTTTTGGTAACTCGGGAATTTTAGGTA
1 ATTCTGGTTTTGGTAACTCAGGAATTTTAGGTA
* *
1422410 ATTCTGGCTTTGGTAACTCAAGAACTTTT-GGTA
1 ATTCTGGTTTTGGTAACTCAGGAA-TTTTAGGTA
*
1422443 ATTCTGGTTTTGGTAAATCAGGAATTTTAGGTA
1 ATTCTGGTTTTGGTAACTCAGGAATTTTAGGTA
*
1422476 ATTCTGGTTTTGGTAATTCAGGAATTTTAGGTA
1 ATTCTGGTTTTGGTAACTCAGGAATTTTAGGTA
* * *
1422509 ATTTTGGTTTTGGTAACTCGGGAATAGTT-GGTA
1 ATTCTGGTTTTGGTAACTCAGGAAT-TTTAGGTA
* * * * *
1422542 TTTCAGGAGCTTTGGTCACCTCAGGAACTTTAGGTA
1 ATTC-TG-GTTTTGGT-AACTCAGGAATTTTAGGTA
1422578 ATTCT
1 ATTCT
1422583 AGCTTCGTTA
Statistics
Matches: 230, Mismatches: 33, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
32 5 0.02
33 193 0.84
34 8 0.03
35 9 0.04
36 15 0.07
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (33 bp):
ATTCTGGTTTTGGTAACTCAGGAATTTTAGGTA
Found at i:1422386 original size:99 final size:98
Alignment explanation
Indices: 1422278--1422582 Score: 394
Period size: 99 Copynumber: 3.1 Consensus size: 98
1422268 ACCTCCGTTG
* * * *
1422278 ATTCAGGTTTTGGTAACTCAGGAGTTTTGGGTAATTTTGGTTTTGGTATCTCGAGAATTTTAGGT
1 ATTCTGGTTTTGGTAACTCAGGAATTTTAGGTAATTTTGGTTTTGGTAACTCGAGAATTTT-GGT
*
1422343 AATTCTGGTTTTGGTAATTCAGGAACTTTAGGTA
65 AATTCTGGTTTTGGTAAATCAGGAACTTTAGGTA
* * * *
1422377 ATTCTGGTTTTGGTAACTCGGGAATTTTAGGTAATTCTGGCTTTGGTAACTCAAGAACTTTTGGT
1 ATTCTGGTTTTGGTAACTCAGGAATTTTAGGTAATTTTGGTTTTGGTAACTCGAGAA-TTTTGGT
*
1422442 AATTCTGGTTTTGGTAAATCAGGAATTTTAGGTA
65 AATTCTGGTTTTGGTAAATCAGGAACTTTAGGTA
* * *
1422476 ATTCTGGTTTTGGTAATTCAGGAATTTTAGGTAATTTTGGTTTTGGTAACTCGGGAATAGTTGGT
1 ATTCTGGTTTTGGTAACTCAGGAATTTTAGGTAATTTTGGTTTTGGTAACTCGAGAAT-TTTGGT
* * * **
1422541 ATTTCAGGAGCTTTGGTCACCTCAGGAACTTTAGGTA
65 AATTC-TG-GTTTTGGT-AAATCAGGAACTTTAGGTA
1422578 ATTCT
1 ATTCT
1422583 AGCTTCGTTA
Statistics
Matches: 178, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
98 1 0.01
99 144 0.81
100 5 0.03
101 7 0.04
102 21 0.12
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (98 bp):
ATTCTGGTTTTGGTAACTCAGGAATTTTAGGTAATTTTGGTTTTGGTAACTCGAGAATTTTGGTA
ATTCTGGTTTTGGTAAATCAGGAACTTTAGGTA
Found at i:1422773 original size:33 final size:33
Alignment explanation
Indices: 1422736--1422806 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
1422726 CACTTTTGGA
1422736 AACTCAGGAACCTTAGGTAA-TTCAGGCTTTGAC
1 AACTCAGGAACCTTAGG-AAGTTCAGGCTTTGAC
*
1422769 AACTCAGGAACCTTAGGAAGTTTAGGCTTTGAC
1 AACTCAGGAACCTTAGGAAGTTCAGGCTTTGAC
1422802 AACTC
1 AACTC
1422807 TGGCATTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.06
33 34 0.94
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (33 bp):
AACTCAGGAACCTTAGGAAGTTCAGGCTTTGAC
Found at i:1422830 original size:84 final size:84
Alignment explanation
Indices: 1422684--1422880 Score: 272
Period size: 84 Copynumber: 2.3 Consensus size: 84
1422674 GCAACTTAAT
* *
1422684 CAACTCAGGAACCTTTGGAAGTTCAGGCTTCGGCAACTCTGGCACTTTTGGAAACTCAGGAACCT
1 CAACTCAGGAACCTTAGGAAGTTCAGGCTTCGACAACTCTGGCACTTTTGGAAACTCAGGAACCT
1422749 TAGGTAATTCAGGCTTTGA
66 TAGGTAATTCAGGCTTTGA
* * **
1422768 CAACTCAGGAACCTTAGGAAGTTTAGGCTTTGACAACTCTGGCA-TTGTTGGAAACTTTGGAACC
1 CAACTCAGGAACCTTAGGAAGTTCAGGCTTCGACAACTCTGGCACTT-TTGGAAACTCAGGAACC
*
1422832 TTAGGTAATTCAGGCTTTGG
65 TTAGGTAATTCAGGCTTTGA
* * *
1422852 TAACTCTGGAACTTTAGGCAA-TTCAGGCT
1 CAACTCAGGAACCTTAGG-AAGTTCAGGCT
1422881 CAGGTACCTC
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
83 2 0.02
84 96 0.96
85 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.29
Consensus pattern (84 bp):
CAACTCAGGAACCTTAGGAAGTTCAGGCTTCGACAACTCTGGCACTTTTGGAAACTCAGGAACCT
TAGGTAATTCAGGCTTTGA
Found at i:1422869 original size:33 final size:33
Alignment explanation
Indices: 1422815--1422880 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1422805 TCTGGCATTG
* *
1422815 TTGGAAACTTTGGAACCTTAGGTAATTCAGGCT
1 TTGGAAACTCTGGAACCTTAGGCAATTCAGGCT
* *
1422848 TTGGTAACTCTGGAACTTTAGGCAATTCAGGCT
1 TTGGAAACTCTGGAACCTTAGGCAATTCAGGCT
1422881 CAGGTACCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (33 bp):
TTGGAAACTCTGGAACCTTAGGCAATTCAGGCT
Found at i:1422896 original size:84 final size:84
Alignment explanation
Indices: 1422684--1422902 Score: 237
Period size: 84 Copynumber: 2.6 Consensus size: 84
1422674 GCAACTTAAT
* * *
1422684 CAACTCAGGAACCTTTGGAAGTTCAGGCTTC-GGCAACTCTGGCACTT-TTGGAAACTCAGGAAC
1 CAACTCAGGAACCTTAGGAAGTTCAGGC-TCAGACAACTCAGGCA-TTGTTGGAAACTCAGGAAC
1422747 CTTAGGTAATTCAGGCTTTGA
64 CTTAGGTAATTCAGGCTTTGA
* ** * **
1422768 CAACTCAGGAACCTTAGGAAGTTTAGGCTTTGACAACTCTGGCATTGTTGGAAACTTTGGAACCT
1 CAACTCAGGAACCTTAGGAAGTTCAGGCTCAGACAACTCAGGCATTGTTGGAAACTCAGGAACCT
*
1422833 TAGGTAATTCAGGCTTTGG
66 TAGGTAATTCAGGCTTTGA
* * * ** * *
1422852 TAACTCTGGAACTTTAGGCAA-TTCAGGCTCAGGTACCTCAGGCATTTTTGG
1 CAACTCAGGAACCTTAGG-AAGTTCAGGCTCAGACAACTCAGGCATTGTTGG
1422903 TATTTTAGGC
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
83 3 0.03
84 109 0.96
85 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.30
Consensus pattern (84 bp):
CAACTCAGGAACCTTAGGAAGTTCAGGCTCAGACAACTCAGGCATTGTTGGAAACTCAGGAACCT
TAGGTAATTCAGGCTTTGA
Found at i:1426359 original size:51 final size:50
Alignment explanation
Indices: 1426304--1426413 Score: 150
Period size: 51 Copynumber: 2.2 Consensus size: 50
1426294 GTGATTATGG
* * *
1426304 TTTTGGTATCTCGGGAA-TATTAGGTAATTCTGGTTTTTGTAACTCTGGAAA
1 TTTTGGTAT-TCGGGAACT-TTAGGTAATTCTGGCTTTGGTAACTCAGGAAA
*
1426355 TTTTGGTAATTCGGGAACTTTAGGTAATTCTGGCTTTGGTAACTCAGGAAC
1 TTTTGGT-ATTCGGGAACTTTAGGTAATTCTGGCTTTGGTAACTCAGGAAA
1426406 TTTTGGTA
1 TTTTGGTA
1426414 ATTATGGTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
50 1 0.02
51 49 0.92
52 3 0.06
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.42
Consensus pattern (50 bp):
TTTTGGTATTCGGGAACTTTAGGTAATTCTGGCTTTGGTAACTCAGGAAA
Found at i:1426363 original size:18 final size:18
Alignment explanation
Indices: 1426337--1426758 Score: 82
Period size: 18 Copynumber: 25.1 Consensus size: 18
1426327 GTAATTCTGG
* *
1426337 TTTTTGTAACTCTGGAAA
1 TTTTGGTAACTCTGGAAC
* *
1426355 TTTTGGTAATTCGGGAAC
1 TTTTGGTAACTCTGGAAC
* *
1426373 TTTAGGTAATTCTGG--C
1 TTTTGGTAACTCTGGAAC
*
1426389 -TTTGGTAACTCAGGAAC
1 TTTTGGTAACTCTGGAAC
* *
1426406 TTTTGGTAATTATGG---
1 TTTTGGTAACTCTGGAAC
* * **
1426421 TTTTGATAATTCACGAAC
1 TTTTGGTAACTCTGGAAC
* * *
1426439 TTTAGGTAATTTTGG--C
1 TTTTGGTAACTCTGGAAC
* * *
1426455 -TTCGATAATTCAT-GAAC
1 TTTTGGTAACTC-TGGAAC
*
1426472 TTTTGGTAATTCTGG--C
1 TTTTGGTAACTCTGGAAC
*
1426488 -TTTGATAACT-TAGGAAC
1 TTTTGGTAACTCT-GGAAC
* *
1426505 TTTAGGTAATTCT-G-AC
1 TTTTGGTAACTCTGGAAC
*
1426521 -TTTGGTAACTCAGGAAC
1 TTTTGGTAACTCTGGAAC
*
1426538 TTTTGGTAATTCTGG---
1 TTTTGGTAACTCTGGAAC
* * **
1426553 TTTTGATAATTCAAGAAC
1 TTTTGGTAACTCTGGAAC
*
1426571 TTTTGGTAATTCTGG---
1 TTTTGGTAACTCTGGAAC
* * **
1426586 TTTTGATAATTCAAGAAC
1 TTTTGGTAACTCTGGAAC
*
1426604 TTTTGGTAATTCT-G-A-
1 TTTTGGTAACTCTGGAAC
* *
1426619 TTTTGGTAACTCGGGAGC
1 TTTTGGTAACTCTGGAAC
* ** * *
1426637 ATTTGGTATTTCAGGAGC
1 TTTTGGTAACTCTGGAAC
* *
1426655 -TTTGGTCACCTCAGGAAC
1 TTTTGGT-AACTCTGGAAC
* * *
1426673 TTTAGGCAATTCTGG--C
1 TTTTGGTAACTCTGGAAC
* * *
1426689 TTCT-GTAATTCAGGAAC
1 TTTTGGTAACTCTGGAAC
* *
1426706 TTTTGGTAACTCAGGAGC
1 TTTTGGTAACTCTGGAAC
* * *
1426724 TTTAGGCAATTCT-G-AC
1 TTTTGGTAACTCTGGAAC
*
1426740 -TTCGGTAACTCTGGAAC
1 TTTTGGTAACTCTGGAAC
1426757 TT
1 TT
1426759 CGACTTCTTT
Statistics
Matches: 291, Mismatches: 77, Indels: 72
0.66 0.17 0.16
Matches are distributed among these distances:
14 1 0.00
15 102 0.35
16 14 0.05
17 21 0.07
18 148 0.51
19 5 0.02
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.40
Consensus pattern (18 bp):
TTTTGGTAACTCTGGAAC
Found at i:1426393 original size:33 final size:33
Alignment explanation
Indices: 1426356--1426714 Score: 353
Period size: 33 Copynumber: 10.8 Consensus size: 33
1426346 CTCTGGAAAT
* *
1426356 TTTGGTAATTCGGGAACTTTAGGTAATTCTGGC
1 TTTGGTAATTCAGGAACTTTTGGTAATTCTGGC
* * *
1426389 TTTGGTAACTCAGGAACTTTTGGTAATTATGGT
1 TTTGGTAATTCAGGAACTTTTGGTAATTCTGGC
* * * *
1426422 TTTGATAATTCACGAACTTTAGGTAATTTTGGC
1 TTTGGTAATTCAGGAACTTTTGGTAATTCTGGC
* * *
1426455 TTCGATAATTCATGAACTTTTGGTAATTCTGGC
1 TTTGGTAATTCAGGAACTTTTGGTAATTCTGGC
* * *
1426488 TTTGATAACTT-AGGAACTTTAGGTAATTCTGAC
1 TTTGGTAA-TTCAGGAACTTTTGGTAATTCTGGC
* *
1426521 TTTGGTAACTCAGGAACTTTTGGTAATTCTGGT
1 TTTGGTAATTCAGGAACTTTTGGTAATTCTGGC
* * *
1426554 TTTGATAATTCAAGAACTTTTGGTAATTCTGGT
1 TTTGGTAATTCAGGAACTTTTGGTAATTCTGGC
* * **
1426587 TTTGATAATTCAAGAACTTTTGGTAATTCTGAT
1 TTTGGTAATTCAGGAACTTTTGGTAATTCTGGC
* * * * * *
1426620 TTTGGTAACTCGGGAGCATTTGGTATTTCAGGAGC
1 TTTGGTAATTCAGGAACTTTTGGTAATTC-TG-GC
** * *
1426655 TTTGGTCACCTCAGGAACTTTAGGCAATTCTGGC
1 TTTGGT-AATTCAGGAACTTTTGGTAATTCTGGC
1426689 TTCT-GTAATTCAGGAACTTTTGGTAA
1 TT-TGGTAATTCAGGAACTTTTGGTAA
1426715 CTCAGGAGCT
Statistics
Matches: 270, Mismatches: 50, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
32 1 0.00
33 236 0.87
34 9 0.03
35 8 0.03
36 16 0.06
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.41
Consensus pattern (33 bp):
TTTGGTAATTCAGGAACTTTTGGTAATTCTGGC
Found at i:1426414 original size:51 final size:51
Alignment explanation
Indices: 1426323--1426758 Score: 217
Period size: 51 Copynumber: 8.7 Consensus size: 51
1426313 CTCGGGAATA
* * * * * *
1426323 TTAGGTAATTCTGGTTTTTGTAACTCTGGAAATTTTGGTAATTCGGGAACT
1 TTAGGTAATTCTGGCTTTGGTAATTCAGGAACTTTTGGTAATTCAGGAACT
*
1426374 TTAGGTAATTCTGGCTTTGGTAACTCAGGAACTTTTGGTAATT-ATGG---T
1 TTAGGTAATTCTGGCTTTGGTAATTCAGGAACTTTTGGTAATTCA-GGAACT
* * * * ** * * *
1426422 TTTGATAATTCACGAACTTTAGGTAATTTTGG--C-TTCGATAATTCATGAACT
1 TTAGGTAATTC-TG-GCTTT-GGTAATTCAGGAACTTTTGGTAATTCAGGAACT
* * * *
1426473 TTTGGTAATTCTGGCTTTGATAACTT-AGGAACTTTAGGTAATTC-TG-ACT
1 TTAGGTAATTCTGGCTTTGGTAA-TTCAGGAACTTTTGGTAATTCAGGAACT
* * * * *
1426522 TT-GGTAACTCAGGAACTTTTGGTAATTCTGG---TTTTGATAATTCAAGAACT
1 TTAGGTAATTCTGG--C-TTTGGTAATTCAGGAACTTTTGGTAATTCAGGAACT
* * * * *
1426572 TTTGGTAATTCTGGTTTTGATAATTCAAGAACTTTTGGTAATTC-TG-A-T
1 TTAGGTAATTCTGGCTTTGGTAATTCAGGAACTTTTGGTAATTCAGGAACT
* * * * * **
1426620 TTTGGTAACTCGGGAGCATTTGGTATTTCAGGAGC-TTTGGTCACCTCAGGAACT
1 TTAGGTAATTC-TG-GC-TTTGGTAATTCAGGAACTTTTGGT-AATTCAGGAACT
* * *
1426674 TTAGGCAATTCTGGCTTCT-GTAATTCAGGAACTTTTGGTAACTCAGGAGCT
1 TTAGGTAATTCTGGCTT-TGGTAATTCAGGAACTTTTGGTAATTCAGGAACT
* * * * *
1426725 TTAGGCAATTCTGACTTCGGTAACTCTGGAACTT
1 TTAGGTAATTCTGGCTTTGGTAATTCAGGAACTT
1426759 CGACTTCTTT
Statistics
Matches: 294, Mismatches: 59, Indels: 64
0.71 0.14 0.15
Matches are distributed among these distances:
48 66 0.22
49 17 0.06
50 24 0.08
51 166 0.56
52 10 0.03
53 2 0.01
54 9 0.03
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.40
Consensus pattern (51 bp):
TTAGGTAATTCTGGCTTTGGTAATTCAGGAACTTTTGGTAATTCAGGAACT
Found at i:1426624 original size:15 final size:15
Alignment explanation
Indices: 1426509--1426627 Score: 76
Period size: 15 Copynumber: 7.3 Consensus size: 15
1426499 AGGAACTTTA
*
1426509 GGTAATTCTGACTTT
1 GGTAATTCTGATTTT
* *
1426524 GGTAACTCAGGAACTTTT
1 GGTAATTC-TG-A-TTTT
*
1426542 GGTAATTCTGGTTTT
1 GGTAATTCTGATTTT
* *
1426557 GATAATTCAAGAACTTTT
1 GGTAATTC-TG-A-TTTT
*
1426575 GGTAATTCTGGTTTT
1 GGTAATTCTGATTTT
* *
1426590 GATAATTCAAGAACTTTT
1 GGTAATTC-TG-A-TTTT
1426608 GGTAATTCTGATTTT
1 GGTAATTCTGATTTT
1426623 GGTAA
1 GGTAA
1426628 CTCGGGAGCA
Statistics
Matches: 78, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
15 38 0.49
16 4 0.05
17 4 0.05
18 32 0.41
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (15 bp):
GGTAATTCTGATTTT
Found at i:1426848 original size:51 final size:51
Alignment explanation
Indices: 1426788--1426900 Score: 147
Period size: 51 Copynumber: 2.2 Consensus size: 51
1426778 CAACTTAGTC
* * *
1426788 AACTCAGGAACCTTTGGAAGTTCAGGCTTT-GACAACTCTGGCACTTTTGGA
1 AACTCAGGAACCTTAGGAAGTTCAAGCTTTGGA-AACTCTGGCACTGTTGGA
** *
1426839 AACTCAGGAACCTTAGTTAGTTCAAGCTTTGGAAACTCTGGCACTGTTGGC
1 AACTCAGGAACCTTAGGAAGTTCAAGCTTTGGAAACTCTGGCACTGTTGGA
*
1426890 AACTCTGGAAC
1 AACTCAGGAAC
1426901 TTCAGGCAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 52 0.96
52 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (51 bp):
AACTCAGGAACCTTAGGAAGTTCAAGCTTTGGAAACTCTGGCACTGTTGGA
Found at i:1427573 original size:22 final size:21
Alignment explanation
Indices: 1427548--1427588 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1427538 GCAACTATGA
*
1427548 TTCTGTGTTTTTATTTATTTGT
1 TTCTGTCTTTTTA-TTATTTGT
*
1427570 TTCTTTCTTTTTATTATTT
1 TTCTGTCTTTTTATTATTT
1427589 TATTTTGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.76
Consensus pattern (21 bp):
TTCTGTCTTTTTATTATTTGT
Found at i:1427840 original size:34 final size:35
Alignment explanation
Indices: 1427794--1427865 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
1427784 ACAACAACAC
*
1427794 TTATTTTTCA-TTTTTTACTTTTATATGTCACATT
1 TTATATTTCATTTTTTTACTTTTATATGTCACATT
1427828 TTATATTTCATTTTTTTACTTTTATATGTCACATT
1 TTATATTTCATTTTTTTACTTTTATATGTCACATT
1427863 TTA
1 TTA
1427866 AATTGTCTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 9 0.25
35 27 0.75
ACGTcount: A:0.22, C:0.11, G:0.03, T:0.64
Consensus pattern (35 bp):
TTATATTTCATTTTTTTACTTTTATATGTCACATT
Found at i:1429695 original size:33 final size:33
Alignment explanation
Indices: 1429658--1429949 Score: 367
Period size: 33 Copynumber: 8.9 Consensus size: 33
1429648 CAGTTGATTA
* * *
1429658 TGGTTTTGTTAATTCAGGAGTTTTGGGTAATTC
1 TGGTTTTGGTAATTCAGGAATTTTAGGTAATTC
*
1429691 TGGTTTTGGT-ATCTCGGGAATTTTAGGTAATTC
1 TGGTTTTGGTAAT-TCAGGAATTTTAGGTAATTC
* * * *
1429724 TGGCTTTGATAACTCTGGAACTTTT-GGTAATTC
1 TGGTTTTGGTAATTCAGGAA-TTTTAGGTAATTC
1429757 TGGTTTTGGTAATTCAGGAATTTTAGGTAATTC
1 TGGTTTTGGTAATTCAGGAATTTTAGGTAATTC
1429790 TGGTTTTGGTAATTCAGGAATTTTAGGTAATTC
1 TGGTTTTGGTAATTCAGGAATTTTAGGTAATTC
* * *
1429823 TGGTTTTGGTAACTCGGGAATTTTAGGTAATTT
1 TGGTTTTGGTAATTCAGGAATTTTAGGTAATTC
** * *
1429856 TGCCTTTGGTAACTCA-GAACATTT-GGTAATTC
1 TGGTTTTGGTAATTCAGGAA-TTTTAGGTAATTC
* *
1429888 TGGTTTTGGTAATTCATGAACTTTAGGTAATTC
1 TGGTTTTGGTAATTCAGGAATTTTAGGTAATTC
*
1429921 TGGTTTTGGTAATTCAGGAACTTTAGGTA
1 TGGTTTTGGTAATTCAGGAATTTTAGGTA
1429950 TTTCAGGAGC
Statistics
Matches: 227, Mismatches: 25, Indels: 14
0.85 0.09 0.05
Matches are distributed among these distances:
32 32 0.14
33 190 0.84
34 5 0.02
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.44
Consensus pattern (33 bp):
TGGTTTTGGTAATTCAGGAATTTTAGGTAATTC
Found at i:1429753 original size:66 final size:66
Alignment explanation
Indices: 1429678--1430018 Score: 364
Period size: 66 Copynumber: 5.1 Consensus size: 66
1429668 AATTCAGGAG
* * *
1429678 TTTTGGGTAATTCTGGTTTTGGT-ATCTCGGGAATTTTAGGTAATTCTGGCTTTGATAACTCTGG
1 TTTT-GGTAATTCTGGTTTTGGTAAT-TCAGGAATTTTAGGTAATTCTGGCTTTGGTAACTCAGG
1429742 AAC
64 AAC
* *
1429745 TTTTGGTAATTCTGGTTTTGGTAATTCAGGAATTTTAGGTAATTCTGGTTTTGGTAATTCAGGAA
1 TTTTGGTAATTCTGGTTTTGGTAATTCAGGAATTTTAGGTAATTCTGGCTTTGGTAACTCAGGAA
1429810 -
66 C
* * * *
1429810 TTTTAGGTAATTCTGGTTTTGGTAACTCGGGAATTTTAGGTAATTTTGCCTTTGGTAACTCA-GA
1 TTTT-GGTAATTCTGGTTTTGGTAATTCAGGAATTTTAGGTAATTCTGGCTTTGGTAACTCAGGA
1429874 AC
65 AC
* * * * *
1429876 ATTTGGTAATTCTGGTTTTGGTAATTCATGAACTTTAGGTAATTCTGGTTTTGGTAATTCAGGAA
1 TTTTGGTAATTCTGGTTTTGGTAATTCAGGAATTTTAGGTAATTCTGGCTTTGGTAACTCAGGAA
1429941 C
66 C
* * * * ** * * ** * * *
1429942 TTTAGGTATTTCAGGAGCTTTGGTCACCTCAGAAACTTTAGGTAATTCTAACTTCGGTAATTCAT
1 TTTTGGTAATTC-TG-GTTTTGGT-AATTCAGGAATTTTAGGTAATTCTGGCTTTGGTAACTCAG
1430007 GAAC
63 GAAC
1430011 TTTTGGTA
1 TTTTGGTA
1430019 GCTTAGGATC
Statistics
Matches: 232, Mismatches: 35, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
65 56 0.24
66 120 0.52
67 7 0.03
68 7 0.03
69 42 0.18
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (66 bp):
TTTTGGTAATTCTGGTTTTGGTAATTCAGGAATTTTAGGTAATTCTGGCTTTGGTAACTCAGGAA
C
Found at i:1430193 original size:33 final size:33
Alignment explanation
Indices: 1430138--1430214 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
1430128 CTCGGGCACT
* *
1430138 TTTGGAAACTCAGGTACCTTAGGTAA-TTCTA-GC
1 TTTGGCAACTCAGGAACCTTAGG-AAGTTC-AGGC
* *
1430171 TTTGGCAACTCATGAACTTTAGGAAGTTCAGGC
1 TTTGGCAACTCAGGAACCTTAGGAAGTTCAGGC
1430204 TTTGGCAACTC
1 TTTGGCAACTC
1430215 TGGCACTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 3 0.08
33 35 0.92
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (33 bp):
TTTGGCAACTCAGGAACCTTAGGAAGTTCAGGC
Found at i:1430202 original size:51 final size:51
Alignment explanation
Indices: 1430093--1430195 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
1430083 CAACTTAGTC
* * * * *
1430093 AACTCAGGAACCTTTGGAAGTTCTGGCTTTGGCAACTCGGGCACTTTTGGA
1 AACTCAGGAACCTTAGGAAGTTCTAGCTTTGGCAACTCAGGAACTTTAGGA
* *
1430144 AACTCAGGTACCTTAGGTAA-TTCTAGCTTTGGCAACTCATGAACTTTAGGA
1 AACTCAGGAACCTTAGG-AAGTTCTAGCTTTGGCAACTCAGGAACTTTAGGA
1430195 A
1 A
1430196 GTTCAGGCTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 42 0.95
52 2 0.05
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.30
Consensus pattern (51 bp):
AACTCAGGAACCTTAGGAAGTTCTAGCTTTGGCAACTCAGGAACTTTAGGA
Done.