Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011792.1 Corchorus capsularis cultivar CVL-1 contig11813, 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: 160054
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3077 original size:20 final size:21
Alignment explanation
Indices: 3038--3079 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3028 TTACAAAGAA
*
3038 AACTCACAATTGCATGAGAGT
1 AACTCACAATTCCATGAGAGT
*
3059 AACTCAC-ATTCCGTGAGAGT
1 AACTCACAATTCCATGAGAGT
3079 A
1 A
3080 GAATCCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (21 bp):
AACTCACAATTCCATGAGAGT
Found at i:4738 original size:29 final size:29
Alignment explanation
Indices: 4677--4739 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
4667 ATGAAATTGT
**
4677 TCTAGTATTTGATTTCAGAATAGACAATT
1 TCTAGTATTTGATTTCAGAATAGACAAAG
*
4706 TCTAGTATTTGATTTCAGAATAGAGAAAG
1 TCTAGTATTTGATTTCAGAATAGACAAAG
4735 TCTAG
1 TCTAG
4740 AATTAAACGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (29 bp):
TCTAGTATTTGATTTCAGAATAGACAAAG
Found at i:26940 original size:11 final size:11
Alignment explanation
Indices: 26926--26963 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
26916 ATTCATAACA
26926 AATTTATAATT
1 AATTTATAATT
26937 AATTTATAATT
1 AATTTATAATT
26948 -ATTTGATAATT
1 AATTT-ATAATT
*
26959 TATTT
1 AATTT
26964 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:28419 original size:30 final size:30
Alignment explanation
Indices: 28359--28421 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
28349 TCTCACGGAA
* *
28359 TGTGAGTTTTCTTTGTAATTTATCGCTTTG
1 TGTGAGTTTCCTTTGTAATTTATCGATTTG
**
28389 TGTGAGTTTCCTTTGTAATTTATTTATTTG
1 TGTGAGTTTCCTTTGTAATTTATCGATTTG
28419 TGT
1 TGT
28422 ATTTAGCATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.14, C:0.08, G:0.19, T:0.59
Consensus pattern (30 bp):
TGTGAGTTTCCTTTGTAATTTATCGATTTG
Found at i:29725 original size:30 final size:32
Alignment explanation
Indices: 29671--29736 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
29661 AACTTTATGT
* *
29671 TTTCCGATTGTACCCTTATTTTT-AAAATATA
1 TTTCCAATTGTACCCTTATTTTTAAAAACATA
29702 TTTCCAATTGTACCCTT-TTTTTAAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAAACATA
29733 TTTC
1 TTTC
29737 TGAATTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.48
Consensus pattern (32 bp):
TTTCCAATTGTACCCTTATTTTTAAAAACATA
Found at i:29954 original size:37 final size:36
Alignment explanation
Indices: 29865--29954 Score: 108
Period size: 37 Copynumber: 2.4 Consensus size: 36
29855 GACTTTTTGT
* * *
29865 TTCCAACGTCCTATTTAATTTTGCCTTTTGTCTTTG
1 TTCCAACGTTCTATTTAATTTTACCTTTTGTCTTCG
* *
29901 TTCCAATCGTTGTATTTAATTTTACTTTTTGTCTTCG
1 TTCCAA-CGTTCTATTTAATTTTACCTTTTGTCTTCG
*
29938 TCTTCAACGTTCTATTT
1 T-TCCAACGTTCTATTT
29955 GGGCTTAGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
36 6 0.13
37 35 0.78
38 4 0.09
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.54
Consensus pattern (36 bp):
TTCCAACGTTCTATTTAATTTTACCTTTTGTCTTCG
Found at i:30041 original size:22 final size:22
Alignment explanation
Indices: 30014--30156 Score: 128
Period size: 22 Copynumber: 6.5 Consensus size: 22
30004 ATCCAATTCA
*
30014 AAAATTTCA-AAACGCGGTTATC
1 AAAATTTCATAAA-GAGGTTATC
* * * *
30036 AAAATTACATAATGTGATTATC
1 AAAATTTCATAAAGAGGTTATC
* * *
30058 AAAATTTCATAGAGGGGTTAAC
1 AAAATTTCATAAAGAGGTTATC
* *
30080 AAAATTTTATAGAGAGGTTATC
1 AAAATTTCATAAAGAGGTTATC
30102 AAAATTTCATAAAGAGGTTATC
1 AAAATTTCATAAAGAGGTTATC
* * * *
30124 AAATTTTCA-AAATATGATTACC
1 AAAATTTCATAAAGA-GGTTATC
30146 AAAATTTCATA
1 AAAATTTCATA
30157 GTGGTATTTC
Statistics
Matches: 98, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
21 4 0.04
22 91 0.93
23 3 0.03
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (22 bp):
AAAATTTCATAAAGAGGTTATC
Found at i:30077 original size:44 final size:44
Alignment explanation
Indices: 30029--30157 Score: 143
Period size: 44 Copynumber: 2.9 Consensus size: 44
30019 TTCAAAACGC
* *
30029 GGTTATCAAAATTACATAATGTGATTATCAAAATTTCATAGAGG
1 GGTTATCAAAATTTCATAATGTGATTATCAAAATTTCATAGAGA
* * * * *
30073 GGTTAACAAAATTTTATAGA-GAGGTTATCAAAATTTCATAAAGA
1 GGTTATCAAAATTTCATA-ATGTGATTATCAAAATTTCATAGAGA
* * * *
30117 GGTTATCAAATTTTCAAAATATGATTACCAAAATTTCATAG
1 GGTTATCAAAATTTCATAATGTGATTATCAAAATTTCATAG
30158 TGGTATTTCT
Statistics
Matches: 67, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
43 1 0.01
44 65 0.97
45 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAATGTGATTATCAAAATTTCATAGAGA
Found at i:30285 original size:22 final size:22
Alignment explanation
Indices: 30257--30421 Score: 129
Period size: 22 Copynumber: 7.5 Consensus size: 22
30247 TCAGGGAGGA
*
30257 TATCAAAATTCCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
30279 TATCAAAATTCCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* *
30301 TTTCAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
* *
30323 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
30344 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
30367 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
30389 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
30411 TATCAAAATTT
1 TATCAAAATTT
30422 GTAGTTATCA
Statistics
Matches: 113, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
21 7 0.06
22 99 0.88
23 7 0.06
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:30351 original size:44 final size:44
Alignment explanation
Indices: 30258--30421 Score: 154
Period size: 44 Copynumber: 3.7 Consensus size: 44
30248 CAGGGAGGAT
* * *
30258 ATCAAAATTCCATATGAAGGTTATCAAAATTCCATAGT-T-TAG
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTATGTAG
* *
30300 TTTTCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTATGTAG
1 --ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTATGTAG
* * * * * *
30346 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGT-T
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGT-ATGTAG
** *
30390 ATCAAAAAATCATAGGGAGGTTATCAAAATTT
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTT
30422 GTAGTTATCA
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
44 94 0.93
45 4 0.04
46 3 0.03
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (44 bp):
ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTATGTAG
Found at i:30430 original size:16 final size:19
Alignment explanation
Indices: 30238--30548 Score: 90
Period size: 22 Copynumber: 14.6 Consensus size: 19
30228 TTTTGAAGTA
* *
30238 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCA-TGAGGTT
*
30258 ATCAAAATTCCATATGAAGGTT
1 ATCAAAATTTC--ATG-AGGTT
*
30280 ATCAAAATTCCAT-AGTTTAGTT
1 ATCAAAATTTCATGAG----GTT
*
30302 TTCAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCAT--G-AGGTT
* *
30324 ATCAAAATTTCATAGTATGTAG
1 ATCAAAATTTCAT-G-AGGT-T
*
30346 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCAT---GAGGTT
*
30368 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTC---ATGAGGTT
**
30390 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCAT---GAGGTT
*
30412 ATCAAAATTT-GT-A-GTT
1 ATCAAAATTTCATGAGGTT
*
30428 ATCAAGATTTCATGAGGTT
1 ATCAAAATTTCATGAGGTT
* *
30447 ATCAAAATTTTACAGGGAGTTTT
1 ATCAAAA-TTT-CA-TGAG-GTT
*
30470 ATCAAAATTTTATTGGAAGGTTT
1 ATCAAAATTTCA-T-G-AGG-TT
*
30493 ATCAAAATTTCATAGCGAGATT
1 ATCAAAATTTCAT---GAGGTT
* *
30515 ATCACAATTTCATAGTATGATT
1 ATCAAAATTTCAT-G-A-GGTT
30537 ATCAAAATTTCA
1 ATCAAAATTTCA
30549 GAGTCTGATT
Statistics
Matches: 221, Mismatches: 36, Indels: 66
0.68 0.11 0.20
Matches are distributed among these distances:
16 12 0.05
17 2 0.01
18 3 0.01
19 11 0.05
20 16 0.07
21 11 0.05
22 132 0.60
23 28 0.13
24 2 0.01
25 2 0.01
26 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (19 bp):
ATCAAAATTTCATGAGGTT
Found at i:30475 original size:23 final size:23
Alignment explanation
Indices: 30445--30502 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
30435 TTTCATGAGG
* *
30445 TTATCAAAATTTTACAGGGAGTT
1 TTATCAAAATTTTACAGGAAGGT
**
30468 TTATCAAAATTTTATTGGAAGGT
1 TTATCAAAATTTTACAGGAAGGT
30491 TTATCAAAATTT
1 TTATCAAAATTT
30503 CATAGCGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (23 bp):
TTATCAAAATTTTACAGGAAGGT
Found at i:30557 original size:22 final size:22
Alignment explanation
Indices: 30491--30559 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
30481 ATTGGAAGGT
*
30491 TTATCAAAATTTCATAG-CGAGA
1 TTATCAAAATTTCATAGTC-TGA
* *
30513 TTATCACAATTTCATAGTATGA
1 TTATCAAAATTTCATAGTCTGA
*
30535 TTATCAAAATTTCAGAGTCTGA
1 TTATCAAAATTTCATAGTCTGA
30557 TTA
1 TTA
30560 CTGACAATTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTCTGA
Found at i:30629 original size:22 final size:23
Alignment explanation
Indices: 30601--30652 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
30591 CATAACGTGT
*
30601 TTATCAATATATTATA-TGGAGG
1 TTATCAACATATTATAGTGGAGG
* **
30623 TTATCAACATCTTATAGTGTTGG
1 TTATCAACATATTATAGTGGAGG
30646 TTATCAA
1 TTATCAA
30653 AATTTCATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (23 bp):
TTATCAACATATTATAGTGGAGG
Found at i:30757 original size:20 final size:22
Alignment explanation
Indices: 30711--30757 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
30701 TTCCTTAGGG
* *
30711 AGGTTAATAAAATTTCATAAGA
1 AGGTTAATAAAAATTCATAAAA
*
30733 TGGTTAA-AAAAATT-ATAAAA
1 AGGTTAATAAAAATTCATAAAA
30753 AGGTT
1 AGGTT
30758 CTCGAAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 9 0.43
21 6 0.29
22 6 0.29
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.32
Consensus pattern (22 bp):
AGGTTAATAAAAATTCATAAAA
Found at i:30883 original size:41 final size:41
Alignment explanation
Indices: 30800--30907 Score: 150
Period size: 41 Copynumber: 2.7 Consensus size: 41
30790 CATAGGAAGG
* * *
30800 TTATCAAAATTTCATAAAG-ACGTCAT-AAAAATAGTGTAA
1 TTATCATAATTTCATAAAGAAAGTTATCAAAAATAGTGTAA
*
30839 TTATCATAATTTCATAAAGAAGGTTATCAAAAATAGTGTAA
1 TTATCATAATTTCATAAAGAAAGTTATCAAAAATAGTGTAA
*
30880 TTATCATAATTTAATAAA-AAAGTTATCA
1 TTATCATAATTTCATAAAGAAAGTTATCA
30908 TAATTTCATA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
39 18 0.29
40 14 0.23
41 30 0.48
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.34
Consensus pattern (41 bp):
TTATCATAATTTCATAAAGAAAGTTATCAAAAATAGTGTAA
Found at i:37495 original size:136 final size:135
Alignment explanation
Indices: 37122--37665 Score: 688
Period size: 136 Copynumber: 4.0 Consensus size: 135
37112 ATCTGGGGAG
*
37122 ATATTTCGTATTTTACAAGATTCGTGCATTAAATATTCATATTATTGAAGACGATCTTTT-ATCA
1 ATATTTCGTATCTTACAAGATTCGTGCATT-AATATTCATATTATTGAAGACGATCTTTTAATC-
* * * *
37186 TACGTTACTTTCTATATCTCGCAATCATATTGAGCACCAACTAATATGAAGCCGAGCCGTACTGG
64 TACGTTACTTTCTATACCTCACAATCATATTGAGCATCAACTAATACGAAGCCGAGCCGTACTGG
*
37251 GTTCGAAA
129 ATTCG-AA
* *
37259 ATATTCCGAATCTTACAATTAGATTCGTGCATTAATATTC--ATTATTGAAGACGATCTTTTAAT
1 ATATTTCGTATCTTAC-A--AGATTCGTGCATTAATATTCATATTATTGAAGACGATCTTTTAAT
* * ** * * *
37322 GTAC-TTCACTTTGTATATTTCACAATCATACTAAGCATCAACTAGTACGAAGCCGAGCCGTACT
63 CTACGTT-ACTTTCTATACCTCACAATCATATTGAGCATCAACTAATACGAAGCCGAGCCGTACT
37386 GGATTCGAA
127 GGATTCGAA
* * *
37395 AGTATTTCGTATCTTACAAGATTTGTGCATTAATATTTATATCATTGAAGACGATCTTTTAATCT
1 A-TATTTCGTATCTTACAAGATTCGTGCATTAATATTCATATTATTGAAGACGATCTTTTAATCT
* * *
37460 ACGTTACTTTCTATGCCTCACAATCATATTGAGCATCAACTAATACGAAGTCGAGCTGTACTGGA
65 ACGTTACTTTCTATACCTCACAATCATATTGAGCATCAACTAATACGAAGCCGAGCCGTACTGGA
37525 TTCGAA
130 TTCGAA
* * *
37531 TATATTGT-GTATCTTACAAGATTCGTGCATTAATATTCATATTATTGAAGACAATCTTTTATTG
1 -ATATT-TCGTATCTTACAAGATTCGTGCATTAATATTCATATTATTGAAGACGATCTTTTAATC
* * * * *
37595 TACGTTACTTTC--TACCTGACAATCATATTGAACATCAACTAGTTCGAAGCCGAGCCGTACTGA
64 TACGTTACTTTCTATACCTCACAATCATATTGAGCATCAACTAATACGAAGCCGAGCCGTACTGG
37658 ATTCGAA
129 ATTCGAA
37665 A
1 A
37666 CGGAAGAAAC
Statistics
Matches: 354, Mismatches: 42, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
133 1 0.00
134 68 0.19
136 154 0.44
137 108 0.31
138 3 0.01
139 7 0.02
140 13 0.04
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (135 bp):
ATATTTCGTATCTTACAAGATTCGTGCATTAATATTCATATTATTGAAGACGATCTTTTAATCTA
CGTTACTTTCTATACCTCACAATCATATTGAGCATCAACTAATACGAAGCCGAGCCGTACTGGAT
TCGAA
Found at i:38836 original size:3 final size:3
Alignment explanation
Indices: 38828--38880 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
38818 TTTTAATTAC
38828 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
38876 CTT CT
1 CTT CT
38881 AACTTCTAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:43151 original size:2 final size:2
Alignment explanation
Indices: 43144--43178 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
43134 GCATTTACAT
43144 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
43179 TTGAAGCAAT
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:46693 original size:28 final size:29
Alignment explanation
Indices: 46623--46693 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
46613 GCTGAGGGGG
* *
46623 CAAAACATCCCAAAATTGAAGTTCAGAGAG
1 CAAAACAT-CCAAAATTGAAATTCAGAGAA
**
46653 CAAAATGTCCAAAATTGAAATTCAG-GAA
1 CAAAACATCCAAAATTGAAATTCAGAGAA
46681 CAAAACATCCAAA
1 CAAAACATCCAAA
46694 CACTACAGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 13 0.37
29 16 0.46
30 6 0.17
ACGTcount: A:0.51, C:0.20, G:0.13, T:0.17
Consensus pattern (29 bp):
CAAAACATCCAAAATTGAAATTCAGAGAA
Found at i:47429 original size:8 final size:8
Alignment explanation
Indices: 47412--47450 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
47402 TTTTTTTTGC
*
47412 GGTTTAGT
1 GGTTTGGT
47420 GGTTTGGT
1 GGTTTGGT
47428 GGTTTGGT
1 GGTTTGGT
*
47436 CGGTTTGGC
1 -GGTTTGGT
47445 GGTTTG
1 GGTTTG
47451 AACCATCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.03, C:0.05, G:0.46, T:0.46
Consensus pattern (8 bp):
GGTTTGGT
Found at i:47563 original size:30 final size:30
Alignment explanation
Indices: 47529--47587 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
47519 AAACCGAACC
47529 TTTTAT-T-TAATATATAATTAAATATATATT
1 TTTTATATATAATA-AT-ATTAAATATATATT
*
47559 TTTTATATATAATAATATTAGATATATAT
1 TTTTATATATAATAATATTAAATATATAT
47588 AATAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 18 0.69
31 3 0.12
32 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTTATATATAATAATATTAAATATATATT
Found at i:48985 original size:34 final size:33
Alignment explanation
Indices: 48929--49020 Score: 141
Period size: 34 Copynumber: 2.8 Consensus size: 33
48919 CGCCACCGGT
** *
48929 GCGGCCTATTCATAGTGAAGCCGCCCCAGTGGG
1 GCGGCCTACCCATGGTGAAGCCGCCCCAGTGGG
48962 GCGGCCTACCCAATGGTGAAGCCGCCCCAGTGGG
1 GCGGCCTACCC-ATGGTGAAGCCGCCCCAGTGGG
48996 GCGGCCTACCCATGGT-AAGCCGCCC
1 GCGGCCTACCCATGGTGAAGCCGCCC
49021 TCTTGGGGCG
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 9 0.16
33 14 0.25
34 32 0.58
ACGTcount: A:0.17, C:0.36, G:0.33, T:0.14
Consensus pattern (33 bp):
GCGGCCTACCCATGGTGAAGCCGCCCCAGTGGG
Found at i:49007 original size:17 final size:17
Alignment explanation
Indices: 48953--49007 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
48943 GTGAAGCCGC
48953 CCCAGTGGGGCGGCCTA
1 CCCAGTGGGGCGGCCTA
* * ** **
48970 CCCAATGGTGAAGCCGC
1 CCCAGTGGGGCGGCCTA
48987 CCCAGTGGGGCGGCCTA
1 CCCAGTGGGGCGGCCTA
49004 CCCA
1 CCCA
49008 TGGTAAGCCG
Statistics
Matches: 26, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.16, C:0.38, G:0.35, T:0.11
Consensus pattern (17 bp):
CCCAGTGGGGCGGCCTA
Found at i:49032 original size:32 final size:34
Alignment explanation
Indices: 48943--49020 Score: 142
Period size: 34 Copynumber: 2.4 Consensus size: 34
48933 CCTATTCATA
48943 GTGAAGCCGCCCCAGTGGGGCGGCCTACCCAATG
1 GTGAAGCCGCCCCAGTGGGGCGGCCTACCCAATG
48977 GTGAAGCCGCCCCAGTGGGGCGGCCTACCC-ATG
1 GTGAAGCCGCCCCAGTGGGGCGGCCTACCCAATG
49010 GT-AAGCCGCCC
1 GTGAAGCCGCCC
49021 TCTTGGGGCG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
32 9 0.20
33 5 0.11
34 30 0.68
ACGTcount: A:0.17, C:0.37, G:0.35, T:0.12
Consensus pattern (34 bp):
GTGAAGCCGCCCCAGTGGGGCGGCCTACCCAATG
Found at i:67570 original size:24 final size:24
Alignment explanation
Indices: 67538--67590 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
67528 TGGTATTGAC
*
67538 CAATCCCTTTCATTTTGCTGTCAT
1 CAATCCCTTTCATTTTGCTGCCAT
* *
67562 CAATTCCTTTTATTTTGCTGCCAT
1 CAATCCCTTTCATTTTGCTGCCAT
67586 CAATC
1 CAATC
67591 TCTTGGTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.19, C:0.28, G:0.08, T:0.45
Consensus pattern (24 bp):
CAATCCCTTTCATTTTGCTGCCAT
Found at i:77431 original size:28 final size:28
Alignment explanation
Indices: 77391--77454 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
77381 ATGGGTGCTA
*
77391 GGTGAGAGTTGCAGTGTGTGTATAAGAG
1 GGTGAGAGTTGCAGTGTGTATATAAGAG
77419 GGTGAGAGTTGCAGTGTGTATATAAGAG
1 GGTGAGAGTTGCAGTGTGTATATAAGAG
*
77447 AGTGAGAG
1 GGTGAGAG
77455 CCATAGAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.28, C:0.03, G:0.42, T:0.27
Consensus pattern (28 bp):
GGTGAGAGTTGCAGTGTGTATATAAGAG
Found at i:80871 original size:12 final size:12
Alignment explanation
Indices: 80854--80881 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
80844 GTAGCCCTTT
80854 ATGATGATTCAG
1 ATGATGATTCAG
80866 ATGATGATTCAG
1 ATGATGATTCAG
80878 ATGA
1 ATGA
80882 AAATGTAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (12 bp):
ATGATGATTCAG
Found at i:84434 original size:12 final size:12
Alignment explanation
Indices: 84417--84441 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
84407 TCGCTACTTG
84417 TACTTTGATTAA
1 TACTTTGATTAA
84429 TACTTTGATTAA
1 TACTTTGATTAA
84441 T
1 T
84442 TTGATAATGA
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:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TACTTTGATTAA
Found at i:92037 original size:1 final size:1
Alignment explanation
Indices: 92031--92056 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
92021 TTGCAACAGG
92031 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
92057 ATGTTAATGC
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:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:111726 original size:81 final size:82
Alignment explanation
Indices: 111591--111754 Score: 267
Period size: 81 Copynumber: 2.0 Consensus size: 82
111581 CCCGGGGAAG
111591 ATTTGTTGTACATTTATTCCAACTTTAGCTTAGATGAGTAGCTAGCCTCAAACAAGAAAATAATC
1 ATTTGTTGTACATTTATTCCAACTTTAGCTTAGATGAGTAGCTAGCCTCAAACAAGAAAATAATC
*
111656 ATTCAT-TAAGACATGA
66 ATTCATCAAAGACATGA
*** * *
111672 ATTTGTTGTACATTTATTTTTACTTTAGCTTAGATGAGTGGCTAGCCTCAAACAAGAAGATAATC
1 ATTTGTTGTACATTTATTCCAACTTTAGCTTAGATGAGTAGCTAGCCTCAAACAAGAAAATAATC
111737 ATTCATCAAAGACATGA
66 ATTCATCAAAGACATGA
111754 A
1 A
111755 AATGTAAACT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
81 66 0.87
82 10 0.13
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (82 bp):
ATTTGTTGTACATTTATTCCAACTTTAGCTTAGATGAGTAGCTAGCCTCAAACAAGAAAATAATC
ATTCATCAAAGACATGA
Found at i:111773 original size:81 final size:81
Alignment explanation
Indices: 111612--111773 Score: 227
Period size: 81 Copynumber: 2.0 Consensus size: 81
111602 ATTTATTCCA
* **
111612 ACTTTAGCTTAGATGAGTAGCTAGCCTCAAACAAGAAAATAATCATTCATTAAGACATGAATTTG
1 ACTTTAGCTTAGATGAGTAGCTAGCCTCAAACAAGAAAATAATCATTCATAAAGACATGAAAATG
**
111677 TTGTACATTTATTTTT
66 TTAAACATTTATTTTT
* *
111693 ACTTTAGCTTAGATGAGTGGCTAGCCTCAAACAAGAAGATAATCATTCATCAAAGACATGAAAAT
1 ACTTTAGCTTAGATGAGTAGCTAGCCTCAAACAAGAAAATAATCATTCAT-AAAGACATGAAAAT
* *
111758 G-TAAACTTTTTTTTTT
65 GTTAAACATTTATTTTT
111774 TCATTAAGAC
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 59 0.83
82 12 0.17
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (81 bp):
ACTTTAGCTTAGATGAGTAGCTAGCCTCAAACAAGAAAATAATCATTCATAAAGACATGAAAATG
TTAAACATTTATTTTT
Found at i:133548 original size:2 final size:2
Alignment explanation
Indices: 133541--133565 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
133531 ATTCTACACC
133541 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 T
133566 TATTGGCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:139312 original size:8 final size:8
Alignment explanation
Indices: 139301--139326 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
139291 ATTCTTAACT
139301 ATTTAAAA
1 ATTTAAAA
139309 ATTTAAAA
1 ATTTAAAA
139317 ATTTAAAA
1 ATTTAAAA
139325 AT
1 AT
139327 CCTAGCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATTTAAAA
Found at i:140288 original size:5 final size:5
Alignment explanation
Indices: 140265--140310 Score: 60
Period size: 5 Copynumber: 9.4 Consensus size: 5
140255 ATTTTTCATA
*
140265 AAAAG AAAA- AATAA- AAAAG GAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
140311 GAGAGATATG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 4 0.11
5 33 0.89
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:148526 original size:21 final size:20
Alignment explanation
Indices: 148500--148540 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
148490 TTTCTCGTTA
*
148500 ATTTCGATTGAACATTTTTTT
1 ATTTCGACTGAAC-TTTTTTT
*
148521 ATTTCGACTGGACTTTTTTT
1 ATTTCGACTGAACTTTTTTT
148541 GTTCGTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.56
Consensus pattern (20 bp):
ATTTCGACTGAACTTTTTTT
Found at i:159974 original size:2 final size:2
Alignment explanation
Indices: 159969--159995 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
159959 TATAGTACTA
159969 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 A
159996 AAAGTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.