Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023774.1 Corchorus olitorius cultivar O-4 contig23807, 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: 87980
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1560 original size:13 final size:12
Alignment explanation
Indices: 1539--1568 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1529 CCGAAAATCA
1539 TTTTTTTGAAAT
1 TTTTTTTGAAAT
1551 TTTTTATTGAAAT
1 TTTTT-TTGAAAT
1564 TTTTT
1 TTTTT
1569 GAAAAAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTTTTTGAAAT
Found at i:2758 original size:22 final size:22
Alignment explanation
Indices: 2706--2758 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
2696 ATAATCATAT
**
2706 TATGAAATTTTGATAATCTCCC
1 TATGAAATTTCAATAATCTCCC
* *
2728 TA-CATAATTTCAATAATCTTCC
1 TATGA-AATTTCAATAATCTCCC
2750 TATGAAATT
1 TATGAAATT
2759 AATTTTATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
21 1 0.04
22 22 0.92
23 1 0.04
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.42
Consensus pattern (22 bp):
TATGAAATTTCAATAATCTCCC
Found at i:2850 original size:22 final size:21
Alignment explanation
Indices: 2788--2993 Score: 80
Period size: 22 Copynumber: 9.5 Consensus size: 21
2778 TCTATGATTT
* * *
2788 TTTGATAACTTCCCTATAAAAA
1 TTTGATAACCTCCATAT-GAAA
* *
2810 TTTCATAACCACACA-ATGAAA
1 TTTGATAACCTC-CATATGAAA
2831 CTTTGATAACCTCCATATGAAA
1 -TTTGATAACCTCCATATGAAA
*
2853 TTTCGATAGCCTCGC-TATGAAA
1 TTT-GATAACCTC-CATATGAAA
* * *
2875 TTTTAGTAATCTCCCTATGAAA
1 TTTGA-TAACCTCCATATGAAA
* * * *
2897 TTTTTATAACCAT-AAAATAAAA
1 -TTTGATAACC-TCCATATGAAA
* **
2919 TTTGATAATCTCTGTATGAAAA
1 TTTGATAACCTCCATATG-AAA
* * * *
2941 TTCGATAATCATAC-TATCAAA
1 TTTGATAA-CCTCCATATGAAA
*
2962 TTTGGAT-ACCTCCTTATGAAA
1 TTT-GATAACCTCCATATGAAA
2983 TTTCGATAACC
1 TTT-GATAACC
2994 ACAACTAAAA
Statistics
Matches: 136, Mismatches: 33, Indels: 30
0.68 0.17 0.15
Matches are distributed among these distances:
20 4 0.03
21 38 0.28
22 85 0.62
23 9 0.07
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (21 bp):
TTTGATAACCTCCATATGAAA
Found at i:4331 original size:22 final size:22
Alignment explanation
Indices: 4306--4349 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
4296 AAATTAAATT
4306 TCATAGCAATTACGCGGTAAAA
1 TCATAGCAATTACGCGGTAAAA
4328 TCATAGCAATTACGCGGTAAAA
1 TCATAGCAATTACGCGGTAAAA
4350 ATGAAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (22 bp):
TCATAGCAATTACGCGGTAAAA
Found at i:4967 original size:44 final size:44
Alignment explanation
Indices: 4912--5034 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 44
4902 TAGTAGTTCC
* ** * *
4912 CTATGAAATTTTGATTATTACAC-TATAAAATTTTGATGACCTTG
1 CTATGAAATTTTGATAACCAC-CTTATAAAAGTTTGATAACCTTG
* *
4956 CTATAAAATTTTGATAACCACCTTATGAAAGTTTGATAACCTTG
1 CTATGAAATTTTGATAACCACCTTATAAAAGTTTGATAACCTTG
* * * *
5000 CTATGAAATTTTGATAATCTCCCTATGAAAGTTTG
1 CTATGAAATTTTGATAACCACCTTATAAAAGTTTG
5035 GTTACTTCCC
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
43 1 0.01
44 66 0.99
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCACCTTATAAAAGTTTGATAACCTTG
Found at i:5025 original size:22 final size:22
Alignment explanation
Indices: 4909--5034 Score: 101
Period size: 22 Copynumber: 5.7 Consensus size: 22
4899 TTCTAGTAGT
* *
4909 TCCCTATGAAATTTTGATTA-T
1 TCCCTATGAAATTTTGATAACC
* * *
4930 TACACTATAAAATTTTGATGACC
1 T-CCCTATGAAATTTTGATAACC
** *
4953 TTGCTATAAAATTTTGATAACC
1 TCCCTATGAAATTTTGATAACC
* * *
4975 ACCTTATGAAAGTTTGATAACC
1 TCCCTATGAAATTTTGATAACC
** *
4997 TTGCTATGAAATTTTGATAATC
1 TCCCTATGAAATTTTGATAACC
*
5019 TCCCTATGAAAGTTTG
1 TCCCTATGAAATTTTG
5035 GTTACTTCCC
Statistics
Matches: 81, Mismatches: 22, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
21 1 0.01
22 79 0.98
23 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (22 bp):
TCCCTATGAAATTTTGATAACC
Found at i:5137 original size:22 final size:22
Alignment explanation
Indices: 5094--5137 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5084 CATGCACACT
* * *
5094 ATGAAATTTTGATAATCTCATA
1 ATGAAATTTTGACAACCACATA
5116 ATGAAATTTTGACAACCACATA
1 ATGAAATTTTGACAACCACATA
5138 GATACAACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (22 bp):
ATGAAATTTTGACAACCACATA
Found at i:6289 original size:96 final size:96
Alignment explanation
Indices: 6125--6324 Score: 249
Period size: 96 Copynumber: 2.1 Consensus size: 96
6115 ATATCATCAA
* * ** * * * *
6125 TGGGACTAACGCCAGAAGCAGAAGCTACAAGTTATTTTGGATAAGGTATTTAGTTGAAGCAAGTA
1 TGGGATTAACGCCAGAACCAGAAGCTACAAGCCATTGTAGATAAGGTATTCAGTTGAAGCAAGGA
* * * *
6190 TTAGTGCGAATAATGTGGAACATGACTTTAG
66 TTAGTGCAAAGAATGAGGAACATCACTTTAG
*
6221 TGGGATTAACGCCAGAACCAGAAGAC-ACAAGCCATTGTAGATAAGGTATTCGGTTGAAGCAAGG
1 TGGGATTAACGCCAGAACCAGAAG-CTACAAGCCATTGTAGATAAGGTATTCAGTTGAAGCAAGG
*
6285 ATTAGTGCAAAGAATGAGGAGCATCACTTTAG
65 ATTAGTGCAAAGAATGAGGAACATCACTTTAG
*
6317 TAGGATTA
1 TGGGATTA
6325 CCAGAAATCG
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
96 87 0.99
97 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.25
Consensus pattern (96 bp):
TGGGATTAACGCCAGAACCAGAAGCTACAAGCCATTGTAGATAAGGTATTCAGTTGAAGCAAGGA
TTAGTGCAAAGAATGAGGAACATCACTTTAG
Found at i:6537 original size:76 final size:76
Alignment explanation
Indices: 6411--6559 Score: 189
Period size: 76 Copynumber: 2.0 Consensus size: 76
6401 TCAACGCCAT
*
6411 AAATTGACAGATTTGAAAGACTTGCGATTAATGAGGAATATGACCGTTGGAGGCAAATCT-AAGT
1 AAATTGACAGATTCGAAAGACTTGCGATTAATGAGGAATATGACCGTTGGAGGCAAATCTGAA-T
*
6475 ATTTAAGGAAAC
65 ATATAAGGAAAC
* * *
6487 AAATTGACAGATTCGACAA-ATTTGC-ATTTAATGTGGAGA-ATGACCGTTGGAGGCAGATCTGA
1 AAATTGACAGATTCGA-AAGACTTGCGA-TTAATGAGGA-ATATGACCGTTGGAGGCAAATCTGA
6549 ATATATAAGGA
63 ATATATAAGGA
6560 CCCAAAAGAA
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
75 1 0.02
76 58 0.91
77 5 0.08
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (76 bp):
AAATTGACAGATTCGAAAGACTTGCGATTAATGAGGAATATGACCGTTGGAGGCAAATCTGAATA
TATAAGGAAAC
Found at i:6746 original size:19 final size:20
Alignment explanation
Indices: 6693--6750 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 20
6683 GCTGCTCTAA
*
6693 TAATCTCATTTGTACAGTACCG
1 TAATCTCATATGTACAGT--CG
*
6715 -AATCTAATATGTACAGT-G
1 TAATCTCATATGTACAGTCG
*
6733 TAATCTCATCTGTACAGT
1 TAATCTCATATGTACAGT
6751 TGCTAAACAG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
21 15 0.48
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
TAATCTCATATGTACAGTCG
Found at i:13091 original size:41 final size:41
Alignment explanation
Indices: 13034--13340 Score: 422
Period size: 41 Copynumber: 7.5 Consensus size: 41
13024 TAATTTCCAA
*
13034 AATCA-GGAGTCAAATTGAACCAATTAATAAG-TATTAACCTC
1 AATCAGGGAG-CAAATTGAACCAATTAA-AAGAAATTAACCTC
* * **
13075 AATCAAGGATG-AAATTGAATCAATTAAAAGATTTTAACCTC
1 AATCAGGGA-GCAAATTGAACCAATTAAAAGAAATTAACCTC
* * * *
13116 AATAAGGGAGCAAATCGAAGCAATTAAAAGATATTAACCTC
1 AATCAGGGAGCAAATTGAACCAATTAAAAGAAATTAACCTC
*
13157 AATCAGGGAGCAAATCGAACCAATTAAAAGAAATTAACCTC
1 AATCAGGGAGCAAATTGAACCAATTAAAAGAAATTAACCTC
* * *
13198 AATTAGGGAGCAAATCGAACCGATTAAAAGAAATTAACCTC
1 AATCAGGGAGCAAATTGAACCAATTAAAAGAAATTAACCTC
*
13239 AATCAGGGAGCAAATTGAATCAATTAAAAGAAATTAACCTC
1 AATCAGGGAGCAAATTGAACCAATTAAAAGAAATTAACCTC
* *
13280 AATCAGGGAGCAAATTGAATCAATTAAAAGACATTAACCTC
1 AATCAGGGAGCAAATTGAACCAATTAAAAGAAATTAACCTC
13321 AATCAGGGAGCAAATTGAAC
1 AATCAGGGAGCAAATTGAAC
13341 AAGAAAAAAT
Statistics
Matches: 244, Mismatches: 18, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
40 4 0.02
41 236 0.97
42 3 0.01
43 1 0.00
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (41 bp):
AATCAGGGAGCAAATTGAACCAATTAAAAGAAATTAACCTC
Found at i:13177 original size:23 final size:23
Alignment explanation
Indices: 13151--13218 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 23
13141 AAAAGATATT
*
13151 AACCTCAATCAGGGAGCAAATCG
1 AACCTCAATTAGGGAGCAAATCG
** *
13174 AA-C-CAATTA-AAAG-AAAT-T
1 AACCTCAATTAGGGAGCAAATCG
13192 AACCTCAATTAGGGAGCAAATCG
1 AACCTCAATTAGGGAGCAAATCG
13215 AACC
1 AACC
13219 GATTAAAAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
18 2 0.06
19 5 0.15
20 8 0.24
21 7 0.21
22 5 0.15
23 6 0.18
ACGTcount: A:0.46, C:0.22, G:0.16, T:0.16
Consensus pattern (23 bp):
AACCTCAATTAGGGAGCAAATCG
Found at i:15940 original size:15 final size:15
Alignment explanation
Indices: 15920--15949 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15910 TCTATTCCTT
*
15920 GTAAAATAGGAAATA
1 GTAAAATAGAAAATA
15935 GTAAAATAGAAAATA
1 GTAAAATAGAAAATA
15950 CCATGTGTGA
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:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (15 bp):
GTAAAATAGAAAATA
Found at i:18843 original size:17 final size:17
Alignment explanation
Indices: 18823--18857 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18813 AAGGGGTAAT
*
18823 TAAAAAAATTGTTTTCA
1 TAAAAAAAGTGTTTTCA
*
18840 TAAAAGAAGTGTTTTCA
1 TAAAAAAAGTGTTTTCA
18857 T
1 T
18858 GATAGAGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (17 bp):
TAAAAAAAGTGTTTTCA
Found at i:19727 original size:19 final size:18
Alignment explanation
Indices: 19703--19738 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19693 TGAAGATTTA
19703 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
19722 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
19739 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:21839 original size:14 final size:14
Alignment explanation
Indices: 21820--21847 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21810 GGTATTACTA
21820 CTGTTCCTTTGGAT
1 CTGTTCCTTTGGAT
21834 CTGTTCCTTTGGAT
1 CTGTTCCTTTGGAT
21848 TGCTATTATG
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:0.07, C:0.21, G:0.21, T:0.50
Consensus pattern (14 bp):
CTGTTCCTTTGGAT
Found at i:26189 original size:21 final size:21
Alignment explanation
Indices: 26163--26219 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
26153 GTTACCGGGC
*
26163 ATGGCCGGGCATGAG-GCTCGG
1 ATGGCCGGGCATG-GTGCGCGG
26184 ATGGCCGGGCATGGTGCGCGG
1 ATGGCCGGGCATGGTGCGCGG
*
26205 ATGGCTGGGCA-GGTG
1 ATGGCCGGGCATGGTG
26220 TCTCGGCGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 5 0.15
21 28 0.85
ACGTcount: A:0.12, C:0.21, G:0.51, T:0.16
Consensus pattern (21 bp):
ATGGCCGGGCATGGTGCGCGG
Found at i:31328 original size:29 final size:29
Alignment explanation
Indices: 31294--31461 Score: 205
Period size: 29 Copynumber: 5.8 Consensus size: 29
31284 ACCTAGGGTA
* * **
31294 TGCAAAAACGACCAAAATGCCCCAGAACA
1 TGCAAAAATGACCAAAATGCCCCTGAATG
* *
31323 TGCAAAAATAACCAAAATGCCCCTAAATG
1 TGCAAAAATGACCAAAATGCCCCTGAATG
** *
31352 TGCAAAAAATGACCAAAATGCTTCTGGATG
1 TGC-AAAAATGACCAAAATGCCCCTGAATG
* * *
31382 CGCAAAAATGACCAAAATACCCCTGGATG
1 TGCAAAAATGACCAAAATGCCCCTGAATG
31411 TGC--AAATGACCAAAATGCCCCTGAATG
1 TGCAAAAATGACCAAAATGCCCCTGAATG
31438 TGCAAAAATGACCAAAATGCCCCT
1 TGCAAAAATGACCAAAATGCCCCT
31462 TGGTATGCGA
Statistics
Matches: 118, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 25 0.21
29 70 0.59
30 23 0.19
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.16
Consensus pattern (29 bp):
TGCAAAAATGACCAAAATGCCCCTGAATG
Found at i:31366 original size:59 final size:58
Alignment explanation
Indices: 31294--31461 Score: 205
Period size: 59 Copynumber: 2.9 Consensus size: 58
31284 ACCTAGGGTA
* * ** *
31294 TGCAAAAACGACCAAAATGCCCCAGAACATGCAAAAATAACCAAAATGCCCCTAAATG
1 TGCAAAAATGACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCCTAAATG
** * * * **
31352 TGCAAAAAATGACCAAAATGCTTCTGGATGCGCAAAAATGACCAAAATACCCCTGGATG
1 TGC-AAAAATGACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCCTAAATG
31411 TGC--AAATGACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCCT
1 TGCAAAAATGACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCCT
31462 TGGTATGCGA
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
56 43 0.47
58 3 0.03
59 46 0.50
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.16
Consensus pattern (58 bp):
TGCAAAAATGACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCCTAAATG
Found at i:31475 original size:56 final size:56
Alignment explanation
Indices: 31303--31475 Score: 177
Period size: 56 Copynumber: 3.0 Consensus size: 56
31293 ATGCAAAAAC
* ** * ***
31303 GACCAAAATGCCCCAGAACATGCAAAAATAACCAAAATGCCCCTAAATGTGCAAAAAAT
1 GACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCCTTGGTGTGC---AAAT
** * * *
31362 GACCAAAATGCTTCTGGATGCGCAAAAATGACCAAAATACCCC-TGGATGTGCAAAT
1 GACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCCTTGG-TGTGCAAAT
* *
31418 GACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCCTTGGTATGCGAAT
1 GACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCCTTGGTGTGCAAAT
31474 GA
1 GA
31476 TCAATTAAGA
Statistics
Matches: 93, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
56 51 0.55
57 3 0.03
59 39 0.42
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (56 bp):
GACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCCTTGGTGTGCAAAT
Found at i:31796 original size:59 final size:60
Alignment explanation
Indices: 31709--32108 Score: 522
Period size: 59 Copynumber: 6.6 Consensus size: 60
31699 TGAAATATAG
* *
31709 ACTCTC-AATCAGAGACCTCGAGCAGGATTTTAAAAACCAGATAAGA-TTTTGAATTGAAA
1 ACTCTCTAA-CAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTTGAATTGAAA
* * *
31768 TCTCTCTAACAGAGACCTCGAACAGGATTTTAAAAAAACAGAATAAGA-TTTTGACTTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACA-AG-ATAAGATTTTTGAATTGAAA
* * *
31829 ACTCTCTAACAAAGACCTCGAACAGGATTTTTTTAAAAAACCATATAAGATTTTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGA---TTTT-AAAAACAAGATAAGA-TTTTTGAATTGAAA
** * *
31894 ACTCTCTAACAGAGACCTCGAACAAAATTTTAAAAACAAGATAAGA-TTTTCACTTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTTGAATTGAAA
*
31953 ACTCTCTAACAGAGATCTCGAACAGGATTTTAAAAACAAGATAAGATTTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTTGAATTGAAA
* *
32013 ACTCTCTAATAGAGACCTCGAACATGA-TTTAAAAACAAGATAAGATTTTTGAATTGAAAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTTGAATTG--AAA
* *
32074 ACTCTCTAACAGAGACCTCGAACATGATTTCAAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAA
32109 GAGAAAGGGG
Statistics
Matches: 300, Mismatches: 28, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
59 114 0.38
60 39 0.13
61 85 0.28
62 10 0.03
63 6 0.02
64 5 0.02
65 41 0.14
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (60 bp):
ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTTGAATTGAAA
Found at i:32992 original size:36 final size:35
Alignment explanation
Indices: 32952--33111 Score: 178
Period size: 41 Copynumber: 4.3 Consensus size: 35
32942 TTTTTATTTA
* *
32952 TTTTTTTTTTCTGACCTCTCTCTGTTTTAGG-CCAAG
1 TTTTTTTTTT-TGACCTCTTTCTATTTTAGGTCC-AG
32988 TTTTTTCTTTTTGACCTCTTTCTATTTTAGGTCCAG
1 TTTTTT-TTTTTGACCTCTTTCTATTTTAGGTCCAG
33024 TTTTTTTCTTTTTCGACCTCTTTCTATTTTAGGTCCAG
1 -TTTTTT-TTTTT-GACCTCTTTCTATTTTAGGTCCAG
33062 TTTTTCTTCTTTTTTTCGACCTCTTTCTATTTTAGGTCCAG
1 ---TT-TT-TTTTTTT-GACCTCTTTCTATTTTAGGTCCAG
*
33103 CTTTTTTTT
1 TTTTTTTTT
33112 AGCTCCTTTT
Statistics
Matches: 113, Mismatches: 3, Indels: 16
0.86 0.02 0.12
Matches are distributed among these distances:
36 31 0.27
37 20 0.18
38 25 0.22
40 3 0.03
41 32 0.28
42 2 0.02
ACGTcount: A:0.10, C:0.21, G:0.11, T:0.59
Consensus pattern (35 bp):
TTTTTTTTTTTGACCTCTTTCTATTTTAGGTCCAG
Found at i:33030 original size:38 final size:38
Alignment explanation
Indices: 32952--33110 Score: 218
Period size: 38 Copynumber: 4.1 Consensus size: 38
32942 TTTTTATTTA
* *
32952 TTTTT-TTTTTCTGACCTCTCTCTGTTTTAGG-CCAAG-T
1 TTTTTCTTTTTC-GACCTCTTTCTATTTTAGGTCC-AGTT
32989 TTTTTCTTTTT-GACCTCTTTCTATTTTAGGTCCAGTT
1 TTTTTCTTTTTCGACCTCTTTCTATTTTAGGTCCAGTT
33026 TTTTTCTTTTTCGACCTCTTTCTATTTTAGGTCCAGTT
1 TTTTTCTTTTTCGACCTCTTTCTATTTTAGGTCCAGTT
33064 TTTCTTCTTTTTTTCGACCTCTTTCTATTTTAGGTCCAGCTT
1 TTT-TTC--TTTTTCGACCTCTTTCTATTTTAGGTCCAG-TT
33106 TTTTT
1 TTTTT
33111 TAGCTCCTTT
Statistics
Matches: 112, Mismatches: 2, Indels: 12
0.89 0.02 0.10
Matches are distributed among these distances:
36 19 0.17
37 19 0.17
38 34 0.30
39 3 0.03
41 32 0.29
42 5 0.04
ACGTcount: A:0.10, C:0.21, G:0.11, T:0.58
Consensus pattern (38 bp):
TTTTTCTTTTTCGACCTCTTTCTATTTTAGGTCCAGTT
Found at i:33099 original size:79 final size:75
Alignment explanation
Indices: 32952--33111 Score: 218
Period size: 79 Copynumber: 2.1 Consensus size: 75
32942 TTTTTATTTA
*
32952 TTTTTTTTTTCTGACCTCTCTCTGTTTTAGGCCAAGTTTTTTCTTTTTGACCTCTTTCTATTTTA
1 TTTTTTTTTTCTGACCTCTCTCTATTTTAGGCCAAGTTTTTTCTTTTTGACCTCTTTCTATTTTA
33017 GGTCCAG-TT
66 GGTCCAGCTT
*
33026 TTTTTCTTTTTC-GACCTCTTTCTATTTTAGGTCC-AGTTTTTCTTCTTTTTTTCGACCTCTTTC
1 TTTTT-TTTTTCTGACCTCTCTCTATTTTAGG-CCAAG-TTTT-TTC--TTTTT-GACCTCTTTC
33089 TATTTTAGGTCCAGCTT
59 TATTTTAGGTCCAGCTT
33106 TTTTTT
1 TTTTTT
33112 AGCTCCTTTT
Statistics
Matches: 76, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
74 24 0.32
75 12 0.16
76 3 0.04
78 5 0.07
79 25 0.33
80 7 0.09
ACGTcount: A:0.10, C:0.21, G:0.11, T:0.59
Consensus pattern (75 bp):
TTTTTTTTTTCTGACCTCTCTCTATTTTAGGCCAAGTTTTTTCTTTTTGACCTCTTTCTATTTTA
GGTCCAGCTT
Found at i:45093 original size:41 final size:41
Alignment explanation
Indices: 45036--45342 Score: 413
Period size: 41 Copynumber: 7.5 Consensus size: 41
45026 TAATTTCCAA
*
45036 AATCA-GGAGTCAAATTGAACCAATTAATAAG-TATTAACCTC
1 AATCAGGGAG-CAAATTGAACCAATTAA-AAGAAATTAACCTC
* * *
45077 AATCAAGGA-CGAAATTGAATCAATTAAAAGATATTAACCTC
1 AATCAGGGAGC-AAATTGAACCAATTAAAAGAAATTAACCTC
* *
45118 AATCAGGGAGCAAATCGAACCAATTAAAAGATATTAACCTC
1 AATCAGGGAGCAAATTGAACCAATTAAAAGAAATTAACCTC
* *
45159 AATCAGGGAGAAAATCGAACCAATTAAAAGAAATTAACCTC
1 AATCAGGGAGCAAATTGAACCAATTAAAAGAAATTAACCTC
* *
45200 AATCAGGGAGCAAATCGAACCGATTAAAAGAAATTAACCTC
1 AATCAGGGAGCAAATTGAACCAATTAAAAGAAATTAACCTC
* * *
45241 AATCAGGGAGCAAATTGAATCAATTAAAAGAAATTAAACTT
1 AATCAGGGAGCAAATTGAACCAATTAAAAGAAATTAACCTC
* * * *
45282 AATCAGGGAGCAAACTGAATCATTTAAAAGACATTAACCTC
1 AATCAGGGAGCAAATTGAACCAATTAAAAGAAATTAACCTC
45323 AATCAGGGAGCAAATTGAAC
1 AATCAGGGAGCAAATTGAAC
45343 AAGAAAACAA
Statistics
Matches: 242, Mismatches: 20, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
40 4 0.02
41 234 0.97
42 4 0.02
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (41 bp):
AATCAGGGAGCAAATTGAACCAATTAAAAGAAATTAACCTC
Found at i:46399 original size:17 final size:17
Alignment explanation
Indices: 46377--46410 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
46367 TCCCCTTAGT
46377 TGTAATTTTCATTTTCC
1 TGTAATTTTCATTTTCC
46394 TGTAATTTTCATTTTCC
1 TGTAATTTTCATTTTCC
46411 CTTTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59
Consensus pattern (17 bp):
TGTAATTTTCATTTTCC
Found at i:46759 original size:14 final size:14
Alignment explanation
Indices: 46740--46767 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46730 GGTATTACTA
46740 CTGTTCCTTTGGAT
1 CTGTTCCTTTGGAT
46754 CTGTTCCTTTGGAT
1 CTGTTCCTTTGGAT
46768 TGCTATTCAG
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:0.07, C:0.21, G:0.21, T:0.50
Consensus pattern (14 bp):
CTGTTCCTTTGGAT
Found at i:47498 original size:18 final size:19
Alignment explanation
Indices: 47465--47500 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
47455 TGAAGATTTA
47465 TTGAAGACAAATTGAAGAT
1 TTGAAGACAAATTGAAGAT
*
47484 TTGAAGAC-CATTGAAGA
1 TTGAAGACAAATTGAAGA
47501 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.25
Consensus pattern (19 bp):
TTGAAGACAAATTGAAGAT
Found at i:48837 original size:35 final size:36
Alignment explanation
Indices: 48798--48867 Score: 90
Period size: 35 Copynumber: 1.9 Consensus size: 36
48788 GAGGGTTTTC
48798 TTAATTATTTTC-TCAATTTATCTT-TTGCTTTCTGA
1 TTAATTATTTTCTTCAATTT-TCTTATTGCTTTCTGA
* *
48833 TTAATTGTTTTCTTTAATTTTCTTGATTGCTTTCT
1 TTAATTATTTTCTTCAATTTTCTT-ATTGCTTTCT
48868 TAGATAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 15 0.50
36 6 0.20
37 9 0.30
ACGTcount: A:0.17, C:0.13, G:0.07, T:0.63
Consensus pattern (36 bp):
TTAATTATTTTCTTCAATTTTCTTATTGCTTTCTGA
Found at i:50001 original size:59 final size:55
Alignment explanation
Indices: 49933--50096 Score: 152
Period size: 59 Copynumber: 2.9 Consensus size: 55
49923 GGGTATAAAA
*
49933 AAATGACCAAAATGCCCTAGAACATGCAAAAATGACCAAAATGGCCCTGAATGTGC
1 AAATAACCAAAATGCCCTAGAAC-TGCAAAAATGACCAAAATGGCCCTGAATGTGC
* * * * *
49989 AAAAATTAACCAAAATGCTTCTGGATGC-GCAAAAATGACCAAAAT-GCCCTTGGATGTTC
1 --AAA-TAACCAAAATGC-CCTAGA-ACTGCAAAAATGACCAAAATGGCCC-TGAATGTGC
* ** *
50048 AAATGACCAAAATGCCCCTAGATGTGCAAAAATGACCAAAATGCCCCTG
1 AAATAACCAAAATG-CCCTAGAACTGCAAAAATGACCAAAATGGCCCTG
50097 GGTATGCGAA
Statistics
Matches: 87, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
56 33 0.38
57 7 0.08
58 7 0.08
59 35 0.40
60 4 0.05
61 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (55 bp):
AAATAACCAAAATGCCCTAGAACTGCAAAAATGACCAAAATGGCCCTGAATGTGC
Found at i:50094 original size:29 final size:29
Alignment explanation
Indices: 49931--50095 Score: 176
Period size: 29 Copynumber: 5.7 Consensus size: 29
49921 TAGGGTATAA
**
49931 AAAAATGACCAAAATG-CCCTAGAACATGC
1 AAAAATGACCAAAATGCCCCTAG-ATGTGC
*
49960 AAAAATGACCAAAATGGCCCT-GAATGTGC
1 AAAAATGACCAAAATGCCCCTAG-ATGTGC
* ** * *
49989 AAAAATTAACCAAAATGCTTCTGGATGCGC
1 AAAAA-TGACCAAAATGCCCCTAGATGTGC
* * *
50019 AAAAATGACCAAAATGCCCTTGGATGTTC
1 AAAAATGACCAAAATGCCCCTAGATGTGC
50048 --AAATGACCAAAATGCCCCTAGATGTGC
1 AAAAATGACCAAAATGCCCCTAGATGTGC
50075 AAAAATGACCAAAATGCCCCT
1 AAAAATGACCAAAATGCCCCT
50096 GGGTATGCGA
Statistics
Matches: 115, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
27 24 0.21
29 64 0.56
30 26 0.23
31 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (29 bp):
AAAAATGACCAAAATGCCCCTAGATGTGC
Found at i:50109 original size:56 final size:56
Alignment explanation
Indices: 49933--50097 Score: 188
Period size: 56 Copynumber: 2.9 Consensus size: 56
49923 GGGTATAAAA
** * *
49933 AAATGACCAAAATG-CCCTAGAACATGCAAAAATGACCAAAATGGCCCTGAATGTGC
1 AAATGACCAAAATGCCCCTAG-ATGTGCAAAAATGACCAAAATGCCCCTGGATGTGC
* ** * * * *
49989 AAAAATTAACCAAAATGCTTCTGGATGCGCAAAAATGACCAAAATGCCCTTGGATGTTC
1 --AAA-TGACCAAAATGCCCCTAGATGTGCAAAAATGACCAAAATGCCCCTGGATGTGC
50048 AAATGACCAAAATGCCCCTAGATGTGCAAAAATGACCAAAATGCCCCTGG
1 AAATGACCAAAATGCCCCTAGATGTGCAAAAATGACCAAAATGCCCCTGG
50098 GTATGCGAAT
Statistics
Matches: 88, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
56 41 0.47
57 3 0.03
58 3 0.03
59 38 0.43
60 3 0.03
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.19
Consensus pattern (56 bp):
AAATGACCAAAATGCCCCTAGATGTGCAAAAATGACCAAAATGCCCCTGGATGTGC
Found at i:54919 original size:96 final size:96
Alignment explanation
Indices: 54731--54929 Score: 247
Period size: 96 Copynumber: 2.1 Consensus size: 96
54721 ATCAAAAAAG
* * * * * **
54731 GGGACTAACGCCAGAAGCAGAAGCTACAAGTTATTTTGGATAAAGTATTCAGTTGAAGCAATTAT
1 GGGATTAACGCCAGAACCAGAAGCTACAAGTCATTGTAGATAAAGTATTCAGTTGAAGCAAGGAT
* * *
54796 TAGTGCTAACAATGTGGAACATGACTTTAGT
66 TAGTGCCAACAATGAGGAACATCACTTTAGT
* * *
54827 GGGATTAACGCCATAACCAGAAGAC-ACAAGTCATTGTAGATAAGGTATTCGGTTGAAGCAAGGA
1 GGGATTAACGCCAGAACCAGAAG-CTACAAGTCATTGTAGATAAAGTATTCAGTTGAAGCAAGGA
* *
54891 TTAGTGCCAACAGTGAGGAGCATCACTTTAGT
65 TTAGTGCCAACAATGAGGAACATCACTTTAGT
54923 GGGATTA
1 GGGATTA
54930 CCAGAAATCG
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
96 86 0.99
97 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.26
Consensus pattern (96 bp):
GGGATTAACGCCAGAACCAGAAGCTACAAGTCATTGTAGATAAAGTATTCAGTTGAAGCAAGGAT
TAGTGCCAACAATGAGGAACATCACTTTAGT
Found at i:57830 original size:2 final size:2
Alignment explanation
Indices: 57788--57819 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
57778 ATTCTTTAGT
57788 TA 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 TA
57820 AAAGTATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:63778 original size:22 final size:23
Alignment explanation
Indices: 63729--63775 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
63719 TTATCAAATT
63729 AAATTCGTTGCAAATTTGGTTGC
1 AAATTCGTTGCAAATTTGGTTGC
* *
63752 TAATT-GTTGTAAATTTGG-TGC
1 AAATTCGTTGCAAATTTGGTTGC
63773 AAA
1 AAA
63776 ATTTGACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
21 5 0.24
22 12 0.57
23 4 0.19
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (23 bp):
AAATTCGTTGCAAATTTGGTTGC
Found at i:68718 original size:22 final size:21
Alignment explanation
Indices: 68639--68856 Score: 79
Period size: 22 Copynumber: 9.8 Consensus size: 21
68629 GTCTTTGTGT
68639 GGTTATCAAAATTTCATAAGGA
1 GGTTATC-AAATTTCATAAGGA
** **
68661 GAATATTTTAATTTCATAAGGA
1 GGTTA-TCAAATTTCATAAGGA
* *
68683 GGTTATCAATATTTTATATGGA
1 GGTTATCAA-ATTTCATAAGGA
*
68705 GGTTATCAGAATTTC-TTAGGAA
1 GGTTATCA-AATTTCATAAGG-A
**
68727 TATTATCAAAATTTCAT--GGTA
1 GGTTATC-AAATTTCATAAGG-A
* * *
68748 TGGTTACCAAAATTTC-TTAGAA
1 -GGTTATC-AAATTTCATAAGGA
*
68770 TGGTTACCAAAATTTCAT-AGGAA
1 -GGTTATC-AAATTTCATAAGG-A
* *
68793 TGTTATCGAAATTTCATAGAGTA
1 GGTTATC-AAATTTCATA-AGGA
*
68816 -GTTATCAAAATTTCATAGGGCCA
1 GGTTATC-AAATTTCATAAGG--A
*
68839 GGTTATTATAATTTCATA
1 GGTTATCA-AATTTCATA
68857 GGTAGCTGGT
Statistics
Matches: 150, Mismatches: 29, Indels: 32
0.71 0.14 0.15
Matches are distributed among these distances:
21 10 0.07
22 114 0.76
23 10 0.07
24 16 0.11
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (21 bp):
GGTTATCAAATTTCATAAGGA
Found at i:68753 original size:44 final size:44
Alignment explanation
Indices: 68705--68834 Score: 140
Period size: 44 Copynumber: 2.9 Consensus size: 44
68695 TTTATATGGA
*
68705 GGTTATCAGAATTTCTTAGGAATATTATCAAAATTTCAT-GGTAT
1 GGTTATCAGAATTTCTTA-GAATATTATCAAAATTTCATAGGAAT
* * * *
68749 GGTTACCAAAATTTCTTAGAATGGTTACCAAAATTTCATAGGAAT
1 GGTTATCAGAATTTCTTAGAAT-ATTATCAAAATTTCATAGGAAT
* *
68794 -GTTATC-GAAATTTCATAGAGTAGTTATCAAAATTTCATAGG
1 GGTTATCAG-AATTTCTTAGAATA-TTATCAAAATTTCATAGG
68835 GCCAGGTTAT
Statistics
Matches: 71, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
43 4 0.06
44 63 0.89
45 4 0.06
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (44 bp):
GGTTATCAGAATTTCTTAGAATATTATCAAAATTTCATAGGAAT
Found at i:68917 original size:44 final size:43
Alignment explanation
Indices: 68866--68970 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 43
68856 AGGTAGCTGG
* * *
68866 TTATCAAAATTTCATAGCGAGATTAACAGAATTTCAT-GGTATA-A
1 TTATCAAAATTTAATAGCGAGATT-ACAAAATTTAATAGG-A-AGA
*
68910 TTATCAAAATTTTATAAG-GAGATTACAAAATTTAATAGGAAGA
1 TTATCAAAATTTAAT-AGCGAGATTACAAAATTTAATAGGAAGA
68953 TTATCAAAATTTAATAGC
1 TTATCAAAATTTAATAGC
68971 ACATAAAAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
42 3 0.06
43 26 0.49
44 22 0.42
45 2 0.04
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (43 bp):
TTATCAAAATTTAATAGCGAGATTACAAAATTTAATAGGAAGA
Found at i:68940 original size:21 final size:22
Alignment explanation
Indices: 68866--68969 Score: 92
Period size: 22 Copynumber: 4.8 Consensus size: 22
68856 AGGTAGCTGG
*
68866 TTATCAAAATTTCATAGCG-AGA
1 TTATCAAAATTTAATAG-GAAGA
* * *
68888 TTAACAGAATTTCAT-GGTATA-A
1 TTATCAAAATTTAATAGG-A-AGA
*
68910 TTATCAAAATTTTATAAGG-AGA
1 TTATCAAAATTTAAT-AGGAAGA
68932 TTA-CAAAATTTAATAGGAAGA
1 TTATCAAAATTTAATAGGAAGA
68953 TTATCAAAATTTAATAG
1 TTATCAAAATTTAATAG
68970 CACATAAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
20 4 0.06
21 18 0.26
22 43 0.63
23 1 0.01
24 2 0.03
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTAATAGGAAGA
Found at i:71558 original size:123 final size:127
Alignment explanation
Indices: 71420--71664 Score: 408
Period size: 131 Copynumber: 1.9 Consensus size: 127
71410 ACTTTTATAA
71420 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-CTT-TA-TA-ATTTTTAC
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACTATATTTTTAC
71481 CATTTTACTATTTAAATTAAAAAACTTATATATATTAGAATTTTTTAAATATACTGTTACAG
66 CATTTTACTATTTAAATTAAAAAACTTATATATATTAGAATTTTTTAAATATACTGTTACAG
*
71543 TTTTATTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACTTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAC-TA---TATTT
*
71608 TTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATA
62 TTACCATTTTACTATTTAAATTAAAAAACTTATATATATTAGAATTTTTTAAATATA
71665 TTTCTTAAAT
Statistics
Matches: 112, Mismatches: 2, Indels: 8
0.92 0.02 0.07
Matches are distributed among these distances:
123 45 0.40
124 3 0.03
125 2 0.02
127 2 0.02
131 60 0.54
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (127 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACTATATTTTTAC
CATTTTACTATTTAAATTAAAAAACTTATATATATTAGAATTTTTTAAATATACTGTTACAG
Found at i:71686 original size:14 final size:13
Alignment explanation
Indices: 71650--71688 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
71640 TATATATTAG
71650 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
71663 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
71677 AATTTTTTAAAT
1 AATTTTTTAAAT
71689 TTTACATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:74215 original size:21 final size:21
Alignment explanation
Indices: 74172--74216 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
74162 CAAAGAAACC
* * **
74172 TTAAGAAAAGTTTTTTTTTTT
1 TTAAAAAAAGTTTTGTTGATT
74193 TTAAAAAAAGTTTTGTTGATT
1 TTAAAAAAAGTTTTGTTGATT
74214 TTA
1 TTA
74217 TAAAGGGTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (21 bp):
TTAAAAAAAGTTTTGTTGATT
Found at i:80771 original size:48 final size:48
Alignment explanation
Indices: 80709--80830 Score: 131
Period size: 49 Copynumber: 2.5 Consensus size: 48
80699 AATTTTGTAC
* * *
80709 AAAAATTGATAAAAAGAGCAATGAAAAGTAAATATTCAATTTTATCT-T
1 AAAAATTGAGAAAAAGAGCAAGGAAAAGTAAAGATTCAATTTTAT-TGT
* * * * *
80757 AAAAATTGAGAAAAAGGTGCGAGGAAAATTAAAGGTTCAATTTTGTTGT
1 AAAAATTGAGAAAAA-GAGCAAGGAAAAGTAAAGATTCAATTTTATTGT
*
80806 AAAAATTGAGAAAAAGTGC-AGGAAA
1 AAAAATTGAGAAAAAGAGCAAGGAAA
80831 TATAAAAGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
47 6 0.09
48 19 0.30
49 39 0.61
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.26
Consensus pattern (48 bp):
AAAAATTGAGAAAAAGAGCAAGGAAAAGTAAAGATTCAATTTTATTGT
Found at i:84463 original size:11 final size:11
Alignment explanation
Indices: 84447--84471 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
84437 GAAAAAAATT
84447 ATTATTTAATA
1 ATTATTTAATA
84458 ATTATTTAATA
1 ATTATTTAATA
84469 ATT
1 ATT
84472 TTCGGTCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTATTTAATA
Found at i:84783 original size:19 final size:19
Alignment explanation
Indices: 84745--84783 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
84735 ATTAAATAAT
* * *
84745 AATGAATGAATTACAGTTA
1 AATGAATAAATTAAAATTA
84764 AATGAATAAATTAAAATTA
1 AATGAATAAATTAAAATTA
84783 A
1 A
84784 CTTGTATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (19 bp):
AATGAATAAATTAAAATTA
Found at i:86095 original size:35 final size:36
Alignment explanation
Indices: 86033--86101 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
86023 GTAAGGTTCT
*
86033 CTCTCTTGCAAGCCACTCAGAGGTCACTCATATTAAC
1 CTCTCTTGCAAACCAC-CAGAGGTCACTCATATTAAC
86070 CTCTCTTGCAAACCA-CAGAGGTCACTCATATT
1 CTCTCTTGCAAACCACCAGAGGTCACTCATATT
86102 CTCGAAATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 17 0.55
37 14 0.45
ACGTcount: A:0.28, C:0.32, G:0.13, T:0.28
Consensus pattern (36 bp):
CTCTCTTGCAAACCACCAGAGGTCACTCATATTAAC
Done.