Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012399.1 Corchorus capsularis cultivar CVL-1 contig12420, 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: 80040
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:11271 original size:2 final size:2
Alignment explanation
Indices: 11264--11298 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
11254 TTTTTGGAAC
*
11264 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11299 AAAACAAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:17262 original size:15 final size:15
Alignment explanation
Indices: 17239--17270 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
17229 TCTATTTCCG
17239 TTTTCTTTTTTGTTT
1 TTTTCTTTTTTGTTT
*
17254 TTTTGTTTTTTGTTT
1 TTTTCTTTTTTGTTT
17269 TT
1 TT
17271 GTATGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (15 bp):
TTTTCTTTTTTGTTT
Found at i:18882 original size:1 final size:1
Alignment explanation
Indices: 18878--18904 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
18868 TTTTGTTGGG
18878 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
18905 GCGTAATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:20221 original size:2 final size:2
Alignment explanation
Indices: 20216--20252 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
20206 AAAGGAAAAA
*
20216 AT AT AT AT AT AT AT AT AT TT AT -T AT AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20253 CTATCTCAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:22721 original size:21 final size:21
Alignment explanation
Indices: 22664--22762 Score: 121
Period size: 20 Copynumber: 4.8 Consensus size: 21
22654 ATATTCTGTC
*
22664 TAAAAATGGCTC-TTTTTGTG
1 TAAAAATGCCTCTTTTTTGTG
*
22684 TAAAATTGCCTCTTTTTTTGTG
1 TAAAAATGCCTC-TTTTTTGTG
* *
22706 TAAAATTGTCTC-TTTTTGTG
1 TAAAAATGCCTCTTTTTTGTG
*
22726 TAAAAATGCCTCTTTTTTGCG
1 TAAAAATGCCTCTTTTTTGTG
*
22747 TAAAAATGTCTCTTTT
1 TAAAAATGCCTCTTTT
22763 GGGCTTGCAT
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
20 28 0.41
21 22 0.32
22 19 0.28
ACGTcount: A:0.23, C:0.13, G:0.14, T:0.49
Consensus pattern (21 bp):
TAAAAATGCCTCTTTTTTGTG
Found at i:22723 original size:42 final size:41
Alignment explanation
Indices: 22664--22762 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 41
22654 ATATTCTGTC
* * *
22664 TAAAAATGGCTCTTTTTGTGTAAAATTGCCTCTTTTTTTGTG
1 TAAAAATGTCTCTTTTTGTGTAAAAATGCCTC-TTTTTTGCG
*
22706 TAAAATTGTCTCTTTTTGTGTAAAAATGCCTCTTTTTTGCG
1 TAAAAATGTCTCTTTTTGTGTAAAAATGCCTCTTTTTTGCG
22747 TAAAAATGTCTCTTTT
1 TAAAAATGTCTCTTTT
22763 GGGCTTGCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
41 23 0.44
42 29 0.56
ACGTcount: A:0.23, C:0.13, G:0.14, T:0.49
Consensus pattern (41 bp):
TAAAAATGTCTCTTTTTGTGTAAAAATGCCTCTTTTTTGCG
Found at i:31034 original size:19 final size:20
Alignment explanation
Indices: 30990--31034 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
30980 TAGATTGTTT
*
30990 CAAAACATATAGGGCCAATTG
1 CAAAACATATAGAGCCAA-TG
31011 CAAAACATATAGAGCCAA-G
1 CAAAACATATAGAGCCAATG
31030 CAAAA
1 CAAAA
31035 GAAAATATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
21 17 0.74
ACGTcount: A:0.51, C:0.20, G:0.16, T:0.13
Consensus pattern (20 bp):
CAAAACATATAGAGCCAATG
Found at i:31476 original size:38 final size:39
Alignment explanation
Indices: 31433--31511 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 39
31423 CTAAGAAAGT
31433 AATTTAAAAACAAGGTCTTTTAAAGTAA-TTTTGTCTTA
1 AATTTAAAAACAAGGTCTTTTAAAGTAATTTTTGTCTTA
31471 AATTTAAAAACAAGGTCTTTTAAAGTAATTTTTGTCTTA
1 AATTTAAAAACAAGGTCTTTTAAAGTAATTTTTGTCTTA
31510 AA
1 AA
31512 ACCACTTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 28 0.70
39 12 0.30
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.42
Consensus pattern (39 bp):
AATTTAAAAACAAGGTCTTTTAAAGTAATTTTTGTCTTA
Found at i:33015 original size:281 final size:283
Alignment explanation
Indices: 32469--33027 Score: 854
Period size: 281 Copynumber: 2.0 Consensus size: 283
32459 AAGATATTTC
* * * * *
32469 CTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCGACCTCACAAAGATTGAAGGTCTT
1 CTCAAATTTTGGCTAAAATACTAATAAAAAATATATAATTCGACCTCAAAAAGATTAAAGGGCTT
*
32534 TTAACGCTTCTAATATTCTATTTTCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGA
66 TTAACGCTTCTAATATTCTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGA
* * * *
32599 TTCGGATACTCGTAAAAAAAAAAAATCCTTAAATCCATTGTGGCTGATATTTGATTAGATGAATA
131 TTCAGATACTCGT--AAAAAAAAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATA
* **
32664 AAGATATTTCAAGAAGTCTCGTTGCCAAAAATCACGCAAAACAGAGTCGTGACCCCGTAACGCGT
194 AAGATATGTCAAGAAGTCTCGTTGCCAAAAATCACGCAAAACAGAGTCGTGACCCCAAAACGCGT
32729 TTTTAGCCGAAAACCGTGATGGTTA
259 TTTTAGCCGAAAACCGTGATGGTTA
* * *
32754 CTCAAATTTTGGCTAAAATGCTAATAAAAAATATATAATTTGACGTCAAAAAGATTAAAGGGCTT
1 CTCAAATTTTGGCTAAAATACTAATAAAAAATATATAATTCGACCTCAAAAAGATTAAAGGGCTT
*
32819 TTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAAT-GAAACAAGA
66 TTAACGCTTCTAATATTCTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGA
** *
32883 TTCAGATGTTCGT-AAAAAAAAATCCTTAAATCCAATGTGGCTAAGATTTGATTATATGAATAAA
131 TTCAGATACTCGTAAAAAAAAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATAAA
* * *
32947 GATATGTCAAGGAGTCTCGTCT-CCAAAAATCATGCAAAACAGAGTCGTGACCTCAAAACGCGTT
196 GATATGTCAAGAAGTCTCGT-TGCCAAAAATCACGCAAAACAGAGTCGTGACCCCAAAACGCGTT
*
33011 TTTAGCTGAAAACCGTG
260 TTTAGCCGAAAACCGTG
33028 GTGGATAGTA
Statistics
Matches: 249, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
281 119 0.48
282 1 0.00
284 19 0.08
285 110 0.44
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (283 bp):
CTCAAATTTTGGCTAAAATACTAATAAAAAATATATAATTCGACCTCAAAAAGATTAAAGGGCTT
TTAACGCTTCTAATATTCTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGA
TTCAGATACTCGTAAAAAAAAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATAAA
GATATGTCAAGAAGTCTCGTTGCCAAAAATCACGCAAAACAGAGTCGTGACCCCAAAACGCGTTT
TTAGCCGAAAACCGTGATGGTTA
Found at i:35409 original size:331 final size:332
Alignment explanation
Indices: 32751--37743 Score: 6230
Period size: 332 Copynumber: 15.2 Consensus size: 332
32741 ACCGTGATGG
* *
32751 TTACTCAAATTTTGGCTAAAATGCTAATAAAAAATATATAATTTGACGTCAAAAAGATTAAAGGG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACGTCAAAAAGATTGAAGGG
32816 CTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAAT-GAAACA
66 CTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * * *
32880 AGATTCAGATGTTCGTAAAAAAAAATCCTTAAATCCAATGTGGCTAAGATTTGATTATATGAATA
131 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
* * * **
32945 AAGATATGTCAAGGAGTCTCGTCTCCAAAAATCATGCAAAACAGAGTCGTGACCTCAAAACGCGT
196 AAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAACGCGT
* * * * *
33010 TTTTAGCTGAAAACCGTGGTGGATAGTACACGATTTAGGCTAAAATTTTGCAAAAATTGAACCGA
261 TTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGA
33075 AAGATAT
326 AAGATAT
** * **
33082 TTACTCAAATTTTGAATAAAATGCTCATAAAAAATATATAATTTGATGTCAAAAAGATAAAAGGG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACGTCAAAAAGATTGAAGGG
33147 CTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAAT-GAAACA
66 CTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * ** *
33211 AGATTCAGATGTTCGTAAAAACAAATCCTTAAATACAATGTACCCGAGATTTGATTAGATGAATA
131 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
* * * * * ** * **
33276 AAGATATTTCAAGAAGTTTCGGCACAAAAAATTTTTGCAAAACCGAG-CTGTGGTCCCGGAACGC
196 AAGATATTTCAAGGAGTCTCGTCGCCAAAAA-TCATGCAAAACAGAGTC-GTGACCCCGGAACGC
* * * *
33340 GTTTTTAGCTGAAAACCGTGATGGTTAGTACACTATTTCGGCTAAAATTTTGTAAAAATTGACCT
259 GTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
33405 GAATA-ATAT
324 GAA-AGATAT
* * * ** * * * *
33414 TTCCTCGATTTTTGGCTAAAATATTTGA-AAAAAATATATAATTCGACGTAAAAAAGATTGGAGG
1 TTACTCAAATTTTGGCTAAAAT-GCTCATAAAAAATATATAATTTGACGTCAAAAAGATTGAAGG
* * *
33478 ACTTTTAACCCTTCTAATATTGTA---T-T-TTTTTTCTGAATTAATTTCTAATTAAATCGAAAC
65 GCTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAAC
* * * *
33538 AAGATTCAGATACTCGTAAAAAAAATATCTTTAAATCCAATGTGGCTGAGTTTTGATTAGATGAA
130 AAGATTCAGATGCTCGTAAAAACAA-ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAA
* *
33603 TAAATATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAATGC
194 TAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAACGC
*
33668 GTTTTTAGCCGAAAACCGTTATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
259 GTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
33733 GAAAGATAT
324 GAAAGATAT
*
33742 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACGTCGAAAAAGATTAAAGG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACGTC-AAAAAGATTGAAGG
33807 GCTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAAT-GAAAC
65 GCTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAAC
* * * * * *
33871 AAGATTAAGATGTTCGTAAAAACAAATCCTTAAATACAATGT-ACTCGAGATTTGGTTAGATAAA
130 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT-GAGATTTGATTAGATGAA
33935 TAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAACGC
194 TAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAACGC
* *
34000 GTTTTTAGCAGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCC
259 GTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
*
34065 GAACGATAT
324 GAAAGATAT
*
34074 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTGGATC-TCAAAAAGATTGAAGG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGA-CGTCAAAAAGATTGAAGG
* * *
34138 TCTTTTAACGCTTCTAATAATGTATTTTCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAAC
65 GCTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAAC
* * * * *
34203 AAGATTCGGATACTTGTAAAAAAAAAATTCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGA
130 AAGATTCAGATGCTCGT-AAAAACAAA-TCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGA
* *
34268 ATAAAGATATTTCAAGGAGTCTCGTCTCCAAAAATCATGCAAAACAGAGTCGTGACCCCTGAACG
193 ATAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAACG
* * *
34333 CGTTTTTAGCCGAAAACCATGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAATATTGACC
258 CGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
*
34398 CGAATA-TTAT
323 CGAA-AGATAT
* * * * * * * ** *
34408 TTCCTCTATTTTTGGCTTAAAT-ATTAGAAAAAAATATATAATTCCACGTCAAAAAGATTGGAGG
1 TTACTCAAATTTTGGCTAAAATGCTCA-TAAAAAATATATAATTTGACGTCAAAAAGATTGAAGG
* *
34472 ACTTTTAACGCTTCTAATATTGTATTTTCTATTTTTT--TAATTAATTTCTAATTAAATCGAAAC
65 GCTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAAC
* * * * *
34535 AAAATTCAGATACTCGTAAAAA-AAATCCTTAAATCCATTGTGCCTGAGATTTGGTTAGATGAAT
130 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* *
34599 AAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAAAGTCGTGAGCCCGGAACGCG
195 AAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAACGCG
* * *
34664 TTTTTAGCCGAAAACCGTGATGCTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTAACCCG
260 TTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCG
34729 AAAGATAT
325 AAAGATAT
* *
34737 TTACTCAAATTTTGGTTAAAATGCTCATAAAAAATATATAATTTGACGTCAAAAAGATTAAAGGG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACGTCAAAAAGATTGAAGGG
*
34802 CTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCCAATTAATTTCTAATTAAAT-GAAACA
66 CTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
** ** * ** *
34866 AGATTCACTTTTTCGTAAAAAAAAATCCTTAAATACCAATGTACCCGAGATTTGATTAGATGAAT
131 AGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CCAATGTGGCTGAGATTTGATTAGATGAAT
* * * * *
34931 AAATATATTTCAAGGAGTCTCATCGCCAAAAATCAAGCAAAATAGGGTCGTGACCCCGGAACGCG
195 AAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAACGCG
* *
34996 TTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGACTCG
260 TTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCG
35061 AAAGATAT
325 AAAGATAT
* * *
35069 TTGCTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACGCCAAAAAGATTAAAGGG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACGTCAAAAAGATTGAAGGG
* * * * *
35134 CTTGTAACGCTTTTAATATTGGATTTTCTATTTTTCCCCAATTAATTTCTAATTAAAT-GAAACA
66 CTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * ** *
35198 AGATTCAGATGTTCGTAAAAACAAATCCTTAAATACAATGTACCCGAGATTTGATTAGATGAATA
131 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
* * **
35263 AGGATATTTCAAGGAGTCTCGTTGCCAAAAATCATGCAAAACAGAGTCGTGACCCCAAAACGCGT
196 AAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAACGCGT
* * * *
35328 TTTTAGTCGAAAACCGTGATGGTTACTATACGATTTCGGCTACAATTTT-CGAAAAATTGACCCG
261 TTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGC-AAAAATTGACCCG
35392 AAAGATAT
325 AAAGATAT
* * * * *
35400 TTACTCAAATTTAGGATAAAATGCTCTTAAAAAATATATAATTTGCCGTCAAAAAGATTAAAGGG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACGTCAAAAAGATTGAAGGG
*
35465 CTTTTAACGCTTCTAATATTGTATTTTC-A-ATTTT-----TTAATTTCTAATTAAATCGAAACA
66 CTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * **
35523 AGATTCAGATGTTCGTAAAAACAAATCCTTAAATCCATTGTACCTGAGATTTGATTAGATGAATA
131 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
* * * ** * **
35588 AAGATATTTCAAGGAGT-TTGTACACAAAAAATTTTGCAAAACAGAGCCGTGGTCCCGGAACGCG
196 AAGATATTTCAAGGAGTCTCGT-CGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAACGCG
* * *
35652 TTTTTAGCCGAAAACCGTGATGGTTAGTTCACGATTTCGACTAAAATTTTGCAAAAATTGACCAG
260 TTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCG
*
35717 AATA-ATGT
325 AA-AGATAT
* * * ** * * *
35725 TTCCTCGATTTTTGGCTAAAATATTCGA-AATAAATATAT-ATTTCTACGTCAAAAAGATTGGAG
1 TTACTCAAATTTTGGCTAAAATGCTC-ATAAAAAATATATAATTT-GACGTCAAAAAGATTGAAG
* * * *
35788 GACTTTTAACGCTTCTAAAATTGTATTTTCTATTTTTTCTGAATTAATTTCTAATTAAATTGAAA
64 GGCTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAA
* * * * * *
35853 CAATATTCAGATACTCGTAAAAAAAAATCCTTAAATCCATTGTGGCTGAGATTTGACTAGAAGAA
129 CAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAA
* *** * * *
35918 TAAAGATATTTCAAGGAGTCTCATCGTTTAAAATTATGCAAAACAGAGTCATGACCCCAGAACGC
194 TAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAACGC
* *
35983 GTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTTCAAAAATTGACTC
259 GTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
36048 GAAAGATAT
324 GAAAGATAT
*
36057 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACG-CAAAAAAGATTAAAGG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACGTC-AAAAAGATTGAAGG
*
36121 GCTTTTAACGCTTCTAATATTGTATTTTCTA--TTTTCCGAATTATTTTCTAATTAAAT-GAAAC
65 GCTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAAC
* * * * **
36183 AAGATTCAGATGATCATAAAAACAAACCCTTAAATCCATTGTACCTGAGATTTGATTAGATGAAT
130 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * * ** * **
36248 AAAGATATTTCAAGGAGT-TTGTACACAAAAAATTTTGCAAAACAGAGCCGTGGTCCCGGAACGC
195 AAAGATATTTCAAGGAGTCTCGT-CGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAACGC
* * *
36312 GTTTTTAGCCGAAAACCGTGATGGTTAGTTCACGATTTCGACTAAAATTTTGCAAAAATTGACCA
259 GTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
*
36377 GAATA-ATGT
324 GAA-AGATAT
* * * ** * * * *
36386 TTCCTCTATTTTTGGCTAAAATATTCGA-AATAAATATAT-ATTTCTACGTCAAAATGATTGGAG
1 TTACTCAAATTTTGGCTAAAATGCTC-ATAAAAAATATATAATTT-GACGTCAAAAAGATTGAAG
* * *
36449 GACTTTTAACGCTTCTAAAATTGTATTTTCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAA
64 GGCTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAA
* * *
36514 CAAGATTCAGATACTCGTAAAAAAAAAT-CTTAAATCCAATGTGGCTAAGATTTGATTAGATGAA
129 CAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAA
* *
36578 TAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAAAGTCGTGACCCCGGAACAC
194 TAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAACGC
* * * *
36643 GTTTTTAGCCGAAAACTGTGATGGTTAGTATACGATTTCGGCTAAAATTTTTCAAAAATTGACCG
259 GTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC
*
36708 GAATA-ACAT
324 GAA-AGATAT
* * * * *
36717 TTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAACTCGACGT-AACAAAGATTGAAGG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACGTCAA-AAAGATTGAAGG
* *
36781 GCTTTAAACACTTCTAATATTGTA-TTTCT-TATTTTTCCGAATTAATTTCTAATTAAATCGAAA
65 GCTTTTAACGCTTCTAATATTGTATTTTCTAT-TTTTTCCGAATTAATTTCTAATTAAATCGAAA
* * * *
36844 CAAGATTCAGTTGCTCATAAAAGCAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAA
129 CAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAA
* * * * * * * *
36909 TATAA-ATATTTCAAAGAGTCTTGACACCAAAAATCATGCGAAACAGAGTCG-GGCCCCGAAACA
194 TA-AAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAACG
* * * * * * *
36972 CGTTTTTTGCCAAAAACCATGATGGTTAGTACACAATTTCGTCTAAAATTTTGCAAAAGTCGACC
258 CGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
37037 CGAAAGATAT
323 CGAAAGATAT
* * * *
37047 TTACTCAATTTTTGGCTAACATGCTCA-AATAAAATATATAATTCGACGTCAAAAAGATTGAATG
1 TTACTCAAATTTTGGCTAAAATGCTCATAA-AAAATATATAATTTGACGTCAAAAAGATTGAAGG
* *
37111 GCTTTTAACGTTTCCAATATTGTA-TTTC-ATATTTTTCCGAATTAATTTCTAATTAAATCGAAA
65 GCTTTTAACGCTTCTAATATTGTATTTTCTAT-TTTTTCCGAATTAATTTCTAATTAAATCGAAA
* * * *
37174 CAAGATTCAGATGCTCGTAAAAACAAATTTTCTTAAATCCAATATAGATGAGATTTGATTAGATG
129 CAAGATTCAGATGCTCGTAAAAACAAA--TCCTTAAATCCAATGTGGCTGAGATTTGATTAGATG
* * * * *
37239 AATAAAGATATTTCAAGGAGTTTCGGCGCCAAAAATCGTTCAAAACAAAGTCGTGACCCCGGAAC
192 AATAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAAC
*** * *
37304 GCGTTTTTATTTGAAAACTGTGATGGTTAGTATACGATTTC-G-----A-----C------T---
257 GCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
*
37349 -----A-ACAT
322 CCGAAAGATAT
* * * * * * *
37354 TTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAACTCGACGTAAAAAAGAATGAAGGG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACGTCAAAAAGATTGAAGGG
*
37419 CTTTTAACACTTCTAATATTGTA-TTTCATATTTTTTCCGAATTAATTTCTAATTAAATCGAAAC
66 CTTTTAACGCTTCTAATATTGTATTTTC-TATTTTTTCCGAATTAATTTCTAATTAAATCGAAAC
* * * *
37483 AAGATTCAGATGCTCGTAAAAACAATTACTTAAATTCAATGTGGCTGAGATTTTG-TTAGTTGAA
130 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA-TTTGATTAGATGAA
* * ** * *
37547 TATAGATATTTCAAGGAGTCTCGACGTAAAAAATCATGCAAAACTA-AGTCGGGACCCCGAAACG
194 TAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAAC-AGAGTCGTGACCCCGGAACG
* * * * **
37611 CGTTTTTTTGCC-AAAACCCGTGATGGTTAATACACGATTTCGCCTAAAATTTTGGAAAAAAAGA
258 CG-TTTTTAGCCGAAAA-CCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA
* *
37675 CCC-AAAAATTT
321 CCCGAAAGATAT
* * * ** *
37686 TTCCTCAAATTTTGGCTAACATACTC--AAATTATATATAATTTAACTGT-AAAAAGATTG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGAC-GTCAAAAAGATTG
37744 GAGGATTTTT
Statistics
Matches: 4050, Mismatches: 507, Indels: 211
0.85 0.11 0.04
Matches are distributed among these distances:
306 86 0.02
307 113 0.03
308 61 0.02
309 2 0.00
313 1 0.00
322 1 0.00
324 24 0.01
325 249 0.06
326 3 0.00
327 35 0.01
328 165 0.04
329 597 0.15
330 347 0.09
331 876 0.22
332 1128 0.28
333 88 0.02
334 272 0.07
335 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (332 bp):
TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACGTCAAAAAGATTGAAGGG
CTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
AAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAACGCGT
TTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGA
AAGATAT
Found at i:36447 original size:661 final size:662
Alignment explanation
Indices: 32751--37714 Score: 6068
Period size: 661 Copynumber: 7.5 Consensus size: 662
32741 ACCGTGATGG
*
32751 TTACTCAAATTTTGGCTAAAATGCTAATAAAAAATATATAATTTGACGTCAAAAAGATTAAAGGG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACG-CAAAAAGATTAAAGGG
32816 CTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAAT-GAAACA
65 CTTTTAACGCTTCTAATATTGTATTTTCTA-TTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * *
32880 AGATTCAGATGTTCGTAAAAAAAAATCCTTAAATCCAATGTGGCTAAGATTTGATTATATGAATA
129 AGATTCAGATGATCGTAAAAAAAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
* * * * **
32945 AAGATATGTCAAGGAGTCTCGT-CTCCAAAAATCATGCAAAACAGAGTCGTGACCTCAAAACGCG
194 AAGATATTTCAAGGAGTCTCGTACACCAAAAATCATGCAAAACAGAGTCGTGGCCCCGGAACGCG
* * * *
33009 TTTTTAGCTGAAAACCGTGGTGGATAGTACACGATTTAGGCTAAAATTTTGCAAAAATTGAACC-
259 TTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTG-ACCA
* ** *
33073 GAAAGATATTTACTCAAATTTTGAATAAAATGCTCATAAAAAATATATAATTT-GATGTCAAAAA
323 GAAAGATATTTCCTCAAATTTTGGCTAAAATGCTCA-AAAAAATATAT-ATTTCGACGTCAAAAA
** *
33137 GATAAAAGGGCTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTA
386 GATTGAAGGACTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTA
* * * *
33202 AA-TGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTAAATACAATGTACCCGAGATTTGAT
451 AATTGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTACCTGAGATTTGAT
* * * * * ** * **
33266 TAGATGAATAAAGATATTTCAAGAAGTTTCGGCACAAAAAATTTTTGCAAAACCGAG-CTGTGGT
516 TAGATGAATAAAGATATTTCAAGGAGTCTCGTCGCCAAAAA-TCATGCAAAACAGAGTC-GTGAC
* *
33330 CCCGGAACGCGTTTTTAGCTGAAAACCGTGATGGTTAGTACACTATTTCGGCTAAAATTTTGT-A
579 CCCGGAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTT-TCA
*
33394 AAAATTGACCTGAATA-ATAT
643 AAAATTGACCCGAA-AGATAT
* * * ** * * * **
33414 TTCCTCGATTTTTGGCTAAAATATTTGA-AAAAAATATATAATTCGACGTAAAAAAGATTGGAGG
1 TTACTCAAATTTTGGCTAAAAT-GCTCATAAAAAATATATAATTTGACG-CAAAAAGATTAAAGG
* * *
33478 ACTTTTAACCCTTCTAATATTGTA--TT-T-TTTTTCTGAATTAATTTCTAATTAAATCGAAACA
64 GCTTTTAACGCTTCTAATATTGTATTTTCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* *
33539 AGATTCAGAT-ACTCGTAAAAAAAATATCTTTAAATCCAATGTGGCTGAGTTTTGATTAGATGAA
129 AGATTCAGATGA-TCGTAAAAAAAA-ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAA
* * * *
33603 TAAATATATTTCAAGGAGTCTCGT-CGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAATG
192 TAAAGATATTTCAAGGAGTCTCGTACACCAAAAATCATGCAAAACAGAGTCGTGGCCCCGGAACG
*
33667 CGTTTTTAGCCGAAAACCGTTATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
257 CGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
* *
33732 CGAAAGATATTTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTT-GACGTCGAAA
322 AGAAAGATATTTCCTCAAATTTTGGCTAAAATGCTCA-AAAAAATATAT-ATTTCGACGTC-AAA
* *
33796 AAGATTAAAGGGCTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAAT
384 AAGATTGAAGGACTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAAT
* * * *
33861 TAAA-TGAAACAAGATTAAGATGTTCGTAAAAACAAATCCTTAAATACAATGTA-CTCGAGATTT
449 TAAATTGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTACCT-GAGATTT
* *
33924 GGTTAGATAAATAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGA
513 GATTAGATGAATAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGA
* *
33989 CCCCGGAACGCGTTTTTAGCAGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACA
578 CCCCGGAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTTCA
*
34054 AAAATTGACCCGAACGATAT
643 AAAATTGACCCGAAAGATAT
* * * *
34074 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTGGATCTCAAAAAGATTGAAGGT
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGA-CGCAAAAAGATTAAAGGG
* *
34139 CTTTTAACGCTTCTAATAATGTATTTTCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACA
65 CTTTTAACGCTTCTAATATTGTATTTTCTA-TTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * *
34204 AGATTCGGAT-ACTTGTAAAAAAAAAATTCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGA
129 AGATTCAGATGA-TCGT-AAAAAAAAA-TCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGA
* * *
34268 ATAAAGATATTTCAAGGAGTCTCGT-CTCCAAAAATCATGCAAAACAGAGTCGTGACCCCTGAAC
191 ATAAAGATATTTCAAGGAGTCTCGTACACCAAAAATCATGCAAAACAGAGTCGTGGCCCCGGAAC
* * *
34332 GCGTTTTTAGCCGAAAACCATGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAATATTGAC
256 GCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
* * * * * ** * * *
34397 CCGAATA-TTATTTCCTCTATTTTTGGCTTAAATATTAGAAAAAAATATATAATTCCACGTCAAA
321 CAGAA-AGATATTTCCTCAAATTTTGGCTAAAATGCT-CAAAAAAATATATATTTCGACGTCAAA
* *
34461 AAGATTGGAGGACTTTTAACGCTTCTAATATTGTATTTTCTATTTTTT--TAATTAATTTCTAAT
384 AAGATTGAAGGACTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAAT
* * * * *
34524 TAAATCGAAACAAAATTCAGATACTCGT-AAAAAAAATCCTTAAATCCATTGTGCCTGAGATTTG
449 TAAATTGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTACCTGAGATTTG
* * *
34588 GTTAGATGAATAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAAAGTCGTGAG
514 ATTAGATGAATAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGAC
*
34653 CCCGGAACGCGTTTTTAGCCGAAAACCGTGATGCTTAGTACACGATTTCGGCTAAAATTTTGT-A
579 CCCGGAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTT-TCA
*
34717 AAAATTAACCCGAAAGATAT
643 AAAATTGACCCGAAAGATAT
*
34737 TTACTCAAATTTTGGTTAAAATGCTCATAAAAAATATATAATTTGACGTCAAAAAGATTAAAGGG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACG-CAAAAAGATTAAAGGG
*
34802 CTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCCAATTAATTTCTAATTAAAT-GAAACA
65 CTTTTAACGCTTCTAATATTGTATTTTCTA-TTTTTCCGAATTAATTTCTAATTAAATCGAAACA
** ** ** *
34866 AGATTCACTTTTTCGTAAAAAAAAATCCTTAAATACCAATGTACCCGAGATTTGATTAGATGAAT
129 AGATTCAGATGATCGTAAAAAAAAATCCTTAAAT-CCAATGTGGCTGAGATTTGATTAGATGAAT
* * * * * * *
34931 AAATATATTTCAAGGAGTCTCAT-CGCCAAAAATCAAGCAAAATAGGGTCGTGACCCCGGAACGC
193 AAAGATATTTCAAGGAGTCTCGTACACCAAAAATCATGCAAAACAGAGTCGTGGCCCCGGAACGC
*
34995 GTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGACTC
258 GTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC-C
* *
35060 -GAAAGATATTTGCTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTT-GACGCCAAAA
322 AGAAAGATATTTCCTCAAATTTTGGCTAAAATGCTCA-AAAAAATATAT-ATTTCGACGTCAAAA
* * * * * * *
35123 AGATTAAAGGGCTTGTAACGCTTTTAATATTGGATTTTCTATTTTTCCCCAATTAATTTCTAATT
385 AGATTGAAGGACTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATT
* * * *
35188 AAA-TGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTAAATACAATGTACCCGAGATTTGA
450 AAATTGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTACCTGAGATTTGA
* *
35252 TTAGATGAATAAGGATATTTCAAGGAGTCTCGTTGCCAAAAATCATGCAAAACAGAGTCGTGACC
515 TTAGATGAATAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACC
** * * * *
35317 CCAAAACGCGTTTTTAGTCGAAAACCGTGATGGTTACTATACGATTTCGGCTACAA-TTTTCGAA
580 CCGGAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTTC-AA
35381 AAATTGACCCGAAAGATAT
644 AAATTGACCCGAAAGATAT
* * * *
35400 TTACTCAAATTTAGGATAAAATGCTCTTAAAAAATATATAATTTGCCGTCAAAAAGATTAAAGGG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACG-CAAAAAGATTAAAGGG
*
35465 CTTTTAACGCTTCTAATATTGTATTTTC-AATTTT-----TTAATTTCTAATTAAATCGAAACAA
65 CTTTTAACGCTTCTAATATTGTATTTTCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACAA
* * * **
35524 GATTCAGATGTTCGTAAAAACAAATCCTTAAATCCATTGTACCTGAGATTTGATTAGATGAATAA
130 GATTCAGATGATCGTAAAAAAAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAA
* * ** * *
35589 AGATATTTCAAGGAGT-TTGTACACAAAAAATTTTGCAAAACAGAGCCGTGGTCCCGGAACGCGT
195 AGATATTTCAAGGAGTCTCGTACACCAAAAATCATGCAAAACAGAGTCGTGGCCCCGGAACGCGT
* *
35653 TTTTAGCCGAAAACCGTGATGGTTAGTTCACGATTTCGACTAAAATTTTGCAAAAATTGACCAGA
260 TTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGA
* * * ** * *
35718 ATA-ATGTTTCCTCGATTTTTGGCTAAAATATTCGAAATAAATATATATTTCTACGTCAAAAAGA
325 A-AGATATTTCCTCAAATTTTGGCTAAAATGCTC-AAAAAAATATATATTTCGACGTCAAAAAGA
* * *
35782 TTGGAGGACTTTTAACGCTTCTAAAATTGTATTTTCTATTTTTTCTGAATTAATTTCTAATTAAA
388 TTGAAGGACTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAA
* * * ** *
35847 TTGAAACAATATTCAGATACTCGTAAAAAAAAATCCTTAAATCCATTGTGGCTGAGATTTGACTA
453 TTGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTACCTGAGATTTGATTA
* * *** * * *
35912 GAAGAATAAAGATATTTCAAGGAGTCTCATCGTTTAAAATTATGCAAAACAGAGTCATGACCCCA
518 GATGAATAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCG
35977 GAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTTCAAAAAT
583 GAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTTCAAAAAT
*
36042 TGACTCGAAAGATAT
648 TGACCCGAAAGATAT
36057 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACGCAAAAAAGATTAAAGGG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACGC-AAAAAGATTAAAGGG
*
36122 CTTTTAACGCTTCTAATATTGTATTTTCTA-TTTTCCGAATTATTTTCTAATTAAAT-GAAACAA
65 CTTTTAACGCTTCTAATATTGTATTTTCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACAA
* * * * **
36185 GATTCAGATGATCATAAAAACAAACCCTTAAATCCATTGTACCTGAGATTTGATTAGATGAATAA
130 GATTCAGATGATCGTAAAAAAAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAA
* * ** * *
36250 AGATATTTCAAGGAGT-TTGTACACAAAAAATTTTGCAAAACAGAGCCGTGGTCCCGGAACGCGT
195 AGATATTTCAAGGAGTCTCGTACACCAAAAATCATGCAAAACAGAGTCGTGGCCCCGGAACGCGT
* *
36314 TTTTAGCCGAAAACCGTGATGGTTAGTTCACGATTTCGACTAAAATTTTGCAAAAATTGACCAGA
260 TTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGA
* * * ** * * *
36379 ATA-ATGTTTCCTCTATTTTTGGCTAAAATATTCGAAATAAATATATATTTCTACGTCAAAATGA
325 A-AGATATTTCCTCAAATTTTGGCTAAAATGCTC-AAAAAAATATATATTTCGACGTCAAAAAGA
* * *
36443 TTGGAGGACTTTTAACGCTTCTAAAATTGTATTTTCTATTTTTTCTGAATTAATTTCTAATTAAA
388 TTGAAGGACTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAA
* * ** *
36508 TCGAAACAAGATTCAGATACTCGTAAAAAAAAAT-CTTAAATCCAATGTGGCTAAGATTTGATTA
453 TTGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTACCTGAGATTTGATTA
*
36572 GATGAATAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAAAGTCGTGACCCCG
518 GATGAATAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCG
* * *
36637 GAACACGTTTTTAGCCGAAAACTGTGATGGTTAGTATACGATTTCGGCTAAAATTTTTCAAAAAT
583 GAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTTCAAAAAT
* *
36702 TGACCGGAATA-ACAT
648 TGACCCGAA-AGATAT
* * * * * * *
36717 TTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAACTCGACGTAACAAAGATTGAAGGG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACGCAA-AAAGATTAAAGGG
* *
36782 CTTTAAACACTTCTAATATTGTA-TTTCTTATTTTTCCGAATTAATTTCTAATTAAATCGAAACA
65 CTTTTAACGCTTCTAATATTGTATTTTC-TATTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * * ** *
36846 AGATTCAGTTGCTCATAAAAGCAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATA
129 AGATTCAGATGATCGTAAAAAAAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
* * * * *
36911 TAA-ATATTTCAAAGAGTCTTG-ACACCAAAAATCATGCGAAACAGAGTCG-GGCCCCGAAACAC
194 -AAGATATTTCAAGGAGTCTCGTACACCAAAAATCATGCAAAACAGAGTCGTGGCCCCGGAACGC
* * * * * * * *
36973 GTTTTTTGCCAAAAACCATGATGGTTAGTACACAATTTCGTCTAAAATTTTGCAAAAGTCGACCC
258 GTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCA
* * * *
37038 GAAAGATATTTACTCAATTTTTGGCTAACATGCTCAAATAAAATATATAATTCGACGTCAAAAAG
323 GAAAGATATTTCCTCAAATTTTGGCTAAAATGCTCAAA-AAAATATATATTTCGACGTCAAAAAG
* *
37103 ATTGAATGG-CTTTTAACGTTTCCAATATTGTA-TTTC-ATATTTTTCCGAATTAATTTCTAATT
387 ATTGAA-GGACTTTTAACGCTTCTAATATTGTATTTTCTAT-TTTTTCCGAATTAATTTCTAATT
* * * * **
37165 AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTTTCTTAAATCCAATATAGATGAGATTT
450 AAATTGAAACAAGATTCAGATGCTCGTAAAAA-AAA-ATCCTTAAATCCAATGTACCTGAGATTT
* * * * *
37230 GATTAGATGAATAAAGATATTTCAAGGAGTTTCGGCGCCAAAAATCGTTCAAAACAAAGTCGTGA
513 GATTAGATGAATAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGA
*** * *
37295 CCCCGGAACGCGTTTTTATTTGAAAACTGTGATGGTTAGTATACGATTTC-G-----A-----C-
578 CCCCGGAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTTCA
*
37348 -----T--------A-ACAT
643 AAAATTGACCCGAAAGATAT
* * * * * * * *
37354 TTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAACTCGACGTAAAAAAGAATGAAGGG
1 TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACG-CAAAAAGATTAAAGGG
*
37419 CTTTTAACACTTCTAATATTGTA-TTTCATATTTTTTCCGAATTAATTTCTAATTAAATCGAAAC
65 CTTTTAACGCTTCTAATATTGTATTTTC-TA-TTTTTCCGAATTAATTTCTAATTAAATCGAAAC
* * * * * *
37483 AAGATTCAGATGCTCGTAAAAACAATTACTTAAATTCAATGTGGCTGAGATTTTG-TTAGTTGAA
128 AAGATTCAGATGATCGTAAAAAAAAATCCTTAAATCCAATGTGGCTGAGA-TTTGATTAGATGAA
* *** *
37547 TATAGATATTTCAAGGAGTCTCG-ACGTAAAAAATCATGCAAAACTA-AGTCG-GGACCCCGAAA
192 TAAAGATATTTCAAGGAGTCTCGTACACCAAAAATCATGCAAAAC-AGAGTCGTGG-CCCCGGAA
* * * * **
37609 CGCGTTTTTTTGCC-AAAACCCGTGATGGTTAATACACGATTTCGCCTAAAATTTTGGAAAAAAA
255 CGCG-TTTTTAGCCGAAAA-CCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATT
* * *
37673 GACCCA-AAA-ATTTTTCCTCAAATTTTGGCTAACATACTCAAA
318 GA-CCAGAAAGATATTTCCTCAAATTTTGGCTAAAATGCTCAAA
37715 TTATATATAA
Statistics
Matches: 3849, Mismatches: 377, Indels: 174
0.87 0.09 0.04
Matches are distributed among these distances:
637 94 0.02
638 129 0.03
639 49 0.01
640 51 0.01
641 2 0.00
646 1 0.00
652 1 0.00
655 7 0.00
656 257 0.07
657 308 0.08
658 32 0.01
659 41 0.01
660 674 0.18
661 933 0.24
662 165 0.04
663 775 0.20
664 22 0.01
665 100 0.03
666 206 0.05
667 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (662 bp):
TTACTCAAATTTTGGCTAAAATGCTCATAAAAAATATATAATTTGACGCAAAAAGATTAAAGGGC
TTTTAACGCTTCTAATATTGTATTTTCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG
ATTCAGATGATCGTAAAAAAAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAAA
GATATTTCAAGGAGTCTCGTACACCAAAAATCATGCAAAACAGAGTCGTGGCCCCGGAACGCGTT
TTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAA
AGATATTTCCTCAAATTTTGGCTAAAATGCTCAAAAAAATATATATTTCGACGTCAAAAAGATTG
AAGGACTTTTAACGCTTCTAATATTGTATTTTCTATTTTTTCCGAATTAATTTCTAATTAAATTG
AAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTACCTGAGATTTGATTAGAT
GAATAAAGATATTTCAAGGAGTCTCGTCGCCAAAAATCATGCAAAACAGAGTCGTGACCCCGGAA
CGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTTCAAAAATTGA
CCCGAAAGATAT
Found at i:38055 original size:1 final size:1
Alignment explanation
Indices: 38049--38078 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
38039 ACAAAACATC
38049 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
38079 AATATTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:39870 original size:41 final size:41
Alignment explanation
Indices: 39824--40109 Score: 455
Period size: 41 Copynumber: 7.2 Consensus size: 41
39814 CACGCGGCAC
39824 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
39865 ATT--CA--C-A---T-CCAAATGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
*
39897 ATTCACATCCAACTTTTCCAAATGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
*
39938 ATTCACATCCAACTTTTCCAAATGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
*
39979 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTG
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
* *
40020 ATTCACTTCCAACTTTCCCAAATGACATTGAACTTGCCTTG
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
*
40061 ATTCACTTCCAACTTTCCCAAATGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
40102 ATTCACAT
1 ATTCACAT
40110 TGTTCCTCAA
Statistics
Matches: 231, Mismatches: 5, Indels: 18
0.91 0.02 0.07
Matches are distributed among these distances:
32 27 0.12
33 1 0.00
34 2 0.01
36 2 0.01
37 2 0.01
39 2 0.01
40 1 0.00
41 194 0.84
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (41 bp):
ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
Found at i:39930 original size:20 final size:20
Alignment explanation
Indices: 39873--40013 Score: 72
Period size: 20 Copynumber: 6.9 Consensus size: 20
39863 TAATTCACAT
39873 CCAAATGACATTGAAC-TTG
1 CCAAATGACATTGAACTTTG
* * ** *
39892 CCTTAATTCACATCCAACTTTT
1 CC--AAATGACATTGAACTTTG
39914 CCAAATGACATTGAAC-TTG
1 CCAAATGACATTGAACTTTG
* * ** *
39933 CCTTAATTCACATCCAACTTTT
1 CC--AAATGACATTGAACTTTG
39955 CCAAATGACATTGAAC-TTG
1 CCAAATGACATTGAACTTTG
* * ** *
39974 CCTTAATTCACATCCAACTTTC
1 CC--AAATGACATTGAACTTTG
39996 CCAAATGACATTGAACTT
1 CCAAATGACATTGAACTT
40014 GCCTTGATTC
Statistics
Matches: 84, Mismatches: 29, Indels: 17
0.65 0.22 0.13
Matches are distributed among these distances:
19 10 0.12
20 32 0.38
21 30 0.36
22 12 0.14
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.33
Consensus pattern (20 bp):
CCAAATGACATTGAACTTTG
Found at i:40394 original size:122 final size:122
Alignment explanation
Indices: 40177--40400 Score: 360
Period size: 122 Copynumber: 1.8 Consensus size: 122
40167 CGAGACAATA
* * * *
40177 AGGCAATCCTTGCTGCCACAAGGATATCCTCAGCTTCAATGGGGAGACAACTGCAGAGGAGAAGA
1 AGGCAATCCTAGCTGCCACAAGGATATCCTCAGATCCAATGGGGAGACAACTGCAGAAGAGAAGA
*** *
40242 AATGTTATCCAGAAACCATCAGAGCAGAAAAAGGAAACTTACAACAAACAAATCTGG
66 AACACTATCAAGAAACCATCAGAGCAGAAAAAGGAAACTTACAACAAACAAATCTGG
40299 AGGCAATCCTAGCTGCCACAAGGATA-CACTCAGATCCAATGGGGAGACAACTGCAGAAGAGAAG
1 AGGCAATCCTAGCTGCCACAAGGATATC-CTCAGATCCAATGGGGAGACAACTGCAGAAGAGAAG
40363 AAACACTATCAAGAAACCATCAGAGCAGAAAAAGGAAA
65 AAACACTATCAAGAAACCATCAGAGCAGAAAAAGGAAA
40401 ATCAGAGCAA
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
121 1 0.01
122 92 0.99
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.14
Consensus pattern (122 bp):
AGGCAATCCTAGCTGCCACAAGGATATCCTCAGATCCAATGGGGAGACAACTGCAGAAGAGAAGA
AACACTATCAAGAAACCATCAGAGCAGAAAAAGGAAACTTACAACAAACAAATCTGG
Found at i:47271 original size:30 final size:30
Alignment explanation
Indices: 47235--47293 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
47225 CCTCATAGAA
47235 GTATAATGCTTTGGTTGAAATGGTTCCAAC
1 GTATAATGCTTTGGTTGAAATGGTTCCAAC
* *
47265 GTATAATTCTTTGGTTGACATGGTTCCAA
1 GTATAATGCTTTGGTTGAAATGGTTCCAA
47294 TGAGTATGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (30 bp):
GTATAATGCTTTGGTTGAAATGGTTCCAAC
Found at i:48076 original size:51 final size:51
Alignment explanation
Indices: 47952--48172 Score: 216
Period size: 51 Copynumber: 4.3 Consensus size: 51
47942 CCAGCTTATT
* * ** *
47952 TTCTAGATTCAGTAGCTGGTTCCAAACTCCTTCCAGCTATTCCAACTTCTC
1 TTCTTGATTCAGCAGCCAGTTCCAAACTCCTCCCAGCTATTCCAACTTCTC
*
48003 TTCTTGATTC-GACTGCCAGTTCCAAACTCCTCCCAGCTATTCCAACTTCTC
1 TTCTTGATTCAG-CAGCCAGTTCCAAACTCCTCCCAGCTATTCCAACTTCTC
* * * * * * * *
48054 TTCTCGATTCAGCAGCCCGTTCCAAGCTTCTCACAGGTATTCTAGCTTCTC
1 TTCTTGATTCAGCAGCCAGTTCCAAACTCCTCCCAGCTATTCCAACTTCTC
* * * *
48105 TTCTGGATTCAGCAG-CATGTTCCAAACTTCTCCCTGAC-ATACCAACTTC-C
1 TTCTTGATTCAGCAGCCA-GTTCCAAACTCCTCCCAG-CTATTCCAACTTCTC
48155 TTTCTTGATTCAGCAGCC
1 -TTCTTGATTCAGCAGCC
48173 TGCTCCAGCC
Statistics
Matches: 139, Mismatches: 25, Indels: 11
0.79 0.14 0.06
Matches are distributed among these distances:
50 3 0.02
51 134 0.96
52 2 0.01
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (51 bp):
TTCTTGATTCAGCAGCCAGTTCCAAACTCCTCCCAGCTATTCCAACTTCTC
Found at i:52579 original size:22 final size:22
Alignment explanation
Indices: 52549--52604 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
52539 AAAAATCCTT
52549 TTAT-AAATTTT-TTAAACTTTC
1 TTATGAAATTTTGTT-AACTTTC
52570 TTATGAAATTTTGTTAACTTTC
1 TTATGAAATTTTGTTAACTTTC
* *
52592 TTAAGGAATTTTG
1 TTATGAAATTTTG
52605 AAGACCTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 4 0.13
22 25 0.81
23 2 0.06
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (22 bp):
TTATGAAATTTTGTTAACTTTC
Found at i:52672 original size:22 final size:23
Alignment explanation
Indices: 52624--52678 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
52614 ATATAAAATT
*
52624 TTGATAACCAACACTATGAGATG
1 TTGATAACCAACACTATGAGATA
** *
52647 TTGATAACCTCCA-TATGATATA
1 TTGATAACCAACACTATGAGATA
52669 TTGATAACCA
1 TTGATAACCA
52679 CTTTATAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (23 bp):
TTGATAACCAACACTATGAGATA
Found at i:52742 original size:22 final size:22
Alignment explanation
Indices: 52708--52763 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
52698 CCTCCATATG
* *
52708 AATTGTTAGTAATCACACTTTAA
1 AATTGTGA-TAATCACACTATAA
* *
52731 AATTTTGATAATCACACTATGA
1 AATTGTGATAATCACACTATAA
52753 AATTGTGATAA
1 AATTGTGATAA
52764 CCTCGCTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (22 bp):
AATTGTGATAATCACACTATAA
Found at i:52800 original size:23 final size:22
Alignment explanation
Indices: 52728--52853 Score: 83
Period size: 22 Copynumber: 5.6 Consensus size: 22
52718 AATCACACTT
* ***
52728 TAAAATTTTGATAATCACACTA
1 TAAAATTTTGATAAACTTTCTA
* * * **
52750 TGAAATTGTGATAACCTCGCTA
1 TAAAATTTTGATAAACTTTCTA
*
52772 TGAAATTTTGATAAATCTTTCTA
1 TAAAATTTTGATAAA-CTTTCTA
* **
52795 TAAAATTTTAATAAACCTCCCTA
1 TAAAATTTTGATAAA-CTTTCTA
52818 TAAAATTTTGAT-AACTTTCTTA
1 TAAAATTTTGATAAACTTTC-TA
* *
52840 TGAAATCTTGATAA
1 TAAAATTTTGATAA
52854 CTACAAATTT
Statistics
Matches: 82, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
21 3 0.04
22 44 0.54
23 35 0.43
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (22 bp):
TAAAATTTTGATAAACTTTCTA
Found at i:52825 original size:46 final size:45
Alignment explanation
Indices: 52728--52831 Score: 120
Period size: 46 Copynumber: 2.3 Consensus size: 45
52718 AATCACACTT
* * *
52728 TAAAATTTTGAT-AATCACACTATGAAATTGTGATAACCTCGCTA
1 TAAAATTTTGATAAATCACACTATAAAATTGTAATAACCTCCCTA
* *** *
52772 TGAAATTTTGATAAATCTTTCTATAAAATTTTAATAAACCTCCCTA
1 TAAAATTTTGATAAATCACACTATAAAATTGTAAT-AACCTCCCTA
52818 TAAAATTTTGATAA
1 TAAAATTTTGATAA
52832 CTTTCTTATG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 11 0.22
45 16 0.33
46 22 0.45
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (45 bp):
TAAAATTTTGATAAATCACACTATAAAATTGTAATAACCTCCCTA
Found at i:52887 original size:22 final size:22
Alignment explanation
Indices: 52861--53028 Score: 80
Period size: 22 Copynumber: 7.6 Consensus size: 22
52851 TAACTACAAA
* * *
52861 TTTTGATAAGCTCCTTATGATT
1 TTTTGATAACCTCATTATGAAT
52883 TTTTGATAACCTCATTATGAAT
1 TTTTGATAACCTCATTATGAAT
* ** *
52905 TTTTG-TGAATCTCCCTATGAAA
1 TTTTGAT-AACCTCATTATGAAT
*
52927 TTTTGAT---CTACATGCTATGAAA
1 TTTTGATAACCT-CAT--TATGAAT
*
52949 TTTTGATAACACTC-TTATGAAA
1 TTTTGATAAC-CTCATTATGAAT
* * * *
52971 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCT-CATTATGAAT
* *
52993 ATTTGATAACCTTCA-TATGAAA
1 TTTTGATAACC-TCATTATGAAT
*
53015 TTTTGATATCCTCA
1 TTTTGATAACCTCA
53029 CTGAATTTTG
Statistics
Matches: 116, Mismatches: 17, Indels: 27
0.73 0.11 0.17
Matches are distributed among these distances:
19 2 0.02
20 3 0.03
21 6 0.05
22 95 0.82
23 5 0.04
24 2 0.02
25 1 0.01
26 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (22 bp):
TTTTGATAACCTCATTATGAAT
Found at i:52968 original size:44 final size:42
Alignment explanation
Indices: 52920--53021 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 42
52910 TGAATCTCCC
* * *
52920 TATGAAATTTTGATCTACATGCTATGAAATTTTGATAACAC-TCT
1 TATGAAATTTTGATCTA-A-ACTATGAAAATTTGATAAC-CTTCA
*
52964 TATGAAATTTTGAAAACTAAACTATGAAAATTTGATAACCTTCA
1 TATGAAATTTTG--ATCTAAACTATGAAAATTTGATAACCTTCA
53008 TATGAAATTTTGAT
1 TATGAAATTTTGAT
53022 ATCCTCACTG
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
42 1 0.02
43 1 0.02
44 43 0.86
45 1 0.02
46 4 0.08
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (42 bp):
TATGAAATTTTGATCTAAACTATGAAAATTTGATAACCTTCA
Found at i:53037 original size:19 final size:18
Alignment explanation
Indices: 53013--53078 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 18
53003 CTTCATATGA
53013 AATTTTGATATCCTCACTG
1 AATTTTGATATCCTC-CTG
53032 AATTTTGATATCCTCCCTG
1 AATTTTGATATCCT-CCTG
* *
53051 AATTTTGGTATCCTCCTAA
1 AATTTTGATATCCTCCT-G
53070 AATTTTGAT
1 AATTTTGAT
53079 TACTCCATCA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 3 0.07
19 38 0.90
20 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.44
Consensus pattern (18 bp):
AATTTTGATATCCTCCTG
Found at i:53206 original size:22 final size:22
Alignment explanation
Indices: 53181--53423 Score: 123
Period size: 22 Copynumber: 11.3 Consensus size: 22
53171 AATCAGATTT
*
53181 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
*
53203 TGAAATTTTGATAACATCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
53225 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
53247 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* * *
53269 TGTAATTTTGATAATCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
53291 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
*
53313 TGGAATTTTGATAA--TCTTCATA
1 TGAAATTTTGATAACCTCTT--TA
*
53335 T-AAATTTTGATAATCATATCTTTA
1 TGAAATTTTGATAA-C--CTCTTTA
*
53359 TGAAATTTCGAT-A-CTC--TA
1 TGAAATTTTGATAACCTCTTTA
* *
53377 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
53397 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
53417 TGAAATT
1 TGAAATT
53424 GAGACTTTTA
Statistics
Matches: 166, Mismatches: 39, Indels: 34
0.69 0.16 0.14
Matches are distributed among these distances:
17 5 0.03
18 7 0.04
19 4 0.02
20 17 0.10
21 17 0.10
22 97 0.58
23 2 0.01
24 4 0.02
25 9 0.05
26 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:53276 original size:44 final size:43
Alignment explanation
Indices: 53156--53347 Score: 165
Period size: 44 Copynumber: 4.4 Consensus size: 43
53146 AAAAATACCA
* * *
53156 CTATGAAATTTTTG-TAATCAGATTTTGAAAATTTGATAACCTCT
1 CTATGAAA-TTTTGATAA-CACATTATGAAATTTTGATAACCTCT
* * * * * *
53200 TTATGAAATTTTGATAACATCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAACA-CATTATGAAATTTTGATAACCTCT
* * *
53244 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAATCTCG
1 CTATGAAATTTTGATAA-CACATTATGAAATTTTGATAACCTCT
* * * *
53288 CTTTGAAATTTTGATAACAACACTATGGAATTTTGATAATCT-T
1 CTATGAAATTTTGATAAC-ACATTATGAAATTTTGATAACCTCT
53331 CATAT-AAATTTTGATAA
1 C-TATGAAATTTTGATAA
53348 TCATATCTTT
Statistics
Matches: 120, Mismatches: 23, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
43 21 0.17
44 97 0.81
45 2 0.02
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.43
Consensus pattern (43 bp):
CTATGAAATTTTGATAACACATTATGAAATTTTGATAACCTCT
Found at i:53320 original size:88 final size:88
Alignment explanation
Indices: 53156--53322 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 88
53146 AAAAATACCA
* * * *
53156 CTATGAAATTTTTGTAATCAGATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACATC
1 CTATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
53221 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* * *
53244 CTATGAAA-TTTTGATAATCACATTATGTAATTTTGATAATCTCGCTT-TGAAATTTTGATAACA
1 CTATGAAATTTTTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACA
**
53307 ACACTATGGAATTTTG
64 ACACTATAAAATTTTG
53323 ATAATCTTCA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
87 5 0.08
88 59 0.89
89 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (88 bp):
CTATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:53353 original size:18 final size:19
Alignment explanation
Indices: 53316--53353 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
53306 AACACTATGG
53316 AATTTTGATAATCTTCATATA
1 AATTTTGATAA--TTCATATA
53337 AATTTTGATAA-TCATAT
1 AATTTTGATAATTCATAT
53354 CTTTATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
21 11 0.65
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.47
Consensus pattern (19 bp):
AATTTTGATAATTCATATA
Found at i:53458 original size:22 final size:22
Alignment explanation
Indices: 53181--53539 Score: 101
Period size: 22 Copynumber: 16.3 Consensus size: 22
53171 AATCAGATTT
* *
53181 TGAAAATTTGATAACC-TCTTTA
1 TGAAATTTTGATAACCTTC-ATA
53203 TGAAATTTTGATAACATCTT--TA
1 TGAAATTTTGATAAC--CTTCATA
* * * *
53225 TAAAATTTTGTTGACCCCTC-TA
1 TGAAATTTTGAT-AACCTTCATA
* *
53247 TGAAATTTTGATAATC-ACATTA
1 TGAAATTTTGATAACCTTCA-TA
* * * *
53269 TGTAATTTTGATAATC-TCGCTT
1 TGAAATTTTGATAACCTTC-ATA
**
53291 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAACCTTCA-TA
* *
53313 TGGAATTTTGATAATCTTCATA
1 TGAAATTTTGATAACCTTCATA
* *
53335 T-AAATTTTGATAATCATATCTTTA
1 TGAAATTTTGATAA-CCT-TC-ATA
*
53359 TGAAATTTCGAT-A-C-TC-TA
1 TGAAATTTTGATAACCTTCATA
*
53377 TGAGA-TTTGATAACCTTC-TA
1 TGAAATTTTGATAACCTTCATA
* * *
53397 TCAAATTTTGGTACTCCTT-ATGAAA
1 TGAAATTTTGATA-ACCTTCAT---A
*
53422 TTGAGACTTTT-ATAACCTTCATA
1 -TGA-AATTTTGATAACCTTCATA
*
53445 TGAAATTTTGATAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
* * **
53467 TAAAATTTTGATAACCTCCCGA
1 TGAAATTTTGATAACCTTCATA
* *
53489 TGAAGTATT-ATTAACCTTC-TAA
1 TGAAATTTTGA-TAACCTTCAT-A
* *
53511 TGAAATTTTGTTAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
53533 TGAAATT
1 TGAAATT
53540 CGTATAACCT
Statistics
Matches: 250, Mismatches: 52, Indels: 70
0.67 0.14 0.19
Matches are distributed among these distances:
17 5 0.02
18 7 0.03
19 1 0.00
20 10 0.04
21 31 0.12
22 155 0.62
23 10 0.04
24 5 0.02
25 15 0.06
26 6 0.02
27 5 0.02
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:53664 original size:24 final size:22
Alignment explanation
Indices: 53603--53765 Score: 100
Period size: 22 Copynumber: 7.3 Consensus size: 22
53593 TTGTGATAAT
* *
53603 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
53625 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* * **
53647 TAACTTGATCCTATGAAATTTTGG
1 TAAC--CAACCTATGAAATTTTAA
**
53671 TAACC-ACTCTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* **
53693 TAA-CTACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
*
53715 TAACC-ACACTATGAAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* * *
53737 TAACC-TCCTCATGGAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
53759 TAACCAA
1 TAACCAA
53766 AGTAAAATAT
Statistics
Matches: 117, Mismatches: 17, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
21 4 0.03
22 95 0.81
23 1 0.01
24 17 0.15
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:53675 original size:46 final size:43
Alignment explanation
Indices: 53610--53740 Score: 147
Period size: 44 Copynumber: 3.0 Consensus size: 43
53600 AATTAACCAC
*** * *
53610 CCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACTTGA
1 CCTATGAAATTTTGGTAACCACA-CTATGAAATTTTGATAAC-T-A
* *
53655 TCCTATGAAATTTTGGTAACCACTCTATGAAATTTTGGTAACTA
1 -CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTA
53699 CACTATGAAATTTTGGTAACCACACTATGAAATTTTGATAAC
1 C-CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAAC
53741 CTCCTCATGG
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
43 1 0.01
44 39 0.53
45 1 0.01
46 33 0.45
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (43 bp):
CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTA
Found at i:53685 original size:22 final size:22
Alignment explanation
Indices: 53657--53741 Score: 143
Period size: 22 Copynumber: 3.9 Consensus size: 22
53647 TAACTTGATC
*
53657 CTATGAAATTTTGGTAACCACT
1 CTATGAAATTTTGGTAACCACA
*
53679 CTATGAAATTTTGGTAACTACA
1 CTATGAAATTTTGGTAACCACA
53701 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
*
53723 CTATGAAATTTTGATAACC
1 CTATGAAATTTTGGTAACC
53742 TCCTCATGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 59 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:53754 original size:22 final size:22
Alignment explanation
Indices: 53603--53741 Score: 129
Period size: 22 Copynumber: 6.2 Consensus size: 22
53593 TTGTGATAAT
* **
53603 TAACCACCCTATGAAATTTCAA
1 TAACCACACTATGAAATTTTGA
* *
53625 TAACCA-ACCTAAGAAATTTTAA
1 TAACCACA-CTATGAAATTTTGA
* *
53647 TAACTTGATC-CTATGAAATTTTGG
1 TAAC--CA-CACTATGAAATTTTGA
* *
53671 TAACCACTCTATGAAATTTTGG
1 TAACCACACTATGAAATTTTGA
* *
53693 TAACTACACTATGAAATTTTGG
1 TAACCACACTATGAAATTTTGA
53715 TAACCACACTATGAAATTTTGA
1 TAACCACACTATGAAATTTTGA
53737 TAACC
1 TAACC
53742 TCCTCATGGA
Statistics
Matches: 99, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.01
22 82 0.83
24 16 0.16
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
TAACCACACTATGAAATTTTGA
Found at i:53763 original size:44 final size:44
Alignment explanation
Indices: 53611--53764 Score: 111
Period size: 44 Copynumber: 3.5 Consensus size: 44
53601 ATTAACCACC
* *
53611 CTATGAAATT-TCAATAACCA-ACCTAAGAAATTTTAATAACTTGATC-
1 CTATGAAATTAT-AATAACCACA-CTATGAAATTTTGATAAC-T-A-CA
* ** * *
53657 CTATGAAATTTTGGTAACCACTCTATGAAATTTTGGTAACTACA
1 CTATGAAATTATAATAACCACACTATGAAATTTTGATAACTACA
* **
53701 CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCT-C-
1 CTATGAAATTATAATAACCACACTATGAAATTTTGATAA-CTACA
*
53744 CTCATGGAATTATAATAACCA
1 CT-ATGAAATTATAATAACCA
53765 AAGTAAAATA
Statistics
Matches: 91, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
43 3 0.03
44 53 0.58
45 3 0.03
46 31 0.34
47 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (44 bp):
CTATGAAATTATAATAACCACACTATGAAATTTTGATAACTACA
Found at i:53882 original size:32 final size:32
Alignment explanation
Indices: 53846--53913 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 32
53836 TTTAGTAATG
53846 ACAATTTAGAAATATGTTTTTAAAAA-AAGGGT
1 ACAATTTAGAAATATG-TTTTAAAAATAAGGGT
*
53878 ACAA-TTGGAAATATGTTTTAAAAATAAGGGT
1 ACAATTTAGAAATATGTTTTAAAAATAAGGGT
53909 ACAAT
1 ACAAT
53914 CGGAAAACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 9 0.27
31 20 0.61
32 4 0.12
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.32
Consensus pattern (32 bp):
ACAATTTAGAAATATGTTTTAAAAATAAGGGT
Found at i:53899 original size:30 final size:32
Alignment explanation
Indices: 53854--53919 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
53844 TGACAATTTA
*
53854 GAAATATGTTTTTAAAAA-AAGGGTACAATTG
1 GAAATATGTTTTTAAAAATAAGGGTACAATCG
53885 GAAATATG-TTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTTAAAAATAAGGGTACAATCG
53916 GAAA
1 GAAA
53920 ACATGAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 9 0.27
31 24 0.73
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.29
Consensus pattern (32 bp):
GAAATATGTTTTTAAAAATAAGGGTACAATCG
Found at i:54129 original size:18 final size:18
Alignment explanation
Indices: 54095--54138 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
54085 TTTTCTACAC
54095 TAATAGAAGACAGTTGGA
1 TAATAGAAGACAGTTGGA
* *
54113 TAATTAGAAGA-ATTTGGC
1 TAA-TAGAAGACAGTTGGA
54131 TAATAGAA
1 TAATAGAA
54139 CAGCATTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 11 0.48
19 7 0.30
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.27
Consensus pattern (18 bp):
TAATAGAAGACAGTTGGA
Found at i:57583 original size:14 final size:14
Alignment explanation
Indices: 57564--57590 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
57554 GGGTGTTACA
57564 TAACAGATATGAAG
1 TAACAGATATGAAG
57578 TAACAGATATGAA
1 TAACAGATATGAA
57591 ATTTGGGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (14 bp):
TAACAGATATGAAG
Found at i:62423 original size:14 final size:15
Alignment explanation
Indices: 62404--62432 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
62394 TTTCCGACAA
62404 CCAATATAG-ATCAT
1 CCAATATAGAATCAT
62418 CCAATATAGAATCAT
1 CCAATATAGAATCAT
62433 GGAGATGGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.28
Consensus pattern (15 bp):
CCAATATAGAATCAT
Found at i:64098 original size:20 final size:20
Alignment explanation
Indices: 64073--64112 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
64063 CATTAACCTC
*
64073 AATCAATCCGGAGTCAAGTA
1 AATCAATCCGGAGCCAAGTA
*
64093 AATCAATTCGGAGCCAAGTA
1 AATCAATCCGGAGCCAAGTA
64113 TCATCCAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCAATCCGGAGCCAAGTA
Found at i:67604 original size:3 final size:3
Alignment explanation
Indices: 67598--67653 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
67588 GTCGTCGTCG
* * * *
67598 TCT TCT TCT TCT TCGT T-A TCC TCT TCT TCC TCT TCC TCT TCT TCT
1 TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
67643 TCT TCT TCT TC
1 TCT TCT TCT TC
67654 AACTTCCTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 1 0.02
3 41 0.93
4 2 0.05
ACGTcount: A:0.02, C:0.38, G:0.02, T:0.59
Consensus pattern (3 bp):
TCT
Found at i:67671 original size:18 final size:18
Alignment explanation
Indices: 67650--67689 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
67640 TCTTCTTCTT
67650 CTTCAACTTCCTCTTCGA
1 CTTCAACTTCCTCTTCGA
*
67668 CTTCTACTTCCTCTTCGA
1 CTTCAACTTCCTCTTCGA
67686 CTTC
1 CTTC
67690 CTCCAGCTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.40, G:0.05, T:0.42
Consensus pattern (18 bp):
CTTCAACTTCCTCTTCGA
Found at i:69543 original size:19 final size:21
Alignment explanation
Indices: 69499--69544 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
69489 TGTGGCACGC
*
69499 CATGTACCAAAAAGTCGTGCCA
1 CATGTACCAAAAAGTC-TGACA
69521 CATGTACCAAAAAGT-T-ACA
1 CATGTACCAAAAAGTCTGACA
69540 CATGT
1 CATGT
69545 CACACCACGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 1 0.04
22 15 0.65
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (21 bp):
CATGTACCAAAAAGTCTGACA
Found at i:69565 original size:53 final size:51
Alignment explanation
Indices: 69466--69566 Score: 130
Period size: 51 Copynumber: 1.9 Consensus size: 51
69456 GACGTGACAC
* ** *
69466 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACACCATGTACCAAAAAGTCGT
* *
69517 GCCACATGTACCAAAAAGTTACACATGTCACACCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACACCA--TGTACCAAAAAGT
69567 AACACGTAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 29 0.69
53 13 0.31
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.18
Consensus pattern (51 bp):
GCCACATGTACCAAAAAGTGACACATGGCACACCATGTACCAAAAAGTCGT
Found at i:73121 original size:24 final size:25
Alignment explanation
Indices: 73093--73141 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
73083 AAGTGAAGCC
73093 CAGATCATGCACAAAA-CCAGATCA
1 CAGATCATGCACAAAACCCAGATCA
73117 CAGATCATGCACAAAACCCAGATCA
1 CAGATCATGCACAAAACCCAGATCA
73142 TGTTGCAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.45, C:0.31, G:0.12, T:0.12
Consensus pattern (25 bp):
CAGATCATGCACAAAACCCAGATCA
Found at i:74067 original size:20 final size:19
Alignment explanation
Indices: 74033--74092 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
74023 TTAGTGTGTG
*
74033 TAATTT-ATTTCTTAATAA
1 TAATTTAATTTTTTAATAA
*
74051 TATTTATAATTTTTTAATAA
1 TAATT-TAATTTTTTAATAA
74071 TAATTTAATTATTTTCAATAA
1 TAATTTAATT-TTTT-AATAA
74092 T
1 T
74093 TAAAACCTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 4 0.11
19 6 0.17
20 19 0.54
21 6 0.17
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATTTAATTTTTTAATAA
Found at i:74085 original size:21 final size:19
Alignment explanation
Indices: 74037--74092 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
74027 TGTGTGTAAT
74037 TTATTTCTTAATAATATTTA
1 TTATTT-TTAATAATATTTA
*
74057 TAATTTTTTAATAATAATTTAA
1 TTA-TTTTTAATAAT-ATTT-A
*
74079 TTATTTTCAATAAT
1 TTATTTTTAATAAT
74093 TAAAACCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 10 0.33
21 17 0.57
22 3 0.10
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTTTTAATAATATTTA
Found at i:75643 original size:29 final size:29
Alignment explanation
Indices: 75578--75658 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
75568 GCTTAATACT
* *
75578 CAAATTAGCCCCTTAACTATCTATTTTGGAA
1 CAAATTGGCCCCTTAACT-T-TTTTTTGGAA
*
75609 CAAATTGGCCCCTTAACTTTTTTTTGGGA
1 CAAATTGGCCCCTTAACTTTTTTTTGGAA
*
75638 TAAATTGGCCCCTTAACTTTT
1 CAAATTGGCCCCTTAACTTTT
75659 AAAAACGAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 28 0.61
30 1 0.02
31 17 0.37
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (29 bp):
CAAATTGGCCCCTTAACTTTTTTTTGGAA
Found at i:76391 original size:28 final size:28
Alignment explanation
Indices: 76350--76406 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
76340 TCTCGTTTTT
* *
76350 AAAAGTTTAGGGGCCAATTTGTCCAAAA
1 AAAAGTTAAGGGGCCAACTTGTCCAAAA
* * *
76378 AAAAGTTAATGGGCTAACTTGTCCCAAA
1 AAAAGTTAAGGGGCCAACTTGTCCAAAA
76406 A
1 A
76407 TGAATAGTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (28 bp):
AAAAGTTAAGGGGCCAACTTGTCCAAAA
Found at i:77591 original size:42 final size:42
Alignment explanation
Indices: 77534--77618 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
77524 AGAAGACTGT
* *
77534 TTAAGAATGATATTGAAATACAAAGGTACATAAAGAACAACC
1 TTAAGAATGAGATTGAAATACAAAGGTAAATAAAGAACAACC
* * *
77576 TTAATAATGAGATTGAAATAGAAAGGTAAATAAAGAACTACC
1 TTAAGAATGAGATTGAAATACAAAGGTAAATAAAGAACAACC
77618 T
1 T
77619 CCGACTCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (42 bp):
TTAAGAATGAGATTGAAATACAAAGGTAAATAAAGAACAACC
Found at i:77779 original size:3 final size:3
Alignment explanation
Indices: 77771--77827 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
77761 CCCTAAACCC
77771 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
77819 ATA ATA ATA
1 ATA ATA ATA
77828 GGAATCTCAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.