Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007989.1 Hibiscus syriacus cultivar Beakdansim tig00110437_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: 510264
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 1 of 2
Found at i:12841 original size:21 final size:19
Alignment explanation
Indices: 12815--12866 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
12805 TTCCATTTCG
*
12815 CGTTGCGATAGTCTATAATGT
1 CGTTGCGATAGTCCA-AAT-T
**
12836 CGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAATT
12855 CGTTGCGATAGT
1 CGTTGCGATAGT
12867 TAAAAAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 11 0.42
20 3 0.12
21 12 0.46
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCCAAATT
Found at i:13473 original size:6 final size:6
Alignment explanation
Indices: 13462--13488 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
13452 TCTCGGGTCA
13462 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
13489 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:13648 original size:19 final size:19
Alignment explanation
Indices: 13588--13651 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
13578 GAATTTTTGT
13588 AACGAATTTGGAAAATCGC
1 AACGAATTTGGAAAATCGC
* * **
13607 AACGATAACTGTAGACTATCGC
1 AACG--AA-TTTGGAAAATCGC
13629 AACGAATTTGGAAAATCGC
1 AACGAATTTGGAAAATCGC
13648 AACG
1 AACG
13652 CGATTTTCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 17 0.50
20 2 0.06
21 2 0.06
22 13 0.38
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (19 bp):
AACGAATTTGGAAAATCGC
Found at i:13683 original size:21 final size:21
Alignment explanation
Indices: 13643--13683 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13633 AATTTGGAAA
** *
13643 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
13664 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
13684 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:13917 original size:2 final size:2
Alignment explanation
Indices: 13910--13940 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13900 TTCGAACATC
13910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13941 AGAATATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15107 original size:24 final size:24
Alignment explanation
Indices: 15078--15133 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
15068 TGAACGGTTC
15078 AGCGGTTCTGGCCGGTTCACTAAT
1 AGCGGTTCTGGCCGGTTCACTAAT
15102 AGCGGTTCTGGCCGGTTCACTAAT
1 AGCGGTTCTGGCCGGTTCACTAAT
15126 AGCGGTTC
1 AGCGGTTC
15134 AACCGATTTA
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:0.16, C:0.25, G:0.30, T:0.29
Consensus pattern (24 bp):
AGCGGTTCTGGCCGGTTCACTAAT
Found at i:18212 original size:20 final size:20
Alignment explanation
Indices: 18168--18213 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
18158 AATAAAAAAA
*
18168 AATTA-AAATATTTTTAATT
1 AATTACAAATATTTTTAAAT
18187 AATTACAAATATTTTTAAAT
1 AATTACAAATATTTTTAAAT
*
18207 ATTTACA
1 AATTACA
18214 TAAAATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTACAAATATTTTTAAAT
Found at i:21613 original size:24 final size:24
Alignment explanation
Indices: 21581--21627 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
21571 TTTAGTCCTA
* *
21581 TTTGCATGTTGTTTTATTTTAATT
1 TTTGCATGTTATTTCATTTTAATT
21605 TTTGCATGTTATTTCATTTTAAT
1 TTTGCATGTTATTTCATTTTAAT
21628 CATTAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.06, G:0.11, T:0.64
Consensus pattern (24 bp):
TTTGCATGTTATTTCATTTTAATT
Found at i:22523 original size:130 final size:130
Alignment explanation
Indices: 22063--22561 Score: 669
Period size: 131 Copynumber: 3.8 Consensus size: 130
22053 TTAATATTGA
* * * *
22063 AAATAGTAATATCTTTTCATTT-AGGTTGGAGTAATAAATGACTGCTTAAAGGCATGAGAGGTCA
1 AAATAGTGATATCTCTTCATTTCA-ATTGGAGTAATAAATGACTGCTTTAAGGCATGAGA-GTCA
* * * * *
22127 TTTATTATCGATTGGAAATAATTAGATATTATAGTTTTCTTTCGAATCAATATTGAATTTTAATA
64 TTTATTCTCAATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAGA
22192 CG
129 CG
* * *
22194 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGATTACTTTAAGGCATGAGAGATCAT
1 AAATAGTGATATCTCTTCATTTCAATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAG-TCAT
* * *
22259 TAATTCTCAATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTTATTTTTAAGAC
65 TTATTCTCAATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAGAC
22324 G
130 G
* * *
22325 GAATAGTGATATCTCTTCATTCCAATTGGAGTAATAAATGACCGCTTTAAGGCATGAGAAGTCAT
1 AAATAGTGATATCTCTTCATTTCAATTGGAGTAATAAATGACTGCTTTAAGGCATGAG-AGTCAT
* * * * *
22390 TTATTCTCAATTGGAAATCATTAGTTATTATCGTTTTCACTCGAATAAATATTGGATTTTAA-AC
65 TTATTCTCAATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAGAC
22454 G
130 G
* *
22455 AAATAGTGATATCTCTTCATTTCAATTGGAGTAATAAATGACTGCTTTAAGGCATAAGATGTCGT
1 AAATAGTGATATCTCTTCATTTCAATTGGAGTAATAAATGACTGCTTTAAGGCATGAGA-GTCAT
* * * * *
22520 TTATTCTCGATTGAAAATCATTAGATATCATCATTTTCTCTC
65 TTATTCTCAATTGGAAATAATTAGATATTATCGTTTTCTCTC
22562 TTAATTTTTT
Statistics
Matches: 324, Mismatches: 40, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
129 1 0.00
130 98 0.30
131 223 0.69
132 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (130 bp):
AAATAGTGATATCTCTTCATTTCAATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGTCATT
TATTCTCAATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAGACG
Found at i:22559 original size:261 final size:262
Alignment explanation
Indices: 22088--22561 Score: 718
Period size: 261 Copynumber: 1.8 Consensus size: 262
22078 TTCATTTAGG
* * *
22088 TTGGAGTAATAAATGACTGCTTAAAGGCATGAGAGGTCATTTATTATCGATTGGAAATAATTAGA
1 TTGGAGTAATAAATGACCGCTTAAAGGCATGAGAAGTCATTTATTATCAATTGGAAATAATTAGA
** * *
22153 TATTATAGTTTTCTTTCGAATCAATATTGAATTTTAATACGAAATAGTGATATCTCTTCATTTCG
66 TATTATAGTTTTCACTCGAATAAATATTGAATTTTAATACGAAATAGTGATATCTCTTCATTTCA
* * *
22218 ATTGGAGTAATAAATGATTACTTTAAGGCATGAGAGATCATTAATTCTCAATTGGAAATAATTAG
131 ATTGGAGTAATAAATGACTACTTTAAGGCATAAGAGATCATTAATTCTCAATTGAAAATAATTAG
* *
22283 ATATTATCGTTTTCTCTCGAATCAATATTTATTTTTAAGACGGAATAGTGATATCTCTTCATTCC
196 ATATCATCATTTTCTCTCGAATCAATATTTATTTTTAAGACGGAATAGTGATATCTCTTCATTCC
22348 AA
261 AA
* * * *
22350 TTGGAGTAATAAATGACCGCTTTAAGGCATGAGAAGTCATTTATTCTCAATTGGAAATCATTAGT
1 TTGGAGTAATAAATGACCGCTTAAAGGCATGAGAAGTCATTTATTATCAATTGGAAATAATTAGA
* *
22415 TATTATCGTTTTCACTCGAATAAATATTGGATTTTAA-ACGAAATAGTGATATCTCTTCATTTCA
66 TATTATAGTTTTCACTCGAATAAATATTGAATTTTAATACGAAATAGTGATATCTCTTCATTTCA
* * * * *
22479 ATTGGAGTAATAAATGACTGCTTTAAGGCATAAGATG-TCGTTTATTCTCGATTGAAAATCATTA
131 ATTGGAGTAATAAATGACTACTTTAAGGCATAAGA-GATCATTAATTCTCAATTGAAAATAATTA
22543 GATATCATCATTTTCTCTC
195 GATATCATCATTTTCTCTC
22562 TTAATTTTTT
Statistics
Matches: 188, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
261 97 0.52
262 91 0.48
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.39
Consensus pattern (262 bp):
TTGGAGTAATAAATGACCGCTTAAAGGCATGAGAAGTCATTTATTATCAATTGGAAATAATTAGA
TATTATAGTTTTCACTCGAATAAATATTGAATTTTAATACGAAATAGTGATATCTCTTCATTTCA
ATTGGAGTAATAAATGACTACTTTAAGGCATAAGAGATCATTAATTCTCAATTGAAAATAATTAG
ATATCATCATTTTCTCTCGAATCAATATTTATTTTTAAGACGGAATAGTGATATCTCTTCATTCC
AA
Found at i:37137 original size:27 final size:27
Alignment explanation
Indices: 37099--37156 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
37089 TTACCCTTTT
37099 AGCTTAGCTTTACACAGTGCCACAAAG
1 AGCTTAGCTTTACACAGTGCCACAAAG
*
37126 AGCTTAGCTTTACACGGTGCCACAAAG
1 AGCTTAGCTTTACACAGTGCCACAAAG
37153 AGCT
1 AGCT
37157 AAACTTTGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (27 bp):
AGCTTAGCTTTACACAGTGCCACAAAG
Found at i:37163 original size:27 final size:27
Alignment explanation
Indices: 37106--37163 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
37096 TTTAGCTTAG
* *
37106 CTTTACACAGTGCCACAAAGAGCTTAG
1 CTTTACACAGTGCCACAAAGAGCTAAA
*
37133 CTTTACACGGTGCCACAAAGAGCTAAA
1 CTTTACACAGTGCCACAAAGAGCTAAA
37160 CTTT
1 CTTT
37164 GAGCAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (27 bp):
CTTTACACAGTGCCACAAAGAGCTAAA
Found at i:39358 original size:21 final size:21
Alignment explanation
Indices: 39328--39375 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
39318 GCAGGGGTAC
* *
39328 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
39349 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
39370 ATGCCA
1 ATGCCA
39376 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:39405 original size:21 final size:21
Alignment explanation
Indices: 39379--39472 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
39369 TATGCCATCT
* *
39379 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
39400 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
39421 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
39442 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
39463 CCGCAGGGTT
1 CCGCAGGGTT
39473 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:40055 original size:33 final size:34
Alignment explanation
Indices: 39996--40092 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
39986 AAATGTTTTT
*
39996 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
40030 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
40063 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
40093 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:40099 original size:34 final size:33
Alignment explanation
Indices: 39994--40099 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
39984 ATAAATGTTT
*
39994 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
40028 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
40060 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
40095 TTAAA
1 TTAAA
40100 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:40723 original size:128 final size:128
Alignment explanation
Indices: 40495--41121 Score: 1164
Period size: 128 Copynumber: 4.9 Consensus size: 128
40485 CCTGATTTAC
40495 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
1 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
*
40560 CGAAATAATGGAAGGTGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAA
66 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAA
40623 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
1 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
*
40688 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
66 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAA
*
40751 CGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
1 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
*
40816 AGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAA
66 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAA
40879 TGATATATCTAGTGTCCCCGAAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
1 TGATATATCTAGTGTCCCCG-AGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
* * * *
40944 ACGAAATAATGAAAGGCGCGCCCCCGGGAAAGTGCCTTCATGTGAATAGTGAAATAATAGGTAC
65 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAA
*
41008 CGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
1 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
41073 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
41122 ACTCCGATTA
Statistics
Matches: 483, Mismatches: 15, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
128 361 0.75
129 122 0.25
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (128 bp):
TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAA
Found at i:41049 original size:257 final size:256
Alignment explanation
Indices: 40496--41121 Score: 1198
Period size: 257 Copynumber: 2.4 Consensus size: 256
40486 CTGATTTACT
40496 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
1 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
*
40561 GAAATAATGGAAGGTGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGA
66 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGA
40626 TATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGA
131 TATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGA
* *
40691 AATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACC
196 AATAATGAAAGGCGCGCCCCCGGGAAAGCGCCTTCATGTGAATAGTGAAATAATAGGTACC
*
40752 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAA
1 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
40817 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGA
66 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGA
40882 TATATCTAGTGTCCCCGAAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
131 TATATCTAGTGTCCCCG-AGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
*
40947 AAATAATGAAAGGCGCGCCCCCGGGAAAGTGCCTTCATGTGAATAGTGAAATAATAGGTACC
195 AAATAATGAAAGGCGCGCCCCCGGGAAAGCGCCTTCATGTGAATAGTGAAATAATAGGTACC
41009 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
1 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
41074 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
41122 ACTCCGATTA
Statistics
Matches: 363, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
256 145 0.40
257 218 0.60
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (256 bp):
GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATGA
TATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGA
AATAATGAAAGGCGCGCCCCCGGGAAAGCGCCTTCATGTGAATAGTGAAATAATAGGTACC
Found at i:41205 original size:8 final size:8
Alignment explanation
Indices: 41192--41230 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
41182 TCACAATCTT
41192 TCAAATTC
1 TCAAATTC
41200 TCAAATTC
1 TCAAATTC
* *
41208 CCAAACTC
1 TCAAATTC
41216 T-AAATTC
1 TCAAATTC
41223 TCAAATTC
1 TCAAATTC
41231 CCTGAAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.33
Consensus pattern (8 bp):
TCAAATTC
Found at i:45217 original size:2 final size:2
Alignment explanation
Indices: 45210--45238 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45200 TCCATACTTT
45210 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45239 TAGTTTGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45294 original size:37 final size:37
Alignment explanation
Indices: 45260--45436 Score: 234
Period size: 37 Copynumber: 4.8 Consensus size: 37
45250 TGGTTTTTGG
*
45260 AAATTATATAATATATATTTTTTAAAAACATTTTTTGAA
1 AAATTATATAATATATAGTTTTTAAAAACA-TTTTT-AA
*
45299 AAA-TATATAATATATAGTTTTT-AAAACATTTTAAA
1 AAATTATATAATATATAGTTTTTAAAAACATTTTTAA
*
45334 AAATTATATAATATATAGTTTTTGAAAACATTTTTAA
1 AAATTATATAATATATAGTTTTTAAAAACATTTTTAA
* *
45371 AAATTATATAATATATAG-TTTTAAAAATATTTTGAAA
1 AAATTATATAATATATAGTTTTTAAAAACATTTT-TAA
* *
45408 ACAATTATATATTATATAGTTTTAAAAAA
1 A-AATTATATAATATATAGTTTTTAAAAA
45437 AACATGTTTG
Statistics
Matches: 125, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
35 5 0.04
36 36 0.29
37 39 0.31
38 34 0.27
39 11 0.09
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (37 bp):
AAATTATATAATATATAGTTTTTAAAAACATTTTTAA
Found at i:45312 original size:36 final size:37
Alignment explanation
Indices: 45260--45435 Score: 209
Period size: 38 Copynumber: 4.7 Consensus size: 37
45250 TGGTTTTTGG
45260 AAATTATATAATATATATTTTTTAAAAACATTTTTTGAA
1 AAATTATATAATATATA-TTTTTAAAAACA-TTTTTGAA
*
45299 AAA-TATATAATATATAGTTTTT-AAAACA-TTTTAAA
1 AAATTATATAATATATA-TTTTTAAAAACATTTTTGAA
*
45334 AAATTATATAATATATAGTTTTTGAAAACATTTTT-AA
1 AAATTATATAATATATA-TTTTTAAAAACATTTTTGAA
* *
45371 AAATTATATAATATATAGTTTTAAAAATA-TTTTGAAA
1 AAATTATATAATATATATTTTTAAAAACATTTTTG-AA
* *
45408 ACAATTATATATTATATAGTTTTAAAAA
1 A-AATTATATAATATATATTTTTAAAAA
45436 AAACATGTTT
Statistics
Matches: 125, Mismatches: 6, Indels: 13
0.87 0.04 0.09
Matches are distributed among these distances:
35 13 0.10
36 28 0.22
37 34 0.27
38 47 0.38
39 3 0.02
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (37 bp):
AAATTATATAATATATATTTTTAAAAACATTTTTGAA
Found at i:45458 original size:73 final size:71
Alignment explanation
Indices: 45260--45495 Score: 201
Period size: 73 Copynumber: 3.2 Consensus size: 71
45250 TGGTTTTTGG
* * * * *
45260 AAATTATATAATATATATTTTTTAAAAACATTTTTTGAAAAATATATAATATATAGTTTTTAAAA
1 AAATTATATAATATATAGTTTTAAAAAACA-TGTTT--AAAA-ATACAATATATAGTTTTAAAAA
*
45325 CATTTT-AAA
62 TATTTTGAAA
** * *
45334 AAATTATATAATATATAGTTTTTGAAAACATTTTTAAAAATTATATAATATATAGTTTTAAAAAT
1 AAATTATATAATATATAGTTTTAAAAAACATGTTT-AAAA--ATACAATATATAGTTTTAAAAAT
45399 ATTTTGAAA
63 ATTTTGAAA
* *
45408 ACAATTATATATTATATAGTTTTAAAAAAAACATGTTT-GAAA-AC-ATATATAGTTTTAAAATA
1 A-AATTATATAATATATAGTTTT--AAAAAACATGTTTAAAAATACAATATATAGTTTTAAAA-A
*
45470 TTTTTTGAAA
62 TATTTTGAAA
*
45480 ATATATTATATTATAT
1 A-A-ATTATATAATAT
45496 GGTTTTGAAA
Statistics
Matches: 141, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
71 16 0.11
72 18 0.13
73 43 0.30
74 32 0.23
75 22 0.16
77 10 0.07
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.45
Consensus pattern (71 bp):
AAATTATATAATATATAGTTTTAAAAAACATGTTTAAAAATACAATATATAGTTTTAAAAATATT
TTGAAA
Found at i:45527 original size:71 final size:69
Alignment explanation
Indices: 45308--45527 Score: 157
Period size: 71 Copynumber: 3.1 Consensus size: 69
45298 AAAATATATA
** * *
45308 ATATATAGTTTTTAAAACA-TTTTAAAAAAT-TA-TATAATATATAGTTTTTGAAAACATTTTTA
1 ATATATAG-TTTTAAAA-ATTTTTTGAAAATATATTATATTATAT-GGTTTTGAAAACATTTTT-
*
45370 AAAATTATAT
62 AAAA-T-CAT
* * * *
45380 AATATATAGTTTTAAAAATATTTTGAAAACA-ATTATATATTATATAGTTTTAAAAAAAACATGT
1 -ATATATAGTTTTAAAAATTTTTTGAAAATATA-T-TATATTATATGGTTTT---GAAAACAT-T
*
45444 TTGAAAA-C--
59 TTTAAAATCAT
*
45452 ATATATAGTTTTAAAATATTTTTTGAAAATATATTATATTATATGGTTTTGAAAGTCATTTTTAA
1 ATATATAGTTTTAAAA-ATTTTTTGAAAATATATTATATTATATGGTTTTGAAA-ACATTTTTAA
45517 AATCAT
64 AATCAT
45523 ATATA
1 ATATA
45528 AAATATAATT
Statistics
Matches: 116, Mismatches: 16, Indels: 32
0.71 0.10 0.20
Matches are distributed among these distances:
68 10 0.09
69 4 0.03
71 37 0.32
72 29 0.25
73 9 0.08
74 4 0.03
75 9 0.08
77 11 0.09
78 3 0.03
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (69 bp):
ATATATAGTTTTAAAAATTTTTTGAAAATATATTATATTATATGGTTTTGAAAACATTTTTAAAA
TCAT
Found at i:46653 original size:24 final size:25
Alignment explanation
Indices: 46626--46681 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
46616 TCAATTCTTA
*
46626 TTTTATT-TTATTATTATT-ATTAT
1 TTTTATTGTTATTAGTATTAATTAT
46649 GTTTTCAATTGTTATTAGTATTAATTAT
1 -TTTT--ATTGTTATTAGTATTAATTAT
46677 TTTTA
1 TTTTA
46682 CTTCATATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
24 4 0.15
25 1 0.04
26 3 0.11
27 14 0.52
28 5 0.19
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (25 bp):
TTTTATTGTTATTAGTATTAATTAT
Found at i:46756 original size:18 final size:17
Alignment explanation
Indices: 46735--46834 Score: 64
Period size: 17 Copynumber: 5.8 Consensus size: 17
46725 TTTAATTTTC
46735 TTATTTATTTATTTAATT
1 TTATTTATTT-TTTAATT
46753 TTATTT-TTAATTTTAA-T
1 TTATTTATT--TTTTAATT
* *
46770 TTACTTCTTTGATTTAATT
1 TTATTTATTT--TTTAATT
* *
46789 TTTTTTATTTTTT--CT
1 TTATTTATTTTTTAATT
**
46804 TTATTTATTTTTTCCTT
1 TTATTTATTTTTTAATT
*
46821 TGATTTATTTTTTA
1 TTATTTATTTTTTA
46835 TATTACTATT
Statistics
Matches: 65, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
15 13 0.20
16 1 0.02
17 24 0.37
18 18 0.28
19 9 0.14
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (17 bp):
TTATTTATTTTTTAATT
Found at i:46765 original size:21 final size:21
Alignment explanation
Indices: 46725--46813 Score: 58
Period size: 21 Copynumber: 4.1 Consensus size: 21
46715 TAATATTTTT
*
46725 TTTAATTTTCTTATTTATTTA
1 TTTAATTTTATTATTTATTTA
46746 TTTAATTTTATT-TTTAATTTTAA
1 TTTAATTTTATTATTT-A-TTT-A
* * *
46769 TTTACTTCTT-TGATTTAATTTT
1 TTTAATT-TTATTATTT-ATTTA
* *
46791 TTTTATTTT-TTCTTTATTTA
1 TTTAATTTTATTATTTATTTA
46811 TTT
1 TTT
46814 TTTCCTTTGA
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
20 10 0.19
21 18 0.33
22 8 0.15
23 11 0.20
24 7 0.13
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.73
Consensus pattern (21 bp):
TTTAATTTTATTATTTATTTA
Found at i:46769 original size:39 final size:40
Alignment explanation
Indices: 46724--46800 Score: 104
Period size: 39 Copynumber: 1.9 Consensus size: 40
46714 ATAATATTTT
*
46724 TTTTAATTTTCTTATTT-ATTT-ATTTAATTTTATTTTTAA
1 TTTTAATTTACTTATTTGATTTAATTT-ATTTTATTTTTAA
* *
46763 TTTTAATTTACTTCTTTGATTTAATTTTTTTTATTTTT
1 TTTTAATTTACTTATTTGATTTAATTTATTTTATTTTT
46801 TCTTTATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 15 0.45
40 14 0.42
41 4 0.12
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (40 bp):
TTTTAATTTACTTATTTGATTTAATTTATTTTATTTTTAA
Found at i:46792 original size:26 final size:24
Alignment explanation
Indices: 46763--46816 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 24
46753 TTATTTTTAA
46763 TTTTAATTTACTTCTTTGATTTAATTT
1 TTTTAATTT-CTTCTTT-ATTT-ATTT
* *
46790 TTTTTATTTTTTCTTTATTTATTT
1 TTTTAATTTCTTCTTTATTTATTT
46814 TTT
1 TTT
46817 CCTTTGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 4 0.16
26 6 0.24
27 8 0.32
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.76
Consensus pattern (24 bp):
TTTTAATTTCTTCTTTATTTATTT
Found at i:46826 original size:17 final size:15
Alignment explanation
Indices: 46792--46833 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 15
46782 TTTAATTTTT
46792 TTTATTTTTTCTTTA
1 TTTATTTTTTCTTTA
46807 TTTATTTTTTCCTTTGA
1 TTTATTTTTT-CTTT-A
46824 TTTATTTTTT
1 TTTATTTTTT
46834 ATATTACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.40
16 4 0.16
17 11 0.44
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTATTTTTTCTTTA
Found at i:47408 original size:18 final size:18
Alignment explanation
Indices: 47385--47433 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
47375 TATAATGTTA
47385 TCTTTTATATTAT-CATCT
1 TCTTTTATATTATACAT-T
47403 TCTTTT-T-TTATACATT
1 TCTTTTATATTATACATT
47419 TGCATTTTATATTAT
1 T-C-TTTTATATTAT
47434 TTTGTTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 6 0.23
17 5 0.19
18 10 0.38
19 1 0.04
20 4 0.15
ACGTcount: A:0.22, C:0.12, G:0.02, T:0.63
Consensus pattern (18 bp):
TCTTTTATATTATACATT
Found at i:49668 original size:146 final size:148
Alignment explanation
Indices: 49175--49816 Score: 815
Period size: 150 Copynumber: 4.3 Consensus size: 148
49165 TAAAGTAGGC
* *
49175 ACAATTTGGCAGCCCAATGTCTATACTGGAAAGGTGGTCCATTTAACAATGAACCGATTTTTTAC
1 ACAATTTGGCAGCCCAATGTCTATACTGGAAAGGTGGTCCATCTAACAATGAA-CGATTTTTGAC
* * **** * *
49240 TGCTAATTT--TCTAGGGGAAAAA-ACTTCTGGCTATTAAAAATTACAAGTCTCATAAGGTTAAT
65 TGTTAATTTACTCGAAAAAAAAAAGACTTTTGACTATTAAAAATTACAAGTCTC---A-GTTAAT
49302 CAAAGTTGATTATATGAATTGAT
126 CAAAGTTGATTATATGAATTGAT
* * *
49325 ACAATTTGGCAGCCCAATGTCTATACTGGAAAGGTGGTCCATCTAACAATGAAAAGACTTTTGAA
1 ACAATTTGGCAGCCCAATGTCTATACTGGAAAGGTGGTCCATCTAACAATG-AACGATTTTTGAC
* * *
49390 TGTTAATTTACTCGAAAAAAAAAAGACTTTTTGACTATTAAAAATTACAAGCCTCGGTTAATTAA
65 TGTTAATTTACTCGAAAAAAAAAAGAC-TTTTGACTATTAAAAATTACAAGTCTCAGTTAATCAA
* * *
49455 AGATGACTATATGAAATGAT
129 AGTTGATTATATGAATTGAT
* *
49475 ACAATTTGGCAGTCCAATGTCTATACTGGAAAGGTGGTCCATTTAACAATGAATCGATTTTTGAC
1 ACAATTTGGCAGCCCAATGTCTATACTGGAAAGGTGGTCCATCTAACAATGAA-CGATTTTTGAC
*
49540 TGTTAATTTTCTCGAAAAAAAAAA-ACTTTTGACTATTAAAAATTACAA-TCTC-GTTAATCAAA
65 TGTTAATTTACTCGAAAAAAAAAAGACTTTTGACTATTAAAAATTACAAGTCTCAGTTAATCAAA
49602 GTTGATTATATGAATTGAT
130 GTTGATTATATGAATTGAT
49621 ACAATTTGGCAGCCCAATGTCTATACTGGAAAGGTGGTCCATCTAACAATGAACAGATTTTTGAC
1 ACAATTTGGCAGCCCAATGTCTATACTGGAAAGGTGGTCCATCTAACAATGAAC-GATTTTTGAC
49686 TGTTAATTTACTCGGAAAAAAAAAAAGACTTTTGACTATTAAAAATTACAAGTCTC-G-T-A--A
65 TGTTAATTTACTC-G-AAAAAAAAAAGACTTTTGACTATTAAAAATTACAAGTCTCAGTTAATCA
* * * * *
49746 GA-TTAATCAAATAAATTGAT
128 AAGTTGATTATATGAATTGAT
* * *
49766 ACAATTTGGCAACCCAATGTCTATACTGAAAAGGTGATCCAT-TGAACAATG
1 ACAATTTGGCAGCCCAATGTCTATACTGGAAAGGTGGTCCATCT-AACAATG
49817 TTGTTTTTTT
Statistics
Matches: 439, Mismatches: 41, Indels: 29
0.86 0.08 0.06
Matches are distributed among these distances:
144 1 0.00
145 61 0.14
146 100 0.23
147 4 0.01
148 33 0.08
149 29 0.07
150 175 0.40
151 2 0.00
152 8 0.02
153 2 0.00
154 24 0.05
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (148 bp):
ACAATTTGGCAGCCCAATGTCTATACTGGAAAGGTGGTCCATCTAACAATGAACGATTTTTGACT
GTTAATTTACTCGAAAAAAAAAAGACTTTTGACTATTAAAAATTACAAGTCTCAGTTAATCAAAG
TTGATTATATGAATTGAT
Found at i:58027 original size:9 final size:9
Alignment explanation
Indices: 58008--58037 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
57998 TTTTAACATT
58008 ATTTATTAAA
1 ATTT-TTAAA
58018 ATTTTTAAA
1 ATTTTTAAA
58027 ATTTTTAAA
1 ATTTTTAAA
58036 AT
1 AT
58038 GATTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:58154 original size:10 final size:10
Alignment explanation
Indices: 58141--58173 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
58131 TTTAAAATAT
58141 TTTAGTTTAA
1 TTTAGTTTAA
*
58151 TTTAGTTTAG
1 TTTAGTTTAA
58161 TTTA-TTTAA
1 TTTAGTTTAA
58170 TTTA
1 TTTA
58174 TTTCCTCGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (10 bp):
TTTAGTTTAA
Found at i:58971 original size:2 final size:2
Alignment explanation
Indices: 58964--58990 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
58954 ATAATTTGAA
58964 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
58991 CAATAGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61839 original size:51 final size:48
Alignment explanation
Indices: 61769--61891 Score: 144
Period size: 47 Copynumber: 2.5 Consensus size: 48
61759 AATTTTTTAA
* *
61769 ATAAATATTATTTTA-AAATTTATAAATTTCCA-CGGAATACATATTGCTATT
1 ATAAAT-TTATTTAACAAATTTAT-AATTT-CATC--AATACATATTGCAATT
*
61820 ATAAATTTATTTAACAAATTTAT-ATTTTATCAATACATATTGCAATT
1 ATAAATTTATTTAACAAATTTATAATTTCATCAATACATATTGCAATT
61867 ATAAATTTATTTAACAAATTATATA
1 ATAAATTTATTTAACAAATT-TATA
61892 TATATATATA
Statistics
Matches: 65, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
47 35 0.54
48 4 0.06
49 5 0.08
50 7 0.11
51 14 0.22
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (48 bp):
ATAAATTTATTTAACAAATTTATAATTTCATCAATACATATTGCAATT
Found at i:61893 original size:2 final size:2
Alignment explanation
Indices: 61886--61920 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
61876 TTTAACAAAT
61886 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61921 ATTTAACTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:74449 original size:17 final size:18
Alignment explanation
Indices: 74427--74463 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
74417 TAAATAGAAA
*
74427 AAAAAGAGAA-AAAAAAC
1 AAAAAGAAAAGAAAAAAC
74444 AAAAAGAAAAGAAAAAAC
1 AAAAAGAAAAGAAAAAAC
74462 AA
1 AA
74464 GGTGGGTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAAC
Found at i:75785 original size:65 final size:65
Alignment explanation
Indices: 75495--75938 Score: 703
Period size: 65 Copynumber: 6.8 Consensus size: 65
75485 GTGCCACTCA
* * * *
75495 AGACAACACAAGTTCAACTTCACGATGAATGGGCCGCTGGTTGTCAAC-AAAATTTCCCAGTTTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTATC
*
75559 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAAC-AAAATTTCCCAGTGTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTATC
* * *
75623 AGACAACGCAAGTTCAACTTCACAACGAAGGGGCCACTGGTTGTCGACAAAAATTTTTTTCCCAG
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAA----TTTCCCAG
75688 TATC
62 TATC
*
75692 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTGTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTATC
* *
75757 AGACAACACAAGTTCAACTTCACGACGAAGGGGCCGCTGGTTGTCGACAAAAATTTCCCAGTATC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTATC
* *
75822 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTATC
* *
75887 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAAA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAA
75939 GACTTCCCCA
Statistics
Matches: 354, Mismatches: 21, Indels: 9
0.92 0.05 0.02
Matches are distributed among these distances:
64 105 0.30
65 188 0.53
69 61 0.17
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (65 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTATC
Found at i:88524 original size:14 final size:15
Alignment explanation
Indices: 88491--88529 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
88481 TACATTTACG
* *
88491 TTTTAATTATTATTA
1 TTTTATTTATTATAA
88506 TTTTATTTATT-TAA
1 TTTTATTTATTATAA
88520 TTTTATTTAT
1 TTTTATTTAT
88530 ACGCACATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTATTTATTATAA
Found at i:88563 original size:4 final size:4
Alignment explanation
Indices: 88554--88580 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
88544 TGTTATTCAT
88554 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
88581 TTCTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:88711 original size:2 final size:2
Alignment explanation
Indices: 88704--88758 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
88694 TTTATTAATT
* * * *
88704 TA TA TA TA TA TA TA TT TA CTA TT TA TT TA TT TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
88746 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
88759 TATTTTTACT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
1 1 0.02
2 40 0.93
3 2 0.05
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:88744 original size:36 final size:35
Alignment explanation
Indices: 88694--88763 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 35
88684 TATTATCAGT
*
88694 TTTATTAATTTATATATATATATATTTACTATTTA
1 TTTATTAATTTATATATATATATATATACTATTTA
* *
88729 TTTATTTATTATATATATATATATATATATTATTT
1 TTTATTAATT-TATATATATATATATATACTATTT
88764 TTACTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 9 0.29
36 22 0.71
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (35 bp):
TTTATTAATTTATATATATATATATATACTATTTA
Found at i:88779 original size:42 final size:40
Alignment explanation
Indices: 88637--88780 Score: 129
Period size: 42 Copynumber: 3.6 Consensus size: 40
88627 TTTACTTTAG
**
88637 TATATATTTTTA-TTTTTTTAGATTATATATATATATATA
1 TATATATTTTTATTTTTTTTTTATTATATATATATATATA
* ***
88676 T-T-TTTTTTTATTATCAGTTTTATTA-AT-T-TATATATA
1 TATATATTTTTATT-TTTTTTTTATTATATATATATATATA
* *
88712 TATATATTTACTATTTATTTATTTATTATATATATATATATA
1 TATATATTT-TTATTT-TTTTTTTATTATATATATATATATA
88754 TATATTATTTTTACTTTTTTTTTTATT
1 TATA-TATTTTTA-TTTTTTTTTTATT
88781 TTTTTTACTT
Statistics
Matches: 80, Mismatches: 14, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
36 9 0.11
37 9 0.11
38 9 0.11
39 19 0.24
40 2 0.03
41 1 0.01
42 23 0.29
43 8 0.10
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (40 bp):
TATATATTTTTATTTTTTTTTTATTATATATATATATATA
Found at i:88782 original size:5 final size:5
Alignment explanation
Indices: 88769--88951 Score: 52
Period size: 5 Copynumber: 36.6 Consensus size: 5
88759 TATTTTTACT
*
88769 TTTTT TTTTA TTTT- TTTTA CTTTT- TTATTA TTTTA -TTTA TTTTA -TTTA
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA
** * *
88817 TTTATA TAAATA TATT- TTTTC TTTT- TCTTTA -TTT- TTTTA TATTTA
1 TTT-TA T-TTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA T-TTTA
* *
88862 TTTTA CTTACTA TTTTA TCTTT- TCTTT- TCTTT- TTTTA TCTTATC TTTTA
1 TTTTA -TT-TTA TTTTA T-TTTA T-TTTA T-TTTA TTTTA T-TT-TA TTTTA
* * *
88911 TTTAA TTTT- TTTTCA TTTTA ATTTA ATTT- TTTTA -TTTA TTT
1 TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTT
88952 CTTACCTTTT
Statistics
Matches: 141, Mismatches: 13, Indels: 48
0.70 0.06 0.24
Matches are distributed among these distances:
4 38 0.27
5 67 0.48
6 32 0.23
7 4 0.03
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:88792 original size:17 final size:17
Alignment explanation
Indices: 88772--88819 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
88762 TTTTACTTTT
*
88772 TTTTTTATTTTTTTTAC
1 TTTTTTATTTATTTTAC
*
88789 TTTTTTA-TTATTTTAT
1 TTTTTTATTTATTTTAC
88805 TTATTTTATTTATTT
1 TT-TTTTATTTATTT
88820 ATATAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 9 0.33
17 12 0.44
18 6 0.22
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTATTTATTTTAC
Found at i:88809 original size:4 final size:4
Alignment explanation
Indices: 88694--88821 Score: 57
Period size: 4 Copynumber: 31.2 Consensus size: 4
88684 TATTATCAGT
* * * * *
88694 TTTA TTAA TTTA TATA TATA TATA TTTA -CTA TTTA TTTA TTTA TTATA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA
* * * * * * *
88742 TATA TATA TATA TATA TTATT TTTA CTTT- TTTT TTTA TTTTT TTTA CTTT-
1 TTTA TTTA TTTA TTTA TT-TA TTTA -TTTA TTTA TTTA -TTTA TTTA -TTTA
88792 TTTA -TTA TTTTA TTTA TTTTA TTTA TTTA T
1 TTTA TTTA -TTTA TTTA -TTTA TTTA TTTA T
88822 ATAAATATAT
Statistics
Matches: 100, Mismatches: 13, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
3 11 0.11
4 67 0.67
5 22 0.22
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:88811 original size:25 final size:25
Alignment explanation
Indices: 88694--88821 Score: 72
Period size: 25 Copynumber: 5.2 Consensus size: 25
88684 TATTATCAGT
* * * *
88694 TTTATTAATTTATATA-TATATATA
1 TTTATTATTTTATTTATTTTATTTA
*
88718 TTTACTA-TTTATTTA-TTTA-TTA
1 TTTATTATTTTATTTATTTTATTTA
* * *
88740 TATATATATATATATATATTATT-TTTA
1 TTTAT-TAT-TTTATTTATT-TTATTTA
* *
88767 CTTT-TTTTTTTATTTTTTTTACTTT-
1 -TTTATTATTTTATTTATTTTA-TTTA
88792 TTTATTATTTTATTTATTTTATTTA
1 TTTATTATTTTATTTATTTTATTTA
88817 TTTAT
1 TTTAT
88822 ATAAATATAT
Statistics
Matches: 78, Mismatches: 15, Indels: 21
0.68 0.13 0.18
Matches are distributed among these distances:
22 5 0.06
23 12 0.15
24 14 0.18
25 33 0.42
26 6 0.08
27 6 0.08
28 2 0.03
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTATTATTTTATTTATTTTATTTA
Found at i:88818 original size:21 final size:21
Alignment explanation
Indices: 88723--88818 Score: 64
Period size: 21 Copynumber: 4.8 Consensus size: 21
88713 ATATATTTAC
*
88723 TATTTA-TTTATTTATTA-TA
1 TATTTATTTTATTTATTATTT
* * *
88742 TATATATATATATATATTATTTT
1 TATTTAT-TTTATTTATTA-TTT
88765 TACTTT-TTTT-TTTA-T-TTT
1 TA-TTTATTTTATTTATTATTT
*
88783 T-TTTACTTT-TTTATTATTT
1 TATTTATTTTATTTATTATTT
88802 TATTTATTTTATTTATT
1 TATTTATTTTATTTATT
88819 TATATAAATA
Statistics
Matches: 58, Mismatches: 9, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
16 3 0.05
17 7 0.12
18 5 0.09
19 9 0.16
20 8 0.14
21 18 0.31
22 2 0.03
23 4 0.07
24 2 0.03
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (21 bp):
TATTTATTTTATTTATTATTT
Found at i:88879 original size:71 final size:71
Alignment explanation
Indices: 88731--88879 Score: 169
Period size: 71 Copynumber: 2.1 Consensus size: 71
88721 ACTATTTATT
* *
88731 TATTTATTATATATATATATATATATATTATTTTTACTTTTTTTTTTATTTTTTTTACTTTTTTA
1 TATTTATTATATATATATATATAAATATTATTTTTACTTTTTTCTTTATTTTTTTTACTTTTTTA
* *
88796 TTATTT
66 TTACTA
* * * * *
88802 TATTTATTTTATTTATTTATATAAATA-TATTTTTTC-TTTTTCTTTATTTTTTTATATTTATTT
1 TATTTATTATATATATATATATAAATATTATTTTTACTTTTTTCTTTATTTTTTT-TACTT-TTT
88865 TACTTACTA
64 TA-TTACTA
88874 T-TTTAT
1 TATTTAT
88880 CTTTTCTTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
69 16 0.24
70 12 0.18
71 33 0.50
72 5 0.08
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (71 bp):
TATTTATTATATATATATATATAAATATTATTTTTACTTTTTTCTTTATTTTTTTTACTTTTTTA
TTACTA
Found at i:88912 original size:115 final size:118
Alignment explanation
Indices: 88681--88935 Score: 258
Period size: 115 Copynumber: 2.2 Consensus size: 118
88671 ATATATTTTT
* *
88681 TTTTATTATCAGTTTTATTAATTTATATATATATATATTTACTATTTATTTATTTATTATATATA
1 TTTTATT-TCA-TTTTATTTATTTATATAAATATATATTTACTATTTATTTATTTATTATATATA
* *
88746 TATATATATATATTATTTTTACTTTTTTTTTTATTTTTTTTACTTTTTTA-TT-A
64 TATATATATATACTATTTTTACTTTTTTTTTTATTTTTTTTACTCTTTTATTTAA
* * * * * *
88799 TTTTATTT-ATTTTATTTATTTATATAAATATATTTTTTCTTTTTCTTTATTT-TTTTATATTTA
1 TTTTATTTCATTTTATTTATTTATATAAATATATATTTACTATTTATTTATTTATTATATATATA
*
88862 T-TTTACT-TACTA-TTTTATCTTTTCTTTTCTT-TTTTTATCTTA-TCTTTTATTTAA
66 TATATA-TATACTATTTTTA-CTTTT-TTTT-TTATTTTT-T-TTACTCTTTTATTTAA
*
88916 TTTTTTTTCATTTTAATTTA
1 TTTTATTTCATTTT-ATTTA
88936 ATTTTTTTAT
Statistics
Matches: 115, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
112 5 0.04
113 12 0.10
114 20 0.17
115 46 0.40
116 6 0.05
117 9 0.08
118 12 0.10
119 5 0.04
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (118 bp):
TTTTATTTCATTTTATTTATTTATATAAATATATATTTACTATTTATTTATTTATTATATATATA
TATATATATACTATTTTTACTTTTTTTTTTATTTTTTTTACTCTTTTATTTAA
Found at i:88919 original size:25 final size:25
Alignment explanation
Indices: 88876--88949 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 25
88866 ACTTACTATT
* **
88876 TTATCTTTTCTTTTCTTTTTTTATC
1 TTATCTTTTATTTAATTTTTTTATC
88901 TTATCTTTTATTTAATTTTTTT-TC
1 TTATCTTTTATTTAATTTTTTTATC
*
88925 --AT-TTTAATTTAATTTTTTTAT-
1 TTATCTTTTATTTAATTTTTTTATC
88946 TTAT
1 TTAT
88950 TTCTTACCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 16 0.38
22 3 0.07
23 2 0.05
24 2 0.05
25 19 0.45
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (25 bp):
TTATCTTTTATTTAATTTTTTTATC
Found at i:93072 original size:15 final size:16
Alignment explanation
Indices: 93052--93092 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
93042 GTTTACTTCA
*
93052 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
93067 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
93083 GAATGATTCA
1 GAATGATTCA
93093 GAGGCTCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:97988 original size:26 final size:26
Alignment explanation
Indices: 97942--98009 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
97932 TTGGGTAATG
* *
97942 AAATGAAAT-TATCTAAAAAAAAGATA
1 AAATAAAATATATTTAAAAAAAAGA-A
*
97968 AAAT-AAATAT-TTTAAATAAAAATAA
1 AAATAAAATATATTTAAA-AAAAAGAA
97993 AAATAAAATATATTTAA
1 AAATAAAATATATTTAA
98010 TAAGTTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
25 14 0.39
26 17 0.47
27 5 0.14
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (26 bp):
AAATAAAATATATTTAAAAAAAAGAA
Found at i:101207 original size:14 final size:14
Alignment explanation
Indices: 101161--101198 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
101151 CGTTGGGCAT
*
101161 CCGAAGCCATCCGA
1 CCGAGGCCATCCGA
*
101175 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
101189 CCGAGGCCAT
1 CCGAGGCCAT
101199 TCGAGCGAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.39, G:0.29, T:0.08
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:101295 original size:29 final size:29
Alignment explanation
Indices: 101254--101359 Score: 203
Period size: 29 Copynumber: 3.7 Consensus size: 29
101244 GAGGAGCAGG
101254 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
101283 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
101312 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
101341 CGGAGTGCATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
101360 TGCTGGGAAG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.24, C:0.27, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:111426 original size:20 final size:20
Alignment explanation
Indices: 111401--111452 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
111391 TAATTGAAAA
*
111401 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
*
111421 TCGCGTTGCGATTTTTCAGT
1 TCGCGTTGCGATTTTCCAGT
*
111441 TCGTGTTGCGAT
1 TCGCGTTGCGAT
111453 AGTCTACAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.10, C:0.21, G:0.25, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:111470 original size:22 final size:22
Alignment explanation
Indices: 111437--111515 Score: 76
Period size: 22 Copynumber: 3.7 Consensus size: 22
111427 TGCGATTTTT
111437 CAGTTCGT-GTTGCGATAGTCTA
1 CAGTT-GTCGTTGCGATAGTCTA
* * *
111459 CAGTTGTCGTTGC-A-ATTTTC
1 CAGTTGTCGTTGCGATAGTCTA
**
111479 CAAAT-TCGTTGCGATAGTCTA
1 CAGTTGTCGTTGCGATAGTCTA
111500 CAGTTGTCGTTGCGAT
1 CAGTTGTCGTTGCGAT
111516 TTTCCAAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
19 7 0.16
20 7 0.16
21 9 0.21
22 20 0.47
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGTTGTCGTTGCGATAGTCTA
Found at i:111490 original size:41 final size:41
Alignment explanation
Indices: 111445--111533 Score: 169
Period size: 41 Copynumber: 2.2 Consensus size: 41
111435 TTCAGTTCGT
111445 GTTGCGATAGTCTACAGTTGTCGTTGCAATTTTCCAAATTC
1 GTTGCGATAGTCTACAGTTGTCGTTGCAATTTTCCAAATTC
*
111486 GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTC
1 GTTGCGATAGTCTACAGTTGTCGTTGCAATTTTCCAAATTC
111527 GTTGCGA
1 GTTGCGA
111534 AAATCGCGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (41 bp):
GTTGCGATAGTCTACAGTTGTCGTTGCAATTTTCCAAATTC
Found at i:111532 original size:19 final size:19
Alignment explanation
Indices: 111465--111533 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
111455 TCTACAGTTG
*
111465 TCGTTGCAATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
111484 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
111505 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
111525 TCGTTGCGA
1 TCGTTGCGA
111534 AAATCGCGTT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 18 0.47
20 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:111626 original size:19 final size:19
Alignment explanation
Indices: 111602--111670 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
111592 TCTACAGTTG
111602 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * * **
111621 TCGTTGCGGTAGTCTACAGTT
1 TCGTTGC-G-ATTTTCCAAAT
*
111642 ATCGTTGCGATTTTCTAAAT
1 -TCGTTGCGATTTTCCAAAT
111662 TCGTTGCGA
1 TCGTTGCGA
111671 AAATTCGTTT
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
19 16 0.44
20 6 0.17
21 7 0.19
22 7 0.19
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:111627 original size:41 final size:41
Alignment explanation
Indices: 111582--111670 Score: 151
Period size: 41 Copynumber: 2.2 Consensus size: 41
111572 TGAAAATCGT
*
111582 GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTC
1 GTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATTC
* *
111623 GTTGCGGTAGTCTACAGTTATCGTTGCGATTTTCTAAATTC
1 GTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATTC
111664 GTTGCGA
1 GTTGCGA
111671 AAATTCGTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (41 bp):
GTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATTC
Found at i:111641 original size:137 final size:136
Alignment explanation
Indices: 111396--111674 Score: 450
Period size: 137 Copynumber: 2.0 Consensus size: 136
111386 TGCGATAATT
** * ** **
111396 GAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTTCAGTTCGTGTTGCGATAGTCTACA
1 GAAAATCGCGTTGCGATTTTCCAGCTCGCGTTGCGATGTTGAAAATCGTGTTGCGATAGTCTACA
*
111461 GTTGTCGTTGCAATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
66 GTTGTCGTTGCAATTTTCCAAATTCGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATT
111526 CGTTGC
131 CGTTGC
111532 GAAAATCGCGTTGCGATTTTCCAGCTCGCGTTGCGATAGTTGAAAATCGTGTTGCGATAGTCTAC
1 GAAAATCGCGTTGCGATTTTCCAGCTCGCGTTGCGAT-GTTGAAAATCGTGTTGCGATAGTCTAC
* * *
111597 AGTTGTCGTTGCGATTTTCCAAATTCGTTGCGGTAGTCTACAGTTATCGTTGCGATTTTCTAAAT
65 AGTTGTCGTTGCAATTTTCCAAATTCGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAAT
111662 TCGTTGC
130 TCGTTGC
111669 GAAAAT
1 GAAAAT
111675 TCGTTTGTGA
Statistics
Matches: 131, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
136 35 0.27
137 96 0.73
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (136 bp):
GAAAATCGCGTTGCGATTTTCCAGCTCGCGTTGCGATGTTGAAAATCGTGTTGCGATAGTCTACA
GTTGTCGTTGCAATTTTCCAAATTCGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATT
CGTTGC
Found at i:111658 original size:22 final size:21
Alignment explanation
Indices: 111582--111652 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 21
111572 TGAAAATCGT
111582 GTTGCGATAGTCTACAGTTGTC
1 GTTGCGATAGTCTACAGTT-TC
* * **
111604 GTTGCGAT--TTTCCAAATTC
1 GTTGCGATAGTCTACAGTTTC
*
111623 GTTGCGGTAGTCTACAGTTATC
1 GTTGCGATAGTCTACAGTT-TC
111645 GTTGCGAT
1 GTTGCGAT
111653 TTTCTAAATT
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
19 9 0.25
20 5 0.14
21 5 0.14
22 17 0.47
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (21 bp):
GTTGCGATAGTCTACAGTTTC
Found at i:111776 original size:6 final size:6
Alignment explanation
Indices: 111765--111803 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
111755 AGACACGTAT
111765 GACCAC GACCAC GACCAC GACCAC GACCAC GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
111804 CGAGACGGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.31, C:0.51, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:112456 original size:20 final size:20
Alignment explanation
Indices: 112431--112585 Score: 130
Period size: 20 Copynumber: 7.6 Consensus size: 20
112421 ATTGTAGACT
*
112431 ATCGCAATGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
112451 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
112471 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
112492 ATAGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
112512 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
** ** *
112533 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGAAATGGAA-A
112554 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
112574 ATCGCAACGCGA
1 ATCGCAACGCGA
112586 TTTCCAACTA
Statistics
Matches: 109, Mismatches: 24, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
20 60 0.55
21 49 0.45
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:112499 original size:41 final size:41
Alignment explanation
Indices: 112454--112544 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
112444 ATGGAAAATC
112454 GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATA
1 GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATA
*
112495 GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATC
1 GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATA
112536 GCAACGCGA
1 GCAACGCGA
112545 TTTTCAATTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (41 bp):
GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATA
Found at i:112500 original size:21 final size:21
Alignment explanation
Indices: 112471--112606 Score: 141
Period size: 21 Copynumber: 6.6 Consensus size: 21
112461 GAAATGGAAA
112471 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* ** ** *
112492 ATAGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
112512 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
112533 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
** ** *
112554 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
*
112574 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTTCAACT
112595 ATCGCAACGCGA
1 ATCGCAACGCGA
112607 AATGCAACAC
Statistics
Matches: 90, Mismatches: 23, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
20 29 0.32
21 61 0.68
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:112504 original size:61 final size:61
Alignment explanation
Indices: 112404--112585 Score: 242
Period size: 61 Copynumber: 3.0 Consensus size: 61
112394 ACAACGAATT
* *
112404 TGGAAAATCGCAACGAC-ATTGT-AGACTATCGCAATGCGAAATGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAAA
* **
112465 TGGAAAATCGCAACGCGATTTTCAACTATAGCAACGCGAAATGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGAAA
** * *
112526 TTCAACTATCGCAACGCGATTTTCAATTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 TGGAA-AATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
112586 TTTCCAACTA
Statistics
Matches: 108, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
60 1 0.01
61 55 0.51
62 52 0.48
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (61 bp):
TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGAAA
Found at i:112561 original size:62 final size:62
Alignment explanation
Indices: 112428--112606 Score: 270
Period size: 62 Copynumber: 2.9 Consensus size: 62
112418 GACATTGTAG
* ** ** *
112428 ACTATCGCAATGCGAAATGGAAAATCGCAACGCGAAATGGAA-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTCCAACTATCGCAACGCGATTTTCA
* *
112489 ACTATAGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTCCAACTATCGCAACGCGATTTTCA
*
112551 ATTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTCCAACTATCGCAACGCGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTCCAACTATCGCAACGCGA
112607 AATGCAACAC
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
61 36 0.34
62 71 0.66
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (62 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTCCAACTATCGCAACGCGATTTTCA
Found at i:112578 original size:41 final size:41
Alignment explanation
Indices: 112533--112610 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
112523 ATTTTCAACT
* *
112533 ATCGCAACGCGATTTTCAATTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTCCAACTATCGCAACGCGAAATGGAAA
112574 ATCGCAACGCGATTTCCAACTATCGCAACGCGAAATG
1 ATCGCAACGCGATTTCCAACTATCGCAACGCGAAATG
112611 CAACACGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGATTTCCAACTATCGCAACGCGAAATGGAAA
Found at i:132311 original size:27 final size:28
Alignment explanation
Indices: 132263--132316 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
132253 TGTGTTAGAA
132263 AAAAAAGGAAAATGAATGATAAAGAAAGT
1 AAAAAAGGAAAATGAA-GATAAAGAAAGT
132292 AAAAAA-GACAAATGAA-ATAAAGAAA
1 AAAAAAGGA-AAATGAAGATAAAGAAA
132317 ATAAGAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.38
28 2 0.08
29 13 0.54
ACGTcount: A:0.70, C:0.02, G:0.17, T:0.11
Consensus pattern (28 bp):
AAAAAAGGAAAATGAAGATAAAGAAAGT
Found at i:132579 original size:23 final size:23
Alignment explanation
Indices: 132514--132579 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 23
132504 CATCTATACC
*
132514 TATATATATAACAAATAACGATAATA
1 TATATATATAAAAAAT-A--ATAATA
* *
132540 TATATATATATATAATAATAATA
1 TATATATATAAAAAATAATAATA
132563 TA-ATATAATAAAAAATA
1 TATATAT-ATAAAAAATA
132580 GAGGAATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
22 4 0.12
23 16 0.47
25 1 0.03
26 13 0.38
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.35
Consensus pattern (23 bp):
TATATATATAAAAAATAATAATA
Found at i:132622 original size:2 final size:2
Alignment explanation
Indices: 132615--132647 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
132605 AATATACTTA
132615 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
132648 CTAATATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:134611 original size:36 final size:36
Alignment explanation
Indices: 134560--134840 Score: 185
Period size: 36 Copynumber: 8.3 Consensus size: 36
134550 ATTAAAAGAT
*
134560 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAA
**
134596 TTTGTTTCAAAGGAAA-TAGAT-TC-A-A-AG---ATT
1 TTTGTTTCAAAGGAAACT-G-TCTCAAGAGAGACAAAA
*
134626 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAA
* *
134662 --T-TTT--AAGAGAAAATGTCTCAAGAGAGACATAA
1 TTTGTTTCAAAG-GAAACTGTCTCAAGAGAGACAAAA
* * * *
134694 TTTGTTTTAAACGAAACTGTCTCAAG-GTAGACGAAT
1 TTTGTTTCAAAGGAAACTGTCTCAAGAG-AGACAAAA
* * *
134730 TTTTTTTC-AAGGAAAACATAT-T-AA-A-AG----AT
1 TTTGTTTCAAAGG-AAAC-TGTCTCAAGAGAGACAAAA
* *
134759 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAA
* * *
134795 ATTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAA
134831 TTTGTTTCAA
1 TTTGTTTCAA
134841 GTTGGGTCAA
Statistics
Matches: 188, Mismatches: 28, Indels: 58
0.69 0.10 0.21
Matches are distributed among these distances:
28 2 0.01
29 14 0.07
30 24 0.13
31 5 0.03
32 25 0.13
33 9 0.05
34 3 0.02
35 11 0.06
36 90 0.48
37 5 0.03
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (36 bp):
TTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAA
Found at i:134780 original size:133 final size:138
Alignment explanation
Indices: 134572--134837 Score: 375
Period size: 134 Copynumber: 2.0 Consensus size: 138
134562 TGTTTCAAGG
* *
134572 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAATAGATTCAAAGATTTTTGTTTCAAG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACAGATTAAAAGATTTTTGTTTCAAG
*
134637 GGAAACTGTCTCAAGAGAGAC-AAAA-T-TTT-AAGAGAAAATGTCTCAAGAGAGACATAATTTG
66 GGAAACTGTCTCAAGAGAGACAAAAATTATTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTG
134698 TTTTAAAC
131 TTTTAAAC
* * * *
134706 GAAACTGTCTCAAG-GTAGACGAATTTTTTTTC-AAGGAAAACATATTAAAAGA-TTTTGTTTCA
1 GAAACTGTCTCAAGAG-AGACAAAATTTGTTTCAAAGG-AAACAGATTAAAAGATTTTTGTTTCA
* * *
134768 AGGGAAATTGTCTCAAGAGAGACAAAAATTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
64 AGGGAAACTGTCTCAAGAGAGACAAAAATTATTTCAAGAGAAAATGTCTCAAGAGAGACAAAATT
134833 TGTTT
129 TGTTT
134838 CAAGTTGGGT
Statistics
Matches: 116, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
133 37 0.32
134 43 0.37
135 1 0.01
136 3 0.03
137 32 0.28
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (138 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACAGATTAAAAGATTTTTGTTTCAAG
GGAAACTGTCTCAAGAGAGACAAAAATTATTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTG
TTTTAAAC
Found at i:134804 original size:65 final size:65
Alignment explanation
Indices: 134499--134811 Score: 287
Period size: 65 Copynumber: 4.8 Consensus size: 65
134489 AGACAAAATT
* * * * * *
134499 TTTCAAGAGAAATTGTCTCGAGAGAGACGAAATTTGTTTAAAGGAAAACAAATTAAAAGATTTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACATATTAAAAGATTTTG
* * *
134564 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGG-AAATAGATTCAAAGATTTT
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTC-AAGGAAAACATATTAAAAGA-TTT
134628 TG
64 TG
** * *
134630 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--T-TTT-AAGAGAAAATGTCTCAAGAGAGACA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG-GAAAACATATTAA-A-AG--A
134691 TAATTTG
61 T--TTTG
* ** * * *
134698 TTTTAAACGAAACTGTCTCAAG-GTAGACGAATTTTTTTTCAAGGAAAACATATTAAAAGATTTT
1 TTTCAAGGGAAACTGTCTCAAGAG-AGACAAAATTTGTTTCAAGGAAAACATATTAAAAGATTTT
134762 G
65 G
* * * *
134763 TTTCAAGGGAAATTGTCTCAAGAGAGACAAAAATTATTTCAAGGGAAAC
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAAC
134812 TGTCTCAAGA
Statistics
Matches: 201, Mismatches: 31, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
61 3 0.01
62 1 0.00
63 9 0.04
64 2 0.01
65 91 0.45
66 43 0.21
67 4 0.02
68 29 0.14
69 2 0.01
70 2 0.01
71 12 0.06
72 3 0.01
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (65 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACATATTAAAAGATTTTG
Found at i:134841 original size:36 final size:36
Alignment explanation
Indices: 134626--134841 Score: 188
Period size: 36 Copynumber: 6.3 Consensus size: 36
134616 TTCAAAGATT
134626 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
134662 --T-TTT-AAGAGAAAATGTCTCAAGAGAGACATAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* ** * *
134694 TTTGTTTTAAACGAAACTGTCTCAAG-GTAGACGAAT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAG-AGACAAAA
* * * *
134730 TTTTTTTCAAGGAAAACATAT-T-AA-A-AG----AT
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
*
134759 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
134795 ATTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
134831 TTTGTTTCAAG
1 TTTGTTTCAAG
134842 TTGGGTCAAT
Statistics
Matches: 140, Mismatches: 25, Indels: 30
0.72 0.13 0.15
Matches are distributed among these distances:
28 2 0.01
29 17 0.12
30 2 0.01
31 1 0.01
32 27 0.19
33 5 0.04
34 2 0.01
35 6 0.04
36 76 0.54
37 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:136893 original size:95 final size:95
Alignment explanation
Indices: 136725--136906 Score: 310
Period size: 95 Copynumber: 1.9 Consensus size: 95
136715 ATATGTAAAT
* * *
136725 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGG
*
136790 ACAGCTCAAGCTTTATTGTATAGTATACTC
66 ACAACTCAAGCTTTATTGTATAGTATACTC
*
136820 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTATAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGG
*
136885 ACAACTCAAGTTTTATTGTATA
66 ACAACTCAAGCTTTATTGTATA
136907 TAATTAATAT
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 81 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGG
ACAACTCAAGCTTTATTGTATAGTATACTC
Found at i:141626 original size:25 final size:25
Alignment explanation
Indices: 141598--141648 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
141588 TTTCCAATTG
141598 TCTTACGTTAAGAAAATTACAGGTT
1 TCTTACGTTAAGAAAATTACAGGTT
141623 TCTTACGTTAAGAAAATTACAGGTT
1 TCTTACGTTAAGAAAATTACAGGTT
141648 T
1 T
141649 AATTAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (25 bp):
TCTTACGTTAAGAAAATTACAGGTT
Found at i:142051 original size:19 final size:20
Alignment explanation
Indices: 142014--142055 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
142004 ATAACGATAT
142014 AAAATATATATATATATAATA
1 AAAATATATATATATATAA-A
142035 AAAATATA-ATATA-ATAAA
1 AAAATATATATATATATAAA
142053 AAA
1 AAA
142056 TAGAGGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 4 0.19
20 5 0.24
21 8 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATATATATATATATAAA
Found at i:142057 original size:17 final size:17
Alignment explanation
Indices: 142021--142054 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
142011 TATAAAATAT
142021 ATATATATATAATAAAA
1 ATATATATATAATAAAA
142038 ATATA-ATATAATAAAA
1 ATATATATATAATAAAA
142054 A
1 A
142055 ATAGAGGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATATATATAATAAAA
Found at i:157478 original size:21 final size:21
Alignment explanation
Indices: 157452--157494 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
157442 GAGTAAGGAG
*
157452 TAAAAATTGAATAAAATATAA
1 TAAAAATGGAATAAAATATAA
157473 TAAAAATGGAATAAAATATAA
1 TAAAAATGGAATAAAATATAA
157494 T
1 T
157495 CTTAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (21 bp):
TAAAAATGGAATAAAATATAA
Found at i:157661 original size:45 final size:44
Alignment explanation
Indices: 157612--157696 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 44
157602 AGTATCAAAT
* *
157612 CTAAATCATTGAATATTT-ATAATAAATAATTATTAGTAATCATTA
1 CTAAATCATTAAAT-TTTAATAATAAATAATTAGTAG-AATCATTA
*
157657 CTAAATCATTAAATTTTAATAATAAATCATTAGTAGAATC
1 CTAAATCATTAAATTTTAATAATAAATAATTAGTAGAATC
157697 GGTACCATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 7 0.19
45 29 0.81
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (44 bp):
CTAAATCATTAAATTTTAATAATAAATAATTAGTAGAATCATTA
Found at i:164588 original size:172 final size:177
Alignment explanation
Indices: 164380--164728 Score: 654
Period size: 173 Copynumber: 2.0 Consensus size: 177
164370 ATATTTTTTT
*
164380 ACTATATAAATAGACAAAAACTTGCAATGTAAAAAACCCATGTCTATACATGCA-GCATTGGTGT
1 ACTATATAAATAGACAAAAACTTGCAATGTAAAAAACCCATGTATATACATGCAGGCATTGGTGT
164444 TTCCTGGTCGCTTTACTTTCAAGTTTGCCCGCTCTGTAACTTAG-AATAAAC-AA-GGTATTCAA
66 TTCCTGGTCGCTTTACTTTCAAGTTTGCCCGCTCTGTAACTTAGAAATAAACAAAGGGTATTCAA
164506 AGAAATTTCTTTCTTTATCATTCCCTCTTTTTTTTTATCATTTCGTC
131 AGAAATTTCTTTCTTTATCATTCCCTCTTTTTTTTTATCATTTCGTC
164553 ACTATATAAATAGAC-AAAACTTGCAATGTAAAAAACCCATGTATATACATGCAGGCATTGGTGT
1 ACTATATAAATAGACAAAAACTTGCAATGTAAAAAACCCATGTATATACATGCAGGCATTGGTGT
164617 TTCCTGGTCGCTTTACTTTCAAGTTTGCCCGCTCTGTAACTTAGAAATAAACAAAGGGTATTCAA
66 TTCCTGGTCGCTTTACTTTCAAGTTTGCCCGCTCTGTAACTTAGAAATAAACAAAGGGTATTCAA
164682 AGAAATTTCTTTCTTTATCATTCCCTCTTTTTTTTTATCATTTCGTC
131 AGAAATTTCTTTCTTTATCATTCCCTCTTTTTTTTTATCATTTCGTC
164729 TCGGAGAAAT
Statistics
Matches: 171, Mismatches: 1, Indels: 5
0.97 0.01 0.03
Matches are distributed among these distances:
172 37 0.22
173 69 0.40
174 7 0.04
175 2 0.01
176 56 0.33
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (177 bp):
ACTATATAAATAGACAAAAACTTGCAATGTAAAAAACCCATGTATATACATGCAGGCATTGGTGT
TTCCTGGTCGCTTTACTTTCAAGTTTGCCCGCTCTGTAACTTAGAAATAAACAAAGGGTATTCAA
AGAAATTTCTTTCTTTATCATTCCCTCTTTTTTTTTATCATTTCGTC
Found at i:168591 original size:37 final size:36
Alignment explanation
Indices: 168532--168650 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 36
168522 ATCCCATTAT
* *
168532 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAAAAACATTTACCAAACTTTG-AAAAC
*
168568 TATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
*
168604 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
168639 CATTTTTTCAAA
1 CA-TTTTTCAAA
168651 GTTGGTTACC
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 34 0.45
36 13 0.17
37 28 0.37
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
Found at i:168607 original size:21 final size:21
Alignment explanation
Indices: 168578--168643 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
168568 TATTTTTCAA
*
168578 AAAAACATTTACCAAACTTTG
1 AAAACCATTTACCAAACTTTG
*
168599 AAAACCATTT-TCAAA----G
1 AAAACCATTTACCAAACTTTG
168615 -AAA-CATTTACCAAACTTTG
1 AAAACCATTTACCAAACTTTG
168634 AAAACCATTT
1 AAAACCATTT
168644 TTTCAAAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
14 5 0.14
15 7 0.20
16 1 0.03
19 1 0.03
20 7 0.20
21 14 0.40
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.29
Consensus pattern (21 bp):
AAAACCATTTACCAAACTTTG
Found at i:168660 original size:35 final size:36
Alignment explanation
Indices: 168534--168678 Score: 133
Period size: 35 Copynumber: 4.1 Consensus size: 36
168524 CCCATTATCA
*
168534 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
* *
168569 ATTTTTCAAAAAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTC-AAAGAACAGTTACCAAACTTTGAAAACCAT
*
168606 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
168642 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
168676 TTT
1 TTT
168679 AATACTTTCA
Statistics
Matches: 96, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
34 17 0.18
35 39 0.41
36 7 0.07
37 32 0.33
38 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:173155 original size:36 final size:37
Alignment explanation
Indices: 173097--173168 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
173087 CATTTTCAAC
*
173097 AACATCTACAAACTTTGAAAAACTA-TTTTTCAAAGA
1 AACATCTACAAACTTTGAAAAACCATTTTTTCAAAGA
*
173133 AACATTTACCAAACTTTG-AAAACCATTTTTTCAAAG
1 AACATCTA-CAAACTTTGAAAAACCATTTTTTCAAAG
173169 TTGGTTACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 13 0.41
37 19 0.59
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (37 bp):
AACATCTACAAACTTTGAAAAACCATTTTTTCAAAGA
Found at i:176779 original size:29 final size:29
Alignment explanation
Indices: 176743--176801 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
176733 GCAGAATAGA
176743 AGACCATCTAAGTAACTCCACAAAATAAT
1 AGACCATCTAAGTAACTCCACAAAATAAT
176772 AGACCATCTAAGTAACTCCACAAAATAAT
1 AGACCATCTAAGTAACTCCACAAAATAAT
176801 A
1 A
176802 TGCAGTAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.24, G:0.07, T:0.20
Consensus pattern (29 bp):
AGACCATCTAAGTAACTCCACAAAATAAT
Found at i:177331 original size:37 final size:37
Alignment explanation
Indices: 177281--177388 Score: 171
Period size: 37 Copynumber: 2.9 Consensus size: 37
177271 TTCTGGATCC
** *
177281 TATTTTTAGGAGTTTGAATTATAGTAGAACTCTATCA
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCA
* *
177318 TATTTTAAGGAGTTTGAATCCTAGTAAAACTCTATCC
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCA
177355 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
177389 ACGCTATGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCA
Found at i:178196 original size:34 final size:35
Alignment explanation
Indices: 178120--178208 Score: 137
Period size: 34 Copynumber: 2.6 Consensus size: 35
178110 AACTCGAGGG
*
178120 TTTG-GTGTTTCAAGAGAAACATTTTCAAAGGCTT
1 TTTGTGTGTTTCAAGAGAAACAATTTCAAAGGCTT
*
178154 TTTGTGTGTTTCAAGAGAAACAATTTCAAA-GTTT
1 TTTGTGTGTTTCAAGAGAAACAATTTCAAAGGCTT
*
178188 TTTTTGTGTTTCAAGAGAAAC
1 TTTGTGTGTTTCAAGAGAAAC
178209 TGTATTCAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
34 27 0.53
35 24 0.47
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.40
Consensus pattern (35 bp):
TTTGTGTGTTTCAAGAGAAACAATTTCAAAGGCTT
Found at i:178217 original size:35 final size:33
Alignment explanation
Indices: 178120--178219 Score: 121
Period size: 35 Copynumber: 2.9 Consensus size: 33
178110 AACTCGAGGG
178120 TTTG-GTGTTTCAAGAGAAACATTTTCAAAGGCTT
1 TTTGTGTGTTTCAAGAGAAAC-TTTTCAAA-GCTT
* *
178154 TTTGTGTGTTTCAAGAGAAACAATTTCAAAGTTT
1 TTTGTGTGTTTCAAGAGAAAC-TTTTCAAAGCTT
*
178188 TTTTTGTGTTTCAAGAGAAACTGTATTCAAAG
1 TTTGTGTGTTTCAAGAGAAACT-T-TTCAAAG
178220 ATTGAAGTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
34 28 0.47
35 31 0.53
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (33 bp):
TTTGTGTGTTTCAAGAGAAACTTTTCAAAGCTT
Found at i:178278 original size:36 final size:36
Alignment explanation
Indices: 178226--178294 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
178216 AAAGATTGAA
* *
178226 GTTTCAAGGGAGACTGTCTCAAAAGAGACAAAATTT
1 GTTTCAAGAGAAACTGTCTCAAAAGAGACAAAATTT
*
178262 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 GTTTCAAGAGAAACTGTCTCAAAAGAGACAAAA
178295 ACTTCCAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGTCTCAAAAGAGACAAAATTT
Found at i:178576 original size:101 final size:100
Alignment explanation
Indices: 178361--178791 Score: 287
Period size: 101 Copynumber: 4.2 Consensus size: 100
178351 CAAAGATTTT
* * * *
178361 GTTTCAAAGGAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAATTGTCTCAAGGGAGACAAAATT
1 GTTTC-AAGGAAACTGTTTTCAATGTTTATGTTTAAAGAGAAACTGTCTCAAGGGAGA-AAAATT
* *
178426 TGTTTC-AAGGAAAAC-GATCTCATA-AGTGACAAAATTCA
64 TG-TTCAAAGG-AAACTG-TCTCA-AGGGAGACAAAATTCA
*
178464 -TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTAAAGAGAAACTGTCTTAAGGGAGATAAAATT
1 GTTTCAA-GGAAACTGTTTTCAATGTTTATGTTTAAAGAGAAACTGTCTCAAGGGAGA-AAAA-T
* **
178527 TTGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAATT-A
63 TTGTT-CAAAGGAAACTGTCTCAAGGGAGACAAAATTCA
* * * * *
178565 GTTTCAAGGAAAACAGATTT-AAT-TATTTTGTTTAAAGGGAAACTGTCTCAAGAGAGAAAAAAT
1 GTTTCAAGG-AAACTGTTTTCAATGT-TTATGTTTAAAGAGAAACTGTCTCAAGGGAG-AAAAAT
*
178628 TTGTTTAAAGGGAAACTGTCTCAAGGGAGACAAAATTTC-
63 TTGTTCAAA-GGAAACTGTCTCAAGGGAGACAAAA-TTCA
* * * * * *
178667 -TTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT-TGTTTCAAGGGAAACTGTCTCAAGAGAG
1 GTTTCAAG-GAAACTGTTTTC-A-A-TG-----TTTATGTTTAAAGAGAAACTGTCTCAAGGGAG
*
178729 ACAAAATTTGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAACTT-A
57 A-AAAATTTG-TTCAAAG-GAAACTGTCTCAAGGGAGACAAAA-TTCA
*
178775 GTTCCAAGAGAAACTGT
1 GTTTCAAG-GAAACTGT
178792 ATTAAGGGAG
Statistics
Matches: 267, Mismatches: 30, Indels: 55
0.76 0.09 0.16
Matches are distributed among these distances:
100 5 0.02
101 92 0.34
102 78 0.29
103 10 0.04
107 2 0.01
108 62 0.23
109 18 0.07
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.28
Consensus pattern (100 bp):
GTTTCAAGGAAACTGTTTTCAATGTTTATGTTTAAAGAGAAACTGTCTCAAGGGAGAAAAATTTG
TTCAAAGGAAACTGTCTCAAGGGAGACAAAATTCA
Found at i:178638 original size:36 final size:36
Alignment explanation
Indices: 178591--179014 Score: 441
Period size: 36 Copynumber: 12.1 Consensus size: 36
178581 ATTTAATTAT
* *
178591 TTTGTTTAAAGGGAAACTGTCTCAAGAGAGAAAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
178627 TTTGTTTAAAGGGAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
178663 TTTCTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
178699 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
178735 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * * * * *
178771 CTTAGTTCCAAGAGAAACTGTATTAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** *
178808 TTAGTTTCAAGGAAAACACAT-TC-A-A-AG----AT
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
*
178837 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
178873 TTTATTTCAAGGGAAACTGTCTCAA-AGGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGA-GAGACAAAA
** *
178909 TTTGTTTCAAGGGAAAACAAAT-TC-A-A-AG----AT
1 TTTGTTTCAAGGG-AAAC-TGTCTCAAGAGAGACAAAA
*
178939 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
178975 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
179011 TTTG
1 TTTG
179015 GGAACTGTCT
Statistics
Matches: 328, Mismatches: 39, Indels: 42
0.80 0.10 0.10
Matches are distributed among these distances:
28 2 0.01
29 24 0.07
30 16 0.05
31 1 0.00
32 4 0.01
33 2 0.01
34 2 0.01
35 2 0.01
36 237 0.72
37 37 0.11
38 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:178746 original size:21 final size:21
Alignment explanation
Indices: 178684--178748 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
178674 AGAAACTGTC
178684 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
178705 TCAAG-G-G---AAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
178720 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
178741 TCAAGAGA
1 TCAAGAGA
178749 AACTGTCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 1 0.03
19 1 0.03
20 4 0.12
21 16 0.47
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:178841 original size:246 final size:240
Alignment explanation
Indices: 178491--179010 Score: 720
Period size: 246 Copynumber: 2.1 Consensus size: 240
178481 TCAATGTTTA
* * * * *
178491 TGTTTAAAGAGAAACTGTCTTAAGGGAGATAAAATTTTGTTCCAAAAGAAACTGTCTCAAGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAACTTAGTTCCAAAAGAAACTGTATCAAGGGAG
* * * **
178556 ACGGAATTAGTTTCAAGGAAAACAGATTTAATTATTTTGTTTAAAGGGAAACTGTCTCAAGAGAG
66 ACGAAATTAGTTTCAAGGAAAACACATTCAAAGATTTTGTTTAAAGGGAAACTGTCTCAAGAGAG
* * **
178621 AAAAAATTTGTTTAAAGGGAAACTGTCTCAAGGGAGACAAAATTTCTTTCAAGAG-AAAC-TGTC
131 AAAAAATTTATTTAAAGGGAAACTGTCTCAAAGGAGACAAAATTTCTTTCAAGAGAAAACAAAT-
178684 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
195 TC-A-A-AG----AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * * *
178737 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAGAAACTGTATTAAGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAACTTAGTTCCAAAAGAAACTGTATCAAGGGAG
*
178802 ACGAAATTAGTTTCAAGGAAAACACATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
66 ACGAAATTAGTTTCAAGGAAAACACATTCAAAGATTTTGTTTAAAGGGAAACTGTCTCAAGAGAG
* * * *
178867 ATAAAATTTATTTCAAGGGAAACTGTCTCAAAGGAGACAAAATTTGTTTCAAGGGAAAACAAATT
131 AAAAAATTTATTTAAAGGGAAACTGTCTCAAAGGAGACAAAATTTCTTTCAAGAGAAAACAAATT
* *
178932 CAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
196 CAAAGAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
178977 TGTTTCAAGGGAAACTGTCTCAAGGGAGATAAAA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAA
179011 TTTGGGAACT
Statistics
Matches: 244, Mismatches: 28, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
240 69 0.28
244 2 0.01
245 1 0.00
246 165 0.68
247 6 0.02
248 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (240 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAACTTAGTTCCAAAAGAAACTGTATCAAGGGAG
ACGAAATTAGTTTCAAGGAAAACACATTCAAAGATTTTGTTTAAAGGGAAACTGTCTCAAGAGAG
AAAAAATTTATTTAAAGGGAAACTGTCTCAAAGGAGACAAAATTTCTTTCAAGAGAAAACAAATT
CAAAGAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:178924 original size:102 final size:102
Alignment explanation
Indices: 178627--179014 Score: 460
Period size: 102 Copynumber: 3.7 Consensus size: 102
178617 AGAGAAAAAA
* * *
178627 TTTGTTTAAAGGGAAACTGTCTCAAGGGAGACAAAATTTCTTTCAAGAGAAACTGTCTC-AAGAG
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAAG-G
** *
178691 AGACAAAATTTGTTTCAAGGG-AAAC-TGTCTCAAGAGAGACAAAA
65 AGACAAAATTTGTTTCAAGGGAAAACAAAT-TC-A-A-AG----AT
* * * * * *
178735 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAGAAACTGTATTAAGGG
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGAGAAACTGTCTCAAAGG
* * *
178800 AGACGAAATTAGTTTCAA-GGAAAACACATTCAAAGAT
65 AGACAAAATTTGTTTCAAGGGAAAACAAATTCAAAGAT
* *
178837 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTATTTCAAGGGAAACTGTCTCAAAGGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAAGGA
178902 GACAAAATTTGTTTCAAGGGAAAACAAATTCAAAGAT
66 GACAAAATTTGTTTCAAGGGAAAACAAATTCAAAGAT
* * * *
178939 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAAGGA
*
179004 GATAAAATTTG
66 GACAAAATTTG
179015 GGAACTGTCT
Statistics
Matches: 245, Mismatches: 30, Indels: 16
0.84 0.10 0.05
Matches are distributed among these distances:
101 35 0.14
102 127 0.52
106 2 0.01
107 1 0.00
108 38 0.16
109 39 0.16
110 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (102 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAAGGA
GACAAAATTTGTTTCAAGGGAAAACAAATTCAAAGAT
Found at i:180259 original size:32 final size:32
Alignment explanation
Indices: 180223--180288 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
180213 ATTCCCAAAG
* *
180223 ATGCCCCAATATTCGATGTTGAATCTAAAAAA
1 ATGCCCCAAAATTCGATGTTAAATCTAAAAAA
* * *
180255 ATGCCCTAAAATTTGATGTTAAATCTCAAAAA
1 ATGCCCCAAAATTCGATGTTAAATCTAAAAAA
180287 AT
1 AT
180289 ACCCTAGCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (32 bp):
ATGCCCCAAAATTCGATGTTAAATCTAAAAAA
Found at i:180294 original size:32 final size:32
Alignment explanation
Indices: 180237--180306 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
180227 CCCAATATTC
* *
180237 GATGTTGAATCTAAAAAAATGCCCTAAAATTT
1 GATGTTAAATCTAAAAAAATACCCTAAAATTT
* **
180269 GATGTTAAATCTCAAAAAATACCCTAGCATTT
1 GATGTTAAATCTAAAAAAATACCCTAAAATTT
180301 GATGTT
1 GATGTT
180307 GAATATTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (32 bp):
GATGTTAAATCTAAAAAAATACCCTAAAATTT
Found at i:181394 original size:25 final size:25
Alignment explanation
Indices: 181353--181411 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
181343 TTTTTCTTCA
* *
181353 ATTTTC-CTTTGTTTTTTCTCTTTTT
1 ATTTTCTCTTTGTCTTTTCTC-TCTT
*
181378 ATTTTCTCTTTG-CTTTTTTCTCTT
1 ATTTTCTCTTTGTCTTTTCTCTCTT
181402 -TTTTCTCTTT
1 ATTTTCTCTTT
181412 TTGTTCTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 10 0.33
24 3 0.10
25 12 0.40
26 5 0.17
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (25 bp):
ATTTTCTCTTTGTCTTTTCTCTCTT
Found at i:181396 original size:14 final size:13
Alignment explanation
Indices: 181354--181402 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
181344 TTTTCTTCAA
181354 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
181366 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
181378 ATTTTCTCTTTGCTT
1 -TTTTCTCTTTG-TT
181393 TTTTCTCTTT
1 TTTTCTCTTT
181403 TTTCTCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
14 10 0.30
15 2 0.06
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:181400 original size:27 final size:25
Alignment explanation
Indices: 181353--181404 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 25
181343 TTTTTCTTCA
181353 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTTTTCTCTTTTT
181378 ATTTTCTCTTTGCTTTTTTCTCTTTTT
1 ATTTTC-CTTTG-TTTTTTCTCTTTTT
181405 TCTCTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (25 bp):
ATTTTCCTTTGTTTTTTCTCTTTTT
Found at i:183594 original size:15 final size:15
Alignment explanation
Indices: 183574--183602 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
183564 CAGAAAATAA
183574 AGCATGAAACAAAGT
1 AGCATGAAACAAAGT
183589 AGCATGAAACAAAG
1 AGCATGAAACAAAG
183603 GCTCTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.14, G:0.21, T:0.10
Consensus pattern (15 bp):
AGCATGAAACAAAGT
Found at i:184498 original size:13 final size:13
Alignment explanation
Indices: 184480--184510 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
184470 TTTGTATGTA
*
184480 AATAGTGTGTTAC
1 AATAGTGAGTTAC
184493 AATAGTGAGTTAC
1 AATAGTGAGTTAC
184506 AATAG
1 AATAG
184511 CTATTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (13 bp):
AATAGTGAGTTAC
Found at i:184584 original size:37 final size:37
Alignment explanation
Indices: 184534--184604 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
184524 TTCTGGATCC
184534 TATTTTTAGGAGTTTGAATCATAGAAAAACTCTATCA
1 TATTTTTAGGAGTTTGAATCATAGAAAAACTCTATCA
* *
184571 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCATAGAAAAACTCTA
184605 ACGCTATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.39
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAGAAAAACTCTATCA
Found at i:193210 original size:3 final size:3
Alignment explanation
Indices: 193191--193225 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
193181 CGTATATATG
*
193191 TAT TAT TAA TAT T-T TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
193226 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:196494 original size:207 final size:207
Alignment explanation
Indices: 195878--196694 Score: 1075
Period size: 207 Copynumber: 4.0 Consensus size: 207
195868 CATGATTCTG
* * *
195878 TGAAGAAGGTATTGTCCGTGGATCCATATAAGGTCTGTAAGGCAATGATCTTACCATTGTTGAAG
1 TGAAGTAGGTACTGTCCGAGGATCCATATAAGGTCTGTAAGGCAATGATCTTACCATTGTTGAAG
* * * * *
195943 AGGATCCAATATCATTGCCGTCTAACTGCTGAAGTACACTCTGGTGATGAAACTTTTGTTGAGGT
66 TGGATCCAATATCATTGCCGGCTAACTGCTGAGGTGCACTCTGGTGATGAAAGTTTTGTTGAGGT
* * * * *
196008 TGATAATAATTTAGGACGGGATCGGCATTGGAATGACGAATTACACCTAAATCATGAGTGGAATG
131 TGATAAGAATTTAGGACGAGATCGGCATTGGAATGATGAATGACACCTAAATCATCAGTGGAATG
*
196073 AACACGTTTTGT
196 AACAGGTTTTGT
*
196085 T---GTAGGTATTGTCCGTA-GATCCATATAAGGTCTGTAAGGCAATGATCTTACCATTGTTGAA
1 TGAAGTAGGTACTGTCCG-AGGATCCATATAAGGTCTGTAAGGCAATGATCTTACCATTGTTGAA
* * * * *
196146 GTGGATCCAATATCATTGCCGGCTAACTGCTGATGTGCACTTTGGCGATGAAA-----ATT-CGG
65 GTGGATCCAATATCATTGCCGGCTAACTGCTGAGGTGCACTCTGGTGATGAAAGTTTTGTTGAGG
* *
196205 TTGATAAGAATTTAGGACGGGATTGGCATTGGAATGATG-ATGGACACCTAAATCATCAGTGGAA
130 TTGATAAGAATTTAGGACGAGATCGGCATTGGAATGATGAAT-GACACCTAAATCATCAGTGGAA
*
196269 TGAACAGATTTTGT
194 TGAACAGGTTTTGT
* *
196283 TGAAGTAGGTACTGTCCGAGGATCCATATAAGGTCTGCAAGGCAATGATCTTACCATTGTTGACG
1 TGAAGTAGGTACTGTCCGAGGATCCATATAAGGTCTGTAAGGCAATGATCTTACCATTGTTGAAG
* * * *
196348 TGGATCCAATATCATTGCTGGC-ATACTGTTGAGGTGCATTCGGGTGATGAAAGTTTTGTTGAGG
66 TGGATCCAATATCATTGCCGGCTA-ACTGCTGAGGTGCACTCTGGTGATGAAAGTTTTGTTGAGG
* * * * *
196412 TTGATAAGATTTTAGTACGAGATTGGCATTGGAATGATGAATGACACCTATATCATCAGTGGACT
130 TTGATAAGAATTTAGGACGAGATCGGCATTGGAATGATGAATGACACCTAAATCATCAGTGGAAT
196477 GAACAGGTTTTGT
195 GAACAGGTTTTGT
* * * *
196490 TGAAGCAGGTACTGCCCGTGGATCCATATAAGGTCTGTAAGACAATGATCTTACCATTGTTGAAG
1 TGAAGTAGGTACTGTCCGAGGATCCATATAAGGTCTGTAAGGCAATGATCTTACCATTGTTGAAG
* * *
196555 TGGATCCAATATCATTGCCGGCAAACTGGTGAGATGCACTCTGGTGATGAAAGTTTTGTTGAGGT
66 TGGATCCAATATCATTGCCGGCTAACTGCTGAGGTGCACTCTGGTGATGAAAGTTTTGTTGAGGT
* * * * * *
196620 TGATAAGAATATAGGGC-ACGATCAGCATTGGATTGATGAATGAAACCTATATCATCAGTGGAAT
131 TGATAAGAATTTAGGACGA-GATCGGCATTGGAATGATGAATGACACCTAAATCATCAGTGGAAT
*
196684 GAACATGTTTT
195 GAACAGGTTTT
196695 TCTTCCTTCG
Statistics
Matches: 538, Mismatches: 56, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
197 2 0.00
198 71 0.13
199 2 0.00
200 2 0.00
201 99 0.18
204 104 0.19
206 3 0.01
207 252 0.47
208 3 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.31
Consensus pattern (207 bp):
TGAAGTAGGTACTGTCCGAGGATCCATATAAGGTCTGTAAGGCAATGATCTTACCATTGTTGAAG
TGGATCCAATATCATTGCCGGCTAACTGCTGAGGTGCACTCTGGTGATGAAAGTTTTGTTGAGGT
TGATAAGAATTTAGGACGAGATCGGCATTGGAATGATGAATGACACCTAAATCATCAGTGGAATG
AACAGGTTTTGT
Found at i:197245 original size:176 final size:175
Alignment explanation
Indices: 196947--197497 Score: 748
Period size: 176 Copynumber: 3.1 Consensus size: 175
196937 TCCAGCATTT
* * *
196947 GGCCTCTCAGATGGTAC-GAAGGTACCACTCGTACCTAATTATAAATGAAAA-ATGTGATGTAAA
1 GGCCTCTCAGAAGGTACAG-AGGTAACACTCGTACCTAATTATAAAGGAAAACATGTGATGTAAA
* * *
197010 ATTCCAGTAGCTCAATAGTAAAAAGATATGGAATTCACAGAAACATAGTTTGTTTTCACCATCTT
65 ATTCCAGTAGCTCAATAGTCAAAAGAAATGGAATTCACAGAAACATAGTTTGCTTTCACCATCTT
* * * *
197075 GCTCT-TGTACATACCAACATCACCATTTTGCAGAGTTGTTGGAATT
130 GCTCTCT-TACATACCAACATCACCATCTTGCTGAGTTGTTGGAGTA
* *
197121 GGCCTCTCAGAAGGTACAGAGGTAACACTCGTACCTAATAATAAAGAAGAAACATGTGATGTAAA
1 GGCCTCTCAGAAGGTACAGAGGTAACACTCGTACCTAATTATAAAGGA-AAACATGTGATGTAAA
* * * * *
197186 ATTTCAGTAGCACAATAGTCAAAAGAAATGGAGTTCACAGAAACATATTTTGCTTTCACCATCTC
65 ATTCCAGTAGCTCAATAGTCAAAAGAAATGGAATTCACAGAAACATAGTTTGCTTTCACCATCTT
* * *
197251 GCTCTCTAACATACCAACATCACCAACTTGCTGAGTGGTTGGAGTA
130 GCTCTCTTACATACCAACATCACCATCTTGCTGAGTTGTTGGAGTA
* * * * * *
197297 GGTCTCTCAGACGGTACAGAGGTAGCATTCGTACCTAATTATGAAAGGCAAAACACGTGATGCAA
1 GGCCTCTCAGAAGGTACAGAGGTAACACTCGTACCTAATTAT-AAAGG-AAAACATGTGATGTAA
*
197362 AATTCCAGTAGCTCAATAGTCAAAAGAAATGGAATTCACAGAAACATAGTTTGCTTTCACCATCC
64 AATTCCAGTAGCTCAATAGTCAAAAGAAATGGAATTCACAGAAACATAGTTTGCTTTCACCATCT
* * *
197427 TGCTCTCTTACATACCAACTTCACCATCTTGCTTAATTGTTGGAGTA
129 TGCTCTCTTACATACCAACATCACCATCTTGCTGAGTTGTTGGAGTA
* *
197474 GGCCTCTCAGAGGGTACAAAGGTA
1 GGCCTCTCAGAAGGTACAGAGGTA
197498 GCAGTCATCC
Statistics
Matches: 328, Mismatches: 43, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
174 41 0.12
175 4 0.01
176 143 0.44
177 139 0.42
178 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (175 bp):
GGCCTCTCAGAAGGTACAGAGGTAACACTCGTACCTAATTATAAAGGAAAACATGTGATGTAAAA
TTCCAGTAGCTCAATAGTCAAAAGAAATGGAATTCACAGAAACATAGTTTGCTTTCACCATCTTG
CTCTCTTACATACCAACATCACCATCTTGCTGAGTTGTTGGAGTA
Found at i:198053 original size:30 final size:30
Alignment explanation
Indices: 198017--198075 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
198007 TGTTGGAGTA
** * *
198017 GGCCTCTCAGATGGTACATATGTAGCACTG
1 GGCCTCTCAGACAGTACAGAGGTAGCACTG
198047 GGCCTCTCAGACAGTACAGAGGTAGCACT
1 GGCCTCTCAGACAGTACAGAGGTAGCACT
198076 AGTACCTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.22
Consensus pattern (30 bp):
GGCCTCTCAGACAGTACAGAGGTAGCACTG
Found at i:198322 original size:148 final size:148
Alignment explanation
Indices: 198047--198324 Score: 411
Period size: 148 Copynumber: 1.9 Consensus size: 148
198037 TGTAGCACTG
* * * *
198047 GGCCTCTCAGACAGTACAGAGGTAGCACTAGTACCTAATTATAAAAGAAGAAACATGTGATGTTA
1 GGCCTCACAGACAGTACAGAGGTAGCACCAGTACCTAATAATAAAAGAAGAAACATGTGATGTAA
* *
198112 AATTCCATTAGCTCAATAGTCAAGAGAAATGGAATTCACAGAAACATAGTTCGCTTGTACCATCT
66 AATTCCAGTAGCTCAAGAGTCAAGAGAAATGGAATTCACAGAAACATAGTTCGCTTGTACCATCT
198177 TGCTGAGTTGTTTGAATA
131 TGCTGAGTTGTTTGAATA
*
198195 GGCCTCACAGACAGTACACG-GGTAGCCCCCA-TACCTAATAATAAAAGAAGAAACATGTGATGT
1 GGCCTCACAGACAGTACA-GAGGTAG-CACCAGTACCTAATAATAAAAGAAGAAACATGTGATGT
* *
198258 AAAATTCCAGTAGCTCAAGAGTCGAA-AGAAATGGACTTCACAGAAACATAGTTTGCTT-TCACC
64 AAAATTCCAGTAGCTCAAGAGTC-AAGAGAAATGGAATTCACAGAAACATAGTTCGCTTGT-ACC
198321 ATCT
127 ATCT
198325 CACACTCTTA
Statistics
Matches: 117, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
147 1 0.01
148 110 0.94
149 6 0.05
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (148 bp):
GGCCTCACAGACAGTACAGAGGTAGCACCAGTACCTAATAATAAAAGAAGAAACATGTGATGTAA
AATTCCAGTAGCTCAAGAGTCAAGAGAAATGGAATTCACAGAAACATAGTTCGCTTGTACCATCT
TGCTGAGTTGTTTGAATA
Found at i:198431 original size:30 final size:30
Alignment explanation
Indices: 198373--198434 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
198363 TTTGAAGTAG
* *
198373 GCCTCTCAGACGGCACAGGGGTATCACTCA
1 GCCTCTCAGACGGCACAGAGGTAGCACTCA
* * *
198403 GCCTCTTAGATGGTACAGAGGTAGCACTCA
1 GCCTCTCAGACGGCACAGAGGTAGCACTCA
198433 GC
1 GC
198435 TTCCCAGGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.19
Consensus pattern (30 bp):
GCCTCTCAGACGGCACAGAGGTAGCACTCA
Found at i:198974 original size:42 final size:42
Alignment explanation
Indices: 198915--198996 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
198905 GCAGTGTGTA
* *
198915 GTTTGCGCTTCTCAGGACGTACATTTCTTCTTTCAGCCTCTC
1 GTTTGCGCTTCCCAGGACATACATTTCTTCTTTCAGCCTCTC
198957 GTTTGCGCTTCCCAGGACATACATTTCTTCTTTCAGCCTC
1 GTTTGCGCTTCCCAGGACATACATTTCTTCTTTCAGCCTC
198997 ATCGCACCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.13, C:0.32, G:0.16, T:0.39
Consensus pattern (42 bp):
GTTTGCGCTTCCCAGGACATACATTTCTTCTTTCAGCCTCTC
Found at i:200959 original size:33 final size:33
Alignment explanation
Indices: 200880--200967 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 33
200870 AAAATGTTAG
**
200880 AGACTAATGCAGACCAAAAATAAACAAATTCAA
1 AGACTAATGTGGACCAAAAATAAACAAATTCAA
* * *
200913 GGACTAATTTGGACCTAAAATAAACAAA-TCACA
1 AGACTAATGTGGACCAAAAATAAACAAATTCA-A
200946 AGACTAATGTGGACCAACAAAT
1 AGACTAATGTGGACCAA-AAAT
200968 TAGAAACTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
32 3 0.07
33 38 0.84
34 4 0.09
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.18
Consensus pattern (33 bp):
AGACTAATGTGGACCAAAAATAAACAAATTCAA
Found at i:202017 original size:397 final size:396
Alignment explanation
Indices: 201108--202956 Score: 1733
Period size: 402 Copynumber: 4.7 Consensus size: 396
201098 GTGAAGAAAG
* * *
201108 TACCTCCAATGCTCAAGAATTCTTTGTTGACACACTGCCTTAGTGCCTGTGATAAGGAGGCCAAG
1 TACCTCCAATGCTCAAGAATTCTCTGTTGACACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
* * * *
201173 GTTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCGAAGGCACCCCCTTCTATGAAAC
66 GTTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCACCTCCTTCTATGGAAC
* *
201238 AACAGAAACATAAATTGTAAGGGCATTTTTTCAGATCAAATTCAATCTTCTATTTTCGAAAAAAG
131 AA-AGGATCATAAATTGTAAGGGCATTTTTTCAGATCAAATTCAATCTTCTATTTTC---AAAA-
* * * *
201303 AAAAAATTGAATTCTAAGAAGAGAAAGATGACCATTGAGAATTGCAATGACTTGATTGCAGAGAG
191 AAAAAATTGAATTCTAAGAAGAGAAAAATGACCTTTGAGAATAGCAATGACTCGATTGCAGAGAG
* * * *
201368 AATT-ATCGTTCTCAGTCTGGTC-ATTATAGTTCAAATCGTTCC-CTTCGTCTTCCTCTTCCTCC
256 -ATTCATCGTTCTCAGTCCGATCAATTATAGTTC----CCTTCCTCTT--TC-TCTTCTTCCT--
* * * * * *** * *
201430 CTGGTTTCATTTCCACTGATGCTATGAAAATT-AATCAAAATTAGAGGGGGGGGACAAAATAATT
311 C-AGTTTCATCTCCACTGATGATATGAAAATTAAATCAAACTTAAAGGGGGAAAACGAATTAATT
* *
201494 CAAAC-AGAAATAGGAATTTAGA
375 GAAACTA-AAATAGGAATTTAAA
* * * * *
201516 TACCCCCAATGCTCAAGAATTCTCTGTTGACACAGTGCCTTACTGCCAGTGATACGAAGGCCATG
1 TACCTCCAATGCTCAAGAATTCTCTGTTGACACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
* *
201581 ATTTCTCAAATAAGCTTTGAGTTCTTTCATGCTTAAGCTTTCTAAGTCACCTCCTTCTATGGAAC
66 GTTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCACCTCCTTCTATGGAAC
** * * * *
201646 ATAAGGATCATAAATTGTAACAGCATTTTATCATATCAAATTCAATCTTCTATTTTCAGAACAAA
131 A-AAGGATCATAAATTGTAAGGGCATTTTTTCAGATCAAATTCAATCTTCTATTTTCAAAAAAAA
* * *
201711 AA-TGAATTCTAAGAAGAGAAAAATGACCTTTGAGAATAGTAACGACTCGAGTGCAGAGAGATTC
195 AATTGAATTCTAAGAAGAGAAAAATGACCTTTGAGAATAGCAATGACTCGATTGCAGAGAGATTC
* **
201775 GTCGTTCTTGGTCCGATC-A-T-TA-TTCCCTTCCTCTTTCTCTTCTTCCTCAGTTTCATCTCCA
260 ATCGTTCTCAGTCCGATCAATTATAGTTCCCTTCCTCTTTCTCTTCTTCCTCAGTTTCATCTCCA
**
201836 CTGATGATATGAAAATTAAATCAAACTTAAAAGGGGGGGCGGGAACGAATTAATTGAAACTAAAA
325 CTGATGATATGAAAATTAAATCAAACTT-AAA---GGGG-GAAAACGAATTAATTGAAACTAAAA
*
201901 TAGGACTTTAAA
385 TAGGAATTTAAA
* * *
201913 TACCTCCAATGCTCAAGAATCCTTTGTTGACACACTGCCTTAGTGCCTGCGATACGGAGGCCATG
1 TACCTCCAATGCTCAAGAATTCTCTGTTGACACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
* * * *
201978 ATTTCTCAAATAAGCCTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCAACTCCTTCTATAGAAC
66 GTTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCACCTCCTTCTATGGAAC
* * * *
202043 ACAAAGATCATAAATTGTAAGGGCAGTTTTGTT-GGATCCAATTCAATATTCTA-TTT-------
131 A-AAGGATCATAAATTGTAAGGGCA-TTTT-TTCAGATCAAATTCAATCTTCTATTTTCAAAAAA
* * * ** *
202099 ----TTG-A----AACAA-A-ATAAATGACCTTTGAGAATGGTGATGACTCGATTGCAGAGAGAG
193 AAAATTGAATTCTAAGAAGAGAAAAATGACCTTTGAGAATAGCAATGACTCGATTGCAGAGAGAT
* * *
202153 TCATCGTTTTCAGTCCGATCATTATTGTCTGAACTGTTCCCTTCCTCTTTCTCTTCTTCCTCATT
258 TCATCGTTCTCAGTCCGATCA--A-T-TAT--A--GTTCCCTTCCTCTTTCTCTTCTTCCTCA-G
* * *
202218 TTTAAT-TCCACTGATGATATGAAAATTATATCAGACTTAAA-GGGGAAAACTGAATTAATTGAA
314 TTTCATCTCCACTGATGATATGAAAATTAAATCAAACTTAAAGGGGGAAAAC-GAATTAATTGAA
* * * * *
202281 ATTGAATTAGGAAATAAAA
378 ACTAAAATAGGAATTTAAA
202300 TACCTCCAATGCTCAAGAATTCTCTGTTGACACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
1 TACCTCCAATGCTCAAGAATTCTCTGTTGACACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
** * * *
202365 GTTTCTCAAATAAGCTTTGTTTTCTTTCAAGCTCATGCTTTCCAAGTCACCTCCTTCTAT-G--C
66 GTTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCACCTCCTTCTATGGAAC
* *** * * *
202427 --A--A-CA-CAATTGTAAGGGTGCTTTTTCGGATTAAATTCAATCTTCTAATTTCAAAACAAAA
131 AAAGGATCATAAATTGTAAGGGCATTTTTTCAGATCAAATTCAATCTTCTATTTTCAAAA-AAAA
* * * *
202486 AATTGAATTCTAAGAAGAGAAAAATTG-CCTTTGAGCATAGCGATGACTTGATTGCAGAGTGATT
195 AATTGAATTCTAAGAAGAGAAAAA-TGACCTTTGAGAATAGCAATGACTCGATTGCAGAGAGATT
* * * *
202550 CATCGTTCTCAGTCCCACCATTATTGTCCAAATTGTTCCCTATGTCTTCCTCTTTCCCTTCTTCC
259 CATCGTTCTCAGTCCGATCA--A-T-T----ATAGTT-CC-----CTTCCTCTTTCTCTTCTTCC
* * * * *
202615 TCAGTTTCATCTCTACTGATTATATGAAAATCAAATCAAACTTAAAGGGGGAAAACGAACTAGTT
310 TCAGTTTCATCTCCACTGATGATATGAAAATTAAATCAAACTTAAAGGGGGAAAACGAATTAATT
* * *
202680 GAAATTGAAATAGGAACTTAAA
375 GAAACTAAAATAGGAATTTAAA
*
202702 TACCTCCAATGCTCAAGAATTCTCTGTATG-CACACTGCCTTGGTGCCTGTGATACGGAGGCCAT
1 TACCTCCAATGCTCAAGAATTCTCTGT-TGACACACTGCCTTAGTGCCTGTGATACGGAGGCCAT
* * *
202766 GGTTTCTCAAATAAGCTTTGAGTTTTTTCAAGCTTAAGCTTTCTAAGTCTCCTCCTTCTATGGAG
65 GGTTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCACCTCCTTCTATGGAA
** * * * *
202831 CACAATTATCAGAAA----AATGGCATTTTTTTA-ATCAAATTCAATCTTCTATTTTTAAAAGAA
130 CA-AAGGATCATAAATTGTAAGGGCATTTTTTCAGATCAAATTCAATCTTCTATTTTCAAAA-AA
** * * * * * * *
202891 AAAACCGAATTCTAAGAAGAGAAAGATGACCTTTGACAATGGCGATAATTCGATTGCAGACAGAT
193 AAAATTGAATTCTAAGAAGAGAAAAATGACCTTTGAGAATAGCAATGACTCGATTGCAGAGAGAT
202956 T
258 T
202957 GGTCGCTCTC
Statistics
Matches: 1203, Mismatches: 165, Indels: 147
0.79 0.11 0.10
Matches are distributed among these distances:
375 2 0.00
376 20 0.02
377 14 0.01
378 2 0.00
379 1 0.00
380 54 0.04
381 2 0.00
382 4 0.00
383 1 0.00
384 1 0.00
386 7 0.01
387 145 0.12
389 4 0.00
390 1 0.00
391 30 0.02
392 67 0.06
393 7 0.01
394 13 0.01
395 3 0.00
396 71 0.06
397 178 0.15
398 21 0.02
399 1 0.00
400 4 0.00
401 7 0.01
402 196 0.16
403 77 0.06
404 5 0.00
405 4 0.00
406 2 0.00
407 78 0.06
408 175 0.15
409 1 0.00
410 1 0.00
411 2 0.00
412 2 0.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (396 bp):
TACCTCCAATGCTCAAGAATTCTCTGTTGACACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
GTTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCACCTCCTTCTATGGAAC
AAAGGATCATAAATTGTAAGGGCATTTTTTCAGATCAAATTCAATCTTCTATTTTCAAAAAAAAA
ATTGAATTCTAAGAAGAGAAAAATGACCTTTGAGAATAGCAATGACTCGATTGCAGAGAGATTCA
TCGTTCTCAGTCCGATCAATTATAGTTCCCTTCCTCTTTCTCTTCTTCCTCAGTTTCATCTCCAC
TGATGATATGAAAATTAAATCAAACTTAAAGGGGGAAAACGAATTAATTGAAACTAAAATAGGAA
TTTAAA
Found at i:211903 original size:24 final size:23
Alignment explanation
Indices: 211871--211926 Score: 85
Period size: 24 Copynumber: 2.4 Consensus size: 23
211861 TTTAATAAAT
*
211871 AAACGAACATAAACTAACACAAAC
1 AAACGAACATAAACGAACAC-AAC
*
211895 AAACGAACATAAACGAACACAAT
1 AAACGAACATAAACGAACACAAC
211918 AAACGAACA
1 AAACGAACA
211927 ACACAAACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.62, C:0.23, G:0.07, T:0.07
Consensus pattern (23 bp):
AAACGAACATAAACGAACACAAC
Found at i:211938 original size:24 final size:24
Alignment explanation
Indices: 211868--211944 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
211858 TCATTTAATA
211868 AATAAACGAACATAAACTAACACA-
1 AATAAACGAACATAAAC-AACACAC
* *
211892 AACAAACGAACATAAACGA-ACAC
1 AATAAACGAACATAAACAACACAC
*
211915 AATAAACGAACA-ACACAAACACAC
1 AATAAACGAACATAAAC-AACACAC
211939 AA-AAAC
1 AATAAAC
211945 ACTTATTCGA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
22 6 0.13
23 17 0.38
24 22 0.49
ACGTcount: A:0.64, C:0.25, G:0.05, T:0.06
Consensus pattern (24 bp):
AATAAACGAACATAAACAACACAC
Found at i:212783 original size:18 final size:18
Alignment explanation
Indices: 212760--212797 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
212750 ACAATTTTAT
*
212760 ATTATCACATCATTAAAA
1 ATTATCACATCAATAAAA
*
212778 ATTATCACATTAATAAAA
1 ATTATCACATCAATAAAA
212796 AT
1 AT
212798 ACCAAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTATCACATCAATAAAA
Found at i:212906 original size:26 final size:26
Alignment explanation
Indices: 212870--212922 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
212860 GAAAGTATCT
*
212870 AATTCAAATATCAATTTATGAATTAA
1 AATTCAAATATCAATTTAAGAATTAA
* * *
212896 AATTTAAATATTAATTTAAGTATTAA
1 AATTCAAATATCAATTTAAGAATTAA
212922 A
1 A
212923 TGTATATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (26 bp):
AATTCAAATATCAATTTAAGAATTAA
Done.