Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012328.1 Corchorus capsularis cultivar CVL-1 contig12349, 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: 122783
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:31 original size:2 final size:2
Alignment explanation
Indices: 26--67 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
16 AAAAAAGGGA
*
26 AT AT AT A- AT AT AT AT AT AT AT AT AA AT A- AT AT 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
66 AT
1 AT
68 GTATTTTCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:48 original size:17 final size:17
Alignment explanation
Indices: 26--66 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
16 AAAAAAGGGA
26 ATATAT-AATATATATAT
1 ATATATAAATA-ATATAT
43 ATATATAAATAATATAT
1 ATATATAAATAATATAT
60 ATATATA
1 ATATATA
67 TGTATTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATATAAATAATATAT
Found at i:3745 original size:167 final size:166
Alignment explanation
Indices: 3456--3777 Score: 581
Period size: 167 Copynumber: 1.9 Consensus size: 166
3446 TAAAATATTG
* *
3456 TACTAAACTTTGCTTTTCCCTAAATGGAAACTATAATCTACAACTATCAAAATTGACTTTAAAAT
1 TACTAAACTTTGATTTTCCCTAAATGGAAACTATAATCTACAACTATCAAAACTGACTTTAAAAT
*
3521 CAATGAAATGCATGAATTGACTCTGTAAAAAGTACCCAATTGCCAGAAATTATGTAATCAATCAT
66 CAATGAAATGCATGAATTGACTCTGTAAAAAGTACCCAATTGCCAGAAATGATGTAATCAATCAT
*
3586 GTGAAATACTTGTTAAAAATAAACTACTTCATGATT
131 GTGAAATACTTGTCAAAAATAAACTACTTCATGATT
* *
3622 TACTAAACTTTGATTTTCCCTAAATGGGAATTATAATCTACAACTATCAAAACTGACTTTAAAAA
1 TACTAAACTTTGATTTTCCCTAAATGGAAACTATAATCTACAACTATCAAAACTGACTTT-AAAA
3687 TCAATGAAATGCATGAATTGACTCTGTAAAAAGTACCCAATTGCCAGAAATGATGTAATCAATCA
65 TCAATGAAATGCATGAATTGACTCTGTAAAAAGTACCCAATTGCCAGAAATGATGTAATCAATCA
3752 TGTGAAATACTTGTCAAAAATAAACT
130 TGTGAAATACTTGTCAAAAATAAACT
3778 CTTTTGCATT
Statistics
Matches: 149, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
166 56 0.38
167 93 0.62
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (166 bp):
TACTAAACTTTGATTTTCCCTAAATGGAAACTATAATCTACAACTATCAAAACTGACTTTAAAAT
CAATGAAATGCATGAATTGACTCTGTAAAAAGTACCCAATTGCCAGAAATGATGTAATCAATCAT
GTGAAATACTTGTCAAAAATAAACTACTTCATGATT
Found at i:6988 original size:31 final size:31
Alignment explanation
Indices: 6945--7016 Score: 119
Period size: 31 Copynumber: 2.3 Consensus size: 31
6935 TACGCGTTAG
6945 TGAGCCTAAACCTTTCAAAAGTT-ACTCAATT
1 TGAGCCTAAACCTTTCAAAAGTTGAC-CAATT
*
6976 TGAGGCTAAACCTTTCAAAAGTTGACCAATT
1 TGAGCCTAAACCTTTCAAAAGTTGACCAATT
7007 TGAGCCTAAA
1 TGAGCCTAAA
7017 AAACAGGTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 36 0.95
32 2 0.05
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (31 bp):
TGAGCCTAAACCTTTCAAAAGTTGACCAATT
Found at i:10693 original size:43 final size:43
Alignment explanation
Indices: 10632--10718 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
10622 TCCTTTTTGG
10632 ATGGTCCGTTGGTCATGTGACTAACGGCCGCTAGTAATGTTGA
1 ATGGTCCGTTGGTCATGTGACTAACGGCCGCTAGTAATGTTGA
* *
10675 ATGGTCTGTTGGTCATGTGACTAACGGCCGTTAGTAATGTTGA
1 ATGGTCCGTTGGTCATGTGACTAACGGCCGCTAGTAATGTTGA
10718 A
1 A
10719 GTGGCTTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (43 bp):
ATGGTCCGTTGGTCATGTGACTAACGGCCGCTAGTAATGTTGA
Found at i:10839 original size:23 final size:23
Alignment explanation
Indices: 10813--10857 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
10803 TTTTTTCATT
*
10813 TTCTCTC-TCTCTCCTTTTTTTCC
1 TTCTCTCTTCT-TCCTTATTTTCC
*
10836 TTCTTTCTTCTTCCTTATTTTC
1 TTCTCTCTTCTTCCTTATTTTC
10858 TTACCCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.64
Consensus pattern (23 bp):
TTCTCTCTTCTTCCTTATTTTCC
Found at i:17354 original size:31 final size:31
Alignment explanation
Indices: 17317--17523 Score: 200
Period size: 31 Copynumber: 6.3 Consensus size: 31
17307 TAAGTAAGTT
*
17317 AGTAAGTCAGTAACTTAATTCAGGATAATTA
1 AGTAAGTCAGTAACTTAATTCAGGGTAATTA
*
17348 AGTAAGTAATAGGTAACTTAATTCAGGGTAATTA
1 AGTAAGT--CA-GTAACTTAATTCAGGGTAATTA
* * *
17382 AGTCAA-TAAATAGCTTAATTCAGGGTAATTA
1 AGT-AAGTCAGTAACTTAATTCAGGGTAATTA
*
17413 AGTAAGGCAGTAACTTAATTCAGGGTAATTA
1 AGTAAGTCAGTAACTTAATTCAGGGTAATTA
* * *
17444 AGTAATTCAGTAATCAACTTAAATCCATGGTAATTA
1 AGTAAGTCAG---T-AACTT-AATTCAGGGTAATTA
*
17480 AGTAAGTCAATAAGTAACTTAGTTCAGGGTAATTA
1 AGTAAGTC----AGTAACTTAATTCAGGGTAATTA
17515 AGTAAGTCA
1 AGTAAGTCA
17524 TTGATCGGCT
Statistics
Matches: 145, Mismatches: 17, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
30 2 0.01
31 60 0.41
32 1 0.01
33 1 0.01
34 26 0.18
35 27 0.19
36 25 0.17
37 1 0.01
40 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (31 bp):
AGTAAGTCAGTAACTTAATTCAGGGTAATTA
Found at i:17522 original size:35 final size:35
Alignment explanation
Indices: 17247--17523 Score: 261
Period size: 35 Copynumber: 8.0 Consensus size: 35
17237 GTGAATCGGT
* * *
17247 AATAAATAACTTAATTCAGGGTAATTAAGTAGGTT
1 AATAAGTAACTTAATTCAGGGTAATTAAGTAAGTC
* * *
17282 AGTGAA-TAATTTAATTCAGGGTAATTAAGTAAGTTAGT
1 AAT-AAGTAACTTAATTCAGGGTAATTAAGTAAG-T--C
* *
17320 AAGTCAGTAACTTAATTCAGGATAATTAAGTAAGT-
1 AA-TAAGTAACTTAATTCAGGGTAATTAAGTAAGTC
*
17355 AATAGGTAACTTAATTCAGGGTAA-T---TAAGTC
1 AATAAGTAACTTAATTCAGGGTAATTAAGTAAGTC
* * *
17386 AATAAATAGCTTAATTCAGGGTAATTAAGTAAGGC
1 AATAAGTAACTTAATTCAGGGTAATTAAGTAAGTC
*
17421 ----AGTAACTTAATTCAGGGTAATTAAGTAATTC
1 AATAAGTAACTTAATTCAGGGTAATTAAGTAAGTC
* * *
17452 AGTAA-TCAACTTAAATCCATGGTAATTAAGTAAGTC
1 AATAAGT-AACTT-AATTCAGGGTAATTAAGTAAGTC
*
17488 AATAAGTAACTTAGTTCAGGGTAATTAAGTAAGTC
1 AATAAGTAACTTAATTCAGGGTAATTAAGTAAGTC
17523 A
1 A
17524 TTGATCGGCT
Statistics
Matches: 199, Mismatches: 25, Indels: 36
0.77 0.10 0.14
Matches are distributed among these distances:
30 5 0.03
31 48 0.24
32 1 0.01
33 1 0.01
34 20 0.10
35 61 0.31
36 32 0.16
37 1 0.01
38 4 0.02
39 26 0.13
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.32
Consensus pattern (35 bp):
AATAAGTAACTTAATTCAGGGTAATTAAGTAAGTC
Found at i:50025 original size:158 final size:158
Alignment explanation
Indices: 49737--50055 Score: 620
Period size: 158 Copynumber: 2.0 Consensus size: 158
49727 CTTCTAAGGA
49737 TTACTTCTAGATTTCTAGACAACTATGAGGATTTTCTTGACTTCTTGTCTTTGATGAATTTGCCA
1 TTACTTCTAGATTTCTAGACAACTATGAGGATTTTCTTGACTTCTTGTCTTTGATGAATTTGCCA
49802 ACCCTTTGAACATTAGAAAAACTCTTATTAATAGTGTTCGAATTAGTAGTTAATTAACCTCTCAT
66 ACCCTTTGAACATTAGAAAAACTCTTATTAATAGTGTTCGAATTAGTAGTTAATTAACCTCTCAT
49867 CCGAATTAATTCAACATGTGAATTGCAT
131 CCGAATTAATTCAACATGTGAATTGCAT
49895 TTACTTCTAGATTTCTAGACAACTATGAGGATTTTCTTGACTTCTTGTCTTTGATGAATTTGCCA
1 TTACTTCTAGATTTCTAGACAACTATGAGGATTTTCTTGACTTCTTGTCTTTGATGAATTTGCCA
* *
49960 ACCCTTTGGACATTAGAAAAACTCTTTTTAATAGTGTTCGAATTAGTAGTTAATTAACCTCTCAT
66 ACCCTTTGAACATTAGAAAAACTCTTATTAATAGTGTTCGAATTAGTAGTTAATTAACCTCTCAT
50025 CCGAATTAATTCAACATGTGAATTGCAT
131 CCGAATTAATTCAACATGTGAATTGCAT
50053 TTA
1 TTA
50056 ATTTGTTCCC
Statistics
Matches: 159, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
158 159 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (158 bp):
TTACTTCTAGATTTCTAGACAACTATGAGGATTTTCTTGACTTCTTGTCTTTGATGAATTTGCCA
ACCCTTTGAACATTAGAAAAACTCTTATTAATAGTGTTCGAATTAGTAGTTAATTAACCTCTCAT
CCGAATTAATTCAACATGTGAATTGCAT
Found at i:61756 original size:30 final size:30
Alignment explanation
Indices: 61717--61793 Score: 136
Period size: 30 Copynumber: 2.6 Consensus size: 30
61707 AGGTGAAGAA
* *
61717 GGAGTTGGTGCCCAAGGGGAAGATGGAGCC
1 GGAGCTGGTGCCCAAGGGGAAGACGGAGCC
61747 GGAGCTGGTGCCCAAGGGGAAGACGGAGCC
1 GGAGCTGGTGCCCAAGGGGAAGACGGAGCC
61777 GGAGCTGGTGCCCAAGG
1 GGAGCTGGTGCCCAAGG
61794 TTCAGTTGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.22, C:0.21, G:0.47, T:0.10
Consensus pattern (30 bp):
GGAGCTGGTGCCCAAGGGGAAGACGGAGCC
Found at i:64019 original size:29 final size:30
Alignment explanation
Indices: 63973--64063 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 30
63963 AAAAAGGCTC
* *
63973 AAATTGAGAGTTCAAT-GGATAAAATGTCCA
1 AAATTAAGAGTTC-ATGGGACAAAATGTCCA
* *
64003 AAATTAAGAGTTCATGGGGCAAAACGTCCA
1 AAATTAAGAGTTCATGGGACAAAATGTCCA
**
64033 AAATTAA-AGTTTTTGGGACAAAATGTCCA
1 AAATTAAGAGTTCATGGGACAAAATGTCCA
64062 AA
1 AA
64064 CACTACAAGT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
29 22 0.42
30 30 0.58
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (30 bp):
AAATTAAGAGTTCATGGGACAAAATGTCCA
Found at i:65664 original size:51 final size:51
Alignment explanation
Indices: 65604--65758 Score: 256
Period size: 51 Copynumber: 3.0 Consensus size: 51
65594 AAGAAGGAGC
* * *
65604 TGGTGCCCAAGGGGAAGATGGAGCGGGAGCTGGTGCCCAAGGTTCAGTTGG
1 TGGTTCCCAAGGGGCAGATGGAGCAGGAGCTGGTGCCCAAGGTTCAGTTGG
* *
65655 TGGTTCCCAAGGGGCAGATGGAGTAGGAGCTGGTGCCCACGGTTCAGTTGG
1 TGGTTCCCAAGGGGCAGATGGAGCAGGAGCTGGTGCCCAAGGTTCAGTTGG
*
65706 TGGTTCCCAAGGGGCAGATGGAGCAGGAGCTGGTGCCCAAGGTTCAGCTGG
1 TGGTTCCCAAGGGGCAGATGGAGCAGGAGCTGGTGCCCAAGGTTCAGTTGG
65757 TG
1 TG
65759 TTGCTGGCGT
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 96 1.00
ACGTcount: A:0.19, C:0.19, G:0.43, T:0.19
Consensus pattern (51 bp):
TGGTTCCCAAGGGGCAGATGGAGCAGGAGCTGGTGCCCAAGGTTCAGTTGG
Found at i:65885 original size:90 final size:90
Alignment explanation
Indices: 65711--65876 Score: 260
Period size: 90 Copynumber: 1.8 Consensus size: 90
65701 GTTGGTGGTT
* * *
65711 CCCAAGGGGCAGATGGAGCAGGAGCTGGTGCCCAAGGTTCAGCTGGTGTTGCTGGCGTAGTTGGT
1 CCCAACGGGAAGATGGAGCAGGAGCTGGTGCCCAAGGTTCAGCTGGTGTTGCTGGCGTAGTTGGA
*
65776 ACCGAAGGTGGGTAAGGAGCCGGTG
66 ACCGAAGATGGGTAAGGAGCCGGTG
* *
65801 CCCAACGGGAAGATGGAGCAGGAGCTGGTGCCCAAGGTTCAGTTGGTGTTGCTGGGGTAGTTGGA
1 CCCAACGGGAAGATGGAGCAGGAGCTGGTGCCCAAGGTTCAGCTGGTGTTGCTGGCGTAGTTGGA
**
65866 ATTGAAGATGG
66 ACCGAAGATGG
65877 AGCCGGAGCT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 68 1.00
ACGTcount: A:0.20, C:0.17, G:0.42, T:0.20
Consensus pattern (90 bp):
CCCAACGGGAAGATGGAGCAGGAGCTGGTGCCCAAGGTTCAGCTGGTGTTGCTGGCGTAGTTGGA
ACCGAAGATGGGTAAGGAGCCGGTG
Found at i:65891 original size:90 final size:90
Alignment explanation
Indices: 65706--65896 Score: 258
Period size: 90 Copynumber: 2.1 Consensus size: 90
65696 GTTCAGTTGG
* * *
65706 TGGTTCCCAAGGGGCAGATGGAGCAGGAGCTGGTGCCCAAGGTTCAGCTGGTGTTGCTGGCGTAG
1 TGGTGCCCAACGGGAAGATGGAGCAGGAGCTGGTGCCCAAGGTTCAGCTGGTGTTGCTGGCGTAG
* *
65771 TTGGTACCGAAGGTGGGTAAGGAGC
66 TTGGAACCGAAGATGGGTAAGGAGC
* * *
65796 CGGTGCCCAACGGGAAGATGGAGCAGGAGCTGGTGCCCAAGGTTCAGTTGGTGTTGCTGGGGTAG
1 TGGTGCCCAACGGGAAGATGGAGCAGGAGCTGGTGCCCAAGGTTCAGCTGGTGTTGCTGGCGTAG
** **
65861 TTGGAATTGAAGATGGAG-CCGGAGC
66 TTGGAACCGAAGATGG-GTAAGGAGC
65886 TGGTGCCCAAC
1 TGGTGCCCAAC
65897 CATATGAATA
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
90 86 0.99
91 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.41, T:0.20
Consensus pattern (90 bp):
TGGTGCCCAACGGGAAGATGGAGCAGGAGCTGGTGCCCAAGGTTCAGCTGGTGTTGCTGGCGTAG
TTGGAACCGAAGATGGGTAAGGAGC
Found at i:67956 original size:36 final size:36
Alignment explanation
Indices: 67909--67983 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
67899 GCTCATATAT
67909 AGGTTGATGATCTTGTTTTGGATGAATAATGGAAAA
1 AGGTTGATGATCTTGTTTTGGATGAATAATGGAAAA
67945 AGGTTGATGATCTTGTTTTGGATGAATAATGGAAAA
1 AGGTTGATGATCTTGTTTTGGATGAATAATGGAAAA
67981 AGG
1 AGG
67984 AAAATAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (36 bp):
AGGTTGATGATCTTGTTTTGGATGAATAATGGAAAA
Found at i:69611 original size:21 final size:21
Alignment explanation
Indices: 69585--69625 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
69575 ATTTAATAAT
*
69585 TAATACTAGTACTTTGATTTG
1 TAATACTAGTACTATGATTTG
*
69606 TAATACTATTACTATGATTT
1 TAATACTAGTACTATGATTT
69626 TTTTGAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.49
Consensus pattern (21 bp):
TAATACTAGTACTATGATTTG
Found at i:70384 original size:18 final size:18
Alignment explanation
Indices: 70361--70395 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
70351 GGTGTGCCTT
70361 TCGCCATGGAATCTTGGA
1 TCGCCATGGAATCTTGGA
70379 TCGCCATGGAATCTTGG
1 TCGCCATGGAATCTTGG
70396 GTTTAAGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (18 bp):
TCGCCATGGAATCTTGGA
Found at i:71621 original size:15 final size:17
Alignment explanation
Indices: 71580--71636 Score: 75
Period size: 16 Copynumber: 3.5 Consensus size: 17
71570 TCAAATACCC
71580 GAACCCGAAAAAACTCA
1 GAACCCGAAAAAACTCA
71597 -AACCCGAAAAAA-TCA
1 GAACCCGAAAAAACTCA
* *
71612 GAACCCAAAAAAAC-CC
1 GAACCCGAAAAAACTCA
71628 GAACCCGAA
1 GAACCCGAA
71637 TCCAAAAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 3 0.09
16 32 0.91
ACGTcount: A:0.54, C:0.32, G:0.11, T:0.04
Consensus pattern (17 bp):
GAACCCGAAAAAACTCA
Found at i:71817 original size:32 final size:32
Alignment explanation
Indices: 71768--71852 Score: 134
Period size: 32 Copynumber: 2.7 Consensus size: 32
71758 AAAGGCTAAA
* *
71768 ACCCAAACTGAACCCGAACCCGAATTAACCTG
1 ACCCAAATTCAACCCGAACCCGAATTAACCTG
* *
71800 ACCCAAATTCAATCCGAACTCGAATTAACCTG
1 ACCCAAATTCAACCCGAACCCGAATTAACCTG
71832 ACCCAAATTCAACCCGAACCC
1 ACCCAAATTCAACCCGAACCC
71853 AACTTAAACC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.38, C:0.38, G:0.09, T:0.15
Consensus pattern (32 bp):
ACCCAAATTCAACCCGAACCCGAATTAACCTG
Found at i:71854 original size:17 final size:16
Alignment explanation
Indices: 71767--71869 Score: 84
Period size: 17 Copynumber: 6.3 Consensus size: 16
71757 AAAAGGCTAA
*
71767 AACCCAAACTGAACCCG
1 AACCCAAA-TTAACCCG
* *
71784 AACCCGAATTAACCTG
1 AACCCAAATTAACCCG
*
71800 -ACCCAAATTCAATCCG
1 AACCCAAATT-AACCCG
* * *
71816 AACTCGAATTAACCTG
1 AACCCAAATTAACCCG
71832 -ACCCAAATTCAACCCG
1 AACCCAAATT-AACCCG
*
71848 AACCCAACTTAAACCCG
1 AACCCAAATT-AACCCG
71865 AACCC
1 AACCC
71870 GAAAACCCGA
Statistics
Matches: 67, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
15 15 0.22
16 19 0.28
17 33 0.49
ACGTcount: A:0.39, C:0.38, G:0.09, T:0.15
Consensus pattern (16 bp):
AACCCAAATTAACCCG
Found at i:81595 original size:36 final size:36
Alignment explanation
Indices: 81548--81616 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
81538 AATAATACTC
81548 CAGACCAAGACAATGATTAGTTGATTTTAAATTACA
1 CAGACCAAGACAATGATTAGTTGATTTTAAATTACA
*
81584 CAGACCAAGACAATGATTAGTTTATTTTAAATT
1 CAGACCAAGACAATGATTAGTTGATTTTAAATT
81617 TAGTAAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (36 bp):
CAGACCAAGACAATGATTAGTTGATTTTAAATTACA
Found at i:81836 original size:33 final size:35
Alignment explanation
Indices: 81794--81877 Score: 136
Period size: 36 Copynumber: 2.4 Consensus size: 35
81784 GTTTTGTAAT
*
81794 TGTTTCACTTATTTTG-A-ACTTCAAAAGTTAAAA
1 TGTTTCACTTATTTTGAAGACCTCAAAAGTTAAAA
81827 TGTTTCACTTATTTTGAAAGACCTCAAAAGTTAAAA
1 TGTTTCACTTATTTTG-AAGACCTCAAAAGTTAAAA
81863 TGTTTCACTTATTTT
1 TGTTTCACTTATTTT
81878 TAATGGGGGG
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 16 0.34
35 1 0.02
36 30 0.64
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (35 bp):
TGTTTCACTTATTTTGAAGACCTCAAAAGTTAAAA
Found at i:85861 original size:23 final size:23
Alignment explanation
Indices: 85831--85896 Score: 109
Period size: 21 Copynumber: 3.0 Consensus size: 23
85821 TTCATCAAAA
85831 TTTATTTAAGTTGTAATTTTAAC
1 TTTATTTAAGTTGTAATTTTAAC
85854 TTTATTTAAGTTGT--TTTTAAC
1 TTTATTTAAGTTGTAATTTTAAC
*
85875 TTTATTTAAGTTGTAAATTTAA
1 TTTATTTAAGTTGTAATTTTAA
85897 GTTAAGTATA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
21 21 0.52
23 19 0.47
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (23 bp):
TTTATTTAAGTTGTAATTTTAAC
Found at i:88133 original size:16 final size:16
Alignment explanation
Indices: 88112--88156 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
88102 GGATCATTTG
88112 GGTTTGGGTCATTTTT
1 GGTTTGGGTCATTTTT
* **
88128 GGTTTGTGTGTTTTTT
1 GGTTTGGGTCATTTTT
88144 GGTTTTGGGTCAT
1 GG-TTTGGGTCAT
88157 ATGGTTCCAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.04, C:0.04, G:0.33, T:0.58
Consensus pattern (16 bp):
GGTTTGGGTCATTTTT
Found at i:89328 original size:29 final size:28
Alignment explanation
Indices: 89249--89334 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 28
89239 CCTATGTGGT
89249 AAGTTGCTCAATTTAGTACT-AAACTTTTA
1 AAGTTGCTCAA-TTAGTACTAAAAC-TTTA
*
89278 AAGAAACT-CTCAAATTAGTACTAAAACTTTA
1 AAG---TTGCTC-AATTAGTACTAAAACTTTA
89309 AAGTTGCTCAATTCAGTACTAAAACT
1 AAGTTGCTCAATT-AGTACTAAAACT
89335 CATCGAATTG
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
28 5 0.10
29 18 0.38
31 18 0.38
32 7 0.15
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (28 bp):
AAGTTGCTCAATTAGTACTAAAACTTTA
Found at i:89802 original size:29 final size:31
Alignment explanation
Indices: 89762--89841 Score: 101
Period size: 29 Copynumber: 2.6 Consensus size: 31
89752 CAAATTGTTG
89762 AGGTTTAGTACTAAATTGAGCATCTT-T-AA
1 AGGTTTAGTACTAAATTGAGCATCTTGTGAA
* *
89791 AGGTTTAGTACTAAATTGGGCATTTTGTGAA
1 AGGTTTAGTACTAAATTGAGCATCTTGTGAA
* **
89822 ATGTTTAGTGTTAAATTGAG
1 AGGTTTAGTACTAAATTGAG
89842 ATTTTAGCCC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 24 0.56
30 1 0.02
31 18 0.42
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (31 bp):
AGGTTTAGTACTAAATTGAGCATCTTGTGAA
Found at i:94060 original size:18 final size:18
Alignment explanation
Indices: 94034--94118 Score: 107
Period size: 18 Copynumber: 4.7 Consensus size: 18
94024 GGAACAGAAT
*
94034 CTGTATTCGGTGCAGGGA
1 CTGTGTTCGGTGCAGGGA
*
94052 CTGTGTTCGGTGCTGGGA
1 CTGTGTTCGGTGCAGGGA
* * *
94070 TTGTGTTTGGTGCTGGGA
1 CTGTGTTCGGTGCAGGGA
* *
94088 CTGTGTTTGGTGCAGGGG
1 CTGTGTTCGGTGCAGGGA
94106 CTGTGTTCGGTGC
1 CTGTGTTCGGTGC
94119 TAGGATTGAG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 59 1.00
ACGTcount: A:0.07, C:0.14, G:0.44, T:0.35
Consensus pattern (18 bp):
CTGTGTTCGGTGCAGGGA
Found at i:98548 original size:21 final size:20
Alignment explanation
Indices: 98517--98559 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
98507 CATCTATATC
98517 TATATCTATACTATACACTA
1 TATATCTATACTATACACTA
*
98537 TATATACTATACTATATACTA
1 TATAT-CTATACTATACACTA
98558 TA
1 TA
98560 ATATTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
TATATCTATACTATACACTA
Found at i:99413 original size:146 final size:143
Alignment explanation
Indices: 99238--99521 Score: 451
Period size: 146 Copynumber: 2.0 Consensus size: 143
99228 ATCTTTACCA
* * *
99238 TTTTACTATTTTTCATTAAAAACTTGGATATATTAAAAATTTTTAATATAAAGTTTTATTCTACT
1 TTTTACTATTTTACATTAAAAACTTGGATATATTAAAAAGTTTTAATATAAAGTTTTATTATACT
* * *
99303 AAAACCTCTATTTTTATTTAATTAAATTCAATATTTTAATAATTATTTTATTTTTACCATTTTAA
66 AAAAACTCTATTTTCATTTAATTAAATTCAATATTTTAATAATTATTTTATGTTTACCATTTTAA
99368 TTTAAAAGTCTAT
131 TTTAAAAGTCTAT
*
99381 TTTTACTATTTTACTATTTTAAAAACTTGGATATATTAAAAAGTTTTAATATACAGTTTTATTAT
1 TTTTACTATTTTAC-A--TTAAAAACTTGGATATATTAAAAAGTTTTAATATAAAGTTTTATTAT
* * *
99446 ATTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATGTTTACTATTT
63 ACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTAATAATTATTTTATGTTTACCATTT
99511 TAATTTAAAAG
128 TAATTTAAAAG
99522 GTTATTGTGG
Statistics
Matches: 128, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
143 13 0.10
144 1 0.01
146 114 0.89
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (143 bp):
TTTTACTATTTTACATTAAAAACTTGGATATATTAAAAAGTTTTAATATAAAGTTTTATTATACT
AAAAACTCTATTTTCATTTAATTAAATTCAATATTTTAATAATTATTTTATGTTTACCATTTTAA
TTTAAAAGTCTAT
Found at i:100183 original size:20 final size:20
Alignment explanation
Indices: 100158--100199 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
100148 TCGCTGCGCA
**
100158 ATGGTTTATTTTGTAATGTC
1 ATGGTTTATTTTACAATGTC
100178 ATGGTTTATTTTACAATGTC
1 ATGGTTTATTTTACAATGTC
100198 AT
1 AT
100200 ATCAAGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.52
Consensus pattern (20 bp):
ATGGTTTATTTTACAATGTC
Found at i:102934 original size:6 final size:6
Alignment explanation
Indices: 102923--102975 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
102913 AAATTGAATC
* *
102923 ATCTAT ATCTAT ATCTAT ATCTAT AGTATCT ATCTAT A-C--T ATCTAT
1 ATCTAT ATCTAT ATCTAT ATCTAT A-TCTAT ATCTAT ATCTAT ATCTAT
102969 A-CTAT AT
1 ATCTAT AT
102976 ATAAAAGTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
3 2 0.05
4 1 0.03
5 6 0.16
6 25 0.66
7 4 0.11
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.47
Consensus pattern (6 bp):
ATCTAT
Found at i:102958 original size:13 final size:13
Alignment explanation
Indices: 102928--102974 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
102918 GAATCATCTA
102928 TATCTATATCTA--
1 TATCTATA-CTATC
*
102940 TATCTATAGTATC
1 TATCTATACTATC
102953 TATCTATACTATC
1 TATCTATACTATC
102966 TATACTATA
1 TAT-CTATA
102975 TATAAAAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 2 0.07
12 8 0.27
13 15 0.50
14 5 0.17
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.47
Consensus pattern (13 bp):
TATCTATACTATC
Found at i:106720 original size:13 final size:13
Alignment explanation
Indices: 106702--106735 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
106692 AAAGAAATTT
106702 AGGTATTAGGTGA
1 AGGTATTAGGTGA
*
106715 AGGTATTTGGGTGA
1 AGGTA-TTAGGTGA
106729 AGGTATT
1 AGGTATT
106736 TGGGTGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.35
Consensus pattern (13 bp):
AGGTATTAGGTGA
Found at i:106729 original size:14 final size:14
Alignment explanation
Indices: 106710--106742 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
106700 TTAGGTATTA
106710 GGTGAAGGTATTTG
1 GGTGAAGGTATTTG
106724 GGTGAAGGTATTTG
1 GGTGAAGGTATTTG
106738 GGTGA
1 GGTGA
106743 TTATGCCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.33
Consensus pattern (14 bp):
GGTGAAGGTATTTG
Found at i:107810 original size:146 final size:146
Alignment explanation
Indices: 107644--107909 Score: 451
Period size: 146 Copynumber: 1.8 Consensus size: 146
107634 CTATTTTTCA
* *
107644 TTAAAAACTAGGATATATTAAAATTTTTTAATCTACAGTTTTATTCTACTAAAAACTCTATTTTC
1 TTAAAAACTAGGATATATTAAAATTTTTTAATATACAATTTTATTCTACTAAAAACTCTATTTTC
* ** *
107709 ATTTAATTAAATTCATTATTTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAGTTGATCT
66 ATTTAATTAAATTCAATAACTTTATAATTATTTTATTTTTACCACTTTAATTTAAAAGTTGATCT
107774 TTACCATTTTACTATT
131 TTACCATTTTACTATT
* *
107790 TTAAAAACTTGGATATATTAAAATTTTTTAATATATAATTTTATTCTACTAAAAACTCTATTTTC
1 TTAAAAACTAGGATATATTAAAATTTTTTAATATACAATTTTATTCTACTAAAAACTCTATTTTC
*
107855 ATTTAATTAAATTCAATAACTTTATAATTATTTTATTTTTACTACTTTAATTTAA
66 ATTTAATTAAATTCAATAACTTTATAATTATTTTATTTTTACCACTTTAATTTAA
107910 CAGGTTGTTG
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
146 111 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (146 bp):
TTAAAAACTAGGATATATTAAAATTTTTTAATATACAATTTTATTCTACTAAAAACTCTATTTTC
ATTTAATTAAATTCAATAACTTTATAATTATTTTATTTTTACCACTTTAATTTAAAAGTTGATCT
TTACCATTTTACTATT
Found at i:111533 original size:187 final size:188
Alignment explanation
Indices: 110988--111549 Score: 1013
Period size: 188 Copynumber: 3.0 Consensus size: 188
110978 AAAAAAAAAA
*
110988 TTTTGGATTGATGGAGATGGGACCCACCAAGGGTATCTTTCTTCCAAAGTTCCCAAAATGCCTTT
1 TTTTGGATAGATGGAGATGGGACCCACCAAGGGTATCTTTCTTCCAAAGTTCCCAAAATGCCTTT
111053 GGTCATCAACTCAAATTACAAAAGAACCAAGCAT-AAATGACCAAAATACCCCTCCCAATTTGTG
66 GGTCATCAACTCAAATTACAAAAGAACCAAGCATAAAATGACCAAAATACCCCTCCCAATTTGTG
111117 CATGAATTCATAAGATCAAATCTTTTGATTGGTTTGTTTTGGTAATTTCAC-TCCTAT
131 CATGAATTCATAAGATCAAATCTTTTGATTGGTTTGTTTTGGTAATTTCACTTCCTAT
* * *
111174 TTTTGGGTAGATGGAGATGGTACCCACCAAGGGTATCTTTCTTCCAAAGTTCCCAAACTGCCTTT
1 TTTTGGATAGATGGAGATGGGACCCACCAAGGGTATCTTTCTTCCAAAGTTCCCAAAATGCCTTT
111239 GGTCATCAACTCAAATTACAAAAGAACCAAGCATAAAATGACCAAAATACCCCTCCCAATTTGTG
66 GGTCATCAACTCAAATTACAAAAGAACCAAGCATAAAATGACCAAAATACCCCTCCCAATTTGTG
111304 CATGAATTCATAAGATCAAATCTTTTGATTGGTTTGTTTTGGTAATTTCACTTCCTAT
131 CATGAATTCATAAGATCAAATCTTTTGATTGGTTTGTTTTGGTAATTTCACTTCCTAT
111362 TTTTGGATAGATGGAGATGGGACCCACCAAGGGTATCTTTCTTCCAAAGTTCCCAAAATGCCTTT
1 TTTTGGATAGATGGAGATGGGACCCACCAAGGGTATCTTTCTTCCAAAGTTCCCAAAATGCCTTT
* * * *
111427 GATCATCAACTCAAATTACAAAATAACCAAGCATAAAATGACTAAAATACCCCTCCCAATTTATG
66 GGTCATCAACTCAAATTACAAAAGAACCAAGCATAAAATGACCAAAATACCCCTCCCAATTTGTG
* *
111492 CATGAATTCATAAGATCAAATCTTTTGATTAGTTT-TTTTGGTAACTTCACTTCCTAT
131 CATGAATTCATAAGATCAAATCTTTTGATTGGTTTGTTTTGGTAATTTCACTTCCTAT
111549 T
1 T
111550 CTTAATGTTT
Statistics
Matches: 361, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
186 95 0.26
187 103 0.29
188 163 0.45
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.33
Consensus pattern (188 bp):
TTTTGGATAGATGGAGATGGGACCCACCAAGGGTATCTTTCTTCCAAAGTTCCCAAAATGCCTTT
GGTCATCAACTCAAATTACAAAAGAACCAAGCATAAAATGACCAAAATACCCCTCCCAATTTGTG
CATGAATTCATAAGATCAAATCTTTTGATTGGTTTGTTTTGGTAATTTCACTTCCTAT
Found at i:113687 original size:25 final size:27
Alignment explanation
Indices: 113626--113687 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
113616 AATAGACTTA
**
113626 ATTTTTCCTTTGTTAGGCGTAGAAAATT
1 ATTTTTCCTGGGTTAGGCGTAG-AAATT
113654 ATTTTTCCTGGGTTAGGCGTAG-AA-T
1 ATTTTTCCTGGGTTAGGCGTAGAAATT
113679 ATTTTTCCT
1 ATTTTTCCT
113688 TTTTTGGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 10 0.31
26 2 0.06
28 20 0.62
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (27 bp):
ATTTTTCCTGGGTTAGGCGTAGAAATT
Done.