Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015950.1 Corchorus olitorius cultivar O-4 contig15983, 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: 65773
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:3483 original size:42 final size:44
Alignment explanation
Indices: 3436--3525 Score: 148
Period size: 45 Copynumber: 2.1 Consensus size: 44
3426 CATTACCTCA
*
3436 ATTCTACT-CT-ATCTCTAGGTAATTCATCAAAATAAAGCTAAT
1 ATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAGCTAAT
3478 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
1 ATTCTACTCCT-CATCTCTAGATAATTCATCAAAATAAAGCTAAT
3523 ATT
1 ATT
3526 AATTGTTGCC
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
42 8 0.18
43 2 0.05
45 34 0.77
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.36
Consensus pattern (44 bp):
ATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAGCTAAT
Found at i:14256 original size:532 final size:526
Alignment explanation
Indices: 12598--14569 Score: 2808
Period size: 528 Copynumber: 3.7 Consensus size: 526
12588 TAACTCGAGT
*
12598 ATTTAATGTAAAATAGTTTGGGGAGTGGAAACAAATCAAAATTGTAACTAGACTTAATTGGCTAA
1 ATTTAATGTAAAATAGTTTGGGGAGTGGAAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAA
* *
12663 ATGTATTTGTAATACTATCTATGAACACACTACTAACACATTTCTATATTATGGCATTTTGTAAA
66 ATGTATTTGTAATACTATCTATGAACACACTACTAACACATTTCTATATTATGACATTGTGTAAA
* * *
12728 GATTCAATTAAATTTTTTTATGTAATTAGCAATTACACAA-TTTTGGGAGACAATATAGAGTTTT
131 GATTCAATTAAATTTTTTTAAGTAATTAGAAATTACACAATTTTTGGG-GACAATATAGA--ATT
** *
12792 GACTTTTGAGATGATATAAATGCAATTATGTGATCATATTACTT-C-AACTCATATTGGGTTTGA
193 -A-TTTTGAGATGATATAAATGCAATTATGTGATCATACCAATTACTAACTCATATTGGGTTTGA
* * * *
12855 GGTCGATCATCTGTCAATTTGCCACAACTTTTGCCACGGGAATCTGTAAACCCGCTGGAAAACCC
256 GGTCAATCATCTCTCAATTTGCCACAGCTTTTGCCACGGGAATCTGTAAACCCGCTGCAAAACCC
* * *
12920 ATTGAAAATTGAAAACTCGTGGCAAAGACTGTGCCAAATAGCCACGAATTTTCCCACGGTTTTTA
321 GTGGAAAATTGAAAACTCGTGGCAAAGACCGTGCCAAATAGCCACGAATTTTCCCACGGTTTTTA
* *
12985 AGAAAACCGTCTCAAAAACCGTGGCAAATATAGAATTAATGTCTCT-AGAATTTTACCCTAAACA
386 AGAAAACCGTTTCAAAAACCGTGGCAAATATAGAATTAATGTCT-TAAAAATTTTACCCTAAACA
*
13049 AAGATAATTTGAAGTTCCTATAAAATTAAAGGTTTTTATGGTACCCTACTT-TGTTTAGCTCGAG
450 AAGATAATTTGAAGTTCCCATAAAATTAAAGGTTTTTATGGTACCCTA-TTGTGTTTAGCTCGAG
13113 TATTTGATGTAGA
514 TATTTGATGTAGA
* *
13126 ATTTAATGTAAAATAGTTTGGGGAGTGGAAAAAAATCAAAACTGTAACTAGATTTAATTGGCTAA
1 ATTTAATGTAAAATAGTTTGGGGAGTGGAAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAA
* *
13191 ATGTATTTGTAATACGATCTATGAACACACTACTGACACATTTCTATATTATGACATTGTGTAAA
66 ATGTATTTGTAATACTATCTATGAACACACTACTAACACATTTCTATATTATGACATTGTGTAAA
* * * *
13256 GATTCAATTAATTTTTTTTAAGTAATTAGCAATCACACAATTTTGGGGGACAATATAGAATTTTG
131 GATTCAATTAAATTTTTTTAAGTAATTAGAAATTACACAATTTTTGGGGACAATATAGAA--TT-
13321 ACTTTTGAGATGATATAAATGCAATTATGTGATCAT----ATTACTTGAACTCATATTGGGTTTG
193 A-TTTTGAGATGATATAAATGCAATTATGTGATCATACCAATTAC-T-AACTCATATTGGGTTTG
* * * * ** * * *
13382 AGGTCGATCATTTGTCAATTTGCTACAGCTTTTGGAACGAGAATTTGTAAACCCGCTGCAAAATC
255 AGGTCAATCATCTCTCAATTTGCCACAGCTTTTGCCACGGGAATCTGTAAACCCGCTGCAAAACC
* * *
13447 CGTTGAAAATTGAAAACTTGTGGCAAAGACCGTGCCAAATAGCCACGAATTTTCCCACGATTTTT
320 CGTGGAAAATTGAAAACTCGTGGCAAAGACCGTGCCAAATAGCCACGAATTTTCCCACGGTTTTT
** * * * *
13512 AAGAAAATTGTTTCAAAAACCATTGCAAATATAGAATTCATGTC--AAAGAATTTTACCATAAAC
385 AAGAAAACCGTTTCAAAAACCGTGGCAAATATAGAATTAATGTCTTAAA-AATTTTACCCTAAAC
* *
13575 AAAGATAATTTGAAATTCCCATAAAATTAAAGGTTTTTATGGTACCCTATTGTGTTTTGCTCGAG
449 AAAGATAATTTGAAGTTCCCATAAAATTAAAGGTTTTTATGGTACCCTATTGTGTTTAGCTCGAG
13640 TATTTGATGTAGA
514 TATTTGATGTAGA
*
13653 ATTTAATGTAAAATAGTTTGGCGAGTGGAAAAAAA-CAAAATTGTAACTAGACTTAATTGGCTAA
1 ATTTAATGTAAAATAGTTTGGGGAGTGGAAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAA
* *
13717 TTGTATTTGTAATACTATCTATGAACACACTACTAACACATTTGTATATTATGACATTGTGTAAA
66 ATGTATTTGTAATACTATCTATGAACACACTACTAACACATTTCTATATTATGACATTGTGTAAA
13782 GATTCAATTAAATTTTTTTAAGTAATTAGAAATTACACAATTTTTGGGGACAATATAGAATT-TT
131 GATTCAATTAAATTTTTTTAAGTAATTAGAAATTACACAATTTTTGGGGACAATATAGAATTATT
*
13846 TGGAGATGATATAAATGCAATTATGTGATCATTAGCCAATTACTAACTCATATAAGTGTAGGGTT
196 TTGAGATGATATAAATGCAATTATGTGATCA-TA-CCAATTACTAACTC--AT-A-T-T-GGGTT
* * *
13911 TGAGGTCAAACATCTCTCAATTTACCACAGCTTTTGCCATGGGAATCTGTAAACCCGCTGCAAAA
253 TGAGGTCAATCATCTCTCAATTTGCCACAGCTTTTGCCACGGGAATCTGTAAACCCGCTGCAAAA
* * * *
13976 CCCGTGGAAAATTGAAAAGTCGTGGCAAAGGCCATGCCAAATAGCCACGACTTTTCCCACGGTTT
318 CCCGTGGAAAATTGAAAACTCGTGGCAAAGACCGTGCCAAATAGCCACGAATTTTCCCACGGTTT
* * *
14041 CTAAGAAAACCGTTTCAAAAACCGTGGCAAATATAGACTGT-ATCTCTTAAAAATTTTACCCTAA
383 TTAAGAAAACCGTTTCAAAAACCGTGGCAAATATAGAAT-TAATGTCTTAAAAATTTTACCCTAA
*
14105 ACAAAGATAATTTGAAGTTCCCATAAAATTAAAGGTTTCTATGGTACCCTATTGTGTTTAGCTCG
447 ACAAAGATAATTTGAAGTTCCCATAAAATTAAAGGTTTTTATGGTACCCTATTGTGTTTAGCTCG
14170 AGTATTTGATGTAGA
512 AGTATTTGATGTAGA
*
14185 ATTTAATGTAAAATCGTTT-GGGAGTGGAAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAA
1 ATTTAATGTAAAATAGTTTGGGGAGTGGAAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAA
* *
14249 ATGTATTTGTAAAACTATCTATGAACACACTACTAACACATTTGTATATTATGACATTGTGTAAA
66 ATGTATTTGTAATACTATCTATGAACACACTACTAACACATTTCTATATTATGACATTGTGTAAA
* **
14314 GATTCAATTAAA--ATTTT---T-A--AGAAATTACACAATTTTTGAAGACAATATAG-A--ATT
131 GATTCAATTAAATTTTTTTAAGTAATTAGAAATTACACAATTTTTGGGGACAATATAGAATTATT
* *
14368 TTGAGATAATATAAATGCAATTATGTGATCATTAGCCAATTACTAACTGATATAAGTGTAGGGTT
196 TTGAGATGATATAAATGCAATTATGTGATCA-TA-CCAATTACTAACT--CAT-A-T-T-GGGTT
*
14433 TGAGGTCAATCATCTCTCAATTTGCCACAGCTTTTGCCACGTGAATCTGTAAACCCGCTGCAAAA
253 TGAGGTCAATCATCTCTCAATTTGCCACAGCTTTTGCCACGGGAATCTGTAAACCCGCTGCAAAA
* * * *
14498 CCCGTGGAAAATTGAAAAGTCGTGGCAAAGGCCGTGCCAAATAGACACGACTTTTCCCACGGTTT
318 CCCGTGGAAAATTGAAAACTCGTGGCAAAGACCGTGCCAAATAGCCACGAATTTTCCCACGGTTT
14563 TTAAGAA
383 TTAAGAA
14570 CTATTTCAAA
Statistics
Matches: 1319, Mismatches: 96, Indels: 64
0.89 0.06 0.04
Matches are distributed among these distances:
521 32 0.02
522 193 0.15
523 1 0.00
524 33 0.03
525 6 0.00
526 149 0.11
527 128 0.10
528 383 0.29
529 7 0.01
530 5 0.00
531 167 0.13
532 212 0.16
533 3 0.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (526 bp):
ATTTAATGTAAAATAGTTTGGGGAGTGGAAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAA
ATGTATTTGTAATACTATCTATGAACACACTACTAACACATTTCTATATTATGACATTGTGTAAA
GATTCAATTAAATTTTTTTAAGTAATTAGAAATTACACAATTTTTGGGGACAATATAGAATTATT
TTGAGATGATATAAATGCAATTATGTGATCATACCAATTACTAACTCATATTGGGTTTGAGGTCA
ATCATCTCTCAATTTGCCACAGCTTTTGCCACGGGAATCTGTAAACCCGCTGCAAAACCCGTGGA
AAATTGAAAACTCGTGGCAAAGACCGTGCCAAATAGCCACGAATTTTCCCACGGTTTTTAAGAAA
ACCGTTTCAAAAACCGTGGCAAATATAGAATTAATGTCTTAAAAATTTTACCCTAAACAAAGATA
ATTTGAAGTTCCCATAAAATTAAAGGTTTTTATGGTACCCTATTGTGTTTAGCTCGAGTATTTGA
TGTAGA
Found at i:14847 original size:21 final size:21
Alignment explanation
Indices: 14787--14851 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 21
14777 TGAGATGATA
14787 TAATATTCCATCAAACAATTG
1 TAATATTCCATCAAACAATTG
*
14808 TAATACACAATTTCATCAAACAATTG
1 TAAT-----ATTCCATCAAACAATTG
14834 TAATATTCCATCAAACAA
1 TAATATTCCATCAAACAA
14852 GTGAAACCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 17 0.46
26 20 0.54
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31
Consensus pattern (21 bp):
TAATATTCCATCAAACAATTG
Found at i:15725 original size:16 final size:16
Alignment explanation
Indices: 15694--15790 Score: 99
Period size: 16 Copynumber: 6.1 Consensus size: 16
15684 AAAGTCAAAT
15694 ACCCGAACCC-AAAAA
1 ACCCGAACCCGAAAAA
15709 ACCCGAACCCGAAAAA
1 ACCCGAACCCGAAAAA
* * *
15725 ACTCAAACCCAAAAAA
1 ACCCGAACCCGAAAAA
*
15741 ACCAGAACCCG-AAAA
1 ACCCGAACCCGAAAAA
* * *
15756 ATCGGAAACCCGATAAA
1 ACCCG-AACCCGAAAAA
*
15773 ACCCGAACCTGAAAAA
1 ACCCGAACCCGAAAAA
15789 AC
1 AC
15791 TCTCCTTGGT
Statistics
Matches: 65, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
15 17 0.26
16 42 0.65
17 6 0.09
ACGTcount: A:0.53, C:0.33, G:0.10, T:0.04
Consensus pattern (16 bp):
ACCCGAACCCGAAAAA
Found at i:15749 original size:32 final size:31
Alignment explanation
Indices: 15699--15792 Score: 116
Period size: 32 Copynumber: 3.0 Consensus size: 31
15689 CAAATACCCG
15699 AACCCAAAAAACCCGAACCCGAAAAAACTCA
1 AACCCAAAAAACCCGAACCCGAAAAAACTCA
* * **
15730 AACCCAAAAAAACCAGAACCCGAAAAATCGGA
1 AACCC-AAAAAACCCGAACCCGAAAAAACTCA
* *
15762 AACCCGATAAAACCCGAACCTGAAAAAACTC
1 AACCC-AAAAAACCCGAACCCGAAAAAACTC
15793 TCCTTGGTAG
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 5 0.10
32 46 0.90
ACGTcount: A:0.53, C:0.32, G:0.10, T:0.05
Consensus pattern (31 bp):
AACCCAAAAAACCCGAACCCGAAAAAACTCA
Found at i:30380 original size:20 final size:21
Alignment explanation
Indices: 30343--30385 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
30333 AACCCGTTAA
*
30343 TTAAAGCGTGTCACTCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
*
30364 TTAAA-CGTGTTAATCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
30384 TT
1 TT
30386 GACACGATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTC
Found at i:30442 original size:42 final size:42
Alignment explanation
Indices: 30373--30454 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
30363 CTTAAACGTG
*
30373 TTAATCGTGTCTTGACACGATAGGACACGAAACACGATAATC
1 TTAATCGTGTCTCGACACGATAGGACACGAAACACGATAATC
*
30415 TTAATCGTGTC-CGACACGATTCA-GACACGAGACACGATAA
1 TTAATCGTGTCTCGACACGA-T-AGGACACGAAACACGATAA
30455 GTCAAACACG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
41 7 0.19
42 28 0.78
43 1 0.03
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (42 bp):
TTAATCGTGTCTCGACACGATAGGACACGAAACACGATAATC
Found at i:31899 original size:13 final size:13
Alignment explanation
Indices: 31881--31921 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
31871 AATTTGACCC
31881 TTAACAGCCGCTT
1 TTAACAGCCGCTT
31894 TTAACAGCCGCTT
1 TTAACAGCCGCTT
*
31907 TTGACAGCCGCTT
1 TTAACAGCCGCTT
31920 TT
1 TT
31922 GAATTGGGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (13 bp):
TTAACAGCCGCTT
Found at i:32359 original size:2 final size:2
Alignment explanation
Indices: 32352--32415 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
32342 AACTTACAGC
* * *
32352 AT AT AT AT AT AT AG AT AT AT AG AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32394 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
32416 GCCCCTCCTC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:34721 original size:16 final size:15
Alignment explanation
Indices: 34673--34746 Score: 58
Period size: 16 Copynumber: 4.7 Consensus size: 15
34663 CTCAGGCAGG
* **
34673 TTCGGGTTCAGGTAC
1 TTCGGGTTCGGGTTT
* *
34688 TTCAGGTTTGGGCTTT
1 TTCGGGTTCGGG-TTT
34704 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGT-TT
*
34720 TTCGGGCTCGGGTTAT
1 TTCGGGTTCGGGTT-T
*
34736 GTCGGGTTCGG
1 TTCGGGTTCGG
34747 TCTCGGGTAG
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
15 11 0.24
16 35 0.76
ACGTcount: A:0.07, C:0.16, G:0.38, T:0.39
Consensus pattern (15 bp):
TTCGGGTTCGGGTTT
Found at i:34767 original size:23 final size:23
Alignment explanation
Indices: 34737--34793 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
34727 TCGGGTTATG
*
34737 TCGGGTTCG-GTCTCGGGTAGGGT
1 TCGGGTTCGAG-CTCGAGTAGGGT
*
34760 TCGGGTTCGAGCTCGAGTCGGGT
1 TCGGGTTCGAGCTCGAGTAGGGT
*
34783 TCGGGCTCGAG
1 TCGGGTTCGAG
34794 TTTGATTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.07, C:0.21, G:0.46, T:0.26
Consensus pattern (23 bp):
TCGGGTTCGAGCTCGAGTAGGGT
Found at i:34780 original size:17 final size:17
Alignment explanation
Indices: 34760--34794 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
34750 CGGGTAGGGT
34760 TCGGGTTCGAGCTCGAG
1 TCGGGTTCGAGCTCGAG
*
34777 TCGGGTTCGGGCTCGAG
1 TCGGGTTCGAGCTCGAG
34794 T
1 T
34795 TTGATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.09, C:0.23, G:0.43, T:0.26
Consensus pattern (17 bp):
TCGGGTTCGAGCTCGAG
Found at i:34943 original size:13 final size:12
Alignment explanation
Indices: 34920--34967 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
34910 AAGTTTATTG
34920 ATAATATATAAT
1 ATAATATATAAT
34932 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
34945 ATAACAT-TATT
1 ATAATATATAAT
34956 ATCAATATATAA
1 AT-AATATATAA
34968 AGATTAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:35248 original size:19 final size:19
Alignment explanation
Indices: 35191--35249 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
35181 AAACTACAAA
35191 ATATATATAGTTAGA-TATAT
1 ATATATATA-TTA-ATTATAT
* *
35211 ATATATATATTTATAATAT
1 ATATATATATTAATTATAT
35230 ATATATATA-TAACTTATAT
1 ATATATATATTAA-TTATAT
35249 A
1 A
35250 ACTTAAAGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 3 0.09
19 21 0.64
20 9 0.27
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (19 bp):
ATATATATATTAATTATAT
Found at i:35249 original size:2 final size:2
Alignment explanation
Indices: 35191--35240 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
35181 AAACTACAAA
* *
35191 AT AT AT AT AGT -T AG AT AT AT AT AT AT AT AT TT AT A- AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35232 AT AT AT AT A
1 AT AT AT AT A
35241 ACTTATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 2 0.05
2 38 0.93
3 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35249 original size:17 final size:15
Alignment explanation
Indices: 35205--35241 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
35195 ATATAGTTAG
35205 ATATAT-ATATATAT
1 ATATATAATATATAT
*
35219 ATTTATAATATATAT
1 ATATATAATATATAT
35234 ATATATAA
1 ATATATAA
35242 CTTATATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATAATATATAT
Found at i:35682 original size:17 final size:17
Alignment explanation
Indices: 35660--35693 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35650 TCAAATTATT
35660 TCGGGTTCGGACTCGGG
1 TCGGGTTCGGACTCGGG
*
35677 TCGGGTTCGGGCTCGGG
1 TCGGGTTCGGACTCGGG
35694 CTGCCTTGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.24, G:0.50, T:0.24
Consensus pattern (17 bp):
TCGGGTTCGGACTCGGG
Found at i:37441 original size:17 final size:17
Alignment explanation
Indices: 37419--37454 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
37409 ATACAAAGAG
37419 CTATCTAGTATAACAAA
1 CTATCTAGTATAACAAA
* *
37436 CTATCTGGTGTAACAAA
1 CTATCTAGTATAACAAA
37453 CT
1 CT
37455 TTACAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (17 bp):
CTATCTAGTATAACAAA
Found at i:41833 original size:17 final size:17
Alignment explanation
Indices: 41811--41846 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41801 ATACAAAGAG
41811 CTATCTAGTATAACAAA
1 CTATCTAGTATAACAAA
* *
41828 CTATCTGGTGTAACAAA
1 CTATCTAGTATAACAAA
41845 CT
1 CT
41847 TTACAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (17 bp):
CTATCTAGTATAACAAA
Found at i:42729 original size:201 final size:201
Alignment explanation
Indices: 42380--42783 Score: 763
Period size: 201 Copynumber: 2.0 Consensus size: 201
42370 AGCATTTTAT
42380 GAATGAATATACACCATGATATACTAATAATTTCACATTTGTTATGAAACTAAAAAGAATGCGAA
1 GAATGAATATACACCATGATATACTAATAATTTCACATTTGTTATGAAACTAAAAAGAATGCGAA
42445 GAACAATATGGAGAGAATGAGAGAGAATTTCTTATTACTCCAGAGAGAAGTGAATACAGAAATGA
66 GAACAATATGGAGAGAATGAGAGAGAATTTCTTATTACTCCAGAGAGAAGTGAATACAGAAATGA
42510 GGTGTGTTTACAACTGAACTGAAGTAGCCTATTTATAGCTGAAAGTTACAACGGACAAGATCATC
131 GGTGTGTTTACAACTGAACTGAAGTAGCCTATTTATAGCTGAAAGTTACAACGGACAAGATCATC
42575 TAAAGA
196 TAAAGA
* *
42581 GAATGAATATACACCATGATATACTAATAATTTCGCATTTGTTATGAAACTAATAAGAATGCGAA
1 GAATGAATATACACCATGATATACTAATAATTTCACATTTGTTATGAAACTAAAAAGAATGCGAA
* *
42646 GAACAATATGGAGAGAATGAGAGAGAATTTCTTATTACTCTAGAGATAAGTGAATACAGAAATGA
66 GAACAATATGGAGAGAATGAGAGAGAATTTCTTATTACTCCAGAGAGAAGTGAATACAGAAATGA
*
42711 GGTGTGTTTACCACTGAACTGAAGTAGCCTATTTATAGCTGAAAGTTACAACGGACAAGATCATC
131 GGTGTGTTTACAACTGAACTGAAGTAGCCTATTTATAGCTGAAAGTTACAACGGACAAGATCATC
42776 TAAAGA
196 TAAAGA
42782 GA
1 GA
42784 TAAAATCTAA
Statistics
Matches: 198, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
201 198 1.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (201 bp):
GAATGAATATACACCATGATATACTAATAATTTCACATTTGTTATGAAACTAAAAAGAATGCGAA
GAACAATATGGAGAGAATGAGAGAGAATTTCTTATTACTCCAGAGAGAAGTGAATACAGAAATGA
GGTGTGTTTACAACTGAACTGAAGTAGCCTATTTATAGCTGAAAGTTACAACGGACAAGATCATC
TAAAGA
Found at i:47397 original size:2 final size:2
Alignment explanation
Indices: 47390--47438 Score: 64
Period size: 2 Copynumber: 24.5 Consensus size: 2
47380 GACTGTTGGT
* *
47390 TA TA TA TA TA TA TA TA TA TA TG TA TA TA CCA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
47432 TA TA TA T
1 TA TA TA T
47439 TGGGGCTACT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:52184 original size:18 final size:18
Alignment explanation
Indices: 52161--52195 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
52151 TTATGTTTAG
52161 GTTTGTGTATGTGAGATT
1 GTTTGTGTATGTGAGATT
*
52179 GTTTGTGTGTGTGAGAT
1 GTTTGTGTATGTGAGAT
52196 AAAAAGCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.37, T:0.49
Consensus pattern (18 bp):
GTTTGTGTATGTGAGATT
Found at i:54680 original size:48 final size:43
Alignment explanation
Indices: 54609--54700 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
54599 AACATTATTA
54609 AATATATTTTAGTTATGCCATTATTATTAAAATATATATAAAATTGCC
1 AATATATTTTAGTTATGCC---ATTATT-AAA-ATATATAAAATTGCC
*
54657 AATATATTTT-GATTATGTCATTATTAAAATATATAAAATTGCC
1 AATATATTTTAG-TTATGCCATTATTAAAATATATAAAATTGCC
54700 A
1 A
54701 TTATTAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
43 16 0.38
44 3 0.07
45 6 0.14
47 1 0.02
48 16 0.38
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (43 bp):
AATATATTTTAGTTATGCCATTATTAAAATATATAAAATTGCC
Found at i:55685 original size:22 final size:22
Alignment explanation
Indices: 55567--55692 Score: 71
Period size: 22 Copynumber: 5.7 Consensus size: 22
55557 ATCATATGGA
*
55567 GGTTATCAAAATTTCATAGAAAG-
1 GGTTATCAAAATTTCAT--AATGT
* * *
55590 GTTTATTAAAATTTCATAGT-T
1 GGTTATCAAAATTTCATAATGT
** *
55611 AGGTTATCAGTATTTCAT--TGG
1 -GGTTATCAAAATTTCATAATGT
* *
55632 GAGTTTATCACAATTTCATAAGGT
1 G-G-TTATCAAAATTTCATAATGT
** *
55656 AATCATCAAAATTTCATAATGT
1 GGTTATCAAAATTTCATAATGT
55678 GGTTATCAAAATTTC
1 GGTTATCAAAATTTC
55693 CTAAAAATAT
Statistics
Matches: 75, Mismatches: 21, Indels: 15
0.68 0.19 0.14
Matches are distributed among these distances:
20 2 0.03
21 2 0.03
22 55 0.73
23 15 0.20
24 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAATGT
Found at i:56694 original size:30 final size:28
Alignment explanation
Indices: 56614--56695 Score: 94
Period size: 27 Copynumber: 2.9 Consensus size: 28
56604 CATTTTAATT
* *
56614 TAAAAAGTTATTGTGATTAAAATTATAC
1 TAAAAAGTTATTGTGATTATAATTCTAC
* * *
56642 TAAAAAGATATT-AGAGTATAATTCTAC
1 TAAAAAGTTATTGTGATTATAATTCTAC
56669 TAACAAGAGTTATTGTGATTATAATTC
1 TAA-AA-AGTTATTGTGATTATAATTC
56696 AGTATTTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
27 14 0.33
28 13 0.30
29 6 0.14
30 10 0.23
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (28 bp):
TAAAAAGTTATTGTGATTATAATTCTAC
Found at i:58106 original size:28 final size:27
Alignment explanation
Indices: 58075--58192 Score: 157
Period size: 28 Copynumber: 4.3 Consensus size: 27
58065 AAAAGAATAA
58075 AACATTTATGTAGCAAAAAAAATAGTTT
1 AACATTTATGTAGC-AAAAAAATAGTTT
58103 AACATTTATGTAGCATAAAAAATAGTTT
1 AACATTTATGTAGCA-AAAAAATAGTTT
* * ****
58131 AACATTTATTTTG-TTTCAAATAGTTT
1 AACATTTATGTAGCAAAAAAATAGTTT
58157 AACATTTATGTAGCAAAAAAATAGTTT
1 AACATTTATGTAGCAAAAAAATAGTTT
58184 AACATTTAT
1 AACATTTAT
58193 TCTCCTTAAG
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
26 20 0.26
27 19 0.25
28 37 0.49
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (27 bp):
AACATTTATGTAGCAAAAAAATAGTTT
Found at i:59689 original size:30 final size:30
Alignment explanation
Indices: 59650--59710 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
59640 ATCATTATAC
* *
59650 CCTTTTCCAACCTTCTT-GTGCTACTGTTTT
1 CCTTCTCCAACCTT-TTCGCGCTACTGTTTT
59680 CCTTCTCCAACCTTTTCGCGCTACTGTTTT
1 CCTTCTCCAACCTTTTCGCGCTACTGTTTT
59710 C
1 C
59711 TTTCCTTGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.10, C:0.34, G:0.10, T:0.46
Consensus pattern (30 bp):
CCTTCTCCAACCTTTTCGCGCTACTGTTTT
Done.