Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011102.1 Corchorus capsularis cultivar CVL-1 contig11123, 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: 79725
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:143 original size:1 final size:1
Alignment explanation
Indices: 139--165 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
129 TTACCCTTAC
139 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
166 CTGGCTTTGG
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:21654 original size:156 final size:156
Alignment explanation
Indices: 21369--21684 Score: 578
Period size: 156 Copynumber: 2.0 Consensus size: 156
21359 AATGGAATCT
*
21369 AAGTTGGAGGTTTTGCCTCAAGAGGTTAATGGTGAGGAATCAAGGGAAAATGAACTAGCTGCTGA
1 AAGTTGGAGGTTTTGCCTCAAGAGGTTAATGGTGAGGAATCAAGAGAAAATGAACTAGCTGCTGA
*
21434 TTATCAAGACAAAAAGGTTGAGGAGTCTGCTGATACTTCTTCTGGTGTGACTGCCAGGCGTCAAG
66 TTATCAAGACAAAAAGGTTGAGGAGTCTGCTGATACTTCTTCTGGTGTGACTACCAGGCGTCAAG
21499 AAGATGAAGTCGAAGCATTGAATGAC
131 AAGATGAAGTCGAAGCATTGAATGAC
* *
21525 AAGTTGGAGGTTTTGCCTCAAGAGGTTAATGGTGAGGAATTAAGAGAAAATGCACTAGCTGCTGA
1 AAGTTGGAGGTTTTGCCTCAAGAGGTTAATGGTGAGGAATCAAGAGAAAATGAACTAGCTGCTGA
*
21590 TTATCAAGACAAAAAGGTTGAGGAGTCTGCTGATACTTCTTCTGGTGTGACTACCAGGCTTCAAG
66 TTATCAAGACAAAAAGGTTGAGGAGTCTGCTGATACTTCTTCTGGTGTGACTACCAGGCGTCAAG
*
21655 AAGATGAAGTTGAAGCATTGAATGAC
131 AAGATGAAGTCGAAGCATTGAATGAC
21681 AAGT
1 AAGT
21685 CAGCTAATGT
Statistics
Matches: 154, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
156 154 1.00
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (156 bp):
AAGTTGGAGGTTTTGCCTCAAGAGGTTAATGGTGAGGAATCAAGAGAAAATGAACTAGCTGCTGA
TTATCAAGACAAAAAGGTTGAGGAGTCTGCTGATACTTCTTCTGGTGTGACTACCAGGCGTCAAG
AAGATGAAGTCGAAGCATTGAATGAC
Found at i:22213 original size:84 final size:84
Alignment explanation
Indices: 22071--22234 Score: 256
Period size: 84 Copynumber: 2.0 Consensus size: 84
22061 GGTGGATGCA
* * *
22071 GTTCGTGATATTCATCCTGTGACTGAAGAACCTGAGAAGAAATTGGAGAAAGATCAGGTAGATAA
1 GTTCGAGATATTCATCCTGTGACTGAAGAACCTGAGAAGAAAGTGGAGAAAGAACAGGTAGATAA
*
22136 GCAAAGCACCCAAGTAACT
66 GCAAAGCAACCAAGTAACT
* * * *
22155 GTTCGAGATATTCATTCTGTGACTGAAGAAGCTGAGAAGAAGGTGGAGAATGAACAGGTAGATAA
1 GTTCGAGATATTCATCCTGTGACTGAAGAACCTGAGAAGAAAGTGGAGAAAGAACAGGTAGATAA
22220 GCAAAGCAACCAAGT
66 GCAAAGCAACCAAGT
22235 GACTCTAGAG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 72 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (84 bp):
GTTCGAGATATTCATCCTGTGACTGAAGAACCTGAGAAGAAAGTGGAGAAAGAACAGGTAGATAA
GCAAAGCAACCAAGTAACT
Found at i:29002 original size:2 final size:2
Alignment explanation
Indices: 28995--29023 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28985 CAAATTGTAA
28995 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 A
29024 CACACACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29129 original size:31 final size:31
Alignment explanation
Indices: 29094--29169 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
29084 TTTGAATTGT
*
29094 CTATTGTATCCTTAATTAACTTTTAATATTC
1 CTATTGTATCCTTAATTAACTATTAATATTC
* *
29125 CTATTGTACCCTTAATTAACTATTAATATTT
1 CTATTGTATCCTTAATTAACTATTAATATTC
*
29156 CTATTATATCCTTA
1 CTATTGTATCCTTA
29170 TTTGTTTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.30, C:0.17, G:0.03, T:0.50
Consensus pattern (31 bp):
CTATTGTATCCTTAATTAACTATTAATATTC
Found at i:29667 original size:31 final size:31
Alignment explanation
Indices: 29619--29679 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
29609 AGTTTTGAGA
*
29619 AACTTTTGAAATACCTATTGTACCCTTATTT
1 AACTTTTGAAATACCTATTATACCCTTATTT
* *
29650 AACTTTT-AATATTCCTATTATATCCTTATT
1 AACTTTTGAA-ATACCTATTATACCCTTATT
29680 AGTTTAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.49
Consensus pattern (31 bp):
AACTTTTGAAATACCTATTATACCCTTATTT
Found at i:31872 original size:52 final size:52
Alignment explanation
Indices: 31746--31893 Score: 236
Period size: 50 Copynumber: 3.0 Consensus size: 52
31736 CTTGGGCATA
*
31746 TGATCATTTATATACAACTTCATACATACTCGAGGAAATGATTAATT-A-AT
1 TGATCATTTATATACAACTTCATACATACTCGAGGAAATTATTAATTAATAT
31796 TGATCATTTATATACAACTTCATACATACTCGAGGAAATTATTAATTAATAT
1 TGATCATTTATATACAACTTCATACATACTCGAGGAAATTATTAATTAATAT
*
31848 TGATCATTTATATACAAC-T--T-CATACTCGAGGAAACTATTAATTAAT
1 TGATCATTTATATACAACTTCATACATACTCGAGGAAATTATTAATTAAT
31894 TTGTTGAATG
Statistics
Matches: 94, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
48 25 0.27
49 1 0.01
50 46 0.49
51 2 0.02
52 20 0.21
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (52 bp):
TGATCATTTATATACAACTTCATACATACTCGAGGAAATTATTAATTAATAT
Found at i:32868 original size:21 final size:21
Alignment explanation
Indices: 32842--32903 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
32832 GTAATTACAT
32842 TATGGTTAATCTTGGCCACCA
1 TATGGTTAATCTTGGCCACCA
* * * *
32863 TATGGTCATTATTGG-CATC-
1 TATGGTTAATCTTGGCCACCA
32882 TATGGTTAATCTTGGCCACCA
1 TATGGTTAATCTTGGCCACCA
32903 T
1 T
32904 GGTCATTATT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
19 12 0.39
20 6 0.19
21 13 0.42
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (21 bp):
TATGGTTAATCTTGGCCACCA
Found at i:32887 original size:19 final size:19
Alignment explanation
Indices: 32863--32919 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
32853 TTGGCCACCA
32863 TATGGTCATTATTGGCATC
1 TATGGTCATTATTGGCATC
* * *
32882 TATGGTTAATCTTGGCCA-C
1 TATGGTCATTATTGG-CATC
*
32901 CATGGTCATTATTGGCATC
1 TATGGTCATTATTGGCATC
32920 ACCAACTTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 2 0.07
19 25 0.86
20 2 0.07
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (19 bp):
TATGGTCATTATTGGCATC
Found at i:32915 original size:38 final size:39
Alignment explanation
Indices: 32842--32919 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 39
32832 GTAATTACAT
32842 TATGGTTAATCTTGGCCACCATATGGTCATTATTGGCATC
1 TATGGTTAATCTTGGCCACCA-ATGGTCATTATTGGCATC
32882 TATGGTTAATCTTGGCCACC-ATGGTCATTATTGGCATC
1 TATGGTTAATCTTGGCCACCAATGGTCATTATTGGCATC
32920 ACCAACTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 18 0.47
40 20 0.53
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (39 bp):
TATGGTTAATCTTGGCCACCAATGGTCATTATTGGCATC
Found at i:34882 original size:2 final size:2
Alignment explanation
Indices: 34869--34911 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
34859 GCTTTACTGA
34869 AT AT AT ACT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34911 A
1 A
34912 ATAGAGTAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44385 original size:60 final size:59
Alignment explanation
Indices: 44291--44452 Score: 225
Period size: 60 Copynumber: 2.7 Consensus size: 59
44281 GCTAATTGTT
* * * *
44291 CAAATAAGGGTCTAACGTTTGACAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGG-CTAACGTTTGACAAAATGCTCAAATAAGGGCCCGATCATTGAATTTGGC
* * *
44351 TAAATAAGGGCATAACGTTTGTCAAAATGCTCAAATAAGGGCCCGGTCATTGAATTTGGC
1 CAAATAAGGGC-TAACGTTTGACAAAATGCTCAAATAAGGGCCCGATCATTGAATTTGGC
*
44411 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGC
1 CAAATAAGGG-CTAACGTTTGACAAAATGCTCAAATAAGGGC
44453 ATGTCTCATG
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
59 1 0.01
60 89 0.98
61 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (59 bp):
CAAATAAGGGCTAACGTTTGACAAAATGCTCAAATAAGGGCCCGATCATTGAATTTGGC
Found at i:44452 original size:31 final size:30
Alignment explanation
Indices: 44290--44452 Score: 108
Period size: 31 Copynumber: 5.4 Consensus size: 30
44280 GGCTAATTGT
*
44290 TCAAATAAGGGTCTAACGTTTGACAAAATGC
1 TCAAATAAGGGCCTAACGTTTG-CAAAATGC
* * * **
44321 TCAAATAAGGGTCTGATC-TTT-TAATTTGGC
1 TCAAATAAGGGCCT-AACGTTTGCAAAAT-GC
*
44351 T-AAATAAGGGCATAACGTTTGTCAAAATGC
1 TCAAATAAGGGCCTAACGTTTG-CAAAATGC
**
44381 TCAAATAAGGGCC---CGGTCATTG-AATTTGGC
1 TCAAATAAGGGCCTAAC-GT--TTGCAAAAT-GC
44411 -CAAATAAGGGCCTAACGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAACGTTTG-CAAAATGC
44441 TCAAATAAGGGC
1 TCAAATAAGGGC
44453 ATGTCTCATG
Statistics
Matches: 101, Mismatches: 15, Indels: 32
0.68 0.10 0.22
Matches are distributed among these distances:
28 3 0.03
29 36 0.36
30 10 0.10
31 49 0.49
32 3 0.03
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (30 bp):
TCAAATAAGGGCCTAACGTTTGCAAAATGC
Found at i:44519 original size:31 final size:30
Alignment explanation
Indices: 44481--44676 Score: 125
Period size: 31 Copynumber: 6.5 Consensus size: 30
44471 AATCTGACAC
44481 TAGGCCCTTATTTGAGCATTTTCGATAACGT
1 TAGGCCCTTATTTGAGCATTTTCGA-AACGT
* *
44512 TAGGCCCTTATTTGAGCATTCTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTTCG-AAACGT
** *
44543 TAGGCCCTTATTT-AGTCAAATT--AAAAGAT
1 TAGGCCCTTATTTGAG-CATTTTCGAAACG-T
** **
44572 CGGGTTCTTATTTGAGCATTTTCGATAACGT
1 TAGGCCCTTATTTGAGCATTTTCGA-AACGT
* ** * *
44603 TAGGCCCTTGTTTG-GCCAAATT--AAAAGA
1 TAGGCCCTTATTTGAG-CATTTTCGAAACGT
* *
44631 TCGGACCTTTATTTGAGCATTTTCGATAACGT
1 TAGG-CCCTTATTTGAGCATTTTCGA-AACGT
*
44663 TAGACCCTTATTTG
1 TAGGCCCTTATTTG
44677 GTCAAATTAA
Statistics
Matches: 120, Mismatches: 32, Indels: 26
0.67 0.18 0.15
Matches are distributed among these distances:
28 10 0.08
29 27 0.22
30 6 0.05
31 68 0.57
32 9 0.08
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (30 bp):
TAGGCCCTTATTTGAGCATTTTCGAAACGT
Found at i:44713 original size:60 final size:60
Alignment explanation
Indices: 44516--44736 Score: 266
Period size: 60 Copynumber: 3.7 Consensus size: 60
44506 TAACGTTAGG
* * * * *
44516 CCCTTATTTGAGCATTCTGGCA-AACGTTAGGCCCTTATTTAGTCAAATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTTCG-ATAACGTTAGACCCTTATTTGGTCAAATTAAAAGATCGGA
** * * *
44576 TTCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTGTTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGTCAAATTAAAAGATCGGA
*
44636 CCTTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGTCAAATTAAAAGATCGGA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGTCAAATTAAAAGATCGGA
* ** * *
44696 CCCTTATTTTAATATTTT-GACAAACATTAGACCCTTATTTG
1 CCCTTATTTGAGCATTTTCGA-TAACGTTAGACCCTTATTTG
44737 AGCAATTAGC
Statistics
Matches: 139, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
59 3 0.02
60 136 0.98
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.37
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGTCAAATTAAAAGATCGGA
Found at i:45003 original size:10 final size:10
Alignment explanation
Indices: 44988--45021 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
44978 GCTAATCACA
44988 TTTTTTCCTT
1 TTTTTTCCTT
44998 TTTTTTCCTT
1 TTTTTTCCTT
*
45008 TTTATT-CTT
1 TTTTTTCCTT
45017 TTTTT
1 TTTTT
45022 GCTGCTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTCCTT
Found at i:47650 original size:17 final size:17
Alignment explanation
Indices: 47612--47644 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
47602 CTCATGATAC
47612 CTAGGTAGTATGAGGTA
1 CTAGGTAGTATGAGGTA
47629 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
47645 GATAGGCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.36, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:49516 original size:17 final size:17
Alignment explanation
Indices: 49494--49527 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
49484 GAGAATCTAT
*
49494 TCTATCGAGTTATTTGA
1 TCTATCCAGTTATTTGA
49511 TCTATCCAGTTATTTGA
1 TCTATCCAGTTATTTGA
49528 AGATGCAGGG
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:0.24, C:0.15, G:0.15, T:0.47
Consensus pattern (17 bp):
TCTATCCAGTTATTTGA
Found at i:54535 original size:13 final size:14
Alignment explanation
Indices: 54512--54540 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
54502 AATTATACAA
54512 CATTCTTAGTTCAT
1 CATTCTTAGTTCAT
54526 CATT-TTAGTTCAT
1 CATTCTTAGTTCAT
54539 CA
1 CA
54541 GCTTTCTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.48
Consensus pattern (14 bp):
CATTCTTAGTTCAT
Found at i:54552 original size:2 final size:2
Alignment explanation
Indices: 54545--54569 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54535 TCATCAGCTT
54545 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
54570 TGACGAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:59211 original size:26 final size:24
Alignment explanation
Indices: 59159--59218 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 24
59149 TATAGTCCCT
* *
59159 TTTAATTTTAATTATTTATTAAAA
1 TTTATTTTTAATTACTTATTAAAA
* * *
59183 TTTGTATTTTTAATTACTTCTTTATA
1 -TT-TATTTTTAATTACTTATTAAAA
59209 TTTATTTTTA
1 TTTATTTTTA
59219 TTTAATGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 8 0.28
25 4 0.14
26 17 0.59
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTATTTTTAATTACTTATTAAAA
Found at i:64590 original size:21 final size:21
Alignment explanation
Indices: 64564--64607 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
64554 GAAAGGGGGG
*
64564 TTGCTAAAT-ACCGCCCTATTT
1 TTGCT-AATCACCGCCCCATTT
*
64585 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
64606 TT
1 TT
64608 TACACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:64710 original size:32 final size:32
Alignment explanation
Indices: 64664--64747 Score: 141
Period size: 32 Copynumber: 2.6 Consensus size: 32
64654 AGCCACGCGG
* *
64664 AGCCTCCCCACTAGGACGGCTCTGGCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
64696 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
*
64728 AGCCGCCCCACTAGGGCGGC
1 AGCCGCCCCACTAGGACGGC
64748 AAGGCTTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.15, C:0.43, G:0.30, T:0.12
Consensus pattern (32 bp):
AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
Found at i:70633 original size:20 final size:20
Alignment explanation
Indices: 70608--70648 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
70598 TGTTATGGAC
70608 TCTGTCTCCAGGACAATATG
1 TCTGTCTCCAGGACAATATG
70628 TCTGTCTCCAGGACAATATG
1 TCTGTCTCCAGGACAATATG
70648 T
1 T
70649 TCACAATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (20 bp):
TCTGTCTCCAGGACAATATG
Found at i:71258 original size:39 final size:39
Alignment explanation
Indices: 71175--71259 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 39
71165 AGTAATAATC
* *
71175 ATATATATAAATATAATTATAAACTAAAACTATATTTTAT
1 ATATATATAAATATAATAATAAAATAAAAC-ATATTTTAT
*
71215 -TATATATATATATAATAATAATAATAAAA-A-ATTATTAT
1 ATATATATAAATATAATAATAA-AATAAAACATATT-TTAT
71253 ATATATA
1 ATATATA
71260 AGTCGGTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
37 3 0.08
38 5 0.13
39 25 0.64
40 6 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.42
Consensus pattern (39 bp):
ATATATATAAATATAATAATAAAATAAAACATATTTTAT
Found at i:77957 original size:332 final size:332
Alignment explanation
Indices: 76136--79725 Score: 4223
Period size: 332 Copynumber: 10.8 Consensus size: 332
76126 ATCTAAGTCT
* * * * * *
76136 TAATTCACCGTAAAAAAGATTGAATGACTTTTCACGTTTCTAATATCGTTTTTCCTA-TTTTTTA
1 TAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTAGTTTTTTT
* * * ** *
76200 AAATTAATTTTAAATTAAATTGAAATAAGATTCGTATGCTCGAAAAAATAAA-TCATTAAATCCA
66 GAATTAATTTCAAATTAGATTGAAATAAGATTCACATGCTCGAAAAAACAAATTC-TTAAATCCA
* * *
76264 ATGTGGCTGATATTTGGTTAGATTAATATAAATATTTCAAGGAGACTTTG-CGCAAAAAATCATG
130 ATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGAC-TTGACGCAAAAAATCATG
** * ** * *
76328 CAAAACTGAGCTAGGGCCTCGAAATGCAATTTTAGCC-AAAAAACAGTAATGGTTAGTACACGAT
194 CAAAACTGAGCCGGGGCCTCGAAACGCGTTTTTAGCCAAAAAAACGGTGATGGTTAGTACACGAT
* * *
76392 TTCGGCTAAAATTTT--TAAAATATGACCCGAAAGTATTTTCCTCAATTTTTTGCCAAAATAATC
259 TTCGGCTAAAATTTTGCAAAAAT-TGACCCGAAAGTATTTTCCTCAATTTTTGGCCAAAATACTC
*
76455 GTAAATATATA
323 ATAAA-ATATA
*
76466 TAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCTTAGTTTTTTT
1 TAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTAGTTTTTTT
* *
76531 GAATTAATTTCAAATTAGATTGAAACAAGATTCACATGCTCGAAAAAACAAATTCTTAAAT-TAA
66 GAATTAATTTCAAATTAGATTGAAATAAGATTCACATGCTCGAAAAAACAAATTCTTAAATCCAA
* * *
76595 TTGTGTGCTGAGATTTGGTTAGATGAATATAGATATTTCATGGAGACTTGGCGGAAAAAATCAAT
131 -TGTG-GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGACTTGACGCAAAAAATC-AT
* *
76660 TCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCC-AAAAAACGGTGATGGTTAGTACACGA
193 GCAAAACTGAGCCGGGGCCTCGAAACGCGTTTTTAGCCAAAAAAACGGTGATGGTTAGTACACGA
*** ** * *
76724 TTTCAATTAAAATTTTGTTAAAATTGACCCGAAAGTAATTTCCTCAATTTTTGGCCAAAATAATC
258 TTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTATTTTCCTCAATTTTTGGCCAAAATACTC
76789 ATAAATATATA
323 ATAAA-ATATA
* * *
76800 TAAATTTAACGTCAAAAAGATTGAAGGGCTTTTCATGCTTCTAATATCATTTTTCCTAGCTTTTT
1 T-AATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTAG-TTTTT
76865 TTGAATTAATTTCAAATTAGATTGAAATAAGATTCACATGCTCGAAAAAACAAATTCTTAAATCC
64 TTGAATTAATTTCAAATTAGATTGAAATAAGATTCACATGCTCGAAAAAACAAATTCTTAAATCC
*
76930 AATGTGGCTGAGTTTTGGTTAGATGAATATAGATATTTCAAGGAGACTTGACGGTTGACGCCAAA
129 AATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA-G-GA---GAC--TTGACG-CAAA
*
76995 AAATCATGCAAAACTGAGCCGGGGCCAT-GAAACACG-TTTTAGCCTAAAAAAACGGT--T--TT
186 AAATCATGCAAAACTGAGCCGGGGCC-TCGAAACGCGTTTTTAGCC-AAAAAAACGGTGATGGTT
* * *
77054 -GTACACGATTTCGGATAAAATTTTGCAAAAATTGACCCGAAAGTATTTTACTCAATTTTTGGTC
249 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTATTTTCCTCAATTTTTGGCC
77118 AAAATACTCATTAAAATATA
314 AAAATACTCA-TAAAATATA
* *
77138 TAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGTTTATAATATCGTTTTTCCTAGTTTTTTT
1 TAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTAG-TTTTTT
*
77203 TGAATTAATTTCAAATTAGATTGAAATAAGATTCACATGCTCGAAAAAATAAATTCTTAAATCCA
65 TGAATTAATTTCAAATTAGATTGAAATAAGATTCACATGCTCGAAAAAACAAATTCTTAAATCCA
* * *
77268 ATGTGGCTGAGATTTGGTTTGATGAATATAGATATTTCAAGGAGACTT-AGCGCCAAAAATGATG
130 ATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGACTTGA-CGCAAAAAATCATG
* *
77332 CAAAACTGAGCCGGGG-CTCCGAAACGCGTTTTTAGCAAAAAAGAAAAAAACGGTGATGGTCAGT
194 CAAAACTGAGCCGGGGCCT-CGAAACGCGTTTTTAGC------CAAAAAAACGGTGATGGTTAGT
* * * * * * ****
77396 ACACGATTTC-GCTAAAATTTGGCAGAAATTGACCCGGATGTATTTTTCTCAATATTTATAAAAA
252 ACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTATTTTCCTCAATTTTTGGCCAAA
77460 ATACTCATAAGAATATA
317 ATACTCATAA-AATATA
* * * * **
77477 TAAATCAACATCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATAGTTTTTCCTTTTTTTTTT
1 TAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTAGTTTTTTT
* * * * * *
77542 TAAGTAATTTCAAATTAGATTGAAATAAGATTCATATGCTCAAAAAAAGAAATCCTTAAATCCAA
66 GAATTAATTTCAAATTAGATTGAAATAAGATTCACATGCTCGAAAAAACAAATTCTTAAATCCAA
*
77607 TATGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGACTTGACGCAAAAAATCATGCA
131 TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGACTTGACGCAAAAAATCATGCA
* ** * *
77672 AAACTGAGCTGGGGCCTCGAAACGCGTTTTTAGCCAAAAAAACTATGATCGTTAGTAAACGATTT
196 AAACTGAGCCGGGGCCTCGAAACGCGTTTTTAGCCAAAAAAACGGTGATGGTTAGTACACGATTT
* * * * **
77737 CGGCTAAAATTTTGCATAAATTAATCTGAAAGTATTTTCCTCAATTTTTGGAAAAAATACTCAT-
261 CGGCTAAAATTTTGCAAAAATTGACCCGAAAGTATTTTCCTCAATTTTTGGCCAAAATACTCATA
77801 AAATATA
326 AAATATA
* * * *
77808 TAATTTAACGTAAAAAAGATTGAAGGGCTTTTTTAACGCTT-TCAATATC-TTTTTCCTAGTTTG
1 TAATTCAACGTCAAAAAGATTGAAGGGC--TTTTCACGCTTCT-AATATCGTTTTTCCTAGTTTT
* * *
77871 TTTGACTTAATTTCAAATTAGATTGAAACAAGATTCACATGCTCGAAAAAATAAATTCTTAAAT-
63 TTTGAATTAATTTCAAATTAGATTGAAATAAGATTCACATGCTCGAAAAAACAAATTCTTAAATC
* * **
77935 CAATTGTGGTTGAGATTTGGTTAGATGAATATAGTTATTTCAAGGAGACTTGGTGCAAAAAAT-A
128 CAA-TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGACTTGACGCAAAAAATCA
* * * * *
77999 TGCAAAACTGAGCCGGGACCCCGAAACGTG-TTTTAGCAAAAAAAAAACGGTGA-GATTAGTACA
192 TGCAAAACTGAGCCGGGGCCTCGAAACGCGTTTTTAGC--CAAAAAAACGGTGATGGTTAGTACA
* * * * *
78062 CGATTTCGGCTAAAATTTGGC-AAAACTGACTCGAAAGTATTCTT-TTCAATGTTTGGCCAAAAT
255 CGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTATT-TTCCTCAATTTTTGGCCAAAAT
78125 ACTCATAAAAATATA
319 ACTCAT-AAAATATA
* * * *
78140 AAATTCAACGTCAAAAAGATTAAAGAGCTTTTCACGCTTC-AA-A-----TAT-C--G-TTTTTT
1 TAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTAGTTTTTTT
* *
78194 -AATTAATTTCAAATTAGATTGAAATAAAATTCATATGCTCGAAAAAACAAATTCTTAAATCCAA
66 GAATTAATTTCAAATTAGATTGAAATAAGATTCACATGCTCGAAAAAACAAATTCTTAAATCCAA
* ** * * * *
78258 TATGGCTGAGATTTTTTTTTAGAAGAATTTAGATATTTCAACGAGACTTCG-CGCAAAAATTCAT
131 TGTGGCTGAGA--TTTGGTTAGATGAATATAGATATTTCAAGGAGACTT-GACGCAAAAAATCAT
* * * * *
78322 GCAAAACTGAGCCGGTGCCCCGAAACACG-TTTTAACC-AAAAAACGGTGATCGTTAGTACACGA
193 GCAAAACTGAGCCGGGGCCTCGAAACGCGTTTTTAGCCAAAAAAACGGTGATGGTTAGTACACGA
* * * *
78385 TTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATTATTTTCCTCATTTTTTGGTCAAAATACTT
258 TTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTATTTTCCTCAATTTTTGGCCAAAATACTC
78450 ATAAAAATATA
323 AT-AAAATATA
* * * * *
78461 TAATTC-ACTGTCTAAAATATTGAATGACTTTTCACGCTTCTAATATCGTTTTTCCTAATTTTTT
1 TAATTCAAC-GTCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTAGTTTTTT
* * * * * *
78525 TGAATTGATTTCAAATTACATGGAAACAA-A---GCATGCTCGAAAAAACAAATCCTTAAATCCA
65 TGAATTAATTTCAAATTAGATTGAAATAAGATTCACATGCTCGAAAAAACAAATTCTTAAATCCA
* * *
78586 ATGTGGCTGATATTTAGG-TAGATGAATATAGATATTTCAAGGAAATTTGACGCAAAAAATCATG
130 ATGTGGCTGAGATTT-GGTTAGATGAATATAGATATTTCAAGGAGACTTGACGCAAAAAATCATG
* * * * * * * * *
78650 CAAGACTGAGCCGGGTCCCCAAAACACGTTTTTAGCATAAAAAAAACGGTGATGATTACTACACA
194 CAAAACTGAGCCGGGGCCTCGAAACGCGTTTTTAGC--CAAAAAAACGGTGATGGTTAGTACACG
* * * * *
78715 ATTTCAGCTAAAATTTTGCATAAATTGACCCGAAAGTATTTTCCCCTATTTTTGTCCAAAATACT
257 ATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTATTTTCCTCAATTTTTGGCCAAAATACT
78780 CATAAAAATATA
322 CAT-AAAATATA
* * *
78792 TAATTCAACATCAAAAAGATTGAAGGGGTTTTCACGCTTGTAATATCG-TTTTCCTA--TTTTTT
1 TAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTAGTTTTTTT
* * * *
78854 AAATTAATTTCAAATTAGATTGAAATTAGATTCATATGCTCG-AAAAA-AAA-TATTAAATCCAA
66 GAATTAATTTCAAATTAGATTGAAATAAGATTCACATGCTCGAAAAAACAAATTCTTAAATCCAA
* * * *
78916 CGCGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGATTTGGCG-ATAAAAATCATG-
131 TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGACTTGACGCA-AAAAATCATGC
* * * * * * *
78979 AATACTGAGCTGGGGTCC-CGAAACGCGTTTTAAGCTAAAAAAAACCGTGATGATCAGTACACGA
195 AAAACTGAGCCGGGG-CCTCGAAACGCGTTTTTAGC-CAAAAAAACGGTGATGGTTAGTACACGA
* * * * *
79043 TTTCGGCTAAAATTTTGAAAAAATTGACCCGGATGTATTTTCCTCAATTTCTGGCCAAAATTCTC
258 TTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTATTTTCCTCAATTTTTGGCCAAAATACTC
79108 ATAAAAATATA
323 AT-AAAATATA
* * * *
79119 TAATTAAATGTCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATA-TTTTGTT
1 TAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTAGTTTT-TT
* * * *
79183 TGAATTAATTTCAAATTTGATTGAAATAAGATTCACTTGCTCTAAATAACAAATTCTTAAAT-CA
65 TGAATTAATTTCAAATTAGATTGAAATAAGATTCACATGCTCGAAAAAACAAATTCTTAAATCCA
* * *
79247 ATTGAGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGACTTGGCGCAAAAAATCATG
130 A-TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGACTTGACGCAAAAAATCATG
* * * *
79312 AAAAACTGAGTCGGGGCCTCGAAATGCGTTTTTAGCC-AAAAAACGGTGATGGTTAGTACACGAG
194 CAAAACTGAGCCGGGGCCTCGAAACGCGTTTTTAGCCAAAAAAACGGTGATGGTTAGTACACGAT
* * * * **
79376 TTCGGTTAAAATTTTGCAAAAATTGACTCGAAAGTATTTTCCTTAATTTCTGATCAAAATACTCA
259 TTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTATTTTCCTCAATTTTTGGCCAAAATACTCA
*
79441 TAAAAATAAA
324 T-AAAATATA
* *
79451 TAATTCAATGTCAAACAA-ATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATA-TTTTGT
1 TAATTCAACGTCAAA-AAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTAGTTTT-T
* *
79514 TTGAATTAATTTCAAATTTGATTGAAATAAGATTCACATGCTCTAAAAAACAAATTCTTAAAT-C
64 TTGAATTAATTTCAAATTAGATTGAAATAAGATTCACATGCTCGAAAAAACAAATTCTTAAATCC
* * *
79578 AGTG-GAGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGCAGACTTGACGAAAAAAATCA
129 AATGTG-G-CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGACTTGACGCAAAAAATCA
* * * * *
79642 TACAAAACTGAGTC-GGGCCTCGAAACGAGCTTTTAGCCAAAAAAAGGGTGATGGTTAGTACACG
192 TGCAAAACTGAGCCGGGGCCTCGAAACGCGTTTTTAGCCAAAAAAACGGTGATGGTTAGTACACG
79706 ATTTCGGCTAAAATTTTGCA
257 ATTTCGGCTAAAATTTTGCA
Statistics
Matches: 2817, Mismatches: 342, Indels: 200
0.84 0.10 0.06
Matches are distributed among these distances:
319 76 0.03
320 40 0.01
321 115 0.04
322 36 0.01
323 2 0.00
324 2 0.00
326 1 0.00
327 199 0.07
328 74 0.03
329 144 0.05
330 167 0.06
331 313 0.11
332 580 0.21
333 228 0.08
334 78 0.03
335 105 0.04
336 73 0.03
337 165 0.06
338 229 0.08
339 116 0.04
340 15 0.01
341 9 0.00
342 32 0.01
343 18 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (332 bp):
TAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTAGTTTTTTT
GAATTAATTTCAAATTAGATTGAAATAAGATTCACATGCTCGAAAAAACAAATTCTTAAATCCAA
TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGACTTGACGCAAAAAATCATGCA
AAACTGAGCCGGGGCCTCGAAACGCGTTTTTAGCCAAAAAAACGGTGATGGTTAGTACACGATTT
CGGCTAAAATTTTGCAAAAATTGACCCGAAAGTATTTTCCTCAATTTTTGGCCAAAATACTCATA
AAATATA
Done.