Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008920.1 Corchorus capsularis cultivar CVL-1 contig08941, 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: 63847
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:656 original size:2 final size:2
Alignment explanation
Indices: 649--689 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
639 GAGTTATGAT
* * *
649 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
690 GGAGTTTAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
TA
Found at i:817 original size:2 final size:2
Alignment explanation
Indices: 810--858 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
800 ATATACATAT
810 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
852 AC AC AC A
1 AC AC AC A
859 TATATATATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3743 original size:2 final size:2
Alignment explanation
Indices: 3693--3729 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3683 ACTAGGCCAC
*
3693 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3730 AAGAAAACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4412 original size:18 final size:18
Alignment explanation
Indices: 4380--4414 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4370 GGAAAAATTA
4380 AAAAGAAAAGAAGAAAGG
1 AAAAGAAAAGAAGAAAGG
4398 AAAAGTAAAAG-AGAAAG
1 AAAAG-AAAAGAAGAAAG
4415 ACCAAACCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (18 bp):
AAAAGAAAAGAAGAAAGG
Found at i:4724 original size:16 final size:16
Alignment explanation
Indices: 4703--4736 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4693 ACCATTCTTT
*
4703 TAATTAAATTAAATAA
1 TAATTAAAATAAATAA
*
4719 TAATTAAAATACATAA
1 TAATTAAAATAAATAA
4735 TA
1 TA
4737 TAACAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATTAAAATAAATAA
Found at i:4792 original size:137 final size:131
Alignment explanation
Indices: 4516--4797 Score: 318
Period size: 141 Copynumber: 2.1 Consensus size: 131
4506 TTTTGACCCA
* *
4516 AAAAAAGAGACACTTGGACTTTATTTATTTTTAATTCCTTATCATTCTTTTAAATAATTAAAATA
1 AAAAAA-AGACACTTGGACTATATTTATTTTTAATTCCTTACCATTCTTTTAAATAATTAAAATA
* * * * * *
4581 CATAATATAACAAATATATATATATATATATATAATTAATATGGAATCAGACACATGGACTTTTT
65 CATAAAATAACAAATATACAAAAAAATATATATAATTAATATGGAATCAGACACATGGAC-TCTT
4646 GGG
129 GGG
*
4649 AAAAAAAAGACACTTGGACTATATTTATTTTTAATTAATTCCTTACCATTCTTTTAATTAAATTA
1 -AAAAAAAGACACTTGGACTATATTTA--TTT--TTAATTCCTTACCATTCTTTTAAAT-AATT-
*
4714 AATAATA-ATTAAAAT-ACATAATATAACAAAAAAATATATATAATTAATATGGAATTTAGACAC
59 AA-AATACA-TAAAATAACA-AATAT-ACAAAAAAATATATATAATTAATATGGAA-TCAGACAC
*
4777 ATGGA-TCTTGGA
119 ATGGACTCTTGGG
4789 AAAAAAAGA
1 AAAAAAAGA
4798 TTTGTATATA
Statistics
Matches: 126, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
133 19 0.15
134 6 0.05
135 3 0.02
137 23 0.18
138 4 0.03
139 15 0.12
140 19 0.15
141 25 0.20
142 12 0.10
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.37
Consensus pattern (131 bp):
AAAAAAAGACACTTGGACTATATTTATTTTTAATTCCTTACCATTCTTTTAAATAATTAAAATAC
ATAAAATAACAAATATACAAAAAAATATATATAATTAATATGGAATCAGACACATGGACTCTTGG
G
Found at i:19095 original size:20 final size:20
Alignment explanation
Indices: 19066--19110 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
19056 CAGAAATTGA
19066 TTTCTCGAAAATAAAC-ACAT
1 TTTCTCGAAAA-AAACTACAT
* *
19086 TTTCTGGAAAAAAACTATAT
1 TTTCTCGAAAAAAACTACAT
19106 TTTCT
1 TTTCT
19111 AAGATCAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.38
Consensus pattern (20 bp):
TTTCTCGAAAAAAACTACAT
Found at i:22503 original size:16 final size:16
Alignment explanation
Indices: 22478--22510 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
22468 TCTCTTTCTC
*
22478 AGAAAGAAACGAAGAA
1 AGAAAAAAACGAAGAA
22494 AGAAAAAAACGAAGAA
1 AGAAAAAAACGAAGAA
22510 A
1 A
22511 AAACGGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.73, C:0.06, G:0.21, T:0.00
Consensus pattern (16 bp):
AGAAAAAAACGAAGAA
Found at i:22936 original size:13 final size:13
Alignment explanation
Indices: 22918--22942 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22908 TTTAGAATTC
22918 AAATAATATTTAT
1 AAATAATATTTAT
22931 AAATAATATTTA
1 AAATAATATTTA
22943 GAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:25000 original size:28 final size:29
Alignment explanation
Indices: 24942--25010 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
24932 GACTCAAACC
*
24942 TTTTAAGTAGAGGGACTAAATTGATTATT
1 TTTTAAGTAGAGGGACTAAATTGACTATT
* * *
24971 TTTTGAGTAGAGGTAC-AAATTTGACTTTT
1 TTTTAAGTAGAGGGACTAAA-TTGACTATT
25000 TCTTGTAAGTA
1 T-TT-TAAGTA
25011 CAGGAACTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 3 0.09
29 22 0.69
30 2 0.06
31 5 0.16
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.43
Consensus pattern (29 bp):
TTTTAAGTAGAGGGACTAAATTGACTATT
Found at i:29904 original size:31 final size:31
Alignment explanation
Indices: 29850--29910 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
29840 CATAAGGACT
* *
29850 AAAAATTGTTAGAGTGTTTGATTATGCCCTC
1 AAAAATTGTTAGAGTGTTCGATTAAGCCCTC
*
29881 AAAAATTGTT-GATTGATTCGATTAAGCCCT
1 AAAAATTGTTAGAGTG-TTCGATTAAGCCCT
29911 TTGAAATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (31 bp):
AAAAATTGTTAGAGTGTTCGATTAAGCCCTC
Found at i:30167 original size:24 final size:24
Alignment explanation
Indices: 30121--30169 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
30111 AATTTGTGAA
* ***
30121 TAAAGATTGAATTTTTTTTTAATT
1 TAAAGATTGAACTTTTAAGTAATT
30145 TAAAGATTGAACTTTTAAGTAATT
1 TAAAGATTGAACTTTTAAGTAATT
30169 T
1 T
30170 TTGTAAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (24 bp):
TAAAGATTGAACTTTTAAGTAATT
Found at i:30762 original size:35 final size:35
Alignment explanation
Indices: 30722--31325 Score: 689
Period size: 35 Copynumber: 17.7 Consensus size: 35
30712 AGTAATAAGT
*
30722 AACTTAATTCAGGGCAATTAAGTAAGTCAGTAAAT-
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGT-AATC
30757 AACTTAATTCAGGGTAATTAAGTAAGTC---AA-C
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* * * *
30788 AACTTAACTCAGGGAAATTAAGTAAGT-AATAGGT-
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTA-ATC
*
30822 AACTCAATTCAGGGTAA-T---TAAGTCAGTAAGT-
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA-TC
* *
30853 AGCTT-ATTCAGGGTAATTAAGTAAAGTCAGTTAGT-
1 AACTTAATTCAGGGTAATTAAGT-AAGTCAG-TAATC
* * *
30888 AACTTAGTTCAGGGAAATTAAGTAAGGCAG---T-
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
30919 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
30954 AACTTAATTCAGGGTGATTAAGCAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
30989 -ACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
31023 AACTTAATTTAGGGTAATTAAGT-AGTTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAG-TCAGTAATC
*
31058 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
31093 AACTT-ATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
31127 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
31162 AACTTAATTCATGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
31197 GACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* * *
31232 AATCTTAA-TCAAGGGTAATTAAGTGAGTTAATAATC
1 AA-CTTAATTC-AGGGTAATTAAGTAAGTCAGTAATC
* *
31268 AACTTAATTCAGGGTAGTTAAGT-AGTTCAATAAGT-
1 AACTTAATTCAGGGTAATTAAGTAAG-TCAGTAA-TC
*
31303 AACTTAATTCAGGGAAATTAAGT
1 AACTTAATTCAGGGTAATTAAGT
31326 TTAGTAAGAA
Statistics
Matches: 494, Mismatches: 47, Indels: 56
0.83 0.08 0.09
Matches are distributed among these distances:
30 16 0.03
31 62 0.13
33 2 0.00
34 82 0.17
35 280 0.57
36 52 0.11
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (35 bp):
AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
Found at i:31052 original size:104 final size:105
Alignment explanation
Indices: 30722--31325 Score: 689
Period size: 104 Copynumber: 5.9 Consensus size: 105
30712 AGTAATAAGT
* *
30722 AACTTAATTCAGGGCAATTAAGTAAGTCAGTAAAT-AACTTAATTCAGGGTAATTAAGTAAGTC-
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGT-AATCAACTTAATTCAGGGTAATTAAGTAAGTCA
* * *
30785 --AA-CAACTTAACTCAGGGAAATTAAGTAAGT-AATAGGT-
65 GTAATCAACTTAATTCAGGGAAATTAAGTAAGTCAGTA-ATC
* *
30822 AACTCAATTCAGGGTAATT-A---AGTCAGTAAGT-AGCTT-ATTCAGGGTAATTAAGTAAAGTC
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAA-TCAACTTAATTCAGGGTAATTAAGT-AAGTC
* * *
30881 AGTTAGT-AACTTAGTTCAGGGAAATTAAGTAAGGCAG---T-
64 AG-TAATCAACTTAATTCAGGGAAATTAAGTAAGTCAGTAATC
* * * *
30919 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATCAACTTAATTCAGGGTGATTAAGCAAGTCAG
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
* *
30984 TAATC-ACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
66 TAATCAACTTAATTCAGGGAAATTAAGTAAGTCAGTAATC
* *
31023 AACTTAATTTAGGGTAATTAAGT-AGTTCAGTAATCAACTTAATTCAGGGTAATTAAGTGAGTCA
1 AACTTAATTCAGGGTAATTAAGTGAG-TCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCA
* *
31087 GTAATCAACTT-ATTCAGGGTAATTAAGTAATTCAGTAATC
65 GTAATCAACTTAATTCAGGGAAATTAAGTAAGTCAGTAATC
* *
31127 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATCAACTTAATTCATGGTAATTAAGTAATTCAG
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
* * *
31192 TAATCGACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
66 TAATCAACTTAATTCAGGGAAATTAAGTAAGTCAGTAATC
* * *
31232 AATCTTAA-TCAAGGGTAATTAAGTGAGTTAATAATCAACTTAATTCAGGGTAGTTAAGT-AGTT
1 AA-CTTAATTC-AGGGTAATTAAGTGAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAG-T
*
31295 CAATAAGT-AACTTAATTCAGGGAAATTAAGT
63 CAGTAA-TCAACTTAATTCAGGGAAATTAAGT
31326 TTAGTAAGAA
Statistics
Matches: 439, Mismatches: 38, Indels: 48
0.84 0.07 0.09
Matches are distributed among these distances:
95 19 0.04
96 17 0.04
97 19 0.04
98 1 0.00
99 1 0.00
100 71 0.16
101 20 0.05
102 15 0.03
103 2 0.00
104 159 0.36
105 38 0.09
106 76 0.17
107 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (105 bp):
AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
TAATCAACTTAATTCAGGGAAATTAAGTAAGTCAGTAATC
Found at i:31088 original size:139 final size:138
Alignment explanation
Indices: 30722--31325 Score: 672
Period size: 139 Copynumber: 4.4 Consensus size: 138
30712 AGTAATAAGT
*
30722 AACTTAATTCAGGGCAATTAAGTAAGTCAGTAAATAACTTAATTCAGGGTAATTAAGTA---AGT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGT-AATAACTTAATTCAGGGTAATTAAGTAGTCAGT
* * * * *
30784 CAA-CAACTTAACTCAGGGAAATTAAGTAAGT-AATAGGT-AACTCAATTCAGGGTAA-T---TA
65 -AATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTA-ATCAACTTAATTCAGGGTAATTAAGTA
30842 AGTCAGTAAGT-
128 AGTCAGTAA-TC
* * * * *
30853 AGCTT-ATTCAGGGTAATTAAGTAAAGTCAGTTAGTAACTTAGTTCAGGGAAATTAAGTAAGGCA
1 AACTTAATTCAGGGTAATTAAGT-AAGTCAG-TAATAACTTAATTCAGGGTAATTAAGT-AGTCA
* * *
30917 G---T-AACTTAATTCAGGGTAATTAAGTAATTCAGTAATCAACTTAATTCAGGGTGATTAAGCA
63 GTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTA
30978 AGTCAGTAATC
128 AGTCAGTAATC
* *
30989 -ACTTAATTCAGGGTAATTAAGTAATTCAGTAATCAACTTAATTTAGGGTAATTAAGTAGTTCAG
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT-AACTTAATTCAGGGTAATTAAGTAG-TCAG
*
31053 TAATCAACTTAATTCAGGGTAATTAAGTGAGTCAGTAATCAACTT-ATTCAGGGTAATTAAGTAA
64 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAA
*
31117 TTCAGTAATC
129 GTCAGTAATC
* * *
31127 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATCAACTTAATTCATGGTAATTAAGTAATTCAG
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT-AACTTAATTCAGGGTAATTAAGT-AGTCAG
* *
31192 TAATCGACTTAATTCAGGGTAATTAAGTGAGTCAGTAATCAATCTTAA-TCAAGGGTAATTAAGT
64 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAA-CTTAATTC-AGGGTAATTAAGT
* * *
31256 GAGTTAATAATC
127 AAGTCAGTAATC
* * *
31268 AACTTAATTCAGGGTAGTTAAGT-AGTTCAATAAGTAACTTAATTCAGGGAAATTAAGT
1 AACTTAATTCAGGGTAATTAAGTAAG-TCAGTAA-TAACTTAATTCAGGGTAATTAAGT
31326 TTAGTAAGAA
Statistics
Matches: 406, Mismatches: 39, Indels: 46
0.83 0.08 0.09
Matches are distributed among these distances:
130 16 0.04
131 59 0.15
132 20 0.05
133 1 0.00
134 5 0.01
135 35 0.09
136 27 0.07
138 27 0.07
139 136 0.33
140 8 0.02
141 71 0.17
142 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (138 bp):
AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATAACTTAATTCAGGGTAATTAAGTAGTCAGTA
ATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGT
CAGTAATC
Found at i:33543 original size:23 final size:25
Alignment explanation
Indices: 33490--33546 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 25
33480 TCCATGCTTT
*
33490 AATAAAAATGGAAAAATTTTCACCA
1 AATAAAAATGGAAAAATTTTCACAA
*
33515 AA-AAAAATGG-AAAATTTTTA-AA
1 AATAAAAATGGAAAAATTTTCACAA
33537 AATAAAAATG
1 AATAAAAATG
33547 TAGTCCATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 3 0.10
23 16 0.55
24 8 0.28
25 2 0.07
ACGTcount: A:0.61, C:0.05, G:0.09, T:0.25
Consensus pattern (25 bp):
AATAAAAATGGAAAAATTTTCACAA
Found at i:34158 original size:21 final size:20
Alignment explanation
Indices: 34132--34172 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
34122 TTCATGGTCT
34132 AACACTTATCTTAAACACTTA
1 AACACTTATCTT-AACACTTA
34153 AACACTTATCTTAACACTTA
1 AACACTTATCTTAACACTTA
34173 TCTTATATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.34
Consensus pattern (20 bp):
AACACTTATCTTAACACTTA
Found at i:34170 original size:12 final size:12
Alignment explanation
Indices: 34131--34177 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
34121 TTTCATGGTC
34131 TAACACTTATCT
1 TAACACTTATCT
34143 TAA-AC--A-CT
1 TAACACTTATCT
34151 TAAACACTTATCT
1 T-AACACTTATCT
34164 TAACACTTATCT
1 TAACACTTATCT
34176 TA
1 TA
34178 TATACCTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
8 3 0.10
9 3 0.10
10 2 0.07
11 2 0.07
12 17 0.57
13 3 0.10
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (12 bp):
TAACACTTATCT
Found at i:37940 original size:1 final size:1
Alignment explanation
Indices: 37899--37933 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
37889 GATCAGAAGT
37899 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
37934 CTAAAAACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:39066 original size:98 final size:99
Alignment explanation
Indices: 38949--39145 Score: 378
Period size: 99 Copynumber: 2.0 Consensus size: 99
38939 CCGCGCCATT
38949 TGGCGCGAGTTGTTTGTTTCCCTT-TGTTTTTCTCAATTGATTACCAATAAAAGGGTTTGAGAAA
1 TGGCGCGAGTTGTTTGTTTCCCTTGTGTTTTTCTCAATTGATTACCAATAAAAGGGTTTGAGAAA
39013 TACTAAGAGAAGCTCAAACAGCAAGTAAGAAAAA
66 TACTAAGAGAAGCTCAAACAGCAAGTAAGAAAAA
*
39047 TGGCGCGGGTTGTTTGTTTCCCTTGTGTTTTTCTCAATTGATTACCAATAAAAGGGTTTGAGAAA
1 TGGCGCGAGTTGTTTGTTTCCCTTGTGTTTTTCTCAATTGATTACCAATAAAAGGGTTTGAGAAA
39112 TACTAAGAGAAGCTCAAACAGCAAGTAAGAAAAA
66 TACTAAGAGAAGCTCAAACAGCAAGTAAGAAAAA
39146 AAATGTGAAT
Statistics
Matches: 97, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
98 23 0.24
99 74 0.76
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.30
Consensus pattern (99 bp):
TGGCGCGAGTTGTTTGTTTCCCTTGTGTTTTTCTCAATTGATTACCAATAAAAGGGTTTGAGAAA
TACTAAGAGAAGCTCAAACAGCAAGTAAGAAAAA
Found at i:44100 original size:87 final size:87
Alignment explanation
Indices: 43954--44127 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
43944 TCTTAACTCA
43954 AACATCCTGCATTCTGTTCTAAAATATTTTTCTTTACCTTGTTCTTCTAATAAAAAATTCAATGT
1 AACATCCTGCATTCTGTTCTAAAATATTTTTCTTTACCTTGTTCTTCTAATAAAAAATTCAATGT
44019 ACCTGCAATAAAAGTCATTGAT
66 ACCTGCAATAAAAGTCATTGAT
44041 AACATCCTGCATTCTGTTCTAAAATATTTTTCTTTACCTTGTTCTTCTAATAAAAAATTCAATGT
1 AACATCCTGCATTCTGTTCTAAAATATTTTTCTTTACCTTGTTCTTCTAATAAAAAATTCAATGT
44106 ACCTGCAATAAAAGTCATTGAT
66 ACCTGCAATAAAAGTCATTGAT
44128 TACCTTTTTC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.40
Consensus pattern (87 bp):
AACATCCTGCATTCTGTTCTAAAATATTTTTCTTTACCTTGTTCTTCTAATAAAAAATTCAATGT
ACCTGCAATAAAAGTCATTGAT
Found at i:51489 original size:19 final size:19
Alignment explanation
Indices: 51465--51525 Score: 86
Period size: 19 Copynumber: 3.1 Consensus size: 19
51455 CATTGTTTAG
51465 ATACTGTACAGATGAGATT
1 ATACTGTACAGATGAGATT
* *
51484 ATACTGTACAGATCAAATT
1 ATACTGTACAGATGAGATT
51503 AGGTACTGTACAGATGAGATT
1 A--TACTGTACAGATGAGATT
51524 AT
1 AT
51526 TAGAGCAGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 19 0.53
21 17 0.47
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (19 bp):
ATACTGTACAGATGAGATT
Found at i:51524 original size:21 final size:20
Alignment explanation
Indices: 51461--51524 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 20
51451 TTGACATTGT
51461 TTAGATACTGTACAGATGAGA
1 TTAG-TACTGTACAGATGAGA
* *
51482 TTA-TACTGTACAGATCAAA
1 TTAGTACTGTACAGATGAGA
51501 TTAGGTACTGTACAGATGAGA
1 TTA-GTACTGTACAGATGAGA
51522 TTA
1 TTA
51525 TTAGAGCAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.46
21 20 0.54
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (20 bp):
TTAGTACTGTACAGATGAGA
Found at i:59930 original size:37 final size:37
Alignment explanation
Indices: 59872--59982 Score: 102
Period size: 37 Copynumber: 3.0 Consensus size: 37
59862 AACAACAAAA
** * * *
59872 AGAGCCTAAGGCTAAAATCCAAGC-AATCATCAACCAC
1 AGAGCCTCGGGCTCAAATCCAAACAAAT-ATCAACAAC
* * * *
59909 TGAGCCTCGGGCTCAAGTCCAAACAAATATCAATAAG
1 AGAGCCTCGGGCTCAAATCCAAACAAATATCAACAAC
59946 AGAGCCTCGGGCTCAAATCC-AACGAAATATCAA-AAC
1 AGAGCCTCGGGCTCAAATCCAAAC-AAATATCAACAAC
59982 A
1 A
59983 TCACAATAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
36 6 0.10
37 51 0.85
38 3 0.05
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.15
Consensus pattern (37 bp):
AGAGCCTCGGGCTCAAATCCAAACAAATATCAACAAC
Found at i:60786 original size:14 final size:13
Alignment explanation
Indices: 60763--60805 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
60753 TAATGCACCC
60763 AAAACATTTAATA
1 AAAACATTTAATA
60776 AAAATCATTT-ATA
1 AAAA-CATTTAATA
*
60789 AAAACAATTTATTA
1 AAAAC-ATTTAATA
60803 AAA
1 AAA
60806 GTAGTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 1 0.04
13 15 0.58
14 10 0.38
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAACATTTAATA
Found at i:61859 original size:27 final size:25
Alignment explanation
Indices: 61829--61899 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 25
61819 CCGTTTGGCA
61829 TCGTTTCTGTTTTTTTGTTTTTTGTTT
1 TCGTTTC-G-TTTTTTGTTTTTTGTTT
*
61856 TCGTTTCG-TTTTTGTTTTAT-TTT
1 TCGTTTCGTTTTTTGTTTTTTGTTT
*
61879 T-GTTACGTTTTTTGTTTTTTG
1 TCGTTTCGTTTTTTGTTTTTTG
61900 AAAACAGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 5 0.13
23 15 0.38
24 11 0.28
26 1 0.03
27 7 0.18
ACGTcount: A:0.03, C:0.07, G:0.15, T:0.75
Consensus pattern (25 bp):
TCGTTTCGTTTTTTGTTTTTTGTTT
Done.