Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009853.1 Corchorus capsularis cultivar CVL-1 contig09874, 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: 63662
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:2870 original size:15 final size:15
Alignment explanation
Indices: 2850--2879 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2840 AAGTTAAGTC
2850 TGTCCCGCTCCTCCT
1 TGTCCCGCTCCTCCT
2865 TGTCCCGCTCCTCCT
1 TGTCCCGCTCCTCCT
2880 CTGCAAGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.53, G:0.13, T:0.33
Consensus pattern (15 bp):
TGTCCCGCTCCTCCT
Found at i:5696 original size:30 final size:30
Alignment explanation
Indices: 5662--5718 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
5652 AAAATTGGTT
5662 TAGGACTTTTACTCATCTTGAAATTAAACC
1 TAGGACTTTTACTCATCTTGAAATTAAACC
5692 TAGGACTTTTACTCATCTTGAAATTAA
1 TAGGACTTTTACTCATCTTGAAATTAA
5719 GCCTTGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.39
Consensus pattern (30 bp):
TAGGACTTTTACTCATCTTGAAATTAAACC
Found at i:10119 original size:15 final size:15
Alignment explanation
Indices: 10099--10128 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10089 ATGAAAAGAC
*
10099 TAGCAGTAAATATAA
1 TAGCAGAAAATATAA
10114 TAGCAGAAAATATAA
1 TAGCAGAAAATATAA
10129 AGAAACATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.13, T:0.23
Consensus pattern (15 bp):
TAGCAGAAAATATAA
Found at i:19688 original size:27 final size:27
Alignment explanation
Indices: 19629--19707 Score: 95
Period size: 27 Copynumber: 2.8 Consensus size: 27
19619 GCTTAATACC
*
19629 CAAATTAGCCCCTTAACTATCCATTTTGGGA
1 CAAATTGGCCCCTTAACT-T---TTTTGGGA
*
19660 CAAATTGGCCCCTTAACTTTTTTTGGA
1 CAAATTGGCCCCTTAACTTTTTTGGGA
*
19687 CAAATTGGTCCCTTAACTTTT
1 CAAATTGGCCCCTTAACTTTT
19708 AAAAACGAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
27 27 0.60
30 1 0.02
31 17 0.38
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (27 bp):
CAAATTGGCCCCTTAACTTTTTTGGGA
Found at i:20433 original size:29 final size:30
Alignment explanation
Indices: 20394--20474 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
20384 TCCCATTTTT
20394 AAAAGTTAAGGGGCCAATTTGTCCCAAAA-
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAAG
* *
20423 AAAAGTTAAGGGGTCAATTTATCCCAAAATG
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA-G
* * *
20454 GATAGTTAAGGGGCTAATTTG
1 AAAAGTTAAGGGGCCAATTTG
20475 GGTACTAAGC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 27 0.63
31 16 0.37
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.26
Consensus pattern (30 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAAAG
Found at i:20597 original size:60 final size:59
Alignment explanation
Indices: 20499--20630 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 59
20489 TATAGCTAAA
* *
20499 TGTTCAAATAGGTTCTTAATGTATATGAAAATGTTCAATTTAGGG-CTCATGCGTTAAATTT
1 TGTT-AAATAGGGTCCTAATGTATATGAAAATGTTCAATTTAGGGCCT-ATGCGTTAAA-TT
* * *
20560 TGTTAAATAGGGTCCTAATGTATGTGAAAAT-TCTCAATTTAGGGCCTATGCTTTGAATT
1 TGTTAAATAGGGTCCTAATGTATATGAAAATGT-TCAATTTAGGGCCTATGCGTTAAATT
20619 TGATTAAATAGG
1 TG-TTAAATAGG
20631 ACCCTTACGT
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
59 5 0.08
60 52 0.83
61 6 0.10
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (59 bp):
TGTTAAATAGGGTCCTAATGTATATGAAAATGTTCAATTTAGGGCCTATGCGTTAAATT
Found at i:20643 original size:60 final size:60
Alignment explanation
Indices: 20519--20643 Score: 139
Period size: 60 Copynumber: 2.1 Consensus size: 60
20509 GGTTCTTAAT
* ** *
20519 GTATATGAAAATGTTCAATTTAGGGCTCATGCGTTAAATTTTGTTAAATAGGGTCCTAAT
1 GTATGTGAAAATGTTCAATTTAGGGCTCATGCGTTAAATTTTGTTAAATAGGACCCTAAC
* * *
20579 GTATGTGAAAAT-TCTCAATTTAGGGC-CTATGCTTTGAA-TTTGATTAAATAGGACCCTTAC
1 GTATGTGAAAATGT-TCAATTTAGGGCTC-ATGCGTTAAATTTTG-TTAAATAGGACCCTAAC
20639 GTATG
1 GTATG
20644 CAAAAATATT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
59 6 0.11
60 49 0.89
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (60 bp):
GTATGTGAAAATGTTCAATTTAGGGCTCATGCGTTAAATTTTGTTAAATAGGACCCTAAC
Found at i:21153 original size:27 final size:27
Alignment explanation
Indices: 21114--21174 Score: 104
Period size: 27 Copynumber: 2.2 Consensus size: 27
21104 ATAGTATTAC
21114 TCCCTCTGTTCCTTTTTAATTGTCCCTT
1 TCCCT-TGTTCCTTTTTAATTGTCCCTT
*
21142 TCCCTTGTTCCTTTTTAATTGTCTCTT
1 TCCCTTGTTCCTTTTTAATTGTCCCTT
21169 TCCCTT
1 TCCCTT
21175 ATTTTCCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.07, C:0.31, G:0.07, T:0.56
Consensus pattern (27 bp):
TCCCTTGTTCCTTTTTAATTGTCCCTT
Found at i:23607 original size:28 final size:26
Alignment explanation
Indices: 23545--23600 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 26
23535 AGTTAAATTT
23545 AAAAAACTTTAACATTGAAGCTAATAAA
1 AAAAAACTTTAACATTGAA-C-AATAAA
23573 AAAAAACTTTAACATTGAA-AAGTAAA
1 AAAAAACTTTAACATTGAACAA-TAAA
23599 AA
1 AA
23601 CATAAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 2 0.07
26 6 0.22
28 19 0.70
ACGTcount: A:0.61, C:0.09, G:0.07, T:0.23
Consensus pattern (26 bp):
AAAAAACTTTAACATTGAACAATAAA
Found at i:26972 original size:319 final size:317
Alignment explanation
Indices: 26315--27713 Score: 1524
Period size: 319 Copynumber: 4.4 Consensus size: 317
26305 ATTTCATATA
* *
26315 TGGCTGAGATTTGGTTCGATGAATATACATATTTCAAGGATTCTTTTCGTCAAAAATCATGCAAA
1 TGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTTCGTCAAAAATCATGCAAA
* * *
26380 TTTGAGCCGGGGCTCCGGAACCCGTTTTTAGCCAAAAACTGTGAT-AGTACATGATTTCGGCTAA
66 ATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACTGTGATAAGTACACGATTTCGGCTAA
* *
26444 AAATTGACCCGAAATGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAAAATATAATTCAA
131 AAATTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAA
** * * * * **
26509 CACCAAAAAGATTGA-CAGTATTTACACGCGTCTAATATCATTTTTCCATTTTTTACCGATTTAA
196 CACCAAAAAGATTGATGGGT-TTT-CACACTTCTAATATCGTTTTTCCATTTTTT-CTGAACTAA
* * * **
26573 TTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAAAAAAT-CTGTATATCCAATA
258 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCT-TATATCCAACG
* * * *
26633 TGGCTGAGATTTGATTCGATGAATATGGATATCTT-AAGGAGTCTTTTCGCCAAAAATCATACAA
1 TGGCTGAGATTTGGTTCGATGAATATAGATAT-TTCAAGGAGTCTTTTCGTCAAAAATCATGCAA
* * * * *
26697 AACTGAGTCAGGGCTCCGGTACGCGTTTTTAGCCAAAAACCGTGATAACGTACACGATTTCGGCT
65 AATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACTGTGATAA-GTACACGATTTCGGCT
26762 AAAAATTGACCC-AACAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGGAAAAAATATATAAT
129 AAAAATTGACCCGAA-AAGTTTTTTCTCAATTTTTTGCCACAATACTCA-GAAAAAATATATAAT
* * *
26826 TTAACACCAAAAAGATTGATGGGTTTTACACATTTCTAATATTGTTTTTCCATTTTTT-TGAACT
192 TCAACACCAAAAAGATTGATGGGTTTT-CACACTTCTAATATCGTTTTTCCATTTTTTCTGAACT
* *
26890 AATTTCTAATTAAATCGAAACAAGATTCATATGCTTGTAAAAATAAATCCTTATATCCAACG
256 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTATATCCAACG
* * * *
26952 TGGCTGACATTTGGTTCGATGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATAATGC
1 TGGCTGAGATTTGGTTC---GATGAATATAGATATTTCAAGGAGTCTTTTCGTCAAAAATCATGC
* * * *
27017 AAAATTGAGTCGGGGCTCTGGAACGCGTTTTTAGCCAAAAACAATGATGGTTAGTACACGA--T-
63 AAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAAC--TG-TGATAAGTACACGATTTC
*
27079 ---T--AAATTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACGATACTCAG-AAAAA-A-A-A
125 GGCTAAAAATTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATA
* * *
27135 ATTCAACACCAAAAAGATTGATGTGCTTTTCACCCTTCTAATATTGTTTTTCCATTTTTTCTGAA
190 ATTCAACACCAAAAAGATTGATG-GGTTTTCACACTTCTAATATCGTTTTTCCATTTTTTCTGAA
* * * *
27200 CTAATTTCTAATTAAATCGAAATAAGATTCATATTCTTGTAAAAATAAATCCTTATATCCAACG
254 CTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTATATCCAACG
* * * * *
27264 TGG-TAGACATTTTGTTGGATGAATATAGATATTTCAAGTAGTCTTTGT-GTCAAAAATCATGTA
1 TGGCT-GAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT-TCGTCAAAAATCATGCA
* * * * *
27327 AGATTGAACCGGGGCTCCGGAACACGTTTTTAGCGAAAAACTGTGATGGTTAA-TACACTATTTC
64 AAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACTGTGA----TAAGTACACGATTTC
* * * *
27391 GGCTAAAAATTGACCTC--AAATTTTTTTCACAATTTTTTGCCACAATACACATAAAAAATATAT
125 GGCTAAAAATTGACC-CGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATAT
* ** *
27454 AATTCAACGCCAAAAAGATTGACAGGTTTTC-CATGCTTTTAATATCG-TTTTCCATTTTTT-TC
189 AATTCAACACCAAAAAGATTGATGGGTTTTCACA--CTTCTAATATCGTTTTTCCATTTTTTCT-
* * * * * *
27516 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGCAAAAACAAATCGTTAAATCGAA
251 GAACTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTATATCCAA
*
27581 TG
316 CG
* * * * *
27583 TGACTGGGATTTGGTTCGATGAATATAGATATTTC-AGTGAGTCTTTACGTTAAAAATCATTCAA
1 TGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAG-GAGTCTTTTCGTCAAAAATCATGCAA
* * ** ** * * * * *
27647 AACTAAGATGGGGC-CTAGAACGCGTTTTTAGCCATAAA-TCGTTATGAGTAAACGATTTCGGTT
65 AATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACT-GTGATAAGTACACGATTTCGGCT
27710 AAAA
129 AAAA
27714 TTTTGCAAAA
Statistics
Matches: 918, Mismatches: 119, Indels: 91
0.81 0.11 0.08
Matches are distributed among these distances:
306 2 0.00
307 2 0.00
309 81 0.09
310 2 0.00
311 53 0.06
312 85 0.09
313 1 0.00
314 7 0.01
315 18 0.02
316 72 0.08
317 17 0.02
318 123 0.13
319 207 0.23
320 93 0.10
321 63 0.07
322 79 0.09
324 9 0.01
325 4 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (317 bp):
TGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTTCGTCAAAAATCATGCAAA
ATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACTGTGATAAGTACACGATTTCGGCTAA
AAATTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAA
CACCAAAAAGATTGATGGGTTTTCACACTTCTAATATCGTTTTTCCATTTTTTCTGAACTAATTT
CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTATATCCAACG
Found at i:27544 original size:631 final size:630
Alignment explanation
Indices: 26315--27680 Score: 1608
Period size: 631 Copynumber: 2.2 Consensus size: 630
26305 ATTTCATATA
* * *
26315 TGGCTGAGATTTGGTTCGATGAATATACATATTTCAAGGATTCTTTTCGTCAAAAATCATGCAAA
1 TGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGTCAAAAATCATGCAAA
* * * * *
26380 TTTGAGCCGGGGCTCCGGAACCCGTTTTTAGCCAAAAACTGTGATAGTACATGATTTCGGCTAAA
66 ATTGAGTCGGGGCTCTGGAACGCGTTTTTAGCCAAAAACTGTGATAGTACACGA-TT---CT-AA
*
26445 AATTGACCCGAAATGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAAAATATAATTCAAC
126 AATTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAG-AAAAAAATATAATTCAAC
* **
26510 ACCAAAAAGATTGACAGTATTTACACGCGTCTAATATCATTTTTCCATTTTTTACCGATTTAATT
190 ACCAAAAAGATTGACAGTATTTACACCCGTCTAATATCATTTTTCCATTTTTTACCGAACTAATT
* *
26575 TCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAAAAAATCTGTATATCCAATATGGCTGA
255 TCTAATTAAATCGAAACAAGATTCAGATGCTCGAAAAAAAAAATCTGTATATCCAACATGGCTGA
* * **
26640 GATTTGATTCGATGAATATGGATATCTTAAGGAGTCTTTTCGCCAAAAATCATACAAAACTGAGT
320 CATTTGATTCGATGAATATAGATATCTTAAGGAGTCTTTTCGCCAAAAATCATACAAAACTGAAC
* *
26705 CAGGGCTCCGGTACGCGTTTTTAGCCAAAAACCGTGATAACGTACACGATTTCGGCTAAAAATTG
385 CAGGGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATAAC-TACACGATTTCGGCTAAAAATTG
* * *
26770 ACCCAACAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGGAAAAAATATATAATTTAACACCA
449 ACCCAACAAGTTTTTTCACAATTTTTTGCCACAATACACAGGAAAAAATATATAATTCAACACCA
** *
26835 AAAAGATTGATGGGTTTTACACATTTCTAATATTGTTTTTCCATTTTTTTGAACTAATTTCTAAT
514 AAAAGATTGACAGGTTTTACACATTTCTAATATCGTTTTTCCATTTTTTTGAACTAATTTCTAAT
* * * * *
26900 TAAATCGAAACAAGATTCATATGCTTGTAAAAATAAATCCTTATATCCAACG
579 TAAATCGAAACAAGATTCAGATGCTCGCAAAAACAAATCCTTAAATCCAACG
* * * *
26952 TGGCTGACATTTGGTTCGATGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATAATGC
1 TGGCTGAGATTTGGTTC---GATGAATATAGATATTTCAAGGAGTCTTTACGTCAAAAATCATGC
*
27017 AAAATTGAGTCGGGGCTCTGGAACGCGTTTTTAGCCAAAAACAATGATGGTTAGTACACGA-T-T
63 AAAATTGAGTCGGGGCTCTGGAACGCGTTTTTAGCCAAAAAC--TG-T-GATAGTACACGATTCT
*
27080 -AAATTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACGATACTCAG-AAAAAA-A-AATTCAA
124 AAAATTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAAATATAATTCAA
* * * * ** *
27141 CACCAAAAAGATTGA-TGTGCTTTTCACCCTTCTAATATTGTTTTTCCATTTTTT-CTGAACTAA
189 CACCAAAAAGATTGACAGT-ATTTACACCCGTCTAATATCATTTTTCCATTTTTTACCGAACTAA
* * * * * * *
27204 TTTCTAATTAAATCGAAATAAGATTCATATTCTTGTAAAAATAAATCCT-TATATCCAACGTGG-
253 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGAAAAAAAAAAT-CTGTATATCCAACATGGC
* * * ** *
27267 TAGACATTTTG-TTGGATGAATATAGATAT-TTCAAGTAGTCTTTGT-GTCAAAAATCATGTAAG
317 T-GACA-TTTGATTCGATGAATATAGATATCTT-AAGGAGTCTTT-TCGCCAAAAATCATACAAA
* * * * *
27329 ATTGAACCGGGGCTCCGGAACACGTTTTTAGCGAAAAACTGTGATGGTTAA-TACACTATTTCGG
378 ACTGAACCAGGGCTCCGGAACACGTTTTTAGCCAAAAACCGTGA----TAACTACACGATTTCGG
* *
27393 CTAAAAATTGACCTC-A-AATTTTTTTCACAATTTTTTGCCACAATACACA-TAAAAAATATATA
439 CTAAAAATTGACC-CAACAAGTTTTTTCACAATTTTTTGCCACAATACACAGGAAAAAATATATA
* *
27455 ATTCAACGCCAAAAAGATTGACAGGTTTT-C-CATGCTTTTAATATCG-TTTTCCATTTTTTTCG
503 ATTCAACACCAAAAAGATTGACAGGTTTTACACAT--TTCTAATATCGTTTTTCCATTTTTTT-G
* * * *
27517 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGCAAAAACAAATCGTTAAATCGAAT
565 AACTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGCAAAAACAAATCCTTAAATCCAAC
27582 G
630 G
* * * *
27583 TGACTGGGATTTGGTTCGATGAATATAGATATTTC-AGTGAGTCTTTACGTTAAAAATCATTCAA
1 TGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAG-GAGTCTTTACGTCAAAAATCATGCAA
* * *
27647 AACTAAGAT-GGGGC-CTAGAACGCGTTTTTAGCCA
65 AATTGAG-TCGGGGCTCTGGAACGCGTTTTTAGCCA
27681 TAAATCGTTA
Statistics
Matches: 626, Mismatches: 80, Indels: 56
0.82 0.10 0.07
Matches are distributed among these distances:
627 21 0.03
628 49 0.08
629 4 0.01
630 18 0.03
631 255 0.41
632 88 0.14
633 27 0.04
634 7 0.01
635 3 0.00
636 45 0.07
637 16 0.03
638 1 0.00
640 78 0.12
642 3 0.00
643 1 0.00
644 10 0.02
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (630 bp):
TGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGTCAAAAATCATGCAAA
ATTGAGTCGGGGCTCTGGAACGCGTTTTTAGCCAAAAACTGTGATAGTACACGATTCTAAAATTG
ACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAAATATAATTCAACACCAAA
AAGATTGACAGTATTTACACCCGTCTAATATCATTTTTCCATTTTTTACCGAACTAATTTCTAAT
TAAATCGAAACAAGATTCAGATGCTCGAAAAAAAAAATCTGTATATCCAACATGGCTGACATTTG
ATTCGATGAATATAGATATCTTAAGGAGTCTTTTCGCCAAAAATCATACAAAACTGAACCAGGGC
TCCGGAACACGTTTTTAGCCAAAAACCGTGATAACTACACGATTTCGGCTAAAAATTGACCCAAC
AAGTTTTTTCACAATTTTTTGCCACAATACACAGGAAAAAATATATAATTCAACACCAAAAAGAT
TGACAGGTTTTACACATTTCTAATATCGTTTTTCCATTTTTTTGAACTAATTTCTAATTAAATCG
AAACAAGATTCAGATGCTCGCAAAAACAAATCCTTAAATCCAACG
Found at i:28706 original size:326 final size:311
Alignment explanation
Indices: 28206--29226 Score: 909
Period size: 326 Copynumber: 3.2 Consensus size: 311
28196 AAAATTTTGC
* ** *
28206 AAAAACTGACTCGAAAA-AAATTTCCTCAAATTTTTTTGCCACAATAGCGAGAAAAAATATATAA
1 AAAAACTGACCCGAAAATTTATTT-CTC-AA-TTTTTTGCCACAATAAC-AGAAAAAATATATAA
* * * * * * *
28270 TTTAATG-CAAAAAAATTGAGGGGC-TTTCACGCGTCAAATATCGTTTTTCTATTTTTTTTCGGA
62 TTAAACGCCAAAAAAATTG-GGGGCTTTTCACGCTTCTAATATCGTTTTTCCA-ATTTTTTCCGA
* * * * * *
28333 ATTTATTTCTAATTAAGTCGAAACTAGATTGAGATCCTCGAAAAAACAAATCCTTAAATCTAATG
125 ATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCG-AAAAACAAATCCTTATATCCAATG
* * *
28398 TATCTGAGATTTGGTTAGATGAATATAGATATTTCAA-AAGACTCTTT-CGGCCATAAATAATGC
189 T-GCTGAGATTTGGTTCGATGAATATAGATATTTCAAGAAGA-T-TTTAC-GCCAAAAATAATGC
*
28461 AAAACTT-AGCCAAGGCCCCCGAAACGCGTTTTTAGCCCAAAAACCGTGATGGTTAGTACACGAT
250 AAAA-TTGAGCC-AGGCCCCCG-AACGCGTTTTTAG-CCAAAAACC---AT-GAT-G-ACACGAT
28525 TTCGACT
305 TTCGACT
* * * * * *
28532 -AAAACATGACCC-AGATTTTTTTATCTGAATTTTTTGCCACAATATTCAGAAAAAATAAATAAT
1 AAAAAC-TGACCCGAAAATTTATT-TCTCAATTTTTTGCCACAATA-ACAGAAAAAATATATAAT
* * * *
28595 TAAACGCCAAAAATATTGGTGGGCTTTTCACACTTCTAATATCATTTTTCCAATTTTTTCCTTAA
63 TAAACGCCAAAAAAATTGG-GGGCTTTTCACGCTTCTAATATCGTTTTTCCAATTTTTTCC-GAA
*
28660 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGT
126 TTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCG-AAAAACAAATCCTTATATCCAATGT
* * * * *
28725 GCTTAACATTTGGTTCGATGAATATAGATATTTCAAGCATATTTTACGCCAAAAATCATGCAAAA
190 GC-TGAGATTTGGTTCGATGAATATAGATATTTCAAGAAGATTTTACGCCAAAAATAATGCAAAA
* * * * *
28790 TTGAGCCGGGGCTCCGAACGCTTTTTTAGCCAAAAACCATGATGACACGATTTCGGCT
254 TTGAGCCAGGCCCCCGAACGCGTTTTTAGCCAAAAACCATGATGACACGATTTCGACT
* *
28848 AAAAACTGACCCGAAAATTTATTTCTCAATTTTTTACCACAATACACA-AAAAAATATATAATTC
1 AAAAACTGACCCGAAAATTTATTTCTCAATTTTTTGCCACAATA-ACAGAAAAAATATATAATTA
* * * * * * *
28912 AACACCAAAAAGATTGACGGTCTTTTCATGCTTCTAATATTGTTTTTCC-ATTTTTTACCGATTT
65 AACGCCAAAAAAATTG-GGGGCTTTTCACGCTTCTAATATCGTTTTTCCAATTTTTT-CCGAATT
* * *
28976 AATTTCTAATTAAATCGAAATAAGATTGAGATGCTCGAAAAAAAAAT-CTGTATATCCAATATGG
128 AATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAACAAATCCT-TATATCCAATGT-G
* * * ** *
29040 CTGAGATTTGATTCGATGAATATACATATTTCAAGGAG-TCTTTGTGCCAAAAATCATGCAAAAT
191 CTGAGATTTGGTTCGATGAATATAGATATTTCAAGAAGAT-TTTACGCCAAAAATAATGCAAAAT
* * *** * * *
29104 TGAGTCGGGATTTCGGAACGCGTTTTTAGCCAAAAACCGTGACAT-ACACGATTTCGGCT
255 TGAGCCAGG-CCCCCGAACGCGTTTTTAGCCAAAAACCATG--ATGACACGATTTCGACT
* * * * * ** *
29163 AAAAATTCACTC-AAAATTTTTTTTCACAATTTTTAACCACAATATACAGAAAAAGTATATAATT
1 AAAAACTGACCCGAAAA-TTTATTTCTCAATTTTTTGCCACAATA-ACAGAAAAAATATATAATT
29227 CAACACTAAA
Statistics
Matches: 584, Mismatches: 87, Indels: 58
0.80 0.12 0.08
Matches are distributed among these distances:
312 3 0.01
313 81 0.14
314 77 0.13
315 106 0.18
316 56 0.10
317 13 0.02
318 2 0.00
319 2 0.00
322 9 0.02
323 12 0.02
324 43 0.07
325 55 0.09
326 122 0.21
327 3 0.01
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (311 bp):
AAAAACTGACCCGAAAATTTATTTCTCAATTTTTTGCCACAATAACAGAAAAAATATATAATTAA
ACGCCAAAAAAATTGGGGGCTTTTCACGCTTCTAATATCGTTTTTCCAATTTTTTCCGAATTAAT
TTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAACAAATCCTTATATCCAATGTGCTGAG
ATTTGGTTCGATGAATATAGATATTTCAAGAAGATTTTACGCCAAAAATAATGCAAAATTGAGCC
AGGCCCCCGAACGCGTTTTTAGCCAAAAACCATGATGACACGATTTCGACT
Found at i:29164 original size:315 final size:310
Alignment explanation
Indices: 28237--29281 Score: 995
Period size: 315 Copynumber: 3.3 Consensus size: 310
28227 TTCCTCAAAT
* * * ** * *
28237 TTTTTTGCCACAATA-GCGAGAAAAAATATATAATTTAA-TGCAAAAAAATTGAGGGGC-TTTCA
1 TTTTTTACCACAATATAC-AGAAAAAATATATAATTCAACACCAAAAAGATTGACGGGCTTTTCA
* * * * *
28299 CGCGTCAAATATCGTTTTTCTATTTTTTTTCGGAATTT-ATTTCTAATTAAGTCGAAACT-AGAT
65 CGCTTCTAATATCGTTTTTCCA--TTTTTTCCG-ATTTAATTTCTAATTAAATCGAAA-TAAGAT
* * * * *
28362 TGAGATCCTCGAAAAAACAAATCCTTAAATCTAATGTATCTGAGATTTGGTTAGATGAATATAGA
126 TGAGATGCTCGAAAAAA-AAATCCTTATATCCAATGT-GCTGAGATTTGGTTCGATGAATATAGA
* * * * * *
28427 TATTTCAAAAGACTCTTTCG-GCCATAAATAATGCAAAACTT-AGCCAAGGCCCCCGAAACGCGT
189 TATTTC-AAGGA-TCTTT-GTGCCAAAAATCATGCAAAA-TTGAGCC--GGGCCTCGGAACGCGT
* * *
28490 TTTTAGCCCAAAAACCGTGATGGTTAGTACACGATTTCGACT-AAAACATGACCCAGATTTTTTT
248 TTTTAG-CCAAAAACCGTGA-----A-TACACGATTTCGGCTAAAAAC-TGACCCAAAATTTTTT
*
28554 ATCTGAA
305 -TCTCAA
* * * * * * **
28561 TTTTTTGCCACAATATTCAGAAAAAATAAATAATTAAACGCCAAAAATATTGGTGGGCTTTTCAC
1 TTTTTTACCACAATATACAGAAAAAATATATAATTCAACACCAAAAAGATTGACGGGCTTTTCAC
* * * * * *
28626 ACTTCTAATATCATTTTTCCAATTTTTTCCTTAATTAATTTCTAATTAAATCGAAACAAGATTCA
66 GCTTCTAATATCGTTTTTCC-ATTTTTTCC-GATTTAATTTCTAATTAAATCGAAATAAGATTGA
* * *
28691 GATGCTCGTAAAAACAAATCCTTATATCCAATGTGCTTAACATTTGGTTCGATGAATATAGATAT
129 GATGCTCG-AAAAAAAAATCCTTATATCCAATGTGC-TGAGATTTGGTTCGATGAATATAGATAT
* * * * *
28756 TTCAAGCATATTT-TACGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCGAACGCTTTTTTAGC
192 TTCAAGGATCTTTGT--GCCAAAAATCATGCAAAATTGAGCCGGGCCTCGGAACGCGTTTTTAGC
* *
28820 CAAAAACCATG-ATGACACGATTTCGGCTAAAAACTGACCCGAAAATTTATTTCTCAA
255 CAAAAACCGTGAAT-ACACGATTTCGGCTAAAAACTGACCC-AAAATTTTTTTCTCAA
* * *
28877 TTTTTTACCACAATACACA-AAAAAATATATAATTCAACACCAAAAAGATTGACGGTCTTTTCAT
1 TTTTTTACCACAATATACAGAAAAAATATATAATTCAACACCAAAAAGATTGACGGGCTTTTCAC
*
28941 GCTTCTAATATTGTTTTTCCATTTTTTACCGATTTAATTTCTAATTAAATCGAAATAAGATTGAG
66 GCTTCTAATATCGTTTTTCCATTTTTT-CCGATTTAATTTCTAATTAAATCGAAATAAGATTGAG
* * *
29006 ATGCTCGAAAAAAAAAT-CTGTATATCCAATATGGCTGAGATTTGATTCGATGAATATACATATT
130 ATGCTCGAAAAAAAAATCCT-TATATCCAATGT-GCTGAGATTTGGTTCGATGAATATAGATATT
* **
29070 TCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGATTTCGGAACGCGTTTTTAGCC
193 TCAAGGA-TCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGG-CCTCGGAACGCGTTTTTAGCC
* * * *
29135 AAAAACCGTGACATACACGATTTCGGCTAAAAATTCACTCAAAATTTTTTTTCACAA
256 AAAAACCGTGA-ATACACGATTTCGGCTAAAAACTGACCCAAAA-TTTTTTTCTCAA
* * * * **
29192 TTTTTAACCACAATATACAGAAAAAGTATATAATTCAACACTAAAAAGATTGACAGGC--AACAC
1 TTTTTTACCACAATATACAGAAAAAATATATAATTCAACACCAAAAAGATTGACGGGCTTTTCAC
*
29255 GCTTCTAATATTAG-TTTTCCATTTTTT
66 GCTTCTAATA-TCGTTTTTCCATTTTTT
29282 TCTGAAAATC
Statistics
Matches: 603, Mismatches: 91, Indels: 64
0.80 0.12 0.08
Matches are distributed among these distances:
312 2 0.00
313 78 0.13
314 106 0.18
315 110 0.18
316 77 0.13
317 12 0.02
322 11 0.02
323 16 0.03
324 39 0.06
325 49 0.08
326 97 0.16
327 6 0.01
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (310 bp):
TTTTTTACCACAATATACAGAAAAAATATATAATTCAACACCAAAAAGATTGACGGGCTTTTCAC
GCTTCTAATATCGTTTTTCCATTTTTTCCGATTTAATTTCTAATTAAATCGAAATAAGATTGAGA
TGCTCGAAAAAAAAATCCTTATATCCAATGTGCTGAGATTTGGTTCGATGAATATAGATATTTCA
AGGATCTTTGTGCCAAAAATCATGCAAAATTGAGCCGGGCCTCGGAACGCGTTTTTAGCCAAAAA
CCGTGAATACACGATTTCGGCTAAAAACTGACCCAAAATTTTTTTCTCAA
Found at i:43044 original size:14 final size:14
Alignment explanation
Indices: 43010--43044 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
43000 ACACTCCAAT
43010 AAAAAAATCAATAA
1 AAAAAAATCAATAA
**
43024 AGCAAAATCAATAA
1 AAAAAAATCAATAA
43038 AAAAAAA
1 AAAAAAA
43045 ACACAAACAG
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.77, C:0.09, G:0.03, T:0.11
Consensus pattern (14 bp):
AAAAAAATCAATAA
Found at i:43877 original size:4 final size:4
Alignment explanation
Indices: 43868--43894 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
43858 AAATATACAA
43868 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
43895 GGTGTCTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:45142 original size:5 final size:5
Alignment explanation
Indices: 45132--45169 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
45122 TTAGATGTAA
45132 TATAT TATATT TATAT TATA- -ATAT TATAT TATAT TATA
1 TATAT TATA-T TATAT TATAT TATAT TATAT TATAT TATA
45170 ATAATTGCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 3 0.10
5 22 0.73
6 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:45158 original size:13 final size:12
Alignment explanation
Indices: 45132--45164 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
45122 TTAGATGTAA
45132 TATATTAT-ATT
1 TATATTATAATT
45143 TATATTATAATAT
1 TATATTATAAT-T
45156 TATATTATA
1 TATATTATA
45165 TTATAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.40
12 2 0.10
13 10 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATATTATAATT
Found at i:46254 original size:102 final size:96
Alignment explanation
Indices: 46049--46265 Score: 335
Period size: 96 Copynumber: 2.2 Consensus size: 96
46039 AGATTTGGCG
*
46049 TAGCATAGTCCCCATTTTCATTTGATCGGCCTGAACTTGCTTCATAGTTGCTTCCATTTCCTTCG
1 TAGCATAGTCCCCATTTTCATTTGATCGGCCAGAACTTGCTTCATAGTTGCTTCCATTTCCTTCG
46114 TCTTGGATTCATGCCTTTGATAAATTTCGCT
66 TCTTGGATTCATGCCTTTGATAAATTTCGCT
* * *
46145 TAGCATAGCCCCCATTTTCATTTGATCGGCCAGAATTTGCTTCAATATAGTTTCTTCCATTTCCT
1 TAGCATAGTCCCCATTTTCATTTGATCGGCCAGAACTTGCTTC---ATAGTTGCTTCCATTTCCT
*
46210 TCGTCTTTGATTCATCTGGCCTTTGATAAATTTCGCT
63 TCGTCTTGGATTCA--T-GCCTTTGATAAATTTCGCT
46247 TAGCATAGTCCCCATTTTC
1 TAGCATAGTCCCCATTTTC
46266 TTCACAGTTT
Statistics
Matches: 109, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
96 40 0.37
99 31 0.28
101 1 0.01
102 37 0.34
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.41
Consensus pattern (96 bp):
TAGCATAGTCCCCATTTTCATTTGATCGGCCAGAACTTGCTTCATAGTTGCTTCCATTTCCTTCG
TCTTGGATTCATGCCTTTGATAAATTTCGCT
Found at i:46345 original size:81 final size:78
Alignment explanation
Indices: 46193--46345 Score: 261
Period size: 78 Copynumber: 1.9 Consensus size: 78
46183 GCTTCAATAT
*
46193 AGTTTCTTCCATTTCCTTCGTCTTTGATTCATCTGGCCTTTGATAAATTTCGCTTAGCATAGTCC
1 AGTTTCTTCCATTTCCTTCGTCTTTGATTCATCTGGCCTTTGATAAAATTCGCTTAGCATAGTCC
46258 CCATTTTCTTCAC
66 CCATTTTCTTCAC
*
46271 AGTTTCTTCCATTTCCTTCGTCTTTGCTTCATCTGGCCTTTGATAGATTAATTCGCTTAGCATAG
1 AGTTTCTTCCATTTCCTTCGTCTTTGATTCATCTGGCCTTTGATA-A--AATTCGCTTAGCATAG
46336 TCCCCATTTT
63 TCCCCATTTT
46346 TTCTTGCCTT
Statistics
Matches: 70, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
78 44 0.63
79 1 0.01
81 25 0.36
ACGTcount: A:0.16, C:0.26, G:0.12, T:0.45
Consensus pattern (78 bp):
AGTTTCTTCCATTTCCTTCGTCTTTGATTCATCTGGCCTTTGATAAAATTCGCTTAGCATAGTCC
CCATTTTCTTCAC
Found at i:47088 original size:2 final size:2
Alignment explanation
Indices: 47081--47106 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47071 GTACTCAATA
47081 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
47107 GAACAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48306 original size:14 final size:14
Alignment explanation
Indices: 48287--48314 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
48277 CTAGTACTTC
48287 CCAAATAAATCCAA
1 CCAAATAAATCCAA
48301 CCAAATAAATCCAA
1 CCAAATAAATCCAA
48315 AAACTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (14 bp):
CCAAATAAATCCAA
Found at i:49789 original size:99 final size:99
Alignment explanation
Indices: 49580--49881 Score: 423
Period size: 99 Copynumber: 3.1 Consensus size: 99
49570 TCCAAGGTAG
* * * *
49580 CCATTTCCATTTGAGT-GGCCAGAATTTTCTTCATTGTTTCTTCCATTTCCTTCGTCTTGGATTC
1 CCATTTTCATTTGA-TCGGCCAGAATTTTCTTCATAGTTTCTTCCATTTCCTTCGTCTTTGCTTC
* **
49644 A-C--GCCTTTGATAAATTTCGCTTAGGACGGTCC
65 ATCTGGCCTTTGATAAATTTCGCTTAGCATAGTCC
* *
49676 CCATTTTCATTTGATCAGCCAGAATTTTCTTCATAGTTTCTTCCATTTCCTTCGTCTTTTCTTCA
1 CCATTTTCATTTGATCGGCCAGAATTTTCTTCATAGTTTCTTCCATTTCCTTCGTCTTTGCTTCA
*
49741 TCTGGCCTTTGATAAATTTCACTTAGCATAGTCC
66 TCTGGCCTTTGATAAATTTCGCTTAGCATAGTCC
* * *
49775 CCATTTTCATTTGATCGGCCTGAATTTTCTTCACAGTTTCTTCAATTTCCTTCGTCTTTGCTTCA
1 CCATTTTCATTTGATCGGCCAGAATTTTCTTCATAGTTTCTTCCATTTCCTTCGTCTTTGCTTCA
* *
49840 TCTGGCCTTTGATAGATTTCGGCTTAGCATAGCCC
66 TCTGGCCTTTGATAAATTTC-GCTTAGCATAGTCC
49875 CCATTTT
1 CCATTTT
49882 TTCTTGCTTT
Statistics
Matches: 183, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
95 1 0.01
96 57 0.31
97 1 0.01
99 105 0.57
100 19 0.10
ACGTcount: A:0.17, C:0.25, G:0.14, T:0.44
Consensus pattern (99 bp):
CCATTTTCATTTGATCGGCCAGAATTTTCTTCATAGTTTCTTCCATTTCCTTCGTCTTTGCTTCA
TCTGGCCTTTGATAAATTTCGCTTAGCATAGTCC
Found at i:51235 original size:2 final size:2
Alignment explanation
Indices: 51230--51260 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
51220 ATAATTGTAG
51230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51261 CTGATACTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51713 original size:42 final size:42
Alignment explanation
Indices: 51654--51741 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
51644 AGCTCATTAT
* *
51654 TTTCATTTTCCTTGTCCTTCTCTCCATGTTTGGCCGACGTCG
1 TTTCATTTTCCTTGTCCTTCCCTCCAAGTTTGGCCGACGTCG
51696 TTTCATTTTCCTTGTCCTTCCCTCCAAGTTTGGCCGACGTCG
1 TTTCATTTTCCTTGTCCTTCCCTCCAAGTTTGGCCGACGTCG
51738 TTTC
1 TTTC
51742 TTTCGTTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.08, C:0.32, G:0.16, T:0.44
Consensus pattern (42 bp):
TTTCATTTTCCTTGTCCTTCCCTCCAAGTTTGGCCGACGTCG
Found at i:57942 original size:20 final size:19
Alignment explanation
Indices: 57917--57983 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 19
57907 TACTTCCTTC
57917 CATCTCCTTCATCTTTGCTT
1 CATCTCCTT-ATCTTTGCTT
*
57937 CATCTCGCCTTATAGTTT-CTT
1 CATCT--CCTTAT-CTTTGCTT
57958 CTATCTCCTTTATCTTTGCTT
1 C-ATCTCC-TTATCTTTGCTT
57979 CATCT
1 CATCT
57984 TGCCTTTGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
20 14 0.36
21 14 0.36
22 11 0.28
ACGTcount: A:0.12, C:0.31, G:0.06, T:0.51
Consensus pattern (19 bp):
CATCTCCTTATCTTTGCTT
Found at i:58229 original size:16 final size:16
Alignment explanation
Indices: 58208--58240 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
58198 GCTGCCTTTT
58208 CTTCAATTGAGCAATG
1 CTTCAATTGAGCAATG
58224 CTTCAATTGAGCAATG
1 CTTCAATTGAGCAATG
58240 C
1 C
58241 CTTTTCTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (16 bp):
CTTCAATTGAGCAATG
Found at i:61489 original size:332 final size:332
Alignment explanation
Indices: 60883--61832 Score: 1497
Period size: 332 Copynumber: 2.9 Consensus size: 332
60873 ATCCGCATCA
** * * * *
60883 ATTGTGTCCAAAAATTGAGGAAAAAATTTTCAGGTCAGTTTTTGCCAATTTTTGGACGAGATCGT
1 ATTGTGTCCAAAAATTGAGGAAAATTTTTTCGGGTCAGTTTTTACCAAATTTTGGACGAAATCGT
* * ** *** * *
60948 GTGCTATCCATCAC-GATTTTGGGCTGAAAATGCGTTCTGGGATCCTTTCTCAGTTTTTAATGAA
66 GTGCTAACCATCACGGATTTT-GGCTGAAAATGCGTTCCGGGGCCCCGGCTCAGTTTTGAATGAT
* * *
61012 TTTTGGTGCCAAGAGTAACTGAAATATCTATATTCATCTATCCTAGTCTCAGCCACATTGGATTT
130 TTTTTGCGCCAAGAGTAATTGAAATATCTATATTCATCTATCCTAGTCTCAGCCACATTGGATTT
*
61077 ATGGATGTCTTTTTACGAGCATATGGATCACATTTCGATTTAATTAGAAATTAATTCGGAAAAAT
195 ATGGATGTCTTTTTACGAGCATCTGGATCACATTTCGATTTAATTAGAAATTAATTCGGAAAAAT
* *
61142 AAGAAAAACGACATTAGAAGCTTGAAAATCCATTATTTTATTTTTGGCGTTGGATTATATATCTT
260 AAGAAAAACGACATTAGAAGCTTGAAAATCCATTATTTTATTTTTGGCATTGAATTATATATCTT
61207 TTATGAGT
325 TTATGAGT
*
61215 ATTGTGTCCAAAAATTGAGGAAAATTTTTTCGGGTCAGTTTTTACCAAAATTTGGACGAAATCGT
1 ATTGTGTCCAAAAATTGAGGAAAATTTTTTCGGGTCAGTTTTTACCAAATTTTGGACGAAATCGT
*
61280 GTACTAACCATCACGGATTTTGGCTGAAAATGCGTTCCGGGGCCCCGGCTCAGTTTTGAATGATT
66 GTGCTAACCATCACGGATTTTGGCTGAAAATGCGTTCCGGGGCCCCGGCTCAGTTTTGAATGATT
* * *
61345 TTTTGCGCCAAGAGTAATTGAAATACCTATATTCATCTATCCTGGTCTCAGCCATATTGGATTTA
131 TTTTGCGCCAAGAGTAATTGAAATATCTATATTCATCTATCCTAGTCTCAGCCACATTGGATTTA
*
61410 TGGATGTCTTTTTACGAGCATCTGGATCACATTTCGATTTAATTAGAAATCAATTCGGAAAAATA
196 TGGATGTCTTTTTACGAGCATCTGGATCACATTTCGATTTAATTAGAAATTAATTCGGAAAAATA
*
61475 AGAAAAACGACATTAGAAGCTTGAAAATCCCTTATTTTATTTTTGGCATTGAATTATATATCTTT
261 AGAAAAACGACATTAGAAGCTTGAAAATCCATTATTTTATTTTTGGCATTGAATTATATATCTTT
61540 TATGAGT
326 TATGAGT
61547 ATTGTGTCCAAAAATTGAGGAAAATTTTTTCGGGTCAGTTTTTACCAAATTTTGGACGAAATCGT
1 ATTGTGTCCAAAAATTGAGGAAAATTTTTTCGGGTCAGTTTTTACCAAATTTTGGACGAAATCGT
* *
61612 GTGCTAACCATCACGGATTTTGGCTGAAAATGCGTTCCGGGGCCCCGGCTTAGTTTTGAATGATC
66 GTGCTAACCATCACGGATTTTGGCTGAAAATGCGTTCCGGGGCCCCGGCTCAGTTTTGAATGATT
* * * * *
61677 TTTTGCGCCAAGAGTAATTGTAATATCTATATTCATCTATTCAAATCTCAGCCACATAGGATTTA
131 TTTTGCGCCAAGAGTAATTGAAATATCTATATTCATCTATCCTAGTCTCAGCCACATTGGATTTA
* * * * * *
61742 AGGATTTGTTTTTACGAGCATCTGGATCACGTTGCGATTTAATTAAAAATTAATTCGGAAAAATA
196 TGGATGTCTTTTTACGAGCATCTGGATCACATTTCGATTTAATTAGAAATTAATTCGGAAAAATA
* *
61807 AGAAAAACGATATTAGAAGCATGAAA
261 AGAAAAACGACATTAGAAGCTTGAAA
61833 GTCCTTTTTT
Statistics
Matches: 568, Mismatches: 49, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
332 562 0.99
333 6 0.01
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (332 bp):
ATTGTGTCCAAAAATTGAGGAAAATTTTTTCGGGTCAGTTTTTACCAAATTTTGGACGAAATCGT
GTGCTAACCATCACGGATTTTGGCTGAAAATGCGTTCCGGGGCCCCGGCTCAGTTTTGAATGATT
TTTTGCGCCAAGAGTAATTGAAATATCTATATTCATCTATCCTAGTCTCAGCCACATTGGATTTA
TGGATGTCTTTTTACGAGCATCTGGATCACATTTCGATTTAATTAGAAATTAATTCGGAAAAATA
AGAAAAACGACATTAGAAGCTTGAAAATCCATTATTTTATTTTTGGCATTGAATTATATATCTTT
TATGAGT
Found at i:63124 original size:984 final size:981
Alignment explanation
Indices: 61215--63662 Score: 4180
Period size: 984 Copynumber: 2.5 Consensus size: 981
61205 TTTTATGAGT
* * * ** *
61215 ATTGTGTCCAAAAATTGAGGAAAATTTTTTCGGGTCAGTTTTTACCAAAATTTGGACGAAATCGT
1 ATTGTGTCCAAAAATTGAGGAAAA-ATTTTCAGGTCAGTTTTTGCCAATTTTTGGACGAGATCGT
* * * * * *
61280 GTACTAACCATCACGGATTTTGGCTGAAAATGCGTTCCGGGGCCCCGGCTCAGTTTTGAATGATT
65 GTGCTATCCATCACGG-TTTTGGCTGAAAATGCGTTCTGGGGTCCCGGCTCAGTTTTCAATGAAT
* * * *
61345 TTTTGCGCCAAGAGTAATTGAAATACCTATATTCATCTATCCTGGTCTCAGCCATATTGGATTTA
129 TTTGGCGCCAAGAGTAATTGAAATATCTATATTCATCTATCCTAGTCTCAGCCACATTGGATTTA
*
61410 TGGATGTCTTTTTACGAGCATCTGGATCACATTTCGATTTAATTAGAAATCAATTCGGAAAAATA
194 TGGATGTCTTTTTACGAGCATCTGGATCACATTTCGATTTAATTAGAAATTAATTCGGAAAAATA
*
61475 AGAAAAACGACATTAGAAGCTTGAAAATCCCTTATTTTATTTTTGGCATTGAATTATATATCTTT
259 AGAAAAACGACATTAGAAGCTTGAAAATCCCTTATTTTATTTTTGGCGTTGAATTATATATCTTT
61540 TATGAGTATTGTGTCCAAAAATTGAGGAAAATTTTTTCGGGTCAGTTTTTACCAAATTTTGGACG
324 TATGAGTATTGTGTCCAAAAATTGAGGAAAATTTTTTCGGGTCAGTTTTTACCAAATTTTGGACG
*
61605 AAATCGTGTGCTAACCATCACGGATTTTGGCTGAAAATGCGTTCCGGGGCCCCGGCTTAGTTTTG
389 AAATCGTGTGCT-A-CATCACGGATTTTGGCTGAAAATGCGTTCCGGGG-CCCGGCTCAGTTTTG
* *
61670 AATGATCTTTTGCGCCAAGAGTAATTGTAATATCTATATTCATCTATTCAAATCTCAGCCACATA
451 AATGATTTTTTGCGCCAAGAGTAATTGAAATATCTATATTCATCTATTCAAATCTCAGCCACATA
*
61735 GGATTTAAGGATTTGTTTTTACGAGCATCTGGATCACGTTGCGATTTAATTAAAAATTAATTCGG
516 GGATTTAAGGATTTGTTTTTACGAGCATCTGGATAACGTTGCGATTTAATTAAAAATTAATTCGG
* *
61800 AAAAATAAGAAAAACGATATTAGAAGCATGAAAGTCCTTTTTTTTTTAATTTTTGGCAAATTAAA
581 AAAAATAAGAAAAACGATATTAGAAGCATGAAAGTCCTTTTTTTTTAAACTTTTGGCAAATTAAA
61865 TAAAAATAAAGAAAGCCCAAAAACAGTCCAAACGGCCCAAAATAACAAAAGCGATAAAAACTAAA
646 TAAAAATAAAGAAAGCCCAAAAACAGTCCAAACGGCCCAAAATAACAAAAGCGATAAAAACTAAA
* *
61930 ACTCGCGACAGAAAACTGTAACGGGCTTTTTAGGCCCTAAACGAAACGTTGAACCGCAATAGCTG
711 ACTCGCGACAGAAAAATGTAACGGGCTTTTTAGGCCCTAAACGAAACGTTCAACCGCAATAGCTG
61995 TTCACCACGTTGTAGTAGACTCGAAACCCTTTCCGAAAAGGTATTATAATAGTCAAACCGACTTA
776 TTCACCACGTTGTAGTAGACTCGAAACCCTTTCCGAAAAGGTATTATAATAGTCAAACCGACTTA
*
62060 CGGTTTGAAAGTTATGCCCTGGTTAAGTTGACCCACCAACAGGAGCTTCAGGCCCAAAATCCAAA
841 CGATTTGAAAGTTATGCCCTGGTTAAGTTGACCCACCAACAGGAGCTTCAGGCCCAAAATCCAAA
62125 ACGTTACACGCCCTTTCGAACGGACTTCTGA-CGTTCCATACGATCCATAAATGTTATGCCTATC
906 ACGTTACACGCCCTTTCGAACGGACTTCTGATCGTT-CATACGATCCATAAATGTTATGCCTATC
62189 TCATCCGCATCA
970 TCATCCGCATCA
62201 ATTGTGTCCAAAAATTGAGGGAAAAATTTTCAGGTCAGTTTTTGCCAATTTTTGGACGAGATCGT
1 ATTGTGTCCAAAAATTGA-GGAAAAATTTTCAGGTCAGTTTTTGCCAATTTTTGGACGAGATCGT
* *
62266 GTGCTATCCATCACGGTTTTGGGCTGAAAATGCGTTATGGGGTCCTGGCTCAGTTTTCAATGAAT
65 GTGCTATCCATCACGGTTTT-GGCTGAAAATGCGTTCTGGGGTCCCGGCTCAGTTTTCAATGAAT
62331 TTTGGCGCCAAGAGTAATTGAAATATCTATATTCATCTATCCTAGTCTCAGCCACATTGGATTTA
129 TTTGGCGCCAAGAGTAATTGAAATATCTATATTCATCTATCCTAGTCTCAGCCACATTGGATTTA
62396 TGGATGTCTTTTTACGAGCATCTGGATCACATTTCGATTTAATTAGAAATTAATTCGGAAAAATA
194 TGGATGTCTTTTTACGAGCATCTGGATCACATTTCGATTTAATTAGAAATTAATTCGGAAAAATA
*
62461 AGAAAAACGACATTAGAAGCTTGAAAATCCCTTATTTTATTTTTGCCGTTGAATTATATATCTTT
259 AGAAAAACGACATTAGAAGCTTGAAAATCCCTTATTTTATTTTTGGCGTTGAATTATATATCTTT
62526 TATGAGTATTGTGTCCAAAAATTGAGGAAAATTTTTTCGGGTCAGTTTTTACCAAATTTTGGACG
324 TATGAGTATTGTGTCCAAAAATTGAGGAAAATTTTTTCGGGTCAGTTTTTACCAAATTTTGGACG
* * *
62591 AAATCGTGTGCGT-TATCACAGATTTTGGCTGAAAATGCGTTCCAGGGCCTCGGCTCAGTTTTGA
389 AAATCGTGTGC-TACATCACGGATTTTGGCTGAAAATGCGTTCCGGGGCC-CGGCTCAGTTTTGA
62655 ATGATTTTTTGCGCCAAGAGTAATTGAAATATCTATATTCATCTATTCAAATCTCAGCCACATAG
452 ATGATTTTTTGCGCCAAGAGTAATTGAAATATCTATATTCATCTATTCAAATCTCAGCCACATAG
62720 GATTTAAGGATTTGTTTTTACGAGCATCTGGATAACGTTGCGATTTAATTAAAAATTAATTCGGA
517 GATTTAAGGATTTGTTTTTACGAGCATCTGGATAACGTTGCGATTTAATTAAAAATTAATTCGGA
*
62785 AAAATAAGAAAAACGATATTGGAAGCATGAAAGTCCTTTTTTTTTAAACTTTTGGCAAATTAAAT
582 AAAATAAGAAAAACGATATTAGAAGCATGAAAGTCCTTTTTTTTTAAACTTTTGGCAAATTAAAT
**
62850 AAAAATAAAGAAAGCCCAAAAACAGTCCAAACGGGTCAAAATAACAAAAGCGATAAAAACTAAAA
647 AAAAATAAAGAAAGCCCAAAAACAGTCCAAACGGCCCAAAATAACAAAAGCGATAAAAACTAAAA
* * ** *
62915 CTCGCGATAGAAAAATGTAACTGGCTTTTTAGGCCCTAAACGAAACGTTCTTCCGCAATAGTTGT
712 CTCGCGACAGAAAAATGTAACGGGCTTTTTAGGCCCTAAACGAAACGTTCAACCGCAATAGCTGT
* * *
62980 TCACCTCGTTGTAGTAGACTCGAAACCCTTTCTGAAAAGGTATTATAATAGTCGAACCGACTTAC
777 TCACCACGTTGTAGTAGACTCGAAACCCTTTCCGAAAAGGTATTATAATAGTCAAACCGACTTAC
* *
63045 GATTTGAAAGTTATGCCCTGTTTAAGTTGACCCACCAATAGGAGCTTCAGGCCCAAAATCCAAAA
842 GATTTGAAAGTTATGCCCTGGTTAAGTTGACCCACCAACAGGAGCTTCAGGCCCAAAATCCAAAA
* * *
63110 CGTTACACGCCCTTTCGAACGGATTTCTGATGGTTCATACGATCCATAAATGTTATGCCTATCTG
907 CGTTACACGCCCTTTCGAACGGACTTCTGATCGTTCATACGATCCATAAATGTTATGCCTATCTC
63175 ATCCGCATCA
972 ATCCGCATCA
* * * *
63185 ATTTTGTCCAAAAATCGATGAAAAAATTTTCAGGTCAGATTTTGCCAATTTTTGGACGAGATCGT
1 ATTGTGTCCAAAAATTGA-GGAAAAATTTTCAGGTCAGTTTTTGCCAATTTTTGGACGAGATCGT
* *
63250 GTGCTATCTATCACGGTTTATGGCTGAAAATGCGTTCTGGGGTCCCGGCTCAGTTTTTAATGAAT
65 GTGCTATCCATCACGGTTT-TGGCTGAAAATGCGTTCTGGGGTCCCGGCTCAGTTTTCAATGAAT
63315 TTTGGCGCCAAGAGTAATTGAAATATCTATATTCATCTATCCTAGTCTCAGCCACATTGGATTTA
129 TTTGGCGCCAAGAGTAATTGAAATATCTATATTCATCTATCCTAGTCTCAGCCACATTGGATTTA
* *
63380 TTGATGTCTTTTTACGAGCATCTGGATCACATTTCGATTTAATTAGAAATTAATTTGGAAAAATA
194 TGGATGTCTTTTTACGAGCATCTGGATCACATTTCGATTTAATTAGAAATTAATTCGGAAAAATA
* * *
63445 AGAAAAACGACATTAGAAGCTTGAAAATCCCATATTTTATTTTTGGGGTTAAATTATATATCTTT
259 AGAAAAACGACATTAGAAGCTTGAAAATCCCTTATTTTATTTTTGGCGTTGAATTATATATCTTT
63510 TATGAGTATTGTGTCCAAAAATTGAGGAAAATTTTTTCGGGTCAGTTTTTACCAAATTTTGGACG
324 TATGAGTATTGTGTCCAAAAATTGAGGAAAATTTTTTCGGGTCAGTTTTTACCAAATTTTGGACG
63575 AAATCGTGTGCTAACCATCACGGATTTTGGCTGAAAATGCGTTCCGGGGTCCCGGCTCAGTTTTG
389 AAATCGTGTGCT-A-CATCACGGATTTTGGCTGAAAATGCGTTCCGGGG-CCCGGCTCAGTTTTG
* * *
63640 AATGAATTTTTCCTCCAAGAGTA
451 AATGATTTTTTGCGCCAAGAGTA
Statistics
Matches: 1382, Mismatches: 70, Indels: 20
0.94 0.05 0.01
Matches are distributed among these distances:
983 3 0.00
984 930 0.67
985 8 0.01
986 432 0.31
987 9 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (981 bp):
ATTGTGTCCAAAAATTGAGGAAAAATTTTCAGGTCAGTTTTTGCCAATTTTTGGACGAGATCGTG
TGCTATCCATCACGGTTTTGGCTGAAAATGCGTTCTGGGGTCCCGGCTCAGTTTTCAATGAATTT
TGGCGCCAAGAGTAATTGAAATATCTATATTCATCTATCCTAGTCTCAGCCACATTGGATTTATG
GATGTCTTTTTACGAGCATCTGGATCACATTTCGATTTAATTAGAAATTAATTCGGAAAAATAAG
AAAAACGACATTAGAAGCTTGAAAATCCCTTATTTTATTTTTGGCGTTGAATTATATATCTTTTA
TGAGTATTGTGTCCAAAAATTGAGGAAAATTTTTTCGGGTCAGTTTTTACCAAATTTTGGACGAA
ATCGTGTGCTACATCACGGATTTTGGCTGAAAATGCGTTCCGGGGCCCGGCTCAGTTTTGAATGA
TTTTTTGCGCCAAGAGTAATTGAAATATCTATATTCATCTATTCAAATCTCAGCCACATAGGATT
TAAGGATTTGTTTTTACGAGCATCTGGATAACGTTGCGATTTAATTAAAAATTAATTCGGAAAAA
TAAGAAAAACGATATTAGAAGCATGAAAGTCCTTTTTTTTTAAACTTTTGGCAAATTAAATAAAA
ATAAAGAAAGCCCAAAAACAGTCCAAACGGCCCAAAATAACAAAAGCGATAAAAACTAAAACTCG
CGACAGAAAAATGTAACGGGCTTTTTAGGCCCTAAACGAAACGTTCAACCGCAATAGCTGTTCAC
CACGTTGTAGTAGACTCGAAACCCTTTCCGAAAAGGTATTATAATAGTCAAACCGACTTACGATT
TGAAAGTTATGCCCTGGTTAAGTTGACCCACCAACAGGAGCTTCAGGCCCAAAATCCAAAACGTT
ACACGCCCTTTCGAACGGACTTCTGATCGTTCATACGATCCATAAATGTTATGCCTATCTCATCC
GCATCA
Done.