Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006551.1 Hibiscus syriacus cultivar Beakdansim tig00016008_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: 70535
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:537 original size:64 final size:65
Alignment explanation
Indices: 379--537 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 65
369 GAATTAATCG
* * *
379 AACATCGAATGCATTCATGCACTGATGCA-CATACCATGCACCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCATTGATGCATTGATGCACCATACCATGCACCGATGCACTCAGGATTTTATGAA
* * * * *
443 AACATCGAATGCATTGATGCATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTT-TG-
1 AACATCGAATGCATTGATGCATTGATGCACCATACCATGCACCGATGCACTCAGGAT-TTTATGA
505 A
65 A
506 AACATCGAATGCACTTGATGCATTGATGCACC
1 AACATCGAATGCA-TTGATGCATTGATGCACC
538 TTAGTACACC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 14 0.17
64 64 0.77
65 5 0.06
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (65 bp):
AACATCGAATGCATTGATGCATTGATGCACCATACCATGCACCGATGCACTCAGGATTTTATGAA
Found at i:1646 original size:8 final size:9
Alignment explanation
Indices: 1616--1650 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1606 CCACATAACA
*
1616 TTTTTTCTT
1 TTTTTTCCT
1625 TTTCTTTCCT
1 TTT-TTTCCT
1635 TTTTTTCCT
1 TTTTTTCCT
1644 TTTTTTC
1 TTTTTTC
1651 TCAATGAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTCCT
Found at i:20586 original size:20 final size:20
Alignment explanation
Indices: 20538--20589 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
20528 TAATACAAAA
*
20538 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
20558 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
20578 TCGCAACGCGAT
1 TCGCAACGCGAT
20590 CTACATAGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:21179 original size:19 final size:19
Alignment explanation
Indices: 21145--21184 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21135 GAGAGAATCA
*
21145 CAACGCGAAATAAAAAACG
1 CAACGCGAAACAAAAAACG
* *
21164 CAACGCGAAACCAAAATCG
1 CAACGCGAAACAAAAAACG
21183 CA
1 CA
21185 TTGCGATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.28, G:0.15, T:0.05
Consensus pattern (19 bp):
CAACGCGAAACAAAAAACG
Found at i:21202 original size:19 final size:19
Alignment explanation
Indices: 21180--21272 Score: 79
Period size: 19 Copynumber: 5.1 Consensus size: 19
21170 GAAACCAAAA
21180 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
21199 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
**
21215 TCG--TTGCGATAGTCATT
1 TCGCATTGCGATTTTCATT
* *
21232 TCGCGTTGCGATTCTCATT
1 TCGCATTGCGATTTTCATT
* *
21251 ATCTCGTTGCGATTTTCATT
1 -TCGCATTGCGATTTTCATT
21271 TC
1 TC
21273 AACCAAAAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
14 6 0.10
16 6 0.10
17 7 0.11
19 25 0.41
20 17 0.28
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:21272 original size:39 final size:33
Alignment explanation
Indices: 21185--21247 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
21175 CAAAATCGCA
21185 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
** *
21218 TTGCGATAGTCATTTCGCGTTGCGATTCTC
1 TTGCGATTTTCATTTCGCATTGCGATTCTC
21248 ATTATCTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:22625 original size:32 final size:33
Alignment explanation
Indices: 22570--22631 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 33
22560 CCTGATCGAC
*
22570 TTTGTCGTTGCGATTTTCATTTCGCGTTGCGAT
1 TTTGTCGTTGCGATTTTCATTTCGCATTGCGAT
22603 TTTGTCGTTGCGA-TTTCATTTCGCATTGC
1 TTTGTCGTTGCGATTTTCATTTCGCATTGC
22632 AATAGCCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (33 bp):
TTTGTCGTTGCGATTTTCATTTCGCATTGCGAT
Found at i:22656 original size:20 final size:20
Alignment explanation
Indices: 22628--22673 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
22618 TCATTTCGCA
*
22628 TTGCAATAGCCATTTCCGTG
1 TTGCGATAGCCATTTCCGTG
* *
22648 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGTG
22668 TTGCGA
1 TTGCGA
22674 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGTG
Found at i:23181 original size:18 final size:18
Alignment explanation
Indices: 23155--23199 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
23145 GTCGATCAGA
*
23155 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
23173 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
23191 TGATGGCTC
1 TGATGGCTC
23200 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:24567 original size:20 final size:20
Alignment explanation
Indices: 24519--24575 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
24509 AGTAGTTTCT
**
24519 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACAC
*
24539 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACAC
**
24559 GAATTTGACTATCGCAA
1 GAAAATGACTATCGCAA
24576 AGAGAGAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
GAAAATGACTATCGCAACAC
Found at i:24868 original size:22 final size:22
Alignment explanation
Indices: 24841--24883 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
24831 ATGGAGATAA
24841 ACGGATTTCGCCGGAGATGGGG
1 ACGGATTTCGCCGGAGATGGGG
*
24863 ACGGATTTCGTCGGAGATGGG
1 ACGGATTTCGCCGGAGATGGG
24884 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.16, G:0.44, T:0.21
Consensus pattern (22 bp):
ACGGATTTCGCCGGAGATGGGG
Found at i:25096 original size:20 final size:20
Alignment explanation
Indices: 25071--25143 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
25061 GATTATGTAT
25071 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
25091 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
25111 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
25131 TATCTCGTTGCGA
1 TATCGCGTTGCGA
25144 TTTTGTATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:25177 original size:20 final size:19
Alignment explanation
Indices: 25051--25185 Score: 108
Period size: 20 Copynumber: 6.7 Consensus size: 19
25041 CGCTTTGAAA
* *
25051 ATCGCATTGCGATTATGTATT
1 ATCGCGTTGCGA-TA-GTAGT
*
25072 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGT-AGT
*
25092 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGT-AGT
*
25112 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGT-AGT
* * *
25132 ATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGA--TAGTAGT
*
25153 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGT-AGT
*
25173 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
25186 TTTCCCAATT
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
19 5 0.05
20 67 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATAGTAGT
Found at i:25203 original size:21 final size:21
Alignment explanation
Indices: 25174--25266 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
25164 ATAGTCAGTA
25174 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
25195 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
25215 TCGTATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
25236 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
25256 TCGCATTGCGA
1 TCGCATTGCGA
25267 ATTGGAAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:25204 original size:41 final size:41
Alignment explanation
Indices: 25073--25247 Score: 133
Period size: 41 Copynumber: 4.3 Consensus size: 41
25063 TTATGTATTA
* * *** *
25073 TCGCGTTGCGAAAGTAAGTATCGCGTTGCGAAAGT--CAGT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* * * ** *
25112 ATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
25153 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
25195 TCGCGTTGCGAT-TTACTTATTCGTATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
25236 TCGCGTTGCGAT
1 TCGCGTTGCGAT
25248 TTACTTATTC
Statistics
Matches: 112, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
40 34 0.30
41 76 0.68
42 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:25248 original size:41 final size:41
Alignment explanation
Indices: 25174--25266 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
25164 ATAGTCAGTA
25174 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
25215 TCGTATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
25256 TCGCATTGCGA
1 TCGCATTGCGA
25267 ATTGGAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:26417 original size:29 final size:29
Alignment explanation
Indices: 26384--26453 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
26374 GAGGACGGAG
* *
26384 ACGGGATGTGAAAAACCCATTTATTTCAA
1 ACGGGACGGGAAAAACCCATTTATTTCAA
* *
26413 ACGGGGACGGGAAAAACCTATTTATTTTAA
1 AC-GGGACGGGAAAAACCCATTTATTTCAA
26443 ACGGGGACGGG
1 AC-GGGACGGG
26454 GACGGGTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 2 0.06
30 34 0.94
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (29 bp):
ACGGGACGGGAAAAACCCATTTATTTCAA
Found at i:26429 original size:30 final size:30
Alignment explanation
Indices: 26393--26453 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
26383 GACGGGATGT
26393 GAAAAACCCATTTATTTCAAACGGGGACGG
1 GAAAAACCCATTTATTTCAAACGGGGACGG
* *
26423 GAAAAACCTATTTATTTTAAACGGGGACGG
1 GAAAAACCCATTTATTTCAAACGGGGACGG
26453 G
1 G
26454 GACGGGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (30 bp):
GAAAAACCCATTTATTTCAAACGGGGACGG
Found at i:26587 original size:24 final size:26
Alignment explanation
Indices: 26560--26616 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
26550 ATATATATAC
*
26560 ATAATATTAATA-A-ATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
26584 ATAA-A-AAATATATATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
26608 ATATATATA
1 ATA-ATATA
26617 TACTCGGCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 4 0.15
23 2 0.07
24 18 0.67
25 1 0.04
26 1 0.04
27 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAATATAAATATATATTTAATTTAA
Found at i:26602 original size:19 final size:19
Alignment explanation
Indices: 26578--26617 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
26568 AATAAATTTA
26578 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
26597 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
26616 AT
1 AT
26618 ACTCGGCCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:26648 original size:11 final size:11
Alignment explanation
Indices: 26632--26667 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
26622 GGCCCGATTC
26632 CCGACCCAATA
1 CCGACCCAATA
26643 CCGACCCAATA
1 CCGACCCAATA
*
26654 CCCAGCCCAATA
1 CCGA-CCCAATA
26666 CC
1 CC
26668 CGTTTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.33, C:0.50, G:0.08, T:0.08
Consensus pattern (11 bp):
CCGACCCAATA
Found at i:27358 original size:14 final size:16
Alignment explanation
Indices: 27329--27363 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
27319 TGGAGAATTT
27329 GAGTTATATAAGAGAG
1 GAGTTATATAAGAGAG
27345 GAGTTATATAAGAGAG
1 GAGTTATATAAGAGAG
27361 GAG
1 GAG
27364 AATATGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.34, T:0.23
Consensus pattern (16 bp):
GAGTTATATAAGAGAG
Found at i:28429 original size:21 final size:21
Alignment explanation
Indices: 28312--28449 Score: 59
Period size: 21 Copynumber: 6.7 Consensus size: 21
28302 ACGCGAAATA
**
28312 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
28332 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
28352 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* * ** *
28373 AAAATCGCGATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* * **
28394 ATATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * * *
28415 ATAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
28435 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
28450 ACACATAAAT
Statistics
Matches: 85, Mismatches: 29, Indels: 8
0.70 0.24 0.07
Matches are distributed among these distances:
19 1 0.01
20 38 0.45
21 44 0.52
22 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:28511 original size:20 final size:20
Alignment explanation
Indices: 28417--28785 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
28407 GATTTTCCAT
* ** *
28417 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
28437 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
28457 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28477 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
28497 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
28517 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28537 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
28557 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
28577 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
28597 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28617 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
28637 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28657 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
28677 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28697 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
28717 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
28737 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
28757 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
28777 AATCACAAC
1 AATCGCAAC
28786 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:29507 original size:24 final size:24
Alignment explanation
Indices: 29468--29514 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
29458 AAATTTGGTC
29468 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
29492 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
29515 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:29706 original size:12 final size:12
Alignment explanation
Indices: 29689--29713 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29679 ATATAATCCT
29689 GAAGAAGAAAAA
1 GAAGAAGAAAAA
29701 GAAGAAGAAAAA
1 GAAGAAGAAAAA
29713 G
1 G
29714 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:32017 original size:19 final size:19
Alignment explanation
Indices: 31995--32301 Score: 376
Period size: 19 Copynumber: 17.4 Consensus size: 19
31985 CGGAAAATAC
*
31995 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
32014 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
32028 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
32048 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
32062 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
32081 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
32100 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
32114 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
32133 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
32152 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
32166 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
32185 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
32204 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
32223 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
32242 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
32256 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
32275 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
32294 AATCGCAA
1 AATCGCAA
32302 CGAGATAATC
Statistics
Matches: 252, Mismatches: 10, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
14 48 0.19
15 2 0.01
16 16 0.06
17 14 0.06
18 3 0.01
19 156 0.62
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:32110 original size:52 final size:52
Alignment explanation
Indices: 32023--32301 Score: 388
Period size: 52 Copynumber: 5.2 Consensus size: 52
32013 AAATCCCAAC
32023 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
32076 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
32128 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
32180 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
32237 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
32289 ATGAAAATCGCAA
1 ATGAAAATCGCAA
32302 CGAGATAATC
Statistics
Matches: 216, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
52 164 0.76
53 16 0.07
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.12
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:32146 original size:71 final size:71
Alignment explanation
Indices: 32062--32301 Score: 373
Period size: 71 Copynumber: 3.4 Consensus size: 71
32052 GCAACGAGAG
*
32062 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
32127 AATGAA
66 AATGAA
* *
32133 AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
32193 TGCGAAATGAA
61 TGCGAAATGAA
32204 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
32269 AATGAA
66 AATGAA
32275 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
32302 CGAGATAATC
Statistics
Matches: 154, Mismatches: 5, Indels: 20
0.86 0.03 0.11
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 5 0.03
71 121 0.79
73 6 0.04
74 3 0.02
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:32247 original size:142 final size:138
Alignment explanation
Indices: 31995--32339 Score: 518
Period size: 142 Copynumber: 2.5 Consensus size: 138
31985 CGGAAAATAC
* * *
31995 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAA--CG
1 AATCGCAATGCGAAATGAAAATCGCAAC--GAAAATCGCAATGC-GAAATTAAAATCGCAATGCG
* *
32058 -AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAA
63 AAGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA
32122 TGCGAAATGAA
128 TGCGAAATGAA
32133 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGAAATTAAAATCGCAATGCG-
32198 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 AA-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
32263 ATGCGAAATGAA
127 ATGCGAAATGAA
*
32275 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTATAAA-CGCATTGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGAAATTA-AAATCGCAATGCG
32339 A
63 A
32340 TTTTCATTTC
Statistics
Matches: 191, Mismatches: 8, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
136 2 0.01
137 16 0.08
138 37 0.19
139 2 0.01
141 2 0.01
142 129 0.68
143 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (138 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAATCGCAATGCGAAATTAAAATCGCAATGCGAAG
AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGC
GAAATGAA
Found at i:32302 original size:52 final size:55
Alignment explanation
Indices: 31995--32323 Score: 332
Period size: 52 Copynumber: 6.3 Consensus size: 55
31985 CGGAAAATAC
* *
31995 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATG-A
*
32048 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
*
32100 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
* *
32152 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
32204 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
*
32256 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAT--
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
32308 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
32324 TATAAACGCA
Statistics
Matches: 257, Mismatches: 6, Indels: 27
0.89 0.02 0.09
Matches are distributed among these distances:
48 9 0.04
49 1 0.00
50 1 0.00
51 2 0.01
52 181 0.70
53 24 0.09
54 7 0.03
55 6 0.02
57 26 0.10
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (55 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
Found at i:32420 original size:19 final size:19
Alignment explanation
Indices: 32330--32412 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
32320 AAATTATAAA
32330 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
32349 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
32369 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
32385 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
32402 CGCATTGCGAT
1 CGCATTGCGAT
32413 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:32538 original size:14 final size:14
Alignment explanation
Indices: 32519--32555 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
32509 CATCAATTAC
32519 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
32533 ACAAATCATCTTTT
1 ACAAATCAACTTTT
32547 ACAAATCAA
1 ACAAATCAA
32556 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:34554 original size:14 final size:14
Alignment explanation
Indices: 34535--34591 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
34525 GCGAAATTAA
*
34535 AATCGCAACGACAG
1 AATCGCAACGAAAG
34549 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
34566 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
34582 AATCGCAACG
1 AATCGCAACG
34592 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:34562 original size:33 final size:33
Alignment explanation
Indices: 34516--34608 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
34506 GCGAAACCAA
* *
34516 AATCGCAACGCGAAATTAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
34549 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
34582 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
34609 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:34573 original size:19 final size:19
Alignment explanation
Indices: 34479--34613 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
34469 TAGTTTACTT
* *
34479 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
34499 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
34518 TCGCAACGCGAAATTAAAA
1 TCGCAACGCGAAATGAAAA
*
34537 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
34551 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
34570 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
34584 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
34603 TCGCAATGCGA
1 TCGCAACGCGA
34614 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.17
16 10 0.10
17 11 0.11
19 47 0.49
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:34631 original size:19 final size:19
Alignment explanation
Indices: 34609--34737 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
34599 AAAATCGCAA
34609 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
34628 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
34642 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
34661 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
34675 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
34694 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
34713 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
34733 TGCGA
1 TGCGA
34738 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:34651 original size:33 final size:33
Alignment explanation
Indices: 34609--34700 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
34599 AAAATCGCAA
34609 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
34642 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
34675 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
34701 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:35163 original size:92 final size:93
Alignment explanation
Indices: 34781--35344 Score: 1105
Period size: 93 Copynumber: 6.1 Consensus size: 93
34771 TTGAATGGAT
34781 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
34846 GTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
34874 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
34939 GTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
34967 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
35032 GTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
35060 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
35124 GTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
35152 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
35216 GTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
35244 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
*
35309 GTTTAGCAGAATTGGCAGCAACCGAATA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
35337 AATTTACT
1 AATTTACT
35345 AAGCAATCTA
Statistics
Matches: 469, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
92 184 0.39
93 285 0.61
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACA
Found at i:35289 original size:185 final size:186
Alignment explanation
Indices: 34781--35344 Score: 1105
Period size: 185 Copynumber: 3.0 Consensus size: 186
34771 TTGAATGGAT
34781 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
34846 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
34911 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
34967 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
35032 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
35097 A-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
35152 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
35216 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
*
35281 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATA
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
35337 AATTTACT
1 AATTTACT
35345 AAGCAATCTA
Statistics
Matches: 376, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
184 92 0.24
185 153 0.41
186 131 0.35
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
Found at i:37066 original size:14 final size:14
Alignment explanation
Indices: 37047--37136 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
37037 TTGAAATGAA
37047 AATCGCAACGAGAG
1 AATCGCAACGAGAG
37061 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
37078 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
37094 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
37113 AATCGCAACGAGAG
1 AATCGCAACGAGAG
37127 AATCGCAACG
1 AATCGCAACG
37137 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:37084 original size:33 final size:33
Alignment explanation
Indices: 37039--37153 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
37029 TCTTTTGGTT
37039 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
37072 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
37105 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
37138 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
37154 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:37085 original size:19 final size:18
Alignment explanation
Indices: 37046--37158 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
37036 GTTGAAATGA
37046 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
37061 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
37078 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
37094 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
37111 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
37127 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
37144 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
37159 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:37189 original size:14 final size:14
Alignment explanation
Indices: 37170--37224 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
37160 TTTGGTTTCG
37170 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
37184 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
37203 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
37217 CGTTGCGA
1 CGTTGCGA
37225 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:37202 original size:33 final size:33
Alignment explanation
Indices: 37154--37224 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
37144 AAAATCGCAA
**
37154 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
37187 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
37220 TGCGA
1 TGCGA
37225 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:37232 original size:33 final size:33
Alignment explanation
Indices: 37165--37246 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
37155 GCGATTTTGG
***
37165 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
37198 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
37231 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
37247 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:37251 original size:20 final size:20
Alignment explanation
Indices: 37177--37265 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
37167 TCGCGTTGCG
37177 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
37197 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
37210 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
37230 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
37250 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
37266 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:37387 original size:33 final size:33
Alignment explanation
Indices: 37345--37415 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
37335 AATACTAACT
*
37345 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
37378 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
37411 TGAAA
1 TGAAA
37416 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:37649 original size:22 final size:22
Alignment explanation
Indices: 37597--37651 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
37587 TGGTTGTGAG
**
37597 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
37619 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
37641 GGATTTCTTCG
1 GGATTTCTTCG
37652 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:37822 original size:20 final size:20
Alignment explanation
Indices: 37797--37989 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
37787 CTTTAAATAT
37797 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
37817 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
37839 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
37858 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
37878 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
37898 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
37918 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
37938 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
37958 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
37978 CGCGTTGCGATT
1 CGCGTTGCGATT
37990 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:37984 original size:60 final size:60
Alignment explanation
Indices: 37797--37989 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
37787 CTTTAAATAT
**
37797 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
37858 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
37918 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
37978 CGCGTTGCGATT
1 CGCGTTGCGATT
37990 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:38070 original size:20 final size:20
Alignment explanation
Indices: 38045--38096 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
38035 AAGAATCGCG
*
38045 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
38065 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
38085 TTGCGATTCTGG
1 TTGCGATTCTGG
38097 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:41677 original size:2 final size:2
Alignment explanation
Indices: 41670--41701 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
41660 CCGCCCCGAT
41670 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41702 TTTATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47426 original size:23 final size:23
Alignment explanation
Indices: 47385--47430 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
47375 ATTTTAAAAT
*
47385 ATTTTAAAAAGAAATATAAATAAA
1 ATTTTAAAAAGAAAGAT-AATAAA
*
47409 ATTTTAAAATG-AAGATAATAAA
1 ATTTTAAAAAGAAAGATAATAAA
47431 TTATAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 4 0.20
24 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (23 bp):
ATTTTAAAAAGAAAGATAATAAA
Found at i:47807 original size:17 final size:19
Alignment explanation
Indices: 47774--47809 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
47764 TTGTGCATTC
47774 TTTTAATAAATTTATATAA
1 TTTTAATAAATTTATATAA
47793 TTTTAA-AAA-TTATATAA
1 TTTTAATAAATTTATATAA
47810 AGCATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 3 0.18
19 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTAATAAATTTATATAA
Found at i:67062 original size:35 final size:35
Alignment explanation
Indices: 67018--67087 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
67008 GCTTAATGGA
67018 TTTTTTAATATTTAAATTTAAAACAATTAAAGGTT
1 TTTTTTAATATTTAAATTTAAAACAATTAAAGGTT
*
67053 TTTTTTAATATTTAAATTTGAAACAATTAAAGGTT
1 TTTTTTAATATTTAAATTTAAAACAATTAAAGGTT
67088 AAGTAATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (35 bp):
TTTTTTAATATTTAAATTTAAAACAATTAAAGGTT
Done.