Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007406.1 Hibiscus syriacus cultivar Beakdansim tig00020010_pilon, 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: 78682
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:465 original size:18 final size:18
Alignment explanation
Indices: 433--467 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
423 AGAAAAAGGC
**
433 AATCAAAATTGCAATCAA
1 AATCAAAATCCCAATCAA
451 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
468 CAACCGGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:776 original size:139 final size:139
Alignment explanation
Indices: 524--804 Score: 519
Period size: 139 Copynumber: 2.0 Consensus size: 139
514 TGCAAACGTG
*
524 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGCATTAGTAACTTGAGT
*
589 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACATATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCA-TTGAATATCGCAACG
654 CGAATTTGAC
130 CGAATTTGAC
*
664 TATTATGTGTATTTTATGTGTAAAC-TTTAACATTTTCAGTTAGGCATGCATTAGTAACTTGATT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGCATTAGTAACTTGAGT
728 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTGAATATCGCAACGC
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTGAATATCGCAACGC
793 GAATTTGAC
131 GAATTTGAC
802 TAT
1 TAT
805 CGCAACGCGA
Statistics
Matches: 138, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
138 28 0.20
139 85 0.62
140 25 0.18
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (139 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGCATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTGAATATCGCAACGC
GAATTTGAC
Found at i:805 original size:20 final size:20
Alignment explanation
Indices: 777--911 Score: 207
Period size: 20 Copynumber: 6.8 Consensus size: 20
767 TACACATTCA
*
777 TTGAATATCGCAACGCGAAT
1 TTGACTATCGCAACGCGAAT
797 TTGACTATCGCAACGCGAAT
1 TTGACTATCGCAACGCGAAT
817 TTGACTATCGCAACGCGAAT
1 TTGACTATCGCAACGCGAAT
*
837 TTGACTATCGCAACGTGAAT
1 TTGACTATCGCAACGCGAAT
*
857 TTGACTATCGCAACGTGAAT
1 TTGACTATCGCAACGCGAAT
* * * *
877 TTGATTATCGCAATGGGAAG
1 TTGACTATCGCAACGCGAAT
897 TTGACTATCGCAACG
1 TTGACTATCGCAACG
912 AGAAAATTGC
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 107 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (20 bp):
TTGACTATCGCAACGCGAAT
Found at i:989 original size:20 final size:20
Alignment explanation
Indices: 950--1027 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
940 GCAACGCGAA
* * *
950 TTGACTTTCACGTTGTGATT
1 TTGACTTTCGCATTGCGATT
*
970 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
990 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
* * *
1010 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGA
1028 AAGTGTACCT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:2614 original size:21 final size:21
Alignment explanation
Indices: 2548--2664 Score: 90
Period size: 21 Copynumber: 5.6 Consensus size: 21
2538 GTGAATCGGG
* * **
2548 CTCTTGAATGGTGGGAGGAAC
1 CTCTTGAACGATGGGAGGGGC
* ** * *
2569 CTCTTCAACGATGACAGTGAC
1 CTCTTGAACGATGGGAGGGGC
*
2590 CTCTTGAACGATGGGAGGGGA
1 CTCTTGAACGATGGGAGGGGC
** **
2611 CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* *
2632 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGATGGGAGGGGC
2653 CTCTTGAACGAT
1 CTCTTGAACGAT
2665 TACAGGTGAG
Statistics
Matches: 72, Mismatches: 24, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 72 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:2615 original size:42 final size:42
Alignment explanation
Indices: 2569--2670 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
2559 TGGGAGGAAC
* * * *
2569 CTCTTCAACGATGACAGTGACCTCTTGAACGATGGGAGGGGA
1 CTCTTGAACGATGACAGGGACCTCTTGAACGATAGGAGAGGA
** * * *
2611 CTCTTGAGGGATGATAGGGGCCTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGATGACAGGGACCTCTTGAACGATAGGAGAGGA
*
2653 CTCTTGAACGATTACAGG
1 CTCTTGAACGATGACAGG
2671 TGAGTCGAGC
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGATGACAGGGACCTCTTGAACGATAGGAGAGGA
Found at i:3170 original size:20 final size:20
Alignment explanation
Indices: 3145--3186 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3135 ATAGTTTCTA
3145 AAACTTAAAATCGCAACACG
1 AAACTTAAAATCGCAACACG
*
3165 AAACTTAAAATCGCAACGCG
1 AAACTTAAAATCGCAACACG
3185 AA
1 AA
3187 TTTGACTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.24, G:0.12, T:0.14
Consensus pattern (20 bp):
AAACTTAAAATCGCAACACG
Found at i:3197 original size:20 final size:20
Alignment explanation
Indices: 3174--3241 Score: 111
Period size: 20 Copynumber: 3.4 Consensus size: 20
3164 GAAACTTAAA
3174 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
3194 ATCGCAACGCGGAA-ATGACT
1 ATCGCAACGC-GAATTTGACT
3214 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
3234 ATCGCAAC
1 ATCGCAAC
3242 AAGATAATCG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.07
20 38 0.86
21 3 0.07
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:3260 original size:34 final size:36
Alignment explanation
Indices: 3173--3261 Score: 103
Period size: 40 Copynumber: 2.4 Consensus size: 36
3163 CGAAACTTAA
3173 AATCGCAACGCGAATTTGACTATCGCAACGCGGAAATG
1 AATCGCAACGCGAATTTGACTATCGCAAC-C-GAAATG
3211 ACTATCGCAACGCGAATTTGACTATCGCAA-C-AAGAT-
1 A--ATCGCAACGCGAATTTGACTATCGCAACCGAA-ATG
*
3247 AATCGCAATGCGAAT
1 AATCGCAACGCGAAT
3262 AAAAATCGCA
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
34 13 0.28
36 3 0.06
37 2 0.04
38 2 0.04
40 27 0.57
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (36 bp):
AATCGCAACGCGAATTTGACTATCGCAACCGAAATG
Found at i:3351 original size:33 final size:34
Alignment explanation
Indices: 3289--3364 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
3279 ACTAAATCCG
*
3289 CGTTGCGATTTTCATTTTCGCATTACGATTTTCA
1 CGTTGCGATTTTCATTTTCGCATTACGATTATCA
* * *
3323 CGTTGCGATTTTTA-TTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTTCGCATTACGATTATCA
3356 CGTTGCGAT
1 CGTTGCGAT
3365 AGTCAAATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
33 25 0.66
34 13 0.34
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTACGATTATCA
Found at i:3383 original size:20 final size:20
Alignment explanation
Indices: 3356--3424 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
3346 GCGATTATCT
*
3356 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
*
3376 CATTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
*
3396 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
3416 CGTTGCGAT
1 CGTTGCGAT
3425 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:5283 original size:20 final size:20
Alignment explanation
Indices: 5260--5310 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5250 TCTGAAACTT
* *
5260 AAAATCGTAACACGAAAATG
1 AAAATCGCAACACAAAAATG
5280 AAAATCGCAACACAAAAATG
1 AAAATCGCAACACAAAAATG
**
5300 ACTATCGCAAC
1 AAAATCGCAAC
5311 GCGAATTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.53, C:0.22, G:0.12, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACAAAAATG
Found at i:5321 original size:20 final size:20
Alignment explanation
Indices: 5298--5375 Score: 129
Period size: 20 Copynumber: 3.9 Consensus size: 20
5288 AACACAAAAA
5298 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATT
*
5318 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATT
*
5338 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATT
*
5358 TGACTATCGCAGCGCGAA
1 TGACTATCGCAACGCGAA
5376 ATGAAAATCG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATT
Found at i:5836 original size:22 final size:22
Alignment explanation
Indices: 5809--5859 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
5799 GATGGAGATA
*
5809 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
5831 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
5853 GACGGAT
1 GACGGAT
5860 GATGCCGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.14, G:0.45, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:6051 original size:20 final size:20
Alignment explanation
Indices: 6026--6098 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
6016 ATTATGTATT
*
6026 ATCGCGTTGCGATAGACAGA
1 ATCGCGTTGCGATAGTCAGA
* *
6046 ATCGCGTTGCAATAGTCATA
1 ATCGCGTTGCGATAGTCAGA
6066 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
6086 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
6099 TTACATATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:6131 original size:21 final size:20
Alignment explanation
Indices: 6085--6132 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
6075 CGATAGTCAG
* *
6085 AATCGCGTTGCGATTTACAT
1 AATCGCATTGCGATTTACAA
* *
6105 ATTCGCATTGCGATTTTATAA
1 AATCGCATTGCGA-TTTACAA
6126 AATCGCA
1 AATCGCA
6133 ACGCGAATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (20 bp):
AATCGCATTGCGATTTACAA
Found at i:6138 original size:21 final size:21
Alignment explanation
Indices: 6114--6154 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6104 TATTCGCATT
* *
6114 GCGATTTTATAAAATCGCAAC
1 GCGAATTTAGAAAATCGCAAC
*
6135 GCGAATTTGGAAAATCGCAA
1 GCGAATTTAGAAAATCGCAA
6155 TCGCATTGCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (21 bp):
GCGAATTTAGAAAATCGCAAC
Found at i:6215 original size:19 final size:19
Alignment explanation
Indices: 6191--6227 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6181 TGCGATACTG
* *
6191 GAGATCGCGTTTCGATTTA
1 GAGATCGCATTGCGATTTA
6210 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
6228 TGTTGGTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:6606 original size:50 final size:51
Alignment explanation
Indices: 6541--6651 Score: 145
Period size: 50 Copynumber: 2.2 Consensus size: 51
6531 GCAGTAAAGT
* * *
6541 GCGCCCCCTGAACCGCGTTATATGCTGATTTGG-CACCACGTGGAGTATAGC
1 GCGCCCCCTGAACCGCGCTATATGCTGACTGGGTCA-CACGTGGAGTATAGC
* * *
6592 GC-CCCCCTGTACCGCGCTATATGCTGACTGGGTTACACGTGGGGTATAGC
1 GCGCCCCCTGAACCGCGCTATATGCTGACTGGGTCACACGTGGAGTATAGC
6642 GCGCCCCCTG
1 GCGCCCCCTG
6652 CTCTGCGCTA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 42 0.81
51 10 0.19
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.23
Consensus pattern (51 bp):
GCGCCCCCTGAACCGCGCTATATGCTGACTGGGTCACACGTGGAGTATAGC
Found at i:8639 original size:18 final size:18
Alignment explanation
Indices: 8616--8652 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
8606 GCGAATGAGA
8616 TGCATCTTACAACGAACT
1 TGCATCTTACAACGAACT
8634 TGCATCTTACAACGAACT
1 TGCATCTTACAACGAACT
8652 T
1 T
8653 CCAGGTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (18 bp):
TGCATCTTACAACGAACT
Found at i:10328 original size:35 final size:34
Alignment explanation
Indices: 10243--10329 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
10233 ATTTGGTATT
*
10243 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
10277 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
10315 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
10330 ATTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:10556 original size:3 final size:3
Alignment explanation
Indices: 10550--10623 Score: 58
Period size: 3 Copynumber: 24.7 Consensus size: 3
10540 GTCATCATCA
* * * * * * * *
10550 TCG TCG TTG TCG TCG TCA CCA TCG TCG TCG TCG TCG TCA CCA TCG TCA
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG
* *
10598 TCG TCG TCA TCG TCA TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TC
10624 CTGAGCAGGT
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.09, C:0.35, G:0.23, T:0.32
Consensus pattern (3 bp):
TCG
Found at i:10572 original size:21 final size:21
Alignment explanation
Indices: 10548--10623 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
10538 CTGTCATCAT
*
10548 CATCGTCGTTGTCGTCGTCAC
1 CATCGTCGTCGTCGTCGTCAC
10569 CATCGTCGTCGTCGTCGTCAC
1 CATCGTCGTCGTCGTCGTCAC
* * **
10590 CATCGTCATCGTCGTCATCGT
1 CATCGTCGTCGTCGTCGTCAC
10611 CATCGTCGTCGTC
1 CATCGTCGTCGTC
10624 CTGAGCAGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.11, C:0.36, G:0.22, T:0.32
Consensus pattern (21 bp):
CATCGTCGTCGTCGTCGTCAC
Found at i:10958 original size:27 final size:27
Alignment explanation
Indices: 10928--10984 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
10918 AGGTGAAGAC
* * *
10928 GGCGGCGGCAGCATCTGGTAATTGAAA
1 GGCGACGGCAGCATATGGTAATGGAAA
* *
10955 GGCGATGGCGGCATATGGTAATGGAAA
1 GGCGACGGCAGCATATGGTAATGGAAA
10982 GGC
1 GGC
10985 TATGATGGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.16, G:0.40, T:0.18
Consensus pattern (27 bp):
GGCGACGGCAGCATATGGTAATGGAAA
Found at i:10994 original size:27 final size:27
Alignment explanation
Indices: 10938--10995 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
10928 GGCGGCGGCA
* * *
10938 GCATCTGGTAATTGAAAGGCGATGGCG
1 GCATATGGTAATGGAAAGGCGATGACG
* *
10965 GCATATGGTAATGGAAAGGCTATGATG
1 GCATATGGTAATGGAAAGGCGATGACG
10992 GCAT
1 GCAT
10996 CATATATGGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.34, T:0.24
Consensus pattern (27 bp):
GCATATGGTAATGGAAAGGCGATGACG
Found at i:11014 original size:18 final size:18
Alignment explanation
Indices: 10991--11025 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
10981 AGGCTATGAT
10991 GGCATCATATATGGCTGC
1 GGCATCATATATGGCTGC
11009 GGCATCATATATGGCTG
1 GGCATCATATATGGCTG
11026 AGGTGGCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (18 bp):
GGCATCATATATGGCTGC
Found at i:12727 original size:111 final size:111
Alignment explanation
Indices: 12533--12860 Score: 558
Period size: 111 Copynumber: 3.0 Consensus size: 111
12523 TTACAAAAAA
*
12533 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATAATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
12598 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
12644 TTAATTCTTAATCTAATAATTATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATAATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* **
12709 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAAAGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
12755 TTAATTCTTAATCTAATAATAATGCATTAAATAAATCAACTAAATATTAC---TAATTT-AATT-
1 TTAATTCTTAATCTAATAATAATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
12815 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
12861 ATGATTTCCA
Statistics
Matches: 207, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
106 42 0.20
107 4 0.02
108 6 0.03
111 155 0.75
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATAATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:24259 original size:21 final size:23
Alignment explanation
Indices: 24233--24277 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
24223 TGGTAAAAAA
24233 TTATCTAAAAAATT-AT-TATTT
1 TTATCTAAAAAATTAATGTATTT
*
24254 TTATCTAAAACATTAATGTATTT
1 TTATCTAAAAAATTAATGTATTT
24277 T
1 T
24278 AACATTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 2 0.10
23 6 0.29
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (23 bp):
TTATCTAAAAAATTAATGTATTT
Found at i:28667 original size:22 final size:21
Alignment explanation
Indices: 28615--28674 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
28605 GATTTCTGGG
28615 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
28636 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
28656 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
28675 CTCAAGCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.56
21 3 0.08
22 13 0.36
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:29598 original size:31 final size:31
Alignment explanation
Indices: 29560--29653 Score: 136
Period size: 31 Copynumber: 3.0 Consensus size: 31
29550 AGGGTCAAGG
29560 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
29591 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * * *
29622 GATTACCTAGGTTTTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
29653 G
1 G
29654 GTCTTTCGGG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 57 0.98
32 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:30141 original size:21 final size:21
Alignment explanation
Indices: 30116--30158 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
30106 AAAGAATATA
30116 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
30137 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
30158 T
1 T
30159 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:33365 original size:21 final size:21
Alignment explanation
Indices: 33339--33378 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
33329 ACAGAACCCA
*
33339 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
33360 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
33379 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:33407 original size:19 final size:20
Alignment explanation
Indices: 33361--33420 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
33351 TTCCCCTGTG
33361 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TC-AA
33384 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
33403 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
33421 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:42788 original size:30 final size:30
Alignment explanation
Indices: 42754--42871 Score: 110
Period size: 30 Copynumber: 4.2 Consensus size: 30
42744 AACACTCCAT
* *
42754 AGGTCACCGTGTGTTCCTGGAGACCTATGG
1 AGGTCACCATGTGCTCCTGGAGACCTATGG
*
42784 AGGTCGCCATGTGCTCCT------C-AT--
1 AGGTCACCATGTGCTCCTGGAGACCTATGG
* *
42805 AGGTCACCGTGTGTTCCTGGAGACCTATGG
1 AGGTCACCATGTGCTCCTGGAGACCTATGG
*
42835 AGGTCGCCATGTGCTCCTGGAGACCTATGG
1 AGGTCACCATGTGCTCCTGGAGACCTATGG
*
42865 TGGTCAC
1 AGGTCAC
42872 TGTAACAATC
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
21 15 0.22
23 2 0.03
24 1 0.01
27 1 0.01
28 2 0.03
30 47 0.69
ACGTcount: A:0.16, C:0.26, G:0.31, T:0.26
Consensus pattern (30 bp):
AGGTCACCATGTGCTCCTGGAGACCTATGG
Found at i:42827 original size:51 final size:51
Alignment explanation
Indices: 42751--42852 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
42741 CACAACACTC
42751 CATAGGTCACCGTGTGTTCCTGGAGACCTATGGAGGTCGCCATGTGCTCCT
1 CATAGGTCACCGTGTGTTCCTGGAGACCTATGGAGGTCGCCATGTGCTCCT
42802 CATAGGTCACCGTGTGTTCCTGGAGACCTATGGAGGTCGCCATGTGCTCCT
1 CATAGGTCACCGTGTGTTCCTGGAGACCTATGGAGGTCGCCATGTGCTCCT
42853 GGAGACCTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.27
Consensus pattern (51 bp):
CATAGGTCACCGTGTGTTCCTGGAGACCTATGGAGGTCGCCATGTGCTCCT
Found at i:46159 original size:2 final size:2
Alignment explanation
Indices: 46152--46195 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
46142 CTTACTTCCC
46152 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46194 AT
1 AT
46196 TCTCTTATCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46806 original size:26 final size:25
Alignment explanation
Indices: 46772--46821 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
46762 TGTTTTGATT
46772 TTTTATTTATAATATTGAAATTTTA
1 TTTTATTTATAATATTGAAATTTTA
** *
46797 TTTTACTTTATGTTATTGTAATTTT
1 TTTTA-TTTATAATATTGAAATTTT
46822 TTACGATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (25 bp):
TTTTATTTATAATATTGAAATTTTA
Found at i:48573 original size:28 final size:27
Alignment explanation
Indices: 48524--48578 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
48514 CTATATCGTT
* * *
48524 TTTAGTTAATTGAACTAGTAAAAATATA
1 TTTAGTTAATCGAACAAAT-AAAATATA
*
48552 TTTAGTTAATCGGACAAATAAAATATA
1 TTTAGTTAATCGAACAAATAAAATATA
48579 GCAGATATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.36
Consensus pattern (27 bp):
TTTAGTTAATCGAACAAATAAAATATA
Found at i:49121 original size:31 final size:31
Alignment explanation
Indices: 49086--49152 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
49076 TTGCAATACA
49086 GTCCCCTAACATTTAGTCCATTTGTAATATG
1 GTCCCCTAACATTTAGTCCATTTGTAATATG
*
49117 GTCCCCTAACATTTAGTCTATTTGTAATATG
1 GTCCCCTAACATTTAGTCCATTTGTAATATG
49148 GTCCC
1 GTCCC
49153 TGATCGTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (31 bp):
GTCCCCTAACATTTAGTCCATTTGTAATATG
Found at i:50484 original size:22 final size:19
Alignment explanation
Indices: 50415--50504 Score: 90
Period size: 19 Copynumber: 4.4 Consensus size: 19
50405 AACGCGATTT
50415 TGAAAAATGTGTTGCGATAG
1 TGAAAAA-GTGTTGCGATAG
* * *
50435 TTAAAATGTGTTGCGAGAG
1 TGAAAAAGTGTTGCGATAG
50454 TTTGAAAAACGTGTTATTGCGATAG
1 --TGAAAAA-GTG---TTGCGATAG
50479 TGAAAAAGTGTTGCGATAG
1 TGAAAAAGTGTTGCGATAG
50498 TGAAAAA
1 TGAAAAA
50505 TCCAAAATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
19 27 0.47
20 5 0.09
21 5 0.09
22 6 0.10
23 7 0.12
25 8 0.14
ACGTcount: A:0.37, C:0.06, G:0.28, T:0.30
Consensus pattern (19 bp):
TGAAAAAGTGTTGCGATAG
Found at i:50992 original size:21 final size:21
Alignment explanation
Indices: 50968--51063 Score: 124
Period size: 21 Copynumber: 4.6 Consensus size: 21
50958 AATTTGGAAA
*
50968 ATCGCATTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
* *
50989 ATCGCGTAGCGATTCTGTATT
1 ATCGCGTTGCGATTTTGTATT
* *
51010 ATCGCGTTGCGA--TAGTCATA
1 ATCGCGTTGCGATTTTGT-ATT
51030 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
51051 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
51064 AGTCAGAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 14 0.22
21 44 0.70
22 3 0.05
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.40
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTGTATT
Found at i:51085 original size:41 final size:41
Alignment explanation
Indices: 50989--51085 Score: 158
Period size: 41 Copynumber: 2.4 Consensus size: 41
50979 ATTTTGTATT
* * *
50989 ATCGCGTAGCGATTCTGTATTATCGCGTTGCGATAGTCATA
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGA
51030 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGA
*
51071 ATTGCGTTGCGATTT
1 ATCGCGTTGCGATTT
51086 ACATATTCGT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGA
Found at i:51123 original size:41 final size:41
Alignment explanation
Indices: 51078--51185 Score: 110
Period size: 41 Copynumber: 2.6 Consensus size: 41
51068 AGAATTGCGT
51078 TGCGATTTACATATTCGTATTGCGATTTTCTAAAATCGCAA
1 TGCGATTTACATATTCGTATTGCGATTTTCTAAAATCGCAA
* * * ** * ** **
51119 TGCGATAGT-CAAAATCGCGTTGCGATTTTGTATTATCGCGT
1 TGCGAT-TTACATATTCGTATTGCGATTTTCTAAAATCGCAA
51160 TGCGATTTACATATTCGTATTGCGAT
1 TGCGATTTACATATTCGTATTGCGAT
51186 AGTTAAAATC
Statistics
Matches: 50, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
40 1 0.02
41 48 0.96
42 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (41 bp):
TGCGATTTACATATTCGTATTGCGATTTTCTAAAATCGCAA
Found at i:51124 original size:21 final size:20
Alignment explanation
Indices: 51098--51147 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
51088 ATATTCGTAT
51098 TGCGATTTTCTAAAATCGCAA
1 TGCGATTTTC-AAAATCGCAA
** **
51119 TGCGATAGTCAAAATCGCGT
1 TGCGATTTTCAAAATCGCAA
51139 TGCGATTTT
1 TGCGATTTT
51148 GTATTATCGC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (20 bp):
TGCGATTTTCAAAATCGCAA
Found at i:60058 original size:23 final size:21
Alignment explanation
Indices: 60024--60067 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
60014 ATCACAAAAA
60024 CTAAGGGAAAAACAGAATATTTT
1 CTAAGGGAAAAA-A-AATATTTT
60047 CTAA-GGAGAAAAAAATATTTT
1 CTAAGGGA-AAAAAAATATTTT
60068 TCAAGAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 8 0.40
22 4 0.20
23 8 0.40
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (21 bp):
CTAAGGGAAAAAAAATATTTT
Found at i:60473 original size:83 final size:83
Alignment explanation
Indices: 60145--60474 Score: 465
Period size: 83 Copynumber: 4.0 Consensus size: 83
60135 AGAATTTCGA
* * *
60145 GAGAGTTTTACTCCAACTAAAACTCTTTTAATATCT-AA---AAATATATTATAATATCTTTTAA
1 GAGAGTTTTACTCCAACCAAAACTCTTTTAATAACTAAATTTAAACATATTATAATATCTTTT--
*
60206 AAAATTTAAAATATTAAATC-T
64 -AAATTTATAATATTAAA-CAT
* * * * * *
60227 CAAAATTTTACT-CTATCAAAACTCTTTTAATATCTAAATTTAAACATATTATAATATCTTTTAA
1 GAGAGTTTTACTCCAACCAAAACTCTTTTAATAACTAAATTTAAACATATTATAATATCTTTTAA
*
60291 ATTTATAATATTAAACTT
66 ATTTATAATATTAAACAT
* *
60309 GAGAGTTTTACTCCAACCAAAACTCTTTTAATAACTAAATTTAAACAAATTATAATATATTTTAA
1 GAGAGTTTTACTCCAACCAAAACTCTTTTAATAACTAAATTTAAACATATTATAATATCTTTTAA
60374 ATTTATAATATTAAACAT
66 ATTTATAATATTAAACAT
60392 GAGAGTTTTACTCCAACCAAAACTCTTTTAATAACTAAATTTAAACATATTATAATATCTTTTAA
1 GAGAGTTTTACTCCAACCAAAACTCTTTTAATAACTAAATTTAAACATATTATAATATCTTTTAA
60457 ATTTATAATATTAAACAT
66 ATTTATAATATTAAACAT
60475 ATATTTCCTC
Statistics
Matches: 223, Mismatches: 19, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
81 21 0.09
82 37 0.17
83 145 0.65
85 20 0.09
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (83 bp):
GAGAGTTTTACTCCAACCAAAACTCTTTTAATAACTAAATTTAAACATATTATAATATCTTTTAA
ATTTATAATATTAAACAT
Found at i:62236 original size:34 final size:34
Alignment explanation
Indices: 62198--62267 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
62188 AAGAAATAAA
* *
62198 ATCAATAATTT-ATTTCTTTTTACAAGATAGAATC
1 ATCAATAATTTAATTAC-TTTTACAAAATAGAATC
*
62232 ATCAATGATTTAATTACTTTTACAAAATAGAATC
1 ATCAATAATTTAATTACTTTTACAAAATAGAATC
62266 AT
1 AT
62268 ACAAGATTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 28 0.88
35 4 0.12
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.41
Consensus pattern (34 bp):
ATCAATAATTTAATTACTTTTACAAAATAGAATC
Found at i:62332 original size:57 final size:57
Alignment explanation
Indices: 62252--62419 Score: 160
Period size: 58 Copynumber: 2.9 Consensus size: 57
62242 TAATTACTTT
* * * * *
62252 TACAAAATAGAATCATACAAGATTCTATGAAAATAAATTTAACAATTTATTTTCTTC
1 TACAAAACATAATCATATAAGATTCTAAGAAAATAAATTTAACAATTTATTTTATTC
** * * * *
62309 TACAAGATGA-AATCA-ATCTAGATTTCTAAGAAAATAAATTTGACATTTTATTTTATTT
1 TACAA-AACATAATCATAT-AAGA-TTCTAAGAAAATAAATTTAACAATTTATTTTATTC
* * *
62367 TACAAAACATAATCATATAAGTTTCATAGGAAAATAAATTCAACAATTTATTT
1 TACAAAACATAATCATATAAGATTC-TAAGAAAATAAATTTAACAATTTATTT
62420 CATTTTTAAA
Statistics
Matches: 88, Mismatches: 17, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
56 1 0.01
57 18 0.20
58 67 0.76
59 2 0.02
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.38
Consensus pattern (57 bp):
TACAAAACATAATCATATAAGATTCTAAGAAAATAAATTTAACAATTTATTTTATTC
Found at i:62439 original size:116 final size:116
Alignment explanation
Indices: 62249--62467 Score: 268
Period size: 116 Copynumber: 1.9 Consensus size: 116
62239 ATTTAATTAC
* * *
62249 TTTTACAAAATAGAATCATACAAGATTCTATGAAAATAAATTTAACAATTTATTTTCTTCTACAA
1 TTTTACAAAACAGAATCATACAAGATTCTAGGAAAATAAATTCAACAATTTATTTTCTTCTACAA
*
62314 GATGAAATCAAT-CTAGATTTCTAAGA-AAATAAATTTGACATTTTATTTTA
66 GATGAAATCAATGCAAGA-TTCTAAGAGAAATAAATTTGACATTTTATTTTA
* * * *
62364 TTTTACAAAACATAATCATATAAGTTTCATAGGAAAATAAATTCAACAATTTA-TTTCATTTTTA
1 TTTTACAAAACAGAATCATACAAGATTC-TAGGAAAATAAATTCAACAATTTATTTTC--TTCTA
*
62428 -AAG-TTAGAATCAATGCAAGATTCTAAGATGAAATAAATTT
63 CAAGATGA-AATCAATGCAAGATTCTAAGA-GAAATAAATTT
62468 TTACAATTTA
Statistics
Matches: 88, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
115 30 0.34
116 40 0.45
117 8 0.09
118 10 0.11
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (116 bp):
TTTTACAAAACAGAATCATACAAGATTCTAGGAAAATAAATTCAACAATTTATTTTCTTCTACAA
GATGAAATCAATGCAAGATTCTAAGAGAAATAAATTTGACATTTTATTTTA
Found at i:64081 original size:83 final size:83
Alignment explanation
Indices: 63918--64241 Score: 394
Period size: 83 Copynumber: 4.0 Consensus size: 83
63908 GAATTTTGAT
* * * *
63918 AGAGTTTTACTTCAACTAAAACTCTTTTAATATCTAAA---AATAGAT-A-ATAATATCTTTTAA
1 AGAGTTTTACTCCAACCAAAACTATTTTAATATCTAAATTTAA-ACATAATATAATATCTTTTAA
* *
63978 ATTTAAAATATTAAATCTG
65 ATTTATAATATTAAACCTG
* ** *
63997 AGAGTTTTACTCTAATAAAAAATATTTTAATATCTAAATTTAAACATAATATAATATCTTTTAAA
1 AGAGTTTTACTCCAACCAAAACTATTTTAATATCTAAATTTAAACATAATATAATATCTTTTAAA
*
64062 ATTATAATATTAAACCTG
66 TTTATAATATTAAACCTG
* * *
64080 AGAGTTTTTCTCCAACCAAAACTATTTTAATATCTAAATTTAAACAGATTATAATATCTTTTAAA
1 AGAGTTTTACTCCAACCAAAACTATTTTAATATCTAAATTTAAACATAATATAATATCTTTTAAA
*
64145 TTTATAATATTAAACATG
66 TTTATAATATTAAACCTG
* * * *
64163 AAAGTTTTACTCCAACCAAAACTCTTTTAATATCTAAATCTAAATAT-ATAATAATAT-TGTTTA
1 AGAGTTTTACTCCAACCAAAACTATTTTAATATCTAAATTTAAACATAAT-ATAATATCT-TTTA
64226 AATTTA-AATATTAAAC
64 AATTTATAATATTAAAC
64242 ATATATTTCC
Statistics
Matches: 212, Mismatches: 26, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
79 32 0.15
81 3 0.01
82 15 0.07
83 162 0.76
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (83 bp):
AGAGTTTTACTCCAACCAAAACTATTTTAATATCTAAATTTAAACATAATATAATATCTTTTAAA
TTTATAATATTAAACCTG
Found at i:66405 original size:133 final size:130
Alignment explanation
Indices: 66170--66425 Score: 388
Period size: 133 Copynumber: 1.9 Consensus size: 130
66160 CTTCCTAAGA
* ** *
66170 GATTTACCTTCTCAGTATCTGATATAACCGACACCTTTAGCAACCATTATCACAGTCACATAAGT
1 GATTTACCTTCTCAATATCTGATATAACAAACACCTTTAGCAACCATTATCACAATCACATAAGT
* *
66235 TTGATGCGATACATTTCGACGGCTGAGTTGGTATCGTATGGACACATTGACATCCTTTTACGAAG
66 TTGATGCGATACATTTCGACGGCTGAGTTAGCATCGTATGGACACATTGACATCCTTTTACGAAG
* *
66300 GATTTACCTTCTCAATGT-TGGATATAACAAACACCTTTAGCAACCATTATTATCACAATCGCAT
1 GATTTACCTTCTCAATATCT-GATATAACAAACACCTTTAGCAACC---ATTATCACAATCACAT
*
66364 AAGTTTGATGCGATACATTTCGATGGCTGAGTTAGCATCGTATGGACACATTGACATCCTTT
62 AAGTTTGATGCGATACATTTCGACGGCTGAGTTAGCATCGTATGGACACATTGACATCCTTT
66426 CACCTGTCAT
Statistics
Matches: 113, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
129 1 0.01
130 39 0.35
133 73 0.65
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (130 bp):
GATTTACCTTCTCAATATCTGATATAACAAACACCTTTAGCAACCATTATCACAATCACATAAGT
TTGATGCGATACATTTCGACGGCTGAGTTAGCATCGTATGGACACATTGACATCCTTTTACGAAG
Found at i:71502 original size:43 final size:43
Alignment explanation
Indices: 71449--71814 Score: 357
Period size: 43 Copynumber: 8.6 Consensus size: 43
71439 TGAGAACAAA
* * * * *
71449 AAACGTCGCAATAGGTCAAGATCTATAGCGGCATTTTTGGAAT
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCATTTTTGGAAC
* *
71492 AAACGCCGCAAAAGGTCGCTATCTATAGCGGCATTTTTAGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCATTTTTGGAAC
* * * *
71535 AAACGTCGCAAAAGGTCGCTATCTATAGCGACCTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCATTTTTGGAAC
* * * * * *
71578 AAACACTGCAAAAGGTCGCTATCTATATCAGCATTTTTAGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCATTTTTGGAAC
* *
71621 AAACGCCGCAAAAGGTTGATATCTATAGCGGCACTTTTGGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCATTTTTGGAAC
* * * * ** *
71664 AAACGTCGCAAAAGGTC-ATATATTTAGCGACGCTTTTAGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCATTTTTGGAAC
**
71706 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGCTTTTGGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCATTTTTGGAAC
* * * *
71748 AAACGTCGCAAAAAGTCAGATA--TATAGCAGCATTTTTTAGATAC
1 AAACGCCGCAAAAGGTC-GATATCTATAGCGGCA-TTTTTGGA-AC
*
71792 AAATGCCGCTAAAA-GTC-ATATCT
1 AAACGCCGC-AAAAGGTCGATATCT
71815 CACAAACGCC
Statistics
Matches: 269, Mismatches: 47, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
42 83 0.31
43 166 0.62
44 16 0.06
45 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGATATCTATAGCGGCATTTTTGGAAC
Found at i:71545 original size:86 final size:86
Alignment explanation
Indices: 71449--71814 Score: 399
Period size: 86 Copynumber: 4.3 Consensus size: 86
71439 TGAGAACAAA
* * * * * *
71449 AAACGTCGCAATAGGTCAAGATCTATAGCGGCATTTTTGGAATAAACGCCGCAAAAGGTCGCTAT
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCACTTTTGGAACAAACGCCGCAAAAGGTCGCTAT
* *
71514 CTATAGCGGCATTTTTAGAAC
66 ATATAGCAGCATTTTTAGAAC
* * * * *
71535 AAACGTCGCAAAAGGTCGCTATCTATAGCGAC-CTTTTTGGAACAAACACTGCAAAAGGTCGCTA
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCAC-TTTTGGAACAAACGCCGCAAAAGGTCGCTA
* *
71599 TCTATATCAGCATTTTTAGAAC
65 TATATAGCAGCATTTTTAGAAC
* * *
71621 AAACGCCGCAAAAGGTTGATATCTATAGCGGCACTTTTGGAACAAACGTCGCAAAAGGTC-ATAT
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCACTTTTGGAACAAACGCCGCAAAAGGTCGCTAT
*
71685 ATTTAGCGACGC--TTTTAGAAC
66 ATATAGC-A-GCATTTTTAGAAC
* * *
71706 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGCTTTTGGAACAAACGTCGCAAAAAGTCAG--A
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCACTTTTGGAACAAACGCCGCAAAAGGTC-GCTA
71768 TATATAGCAGCATTTTTTAGATAC
65 TATATAGCAGCA-TTTTTAGA-AC
*
71792 AAATGCCGCTAAAA-GTC-ATATCT
1 AAACGCCGC-AAAAGGTCGATATCT
71815 CACAAACGCC
Statistics
Matches: 242, Mismatches: 27, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
82 2 0.01
83 1 0.00
84 48 0.20
85 39 0.16
86 145 0.60
87 7 0.03
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (86 bp):
AAACGCCGCAAAAGGTCGATATCTATAGCGGCACTTTTGGAACAAACGCCGCAAAAGGTCGCTAT
ATATAGCAGCATTTTTAGAAC
Found at i:73055 original size:27 final size:30
Alignment explanation
Indices: 73017--73086 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 30
73007 TTTCAAATGG
*
73017 AACTCCTTTATA-TTT-ATA-ACCAGTGTT
1 AACTCCTTTATATTTTGAAAGACCAGTGTT
73044 AACTCCTTTATATTTTGAAAGTACCAGTGTT
1 AACTCCTTTATATTTTGAAAG-ACCAGTGTT
73075 AACTCCTTTATA
1 AACTCCTTTATA
73087 ACTAGTGTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
27 12 0.32
28 3 0.08
29 2 0.05
31 21 0.55
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.43
Consensus pattern (30 bp):
AACTCCTTTATATTTTGAAAGACCAGTGTT
Found at i:74807 original size:42 final size:42
Alignment explanation
Indices: 74756--75146 Score: 273
Period size: 42 Copynumber: 9.4 Consensus size: 42
74746 GCATTTTTTA
* *
74756 AAAATGCCACTAAAGTACGTGTAATTAGCAGCGTTTGTGCAT
1 AAAACGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCAT
* *
74798 AAAACGCCACAAAAGTACGTGTAATTAGCGGCGTTTGTGCTT
1 AAAACGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCAT
** * ** * ** * *
74840 GCAACACCACTAAAGTAC-AATATTTCTCGGCATTTAT--AT
1 AAAACGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCAT
* * * *
74879 AAAATGCAACTAGAGTACGTGTAATTAGCGGCGTTTGTGTAT
1 AAAACGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCAT
* * *
74921 AAAACGCCACTAAAGAACATGTAATTAGCGGCGCGTTTGTGCTT
1 AAAACGCCACTAAAGTACGTGTAATTAGC-G-GCGTTTGTGCAT
* ** *
74965 AAAATGCCACTAAAGTACGACCT--TTAGCGACGTTTGT--AT
1 AAAACGCCACTAAAGTACG-TGTAATTAGCGGCGTTTGTGCAT
* * * ** *
75004 AAAAATGCCACTAAAGTAC-AGTATTTATTGGC-TGTTAT--AT
1 -AAAACGCCACTAAAGTACGTGTAATTAGCGGCGT-TTGTGCAT
* * ** ** *
75044 AAAAACGTCACTATAGTGTGTGTAATTAGCAACGTTTGTGCGT
1 -AAAACGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCAT
* *
75087 AAAACGCCATTAAAGTACGTGTAATTAGCGGCGTTTGTGCTT
1 AAAACGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCAT
* *
75129 AAAATGTCACTAAAGTAC
1 AAAACGCCACTAAAGTAC
75147 ATTATTTTCT
Statistics
Matches: 262, Mismatches: 73, Indels: 28
0.72 0.20 0.08
Matches are distributed among these distances:
38 1 0.00
39 15 0.06
40 54 0.21
41 29 0.11
42 129 0.49
43 7 0.03
44 26 0.10
45 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (42 bp):
AAAACGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCAT
Found at i:75112 original size:166 final size:163
Alignment explanation
Indices: 74756--75146 Score: 410
Period size: 166 Copynumber: 2.4 Consensus size: 163
74746 GCATTTTTTA
* * * * * * * **
74756 AAAATGCCACTAAAGTACGTGTAATTAGCAGCGTTTGTGCATAAAACGCCACAAAAGTACG-TGT
1 AAAACGCCACTAAAGAACATGTAATTAGCGGCGTTTGTGCTTAAAATGCCACTAAAGTACGACCT
* * *** ** * *
74820 AATTAGCGGCGTTTGTGCTTGCAACACCACTAAAGTACAATATTTCTCGGCATTTATATAAAATG
66 --TTAGCGACGTTTGT-ATAAAAATGCCACTAAAGTACAATATTTATCGGCATTTATATAAAACG
** *
74885 CAACTAGAGTACGTGTAATTAGCGGCGTTTGTGTAT
128 CAACTAGAGTACGTGTAATTAGCAACGTTTGTGCAT
74921 AAAACGCCACTAAAGAACATGTAATTAGCGGCGCGTTTGTGCTTAAAATGCCACTAAAGTACGAC
1 AAAACGCCACTAAAGAACATGTAATTAGC-G-GCGTTTGTGCTTAAAATGCCACTAAAGTACGAC
* *
74986 CTTTAGCGACGTTTGTATAAAAATGCCACTAAAGTACAGTATTTATTGGC-TGTTATATAAAAAC
64 CTTTAGCGACGTTTGTATAAAAATGCCACTAAAGTACAATATTTATCGGCAT-TTATAT-AAAAC
* ** *
75050 GTC-ACTATAGTGTGTGTAATTAGCAACGTTTGTGCGT
127 G-CAACTAGAGTACGTGTAATTAGCAACGTTTGTGCAT
* * * *
75087 AAAACGCCATTAAAGTACGTGTAATTAGCGGCGTTTGTGCTTAAAATGTCACTAAAGTAC
1 AAAACGCCACTAAAGAACATGTAATTAGCGGCGTTTGTGCTTAAAATGCCACTAAAGTAC
75147 ATTATTTTCT
Statistics
Matches: 189, Mismatches: 31, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
164 30 0.16
165 58 0.31
166 71 0.38
167 29 0.15
168 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (163 bp):
AAAACGCCACTAAAGAACATGTAATTAGCGGCGTTTGTGCTTAAAATGCCACTAAAGTACGACCT
TTAGCGACGTTTGTATAAAAATGCCACTAAAGTACAATATTTATCGGCATTTATATAAAACGCAA
CTAGAGTACGTGTAATTAGCAACGTTTGTGCAT
Done.