Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009814.1 Corchorus capsularis cultivar CVL-1 contig09835, 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: 83157
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:148 original size:87 final size:87
Alignment explanation
Indices: 2--167 Score: 305
Period size: 87 Copynumber: 1.9 Consensus size: 87
1 A
*
2 ATAAATAAATTATAAAGATTGAGCTAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGA
1 ATAAATAAATTATAAAGATTGAGCTAATAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGGA
*
67 GATTTAGGAGATATTTTAAGAT
66 GATTTAGAAGATATTTTAAGAT
*
89 ATAAATAAATTATAAAGATTGAGTTAATAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGGA
1 ATAAATAAATTATAAAGATTGAGCTAATAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGGA
154 GATTTAGAAGATAT
66 GATTTAGAAGATAT
168 AGAAAAAGAA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 76 1.00
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.35
Consensus pattern (87 bp):
ATAAATAAATTATAAAGATTGAGCTAATAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGGA
GATTTAGAAGATATTTTAAGAT
Found at i:398 original size:26 final size:26
Alignment explanation
Indices: 362--418 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
352 GACTAAATAA
*
362 TAAAGATATGATTAAAATTCAAAAAC
1 TAAAAATATGATTAAAATTCAAAAAC
388 TAAAAATATGATTAAAATTCAAAAAC
1 TAAAAATATGATTAAAATTCAAAAAC
414 TAAAA
1 TAAAA
419 GAAAGATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.26
Consensus pattern (26 bp):
TAAAAATATGATTAAAATTCAAAAAC
Found at i:426 original size:26 final size:26
Alignment explanation
Indices: 362--426 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
352 GACTAAATAA
* *
362 TAAAGATATGATTAAAATTCAAAAAC
1 TAAAAATAAGATTAAAATTCAAAAAC
*
388 TAAAAATATGATTAAAATTCAAAAAC
1 TAAAAATAAGATTAAAATTCAAAAAC
414 TAAAAGA-AAGATT
1 TAAAA-ATAAGATT
427 TGCAATAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 35 0.97
27 1 0.03
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.26
Consensus pattern (26 bp):
TAAAAATAAGATTAAAATTCAAAAAC
Found at i:1223 original size:13 final size:12
Alignment explanation
Indices: 1199--1228 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1189 ACCCACGGAG
1199 GTCAATGTCAAA
1 GTCAATGTCAAA
1211 GTCAATGGTCAAA
1 GTCAAT-GTCAAA
1224 GTCAA
1 GTCAA
1229 CGGCTGATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (12 bp):
GTCAATGTCAAA
Found at i:1359 original size:20 final size:20
Alignment explanation
Indices: 1312--1352 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1302 GTACACTTGC
*
1312 TGACATGG-CAGTCAACGGA
1 TGACATGGCCGGTCAACGGA
1331 TGACATGGCCGGTCAACGGA
1 TGACATGGCCGGTCAACGGA
1351 TG
1 TG
1353 GTGTGGCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.27, C:0.22, G:0.34, T:0.17
Consensus pattern (20 bp):
TGACATGGCCGGTCAACGGA
Found at i:3329 original size:14 final size:15
Alignment explanation
Indices: 3310--3338 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3300 ATGTATTTAA
3310 TTAATTA-TTATACT
1 TTAATTAGTTATACT
3324 TTAATTAGTTATACT
1 TTAATTAGTTATACT
3339 ACACGATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.55
Consensus pattern (15 bp):
TTAATTAGTTATACT
Found at i:5381 original size:13 final size:13
Alignment explanation
Indices: 5363--5389 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5353 GGAGGTCAAT
5363 GTCAAAGTCAACG
1 GTCAAAGTCAACG
5376 GTCAAAGTCAACG
1 GTCAAAGTCAACG
5389 G
1 G
5390 CTGACGCGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (13 bp):
GTCAAAGTCAACG
Found at i:22323 original size:18 final size:19
Alignment explanation
Indices: 22284--22323 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
22274 GCTCATCAAT
*
22284 ATCTTCATGTTCTCCATGC
1 ATCTTCATGCTCTCCATGC
*
22303 ATCTTCATGCT-TCCTTGC
1 ATCTTCATGCTCTCCATGC
22321 ATC
1 ATC
22324 CCTTGCACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.15, C:0.33, G:0.10, T:0.42
Consensus pattern (19 bp):
ATCTTCATGCTCTCCATGC
Found at i:23367 original size:36 final size:34
Alignment explanation
Indices: 23325--24124 Score: 787
Period size: 36 Copynumber: 22.8 Consensus size: 34
23315 TTTAATTTCC
*
23325 ACTTAATTA-CCTAGAATTAAGTTCTTTGTTGACTCT
1 ACTTAATTACCCT-GAATTAAG-TCTTTGTTGA-TTT
* * * *
23361 ACTTAATTTCCCTGAATTAAATTCTTTATTGACTCT
1 ACTTAATTACCCTGAATT-AAGTCTTTGTTGA-TTT
* * * *
23397 ACTTAATTTCCATGAATTAAGTCCTTTATTGACTCT
1 ACTTAATTACCCTGAATTAAGT-CTTTGTTGA-TTT
* * *
23433 ATTTAATTACCCTGAATTAA------GTT-CTTC
1 ACTTAATTACCCTGAATTAAGTCTTTGTTGATTT
* *
23460 ACTTAA-TCCCCTTGGATTAAGTCTTTGATTGATCTT
1 ACTTAATTACCC-TGAATTAAGTCTTTG-TTGAT-TT
* * * *
23496 ACTTAATAATCTTGGATTAAGTCTTTGTTGATTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGTTGA-TTT
* ** * *
23531 ACTTAATTTCTTTGAAACTAAGTCTTTGCTGATTT
1 ACTTAATTACCCTG-AATTAAGTCTTTGTTGATTT
* * *
23566 ACTTAATTACCTTGAATTAAGTCATTGGCTGATTTT
1 ACTTAATTACCCTGAATTAAGTC-TTTGTTGA-TTT
*
23602 ACTTAATTACCCTGAATTAAGTCTTTCCTTGATTTT
1 ACTTAATTACCCTGAATTAAGTCTTT-GTTGA-TTT
*
23638 ACTTAATTACTCTGAATTAAGTCTTTGCTTGATTT
1 ACTTAATTACCCTGAATTAAGTCTTTG-TTGATTT
*
23673 ACTTAATTACCCTGAATTAAGTCTAACTG-T-ATTT
1 ACTTAATTACCCTGAATTAAGTCT--TTGTTGATTT
** * *
23707 ACTTAATTACCCTGAATTAAGTCTCTAACTGGTTTT
1 ACTTAATTACCCTGAATTAAGTCT-T-TGTTGATTT
*
23743 ACTTAATTACCCTAAATTAAGTCTTTGTCTGATTT
1 ACTTAATTACCCTGAATTAAGTCTTTGT-TGATTT
* *
23778 ACTTAATAACCCTGAATTAAGTCTTTGCTGATTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGTTGA-TTT
* * * *
23813 ACTTAATTGCCATGAATTAAGACTTTCTTGATTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGTTGA-TTT
*
23848 ACTTAATTATCCTGAATTAAGTCTTTGCTTGAATTT
1 ACTTAATTACCCTGAATTAAGTCTTTG-TTG-ATTT
23884 ACTTAATTACCCTGAATTAAGTCTTTGTTTGAATTT
1 ACTTAATTACCCTGAATTAAGTCTTTG-TTG-ATTT
*
23920 ACTTAATTACCCTGAATTAAGTATTTGTTTGATTT
1 ACTTAATTACCCTGAATTAAGTCTTTG-TTGATTT
23955 ACTTAATTACCCTGAATTAAGTCTTTGTTTGATTT
1 ACTTAATTACCCTGAATTAAGTCTTTG-TTGATTT
23990 ACTTAATTACCCTGAATTAAGTCTTTGCTTGAATTT
1 ACTTAATTACCCTGAATTAAGTCTTTG-TTG-ATTT
24026 ACTTAATTACCCTGAATTAAGTCTTTGACTGTG-TTT
1 ACTTAATTACCCTGAATTAAGTCTTTG--T-TGATTT
**
24062 ACTTAATTACCCTTCATTAAGTCTTTGCTTGAATTT
1 ACTTAATTACCCTGAATTAAGTCTTTG-TTG-ATTT
24098 ACTTAATTACCCTGAATTAAGTCTTTG
1 ACTTAATTACCCTGAATTAAGTCTTTG
24125 ACTGTGTTTA
Statistics
Matches: 656, Mismatches: 74, Indels: 68
0.82 0.09 0.09
Matches are distributed among these distances:
26 4 0.01
27 13 0.02
29 2 0.00
33 1 0.00
34 44 0.07
35 225 0.34
36 354 0.54
37 11 0.02
38 2 0.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (34 bp):
ACTTAATTACCCTGAATTAAGTCTTTGTTGATTT
Found at i:23534 original size:35 final size:36
Alignment explanation
Indices: 23475--24124 Score: 803
Period size: 36 Copynumber: 18.3 Consensus size: 36
23465 ATCCCCTTGG
* * * * * *
23475 ATTAAGTCTTTGATTGATCTTACTTAATAATCTTGG
1 ATTAAGTCTTTGCTTGATTTTACTTAATTACCCTGA
* **
23511 ATTAAGTCTTTG-TTGATTTTACTTAATTTCTTTGAA
1 ATTAAGTCTTTGCTTGATTTTACTTAATTACCCTG-A
* *
23547 ACTAAGTCTTTGC-TGA-TTTACTTAATTACCTTGA
1 ATTAAGTCTTTGCTTGATTTTACTTAATTACCCTGA
*
23581 ATTAAGTCATTGGC-TGATTTTACTTAATTACCCTGA
1 ATTAAGTC-TTTGCTTGATTTTACTTAATTACCCTGA
* *
23617 ATTAAGTCTTTCCTTGATTTTACTTAATTACTCTGA
1 ATTAAGTCTTTGCTTGATTTTACTTAATTACCCTGA
23653 ATTAAGTCTTTGCTTGA-TTTACTTAATTACCCTGA
1 ATTAAGTCTTTGCTTGATTTTACTTAATTACCCTGA
**
23688 ATTAAGTC-TAAC-TG-TATTTACTTAATTACCCTGA
1 ATTAAGTCTTTGCTTGAT-TTTACTTAATTACCCTGA
** * *
23722 ATTAAGTCTCTAAC-TGGTTTTACTTAATTACCCTAA
1 ATTAAGTCT-TTGCTTGATTTTACTTAATTACCCTGA
*
23758 ATTAAGTCTTTG-TCTGA-TTTACTTAATAACCCTGA
1 ATTAAGTCTTTGCT-TGATTTTACTTAATTACCCTGA
* *
23793 ATTAAGTCTTTGC-TGATTTTACTTAATTGCCATGA
1 ATTAAGTCTTTGCTTGATTTTACTTAATTACCCTGA
* *
23828 ATTAAGACTTT-CTTGATTTTACTTAATTATCCTGA
1 ATTAAGTCTTTGCTTGATTTTACTTAATTACCCTGA
*
23863 ATTAAGTCTTTGCTTGAATTTACTTAATTACCCTGA
1 ATTAAGTCTTTGCTTGATTTTACTTAATTACCCTGA
* *
23899 ATTAAGTCTTTGTTTGAATTTACTTAATTACCCTGA
1 ATTAAGTCTTTGCTTGATTTTACTTAATTACCCTGA
* *
23935 ATTAAGTATTTGTTTGA-TTTACTTAATTACCCTGA
1 ATTAAGTCTTTGCTTGATTTTACTTAATTACCCTGA
*
23970 ATTAAGTCTTTGTTTGA-TTTACTTAATTACCCTGA
1 ATTAAGTCTTTGCTTGATTTTACTTAATTACCCTGA
*
24005 ATTAAGTCTTTGCTTGAATTTACTTAATTACCCTGA
1 ATTAAGTCTTTGCTTGATTTTACTTAATTACCCTGA
**
24041 ATTAAGTCTTTGAC-TG-TGTTTACTTAATTACCCTTC
1 ATTAAGTCTTTG-CTTGAT-TTTACTTAATTACCCTGA
*
24077 ATTAAGTCTTTGCTTGAATTTACTTAATTACCCTGA
1 ATTAAGTCTTTGCTTGATTTTACTTAATTACCCTGA
24113 ATTAAGTCTTTG
1 ATTAAGTCTTTG
24125 ACTGTGTTTA
Statistics
Matches: 548, Mismatches: 45, Indels: 42
0.86 0.07 0.07
Matches are distributed among these distances:
33 2 0.00
34 40 0.07
35 219 0.40
36 285 0.52
37 2 0.00
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.46
Consensus pattern (36 bp):
ATTAAGTCTTTGCTTGATTTTACTTAATTACCCTGA
Found at i:23997 original size:142 final size:139
Alignment explanation
Indices: 23325--24124 Score: 815
Period size: 142 Copynumber: 5.7 Consensus size: 139
23315 TTTAATTTCC
* * *
23325 ACTTAATTA-CCTAGAATTAAGTTCTTTG-TTGACTCTACTTAATTTCCCTGAATTAAATTCTTT
1 ACTTAATTACCCT-GAATTAAG-TCTTTGATTGA-TTTACTTAATTACCCTGAATT-AAGTCTTT
* * * * * * *
23388 ATTGACTCTACTTAATTTCCATGAATTAAGTCCTTT-ATTGACTCTATTTAATTACCCTGAATTA
62 GTTGA-TTTACTTAATTACCCTGAATTAAGT-CTTTGTTTGA-TTTACTTAATTACCCTGAATTA
*
23452 AG---TT-C----TTC
124 AGTCTTTGCTGAATTT
* * * * * *
23460 ACTTAA-TCCCCTTGGATTAAGTCTTTGATTGATCTTACTTAATAATCTTGGATTAAGTCTTTGT
1 ACTTAATTACCC-TGAATTAAGTCTTTGATTGAT-TTACTTAATTACCCTGAATTAAGTCTTTGT
* ** * * *
23524 TGATTTTACTTAATTTCTTTGAAACTAAGTCTTTG-CTGATTTACTTAATTACCTTGAATTAAGT
64 TGA-TTTACTTAATTACCCTG-AATTAAGTCTTTGTTTGATTTACTTAATTACCCTGAATTAAGT
* *
23588 CATTGGCTGATTTT
127 C-TTTGCTGAATTT
** *
23602 ACTTAATTACCCTGAATTAAGTCTTTCCTTGATTTTACTTAATTACTCTGAATTAAGTCTTTGCT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTGA-TTTACTTAATTACCCTGAATTAAGTCTTTG-T
*** *
23667 TGATTTACTTAATTACCCTGAATTAAGTCTAACTGT-ATTTACTTAATTACCCTGAATTAAGTCT
64 TGATTTACTTAATTACCCTGAATTAAGTCTTTGTTTGATTTACTTAATTACCCTGAATTAAGTCT
** **
23731 CTAACTGGTTTT
129 -TTGCTGAATTT
* * *
23743 ACTTAATTACCCTAAATTAAGTCTTTG-TCTGATTTACTTAATAACCCTGAATTAAGTCTTTGCT
1 ACTTAATTACCCTGAATTAAGTCTTTGAT-TGATTTACTTAATTACCCTGAATTAAGTCTTTGTT
* * * * *
23807 GATTTTACTTAATTGCCATGAATTAAGACTTT-CTTGATTTTACTTAATTATCCTGAATTAAGTC
65 GA-TTTACTTAATTACCCTGAATTAAGTCTTTGTTTGA-TTTACTTAATTACCCTGAATTAAGTC
23871 TTTGCTTGAATTT
128 TTTGC-TGAATTT
* *
23884 ACTTAATTACCCTGAATTAAGTCTTTGTTTGAATTTACTTAATTACCCTGAATTAAGTATTTGTT
1 ACTTAATTACCCTGAATTAAGTCTTTGATTG-ATTTACTTAATTACCCTGAATTAAGTCTTTG-T
23949 TGATTTACTTAATTACCCTGAATTAAGTCTTTGTTTGATTTACTTAATTACCCTGAATTAAGTCT
64 TGATTTACTTAATTACCCTGAATTAAGTCTTTGTTTGATTTACTTAATTACCCTGAATTAAGTCT
24014 TTGCTTGAATTT
129 TTGC-TGAATTT
**
24026 ACTTAATTACCCTGAATTAAGTCTTTGACTGTG-TTTACTTAATTACCCTTCATTAAGTCTTTGC
1 ACTTAATTACCCTGAATTAAGTCTTTGA-T-TGATTTACTTAATTACCCTGAATTAAGTCTTTG-
24090 TTGAATTTACTTAATTACCCTGAATTAAGTCTTTG
63 TTG-ATTTACTTAATTACCCTGAATTAAGTCTTTG
24125 ACTGTGTTTA
Statistics
Matches: 560, Mismatches: 73, Indels: 56
0.81 0.11 0.08
Matches are distributed among these distances:
133 21 0.04
134 40 0.07
135 40 0.07
136 1 0.00
137 1 0.00
138 1 0.00
139 4 0.01
140 57 0.10
141 130 0.23
142 215 0.38
143 48 0.09
144 2 0.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (139 bp):
ACTTAATTACCCTGAATTAAGTCTTTGATTGATTTACTTAATTACCCTGAATTAAGTCTTTGTTG
ATTTACTTAATTACCCTGAATTAAGTCTTTGTTTGATTTACTTAATTACCCTGAATTAAGTCTTT
GCTGAATTT
Found at i:27164 original size:21 final size:21
Alignment explanation
Indices: 27138--27182 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
27128 TAAATGCTTT
27138 TGTTTTGTATTTTGCAAAGCC
1 TGTTTTGTATTTTGCAAAGCC
*
27159 TGTTTTGTATTTTGTAAAGCC
1 TGTTTTGTATTTTGCAAAGCC
27180 TGT
1 TGT
27183 AAACTAATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.11, G:0.20, T:0.51
Consensus pattern (21 bp):
TGTTTTGTATTTTGCAAAGCC
Found at i:35670 original size:26 final size:26
Alignment explanation
Indices: 35628--35703 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
35618 AAACTCATTG
*
35628 CTTCTTCTTTTGATTCCCTTCCTTTT
1 CTTCTTCTTTTCATTCCCTTCCTTTT
* *** *
35654 CTTCTTCTTTTCTTTCCAAACTTTTT
1 CTTCTTCTTTTCATTCCCTTCCTTTT
*
35680 CTTCTTC-TTTCCTTCTCCTTCCTT
1 CTTCTTCTTTTCATTC-CCTTCCTT
35704 GCCTGATTCT
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
25 7 0.18
26 31 0.82
ACGTcount: A:0.05, C:0.33, G:0.01, T:0.61
Consensus pattern (26 bp):
CTTCTTCTTTTCATTCCCTTCCTTTT
Found at i:36832 original size:30 final size:32
Alignment explanation
Indices: 36782--36867 Score: 104
Period size: 33 Copynumber: 2.7 Consensus size: 32
36772 GCCGCGCAAC
*
36782 ACCGGCCACATGACCGGCCATCGCATGG-G-GCA
1 ACCGGCCACA--ACCGGCCATCGCATGGCGACCA
* *
36814 ACCGGCCACAAGCGGCCATCGCTTGGCGCACCA
1 ACCGGCCACAACCGGCCATCGCATGGCG-ACCA
36847 ACCGGCCACAACCGGCCATCG
1 ACCGGCCACAACCGGCCATCG
36868 TTTGGGCCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 14 0.30
31 1 0.02
32 10 0.21
33 22 0.47
ACGTcount: A:0.22, C:0.42, G:0.28, T:0.08
Consensus pattern (32 bp):
ACCGGCCACAACCGGCCATCGCATGGCGACCA
Found at i:45440 original size:22 final size:22
Alignment explanation
Indices: 45414--45482 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
45404 CTAACTACTT
45414 TTCTGCTAATTGTGTTACATAA
1 TTCTGCTAATTGTGTTACATAA
*
45436 TTCTG-TAATT-TG-GACTAACTAA
1 TTCTGCTAATTGTGTTAC--A-TAA
45458 TT-TGC-AATTGTGTTACATAA
1 TTCTGCTAATTGTGTTACATAA
45478 TTCTG
1 TTCTG
45483 TTATCTACCA
Statistics
Matches: 38, Mismatches: 2, Indels: 15
0.69 0.04 0.27
Matches are distributed among these distances:
19 2 0.05
20 7 0.18
21 15 0.39
22 12 0.32
23 2 0.05
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (22 bp):
TTCTGCTAATTGTGTTACATAA
Found at i:45478 original size:42 final size:45
Alignment explanation
Indices: 45394--45483 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 45
45384 GAGCTGGTAA
* *
45394 GTAATTTGTACTAACTACTTTTCTGCTAATTGTGTTACATAATTCT
1 GTAATTTGGACTAACTAC-ATTCTGCTAATTGTGTTACATAATTCT
45440 GTAATTTGGACTAACTA-ATT-TGC-AATTGTGTTACATAATTCT
1 GTAATTTGGACTAACTACATTCTGCTAATTGTGTTACATAATTCT
45482 GT
1 GT
45484 TATCTACCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
42 21 0.50
43 3 0.07
44 2 0.05
46 16 0.38
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (45 bp):
GTAATTTGGACTAACTACATTCTGCTAATTGTGTTACATAATTCT
Found at i:54018 original size:30 final size:30
Alignment explanation
Indices: 53978--54042 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
53968 CAAGAAAGAG
53978 ATGGAATCGCACCAAAGATGCCATTAGGTA
1 ATGGAATCGCACCAAAGATGCCATTAGGTA
* *
54008 ATGGATTCGCACCAAAGATGCCATTAGGTC
1 ATGGAATCGCACCAAAGATGCCATTAGGTA
54038 ATGGA
1 ATGGA
54043 GATGCCAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.22
Consensus pattern (30 bp):
ATGGAATCGCACCAAAGATGCCATTAGGTA
Found at i:54557 original size:18 final size:18
Alignment explanation
Indices: 54534--54579 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
54524 TTATAAACAG
54534 AAGTTGAGTTGATTAATA
1 AAGTTGAGTTGATTAATA
54552 AAGTTGAGTTGATTAATA
1 AAGTTGAGTTGATTAATA
54570 AAGTTGAGTT
1 AAGTTGAGTT
54580 TTACACCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (18 bp):
AAGTTGAGTTGATTAATA
Found at i:62403 original size:21 final size:21
Alignment explanation
Indices: 62375--62414 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
62365 AAAAACAATC
62375 CTATTTTTATGGT-TATTTTA
1 CTATTTTTATGGTCTATTTTA
*
62395 CTATGTTTTTTGGTCTATTT
1 CTAT-TTTTATGGTCTATTT
62415 ATGCTCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.15, C:0.07, G:0.12, T:0.65
Consensus pattern (21 bp):
CTATTTTTATGGTCTATTTTA
Found at i:63916 original size:32 final size:33
Alignment explanation
Indices: 63880--64000 Score: 86
Period size: 33 Copynumber: 3.7 Consensus size: 33
63870 TACCGTGGCG
* *
63880 AAGCCGCCCCACTTGGGAGGCTTCGCCA-CGGC
1 AAGCCGCCCCACTGGGGAGGCTTCACCATCGGC
* * *
63912 AAGCCTCCCTCA-TGGGGCGGCTTCACCATGGGC
1 AAGCCGCCC-CACTGGGGAGGCTTCACCATCGGC
* * * * **
63945 AGGCCGCCCCACTGGCGCGGCTTCCCCAT-GAA
1 AAGCCGCCCCACTGGGGAGGCTTCACCATCGGC
* *
63977 AAGGCCGCCCCACTAGGGCGGCTT
1 AA-GCCGCCCCACTGGGGAGGCTT
64001 AGCCAGGGTA
Statistics
Matches: 71, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
32 25 0.35
33 46 0.65
ACGTcount: A:0.16, C:0.40, G:0.31, T:0.14
Consensus pattern (33 bp):
AAGCCGCCCCACTGGGGAGGCTTCACCATCGGC
Found at i:63966 original size:33 final size:33
Alignment explanation
Indices: 63926--64000 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
63916 CTCCCTCATG
***
63926 GGGCGGCTTCACCATGGGCAGGCCGCCCCACT-
1 GGGCGGCTTCACCATGAAAAGGCCGCCCCACTA
*
63958 GGCGCGGCTTCCCCATGAAAAGGCCGCCCCACTA
1 GG-GCGGCTTCACCATGAAAAGGCCGCCCCACTA
63992 GGGCGGCTT
1 GGGCGGCTT
64001 AGCCAGGGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 2 0.05
33 33 0.89
34 2 0.05
ACGTcount: A:0.15, C:0.39, G:0.33, T:0.13
Consensus pattern (33 bp):
GGGCGGCTTCACCATGAAAAGGCCGCCCCACTA
Found at i:64161 original size:33 final size:33
Alignment explanation
Indices: 64124--64220 Score: 101
Period size: 33 Copynumber: 2.9 Consensus size: 33
64114 GGCGGCTGAG
64124 CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA
1 CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA
* * * *
64157 CCATGGCCAGGCCG-CTTCCCTGGGACGGCCCTA
1 CCATGGCCAAGCCGCCCT-CCTGGGGCGGCACTA
*
64190 CCATGG--ATAGACCGCCCCCCTGGGGCGGCAC
1 CCATGGCCA-AG-CCGCCCTCCTGGGGCGGCAC
64221 CGGTACTAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
31 1 0.02
32 3 0.06
33 46 0.90
34 1 0.02
ACGTcount: A:0.14, C:0.42, G:0.31, T:0.12
Consensus pattern (33 bp):
CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA
Found at i:64335 original size:32 final size:32
Alignment explanation
Indices: 64284--64426 Score: 225
Period size: 32 Copynumber: 4.4 Consensus size: 32
64274 AAAAAGCCTT
* *
64284 GCCGCCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
64316 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
64348 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
* *
64380 GCCGTCCTAATGGGGA-GGCTCCGCCGTGGCAGA
1 GCCGTCCTAGT-GGGACGGCT-AGCCGTGGCAGA
64413 GCCGTCCTAGTGGG
1 GCCGTCCTAGTGGG
64427 GAGGCTCCGC
Statistics
Matches: 104, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
32 79 0.76
33 25 0.24
ACGTcount: A:0.14, C:0.29, G:0.41, T:0.15
Consensus pattern (32 bp):
GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
Found at i:74616 original size:16 final size:16
Alignment explanation
Indices: 74595--74626 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
74585 GAGGTAATTT
74595 ACACAGCAACACAACA
1 ACACAGCAACACAACA
*
74611 ACACAGCAATACAACA
1 ACACAGCAACACAACA
74627 GATGAATCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.34, G:0.06, T:0.03
Consensus pattern (16 bp):
ACACAGCAACACAACA
Found at i:74688 original size:31 final size:31
Alignment explanation
Indices: 74650--74708 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
74640 ACCCAATCTC
74650 AGTTGGTTACATTTTAGAGAAATTACCTGTT
1 AGTTGGTTACATTTTAGAGAAATTACCTGTT
74681 AGTTGGTTACATTTTAGAGAAATTACCT
1 AGTTGGTTACATTTTAGAGAAATTACCT
74709 ACCACCTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.41
Consensus pattern (31 bp):
AGTTGGTTACATTTTAGAGAAATTACCTGTT
Found at i:76831 original size:29 final size:27
Alignment explanation
Indices: 76785--76840 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
76775 GGATAAGGAT
*
76785 AAAATAAAAAAAGAGAAGTAATCAGTA
1 AAAAGAAAAAAAGAGAAGTAATCAGTA
*
76812 AAAAGAAATAAAAGAGGAAGTGATCAGTA
1 AAAAGAAA-AAAAGA-GAAGTAATCAGTA
76841 GAATGGAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.28
28 6 0.24
29 12 0.48
ACGTcount: A:0.62, C:0.04, G:0.20, T:0.14
Consensus pattern (27 bp):
AAAAGAAAAAAAGAGAAGTAATCAGTA
Found at i:76870 original size:32 final size:33
Alignment explanation
Indices: 76828--76904 Score: 115
Period size: 32 Copynumber: 2.4 Consensus size: 33
76818 AATAAAAGAG
*
76828 GAAGTGATCAGTAG-AATGGAGTGAAAG-TAAAA
1 GAAGTAATCAGTAGAAATGGAGT-AAAGCTAAAA
76860 GAAGTAATCAGT-GAAATGGAGTAAAGCTAAAA
1 GAAGTAATCAGTAGAAATGGAGTAAAGCTAAAA
76892 GAAGTAATCAGTA
1 GAAGTAATCAGTA
76905 AGTTGGTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
31 5 0.12
32 36 0.88
ACGTcount: A:0.48, C:0.05, G:0.27, T:0.19
Consensus pattern (33 bp):
GAAGTAATCAGTAGAAATGGAGTAAAGCTAAAA
Found at i:76923 original size:40 final size:40
Alignment explanation
Indices: 76878--76990 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 40
76868 CAGTGAAATG
*
76878 GAGT-AAAGCTAAAAGAAGTAATCAGTAAGTTGGTAATTAA
1 GAGTAAAAG-TAAAAGAAGTAATCAGTAAATTGGTAATTAA
* * ** * *
76918 GAGTAAAAGTAAAAGAGGCAATTTGTAAAATGGTAGTTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAATTGGTAATTAA
*
76958 GAGTAAAAGTAAAAGAAATAATCAGTAAATTGG
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAATTGG
76991 AAAAGAGTGA
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
40 55 0.93
41 4 0.07
ACGTcount: A:0.50, C:0.04, G:0.23, T:0.24
Consensus pattern (40 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAATTGGTAATTAA
Found at i:77103 original size:32 final size:33
Alignment explanation
Indices: 77059--77120 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 33
77049 TAAAATGGTA
77059 AAATGGTAATTAAATTCAAAGAGT-AAAATGAC
1 AAATGGTAATTAAATTCAAAGAGTGAAAATGAC
*
77091 AAATGGTGATTAAATTCAAAGAGTGAAAAT
1 AAATGGTAATTAAATTCAAAGAGTGAAAAT
77121 AGTAATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 23 0.82
33 5 0.18
ACGTcount: A:0.52, C:0.05, G:0.18, T:0.26
Consensus pattern (33 bp):
AAATGGTAATTAAATTCAAAGAGTGAAAATGAC
Found at i:77128 original size:26 final size:26
Alignment explanation
Indices: 77058--77152 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 26
77048 GTAAAATGGT
*
77058 AAAATGGTAATTAAATTCAAAGAGTAAAATG
1 AAAATAGTAATTAAATTCAAAGAG-----TG
* *
77089 ACAAATGGTGATTAAATTCAAAGAGTG
1 A-AAATAGTAATTAAATTCAAAGAGTG
77116 AAAATAGTAATTAAATTCAAGAGAGT-
1 AAAATAGTAATTAAATTCAA-AGAGTG
77142 AAAATAGTAAT
1 AAAATAGTAAT
77153 CAGTAAAGAG
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
26 28 0.47
27 8 0.14
31 1 0.02
32 22 0.37
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.26
Consensus pattern (26 bp):
AAAATAGTAATTAAATTCAAAGAGTG
Found at i:77185 original size:14 final size:14
Alignment explanation
Indices: 77147--77278 Score: 126
Period size: 14 Copynumber: 9.4 Consensus size: 14
77137 AGAGTAAAAT
77147 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
* **
77161 AGGAAAAAGTAAAG
1 AGTAATCAGTAAAG
*
77175 AGTAATCAGTAAAA
1 AGTAATCAGTAAAG
**
77189 AGTAAAAATGGTAAA-
1 AGTAATCA--GTAAAG
77204 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
77218 AGTAATCAGTAAA-
1 AGTAATCAGTAAAG
**
77231 AGTAAAAATGGTAAA-
1 AGTAATCA--GTAAAG
77246 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
*
77260 AGTAATCAGTAAAA
1 AGTAATCAGTAAAG
77274 AGTAA
1 AGTAA
77279 AAATGGCAAA
Statistics
Matches: 96, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
13 16 0.17
14 58 0.60
15 17 0.18
16 5 0.05
ACGTcount: A:0.56, C:0.05, G:0.20, T:0.20
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:77192 original size:7 final size:7
Alignment explanation
Indices: 77139--77281 Score: 67
Period size: 7 Copynumber: 20.1 Consensus size: 7
77129 AATTCAAGAG
77139 AGTAAAA
1 AGTAAAA
**
77146 TAGTAATC
1 -AGTAAAA
*
77154 AGTAAAG
1 AGTAAAA
*
77161 AGGAAAA
1 AGTAAAA
*
77168 AGTAAAG
1 AGTAAAA
**
77175 AGTAATC
1 AGTAAAA
77182 AGTAAAA
1 AGTAAAA
77189 AGTAAAA
1 AGTAAAA
77196 ATGGT-AAA
1 A--GTAAAA
**
77204 AGTAATC
1 AGTAAAA
*
77211 AGTAAAG
1 AGTAAAA
**
77218 AGTAATC
1 AGTAAAA
77225 AGT-AAA
1 AGTAAAA
77231 AGTAAAA
1 AGTAAAA
77238 ATGGT-AAA
1 A--GTAAAA
**
77246 AGTAATC
1 AGTAAAA
*
77253 AGTAAAG
1 AGTAAAA
**
77260 AGTAATC
1 AGTAAAA
77267 AGTAAAA
1 AGTAAAA
77274 AGTAAAA
1 AGTAAAA
77281 A
1 A
77282 TGGCAAAGAG
Statistics
Matches: 100, Mismatches: 28, Indels: 15
0.70 0.20 0.10
Matches are distributed among these distances:
6 8 0.08
7 75 0.75
8 13 0.13
9 4 0.04
ACGTcount: A:0.57, C:0.04, G:0.19, T:0.20
Consensus pattern (7 bp):
AGTAAAA
Found at i:77233 original size:42 final size:43
Alignment explanation
Indices: 77168--77293 Score: 227
Period size: 42 Copynumber: 2.9 Consensus size: 43
77158 AAGAGGAAAA
77168 AGTAAAGAGTAATCAGTAAAAAGTAAAAATGGTAAAAGTAATC
1 AGTAAAGAGTAATCAGTAAAAAGTAAAAATGGTAAAAGTAATC
77211 AGTAAAGAGTAATCAGT-AAAAGTAAAAATGGTAAAAGTAATC
1 AGTAAAGAGTAATCAGTAAAAAGTAAAAATGGTAAAAGTAATC
*
77253 AGTAAAGAGTAATCAGTAAAAAGTAAAAATGGCAAAGAGTA
1 AGTAAAGAGTAATCAGTAAAAAGTAAAAATGGTAAA-AGTA
77294 GTAAAAGGTA
Statistics
Matches: 80, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
42 42 0.52
43 34 0.43
44 4 0.05
ACGTcount: A:0.56, C:0.05, G:0.20, T:0.20
Consensus pattern (43 bp):
AGTAAAGAGTAATCAGTAAAAAGTAAAAATGGTAAAAGTAATC
Found at i:77384 original size:16 final size:16
Alignment explanation
Indices: 77363--77393 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
77353 AAGAGTAAAG
77363 GGTAATCAATAAAGAT
1 GGTAATCAATAAAGAT
*
77379 GGTAATCAGTAAAGA
1 GGTAATCAATAAAGA
77394 GTAAAATAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.23, T:0.23
Consensus pattern (16 bp):
GGTAATCAATAAAGAT
Found at i:77429 original size:44 final size:43
Alignment explanation
Indices: 77379--77556 Score: 194
Period size: 44 Copynumber: 4.3 Consensus size: 43
77369 CAATAAAGAT
77379 GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAA
1 GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAA-AA
77423 GGTAATCAGTAAAGAGTAAAATAGTAATC-------AGTAAAA
1 GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAAA
* * *
77459 GGTAATCAGT-AAGAGTAAAATAGTAATTAGTAGAAAGCAAAA
1 GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAAA
* * *
77501 TGGTAATTAGT-AAGAATAAAAATAGTAATCAGTAAAGAGTAAAA
1 -GGTAATCAGTAAAGAGT-AAAATAGTAATCAGTAAAAAGTAAAA
* *
77545 AGTGATCAGTAA
1 GGTAATCAGTAA
77557 TTCAAAGAGT
Statistics
Matches: 113, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
35 17 0.15
36 12 0.11
37 5 0.04
42 6 0.05
43 21 0.19
44 52 0.46
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (43 bp):
GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAAA
Found at i:77463 original size:22 final size:22
Alignment explanation
Indices: 77380--77457 Score: 122
Period size: 22 Copynumber: 3.5 Consensus size: 22
77370 AATAAAGATG
77380 GTAATCAGTAAAGAGTAAAATA
1 GTAATCAGTAAAGAGTAAAATA
* *
77402 GTAATCAGTAAAAAGTAAGAA-G
1 GTAATCAGTAAAGAGTAA-AATA
77424 GTAATCAGTAAAGAGTAAAATA
1 GTAATCAGTAAAGAGTAAAATA
77446 GTAATCAGTAAA
1 GTAATCAGTAAA
77458 AGGTAATCAG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.04
22 46 0.92
23 2 0.04
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.22
Consensus pattern (22 bp):
GTAATCAGTAAAGAGTAAAATA
Found at i:77480 original size:35 final size:36
Alignment explanation
Indices: 77415--77495 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 36
77405 ATCAGTAAAA
77415 AGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATC
1 AGTAA-AAGGTAATCAGTAAAGAGTAAAATAGTAATC
*
77452 AGTAAAAGGTAATCAGT-AAGAGTAAAATAGTAATT
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
77487 AGTAGAAAG
1 AGTA-AAAG
77496 CAAAATGGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 21 0.50
36 16 0.38
37 5 0.12
ACGTcount: A:0.52, C:0.04, G:0.22, T:0.22
Consensus pattern (36 bp):
AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
Found at i:77485 original size:79 final size:82
Alignment explanation
Indices: 77364--77538 Score: 243
Period size: 79 Copynumber: 2.2 Consensus size: 82
77354 AGAGTAAAGG
* *
77364 GTAATCAATAAAGATGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAA-GGTAA
1 GTAATCAGTAAAGATGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGCAA-AATGGTAA
*
77428 TCAGTAAAGAGT-AAAATA
65 TCAGT-AAGAATAAAAATA
* *
77446 GTAATCAGTAAA-A-GGTAATCAGT-AAGAGTAAAATAGTAATTAGTAGAAAGCAAAATGGTAAT
1 GTAATCAGTAAAGATGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGCAAAATGGTAAT
*
77508 TAGTAAGAATAAAAATA
66 CAGTAAGAATAAAAATA
77525 GTAATCAGTAAAGA
1 GTAATCAGTAAAGA
77539 GTAAAAAGTG
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
78 7 0.08
79 54 0.64
80 11 0.13
81 1 0.01
82 11 0.13
ACGTcount: A:0.53, C:0.05, G:0.19, T:0.23
Consensus pattern (82 bp):
GTAATCAGTAAAGATGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGCAAAATGGTAAT
CAGTAAGAATAAAAATA
Found at i:77522 original size:22 final size:22
Alignment explanation
Indices: 77460--77545 Score: 79
Period size: 22 Copynumber: 3.9 Consensus size: 22
77450 TCAGTAAAAG
*
77460 GTAATCAGTAAGAGT-AAAATA
1 GTAATCAGTAAGAATAAAAATA
* *
77481 GTAATTAGT-AGAA-AGCAAAATG
1 GTAATCAGTAAGAATA--AAAATA
*
77503 GTAATTAGTAAGAATAAAAATA
1 GTAATCAGTAAGAATAAAAATA
*
77525 GTAATCAGTAAAGAGTAAAAA
1 GTAATCAGT-AAGAATAAAAA
77546 GTGATCAGTA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
20 3 0.06
21 8 0.15
22 27 0.51
23 14 0.26
24 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.19, T:0.23
Consensus pattern (22 bp):
GTAATCAGTAAGAATAAAAATA
Found at i:78280 original size:28 final size:26
Alignment explanation
Indices: 78231--78299 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 26
78221 TTTTTACTCT
78231 TTTCTTACTCT-TTTACTAATTACCC
1 TTTCTTACTCTCTTTACTAATTACCC
* *
78256 TTTCCTTACTCTCTTTCATTGATTACCAC
1 TTT-CTTACTCTCTTT-ACTAATTACC-C
78285 TTT-TTACTCTTCTTT
1 TTTCTTACTC-TCTTT
78300 TTCTCTTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
25 3 0.08
26 8 0.22
27 9 0.24
28 13 0.35
29 4 0.11
ACGTcount: A:0.16, C:0.28, G:0.01, T:0.55
Consensus pattern (26 bp):
TTTCTTACTCTCTTTACTAATTACCC
Found at i:78427 original size:28 final size:27
Alignment explanation
Indices: 78404--78457 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
78394 GATTACTATT
78404 TTACTATGA-CTGATTACCTTTTACTGA
1 TTACTATGATCTGATTACCTTTTACT-A
* *
78431 TTACTATTATCTGATTACTTTTTACTA
1 TTACTATGATCTGATTACCTTTTACTA
78458 CTCTTTGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (27 bp):
TTACTATGATCTGATTACCTTTTACTA
Found at i:78431 original size:14 final size:14
Alignment explanation
Indices: 78412--78456 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
78402 TTTTACTATG
78412 ACTGATTACCTTTT
1 ACTGATTACCTTTT
*
78426 ACTGATTA-CTATT
1 ACTGATTACCTTTT
*
78439 ATCTGATTACTTTTT
1 A-CTGATTACCTTTT
78454 ACT
1 ACT
78457 ACTCTTTGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 5 0.19
14 17 0.65
15 4 0.15
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.51
Consensus pattern (14 bp):
ACTGATTACCTTTT
Found at i:78493 original size:14 final size:14
Alignment explanation
Indices: 78471--78516 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
78461 TTTGCCATTT
78471 TTACT-TTTACTGA
1 TTACTCTTTACTGA
**
78484 TTACTCTTTACTTT
1 TTACTCTTTACTGA
*
78498 TTCCTCTTTACTGA
1 TTACTCTTTACTGA
78512 TTACT
1 TTACT
78517 ATTTTACCCT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 5 0.19
14 21 0.81
ACGTcount: A:0.17, C:0.22, G:0.04, T:0.57
Consensus pattern (14 bp):
TTACTCTTTACTGA
Found at i:78557 original size:26 final size:27
Alignment explanation
Indices: 78511--78578 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
78501 CTCTTTACTG
**
78511 ATTACTATTTT-ACCCTCTTGAACTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
*
78537 ATTACTATTTTCATTCT-TTGAATTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
* *
78563 ATCACCATTTGTCATT
1 ATTACTATTT-TCATT
78579 TTACTCTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 27 0.77
27 8 0.23
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.50
Consensus pattern (27 bp):
ATTACTATTTTCATTCTCTTGAACTTA
Found at i:78692 original size:40 final size:39
Alignment explanation
Indices: 78648--78764 Score: 155
Period size: 40 Copynumber: 2.9 Consensus size: 39
78638 TTTTTACTCT
*
78648 TTACCGATTTACTGATTACTTCTTTTACTCTT-ACTCTTAA
1 TTACC-ATTTACTGATTACTTCTTTTACT-TTAACTCATAA
*
78688 TTACCATTTTACTAATTACTTCTTTTACTTTAACTCATAA
1 TTACCA-TTTACTGATTACTTCTTTTACTTTAACTCATAA
* *
78728 TTACCAACTTACTGATTACTTCTTTTACTTTCACTCA
1 TTACC-ATTTACTGATTACTTCTTTTACTTTAACTCA
78765 ATTTTACTGA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
39 3 0.04
40 65 0.94
41 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.49
Consensus pattern (39 bp):
TTACCATTTACTGATTACTTCTTTTACTTTAACTCATAA
Found at i:78862 original size:36 final size:36
Alignment explanation
Indices: 78655--78896 Score: 145
Period size: 40 Copynumber: 6.3 Consensus size: 36
78645 TCTTTACCGA
*
78655 TTTACTGATTACTTCTTTTACTCTTACTCTTAATTACCAT
1 TTTACTGATTACTTCTTTTACTTTTACTCTT--TTA-C-T
* * * *
78695 TTTACTAATTACTTCTTTTACTTTAACTCATAATTACCAA
1 TTTACTGATTACTTCTTTTACTTTTACTC-T-TTTA-C-T
* * *
78735 CTTACTGATTACTTCTTTTACTTTCACTC----AAT
1 TTTACTGATTACTTCTTTTACTTTTACTCTTTTACT
78767 TTTACTGATTACTT-TTTCTACGAGTTACTT-CTCTTGATTACCAT
1 TTTACTGATTACTTCTTT-TAC---TT--TTACTCTT--TTA-C-T
* * **
78811 TTTTCTGATTACTTCTTTTATTTTTGTTCTTTTACT
1 TTTACTGATTACTTCTTTTACTTTTACTCTTTTACT
78847 TTTACTGATTACTTCTTTTACTTTTACTCTTTTACT
1 TTTACTGATTACTTCTTTTACTTTTACTCTTTTACT
78883 GACTTTACTGATTA
1 ---TTTACTGATTA
78897 ATCCCTTACC
Statistics
Matches: 161, Mismatches: 20, Indels: 43
0.72 0.09 0.19
Matches are distributed among these distances:
31 3 0.02
32 16 0.10
34 1 0.01
35 2 0.01
36 36 0.22
37 2 0.01
38 3 0.02
39 13 0.08
40 62 0.39
41 3 0.02
42 1 0.01
44 16 0.10
45 3 0.02
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.54
Consensus pattern (36 bp):
TTTACTGATTACTTCTTTTACTTTTACTCTTTTACT
Found at i:78877 original size:76 final size:72
Alignment explanation
Indices: 78693--78877 Score: 158
Period size: 76 Copynumber: 2.5 Consensus size: 72
78683 CTTAATTACC
* * *
78693 ATTTTACTAATTACTTCTTTTACTTTAACTCATAATTACCAACTTACTGATTACTTCTTTTACTT
1 ATTTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAACTTACTGATTACTTCTTTTACTT
78758 TCACTCA
66 TCACTCA
* ** *
78765 ATTTTACTGATTACTT-TTTCTACGAGTTACTT-CTCTTGATTACCATTTTTCTGATTACTTCTT
1 ATTTTACTGATTACTTCTTT-TAC---TT--TTACTCTTAATTACCAACTTACTGATTACTTCTT
* ** *
78828 TTATTTTTGTTCTTTTA
60 TTA---CT-TTCACTCA
*
78845 CTTTTACTGATTACTTCTTTTACTTTTACTCTT
1 ATTTTACTGATTACTTCTTTTACTTTTACTCTT
78878 TTACTGACTT
Statistics
Matches: 89, Mismatches: 12, Indels: 20
0.74 0.10 0.17
Matches are distributed among these distances:
71 3 0.03
72 18 0.20
75 4 0.04
76 34 0.38
77 3 0.03
79 1 0.01
80 23 0.26
81 3 0.03
ACGTcount: A:0.21, C:0.19, G:0.04, T:0.55
Consensus pattern (72 bp):
ATTTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAACTTACTGATTACTTCTTTTACTT
TCACTCA
Found at i:78879 original size:14 final size:16
Alignment explanation
Indices: 78736--78884 Score: 61
Period size: 16 Copynumber: 9.4 Consensus size: 16
78726 AATTACCAAC
78736 TTACTGATTACTTCTT
1 TTACTGATTACTTCTT
78752 TTACT--TTCAC-TCAATT
1 TTACTGATT-ACTTC--TT
78768 TTACTGATTACTT-TT
1 TTACTGATTACTTCTT
78783 TCTAC-GAGTTACTTC-T
1 T-TACTGA-TTACTTCTT
*
78799 CT--TGATTAC--CATT
1 TTACTGATTACTTC-TT
*
78812 TTTCTGATTACTTCTT
1 TTACTGATTACTTCTT
* ** *
78828 TTATTTTTGTTCTTTTACTT
1 TTACTGAT-TAC--TT-CTT
78848 TTACTGATTACTTCTT
1 TTACTGATTACTTCTT
*
78864 TTACT-TTTAC-TCTT
1 TTACTGATTACTTCTT
78878 TTACTGA
1 TTACTGA
78885 CTTTACTGAT
Statistics
Matches: 99, Mismatches: 13, Indels: 43
0.64 0.08 0.28
Matches are distributed among these distances:
11 1 0.01
13 6 0.06
14 15 0.15
15 19 0.19
16 36 0.36
17 7 0.07
18 3 0.03
19 4 0.04
20 8 0.08
ACGTcount: A:0.18, C:0.19, G:0.06, T:0.57
Consensus pattern (16 bp):
TTACTGATTACTTCTT
Found at i:79768 original size:2 final size:2
Alignment explanation
Indices: 79761--79789 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
79751 ACTTACTTAG
79761 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 T
79790 CCTAAAACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:82875 original size:18 final size:18
Alignment explanation
Indices: 82833--82868 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
82823 ATGCGGGTTA
*
82833 GAATGATAATGCAATGTC
1 GAATGCTAATGCAATGTC
*
82851 GAATGCTAATGTAATGTC
1 GAATGCTAATGCAATGTC
82869 ATATGCTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (18 bp):
GAATGCTAATGCAATGTC
Done.