Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015538.1 Corchorus capsularis cultivar CVL-1 contig15559, 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: 17343
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:2504 original size:30 final size:32
Alignment explanation
Indices: 2442--2509 Score: 104
Period size: 30 Copynumber: 2.2 Consensus size: 32
2432 AGAAAATTTT
* *
2442 ATATTTTCCGATTGTACCCTTATTTTTAAAAC
1 ATATTTTCCAATTGTACCCTTATTTGTAAAAC
2474 ATATTTT-CAATTGTACCCTT-TTTGTAAAAC
1 ATATTTTCCAATTGTACCCTTATTTGTAAAAC
2504 ATATTT
1 ATATTT
2510 CTAAATTGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 15 0.44
31 12 0.35
32 7 0.21
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.49
Consensus pattern (32 bp):
ATATTTTCCAATTGTACCCTTATTTGTAAAAC
Found at i:2517 original size:31 final size:31
Alignment explanation
Indices: 2452--2517 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
2442 ATATTTTCCG
* *
2452 ATTGTACCCTTATTTTTAAAACATATTTTCA
1 ATTGTACCCTTATTTGTAAAACATATTTTAA
2483 ATTGTACCCTT-TTTGTAAAACATATTTCTAA
1 ATTGTACCCTTATTTGTAAAACATATTT-TAA
2514 ATTG
1 ATTG
2518 CCATTACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.47
Consensus pattern (31 bp):
ATTGTACCCTTATTTGTAAAACATATTTTAA
Found at i:2858 original size:22 final size:22
Alignment explanation
Indices: 2833--2916 Score: 150
Period size: 22 Copynumber: 3.8 Consensus size: 22
2823 CCATGAGGAG
2833 GTTACCAAAATTTCATAGTGTA
1 GTTACCAAAATTTCATAGTGTA
2855 GTTACCAAAATTTCATAGTGTA
1 GTTACCAAAATTTCATAGTGTA
* *
2877 GTTACCAAAATTTCATAGAGTG
1 GTTACCAAAATTTCATAGTGTA
2899 GTTACCAAAATTTCATAG
1 GTTACCAAAATTTCATAG
2917 GATCAGGTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (22 bp):
GTTACCAAAATTTCATAGTGTA
Found at i:2932 original size:24 final size:22
Alignment explanation
Indices: 2788--2969 Score: 106
Period size: 22 Copynumber: 8.2 Consensus size: 22
2778 GTCTCAATGT
* *
2788 GGTTATCAAAATTTCATAAG-A
1 GGTTATTAAAATTTCATAGGTA
* * *
2809 TGATTATTATAATTCCATGAGG-A
1 -GGTTATTAAAATTTCAT-AGGTA
**
2832 GGTTACCAAAATTTCATAGTGTA
1 GGTTATTAAAATTTCATAG-GTA
**
2855 -GTTACCAAAATTTCATAGTGTA
1 GGTTATTAAAATTTCATAG-GTA
**
2877 -GTTACCAAAATTTCATAGAGT-
1 GGTTATTAAAATTTCATAG-GTA
**
2898 GGTTACCAAAATTTCATAGGATCA
1 GGTTATTAAAATTTCATAGG-T-A
* *
2922 GGTTATTAAAATTTCTTAGGTT
1 GGTTATTAAAATTTCATAGGTA
* *
2944 GGTTATTGAAA-TTCATAGGTT
1 GGTTATTAAAATTTCATAGGTA
2965 GGTTA
1 GGTTA
2970 ATTATCACAA
Statistics
Matches: 136, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
21 17 0.12
22 97 0.71
23 5 0.04
24 17 0.12
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
GGTTATTAAAATTTCATAGGTA
Found at i:2950 original size:22 final size:21
Alignment explanation
Indices: 2922--2969 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
2912 CATAGGATCA
*
2922 GGTTATTAAAATTTCTTAGGTT
1 GGTTATTAAAA-TTCATAGGTT
*
2944 GGTTATTGAAATTCATAGGTT
1 GGTTATTAAAATTCATAGGTT
2965 GGTTA
1 GGTTA
2970 ATTATCACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.27, C:0.04, G:0.23, T:0.46
Consensus pattern (21 bp):
GGTTATTAAAATTCATAGGTT
Found at i:3137 original size:22 final size:22
Alignment explanation
Indices: 3090--3374 Score: 78
Period size: 22 Copynumber: 12.8 Consensus size: 22
3080 TCATCGGGAG
*
3090 GTTATCAAAATTTTATAGTG--T
1 GTTATCAAAATTTCATA-TGAAT
3111 GGTTATCAAAATTTCATATGAAT
1 -GTTATCAAAATTTCATATGAAT
* *
3134 GTTAT-AAAAGTCTCAATTTCAT-AAG
1 GTTATCAAAA-TTTC-A--T-ATGAAT
* * * *
3159 GAGTACCAAAATTTGATA-GAAG
1 G-TTATCAAAATTTCATATGAAT
* *
3181 GTTATC-AAATCTCATA-GAGT
1 GTTATCAAAATTTCATATGAAT
* **
3201 GATTATCGAAATTTCATAAAAAT
1 G-TTATCAAAATTTCATATGAAT
*
3224 AGGATGATCAAAATTT-ATATGAA-
1 --G-TTATCAAAATTTCATATGAAT
*
3247 GATTATCAAAATTTCATAATG-TT
1 G-TTATCAAAATTTCAT-ATGAAT
* * *
3270 GTTATCAAAATTTCA-AAGCGAG
1 GTTATCAAAATTTCATATG-AAT
*
3292 GTTATCAAAATTACATAATG--T
1 GTTATCAAAATTTCAT-ATGAAT
**
3313 GATTATCAAAATTTCATA-GAGGG
1 G-TTATCAAAATTTCATATGA-AT
* * * *
3336 GTCAACAAAATTTTATA-AAGAT
1 GTTATCAAAATTTCATATGA-AT
3358 GTTATCAAAATTTCATA
1 GTTATCAAAATTTCATA
3375 AAGAGGTTAT
Statistics
Matches: 198, Mismatches: 39, Indels: 52
0.69 0.13 0.18
Matches are distributed among these distances:
20 14 0.07
21 29 0.15
22 111 0.56
23 10 0.05
24 7 0.04
25 17 0.09
26 6 0.03
27 4 0.02
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTCATATGAAT
Found at i:3303 original size:44 final size:44
Alignment explanation
Indices: 3249--3416 Score: 182
Period size: 44 Copynumber: 3.8 Consensus size: 44
3239 TATATGAAGA
*
3249 TTATCAAAATTTCATAATGTTG-TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAATG-TGATTATCAAAATTTCAAAGAGAGG
* * *
3293 TTATCAAAATTACATAATGTGATTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAATGTGATTATCAAAATTTCAAAGAGAGG
* * * *
3337 TCAACAAAATTTTATAAAGATG-TTATCAAAATTTCATAA-AGAGG
1 TTATCAAAATTTCATAATG-TGATTATCAAAATTTCA-AAGAGAGG
* *
3381 TTATCAAATTTTCAAAATGTGATTA-CAAAAATTTCA
1 TTATCAAAATTTCATAATGTGATTATC-AAAATTTCA
3417 TAGTGGTATT
Statistics
Matches: 102, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
43 5 0.05
44 94 0.92
45 3 0.03
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (44 bp):
TTATCAAAATTTCATAATGTGATTATCAAAATTTCAAAGAGAGG
Found at i:3345 original size:66 final size:66
Alignment explanation
Indices: 3246--3399 Score: 159
Period size: 66 Copynumber: 2.3 Consensus size: 66
3236 ATTTATATGA
** * * *
3246 AGATTATCAAAATTTCATAATGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAA
1 AGATTATCAAAATTTCATAATGGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACATAA
*
3310 TG
65 AG
* * * *
3312 TGATTATCAAAATTTCATAGA-GGGGTCAACAAAATTTTATAAAGATGTTATCAAAATTTCATAA
1 AGATTATCAAAATTTCATA-ATGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAA
3376 AG
65 AG
* * *
3378 AGGTTATCAAATTTTCAAAATG
1 AGATTATCAAAATTTCATAATG
3400 TGATTACAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
65 1 0.01
66 67 0.94
67 3 0.04
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (66 bp):
AGATTATCAAAATTTCATAATGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAAA
G
Found at i:3347 original size:88 final size:88
Alignment explanation
Indices: 3253--3419 Score: 239
Period size: 88 Copynumber: 1.9 Consensus size: 88
3243 TGAAGATTAT
* * * *
3253 CAAAATTTCATAATGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTCATAAAGATGTTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATGTGATT
3317 ATC-AAAATTTCATAGAGGGGTCAA
65 A-CAAAAATTTCATAGAGGGGTCAA
* * *
3341 CAAAATTTTATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTA
1 CAAAATTTCATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
3406 CAAAAATTTCATAG
66 CAAAAATTTCATAG
3420 TGGTATTTCT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
87 1 0.01
88 67 0.96
89 2 0.03
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (88 bp):
CAAAATTTCATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
CAAAAATTTCATAGAGGGGTCAA
Found at i:3375 original size:22 final size:22
Alignment explanation
Indices: 3148--3418 Score: 138
Period size: 22 Copynumber: 12.4 Consensus size: 22
3138 TAAAAGTCTC
* *
3148 AATTTCATAAGGA-G-TACCAA
1 AATTTCATAAAGATGTTATCAA
*
3168 AATTTGATAGAAG--GTTATC-A
1 AATTTCATA-AAGATGTTATCAA
* * *
3188 AATCTCATAGAG-TGATTATCGA
1 AATTTCATAAAGATG-TTATCAA
* *
3210 AATTTCATAAAAATAGGATGATCAA
1 AATTTCATAAAGAT--G-TTATCAA
3235 AATTT-ATATGAAGA--TTATCAA
1 AATTTCATA--AAGATGTTATCAA
* *
3256 AATTTCATAATGTTGTTATCAA
1 AATTTCATAAAGATGTTATCAA
* *
3278 AATTTCA-AAGCGAGGTTATCAA
1 AATTTCATAA-AGATGTTATCAA
* *
3300 AATTACATAATG-TGATTATCAA
1 AATTTCATAAAGATG-TTATCAA
* ** * *
3322 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAAAGATGTTATCAA
*
3344 AATTTTATAAAGATGTTATCAA
1 AATTTCATAAAGATGTTATCAA
*
3366 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAAAGATGTTATCAA
*
3388 ATTTTCA-AAATG-TGATTA-CAAA
1 AATTTCATAAA-GATG-TTATC-AA
3410 AATTTCATA
1 AATTTCATA
3419 GTGGTATTTC
Statistics
Matches: 192, Mismatches: 38, Indels: 39
0.71 0.14 0.14
Matches are distributed among these distances:
19 2 0.01
20 20 0.10
21 29 0.15
22 118 0.61
23 5 0.03
24 3 0.02
25 12 0.06
26 3 0.02
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.34
Consensus pattern (22 bp):
AATTTCATAAAGATGTTATCAA
Found at i:3532 original size:19 final size:19
Alignment explanation
Indices: 3500--3566 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
3490 TGATGAAGTA
3500 ATCAAAATTTCAGGGAGGAT
1 ATCAAAA-TTCAGGGAGGAT
*
3520 ACCAAAATTCAGGGAGGAT
1 ATCAAAATTCAGGGAGGAT
*
3539 ATCAAAATTCAGTGAGGAT
1 ATCAAAATTCAGGGAGGAT
3558 ATCAAAATT
1 ATCAAAATT
3567 TCATATGAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 38 0.86
20 6 0.14
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (19 bp):
ATCAAAATTCAGGGAGGAT
Found at i:3585 original size:22 final size:22
Alignment explanation
Indices: 3557--3637 Score: 83
Period size: 22 Copynumber: 3.7 Consensus size: 22
3547 TCAGTGAGGA
3557 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
3579 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
3601 TTTCAAGATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
3623 TATCAAAATTTCATA
1 TATCAAAATTTCATA
3638 GTATATGTAG
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
22 43 0.96
23 2 0.04
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:3614 original size:44 final size:45
Alignment explanation
Indices: 3558--3679 Score: 140
Period size: 44 Copynumber: 2.7 Consensus size: 45
3548 CAGTGAGGAT
* *
3558 ATCAAAATTTCATATGAAGGTTATCAAATTTTCATAGTTTA-GT-T
1 ATCAAAATTTCATA-GAAGGTTATCAAATTTTCATAGTATATGTAG
* * * *
3602 TTCAAGATTTCATAAGAGGGTTATCAAAATTTCATAGTATATGTAG
1 ATCAAAATTTCAT-AGAAGGTTATCAAATTTTCATAGTATATGTAG
*
3648 ATCAAAATTTCATAAAGAGGTTATCAAATTTT
1 ATCAAAATTTCATAGA-AGGTTATCAAATTTT
3680 TAAAATGTGA
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
44 34 0.54
45 5 0.08
46 24 0.38
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (45 bp):
ATCAAAATTTCATAGAAGGTTATCAAATTTTCATAGTATATGTAG
Found at i:3688 original size:287 final size:287
Alignment explanation
Indices: 3318--3948 Score: 1133
Period size: 287 Copynumber: 2.2 Consensus size: 287
3308 AATGTGATTA
* * * * * *
3318 TCAAAATTTCAT-AGAGGGGTCAACAAAATTTTATA-AAGATGT-TATCAAAATTTCATAAAGAG
1 TCAAAATTTCATAAGA-GGGTTATCAAAATTTCATAGTATATGTAGATCAAAATTTCATAAAGAG
3380 GTTATCAAATTTTCAAAATGTGATTACAAAAATTTCATAGTGGTATTTCTGGGAAGGTTATCAAA
65 GTTATCAAATTTTCAAAATGTGATTACAAAAATTTCATAGTGGTATTTCTGGGAAGGTTATCAAA
3445 ATTTCATAGTATGGTTACCAAATTAGGAAGGTTATTAAACTTTCATGATGAAGTAATCAAAATTT
130 ATTTCATAGTATGGTTACCAAATTAGGAAGGTTATTAAACTTTCATGATGAAGTAATCAAAATTT
3510 CAGGGAGGATACCAAAATTCAGGGAGGATATCAAAATTCAGTGAGGATATCAAAATTTCATATGA
195 CAGGGAGGATACCAAAATTCAGGGAGGATATCAAAATTCAGTGAGGATATCAAAATTTCATATGA
3575 AGGTTATCAAATTTTCATAGTTTAGTTT
260 AGGTTATCAAATTTTCATAGTTTAGTTT
*
3603 TCAAGATTTCATAAGAGGGTTATCAAAATTTCATAGTATATGTAGATCAAAATTTCATAAAGAGG
1 TCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATATGTAGATCAAAATTTCATAAAGAGG
* *
3668 TTATCAAATTTTTAAAATGTGATTACAAAAATTTCATAGTGGTATTTCTGGGGAGGTTATCAAAA
66 TTATCAAATTTTCAAAATGTGATTACAAAAATTTCATAGTGGTATTTCTGGGAAGGTTATCAAAA
*
3733 TTTCATAGTATGGTTACCAAATTAGGAAGGTTATTAAACTTTCATGATGGAGTAATCAAAATTTC
131 TTTCATAGTATGGTTACCAAATTAGGAAGGTTATTAAACTTTCATGATGAAGTAATCAAAATTTC
*
3798 AGGGAGGATACCAAAATTCAGGGAGGATATCGAAATTCAGTGAGGATATCAAAATTTCATATGAA
196 AGGGAGGATACCAAAATTCAGGGAGGATATCAAAATTCAGTGAGGATATCAAAATTTCATATGAA
3863 GGTTATCAAATTTTCATAGTTTAGTTT
261 GGTTATCAAATTTTCATAGTTTAGTTT
3890 TCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATATGTAGATCAAAATTTCATA
1 TCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATATGTAGATCAAAATTTCATA
3949 GGGAGATGAA
Statistics
Matches: 331, Mismatches: 12, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
285 27 0.08
286 8 0.02
287 296 0.89
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (287 bp):
TCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATATGTAGATCAAAATTTCATAAAGAGG
TTATCAAATTTTCAAAATGTGATTACAAAAATTTCATAGTGGTATTTCTGGGAAGGTTATCAAAA
TTTCATAGTATGGTTACCAAATTAGGAAGGTTATTAAACTTTCATGATGAAGTAATCAAAATTTC
AGGGAGGATACCAAAATTCAGGGAGGATATCAAAATTCAGTGAGGATATCAAAATTTCATATGAA
GGTTATCAAATTTTCATAGTTTAGTTT
Found at i:3817 original size:19 final size:19
Alignment explanation
Indices: 3787--3853 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
3777 TGATGGAGTA
3787 ATCAAAATTTCAGGGAGGAT
1 ATCAAAA-TTCAGGGAGGAT
*
3807 ACCAAAATTCAGGGAGGAT
1 ATCAAAATTCAGGGAGGAT
* *
3826 ATCGAAATTCAGTGAGGAT
1 ATCAAAATTCAGGGAGGAT
3845 ATCAAAATT
1 ATCAAAATT
3854 TCATATGAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 36 0.86
20 6 0.14
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (19 bp):
ATCAAAATTCAGGGAGGAT
Found at i:3870 original size:22 final size:22
Alignment explanation
Indices: 3844--4121 Score: 160
Period size: 22 Copynumber: 12.7 Consensus size: 22
3834 TCAGTGAGGA
*
3844 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATAGGAAGGT
* **
3866 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATAG-GAAGGT
* * *
3888 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATAGGAAGGT
* *
3910 TATCAAAATTTCATAGTATATGT
1 TATCAAAATTTCATAGGA-AGGT
* * *
3933 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAGGAAGGT
* * *
3956 GAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-AGGAAGGT
* ** * *
3978 AATCAAAAAATCATAGGGAGCT
1 TATCAAAATTTCATAGGAAGGT
*
4000 TATCAAAA-TT--T--GTA-GT
1 TATCAAAATTTCATAGGAAGGT
* * *
4016 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATAGGAAGGT
* *
4038 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGGAAGG-T
* * *
4061 TATTAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGGAAG-GT
4084 TATCAAAATTTCATAGCG-AGGT
1 TATCAAAATTTCATAG-GAAGGT
*
4106 TATCACAATTTCATAG
1 TATCAAAATTTCATAG
4122 TGTAATATAT
Statistics
Matches: 194, Mismatches: 47, Indels: 30
0.72 0.17 0.11
Matches are distributed among these distances:
16 8 0.04
17 4 0.02
19 2 0.01
21 5 0.03
22 116 0.60
23 43 0.22
24 16 0.08
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGGAAGGT
Found at i:4068 original size:23 final size:23
Alignment explanation
Indices: 4037--4121 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
4027 CATAAGAAAG
4037 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* * *
4060 TTATTAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
4083 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
* *
4105 TTATCACAATTTCATAG
1 TTATCAAAATTTTATAG
4122 TGTAATATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:4220 original size:22 final size:23
Alignment explanation
Indices: 4192--4270 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 23
4182 TTTATAAAGT
*
4192 GGTTATCAATATATCATA-TGGA
1 GGTTATCAAAATATCATAGTGGA
* * **
4214 GGTTATCAACATCTCATAGTGTT
1 GGTTATCAAAATATCATAGTGGA
* *
4237 GGTTATCAAAATTTCATACT-GA
1 GGTTATCAAAATATCATAGTGGA
4259 GGTCT-TCAAAAT
1 GGT-TATCAAAAT
4271 TCCTTGGGGA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 26 0.57
23 20 0.43
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (23 bp):
GGTTATCAAAATATCATAGTGGA
Found at i:4244 original size:23 final size:22
Alignment explanation
Indices: 4190--4254 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
4180 TTTTTATAAA
*
4190 GTGGTTATCAATATATCATATG
1 GTGGTTATCAAAATATCATATG
* * *
4212 GAGGTTATCAACATCTCATAGTG
1 GTGGTTATCAAAATATCATA-TG
* *
4235 TTGGTTATCAAAATTTCATA
1 GTGGTTATCAAAATATCATA
4255 CTGAGGTCTT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (22 bp):
GTGGTTATCAAAATATCATATG
Found at i:5335 original size:33 final size:33
Alignment explanation
Indices: 5298--5371 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 33
5288 GCACCCCGGA
5298 CCGCCACCCCCGCCGCACCATCATCAT-CCGCCT
1 CCGCCA-CCCCGCCGCACCATCATCATGCCGCCT
* *
5331 CCGCCA--CCGCCTCATCATCATCATGGGCCGCCT
1 CCGCCACCCCGCCGCACCATCATCAT--GCCGCCT
5364 CCGCCACC
1 CCGCCACC
5372 ACCACCTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
30 16 0.47
33 18 0.53
ACGTcount: A:0.15, C:0.57, G:0.15, T:0.14
Consensus pattern (33 bp):
CCGCCACCCCGCCGCACCATCATCATGCCGCCT
Found at i:5381 original size:36 final size:36
Alignment explanation
Indices: 5334--5406 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
5324 TCCGCCTCCG
* *
5334 CCACCGCCTCATCATCATCATGGGCCGCCTCCGCCA
1 CCACCACCTCATCATCACCATGGGCCGCCTCCGCCA
* *
5370 CCACCACCTCATCATCACCATGGTCCGCCTCCTCCA
1 CCACCACCTCATCATCACCATGGGCCGCCTCCGCCA
5406 C
1 C
5407 GTCGTCGTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.18, C:0.52, G:0.12, T:0.18
Consensus pattern (36 bp):
CCACCACCTCATCATCACCATGGGCCGCCTCCGCCA
Found at i:6635 original size:19 final size:19
Alignment explanation
Indices: 6611--6699 Score: 109
Period size: 19 Copynumber: 5.0 Consensus size: 19
6601 CTCATTACTG
6611 CAATTTCAGAATCAAACCC
1 CAATTTCAGAATCAAACCC
* *
6630 CAATTTTAGAATCAAACCT
1 CAATTTCAGAATCAAACCC
6649 CAATTTCAGAATCAAACCC
1 CAATTTCAGAATCAAACCC
*
6668 CAA---C-TAA--AAACCC
1 CAATTTCAGAATCAAACCC
6681 CAATTTCAGAATCAAACCC
1 CAATTTCAGAATCAAACCC
6700 TAACTTAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
13 9 0.16
15 2 0.03
16 2 0.03
17 2 0.03
19 43 0.74
ACGTcount: A:0.44, C:0.30, G:0.04, T:0.21
Consensus pattern (19 bp):
CAATTTCAGAATCAAACCC
Found at i:6685 original size:32 final size:34
Alignment explanation
Indices: 6611--6704 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 34
6601 CTCATTACTG
* *
6611 CAATTTCAGAATCAAACCCCAATTTTAGAATCAAACCT
1 CAATTTCAGAATCAAACCCCAA--CTA-AA-CAAACCC
6649 CAATTTCAGAATCAAACCCCAACT-AA-AAACCC
1 CAATTTCAGAATCAAACCCCAACTAAACAAACCC
*
6681 CAATTTCAGAATCAAACCCTAACT
1 CAATTTCAGAATCAAACCCCAACT
6705 TAATTTTTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
32 28 0.53
34 2 0.04
36 1 0.02
38 22 0.42
ACGTcount: A:0.44, C:0.30, G:0.04, T:0.22
Consensus pattern (34 bp):
CAATTTCAGAATCAAACCCCAACTAAACAAACCC
Found at i:8800 original size:66 final size:66
Alignment explanation
Indices: 8690--8817 Score: 195
Period size: 66 Copynumber: 1.9 Consensus size: 66
8680 TAAGTAAGAT
* *
8690 GCACCATCATTCACACCACCACCACCACCACGCGCCACATCCAGGGCCGTCC-CCACCGCCACCG
1 GCACCATCATTCACACCACCACCACCACCACGCGCCAAAGCCAGGGCCG-CCGCCACCGCCACCG
8754 CA
65 CA
* * *
8756 GCACCATCATTCACACCACCACCACCACCATGGGCCAAAGCCAGGGCCGCCGCCGCCGCCAC
1 GCACCATCATTCACACCACCACCACCACCACGCGCCAAAGCCAGGGCCGCCGCCACCGCCAC
8818 ACCATCCACA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 2 0.04
66 54 0.96
ACGTcount: A:0.24, C:0.52, G:0.16, T:0.07
Consensus pattern (66 bp):
GCACCATCATTCACACCACCACCACCACCACGCGCCAAAGCCAGGGCCGCCGCCACCGCCACCGC
A
Found at i:8871 original size:33 final size:33
Alignment explanation
Indices: 8796--8872 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
8786 TGGGCCAAAG
* *
8796 CCAGGGCCGCCGCCGCCGCCACACCATCCACAC
1 CCAGGGCCGCCACCACCGCCACACCATCCACAC
** * * *
8829 CCACAGCCGCCACCACCGCCCCATCATCCACAT
1 CCAGGGCCGCCACCACCGCCACACCATCCACAC
8862 CCAGGGCCGCC
1 CCAGGGCCGCC
8873 TCACCATCCA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.19, C:0.57, G:0.18, T:0.05
Consensus pattern (33 bp):
CCAGGGCCGCCACCACCGCCACACCATCCACAC
Found at i:8872 original size:24 final size:24
Alignment explanation
Indices: 8844--8902 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
8834 GCCGCCACCA
* *
8844 CCGCCCCATCATCCACATCCAGGG
1 CCGCCCCACCATCCACACCCAGGG
* *
8868 CCGCCTCACCATCCACACCCGGGG
1 CCGCCCCACCATCCACACCCAGGG
*
8892 CCTCCGCCACC
1 CCGCC-CCACC
8903 TCCTGTCCAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.17, C:0.56, G:0.17, T:0.10
Consensus pattern (24 bp):
CCGCCCCACCATCCACACCCAGGG
Found at i:9261 original size:2 final size:2
Alignment explanation
Indices: 9254--9293 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
9244 GAGACACTCC
*
9254 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9294 TTCCTAAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:14486 original size:27 final size:27
Alignment explanation
Indices: 14447--14498 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
14437 GTGGTGGTTT
14447 TTCAAATGGTGGGGATAAGGCTGGACC
1 TTCAAATGGTGGGGATAAGGCTGGACC
* *
14474 TTCAAATGTTGGGGATGAGGCTGGA
1 TTCAAATGGTGGGGATAAGGCTGGA
14499 TTTTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.12, G:0.38, T:0.25
Consensus pattern (27 bp):
TTCAAATGGTGGGGATAAGGCTGGACC
Done.