Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold404
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: 308352
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.33
Warning! 11147 characters in sequence are not A, C, G, or T
Found at i:8081 original size:50 final size:50
Alignment explanation
Indices: 7985--8590 Score: 163
Period size: 49 Copynumber: 12.6 Consensus size: 50
7975 ATTGCAATTT
* * * * * * *
7985 AAAAGATTGAAGCTACAACAACGAATCTCACCTCCCTGGCAATGCAGTGG
1 AAAAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGACATTGCAGTGG
* * * * **
8035 AACAGATTGAAGCTACAATTGCGGATCATACTTCCCCGACATTGCAGTTT
1 AAAAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGACATTGCAGTGG
* * ** * * **
8085 AAAAGATCGAAGCCACAACGGCGAATCTTACCTT--CAGGCGA-TGCAACGG
1 AAAAGATTGAAGCTACAATAGCGAATCTTA-CTTCCCCGAC-ATTGCAGTGG
* **
8134 AATAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGACATTGCAGTTT
1 AAAAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGACATTGCAGTGG
** * * * * * * **
8184 AAAAGATCAAAGCCACAACAACGAATCTTA-TTTCCAGGCGA-TGCAGCAG
1 AAAAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGAC-ATTGCAGTGG
* ** * *
8233 AACAGATTGAAGCTACAACGGCGAGTCTCACTT-CCC--CATTGC-GT--
1 AAAAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGACATTGCAGTGG
* * * ** * * *
8277 --TAGATCGAAGCCACAACGGCGAATCTTACTT-CCAGGCGA-TGCAGCGG
1 AAAAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGAC-ATTGCAGTGG
** * *
8324 AACAA-ATTGAAGCTACAACGGCGAGTCTCACTT-CCC--CATTGC-GT--
1 AA-AAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGACATTGCAGTGG
* * * ** * * *
8368 --TAGATCGAAGCCACAACGGCGAATCTTACTT-CCAGGCGA-TGCAGCGG
1 AAAAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGAC-ATTGCAGTGG
* * * * * * *
8415 AATAGATTAAAGCTACAACAGCGAGTCTCACTTCCCCGACATTGCAAT-T
1 AAAAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGACATTGCAGTGG
* * ** * * * ** ** *
8464 AAAAGATTGAAGCCATAACGGTGAATCTCATTTCCTTG-CGGTGTAGTGG
1 AAAAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGACATTGCAGTGG
* * * ** * *
8513 AACAGATTGAAGCTACGATGGCGAATCTCGCTTCCCCAACATTGCAGT-C
1 AAAAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGACATTGCAGTGG
* *
8562 AAATAGATTGAAGCTACAACAGTGAATCT
1 AAA-AGATTGAAGCTACAATAGCGAATCT
8591 CACATCATTA
Statistics
Matches: 398, Mismatches: 126, Indels: 64
0.68 0.21 0.11
Matches are distributed among these distances:
41 1 0.00
42 54 0.14
44 8 0.02
45 4 0.01
46 4 0.01
47 8 0.02
48 8 0.02
49 177 0.44
50 131 0.33
51 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (50 bp):
AAAAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGACATTGCAGTGG
Found at i:8173 original size:99 final size:99
Alignment explanation
Indices: 7975--8630 Score: 609
Period size: 91 Copynumber: 6.8 Consensus size: 99
7965 GTAACCATAG
* * * ** * * * * *
7975 ATTGCAATTTAAAAGATTGAAGCTACAACAACGAATCTCACCTCCCTGGCAATGCAGTGGAACAG
1 ATTGCAGTTTAAAAGATCGAAGCCACAACGGCGAATCTTA-CTTCCAGGCGATGCAGCGGAACAG
**
8040 ATTGAAGCTACAATTGCG-GATCAT-ACTTCCCCGAC
65 ATTGAAGCTACAACAGCGAG-TC-TCACTTCCCCGAC
* *
8075 ATTGCAGTTTAAAAGATCGAAGCCACAACGGCGAATCTTACCTT-CAGGCGATGCAACGGAATAG
1 ATTGCAGTTTAAAAGATCGAAGCCACAACGGCGAATCTTA-CTTCCAGGCGATGCAGCGGAACAG
* * *
8139 ATTGAAGCTACAATAGCGAATCTTACTTCCCCGAC
65 ATTGAAGCTACAACAGCGAGTCTCACTTCCCCGAC
* ** * *
8174 ATTGCAGTTTAAAAGATCAAAGCCACAACAACGAATCTTATTTCCAGGCGATGCAGCAGAACAGA
1 ATTGCAGTTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
*
8239 TTGAAGCTACAACGGCGAGTCTCACTT-CCC--C
66 TTGAAGCTACAACAGCGAGTCTCACTTCCCCGAC
*
8270 ATTGC-G-TT---AGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAAA
1 ATTGCAGTTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
*
8330 TTGAAGCTACAACGGCGAGTCTCACTT-CCC--C
66 TTGAAGCTACAACAGCGAGTCTCACTTCCCCGAC
*
8361 ATTGC-G-TT---AGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAATAGA
1 ATTGCAGTTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
*
8421 TTAAAGCTACAACAGCGAGTCTCACTTCCCCGAC
66 TTGAAGCTACAACAGCGAGTCTCACTTCCCCGAC
* * * * * * ** * * *
8455 ATTGCA-ATTAAAAGATTGAAGCCATAACGGTGAATCTCATTTCCTTGCGGTGTAGTGGAACAGA
1 ATTGCAGTTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
* ** * * *
8519 TTGAAGCTACGATGGCGAATCTCGCTTCCCCAAC
66 TTGAAGCTACAACAGCGAGTCTCACTTCCCCGAC
* * * * * * * * * *
8553 ATTGCAG-TCAAATAGATTGAAGCTACAACAGTGAATCTCACAT-CATTAGCGATACAGTGGAAC
1 ATTGCAGTTTAAA-AGATCGAAGCCACAACGGCGAATCTTACTTCCA--GGCGATGCAGCGGAAC
8616 AGATTGAAGCTACAA
63 AGATTGAAGCTACAA
8631 TGGCGAACCT
Statistics
Matches: 476, Mismatches: 65, Indels: 30
0.83 0.11 0.05
Matches are distributed among these distances:
91 160 0.34
92 3 0.01
94 8 0.02
95 3 0.01
96 6 0.01
98 85 0.18
99 148 0.31
100 63 0.13
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (99 bp):
ATTGCAGTTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGA
TTGAAGCTACAACAGCGAGTCTCACTTCCCCGAC
Found at i:8293 original size:42 final size:42
Alignment explanation
Indices: 8236--8400 Score: 150
Period size: 42 Copynumber: 3.8 Consensus size: 42
8226 GCAGCAGAAC
* * *
8236 AGATTGAAGCTACAACGGCGAGTCTCACTTCCCCATTGCGTT
1 AGATCGAAGCCACAACGGCGAATCTCACTTCCCCATTGCGTT
* * * **
8278 AGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAAC
1 AGATCGAAGCCACAACGGCGAATCTCACTTCC---CCAT--TGC-G-TT
* * * *
8327 AAATTGAAGCTACAACGGCGAGTCTCACTTCCCCATTGCGTT
1 AGATCGAAGCCACAACGGCGAATCTCACTTCCCCATTGCGTT
*
8369 AGATCGAAGCCACAACGGCGAATCTTACTTCC
1 AGATCGAAGCCACAACGGCGAATCTCACTTCC
8401 AGGCGATGCA
Statistics
Matches: 94, Mismatches: 22, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
42 55 0.59
43 1 0.01
44 2 0.02
45 3 0.03
46 3 0.03
47 2 0.02
48 1 0.01
49 27 0.29
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (42 bp):
AGATCGAAGCCACAACGGCGAATCTCACTTCCCCATTGCGTT
Found at i:11394 original size:5 final size:5
Alignment explanation
Indices: 11384--11408 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11374 AAAATTTTAT
11384 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
11409 TTATTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:19613 original size:22 final size:23
Alignment explanation
Indices: 19580--19638 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
19570 AGAATGATAC
*
19580 ATGA-AAACTTAAAATAAT-TAT
1 ATGATAAATTTAAAATAATATAT
19601 ATGATAAATTTAAAATAATAATAT
1 ATGATAAATTTAAAATAAT-ATAT
*
19625 GTGATAAATTTAAA
1 ATGATAAATTTAAA
19639 CAACATTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 13 0.39
24 16 0.48
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (23 bp):
ATGATAAATTTAAAATAATATAT
Found at i:23603 original size:16 final size:16
Alignment explanation
Indices: 23584--23617 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
23574 ATATCTTTTG
*
23584 TTATTTTTTTAAAATT
1 TTATTTTTATAAAATT
*
23600 TTATTTTTATATAATT
1 TTATTTTTATAAAATT
23616 TT
1 TT
23618 TCTACATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTTTATAAAATT
Found at i:27668 original size:23 final size:22
Alignment explanation
Indices: 27642--27687 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
27632 TGTAACTTTG
* *
27642 TATTTGTCTGATTTATGATTTCT
1 TATTTGTCTAATTT-GGATTTCT
*
27665 TATTTTTCTAATTTGGATTTCT
1 TATTTGTCTAATTTGGATTTCT
27687 T
1 T
27688 TCCTAATCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.63
Consensus pattern (22 bp):
TATTTGTCTAATTTGGATTTCT
Found at i:31609 original size:15 final size:15
Alignment explanation
Indices: 31589--31623 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
31579 GGTTTGTCTC
31589 TTTGTTTGTTTTTA-T
1 TTTGTTT-TTTTTACT
31604 TTTGTTTTTTTTACT
1 TTTGTTTTTTTTACT
31619 TTTGT
1 TTTGT
31624 CTCTTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.06, C:0.03, G:0.11, T:0.80
Consensus pattern (15 bp):
TTTGTTTTTTTTACT
Found at i:35931 original size:45 final size:45
Alignment explanation
Indices: 35867--35958 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
35857 TTAATGCACA
35867 CTTGGCGGAAATTCAATCGAGTTGCAGATCATTGGACACTGGTTG
1 CTTGGCGGAAATTCAATCGAGTTGCAGATCATTGGACACTGGTTG
35912 CTTGGCGGAAATTCAATCGAGTTGCAGATCATTGGACACTGGTTG
1 CTTGGCGGAAATTCAATCGAGTTGCAGATCATTGGACACTGGTTG
35957 CT
1 CT
35959 GATTTGAACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (45 bp):
CTTGGCGGAAATTCAATCGAGTTGCAGATCATTGGACACTGGTTG
Found at i:38882 original size:32 final size:32
Alignment explanation
Indices: 38838--38910 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
38828 AGCTACAAGA
*
38838 ATGGA-AGTGCTACATTGCATCAAGGATACCG
1 ATGGATAGAGCTACATTGCATCAAGGATACCG
*
38869 ATGGATAGAGCTACATTGGATCAAGGATACCG
1 ATGGATAGAGCTACATTGCATCAAGGATACCG
38901 ATGGATAGAG
1 ATGGATAGAG
38911 ACTTTCCAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 5 0.13
32 34 0.87
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.22
Consensus pattern (32 bp):
ATGGATAGAGCTACATTGCATCAAGGATACCG
Found at i:39460 original size:45 final size:45
Alignment explanation
Indices: 39396--39652 Score: 478
Period size: 45 Copynumber: 5.7 Consensus size: 45
39386 GCCATATCCT
39396 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
1 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
39441 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
1 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
* *
39486 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATACCCTTCTTCC
1 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
39531 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
1 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
*
39576 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTTCC
1 TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
*
39621 TCTTCCTCGGATCTACCATAACTTGGTTTCCT
1 TCTTCCTCGGATCTACCATAACTTGGCTTCCT
39653 CTCATACCCG
Statistics
Matches: 206, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 206 1.00
ACGTcount: A:0.16, C:0.35, G:0.11, T:0.39
Consensus pattern (45 bp):
TCTTCCTCGGATCTACCATAACTTGGCTTCCTATATCCTTCTGCC
Found at i:39967 original size:54 final size:54
Alignment explanation
Indices: 39904--40015 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
39894 TGTTCGCCAT
* *
39904 ATTCGGGTCTCCGGCCATGCCCAGATT-CAAATTCAGGAGGCGGAGGCTGCTCAA
1 ATTCGGGTCTCCGGCCATACCCAG-TTCCAAACTCAGGAGGCGGAGGCTGCTCAA
* * *
39958 ATTCGGGTCTCCGTCGATACCCAGTTCCAAACTCAGGCGGCGGAGGCTGCTCAA
1 ATTCGGGTCTCCGGCCATACCCAGTTCCAAACTCAGGAGGCGGAGGCTGCTCAA
40012 ATTC
1 ATTC
40016 TGATCTACGG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
53 2 0.04
54 50 0.96
ACGTcount: A:0.21, C:0.29, G:0.28, T:0.21
Consensus pattern (54 bp):
ATTCGGGTCTCCGGCCATACCCAGTTCCAAACTCAGGAGGCGGAGGCTGCTCAA
Found at i:41181 original size:21 final size:19
Alignment explanation
Indices: 41156--41210 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 19
41146 TGCGACATAC
*
41156 CAACTAAATATTTAACATTGT
1 CAACTAAATATTTAA-A-TAT
*
41177 TAACTTAAAATATTTAAATAT
1 CAAC-T-AAATATTTAAATAT
41198 CAACTAAATATTT
1 CAACTAAATATTT
41211 TTAGACAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 8 0.28
20 1 0.03
21 8 0.28
22 2 0.07
23 10 0.34
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (19 bp):
CAACTAAATATTTAAATAT
Found at i:43275 original size:64 final size:65
Alignment explanation
Indices: 43184--43312 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 65
43174 ACAATCTTAG
43184 AAAAGAGACACACACATTAGATTAGAACACATAACACATTCAGAGAATTTTGTGTTTACGTTTTC
1 AAAAGAGACACACACATTAGATTAGAACACATAACACATTCAGAGAATTTTGTGTTTACGTTTTC
43249 AAAAGAGACA-ACACATTAGATTAGAACACATAACACATTCAGAGAATTTTGTGTTTACGTTTTC
1 AAAAGAGACACACACATTAGATTAGAACACATAACACATTCAGAGAATTTTGTGTTTACGTTTTC
43313 GGGTTCTTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
64 54 0.84
65 10 0.16
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (65 bp):
AAAAGAGACACACACATTAGATTAGAACACATAACACATTCAGAGAATTTTGTGTTTACGTTTTC
Found at i:43337 original size:15 final size:16
Alignment explanation
Indices: 43308--43337 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43298 TGTGTTTACG
43308 TTTTCGGGTTCTTTAT
1 TTTTCGGGTTCTTTAT
43324 TTTTCGGGTT-TTTA
1 TTTTCGGGTTCTTTA
43338 GGTTTTCTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.07, C:0.10, G:0.20, T:0.63
Consensus pattern (16 bp):
TTTTCGGGTTCTTTAT
Found at i:43343 original size:16 final size:16
Alignment explanation
Indices: 43302--43344 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
43292 GAATTTTGTG
43302 TTTACGTTTTCGGGTTC
1 TTTA-GTTTTCGGGTTC
*
43319 TTTATTTTTCGGGTT-
1 TTTAGTTTTCGGGTTC
43334 TTTAGGTTTTC
1 TTTA-GTTTTC
43345 TCCATCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 15 0.65
17 4 0.17
ACGTcount: A:0.07, C:0.12, G:0.21, T:0.60
Consensus pattern (16 bp):
TTTAGTTTTCGGGTTC
Found at i:46212 original size:30 final size:30
Alignment explanation
Indices: 46178--46282 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 30
46168 AATGTGACCA
46178 ATTACAGGCTATGACAGGTAAATGCAAATG
1 ATTACAGGCTATGACAGGTAAATGCAAATG
** ***
46208 ATTACAAGG-TATGA-AAATAAAAATG-TGTTCG
1 ATTAC-AGGCTATGACAGGT--AAATGCAAAT-G
46239 ATTACAGGCTATGACAGGTAAATGCAAATG
1 ATTACAGGCTATGACAGGTAAATGCAAATG
* *
46269 ATTGCAGGGTATGA
1 ATTACAGGCTATGA
46283 TAATGCAAAT
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
29 2 0.04
30 32 0.57
31 20 0.36
32 2 0.04
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (30 bp):
ATTACAGGCTATGACAGGTAAATGCAAATG
Found at i:46249 original size:61 final size:61
Alignment explanation
Indices: 46149--46282 Score: 223
Period size: 61 Copynumber: 2.2 Consensus size: 61
46139 TAGTACAGTG
46149 TACAGGGTATGAAAATAAAAATGTGACCAATTACAGGCTATGACAGGTAAATGCAAATGAT
1 TACAGGGTATGAAAATAAAAATGTGACCAATTACAGGCTATGACAGGTAAATGCAAATGAT
* ** *
46210 TACAAGGTATGAAAATAAAAATGTGTTCGATTACAGGCTATGACAGGTAAATGCAAATGAT
1 TACAGGGTATGAAAATAAAAATGTGACCAATTACAGGCTATGACAGGTAAATGCAAATGAT
*
46271 TGCAGGGTATGA
1 TACAGGGTATGA
46283 TAATGCAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 67 1.00
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (61 bp):
TACAGGGTATGAAAATAAAAATGTGACCAATTACAGGCTATGACAGGTAAATGCAAATGAT
Found at i:58267 original size:13 final size:13
Alignment explanation
Indices: 58249--58275 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58239 ATATATTTTT
58249 AGATTTAAAATTA
1 AGATTTAAAATTA
58262 AGATTTAAAATTA
1 AGATTTAAAATTA
58275 A
1 A
58276 CAATAATAAT
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:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
AGATTTAAAATTA
Found at i:64594 original size:12 final size:11
Alignment explanation
Indices: 64582--64621 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
64572 TTTCTTTAAT
64582 TTTCTCTCAAA
1 TTTCTCTCAAA
*
64593 TTTATCTCAAA
1 TTTCTCTCAAA
64604 TTTCTCTCTAAA
1 TTTCTCTC-AAA
64616 TTTCTC
1 TTTCTC
64622 AAAGCTCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (11 bp):
TTTCTCTCAAA
Found at i:64630 original size:21 final size:22
Alignment explanation
Indices: 64584--64631 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
64574 TCTTTAATTT
**
64584 TCTCTCAAATTTATCTCAAATT
1 TCTCTCAAATTTATCTCAAAGC
64606 TCTCTCTAAA-TT-TCTCAAAGC
1 TCTCTC-AAATTTATCTCAAAGC
64627 TCTCT
1 TCTCT
64632 TTACTTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 12 0.52
22 8 0.35
23 3 0.13
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.44
Consensus pattern (22 bp):
TCTCTCAAATTTATCTCAAAGC
Found at i:67732 original size:33 final size:32
Alignment explanation
Indices: 67691--67774 Score: 87
Period size: 33 Copynumber: 2.6 Consensus size: 32
67681 ACTTGAGTTG
* *
67691 GGAGGAGTGTTGTATTGTGGTAGATACGACCC
1 GGAGGAGTGCTGTATTGCGGTAGATACGACCC
** * **
67723 AGGAGGAGTGGAGTAATGCGGTAGATACGGGCC
1 -GGAGGAGTGCTGTATTGCGGTAGATACGACCC
67756 GAGAGGAGTGCTGTATTGC
1 G-GAGGAGTGCTGTATTGC
67775 AGTGGTACTA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
32 1 0.02
33 40 0.98
ACGTcount: A:0.24, C:0.12, G:0.42, T:0.23
Consensus pattern (32 bp):
GGAGGAGTGCTGTATTGCGGTAGATACGACCC
Found at i:77259 original size:16 final size:16
Alignment explanation
Indices: 77230--77275 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
77220 ATAAAGTTTC
* *
77230 ACTGGAATGGAATAAT
1 ACTGTAATGGAATAAA
* *
77246 ATTGTAATGAAATAAA
1 ACTGTAATGGAATAAA
77262 ACTGTAATGGAATA
1 ACTGTAATGGAATA
77276 GAGTTGTAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.48, C:0.04, G:0.20, T:0.28
Consensus pattern (16 bp):
ACTGTAATGGAATAAA
Found at i:77317 original size:46 final size:44
Alignment explanation
Indices: 77264--77354 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 44
77254 GAAATAAAAC
**
77264 TGTAATGGAATAGAGTTGTAATCAGTGATTCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAACTGTAAT-AGT-ATT-AATGTGTTTGGTTGAA
* *
77310 TGTAATGGAATATAACTGTAATAGTATTATTGTGTTTGGTTGAA
1 TGTAATGGAATAGAACTGTAATAGTATTAATGTGTTTGGTTGAA
77354 T
1 T
77355 AAAATAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
43 2 0.05
44 16 0.40
45 3 0.08
46 19 0.47
ACGTcount: A:0.31, C:0.03, G:0.24, T:0.42
Consensus pattern (44 bp):
TGTAATGGAATAGAACTGTAATAGTATTAATGTGTTTGGTTGAA
Found at i:83797 original size:10 final size:11
Alignment explanation
Indices: 83778--83807 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
83768 AATGACACGG
83778 GAAGAAAAAAA
1 GAAGAAAAAAA
83789 GAA-AAAAAAA
1 GAAGAAAAAAA
83799 GAAGAAAAA
1 GAAGAAAAA
83808 CTCCAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
GAAGAAAAAAA
Found at i:97480 original size:689 final size:690
Alignment explanation
Indices: 96152--97531 Score: 2753
Period size: 689 Copynumber: 2.0 Consensus size: 690
96142 TTTATTAATT
96152 TAATATTAATGTAATTAATTCTAATCCTAGTTAAATTCTCTCTAAACTCTCTCTATATAAGGAGA
1 TAATATTAATGTAATTAATTCTAATCCTAGTTAAATTCTCTCTAAACTCTCTCTATATAAGGAGA
96217 ACTTAGGTCATTATTCTCAAACATTTGAATTTAAGAAAAGTTGTAGAGAGAATTTTTTAAAAAAA
66 ACTTAGGTCATTATTCTCAAACATTTGAATTTAAGAAAAGTTGTAGAGAGAATTTTTTAAAAAAA
96282 ATATTTTAGAAAATTTTTAGAGATATTCTTTTTATTTATTACTTGATCTCAAAAGTTTAAAGAAA
131 ATATTTTAGAAAATTTTTAGAGATATTCTTTTTATTTATTACTTGATCTCAAAAGTTTAAAGAAA
96347 TTACGAAATTGCCTCACTCGTAATTTTGTGAAAAATTTTCTGATTCAAAATAAGTCCACACTCGA
196 TTACGAAATTGCCTCACTCGTAATTTTGTGAAAAATTTTCTGATTCAAAATAAGTCCACACTCGA
96412 CAGACGTGAGTTTGAGGATGGCGGAGAAGACTACTCCGTCGAAGCATTCATTCTAGACGAATCAT
261 CAGACGTGAGTTTGAGGATGGCGGAGAAGACTACTCCGTCGAAGCATTCATTCTAGACGAATCAT
96477 AAAGATATCATTTTGATTAAGCGTTTATTACTTTAGATAACACAATCAAGTTCTTATTTTGGAAA
326 AAAGATATCATTTTGATTAAGCGTTTATTACTTTAGATAACACAATCAAGTTCTTATTTTGGAAA
96542 AAAAATTTAAAACTCTGGTTTTCCTTAAACTTATATTTTCCAACATCTTATGTTTCATTATTTAT
391 AAAAATTTAAAACTCTGGTTTTCCTTAAACTTATATTTTCCAACATCTTATGTTTCATTATTTAT
96607 TATATGTTATGTTAAAACACATCTATGATCTAAATGCATGGTTTCCACATGTAAATCCGTGTAAA
456 TATATGTTATGTTAAAACACATCTATGATCTAAATGCATGGTTTCCACATGTAAATCCGTGTAAA
96672 TTTTTTAGAAAAAAATAATTAAAACTTGCTAAACACAAAAATAACCATATTTGTTAGTAGGGTTA
521 TTTTTTAGAAAAAAATAATTAAAACTTGCTAAACACAAAAATAACCATATTTGTTAGTAGGGTTA
96737 ATGTACTATTTACCCCCAAAAGTTGCACCCAATTATCACAACGTCAAACACGTTACCCTAACCAT
586 ATGTACTATTTACCCCCAAAAGTTGCACCCAATTATCACAACGTCAAACACGTTACCCTAACCAT
96802 TACCAAAAAAGATAACATGGATCGCTGGGAGCGCGCCACG
651 TACCAAAAAAGATAACATGGATCGCTGGGAGCGCGCCACG
96842 TAATATTAAT-TAATTAATTCTAATCCTAGTTAAATTCTCTCTAAACTCTCTCTATATAAGGAGA
1 TAATATTAATGTAATTAATTCTAATCCTAGTTAAATTCTCTCTAAACTCTCTCTATATAAGGAGA
96906 ACTTAGGTCATTATTCTCAAACATTTGAATTTAAGAAAAGTTGTAGAGAGAATTTTTTAAAAAAA
66 ACTTAGGTCATTATTCTCAAACATTTGAATTTAAGAAAAGTTGTAGAGAGAATTTTTTAAAAAAA
96971 ATATTTTAGAAAATTTTTAGAGATATTCTTTTTATTTATTACTTGATCTCAAAAGTTTAAAGAAA
131 ATATTTTAGAAAATTTTTAGAGATATTCTTTTTATTTATTACTTGATCTCAAAAGTTTAAAGAAA
97036 TTACGAAATTGCCTCACTCGTAATTTTGTGAAAAATTTTCTGATTCAAAATAAGTCCACACTCGA
196 TTACGAAATTGCCTCACTCGTAATTTTGTGAAAAATTTTCTGATTCAAAATAAGTCCACACTCGA
97101 CAGACGTGAGTTTGAGGATGGCGGAGAAGACTACTCCGTCGAAGCATTCATTCTAGACGAATCAT
261 CAGACGTGAGTTTGAGGATGGCGGAGAAGACTACTCCGTCGAAGCATTCATTCTAGACGAATCAT
97166 AAAGATATCATTTTGATTAAGCGTTTATTACTTTAGATAACACAATCAAGTTCTTATTTTGGAAA
326 AAAGATATCATTTTGATTAAGCGTTTATTACTTTAGATAACACAATCAAGTTCTTATTTTGGAAA
97231 AAAAATTTAAAACTCTGGTTTTCCTTAAACTTATATTTTCCAACATCTTATGTTTCATTATTTAT
391 AAAAATTTAAAACTCTGGTTTTCCTTAAACTTATATTTTCCAACATCTTATGTTTCATTATTTAT
97296 TATATGTTATGTTAAAACACATCTATGATCTAAATGCATGGTTTCCACATGTAAATCCGTGTAAA
456 TATATGTTATGTTAAAACACATCTATGATCTAAATGCATGGTTTCCACATGTAAATCCGTGTAAA
97361 TTTTTTAGAAAAAAATAATTAAAACTTGCTAAACACAAAAATAACCATATTTGTTAGTAGGGTTA
521 TTTTTTAGAAAAAAATAATTAAAACTTGCTAAACACAAAAATAACCATATTTGTTAGTAGGGTTA
97426 ATGTACTATTTACCCCCAAAAGTTGCACCCAATTATCACAACGTCAAACACGTTACCCTAACCAT
586 ATGTACTATTTACCCCCAAAAGTTGCACCCAATTATCACAACGTCAAACACGTTACCCTAACCAT
97491 TACCAAAAAAGATAACATGGATCGCTGGGAGCGCGCCACG
651 TACCAAAAAAGATAACATGGATCGCTGGGAGCGCGCCACG
97531 T
1 T
97532 CACCTAATTT
Statistics
Matches: 690, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
689 680 0.99
690 10 0.01
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (690 bp):
TAATATTAATGTAATTAATTCTAATCCTAGTTAAATTCTCTCTAAACTCTCTCTATATAAGGAGA
ACTTAGGTCATTATTCTCAAACATTTGAATTTAAGAAAAGTTGTAGAGAGAATTTTTTAAAAAAA
ATATTTTAGAAAATTTTTAGAGATATTCTTTTTATTTATTACTTGATCTCAAAAGTTTAAAGAAA
TTACGAAATTGCCTCACTCGTAATTTTGTGAAAAATTTTCTGATTCAAAATAAGTCCACACTCGA
CAGACGTGAGTTTGAGGATGGCGGAGAAGACTACTCCGTCGAAGCATTCATTCTAGACGAATCAT
AAAGATATCATTTTGATTAAGCGTTTATTACTTTAGATAACACAATCAAGTTCTTATTTTGGAAA
AAAAATTTAAAACTCTGGTTTTCCTTAAACTTATATTTTCCAACATCTTATGTTTCATTATTTAT
TATATGTTATGTTAAAACACATCTATGATCTAAATGCATGGTTTCCACATGTAAATCCGTGTAAA
TTTTTTAGAAAAAAATAATTAAAACTTGCTAAACACAAAAATAACCATATTTGTTAGTAGGGTTA
ATGTACTATTTACCCCCAAAAGTTGCACCCAATTATCACAACGTCAAACACGTTACCCTAACCAT
TACCAAAAAAGATAACATGGATCGCTGGGAGCGCGCCACG
Found at i:102208 original size:20 final size:21
Alignment explanation
Indices: 102171--102209 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
102161 ATTAATGTTA
102171 GATTAAATTTAATATTAAAGT
1 GATTAAATTTAATATTAAAGT
102192 GATT-AATTT-ATAGTTAAA
1 GATTAAATTTAATA-TTAAA
102210 TTCTCTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 10 0.59
21 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (21 bp):
GATTAAATTTAATATTAAAGT
Found at i:104740 original size:26 final size:26
Alignment explanation
Indices: 104708--104766 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
104698 TATTTTCTCG
104708 AAATTTTACCAGGGGCAAAATCGATA
1 AAATTTTACCAGGGGCAAAATCGATA
* * * *
104734 AAGTTTTACCATGGGTAAAATCGTTA
1 AAATTTTACCAGGGGCAAAATCGATA
104760 AAATTTT
1 AAATTTT
104767 GCTAGAGGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (26 bp):
AAATTTTACCAGGGGCAAAATCGATA
Found at i:109466 original size:25 final size:24
Alignment explanation
Indices: 109438--109486 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
109428 ATCCAAAATA
109438 CTAAAAACATT-AAAATAAATGTTTT
1 CTAAAAA-ATTGAAAATAAAT-TTTT
*
109463 CTAACAAATTGAAAATAAATTTTT
1 CTAAAAAATTGAAAATAAATTTTT
109487 AAAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
CTAAAAAATTGAAAATAAATTTTT
Found at i:111062 original size:9 final size:9
Alignment explanation
Indices: 111033--111069 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
111023 TGAGTTTTCA
111033 AATTCGAAT
1 AATTCGAAT
*
111042 AACTCGAAT
1 AATTCGAAT
111051 AATTCGAAT
1 AATTCGAAT
*
111060 AATTTGAAT
1 AATTCGAAT
111069 A
1 A
111070 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:112897 original size:29 final size:29
Alignment explanation
Indices: 112864--112931 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
112854 AACAAATGCA
* *
112864 ACAATTTCCAGTTTGGA-TGAAAACAGCAG
1 ACAATTTCCAATTT-CATTGAAAACAGCAG
*
112893 ACAATTTCCAATTTCATTGAAAACTGCAG
1 ACAATTTCCAATTTCATTGAAAACAGCAG
*
112922 ACGATTTCCA
1 ACAATTTCCA
112932 TTGCAACAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 1 0.03
29 33 0.97
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.28
Consensus pattern (29 bp):
ACAATTTCCAATTTCATTGAAAACAGCAG
Found at i:113927 original size:14 final size:15
Alignment explanation
Indices: 113894--113927 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
113884 AGTGTTCATC
*
113894 CAAAACAGAACCATA
1 CAAAACAGAAACATA
113909 CAAAACAGAAACA-A
1 CAAAACAGAAACATA
113923 CAAAA
1 CAAAA
113928 TCTGCTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.68, C:0.24, G:0.06, T:0.03
Consensus pattern (15 bp):
CAAAACAGAAACATA
Found at i:115220 original size:5 final size:5
Alignment explanation
Indices: 115210--115235 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
115200 GAACAAATAT
115210 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
115236 ATTTCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:115335 original size:5 final size:5
Alignment explanation
Indices: 115325--115355 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
115315 CTCGAAAATT
115325 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
115356 CGAATGCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:117334 original size:14 final size:14
Alignment explanation
Indices: 117315--117350 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
117305 TTTATGAACT
117315 TTTTTATTTTTTAA
1 TTTTTATTTTTTAA
117329 TTTTTA-TTTTTAA
1 TTTTTATTTTTTAA
117342 TTATTTATT
1 TT-TTTATT
117351 GATATGACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.45
14 10 0.50
15 1 0.05
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTATTTTTTAA
Found at i:118343 original size:86 final size:84
Alignment explanation
Indices: 118195--118411 Score: 249
Period size: 86 Copynumber: 2.5 Consensus size: 84
118185 CCTCAAACTT
* * ** * * *
118195 CTTCAAAAAAAAGTAATTAAGTCCTTACTTTTTTATACTCAATTGGGTACTTGAACTTTCAAAAT
1 CTTCAAAAAAAA-CAATTAAGTCCTT-TTTTTTTGCACTCAATTGAGTACTTAAACTGTCAAAAT
118260 GCATCAAAAAGGCTCTCAA-A
64 GCATCAAAAAGGCTCTCAAGA
*
118280 CTT-AAAAAAAACAATTAAGTCCTGTTTTTTTTTTTGCACTCAATTGAGTATTTAAACTGTCAAA
1 CTTCAAAAAAAACAATTAAGTCC----TTTTTTTTTGCACTCAATTGAGTACTTAAACTGTCAAA
*
118344 ATGCATCAAAAAGGCTCTCAAGGTT
62 ATGCATCAAAAAGGCTCTCAA-G-A
* *
118369 TTTCAAAAAAAGCAATTAAGTCCTTTTTTTTTGCACTCAATTG
1 CTTCAAAAAAAACAATTAAGTCCTTTTTTTTTGCACTCAATTG
118412 GGTAATTTCA
Statistics
Matches: 113, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
83 10 0.09
84 8 0.07
85 3 0.03
86 70 0.62
87 2 0.02
89 2 0.02
90 18 0.16
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (84 bp):
CTTCAAAAAAAACAATTAAGTCCTTTTTTTTTGCACTCAATTGAGTACTTAAACTGTCAAAATGC
ATCAAAAAGGCTCTCAAGA
Found at i:118542 original size:10 final size:9
Alignment explanation
Indices: 118503--118653 Score: 78
Period size: 9 Copynumber: 16.4 Consensus size: 9
118493 GACATGCAAA
*
118503 AAAAAATAT
1 AAAAATTAT
118512 AAAAA-T-T
1 AAAAATTAT
*
118519 AAAAATCAGT
1 AAAAATTA-T
*
118529 AAAAGTTAT
1 AAAAATTAT
118538 AAAAATTAT
1 AAAAATTAT
*
118547 AAAAATTTTT
1 AAAAA-TTAT
***
118557 AATTTTTAAT
1 AAAAATT-AT
118567 AAAAA-TATT
1 AAAAATTA-T
*
118576 AAAATTTTATT
1 AAAA-ATTA-T
* *
118587 GAAAACTAT
1 AAAAATTAT
118596 AAAAA-TAT
1 AAAAATTAT
*
118604 AAAAATCAT
1 AAAAATTAT
118613 AAAAA-TAT
1 AAAAATTAT
*
118621 AAAATTTTAT
1 AAAA-ATTAT
*
118631 AAAAATCAT
1 AAAAATTAT
118640 AAAAAATTAT
1 -AAAAATTAT
118650 AAAA
1 AAAA
118654 TGCATAAAAA
Statistics
Matches: 107, Mismatches: 23, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
7 6 0.06
8 16 0.15
9 46 0.43
10 32 0.30
11 7 0.07
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:118551 original size:19 final size:18
Alignment explanation
Indices: 118503--118653 Score: 78
Period size: 19 Copynumber: 8.2 Consensus size: 18
118493 GACATGCAAA
*
118503 AAAAAATATAAAAA-T-T
1 AAAAATTATAAAAATTAT
* *
118519 AAAAATCAGTAAAAGTTAT
1 AAAAATTA-TAAAAATTAT
*
118538 AAAAATTATAAAAATTTTT
1 AAAAATTATAAAAA-TTAT
***
118557 AATTTTTAATAAAAA-TATT
1 AAAAATT-ATAAAAATTA-T
* * *
118576 AAAATTTTATTGAAAACTAT
1 AAAA-ATTA-TAAAAATTAT
*
118596 AAAAA-TATAAAAATCAT
1 AAAAATTATAAAAATTAT
*
118613 AAAAA-TATAAAATTTTAT
1 AAAAATTATAAAA-ATTAT
*
118631 AAAAATCATAAAAAATTAT
1 AAAAATTAT-AAAAATTAT
118650 AAAA
1 AAAA
118654 TGCATAAAAA
Statistics
Matches: 102, Mismatches: 21, Indels: 21
0.71 0.15 0.15
Matches are distributed among these distances:
16 6 0.06
17 24 0.24
18 17 0.17
19 29 0.28
20 24 0.24
21 2 0.02
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAAATTATAAAAATTAT
Found at i:118583 original size:20 final size:20
Alignment explanation
Indices: 118545--118584 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
118535 TATAAAAATT
* * *
118545 ATAAAAATTTTTAATTTTTA
1 ATAAAAATATTAAAATTTTA
118565 ATAAAAATATTAAAATTTTA
1 ATAAAAATATTAAAATTTTA
118585 TTGAAAACTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAAAAATATTAAAATTTTA
Found at i:118599 original size:8 final size:8
Alignment explanation
Indices: 118588--118644 Score: 60
Period size: 8 Copynumber: 6.6 Consensus size: 8
118578 AATTTTATTG
*
118588 AAAACTAT
1 AAAAATAT
118596 AAAAATAT
1 AAAAATAT
118604 AAAAATCAT
1 AAAAAT-AT
118613 AAAAATAT
1 AAAAATAT
*
118621 AAAATTTTAT
1 AAAA--ATAT
118631 AAAAATCAT
1 AAAAAT-AT
118640 AAAAA
1 AAAAA
118645 ATTATAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
8 20 0.48
9 15 0.36
10 7 0.17
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAAATAT
Found at i:118619 original size:46 final size:46
Alignment explanation
Indices: 118565--118663 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
118555 TTAATTTTTA
*
118565 ATAAAAATATTAAAATTTTATTGAAAA-C-TATAAAAA-TATAAAAAT-C
1 ATAAAAATA-TAAAATTTTA-TAAAAATCATA-AAAAATTAT-AAAATGC
118611 ATAAAAATATAAAATTTTATAAAAATCATAAAAAATTATAAAATGC
1 ATAAAAATATAAAATTTTATAAAAATCATAAAAAATTATAAAATGC
118657 ATAAAAA
1 ATAAAAA
118664 GACCCTTAAC
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
44 5 0.10
45 21 0.44
46 22 0.46
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (46 bp):
ATAAAAATATAAAATTTTATAAAAATCATAAAAAATTATAAAATGC
Found at i:118638 original size:27 final size:29
Alignment explanation
Indices: 118601--118654 Score: 94
Period size: 27 Copynumber: 1.9 Consensus size: 29
118591 ACTATAAAAA
118601 TATAAAAATCAT-AAAAA-TATAAAATTT
1 TATAAAAATCATAAAAAATTATAAAATTT
118628 TATAAAAATCATAAAAAATTATAAAAT
1 TATAAAAATCATAAAAAATTATAAAAT
118655 GCATAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 12 0.48
28 5 0.20
29 8 0.32
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (29 bp):
TATAAAAATCATAAAAAATTATAAAATTT
Found at i:118659 original size:19 final size:19
Alignment explanation
Indices: 118588--118663 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 19
118578 AATTTTATTG
*
118588 AAAACTATAAAAAT-AT-A
1 AAAATTATAAAAATCATAA
*
118605 AAAATCATAAAAAT-ATAA
1 AAAATTATAAAAATCATAA
**
118623 AATTTTATAAAAATCATAA
1 AAAATTATAAAAATCATAA
118642 AAAATTAT-AAAATGCATAA
1 AAAATTATAAAAAT-CATAA
118661 AAA
1 AAA
118664 GACCCTTAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
17 14 0.29
18 17 0.35
19 18 0.37
ACGTcount: A:0.67, C:0.05, G:0.01, T:0.26
Consensus pattern (19 bp):
AAAATTATAAAAATCATAA
Found at i:122113 original size:29 final size:33
Alignment explanation
Indices: 122081--122148 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 33
122071 TAATAATACA
*
122081 AATAAA-A-AAATTTCATTATAT-AATA-AAGT
1 AATAAACATAAATTTCATTATATAAATATAAAT
* *
122110 AATAAACATATATTTTATTATATAAATATAAAT
1 AATAAACATAAATTTCATTATATAAATATAAAT
122143 AATAAA
1 AATAAA
122149 TGTTTTGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 6 0.19
30 1 0.03
31 12 0.38
32 4 0.12
33 9 0.28
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (33 bp):
AATAAACATAAATTTCATTATATAAATATAAAT
Found at i:123259 original size:27 final size:25
Alignment explanation
Indices: 123211--123260 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
123201 TTTGACTCTA
*
123211 ATTTTTTTTAAATTTCTCTCAATTT
1 ATTTTTTTTAAATTTATCTCAATTT
*
123236 ATTTATTTTTAACTTTATCGTCAAT
1 ATTT-TTTTTAAATTTATC-TCAAT
123261 ATGCTTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 12 0.57
27 5 0.24
ACGTcount: A:0.26, C:0.12, G:0.02, T:0.60
Consensus pattern (25 bp):
ATTTTTTTTAAATTTATCTCAATTT
Found at i:123355 original size:11 final size:11
Alignment explanation
Indices: 123335--123378 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
123325 CTCAACACCA
123335 AAATTGAGAGG
1 AAATTGAGAGG
*
123346 AAATTTAGAGG
1 AAATTGAGAGG
*
123357 AAACTGAGAGG
1 AAATTGAGAGG
123368 AAATTTGAGAG
1 AAA-TTGAGAG
123379 ATGATTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 22 0.79
12 6 0.21
ACGTcount: A:0.45, C:0.02, G:0.32, T:0.20
Consensus pattern (11 bp):
AAATTGAGAGG
Found at i:125588 original size:3 final size:3
Alignment explanation
Indices: 125580--125604 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
125570 TAACAATCAA
125580 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
125605 GCATCTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:131480 original size:22 final size:22
Alignment explanation
Indices: 131445--131500 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
131435 ATGGTTATTC
* * *
131445 ATTTTTTTATAATTTTGTATGT
1 ATTTTTATAAAATTTTATATGT
*
131467 ATTTTTATAAAATTTTATGTGT
1 ATTTTTATAAAATTTTATATGT
*
131489 TTTTTTATAAAA
1 ATTTTTATAAAA
131501 AAACGAACTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (22 bp):
ATTTTTATAAAATTTTATATGT
Found at i:131485 original size:20 final size:20
Alignment explanation
Indices: 131448--131492 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
131438 GTTATTCATT
*
131448 TTTTTATAATTTTGTATGTA
1 TTTTTATAAATTTGTATGTA
*
131468 TTTTTATAAAATTT-TATGTG
1 TTTTTAT-AAATTTGTATGTA
131488 TTTTT
1 TTTTT
131493 TTATAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (20 bp):
TTTTTATAAATTTGTATGTA
Found at i:131553 original size:10 final size:10
Alignment explanation
Indices: 131538--131571 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
131528 GAAAGTTTTT
131538 ATTTTTTAAA
1 ATTTTTTAAA
131548 ATTTTTT-AA
1 ATTTTTTAAA
131557 A-TTTTTAAA
1 ATTTTTTAAA
131566 ATTTTT
1 ATTTTT
131572 AAGAATCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 5 0.23
9 6 0.27
10 11 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:131572 original size:9 final size:9
Alignment explanation
Indices: 131540--131573 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
131530 AAGTTTTTAT
131540 TTTTTAAAA
1 TTTTTAAAA
*
131549 TTTTTTAAA
1 TTTTTAAAA
131558 TTTTTAAAA
1 TTTTTAAAA
131567 TTTTTAA
1 TTTTTAA
131574 GAATCAAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:132680 original size:5 final size:5
Alignment explanation
Indices: 132670--132696 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
132660 TTGCATTTTA
132670 CATAC CATAC CATAC CATAC CATAC CA
1 CATAC CATAC CATAC CATAC CATAC CA
132697 CTTTACAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.19
Consensus pattern (5 bp):
CATAC
Found at i:137491 original size:21 final size:18
Alignment explanation
Indices: 137460--137518 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 18
137450 AATTTATTGT
137460 AATATTATTTAAATTTTTA
1 AATATTATTT-AATTTTTA
137479 AATATCTATTTTAA-TTTT-
1 AATAT-TA-TTTAATTTTTA
*
137497 AATAGTGTATTTAATTTATA
1 AATA-T-TATTTAATTTTTA
137517 AA
1 AA
137519 AGTATTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 9 0.27
19 15 0.45
20 6 0.18
21 3 0.09
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (18 bp):
AATATTATTTAATTTTTA
Found at i:141163 original size:3 final size:3
Alignment explanation
Indices: 141155--141180 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
141145 ACGTTAACAT
141155 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
141181 TATATGTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:146278 original size:4 final size:5
Alignment explanation
Indices: 146253--146281 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
146243 CCTAATTCAA
146253 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
146282 TTAATGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:170925 original size:39 final size:39
Alignment explanation
Indices: 170871--170947 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
170861 GATTTAAGAC
170871 TCGTTTTTGTATGAATGCCATGAATGATGATTGGTTATA
1 TCGTTTTTGTATGAATGCCATGAATGATGATTGGTTATA
170910 TCGTTTTTGTATGAATGCCATGAATGATGATTGGTTAT
1 TCGTTTTTGTATGAATGCCATGAATGATGATTGGTTAT
170948 GTATAGTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (39 bp):
TCGTTTTTGTATGAATGCCATGAATGATGATTGGTTATA
Found at i:176893 original size:25 final size:25
Alignment explanation
Indices: 176860--176929 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
176850 TTAAAATTTG
* * **
176860 AAAAGTAAAAGAACTAAAAATGACC
1 AAAATTAAAGGAACTAAAAATGAAA
176885 AAAATTAAAGGAACTAAAAATGAAA
1 AAAATTAAAGGAACTAAAAATGAAA
176910 AAAATTAAAGGAACTAAAAA
1 AAAATTAAAGGAACTAAAAA
176930 AAAATTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.67, C:0.07, G:0.11, T:0.14
Consensus pattern (25 bp):
AAAATTAAAGGAACTAAAAATGAAA
Found at i:201665 original size:37 final size:35
Alignment explanation
Indices: 201615--201723 Score: 89
Period size: 37 Copynumber: 3.0 Consensus size: 35
201605 TATTCCAAAA
*
201615 AATATTATTTTAATAGT-TTAATATTAAATTTAATGT
1 AATATTATCTTAATAGTATT-ATATT-AATTTAATGT
* *
201651 AATACTTATCTTAATAGTATTTTATTAATTTAATTTT
1 AATA-TTATCTTAATAGTATTATATTAATTTAA-TGT
* *
201688 AAAGTGATTATCTTAATATTA-AAT-TTAATTTAATGT
1 -AA-T-ATTATCTTAATAGTATTATATTAATTTAATGT
201724 TTACCTTATA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
36 13 0.22
37 27 0.45
38 5 0.08
39 14 0.23
40 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (35 bp):
AATATTATCTTAATAGTATTATATTAATTTAATGT
Found at i:201689 original size:25 final size:27
Alignment explanation
Indices: 201661--201716 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
201651 AATACTTATC
* *
201661 TTAATAGT-ATTTTATTAAT-TTAATT
1 TTAATAGTGATTATATTAATATTAAAT
*
201686 TTAA-AGTGATTATCTTAATATTAAAT
1 TTAATAGTGATTATATTAATATTAAAT
201712 TTAAT
1 TTAAT
201717 TTAATGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 3 0.12
25 13 0.52
26 9 0.36
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (27 bp):
TTAATAGTGATTATATTAATATTAAAT
Found at i:206692 original size:13 final size:13
Alignment explanation
Indices: 206658--206706 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
206648 GACATGGGCG
*
206658 TGTGACTCAGCCA
1 TGTGACACAGCCA
*
206671 TGTGAGACACAGCCT
1 TGT--GACACAGCCA
*
206686 TGTGACACGGCCA
1 TGTGACACAGCCA
206699 TGTGACAC
1 TGTGACAC
206707 CTGATGGTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 19 0.63
15 11 0.37
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (13 bp):
TGTGACACAGCCA
Found at i:206773 original size:25 final size:25
Alignment explanation
Indices: 206739--206796 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
206729 TCAATGAGTT
* *
206739 ACACGGCCTGGCACACAGGTGTGTG
1 ACACGGCCTGGCACACAAGCGTGTG
*
206764 ACACGGCCTGGCACATAAGCGTGTG
1 ACACGGCCTGGCACACAAGCGTGTG
206789 ACACGGCC
1 ACACGGCC
206797 GTGTGACCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.22, C:0.31, G:0.33, T:0.14
Consensus pattern (25 bp):
ACACGGCCTGGCACACAAGCGTGTG
Found at i:212634 original size:16 final size:17
Alignment explanation
Indices: 212612--212651 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
212602 TCACTATTAG
*
212612 ATTTTATTATA-TTTAT
1 ATTTTATCATATTTTAT
*
212628 GTTTTATCATATTTTAT
1 ATTTTATCATATTTTAT
212645 ATTTTAT
1 ATTTTAT
212652 AATTTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTATCATATTTTAT
Found at i:214321 original size:49 final size:49
Alignment explanation
Indices: 214201--214323 Score: 151
Period size: 49 Copynumber: 2.5 Consensus size: 49
214191 ATGGTATTAA
* * * *
214201 ACTTGAACCCGTGACTATATAATCACCGTCAACTAGGGACCCGAGTTAT
1 ACTTCAACCCATGACTGTATAACCACCGTCAACTAGGGACCCGAGTTAT
* * *
214250 ACTTCAACCTATGACTGCATAACCACCGTCAACTA-GGAGCCCTAGTTAT
1 ACTTCAACCCATGACTGTATAACCACCGTCAACTAGGGA-CCCGAGTTAT
214299 ACTTCAACCCATGA-TCGTATAACCA
1 ACTTCAACCCATGACT-GTATAACCA
214324 TTGTGAACTG
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
48 4 0.06
49 59 0.94
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (49 bp):
ACTTCAACCCATGACTGTATAACCACCGTCAACTAGGGACCCGAGTTAT
Found at i:219715 original size:19 final size:18
Alignment explanation
Indices: 219693--219737 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
219683 ATTTTTTAAG
**
219693 TTCATTTTTATTTTTATTT
1 TTCATTTTTATTTGCA-TT
*
219712 TTCATTTATATTTGCATT
1 TTCATTTTTATTTGCATT
219730 TTCATTTT
1 TTCATTTT
219738 GGAGAAAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.71
Consensus pattern (18 bp):
TTCATTTTTATTTGCATT
Found at i:220541 original size:17 final size:17
Alignment explanation
Indices: 220519--220557 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
220509 ACTTAATCAC
220519 TTTAATATTAAAT-TTAA
1 TTTAATA-TAAATATTAA
220536 TTTAATATAAATATTAA
1 TTTAATATAAATATTAA
*
220553 ATTAA
1 TTTAA
220558 CTTTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAATATAAATATTAA
Found at i:221021 original size:20 final size:20
Alignment explanation
Indices: 221005--221041 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
220995 TTGATTTTGG
221005 GATCCCAGGCCCAA-TTTAC
1 GATCCCAGGCCCAATTTTAC
*
221024 GATCCCAGGTCCAATTTT
1 GATCCCAGGCCCAATTTT
221042 CAAGTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 13 0.81
20 3 0.19
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.27
Consensus pattern (20 bp):
GATCCCAGGCCCAATTTTAC
Found at i:221127 original size:9 final size:9
Alignment explanation
Indices: 221103--221142 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
221093 AAAATATCAT
221103 ATTAATTTTA
1 ATTAA-TTTA
*
221113 ATTAATTTG
1 ATTAATTTA
221122 ATTAATTTA
1 ATTAATTTA
221131 ATTAATTTA
1 ATTAATTTA
221140 ATT
1 ATT
221143 TTACTTCATC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
9 23 0.82
10 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
ATTAATTTA
Found at i:227681 original size:32 final size:32
Alignment explanation
Indices: 227639--227699 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
227629 TCAACTCAAA
227639 TATATCATGTTATAA-AAAAATTATTATATTAAT
1 TATATCATGTTA-AATAAAAATTA-TATATTAAT
*
227672 TATAT-ATGTTAAATAATAATTATATATT
1 TATATCATGTTAAATAAAAATTATATATT
227700 TTTATATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 8 0.31
32 13 0.50
33 5 0.19
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (32 bp):
TATATCATGTTAAATAAAAATTATATATTAAT
Found at i:227960 original size:224 final size:225
Alignment explanation
Indices: 227658--228108 Score: 895
Period size: 224 Copynumber: 2.0 Consensus size: 225
227648 TTATAAAAAA
227658 ATTATTATATTAATTATATATGTTAAATAATAATTATATATTTTTATATTTATATTAAATGTCTA
1 ATTATTATATTAATTATATATGTTAAATAATAATTATATATTTTTATATTTATATTAAATGTCTA
227723 ACTCAATAACAATTAACTACCCATTTCTCTAAAATCTTAACGTTCAACTCATTAAATGGGCGTAA
66 ACTCAATAACAATTAACTACCCATTTCTCTAAAATCTTAACGTTCAACTCATTAAATGGGCGTAA
227788 CTTTATAAATTTATCACGTCTGTGGTTTACATTGGTAAAAGCCACATTTTGTTCTCTGTTTTTAG
131 CTTTATAAATTTATCACGTCTGTGGTTTACATTGGTAAAAGCCACATTTTGTTCTCTGTTTTTAG
227853 TTGCAGACTGGCACCGTATTTTATCTCCAT
196 TTGCAGACTGGCACCGTATTTTATCTCCAT
227883 ATTATTATATT-ATTATATATGTTAAATAATAATTATATATTTTTATATTTATATTAAATGTCTA
1 ATTATTATATTAATTATATATGTTAAATAATAATTATATATTTTTATATTTATATTAAATGTCTA
227947 ACTCAATAACAATTAACTACCCATTTCTCTAAAATCTTAACGTTCAACTCATTAAATGGGCGTAA
66 ACTCAATAACAATTAACTACCCATTTCTCTAAAATCTTAACGTTCAACTCATTAAATGGGCGTAA
228012 CTTTATAAATTTATCACGTCTGTGGTTTACATTGGTAAAAGCCACATTTTGTTCTCTGTTTTTAG
131 CTTTATAAATTTATCACGTCTGTGGTTTACATTGGTAAAAGCCACATTTTGTTCTCTGTTTTTAG
228077 TTGCAGACTGGCACCGTATTTTATCTCCAT
196 TTGCAGACTGGCACCGTATTTTATCTCCAT
228107 AT
1 AT
228109 GATTCCTGTT
Statistics
Matches: 226, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
224 215 0.95
225 11 0.05
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (225 bp):
ATTATTATATTAATTATATATGTTAAATAATAATTATATATTTTTATATTTATATTAAATGTCTA
ACTCAATAACAATTAACTACCCATTTCTCTAAAATCTTAACGTTCAACTCATTAAATGGGCGTAA
CTTTATAAATTTATCACGTCTGTGGTTTACATTGGTAAAAGCCACATTTTGTTCTCTGTTTTTAG
TTGCAGACTGGCACCGTATTTTATCTCCAT
Found at i:232666 original size:2 final size:2
Alignment explanation
Indices: 232659--232683 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
232649 TAAATTCATT
232659 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
232684 TGTTGGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:245682 original size:48 final size:48
Alignment explanation
Indices: 245616--245723 Score: 189
Period size: 48 Copynumber: 2.2 Consensus size: 48
245606 CTATTTAATC
* *
245616 ATCAATTAAATCATTTTTTTTATAATTTTTAATAATTTATTCAATCAA
1 ATCAATTAAATTAATTTTTTTATAATTTTTAATAATTTATTCAATCAA
*
245664 ATCAATTAAATTAATTTTTTTATAATTTTTAATAATTTATTGAATCAA
1 ATCAATTAAATTAATTTTTTTATAATTTTTAATAATTTATTCAATCAA
245712 ATCAATTAAATT
1 ATCAATTAAATT
245724 GATGGCTTGA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (48 bp):
ATCAATTAAATTAATTTTTTTATAATTTTTAATAATTTATTCAATCAA
Found at i:250764 original size:4 final size:4
Alignment explanation
Indices: 250757--250846 Score: 180
Period size: 4 Copynumber: 22.5 Consensus size: 4
250747 ACACACACAT
250757 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
250805 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
250847 GATTTGTTAC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 86 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:253231 original size:4 final size:4
Alignment explanation
Indices: 253222--253437 Score: 414
Period size: 4 Copynumber: 54.0 Consensus size: 4
253212 GAAAATAAAC
253222 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
253270 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
253318 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
253366 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
253414 GTAT GTAT GTTT GTTT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT
253438 TCATTTATTT
Statistics
Matches: 210, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 210 1.00
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
GTAT
Found at i:262045 original size:14 final size:14
Alignment explanation
Indices: 262026--262065 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
262016 TTGATTGCCA
262026 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
262040 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
262054 GGAAAATGTTTT
1 GTAAAATGTTTT
262066 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:262074 original size:20 final size:20
Alignment explanation
Indices: 262049--262089 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
262039 CGTAAAATGA
*
262049 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
262069 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
262089 T
1 T
262090 GAAAATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:262078 original size:34 final size:35
Alignment explanation
Indices: 262034--262100 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
262024 CAGTAAAATG
*
262034 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
* *
262068 TTTTCTGTAAAATGATTTACTTGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
262101 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:265507 original size:2 final size:2
Alignment explanation
Indices: 265500--265557 Score: 53
Period size: 2 Copynumber: 29.0 Consensus size: 2
265490 GCCGGTAAAT
* * * * * *
265500 TC TC TC TC TC TC TC CC CC CC TC TC CC TC TC CC TC CC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
265542 CC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
265558 ATTTTTTTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (2 bp):
TC
Found at i:265528 original size:16 final size:18
Alignment explanation
Indices: 265501--265557 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
265491 CCGGTAAATT
*
265501 CTCTCTCTCTCTCCC-CC
1 CTCTCTCCCTCTCCCTCC
265518 C-CTCTCCCTCTCCCTCC
1 CTCTCTCCCTCTCCCTCC
* *
265535 CTCTCTCCCTCTCTCTCT
1 CTCTCTCCCTCTCCCTCC
265553 CTCTC
1 CTCTC
265558 ATTTTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
16 12 0.34
17 4 0.11
18 19 0.54
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (18 bp):
CTCTCTCCCTCTCCCTCC
Found at i:268590 original size:50 final size:50
Alignment explanation
Indices: 268515--268613 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
268505 TGAATTTTTA
*
268515 TACTTATAATATGTAGTAGGTTTATTCATTAGCTTGAATAATTAGATATT
1 TACTTATAATATGTAGTAGGTTTATTCATTAGCTTCAATAATTAGATATT
268565 TACTTATAATATGTAGTAGGTTTATTCATTAGCTTCAATAATTAGATAT
1 TACTTATAATATGTAGTAGGTTTATTCATTAGCTTCAATAATTAGATAT
268614 CATAGTTCTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.45
Consensus pattern (50 bp):
TACTTATAATATGTAGTAGGTTTATTCATTAGCTTCAATAATTAGATATT
Found at i:273373 original size:2 final size:2
Alignment explanation
Indices: 273366--273400 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
273356 TAAAATATGC
273366 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
273401 CTCAGTATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:273683 original size:20 final size:19
Alignment explanation
Indices: 273636--273683 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
273626 TAAACCGCAG
* *
273636 TTAAACTCACCCTAAGTTT
1 TTAATCTCACCCTAAGTAT
* *
273655 TTTATCTCACGCTATAGTAT
1 TTAATCTCACCCTA-AGTAT
273675 TTAATCTCA
1 TTAATCTCA
273684 ACGCCACTAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (19 bp):
TTAATCTCACCCTAAGTAT
Found at i:273709 original size:78 final size:78
Alignment explanation
Indices: 273575--273730 Score: 240
Period size: 78 Copynumber: 2.0 Consensus size: 78
273565 TTTAGCTTAC
* * *
273575 TTTTTGTCTCACGCTATAATATCTAATATCAACGCCACCACTATTTTTACATAAACCGCAGTTAA
1 TTTTTATCTCACGCTATAATATCTAATATCAACGCCACCACTATTTTAACACAAACCGCAGTTAA
273640 ACTCACCCTAAGT
66 ACTCACCCTAAGT
* * * * *
273653 TTTTTATCTCACGCTATAGTATTTAATCTCAACGCCACTACTGTTTTAACACAAACCGCAGTTAA
1 TTTTTATCTCACGCTATAATATCTAATATCAACGCCACCACTATTTTAACACAAACCGCAGTTAA
273718 ACTCACCCTAAGT
66 ACTCACCCTAAGT
273731 GAGTTTTTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.33
Consensus pattern (78 bp):
TTTTTATCTCACGCTATAATATCTAATATCAACGCCACCACTATTTTAACACAAACCGCAGTTAA
ACTCACCCTAAGT
Found at i:287614 original size:44 final size:44
Alignment explanation
Indices: 287551--287713 Score: 229
Period size: 44 Copynumber: 3.6 Consensus size: 44
287541 TTTGAGTACT
* *
287551 TCTGATCAGTGACAAGTGATTAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGGGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
287595 TCTGATTAGGGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGGGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
287639 TCTGATCAATGACAAGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTA
1 TCTGATC-A-G----G-GACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
287689 TCTGATCAGGGACAAGTGATAAGTG
1 TCTGATCAGGGACAAGTGATAAGTG
287714 ATCATACGTA
Statistics
Matches: 108, Mismatches: 4, Indels: 15
0.85 0.03 0.12
Matches are distributed among these distances:
43 15 0.14
44 48 0.44
45 1 0.01
46 1 0.01
48 1 0.01
49 1 0.01
50 21 0.19
51 20 0.19
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (44 bp):
TCTGATCAGGGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:287703 original size:50 final size:51
Alignment explanation
Indices: 287605--287715 Score: 188
Period size: 50 Copynumber: 2.2 Consensus size: 51
287595 TCTGATTAGG
*
287605 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAAGT
1 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGGACAAGT
*
287656 GACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGGGACAAGT
1 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGGACAAGT
*
287706 GATAAGTGAT
1 GACAAGTGAT
287716 CATACGTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
50 37 0.65
51 20 0.35
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.28
Consensus pattern (51 bp):
GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGGACAAGT
Done.