Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020823.1 Corchorus olitorius cultivar O-4 contig20856, 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: 103914
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--43 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1 C
*
2 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44 TAGTTATTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21709 original size:126 final size:125
Alignment explanation
Indices: 21545--21815 Score: 470
Period size: 126 Copynumber: 2.2 Consensus size: 125
21535 GGTAGTGCTC
*
21545 CCTTTGCTTGCTTGGTTTCTGGAGCAGTAGCCTGCACTGATGCCTGTTTATTCTCCCTAGCAGGC
1 CCTTTGCTTGCTTGGTTTCTGGAGCAGTAGCCTGCACTGATGCCTGTTTATTCTCCCTAGAAGGC
*
21610 TTCATACCATTTGCAGGTAACATTGCTTCATCCTTATCAAAGAAGTCAGCAGGAAGTGAA
66 TTCATACCATTCGCAGGTAACATTGCTTCATCCTTATCAAAGAAGTCAGCAGGAAGTGAA
* * *
21670 CCTTTCGCTTGCTTGGTTTCTGGAGCGGTAGCCTTCACTGATGCCTGTTTATTCTCCCTGGAAGG
1 CCTTT-GCTTGCTTGGTTTCTGGAGCAGTAGCCTGCACTGATGCCTGTTTATTCTCCCTAGAAGG
*
21735 CTTCATACCATTCGCAGGTAACCTTGCTTCATCCTTATCAAAGAAGTCAGCAGGAAGTGAA
65 CTTCATACCATTCGCAGGTAACATTGCTTCATCCTTATCAAAGAAGTCAGCAGGAAGTGAA
21796 CCTTTTGCTTGCTTGGTTTC
1 CC-TTTGCTTGCTTGGTTTC
21816 CAACACTGTG
Statistics
Matches: 138, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
125 5 0.04
126 130 0.94
127 3 0.02
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.34
Consensus pattern (125 bp):
CCTTTGCTTGCTTGGTTTCTGGAGCAGTAGCCTGCACTGATGCCTGTTTATTCTCCCTAGAAGGC
TTCATACCATTCGCAGGTAACATTGCTTCATCCTTATCAAAGAAGTCAGCAGGAAGTGAA
Found at i:24843 original size:3 final size:3
Alignment explanation
Indices: 24835--24902 Score: 86
Period size: 3 Copynumber: 23.0 Consensus size: 3
24825 ATTTATTTAT
* * *
24835 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTT ATT ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
24883 AT- ATA ATTA ATA ATA A-A ATA
1 ATA ATA A-TA ATA ATA ATA ATA
24903 TTTTTTTATT
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 4 0.07
3 51 0.88
4 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:38062 original size:2 final size:2
Alignment explanation
Indices: 38055--38089 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
38045 ACTAAATTAG
38055 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38090 GGAGATGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39094 original size:29 final size:28
Alignment explanation
Indices: 39053--39108 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
39043 GTTATTCCAC
* *
39053 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
1 GTTCTTGAACGTTCTTGAA-ATTAGAAAT
39082 GTTCTTGAACGTTCTTGAAATTAGAAA
1 GTTCTTGAACGTTCTTGAAATTAGAAA
39109 GTTTGAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (28 bp):
GTTCTTGAACGTTCTTGAAATTAGAAAT
Found at i:48978 original size:118 final size:117
Alignment explanation
Indices: 48748--48983 Score: 418
Period size: 118 Copynumber: 2.0 Consensus size: 117
48738 ATTATTTTCC
* * * *
48748 TGTAAATAAGTACTTTATTTTGGCGGTAGGAGGATGGGTGTCCAATATAAATGTATGAAGGTCTA
1 TGTAAATAAGTACATTATTTTGGCGGTAGGAGGATGGGTGTCCAATATAAATGCACGAAAGTCTA
*
48813 AGTTGTAAGAATTTGTTGCCTTATTTTATGCATGCAAGTGTATCATTTTTGG
66 AGTTGTAAGAATTTGTTGCCTTATTTTATGCATGCAAGTATATCATTTTTGG
48865 TGTAAATAAGTACATTATTTTGGCGGTAGGAGGATGGGTGTCCAATATAAATGCACGTAAAGTCT
1 TGTAAATAAGTACATTATTTTGGCGGTAGGAGGATGGGTGTCCAATATAAATGCACG-AAAGTCT
48930 AAGTTGTAAGAATTTGTTGCCTTATTTTATGCATGCAAGTATATCATTTTTGG
65 AAGTTGTAAGAATTTGTTGCCTTATTTTATGCATGCAAGTATATCATTTTTGG
48983 T
1 T
48984 ATTAAATGAA
Statistics
Matches: 113, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
117 54 0.48
118 59 0.52
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (117 bp):
TGTAAATAAGTACATTATTTTGGCGGTAGGAGGATGGGTGTCCAATATAAATGCACGAAAGTCTA
AGTTGTAAGAATTTGTTGCCTTATTTTATGCATGCAAGTATATCATTTTTGG
Found at i:52554 original size:27 final size:27
Alignment explanation
Indices: 52523--52576 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
52513 AATCACATGA
*
52523 GACGAGCCTAACGTTGCTCAAAATTTG
1 GACGAGCCTAACATTGCTCAAAATTTG
52550 GACGAGCCTAACATTGCTCAAAATTTG
1 GACGAGCCTAACATTGCTCAAAATTTG
52577 TGTGGAAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (27 bp):
GACGAGCCTAACATTGCTCAAAATTTG
Found at i:54280 original size:56 final size:56
Alignment explanation
Indices: 54194--54306 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
54184 CCGCTTGTGG
* *
54194 AGTCTAAAATTTACATTGATAATATATGGTATAATCATCCTAGAAAAATGAAAATT
1 AGTCTAAAAATTACACTGATAATATATGGTATAATCATCCTAGAAAAATGAAAATT
*
54250 AGTCTAAAAATTACACTGATAATATATGGTATAATCATCCTAGAAGAATGAAAATT
1 AGTCTAAAAATTACACTGATAATATATGGTATAATCATCCTAGAAAAATGAAAATT
54306 A
1 A
54307 TACCATACAC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.32
Consensus pattern (56 bp):
AGTCTAAAAATTACACTGATAATATATGGTATAATCATCCTAGAAAAATGAAAATT
Found at i:56554 original size:22 final size:22
Alignment explanation
Indices: 56487--57191 Score: 311
Period size: 22 Copynumber: 32.2 Consensus size: 22
56477 GAAATTTCAG
*
56487 TAACCTCACTATCAATATTTTGA
1 TAACCTCACTATGAA-ATTTTGA
* * * *
56510 TAAAATCTC-CTTATAAAAGTTTGC
1 T--AACCTCAC-TATGAAATTTTGA
56534 TAACCTCACTATGAAATTTTGA
1 TAACCTCACTATGAAATTTTGA
* * *
56556 TAGCCTCATTATGAAATTTTAATTA
1 TAACCTCACTATGAAA-TTT--TGA
* *
56581 TAACCTC-CATATGAAATTTAGC
1 TAACCTCAC-TATGAAATTTTGA
* * *
56603 TAACCTCCCTATGAAAATTCGA
1 TAACCTCACTATGAAATTTTGA
* *
56625 TAACCATC-GTATGAAATTTTGG
1 TAACC-TCACTATGAAATTTTGA
* * * **
56647 T-ACTTCCCTATGAAAATTCAA
1 TAACCTCACTATGAAATTTTGA
** *
56668 TAACCAT-GGTATGAAATATTGA
1 TAACC-TCACTATGAAATTTTGA
56690 T-ACCT--CTATGAAATTTTGA
1 TAACCTCACTATGAAATTTTGA
* ** * *
56709 TAACCACAAAATAAAAATTTGA
1 TAACCTCACTATGAAATTTTGA
* *
56731 TAACCTTACTATAAAATTTTGA
1 TAACCTCACTATGAAATTTTGA
56753 TAA-CTACACTATGAAATTTTGA
1 TAACCT-CACTATGAAATTTTGA
* *
56775 TAACAACTTC-CTTCTAAAATTTTGA
1 TAAC--C-TCAC-TATGAAATTTTGA
* * *
56800 TAACTTCATTATGAAATTTCGA
1 TAACCTCACTATGAAATTTTGA
* * ***
56822 TAACGT-TCT-T--AATGAAGA
1 TAACCTCACTATGAAATTTTGA
*
56840 TAACCTCCCTAT-AATATTTATGA
1 TAACCTCACTATGAA-ATTT-TGA
* *
56863 TAAGCTAACTATGAAATTTTGA
1 TAACCTCACTATGAAATTTTGA
* *
56885 TAACCTC-CCATTAAAATTTTGA
1 TAACCTCACTA-TGAAATTTTGA
* *
56907 TAACCACACAATG-AATATTTGA
1 TAACCTCACTATGAAAT-TTTGA
* *
56929 TAACC-CTGCTATGAAATTTTAA
1 TAACCTC-ACTATGAAATTTTGA
*
56951 TAA-CTACAGTATGAAATTTTGA
1 TAACCT-CACTATGAAATTTTGA
*
56973 TAACAACT-TCTA--AAATTTTGA
1 TAAC--CTCACTATGAAATTTTGA
* * *
56994 TAACTTCATTATGAAATTTCGA
1 TAACCTCACTATGAAATTTTGA
** **
57016 TAATGT-TTTATGAAA-----A
1 TAACCTCACTATGAAATTTTGA
* * *
57032 TAA-CTCCCTATGATATTCATGA
1 TAACCTCACTATGAAATT-TTGA
* *
57054 TAAGCTAACTATGAAATTTTGA
1 TAACCTCACTATGAAATTTTGA
*
57076 TAACCTC-CTTTTGAAATTTTGA
1 TAACCTCAC-TATGAAATTTTGA
* *
57098 TAACCGCATTATGAAATTTTGA
1 TAACCTCACTATGAAATTTTGA
* *
57120 TAATCACACTATGAAATTTTGA
1 TAACCTCACTATGAAATTTTGA
* *
57142 TAAATCTCTCTAT-AAATTTATGA
1 T-AACCTCACTATGAAATTT-TGA
*
57165 TAACCTCACAATGAAATTTTGA
1 TAACCTCACTATGAAATTTTGA
57187 TAACC
1 TAACC
57192 ATACAGAGAC
Statistics
Matches: 512, Mismatches: 115, Indels: 111
0.69 0.16 0.15
Matches are distributed among these distances:
15 1 0.00
16 10 0.02
18 10 0.02
19 16 0.03
20 10 0.02
21 48 0.09
22 297 0.58
23 62 0.12
24 13 0.03
25 44 0.09
26 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (22 bp):
TAACCTCACTATGAAATTTTGA
Found at i:56671 original size:43 final size:44
Alignment explanation
Indices: 56590--56684 Score: 138
Period size: 43 Copynumber: 2.2 Consensus size: 44
56580 ATAACCTCCA
*
56590 TATGAAATTTAGCTAACCTCCCTATGAAAATTCGATAACCATCG
1 TATGAAATTTAGCTAACCTCCCTATGAAAATTCAATAACCATCG
* * * *
56634 TATGAAATTTTGGT-ACTTCCCTATGAAAATTCAATAACCATGG
1 TATGAAATTTAGCTAACCTCCCTATGAAAATTCAATAACCATCG
56677 TATGAAAT
1 TATGAAAT
56685 ATTGATACCT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 34 0.74
44 12 0.26
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.33
Consensus pattern (44 bp):
TATGAAATTTAGCTAACCTCCCTATGAAAATTCAATAACCATCG
Found at i:56800 original size:47 final size:44
Alignment explanation
Indices: 56677--56825 Score: 142
Period size: 47 Copynumber: 3.4 Consensus size: 44
56667 ATAACCATGG
* * *
56677 TATGAAATATTGAT-ACC-T-CTATGAAATTTTGATAACCACAA
1 TATGAAATTTTGATAACCTTACTATAAAATTTTGATAACTACAA
* * * *
56718 AATAAAAATTTGATAACCTTACTATAAAATTTTGATAACTACAC
1 TATGAAATTTTGATAACCTTACTATAAAATTTTGATAACTACAA
* * * *
56762 TATGAAATTTTGATAACAACTTCCTTCTAAAATTTTGATAACTTCAT
1 TATGAAATTTTGATAAC--CTTAC-TATAAAATTTTGATAACTACAA
*
56809 TATGAAATTTCGATAAC
1 TATGAAATTTTGATAAC
56826 GTTCTTAATG
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
41 10 0.11
42 3 0.03
43 1 0.01
44 34 0.39
46 4 0.05
47 35 0.40
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTTACTATAAAATTTTGATAACTACAA
Found at i:56956 original size:198 final size:191
Alignment explanation
Indices: 56700--57102 Score: 608
Period size: 198 Copynumber: 2.1 Consensus size: 191
56690 TACCTCTATG
* *
56700 AAATTTTGATAACCACAAAATAAAAATTTGATAACCTTACTATAAAATTTTGATAACTACACTAT
1 AAATTTTGATAACCACAAAATAAAAATTTGATAACCCTACTATAAAATTTTAATAACTACACTAT
56765 GAAATTTTGATAACAACTTCCTTCTAAAATTTTGATAACTTCATTATGAAATTTCGATAACGTTC
66 GAAATTTTGATAACAA----CTTCTAAAATTTTGATAACTTCATTATGAAATTTCGATAACGTT-
* *
56830 TTAATGAAGATAACCTCCCTATAATATTTATGATAAGCTAACTATGAAATTTTGATAACCTCCCA
126 TT-ATGAAAATAA-CTCCCTATAATATTCATGATAAGCTAACTATGAAATTTTGATAACCTCCCA
56895 TTA
189 TTA
* * * * * *
56898 AAATTTTGATAACCACACAATGAATATTTGATAACCCTGCTATGAAATTTTAATAACTACAGTAT
1 AAATTTTGATAACCACAAAATAAAAATTTGATAACCCTACTATAAAATTTTAATAACTACACTAT
*
56963 GAAATTTTGATAACAACTTCTAAAATTTTGATAACTTCATTATGAAATTTCGATAATGTTTTATG
66 GAAATTTTGATAACAACTTCTAAAATTTTGATAACTTCATTATGAAATTTCGATAACGTTTTATG
* ** *
57028 AAAATAACTCCCTATGATATTCATGATAAGCTAACTATGAAATTTTGATAACCTCCTTTTG
131 AAAATAACTCCCTATAATATTCATGATAAGCTAACTATGAAATTTTGATAACCTCCCATTA
57089 AAATTTTGATAACC
1 AAATTTTGATAACC
57103 GCATTATGAA
Statistics
Matches: 190, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
191 63 0.33
192 9 0.05
193 2 0.01
194 43 0.23
198 73 0.38
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (191 bp):
AAATTTTGATAACCACAAAATAAAAATTTGATAACCCTACTATAAAATTTTAATAACTACACTAT
GAAATTTTGATAACAACTTCTAAAATTTTGATAACTTCATTATGAAATTTCGATAACGTTTTATG
AAAATAACTCCCTATAATATTCATGATAAGCTAACTATGAAATTTTGATAACCTCCCATTA
Found at i:57121 original size:191 final size:194
Alignment explanation
Indices: 56700--57144 Score: 603
Period size: 191 Copynumber: 2.3 Consensus size: 194
56690 TACCTCTATG
* * * * ** * * *
56700 AAATTTTGATAACCACAAAATAAAAATTTGATAACCTTACTATAAAATTTTGATAACTACACTAT
1 AAATTTTGATAACCACACAATGAATATTTGATAATCACACTATGAAATTTTAATAACTACAGTAT
56765 GAAATTTTGATAACAACTTCCTTCTAAAATTTTGATAACTTCATTATGAAATTTCGATAACGTTC
66 GAAATTTTGATAACAA----CTTCTAAAATTTTGATAACTTCATTATGAAATTTCGATAACGTTC
* *
56830 TTAATGAAGATAACCTCCCTATAATATTTATGATAAGCTAACTATGAAATTTTGATAACCTCCCA
127 TTAATGAAAATAACCTCCCTATAATATTCATGATAAGCTAACTATGAAATTTTGATAACCTCCCA
56895 TTA
192 TTA
* *
56898 AAATTTTGATAACCACACAATGAATATTTGATAA-CCCTGCTATGAAATTTTAATAACTACAGTA
1 AAATTTTGATAACCACACAATGAATATTTGATAATCAC-ACTATGAAATTTTAATAACTACAGTA
*
56962 TGAAATTTTGATAACAACTTCTAAAATTTTGATAACTTCATTATGAAATTTCGATAATGTT-TT-
65 TGAAATTTTGATAACAACTTCTAAAATTTTGATAACTTCATTATGAAATTTCGATAACGTTCTTA
* ** *
57025 ATGAAAATAA-CTCCCTATGATATTCATGATAAGCTAACTATGAAATTTTGATAACCTCCTTTTG
130 ATGAAAATAACCTCCCTATAATATTCATGATAAGCTAACTATGAAATTTTGATAACCTCCCATTA
* ** *
57089 AAATTTTGATAACCGCATTATGAA-ATTTTGATAATCACACTATGAAATTTTGATAA
1 AAATTTTGATAACCACACAATGAATA-TTTGATAATCACACTATGAAATTTTAATAA
57145 ATCTCTCTAT
Statistics
Matches: 222, Mismatches: 22, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
190 1 0.00
191 94 0.42
192 11 0.05
193 2 0.01
194 43 0.19
197 1 0.00
198 70 0.32
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (194 bp):
AAATTTTGATAACCACACAATGAATATTTGATAATCACACTATGAAATTTTAATAACTACAGTAT
GAAATTTTGATAACAACTTCTAAAATTTTGATAACTTCATTATGAAATTTCGATAACGTTCTTAA
TGAAAATAACCTCCCTATAATATTCATGATAAGCTAACTATGAAATTTTGATAACCTCCCATTA
Found at i:57674 original size:37 final size:37
Alignment explanation
Indices: 57633--57707 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
57623 AGTCTAGTTT
57633 TAAGTAATGATTGATTAAAATTTAAGTCCAAATCAAC
1 TAAGTAATGATTGATTAAAATTTAAGTCCAAATCAAC
57670 TAAGTAATGATTGATTAAAATTTAAGTCCAAATCAAC
1 TAAGTAATGATTGATTAAAATTTAAGTCCAAATCAAC
57707 T
1 T
57708 TAAGATAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (37 bp):
TAAGTAATGATTGATTAAAATTTAAGTCCAAATCAAC
Found at i:57708 original size:93 final size:93
Alignment explanation
Indices: 57586--57763 Score: 329
Period size: 93 Copynumber: 1.9 Consensus size: 93
57576 TTTTAACAAC
*
57586 ATTGAATAAGATTTAAGTCCAAATCAACTTAAGATAAAGTCTAGTTTTAAGTAATGATTGATTAA
1 ATTGAATAAAATTTAAGTCCAAATCAACTTAAGATAAAGTCTAGTTTTAAGTAATGATTGATTAA
57651 AATTTAAGTCCAAATCAACTAAGTAATG
66 AATTTAAGTCCAAATCAACTAAGTAATG
*
57679 ATTGATTAAAATTTAAGTCCAAATCAACTTAAGATAAAGTCTAGTTTTAAGTAATGATTGATTAA
1 ATTGAATAAAATTTAAGTCCAAATCAACTTAAGATAAAGTCTAGTTTTAAGTAATGATTGATTAA
*
57744 AATTTAAGTCTAAATCAACT
66 AATTTAAGTCCAAATCAACT
57764 TAAAATAAAA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 82 1.00
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.35
Consensus pattern (93 bp):
ATTGAATAAAATTTAAGTCCAAATCAACTTAAGATAAAGTCTAGTTTTAAGTAATGATTGATTAA
AATTTAAGTCCAAATCAACTAAGTAATG
Found at i:60660 original size:12 final size:12
Alignment explanation
Indices: 60643--60667 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60633 TCTCAATTCA
60643 CAAAATTCAAAT
1 CAAAATTCAAAT
60655 CAAAATTCAAAT
1 CAAAATTCAAAT
60667 C
1 C
60668 TGAAACGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (12 bp):
CAAAATTCAAAT
Found at i:65513 original size:22 final size:22
Alignment explanation
Indices: 65488--65536 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
65478 CCTTACCTGC
*
65488 AGTTTTATTCATGCCATAAGAA
1 AGTTCTATTCATGCCATAAGAA
65510 AGTTCTATTCATGCCATAAGAA
1 AGTTCTATTCATGCCATAAGAA
65532 AGTTC
1 AGTTC
65537 GTTAACTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (22 bp):
AGTTCTATTCATGCCATAAGAA
Found at i:69730 original size:1 final size:1
Alignment explanation
Indices: 69724--69748 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
69714 TCTGGCCAAG
69724 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
69749 TCACTCGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:72003 original size:32 final size:32
Alignment explanation
Indices: 71967--72032 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
71957 CATTGCAGGA
71967 GATTCTAGCATAAGAGAGCATTCTGCTCTCAG
1 GATTCTAGCATAAGAGAGCATTCTGCTCTCAG
71999 GATTCTAGCATAAGAGAGCATTCTGCTCTCAG
1 GATTCTAGCATAAGAGAGCATTCTGCTCTCAG
72031 GA
1 GA
72033 AGTAAATGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (32 bp):
GATTCTAGCATAAGAGAGCATTCTGCTCTCAG
Found at i:75292 original size:20 final size:20
Alignment explanation
Indices: 75260--75298 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
75250 AGCATGAAGT
*
75260 AAAATATAAAACTTATAAAG
1 AAAATATAAAACTAATAAAG
75280 AAAA-ATAACAACTAATAAA
1 AAAATATAA-AACTAATAAA
75299 TAGGAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.21
Consensus pattern (20 bp):
AAAATATAAAACTAATAAAG
Found at i:77306 original size:2 final size:2
Alignment explanation
Indices: 77299--77327 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
77289 ATTAATTACC
77299 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
77328 GTGGTCAGAC
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:78578 original size:308 final size:308
Alignment explanation
Indices: 78018--78827 Score: 1000
Period size: 308 Copynumber: 2.7 Consensus size: 308
78008 GAAGCTACTT
*
78018 TTTTTTTAGGAAAATAAGCTACTATCTTAAGTACATACTTAAGTAGCTAGTTAATTTTAGTTAAA
1 TTTTTTTAGGAAAAGAAGCTACTATCTTAAGTACATACTTAAGTAGCTAGTTAATTTTAGTTAAA
* *
78083 TATGTCATGATTTATACATGCGCTGTCATTTCTTTAAAAGAAATCATAGACTCAGTTTGTTGAGC
66 TATGTCATGA--TATACATGCGCTGTCATTTCTTTAAAAAAAATCATAGACTCAATTTGTTGAGC
*
78148 GTTACAGTCAAGACTTATAAAGATGCTACCATCTAAACTACATACTTAAGTAGCTGATTAATTTT
129 GTTACAGTCAAGACTTATAAAGATACTACCATCTAAACTACATACTTAAGTAGCTGATTAATTTT
*
78213 AGTTAAATATATCATAATTTATACATTATTTCTTAAACAAAAATTGTGGACTCAACTCATAAGCG
194 AGTTAAATATATCATAATTTATACATCATTTCTTAAACAAAAATTGTGGACTCAACTCATAAGCG
* * *
78278 TTACAGTCGATAATTATTAAGAAGCTATTTTTTTCACAAAAAAAAAGCTA
259 TTACAATCAATAATTATTAAGAAGCCATTTTTTTCACAAAAAAAAAGCTA
* *
78328 TTTTTTTAGGAAAAGAAGCTACTATCTTAAGTACATACTTAAGTAGTTGGTTAATTTTAGTTAAA
1 TTTTTTTAGGAAAAGAAGCTACTATCTTAAGTACATACTTAAGTAGCTAGTTAATTTTAGTTAAA
*
78393 TATGTCAT-A-ATACATGCGCTGTCATTT-TTTAAAAAAAATCATGGACTCAATTTGTTGAGCGT
66 TATGTCATGATATACATGCGCTGTCATTTCTTTAAAAAAAATCATAGACTCAATTTGTTGAGCGT
* * *
78455 TACAGTCAATACTTATTAAGATACTACCATCTAAACTACATAATTTATAAGTAGCTGATTAATTT
131 TACAGTCAAGACTTATAAAGATACTACCATCTAAACTACAT-A-CT-TAAGTAGCTGATTAATTT
* * * *
78520 TAGTTAATTATATCATGATTTATACATCATTTCTTAAACAGAAATTGTGGACTCAACTCATGAGC
193 TAGTTAAATATATCATAATTTATACATCATTTCTTAAACAAAAATTGTGGACTCAACTCATAAGC
78585 GTTACAATCAATAATTATTAAGAAGCCA-TTTTTT--------------TA
258 GTTACAATCAATAATTATTAAGAAGCCATTTTTTTCACAAAAAAAAAGCTA
*
78621 -------AGGAAAAGAAGCTACTATCTTAAGTACATACTTAAGTAGCTGGTTAATTTTAGTTAAA
1 TTTTTTTAGGAAAAGAAGCTACTATCTTAAGTACATACTTAAGTAGCTAGTTAATTTTAGTTAAA
* * * * * *
78679 TATGTCATAATTTATACATACACTGTCATTTC-TTAAAAAGAAATCCT-GAACTCAGTTTGCTGA
66 TATGTCATGA--TATACATGCGCTGTCATTTCTTTAAAAA-AAATCATAG-ACTCAATTTGTTGA
** * * * * * *
78742 GCGTTATGGTCAAAAATTATTAAGA-AGTTACCATCTTAACTACATA---AA-TAGCCGATTAAT
127 GCGTTACAGTCAAGACTTATAAAGATA-CTACCATCTAAACTACATACTTAAGTAGCTGATTAAT
*
78802 TTTAGTTAAATATATAATAATTTATA
191 TTTAGTTAAATATATCATAATTTATA
78828 TATTTTACAT
Statistics
Matches: 455, Mismatches: 34, Indels: 48
0.85 0.06 0.09
Matches are distributed among these distances:
284 34 0.07
285 2 0.00
286 65 0.14
287 1 0.00
290 26 0.06
291 55 0.12
293 2 0.00
305 70 0.15
306 19 0.04
307 7 0.02
308 103 0.23
309 1 0.00
310 70 0.15
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (308 bp):
TTTTTTTAGGAAAAGAAGCTACTATCTTAAGTACATACTTAAGTAGCTAGTTAATTTTAGTTAAA
TATGTCATGATATACATGCGCTGTCATTTCTTTAAAAAAAATCATAGACTCAATTTGTTGAGCGT
TACAGTCAAGACTTATAAAGATACTACCATCTAAACTACATACTTAAGTAGCTGATTAATTTTAG
TTAAATATATCATAATTTATACATCATTTCTTAAACAAAAATTGTGGACTCAACTCATAAGCGTT
ACAATCAATAATTATTAAGAAGCCATTTTTTTCACAAAAAAAAAGCTA
Found at i:78961 original size:21 final size:19
Alignment explanation
Indices: 78936--78978 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
78926 TATAATTGAC
78936 ATATACTATA-CATTTATAT
1 ATATA-TATATCATTTATAT
* *
78955 ATATATATATTATTTTTAT
1 ATATATATATCATTTATAT
78974 ATATA
1 ATATA
78979 ATTCCATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATATATATCATTTATAT
Found at i:83932 original size:3 final size:3
Alignment explanation
Indices: 83924--83949 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
83914 GGCTTAGAAT
83924 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
83950 TTGATGAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:86775 original size:47 final size:47
Alignment explanation
Indices: 86706--86894 Score: 337
Period size: 47 Copynumber: 4.0 Consensus size: 47
86696 ATCAGGTATC
86706 AAGCATTGTTCTTTGAATGCAAAATTTCTAGTTTCATAATTAAGGTT
1 AAGCATTGTTCTTTGAATGCAAAATTTCTAGTTTCATAATTAAGGTT
86753 AAGCATTGTTCTTTGAATGCAAAATTTCTAGTTTCATAATTAAGGTT
1 AAGCATTGTTCTTTGAATGCAAAATTTCTAGTTTCATAATTAAGGTT
86800 AAGCATTGTTCTTTGAATGCAAAATTTCTAGTTTCATAATTAAGGTT
1 AAGCATTGTTCTTTGAATGCAAAATTTCTAGTTTCATAATTAAGGTT
*
86847 AAGCATTGCTT-TTTGAATGGAAAATTTCTAGTTTC-TCAATTAAGGTT
1 AAGCATTG-TTCTTTGAATGCAAAATTTCTAGTTTCAT-AATTAAGGTT
86894 A
1 A
86895 TATGTTATGT
Statistics
Matches: 139, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
46 1 0.01
47 136 0.98
48 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (47 bp):
AAGCATTGTTCTTTGAATGCAAAATTTCTAGTTTCATAATTAAGGTT
Found at i:90966 original size:17 final size:17
Alignment explanation
Indices: 90930--90967 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
90920 GTAATAATCA
90930 ACTTAAACTAATCCGAAG
1 ACTTAAACTAAT-CGAAG
90948 ACTTAAAACTAAT-GAAG
1 ACTT-AAACTAATCGAAG
90965 ACT
1 ACT
90968 CTTAACATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (17 bp):
ACTTAAACTAATCGAAG
Found at i:91384 original size:2 final size:2
Alignment explanation
Indices: 91373--91402 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
91363 CACATCCAAT
91373 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
91403 TCTCTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:92101 original size:2 final size:2
Alignment explanation
Indices: 92094--92123 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
92084 TATGCAAGAT
92094 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
92124 CACAAATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:92418 original size:1 final size:1
Alignment explanation
Indices: 92412--92437 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
92402 TTTTAGTCTT
92412 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
92438 CTTAATTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:95994 original size:60 final size:60
Alignment explanation
Indices: 95899--96060 Score: 211
Period size: 60 Copynumber: 2.7 Consensus size: 60
95889 CTAATTGCTT
* *
95899 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAA-GAGCCTGATATTTTAATTTGACC
1 AAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGA-CCCGATATTTTAATTTGACC
* * * * *
95959 AAATAAGGACCTAATGTTTGCCAAAATGCTTAAATAAGGACCCGGTCTTTTAATTTGGCC
1 AAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGACCCGATATTTTAATTTGACC
* *
96019 AAATAAGGGCCTAATGTTAT-CGAAAATACTCAAATAAGGACC
1 AAATAAGGGCCTAATGTT-TGCCAAAATGCTCAAATAAGGACC
96061 TGACGTCAAT
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
60 86 0.97
61 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (60 bp):
AAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGACCCGATATTTTAATTTGACC
Found at i:95997 original size:31 final size:31
Alignment explanation
Indices: 95894--96000 Score: 87
Period size: 31 Copynumber: 3.5 Consensus size: 31
95884 ACCGGCTAAT
* * *
95894 TGCTTAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGACCTAATGTTTGCCAAAA
* * * **
95925 TGCTCAAATAA-GAGCCTGATATTT--TAATT
1 TGCTCAAATAAGGA-CCTAATGTTTGCCAAAA
95954 TGAC-CAAATAAGGACCTAATGTTTGCCAAAA
1 TG-CTCAAATAAGGACCTAATGTTTGCCAAAA
*
95985 TGCTTAAATAAGGACC
1 TGCTCAAATAAGGACC
96001 CGGTCTTTTA
Statistics
Matches: 56, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
29 19 0.34
30 5 0.09
31 32 0.57
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGACCTAATGTTTGCCAAAA
Found at i:96200 original size:60 final size:60
Alignment explanation
Indices: 96101--96262 Score: 184
Period size: 60 Copynumber: 2.7 Consensus size: 60
96091 TTCGACACCA
** * *
96101 GGCCCTTATTTGAGAATTTTTGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGAATTTTCAATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCG
* *
96161 GGCCCTTTTTTGAGTATTTTCAATAACATTA-GCCTCTTATTTGACCAAATTAAAAGATCG
1 GGCCCTTATTTGAGAATTTTCAATAACATTAGGCC-CTTATTTGACCAAATTAAAAGATCG
** ** * *
96221 AACCCTTATTTGATCATTTTGACA-AATATTAGGCCCTTATTT
1 GGCCCTTATTTGAGAATTTTCA-ATAACATTAGGCCCTTATTT
96263 AAGCAATTAG
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 3 0.03
60 79 0.92
61 4 0.05
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (60 bp):
GGCCCTTATTTGAGAATTTTCAATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCG
Found at i:97800 original size:21 final size:21
Alignment explanation
Indices: 97776--97827 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
97766 CAACACTGTA
*
97776 AAAAAAAAACGAAAATGAGAC
1 AAAAAAAAACGAAAACGAGAC
*
97797 AAAAACAAACGAAAACGAGAC
1 AAAAAAAAACGAAAACGAGAC
97818 AAAAACAAAA
1 AAAAA-AAAA
97828 AACTGAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.73, C:0.13, G:0.12, T:0.02
Consensus pattern (21 bp):
AAAAAAAAACGAAAACGAGAC
Found at i:102477 original size:12 final size:12
Alignment explanation
Indices: 102434--102481 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
102424 ACCATAATAT
102434 TATATTATTATA
1 TATATTATTATA
* * *
102446 TATAGTATAACA
1 TATATTATTATA
102458 TATGATTATTATA
1 TAT-ATTATTATA
102471 TATATTATTAT
1 TATATTATTAT
102482 TATTTGAAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
12 20 0.69
13 9 0.31
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (12 bp):
TATATTATTATA
Found at i:102812 original size:2 final size:2
Alignment explanation
Indices: 102805--102844 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
102795 GAATCTCTAG
102805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
102845 GGTTTAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.