Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022105.1 Corchorus olitorius cultivar O-4 contig22138, 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: 84862
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:2760 original size:1 final size:1
Alignment explanation
Indices: 2756--2782 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
2746 TCTTTTTTTT
2756 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
2783 GAAGGCTGCA
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2962 original size:17 final size:17
Alignment explanation
Indices: 2942--2987 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
2932 TTTATTATTG
* *
2942 TAAATATTTTAATAATT
1 TAAATATTTTAAAAAAT
2959 TAAAT-TTTTAAAAAAT
1 TAAATATTTTAAAAAAT
2975 T-AATA-TTTAAAAA
1 TAAATATTTTAAAAA
2988 GTATTTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 11 0.42
16 10 0.38
17 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATATTTTAAAAAAT
Found at i:4036 original size:37 final size:37
Alignment explanation
Indices: 3986--4059 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
3976 CTACATGATT
3986 AGCTACAATACCGATAATCTATGAGCCAACAAACCCC
1 AGCTACAATACCGATAATCTATGAGCCAACAAACCCC
4023 AGCTACAATACCGATAATCTATGAGCCAACAAACCCC
1 AGCTACAATACCGATAATCTATGAGCCAACAAACCCC
4060 TTCCCCAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.32, G:0.11, T:0.16
Consensus pattern (37 bp):
AGCTACAATACCGATAATCTATGAGCCAACAAACCCC
Found at i:4867 original size:179 final size:178
Alignment explanation
Indices: 4597--4935 Score: 504
Period size: 179 Copynumber: 1.9 Consensus size: 178
4587 CCAATTAAGG
* *
4597 TGATTTAAGTCTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGTAGGACTCGAAAACTA
1 TGATTCAAGTCTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
* * * *
4662 AATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAA-AATTTGTTGTTTTGCTTAACGGGAAATA
66 AATTTAATGTTTCAAGTATAAAAAATGCTTCC-AAAGAATTAGTTGTTTCGCTAAAC-GGAAATA
*
4726 GACGGTCCACTTAATATTATATAACTTT-TGCTCCAGATGTCTGATTGAGA
129 GACGGTCCACTTAATATTACATAA-TTTGTGCTCCAGATGTCTGATTGAGA
* * * *
4776 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTCTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
*
4841 AATTTAATG-TTCAAGGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTAAACGGAAATAG
66 AATTTAATGTTTCAA-GTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGCTAAACGGAAATAG
*
4905 ACGGTCTACTTAATATTACATAATTTGTGCT
130 ACGGTCCACTTAATATTACATAATTTGTGCT
4936 TATGGTGGAA
Statistics
Matches: 144, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
177 3 0.02
178 41 0.28
179 100 0.69
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (178 bp):
TGATTCAAGTCTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGCTAAACGGAAATAGA
CGGTCCACTTAATATTACATAATTTGTGCTCCAGATGTCTGATTGAGA
Found at i:14092 original size:45 final size:45
Alignment explanation
Indices: 14043--14172 Score: 251
Period size: 45 Copynumber: 2.9 Consensus size: 45
14033 CTAAATTCTA
14043 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
1 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
*
14088 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTC
1 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
14133 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
1 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
14173 ATTGTTGCTT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 83 1.00
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (45 bp):
CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
Found at i:19976 original size:2 final size:2
Alignment explanation
Indices: 19963--20003 Score: 55
Period size: 2 Copynumber: 19.5 Consensus size: 2
19953 ACTAAAAATA
*
19963 AT AT AT AGT AT AT AT AT AT AT AT AT AT CT AT ACT AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
20004 AAAGTACGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 31 0.89
3 4 0.11
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:19987 original size:19 final size:19
Alignment explanation
Indices: 19963--20003 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
19953 ACTAAAAATA
19963 ATATATAGTATATA-TATAT
1 ATATATA-TATATACTATAT
*
19982 ATATATATCTATACTATAT
1 ATATATATATATACTATAT
20001 ATA
1 ATA
20004 AAAGTACGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (19 bp):
ATATATATATATACTATAT
Found at i:21003 original size:22 final size:22
Alignment explanation
Indices: 20923--21006 Score: 100
Period size: 21 Copynumber: 3.9 Consensus size: 22
20913 TCTCACAGAG
*
20923 AGGTTATCAAAA-ATCATAGGA
1 AGGTTATCAAAATTTCATAGGA
20944 AGGTTA-CAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
* **
20965 AGGTTTATTAAAATTTCATAGTT
1 AGG-TTATCAAAATTTCATAGGA
*
20988 AGGTTATCAAAGTTTCATA
1 AGGTTATCAAAATTTCATA
21007 TTTCATAGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
20 5 0.09
21 17 0.31
22 17 0.31
23 15 0.28
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:21010 original size:29 final size:29
Alignment explanation
Indices: 20977--21035 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
20967 GTTTATTAAA
* ** *
20977 ATTTCATAGTTAGGTTATCAAAGTTTCAT
1 ATTTCATAGGTAAATTATCAAAATTTCAT
21006 ATTTCATAGGTAAATTATCAAAATTTCAT
1 ATTTCATAGGTAAATTATCAAAATTTCAT
21035 A
1 A
21036 GCGTGGTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (29 bp):
ATTTCATAGGTAAATTATCAAAATTTCAT
Found at i:21032 original size:22 final size:21
Alignment explanation
Indices: 21006--21079 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 21
20996 AAAGTTTCAT
*
21006 ATTTCATAGGTAAATTATCAAA
1 ATTTCATAGGT-AGTTATCAAA
*
21028 ATTTCATAGCGTGGTTATCAAA
1 ATTTCATAG-GTAGTTATCAAA
21050 ATTT-AGTAAGGTAGTTATCAAA
1 ATTTCA-T-AGGTAGTTATCAAA
21072 ATTTCATA
1 ATTTCATA
21080 AAAATATTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
21 2 0.04
22 38 0.84
23 5 0.11
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (21 bp):
ATTTCATAGGTAGTTATCAAA
Found at i:21363 original size:21 final size:21
Alignment explanation
Indices: 21326--21368 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
21316 TTTTCTTGTT
*
21326 TACTATATATAGCTTATATAA
1 TACTATATATAGATTATATAA
*
21347 TACTATATA-AGTATTATTTAA
1 TACTATATATAG-ATTATATAA
21368 T
1 T
21369 TGAGGTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (21 bp):
TACTATATATAGATTATATAA
Found at i:22181 original size:18 final size:18
Alignment explanation
Indices: 22158--22192 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22148 GTATCAAATA
*
22158 AAAGAAGTGATTTACAAT
1 AAAGAAGTAATTTACAAT
22176 AAAGAAGTAATTTACAA
1 AAAGAAGTAATTTACAA
22193 GATAAAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (18 bp):
AAAGAAGTAATTTACAAT
Found at i:27903 original size:15 final size:16
Alignment explanation
Indices: 27865--27933 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
27855 AAGTAATTTC
27865 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
*
27881 TCGAGTCATAT-GGG-T
1 TCGGGTCAT-TCGGGTT
27896 TCGGGTCATTCGGGTCT
1 TCGGGTCATTCGGGT-T
*
27913 T-GGGTC-TACCGGGTT
1 TCGGGTCAT-TCGGGTT
27928 TCGGGT
1 TCGGGT
27934 TGGACGAGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
14 1 0.02
15 15 0.34
16 25 0.57
17 3 0.07
ACGTcount: A:0.09, C:0.19, G:0.38, T:0.35
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:28746 original size:16 final size:16
Alignment explanation
Indices: 28725--28758 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
28715 TAGCTGCTAA
28725 AAAAATGATAATTTAG
1 AAAAATGATAATTTAG
28741 AAAAATGATAATTTAG
1 AAAAATGATAATTTAG
28757 AA
1 AA
28759 TAAGTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (16 bp):
AAAAATGATAATTTAG
Found at i:34362 original size:3 final size:3
Alignment explanation
Indices: 34354--34384 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
34344 GTCGACGTGC
34354 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
34385 CATTATTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:48519 original size:23 final size:23
Alignment explanation
Indices: 48493--48541 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
48483 CACAAACATC
48493 AATTAACATAATGTCTAATTTCT
1 AATTAACATAATGTCTAATTTCT
48516 AATTAACATAATGTCTAATTTCT
1 AATTAACATAATGTCTAATTTCT
48539 AAT
1 AAT
48542 GAAAAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (23 bp):
AATTAACATAATGTCTAATTTCT
Found at i:48757 original size:46 final size:46
Alignment explanation
Indices: 48688--48817 Score: 192
Period size: 46 Copynumber: 2.9 Consensus size: 46
48678 TTTAAGCGTG
* * * *
48688 TTAGTCGTATTTTAACACACATAGAAATTGAAACACGATACACATA
1 TTAGTCATGTTTTAACACACATAGAAATTGAAAAACGATACACACA
* *
48734 TTAGTCATGTTTTAACACGCATAGAAATTGAAATACGATACACACA
1 TTAGTCATGTTTTAACACACATAGAAATTGAAAAACGATACACACA
48780 TTAGTCATGTTTTAACACACA-A-AAATTGAAAAACGATA
1 TTAGTCATGTTTTAACACACATAGAAATTGAAAAACGATA
48818 ATCATAATTG
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 15 0.19
45 1 0.01
46 61 0.79
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (46 bp):
TTAGTCATGTTTTAACACACATAGAAATTGAAAAACGATACACACA
Found at i:56466 original size:21 final size:19
Alignment explanation
Indices: 56436--56476 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
56426 AACTTTGGTG
56436 CAAAACACAAAGCCCCATATA
1 CAAAACACAAA-CCCCA-ATA
*
56457 CAAAATACAAACCCCAATA
1 CAAAACACAAACCCCAATA
56476 C
1 C
56477 TGAAACAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 10 0.53
ACGTcount: A:0.54, C:0.34, G:0.02, T:0.10
Consensus pattern (19 bp):
CAAAACACAAACCCCAATA
Found at i:60132 original size:24 final size:26
Alignment explanation
Indices: 60105--60153 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
60095 GAGATGGTGT
60105 TTTCGCAGG-AAA-AAGCAAGAGAGC
1 TTTCGCAGGAAAAGAAGCAAGAGAGC
60129 TTTCGCAGGAAAAGAAGCAAGAGAG
1 TTTCGCAGGAAAAGAAGCAAGAGAG
60154 ATTAGCTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 9 0.39
25 3 0.13
26 11 0.48
ACGTcount: A:0.43, C:0.14, G:0.31, T:0.12
Consensus pattern (26 bp):
TTTCGCAGGAAAAGAAGCAAGAGAGC
Found at i:69415 original size:9 final size:9
Alignment explanation
Indices: 69393--69437 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
69383 AGGGCTATTT
69393 GATGATGAA
1 GATGATGAA
* *
69402 AATGAGGAA
1 GATGATGAA
69411 GATGATGAA
1 GATGATGAA
* *
69420 GATGGTGAT
1 GATGATGAA
69429 GATGATGAA
1 GATGATGAA
69438 ATTGATAATG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.36, T:0.22
Consensus pattern (9 bp):
GATGATGAA
Found at i:72320 original size:41 final size:41
Alignment explanation
Indices: 72263--72345 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
72253 TATATTTCTC
* *
72263 TTAAGGGATCAGTCGACAGAAAAGAGATAAGGCAGAAAGCT
1 TTAAGAGATCAGTCGACAGAAAAGAGATAACGCAGAAAGCT
72304 TTAAGAGATCAGTCGACAGAAAAGAGATAACGCAGAAAGCT
1 TTAAGAGATCAGTCGACAGAAAAGAGATAACGCAGAAAGCT
72345 T
1 T
72346 GTGATTCATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.45, C:0.13, G:0.27, T:0.16
Consensus pattern (41 bp):
TTAAGAGATCAGTCGACAGAAAAGAGATAACGCAGAAAGCT
Found at i:72330 original size:19 final size:19
Alignment explanation
Indices: 72269--72331 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
72259 TCTCTTAAGG
72269 GATCAGTCGACAGAAAAGA
1 GATCAGTCGACAGAAAAGA
* * * **
72288 GATAAGGCAGAAAGCTTTAAGA
1 GATCAGTC-GACAG--AAAAGA
72310 GATCAGTCGACAGAAAAGA
1 GATCAGTCGACAGAAAAGA
72329 GAT
1 GAT
72332 AACGCAGAAA
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
19 13 0.42
20 4 0.13
21 4 0.13
22 10 0.32
ACGTcount: A:0.46, C:0.13, G:0.27, T:0.14
Consensus pattern (19 bp):
GATCAGTCGACAGAAAAGA
Found at i:76476 original size:6 final size:6
Alignment explanation
Indices: 76465--76501 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
76455 GCTGGGGGGA
76465 TTTTCC TTTTCC TTTTCC TTTTTCC TTTTCC TTTTCC
1 TTTTCC TTTTCC TTTTCC -TTTTCC TTTTCC TTTTCC
76502 AACATTGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTCC
Found at i:76489 original size:13 final size:13
Alignment explanation
Indices: 76465--76499 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
76455 GCTGGGGGGA
76465 TTTTCC-TTTTCC
1 TTTTCCTTTTTCC
76477 TTTTCCTTTTTCC
1 TTTTCCTTTTTCC
76490 TTTTCCTTTT
1 TTTTCCTTTT
76500 CCAACATTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTCCTTTTTCC
Found at i:76489 original size:19 final size:19
Alignment explanation
Indices: 76465--76501 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
76455 GCTGGGGGGA
76465 TTTTCCTTTTCCTTTTCCT
1 TTTTCCTTTTCCTTTTCCT
76484 TTTTCCTTTTCCTTTTCC
1 TTTTCCTTTTCCTTTTCC
76502 AACATTGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTCCTTTTCCTTTTCCT
Found at i:83672 original size:21 final size:21
Alignment explanation
Indices: 83648--83750 Score: 82
Period size: 21 Copynumber: 4.8 Consensus size: 21
83638 CCAGAGTAAA
*
83648 TTCCTCATCATCATCTTCCTC
1 TTCCTCTTCATCATCTTCCTC
83669 TTCCTCTTCATC-TACTTCCTCC
1 TTCCTCTTCATCAT-CTTCCT-C
* *
83691 TCCTCCTCTTCCTCTTCTTCCTC
1 T--TCCTCTTCATCATCTTCCTC
* ** * *
83714 CTCCTCCACATAATCTTCATC
1 TTCCTCTTCATCATCTTCCTC
*
83735 TTCCTCTTCTTCATCT
1 TTCCTCTTCATCATCT
83751 GATGCACTTT
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
20 1 0.02
21 42 0.67
22 2 0.03
23 1 0.02
24 16 0.25
25 1 0.02
ACGTcount: A:0.11, C:0.45, G:0.00, T:0.45
Consensus pattern (21 bp):
TTCCTCTTCATCATCTTCCTC
Found at i:83686 original size:15 final size:15
Alignment explanation
Indices: 83664--83719 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
83654 ATCATCATCT
83664 TCCTCTTCCTCTTCA
1 TCCTCTTCCTCTTCA
* *
83679 T-CTACTTCCTCCTCC
1 TCCT-CTTCCTCTTCA
*
83694 TCCTCTTCCTCTTCT
1 TCCTCTTCCTCTTCA
*
83709 TCCTCCTCCTC
1 TCCTCTTCCTC
83720 CACATAATCT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
14 2 0.06
15 30 0.88
16 2 0.06
ACGTcount: A:0.04, C:0.52, G:0.00, T:0.45
Consensus pattern (15 bp):
TCCTCTTCCTCTTCA
Found at i:83904 original size:102 final size:102
Alignment explanation
Indices: 83714--83915 Score: 350
Period size: 102 Copynumber: 2.0 Consensus size: 102
83704 CTTCTTCCTC
* * *
83714 CTCCTCCACATAATCTTCATCTTCCTCTTCTTCATCTGATGCACTTTTCTGCTTTCGGGATTTTC
1 CTCCTCCACATAATCTTCATCTTCCTCTTCTTCATCCGAAGCACTTTTCCGCTTTCGGGATTTTC
83779 TACCCACAATCTTCATCTCCTTTGGTGAAGGCATCTT
66 TACCCACAATCTTCATCTCCTTTGGTGAAGGCATCTT
83816 CTCCTCCACATAATCTTCATCTTCCTCTTCTTCATCCGAAGCACTTTTCCGCTTTCGGGATTTTC
1 CTCCTCCACATAATCTTCATCTTCCTCTTCTTCATCCGAAGCACTTTTCCGCTTTCGGGATTTTC
** *
83881 TACCCACGGTCTTCCTCTCCTTTGGTGAAGGCATC
66 TACCCACAATCTTCATCTCCTTTGGTGAAGGCATC
83916 CGTCTAGCTT
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 94 1.00
ACGTcount: A:0.16, C:0.33, G:0.12, T:0.39
Consensus pattern (102 bp):
CTCCTCCACATAATCTTCATCTTCCTCTTCTTCATCCGAAGCACTTTTCCGCTTTCGGGATTTTC
TACCCACAATCTTCATCTCCTTTGGTGAAGGCATCTT
Found at i:84834 original size:2 final size:2
Alignment explanation
Indices: 84827--84861 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
84817 ATAAGAGTTA
84827 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
84862 A
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.