Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011591.1 Kokia drynarioides strain JFW-HI SEQ_126581, 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: 412326
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 224 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:309 original size:15 final size:15
Alignment explanation
Indices: 273--301 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
263 TGCTTATAAT
273 ATAATTTTTATAAAA
1 ATAATTTTTATAAAA
288 ATAATTTTT-TAAAA
1 ATAATTTTTATAAAA
302 TTGAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATTTTTATAAAA
Found at i:1253 original size:19 final size:20
Alignment explanation
Indices: 1229--1273 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1219 ATTTTTATCT
1229 TAAAAAAATTAAAATT-AAA
1 TAAAAAAATTAAAATTAAAA
**
1248 TAAAAATCTTAAAATTCAAAA
1 TAAAAAAATTAAAATT-AAAA
1269 TAAAA
1 TAAAA
1274 TTATTGATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
21 8 0.36
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (20 bp):
TAAAAAAATTAAAATTAAAA
Found at i:16224 original size:27 final size:27
Alignment explanation
Indices: 16185--16251 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
16175 TCAAATGTAT
*
16185 GAAAAATTGAAACCTTTTGAAAGAAAA
1 GAAATATTGAAACCTTTTGAAAGAAAA
*
16212 GAATTATTGAAACCTTTTGAAAGAAAA
1 GAAATATTGAAACCTTTTGAAAGAAAA
16239 GAAATATTGAAAC
1 GAAATATTGAAAC
16252 TTTAAATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.25
Consensus pattern (27 bp):
GAAATATTGAAACCTTTTGAAAGAAAA
Found at i:19109 original size:23 final size:24
Alignment explanation
Indices: 19083--19134 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
19073 GAAGATTTAG
*
19083 TATTTATTAGCATAATAT-TTTGA
1 TATTTATTAGCATAAAATCTTTGA
* *
19106 TATTTATTAGTATAAAATCTTTGT
1 TATTTATTAGCATAAAATCTTTGA
19130 TATTT
1 TATTT
19135 CTTTCCTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.56
Consensus pattern (24 bp):
TATTTATTAGCATAAAATCTTTGA
Found at i:24116 original size:368 final size:362
Alignment explanation
Indices: 23279--24278 Score: 1251
Period size: 365 Copynumber: 2.8 Consensus size: 362
23269 ATAATACCTG
* *
23279 AAAATTAACCAAGACCTCGTAAAATAATTAAAAATTAATAAAATTCTCTACATAAACATTTTTCC
1 AAAATTAATCAAGACCTCGTAAAATAATTAAAAATTAATAAAATTCTCCACATAAACATTTTTCC
* * * * **
23344 ACATCAAATGCCACATTAGTCGCCAGATCATCATTTTTCCACGATAGCTACCTCATCACTAGT-C
66 ACGTCAAATGCCACATTAGTCGCCACATCATCATTTTTCCACGCTAGCTACCACATCAC-CCTCC
* **
23408 ATGTCACTTGCCACATCAACTCTTAACGGTCTATTAAGGGTGTAACACTTTAAGCCTAAGCTCAA
130 ATGTCACTTGCCAC-GCAACTCTTAACGGTCTATTAAGGGTGTAACACCCTAAGCCTAAGCTCAA
* * * * * * *
23473 CTTGAAAGTCCAGTCAAATTTAGAGTGTCACAATGATTGT-TGAAGCGACC-CATTCGATCAATC
194 CTCGAAAGTCCAGTAAAATATAGAGTGTCATAGTGATTGTCGGAA-TGACCGC--TCGATCAATC
* * *
23536 ATTTAATTATACATAGAAAAAAATGAAAATAAAAAGTATAAACAATAATAAATAATTTAACACAA
256 ATTCAATTATACATAG--AAAAATGAAAACAAAAAATATAAACAATAATAAATAATTTAACACAA
*
23601 TCATGCTTAAAAATAAATTAAAATCATTAAACACAAATTTCTAA
319 TCATGCTTAAAAATAAATTAAAATAATTAAACACAAATTTCTAA
* *
23645 AAAA-TAATCAAGAACTCGTAAAATAATTAAAAATTAATAAAATCCTCCACATAAACATTTTTCC
1 AAAATTAATCAAGACCTCGTAAAATAATTAAAAATTAATAAAATTCTCCACATAAACATTTTTCC
* * *
23709 AAGTCAAATGCCACATGAGTTGCCACATCATCATTTTTCCACGCTAGCTACCACATCACCCTCCA
66 ACGTCAAATGCCACATTAGTCGCCACATCATCATTTTTCCACGCTAGCTACCACATCACCCTCCA
* *
23774 TGTCACTTGCCACGCCAACTCTTAACGGTCTATCAAGTGTGTAACACCCTAAGCCTAAGCTCAAC
131 TGTCACTTGCCACG-CAACTCTTAACGGTCTATTAAGGGTGTAACACCCTAAGCCTAAGCTCAAC
* * * *
23839 CCGAAAGTCCGGTAAAATCTAGAGTGCCATAGTGATTGTCGGAATGATCCGCTCGATCAATCATT
195 TCGAAAGTCCAGTAAAATATAGAGTGTCATAGTGATTGTCGGAATGA-CCGCTCGATCAATCATT
* * *
23904 CAATTATACATAGAAAATTGAAAACAAAAAATTTAAACATGCAAATAATAAATCATTTAACACAA
259 CAATTATACATAGAAAAATGAAAACAAAAAATAT-AA-A--C-AATAATAAATAATTTAACACAA
*
23969 TCATGCTTAAAAATAAGTTAAAATAATTAAACACAAATTTC-AA
319 TCATGCTTAAAAATAAATTAAAATAATTAAACACAAATTTCTAA
* * * * *
24012 AAAATTAATTAAGACCTCATAAAATAATTAAAAATGAATAAAATTTTCCACATAAATATTTTTCC
1 AAAATTAATCAAGACCTCGTAAAATAATTAAAAATTAATAAAATTCTCCACATAAACATTTTTCC
* * * *
24077 ACGTCAAATGCCACATTAATCACCACATTATCATTTTTCCATGCTAGCTACCACATCA-CCTGCC
66 ACGTCAAATGCCACATTAGTCGCCACATCATCATTTTTCCACGCTAGCTACCACATCACCCT-CC
* * * *
24141 ATG-----T--CA-G---CTCTTAACGGTCTATTAGGGGTGTAATACCCTAAGCCTAAGCCCGAC
130 ATGTCACTTGCCACGCAACTCTTAACGGTCTATTAAGGGTGTAACACCCTAAGCCTAAGCTCAAC
* * * *
24195 TCGAAAGTCCAGTTAAATATAGAGTGTCGTAGTGATTGTCGGAGTGACTTGCTCGATCAATCATT
195 TCGAAAGTCCAGTAAAATATAGAGTGTCATAGTGATTGTCGGAATGAC-CGCTCGATCAATCATT
24260 CAATTATACATAGAAAAAT
259 CAATTATACATAGAAAAAT
24279 AACCAAACAA
Statistics
Matches: 556, Mismatches: 65, Indels: 36
0.85 0.10 0.05
Matches are distributed among these distances:
355 1 0.00
356 114 0.21
360 1 0.00
361 2 0.00
363 18 0.03
364 3 0.01
365 228 0.41
366 9 0.02
367 11 0.02
368 169 0.30
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (362 bp):
AAAATTAATCAAGACCTCGTAAAATAATTAAAAATTAATAAAATTCTCCACATAAACATTTTTCC
ACGTCAAATGCCACATTAGTCGCCACATCATCATTTTTCCACGCTAGCTACCACATCACCCTCCA
TGTCACTTGCCACGCAACTCTTAACGGTCTATTAAGGGTGTAACACCCTAAGCCTAAGCTCAACT
CGAAAGTCCAGTAAAATATAGAGTGTCATAGTGATTGTCGGAATGACCGCTCGATCAATCATTCA
ATTATACATAGAAAAATGAAAACAAAAAATATAAACAATAATAAATAATTTAACACAATCATGCT
TAAAAATAAATTAAAATAATTAAACACAAATTTCTAA
Found at i:24297 original size:22 final size:22
Alignment explanation
Indices: 24269--24313 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
24259 TCAATTATAC
24269 ATAGAAAAATAACCAAACAATT
1 ATAGAAAAATAACCAAACAATT
24291 ATAGAAAAATAACCAAACAATT
1 ATAGAAAAATAACCAAACAATT
24313 A
1 A
24314 ACACAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.64, C:0.13, G:0.04, T:0.18
Consensus pattern (22 bp):
ATAGAAAAATAACCAAACAATT
Found at i:27991 original size:70 final size:70
Alignment explanation
Indices: 27878--28017 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
27868 GTGAAGGTCG
27878 TCGCATGCAGATTTGATTGCTGCTTGATATGGTCCAATCTCACCAGGGTCATCGTAAGGCTAGGC
1 TCGCATGCAGATTTGATTGCTGCTTGATATGGTCCAATCTCACCAGGGTCATCGTAAGGCTAGGC
27943 TCCGT
66 TCCGT
27948 TCGCATGCAGATTTGATTGCTGCTTGATATGGTCCAATCTCACCAGGGTCATCGTAAGGCTAGGC
1 TCGCATGCAGATTTGATTGCTGCTTGATATGGTCCAATCTCACCAGGGTCATCGTAAGGCTAGGC
28013 TCCGT
66 TCCGT
28018 CCGAATGGGT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (70 bp):
TCGCATGCAGATTTGATTGCTGCTTGATATGGTCCAATCTCACCAGGGTCATCGTAAGGCTAGGC
TCCGT
Found at i:29873 original size:193 final size:193
Alignment explanation
Indices: 29505--29874 Score: 440
Period size: 194 Copynumber: 1.9 Consensus size: 193
29495 TACCAGTACT
* * * **
29505 CGATGATGCTCACACGAGCTGTCGAGGACTCGCAACGTATGCGGTACCCCATCCATCGGTACGGT
1 CGATGATGCTCACACGAGCTGTCAAGGACTCGCAACATATGCGGTACCCCAGCCATCAATACGGT
* * * * * *
29570 GTTTGTCTGTACTATAAACTATTCCCTAACAATGCTGCCACACGAGTTATCGAGAGTATGCAATA
66 ATCTG-CTGCACTATAAACTATTCCCTAACAATGCTGCCACACGAGCTATCAAGAATATGCAATA
* * *
29635 AGTATAGTCCCAGCCATCGTAGGGCCTATAAACCATTTAGGATCCATATCTCTTTCTCGAGTCA
130 AGCATAATCCCAACCATCGTAGGGCCTATAAACCATTTAGGATCCATATCTCTTTCTCGAGTCA
* * * *
29699 CGATGCTGCTCACATGAGCTGTCAAGGACTCGCAACATATGTGGTACCTCAGCCATCAATACGGT
1 CGATGATGCTCACACGAGCTGTCAAGGACTCGCAACATATGCGGTACCCCAGCCATCAATACGGT
* * * *
29764 ATCTG-TGCA-TAT-AACTGTTCCCTAACGATGTTGCTCACACGAGCTATCAAGAATATGCACTT
66 ATCTGCTGCACTATAAACTATTCCCTAACAATGCTGC-CACACGAGCTATCAAGAATATGCA-AT
* * * * *
29826 ATGCATAAATCTCAACCATCGTAGGGCCTGTTATCCATTTAGGATCCAT
129 AAGCAT-AATCCCAACCATCGTAGGGCCTATAAACCATTTAGGATCCAT
29875 GTTCCTTTTC
Statistics
Matches: 146, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
190 19 0.13
191 24 0.16
192 8 0.05
193 36 0.25
194 59 0.40
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (193 bp):
CGATGATGCTCACACGAGCTGTCAAGGACTCGCAACATATGCGGTACCCCAGCCATCAATACGGT
ATCTGCTGCACTATAAACTATTCCCTAACAATGCTGCCACACGAGCTATCAAGAATATGCAATAA
GCATAATCCCAACCATCGTAGGGCCTATAAACCATTTAGGATCCATATCTCTTTCTCGAGTCA
Found at i:46630 original size:14 final size:15
Alignment explanation
Indices: 46611--46643 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
46601 AAAGAGACTG
*
46611 AAATTTTTT-TGGCA
1 AAATTTTTTCTAGCA
46625 AAATTTTTTCTAGCA
1 AAATTTTTTCTAGCA
46640 AAAT
1 AAAT
46644 CTATGGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (15 bp):
AAATTTTTTCTAGCA
Found at i:47418 original size:13 final size:13
Alignment explanation
Indices: 47400--47428 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
47390 AAAATTAACA
47400 AAATTAATAAACT
1 AAATTAATAAACT
47413 AAATTAATAAACT
1 AAATTAATAAACT
47426 AAA
1 AAA
47429 GAACACAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATTAATAAACT
Found at i:52977 original size:3 final size:3
Alignment explanation
Indices: 52969--53059 Score: 94
Period size: 3 Copynumber: 30.3 Consensus size: 3
52959 ACATGAACAT
* * * * * *
52969 ATA ATA ATA ATA ATA GTA ATA CTA CTA TTA CTA ATA ATA ATA AGA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
53017 ATA ATA A-A ACTC ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53060 ACGAAAGGAG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
2 2 0.03
3 72 0.96
4 1 0.01
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:56841 original size:20 final size:21
Alignment explanation
Indices: 56814--56858 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
56804 AATAAAAGGG
*
56814 AAAA-ATTAAATTAAAAA-TA
1 AAAATATTAAAATAAAAATTA
56833 AAAATATTAAAATAAAAATTA
1 AAAATATTAAAATAAAAATTA
56854 AAAAT
1 AAAAT
56859 GGCTAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.17
20 12 0.52
21 7 0.30
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAATATTAAAATAAAAATTA
Found at i:74560 original size:17 final size:17
Alignment explanation
Indices: 74538--74576 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
74528 AAGTGAAAAA
* * *
74538 CTTGTTCGTTGAGAGTT
1 CTTGTTCATAGAGAATT
74555 CTTGTTCATAGAGAATT
1 CTTGTTCATAGAGAATT
74572 CTTGT
1 CTTGT
74577 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCATAGAGAATT
Found at i:74623 original size:41 final size:41
Alignment explanation
Indices: 74566--74661 Score: 167
Period size: 41 Copynumber: 2.3 Consensus size: 41
74556 TTGTTCATAG
*
74566 AGAATTCTTGTCAAGGTGGAGATTGTTAGAATT-AGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGA-GTGACT
74607 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGAGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGAGTGACT
74648 AGAATTCTTGTTAA
1 AGAATTCTTGTTAA
74662 AATAAAATTC
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
41 52 0.98
42 1 0.02
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.36
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGAGTGACT
Found at i:83695 original size:3 final size:3
Alignment explanation
Indices: 83689--83726 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
83679 AAAAAGAAGA
83689 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
83727 AGAAGAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:86913 original size:23 final size:22
Alignment explanation
Indices: 86887--86930 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
86877 AGCCTAACTC
86887 ATTTTTAAATATTATATTATTTT
1 ATTTTTAAATATTATA-TATTTT
*
86910 ATTTTTATATATTATATATTT
1 ATTTTTAAATATTATATATTT
86931 ATGGTGGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTTTAAATATTATATATTTT
Found at i:89719 original size:28 final size:28
Alignment explanation
Indices: 89680--89756 Score: 118
Period size: 28 Copynumber: 2.8 Consensus size: 28
89670 ATGGTTTTGG
*
89680 AAAAATAATTTTGACGAGATGTGTTGTA
1 AAAAATAATTTTGACGAGATGTGTTATA
* * *
89708 AAAAATAATTTTGACGTGATATGTTATG
1 AAAAATAATTTTGACGAGATGTGTTATA
89736 AAAAATAATTTTGACGAGATG
1 AAAAATAATTTTGACGAGATG
89757 GATTTTGTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (28 bp):
AAAAATAATTTTGACGAGATGTGTTATA
Found at i:94961 original size:20 final size:20
Alignment explanation
Indices: 94936--94975 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
94926 TAAATCTTTC
94936 GATTTTAGCTCGTTTTCGCT
1 GATTTTAGCTCGTTTTCGCT
94956 GATTTTAGCTCGTTTTCGCT
1 GATTTTAGCTCGTTTTCGCT
94976 CCTTTTGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.50
Consensus pattern (20 bp):
GATTTTAGCTCGTTTTCGCT
Found at i:94981 original size:20 final size:20
Alignment explanation
Indices: 94937--94985 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
94927 AAATCTTTCG
*
94937 ATTTTAGCTCGTTTTCGCTG
1 ATTTTAGCTCGTTTTCGCTC
94957 ATTTTAGCTCGTTTTCGCTC
1 ATTTTAGCTCGTTTTCGCTC
*
94977 CTTTT-GCTC
1 ATTTTAGCTC
94986 TCAAATGCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.08, C:0.24, G:0.16, T:0.51
Consensus pattern (20 bp):
ATTTTAGCTCGTTTTCGCTC
Found at i:95340 original size:12 final size:12
Alignment explanation
Indices: 95323--95348 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
95313 GGATTTTAAA
95323 TTCATTTCACCC
1 TTCATTTCACCC
95335 TTCATTTCACCC
1 TTCATTTCACCC
95347 TT
1 TT
95349 TATAATCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.46
Consensus pattern (12 bp):
TTCATTTCACCC
Found at i:107179 original size:11 final size:11
Alignment explanation
Indices: 107165--107198 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
107155 TACTTTTATT
107165 TTAGTTTTTAA
1 TTAGTTTTTAA
107176 TTAGTTTTTAA
1 TTAGTTTTTAA
*
107187 TTGTGTTTTTAA
1 TT-AGTTTTTAA
107199 GTTTCTAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (11 bp):
TTAGTTTTTAA
Found at i:107390 original size:38 final size:38
Alignment explanation
Indices: 107348--107424 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
107338 ATGCATAAGT
* *
107348 AAAGAAAATTAGTGTATTATAAAGCAAGGTATCAAACA
1 AAAGAAAATAAGTGTATTATAAAGCAAGGTACCAAACA
107386 AAAGAAAATAAGTGTATTATAAAGCAAGGTACCAAACA
1 AAAGAAAATAAGTGTATTATAAAGCAAGGTACCAAACA
107424 A
1 A
107425 TTTAAGAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.55, C:0.09, G:0.16, T:0.21
Consensus pattern (38 bp):
AAAGAAAATAAGTGTATTATAAAGCAAGGTACCAAACA
Found at i:108283 original size:14 final size:15
Alignment explanation
Indices: 108260--108301 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
108250 ATCATTAGTT
* *
108260 TTTTAAATATTT-AC
1 TTTTATATATTTAAA
108274 TTTTATATATTTTAAA
1 TTTTATATA-TTTAAA
108290 TTTTATATATTT
1 TTTTATATATTT
108302 TTATTTCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 8 0.33
15 6 0.25
16 10 0.42
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTATATATTTAAA
Found at i:109909 original size:45 final size:45
Alignment explanation
Indices: 109858--109954 Score: 158
Period size: 45 Copynumber: 2.2 Consensus size: 45
109848 AGCGAAACGT
* *
109858 ATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACC
1 ATATCATGCATATCATATAACATAATCAATCAAATAATATTTACC
**
109903 ATATCATGCATATCATATAACATAATCAATCAAATAATATTTGTC
1 ATATCATGCATATCATATAACATAATCAATCAAATAATATTTACC
109948 ATATCAT
1 ATATCAT
109955 TGTTAGAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.35
Consensus pattern (45 bp):
ATATCATGCATATCATATAACATAATCAATCAAATAATATTTACC
Found at i:110565 original size:11 final size:11
Alignment explanation
Indices: 110551--110626 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
110541 GATAATCAAT
110551 TTAATATTAAA
1 TTAATATTAAA
110562 TTAATA--AAA
1 TTAATATTAAA
*
110571 -TACTATTAAA
1 TTAATATTAAA
*
110581 ATAAGTATTAAA
1 TTAA-TATTAAA
110593 TTAA-ATTTAATA
1 TTAATA-TTAA-A
110605 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
110618 ATAATATTA
1 TTAATATTA
110627 TTTTTGAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 4 0.08
11 17 0.33
12 15 0.29
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:110613 original size:37 final size:36
Alignment explanation
Indices: 110551--110626 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
110541 GATAATCAAT
110551 TTAATATTAAATTAATAAAATACTATTAAAATAAGTA
1 TTAATATTAAATTAATAAAATACTATTAAAATAA-TA
*
110588 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAATA
1 TTAATATTAAA-TTAATA-AAATACTATTAAAATAATA
110624 TTA
1 TTA
110627 TTTTTGAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 11 0.31
37 23 0.64
38 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAATA
Found at i:115534 original size:36 final size:35
Alignment explanation
Indices: 115482--115582 Score: 157
Period size: 36 Copynumber: 2.8 Consensus size: 35
115472 TCATTATTCG
*
115482 TTTTACTCCCTGTTGACACATAGGTCATGATGCTCA
1 TTTTACTCCCTGTTGACCCA-AGGTCATGATGCTCA
*
115518 TTTTACTCCCTATTGACCCAAAGGTCATGATGCTCA
1 TTTTACTCCCTGTTGACCC-AAGGTCATGATGCTCA
115554 TTTTACTCCCTGTTGATCCCAAGGTCATG
1 TTTTACTCCCTGTTGA-CCCAAGGTCATG
115583 CCTGTTACCT
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
36 56 0.93
37 4 0.07
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.36
Consensus pattern (35 bp):
TTTTACTCCCTGTTGACCCAAGGTCATGATGCTCA
Found at i:119804 original size:24 final size:24
Alignment explanation
Indices: 119777--119832 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
119767 AGCCCACACG
*
119777 AGCCCATAATGGTTAGCTCTTACT
1 AGCCCAGAATGGTTAGCTCTTACT
119801 AGCCCAGAATGGTTAGCTCTTACT
1 AGCCCAGAATGGTTAGCTCTTACT
119825 AGCCCAGA
1 AGCCCAGA
119833 TAGAGTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (24 bp):
AGCCCAGAATGGTTAGCTCTTACT
Found at i:123568 original size:21 final size:20
Alignment explanation
Indices: 123528--123571 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
123518 ATATTAGAAA
123528 TAAATAGGATTAATTAAAGC
1 TAAATAGGATTAATTAAAGC
123548 TAAATAAGTGATTAA-TAAAGC
1 TAAAT-AG-GATTAATTAAAGC
123569 TAA
1 TAA
123572 TTATGAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.23
21 11 0.50
22 6 0.27
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.30
Consensus pattern (20 bp):
TAAATAGGATTAATTAAAGC
Found at i:147098 original size:24 final size:24
Alignment explanation
Indices: 147071--147119 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
147061 TTTTTATTTG
*
147071 AGTGGCTAACGAGCATAAATGTAT
1 AGTGGCTAACGAGCATAAACGTAT
* * *
147095 AGTGGGTTATGAGCATAAACGTAT
1 AGTGGCTAACGAGCATAAACGTAT
147119 A
1 A
147120 TTAGCTGACG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (24 bp):
AGTGGCTAACGAGCATAAACGTAT
Found at i:151733 original size:45 final size:45
Alignment explanation
Indices: 151659--152052 Score: 431
Period size: 45 Copynumber: 8.7 Consensus size: 45
151649 TCAATCATAT
* * * *
151659 ATATCTTATAGCATAATTAATCAAATAATATTTACCATATCGTGC
1 ATATCGTATAACATAATCAATCAAATAATATTTACCATATCATGC
* * * *
151704 ATATCATATAACACAATCAACCAAGTAATATTTACCATATCATGC
1 ATATCGTATAACATAATCAATCAAATAATATTTACCATATCATGC
* * *
151749 ATATTGTATAAC---AT-AATC-AATAGTATTTACCATATCAAGC
1 ATATCGTATAACATAATCAATCAAATAATATTTACCATATCATGC
* * * *
151789 ATATCTTATATCATAATCAATCAAATAATATCTACCAAATCATGC
1 ATATCGTATAACATAATCAATCAAATAATATTTACCATATCATGC
* * * * *
151834 ATATCGTATAGCATAATTAATTAAATTACATTTACCATATCATGC
1 ATATCGTATAACATAATCAATCAAATAATATTTACCATATCATGC
*
151879 ATATCGTATTAACATAATCAAAT-AAATAATACTTACCATATCATGC
1 ATATCGTA-TAACATAATC-AATCAAATAATATTTACCATATCATGC
* * *
151925 ATATCGTACAACATAATTAATCAAATAATAATATTTATCATATCATGC
1 ATATCGTATAACATAATCAATC--A-AATAATATTTACCATATCATGC
*
151973 ATATCGTACAACATAATCAATCAAATAATAATATTTACCATATCATGC
1 ATATCGTATAACATAATCAATC--A-AATAATATTTACCATATCATGC
* *
152021 ATATCGTACAACATAATTAATCAAATAATATT
1 ATATCGTATAACATAATCAATCAAATAATATT
152053 ACTTCATGGT
Statistics
Matches: 298, Mismatches: 40, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
40 28 0.09
41 3 0.01
42 2 0.01
43 2 0.01
44 7 0.02
45 128 0.43
46 37 0.12
47 4 0.01
48 87 0.29
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (45 bp):
ATATCGTATAACATAATCAATCAAATAATATTTACCATATCATGC
Found at i:151777 original size:85 final size:86
Alignment explanation
Indices: 151676--152037 Score: 375
Period size: 85 Copynumber: 4.0 Consensus size: 86
151666 ATAGCATAAT
* * * *
151676 TAATCAAATAATATTTACCATATCGTGCATATCATATAACACAATCAACCAAGTAATATTTACCA
1 TAATCAAATAATATTTACCATATCATGCATATCGTATAACATAATCAACCAAATAATATTTACCA
* *
151741 TATCATGCATATTGTATAACA
66 TATCATGCATATCGTACAACA
* * * * * *
151762 TAATC-AATAGTATTTACCATATCAAGCATATCTTATATCATAATCAATCAAATAATATCTACCA
1 TAATCAAATAATATTTACCATATCATGCATATCGTATAACATAATCAACCAAATAATATTTACCA
* * *
151826 AATCATGCATATCGTATAGCA
66 TATCATGCATATCGTACAACA
* * ** *
151847 TAATTAATTAAATTACATTTACCATATCATGCATATCGTATTAACATAATCAAATAAATAATACT
1 TAATCAAAT-AA-T--ATTTACCATATCATGCATATCGTA-TAACATAATCAACCAAATAATATT
151912 TACCATATCATGCATATCGTACAACATAA
61 TACCATATCATGCATATCGTACAAC---A
* * *
151941 TTAATCAAATAATAATATTTATCATATCATGCATATCGTACAACATAATCAATCAAATAATAATA
1 -TAATC--A-AATAATATTTACCATATCATGCATATCGTATAACATAATCAA-C-CA-AATAATA
152006 TTTACCATATCATGCATATCGTACAACA
59 TTTACCATATCATGCATATCGTACAACA
152034 TAAT
1 TAAT
152038 TAATCAAATA
Statistics
Matches: 228, Mismatches: 32, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
85 72 0.32
86 7 0.03
87 1 0.00
88 1 0.00
90 22 0.10
91 41 0.18
92 4 0.02
93 12 0.05
94 24 0.11
95 5 0.02
96 34 0.15
97 3 0.01
98 2 0.01
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (86 bp):
TAATCAAATAATATTTACCATATCATGCATATCGTATAACATAATCAACCAAATAATATTTACCA
TATCATGCATATCGTACAACA
Found at i:151974 original size:48 final size:48
Alignment explanation
Indices: 151767--152050 Score: 336
Period size: 48 Copynumber: 6.1 Consensus size: 48
151757 TAACATAATC
* * * * * *
151767 AATAGTATTTACCATATCAAGCATATCTTATATCATAATCAATC--A-
1 AATAATATTTACCATATCATGCATATCGTACAACATAATTAATCAAAT
* * * * *
151812 AATAATATCTACCAAATCATGCATATCGTATAGCATAATTAATTAAAT
1 AATAATATTTACCATATCATGCATATCGTACAACATAATTAATCAAAT
* *
151860 --T-ACATTTACCATATCATGCATATCGTATTAAC---A-TAATCAAAT
1 AATAATATTTACCATATCATGCATATCGTA-CAACATAATTAATCAAAT
*
151902 AAATAATACTTACCATATCATGCATATCGTACAACATAATTAATCAAAT
1 -AATAATATTTACCATATCATGCATATCGTACAACATAATTAATCAAAT
* *
151951 AATAATATTTATCATATCATGCATATCGTACAACATAATCAATCAAAT
1 AATAATATTTACCATATCATGCATATCGTACAACATAATTAATCAAAT
151999 AATAATATTTACCATATCATGCATATCGTACAACATAATTAATCAAAT
1 AATAATATTTACCATATCATGCATATCGTACAACATAATTAATCAAAT
152047 AATA
1 AATA
152051 TTACTTCATG
Statistics
Matches: 206, Mismatches: 21, Indels: 21
0.83 0.08 0.08
Matches are distributed among these distances:
42 8 0.04
43 1 0.00
45 63 0.31
46 28 0.14
47 1 0.00
48 96 0.47
49 9 0.04
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (48 bp):
AATAATATTTACCATATCATGCATATCGTACAACATAATTAATCAAAT
Found at i:152023 original size:96 final size:94
Alignment explanation
Indices: 151767--152050 Score: 373
Period size: 91 Copynumber: 3.0 Consensus size: 94
151757 TAACATAATC
* * * * * *
151767 AATAGTATTTACCATATCAAGCATATCTTATATCATAATCAATC-AAATAATATCTACCAAATCA
1 AATAATATTTACCATATCATGCATATCGTATAACATAATCAATCAAAATAATATTTACCATATCA
* * *
151831 TGCATATCGTATAGCATAATTAATTAAAT
66 TGCATATCGTACAACATAATTAATCAAAT
* *
151860 --T-ACATTTACCATATCATGCATATCGTATTAACATAATCAA--ATAAATAATACTTACCATAT
1 AATAATATTTACCATATCATGCATATCGTA-TAACATAATCAATCA-AAATAATATTTACCATAT
151920 CATGCATATCGTACAACATAATTAATCAAAT
64 CATGCATATCGTACAACATAATTAATCAAAT
* *
151951 AATAATATTTATCATATCATGCATATCGTACAACATAATCAATCAAATAATAATATTTACCATAT
1 AATAATATTTACCATATCATGCATATCGTATAACATAATCAATC-AA-AATAATATTTACCATAT
152016 CATGCATATCGTACAACATAATTAATCAAAT
64 CATGCATATCGTACAACATAATTAATCAAAT
152047 AATA
1 AATA
152051 TTACTTCATG
Statistics
Matches: 166, Mismatches: 15, Indels: 17
0.84 0.08 0.09
Matches are distributed among these distances:
90 22 0.13
91 55 0.33
93 12 0.07
94 24 0.14
95 1 0.01
96 52 0.31
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (94 bp):
AATAATATTTACCATATCATGCATATCGTATAACATAATCAATCAAAATAATATTTACCATATCA
TGCATATCGTACAACATAATTAATCAAAT
Found at i:154443 original size:18 final size:19
Alignment explanation
Indices: 154420--154466 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
154410 TAGAGGGAAT
* *
154420 AGCAATATTGCCTCGT-TG
1 AGCAATACTGCCTCGTAAG
*
154438 AGCAATACTGGCTCGTAAG
1 AGCAATACTGCCTCGTAAG
154457 AGCAATACTG
1 AGCAATACTG
154467 GATCGTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (19 bp):
AGCAATACTGCCTCGTAAG
Found at i:154461 original size:19 final size:19
Alignment explanation
Indices: 154437--154474 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
154427 TTGCCTCGTT
*
154437 GAGCAATACTGGCTCGTAA
1 GAGCAATACTGGATCGTAA
154456 GAGCAATACTGGATCGTAA
1 GAGCAATACTGGATCGTAA
154475 AGGGTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.21
Consensus pattern (19 bp):
GAGCAATACTGGATCGTAA
Found at i:155111 original size:21 final size:21
Alignment explanation
Indices: 155085--155136 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
155075 GTGTTTAGAA
155085 GTATCGGTAGTTTGTGTACTT
1 GTATCGGTAGTTTGTGTACTT
155106 GTATCGGTAGTTTGTGTACTT
1 GTATCGGTAGTTTGTGTACTT
155127 GTATCGGTAG
1 GTATCGGTAG
155137 AAGTTGTAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.15, C:0.10, G:0.31, T:0.44
Consensus pattern (21 bp):
GTATCGGTAGTTTGTGTACTT
Found at i:155216 original size:21 final size:21
Alignment explanation
Indices: 155192--155249 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
155182 TAGAAGTAAG
* * *
155192 ACTTGTTTCAGTAGAAGAGTC
1 ACTTGTATCGGTAGAACAGTC
*
155213 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGGTAGAACAGTC
155234 ACTTGTATCGGTAGAA
1 ACTTGTATCGGTAGAA
155250 ATTTGTACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:155991 original size:6 final size:6
Alignment explanation
Indices: 155982--156008 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
155972 AAGGAAAAGC
155982 ATATAA ATATAA ATATAA ATATAA ATA
1 ATATAA ATATAA ATATAA ATATAA ATA
156009 AAAAGAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAA
Found at i:156992 original size:31 final size:31
Alignment explanation
Indices: 156942--157018 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
156932 TCCGGCCATG
* * * *
156942 GCTCCGTCGCCGACCCACCGC-CAGTCATTGA
1 GCTCCGTCGTCGGCCCACCGCTCACT-ATCGA
* *
156973 GCTCCGTCGTCGGCTCACCGCTCACTGTCGA
1 GCTCCGTCGTCGGCCCACCGCTCACTATCGA
157004 GCTCCGTCGTCGGCC
1 GCTCCGTCGTCGGCC
157019 TACCACCATG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 35 0.92
32 3 0.08
ACGTcount: A:0.10, C:0.44, G:0.26, T:0.19
Consensus pattern (31 bp):
GCTCCGTCGTCGGCCCACCGCTCACTATCGA
Found at i:158484 original size:38 final size:38
Alignment explanation
Indices: 158381--158823 Score: 376
Period size: 38 Copynumber: 11.4 Consensus size: 38
158371 TAAGATGATA
* * *
158381 GCTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGTAT
1 GCTTCAATCTGCCCCATGATCAGGGTAAAAGATTGG-AT
* * * *
158420 GTCTTCAATCTGCCTTC-TAATTAAGGTAAAAGATTGGAT
1 G-CTTCAATCTGCC-CCATGATCAGGGTAAAAGATTGGAT
* * *
158459 GCTTCAATCTACCCCATGATCAAGGTAAGAGATTGGAT
1 GCTTCAATCTGCCCCATGATCAGGGTAAAAGATTGGAT
* * *
158497 GGTTACAATCTGCCCCATGATTAGGGTCAAAGATTGGAT
1 GCTT-CAATCTGCCCCATGATCAGGGTAAAAGATTGGAT
* * * *
158536 GGCTGCAATTTGCCCCATGATCGGGGTAAGAGATTGGAT
1 -GCTTCAATCTGCCCCATGATCAGGGTAAAAGATTGGAT
* * *
158575 GCTTCAATCTGCCCTATGGTC-GAGGTAAGAGATTGGAT
1 GCTTCAATCTGCCCCATGATCAG-GGTAAAAGATTGGAT
* * *
158613 GGTATTCAATCTGCCCTC-TGATTAGGATAAAAGATTGGAT
1 -G-CTTCAATCTGCCC-CATGATCAGGGTAAAAGATTGGAT
* * *
158653 GCATCAATTTGCCCCATGATC-GGAATAAAAGATTGGAT
1 GCTTCAATCTGCCCCATGATCAGG-GTAAAAGATTGGAT
* * *
158691 GGTCTTCAATCTGCCCTATGGTC-GGGTAAGAGATTGGAT
1 -G-CTTCAATCTGCCCCATGATCAGGGTAAAAGATTGGAT
* * *
158730 GATCTTCAATCTGTCCTC-TAATTAGGGTAAAAGATTGGAT
1 G--CTTCAATCTG-CCCCATGATCAGGGTAAAAGATTGGAT
* * *
158770 GCTTCAATCTGCCCCATGATTAGGGTAAAAGACTAGAT
1 GCTTCAATCTGCCCCATGATCAGGGTAAAAGATTGGAT
* *
158808 TCTTCAATTTGCCCCA
1 GCTTCAATCTGCCCCA
158824 CCATAACTTA
Statistics
Matches: 331, Mismatches: 55, Indels: 37
0.78 0.13 0.09
Matches are distributed among these distances:
37 8 0.02
38 137 0.41
39 90 0.27
40 93 0.28
41 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (38 bp):
GCTTCAATCTGCCCCATGATCAGGGTAAAAGATTGGAT
Found at i:158552 original size:78 final size:77
Alignment explanation
Indices: 158381--158823 Score: 407
Period size: 78 Copynumber: 5.7 Consensus size: 77
158371 TAAGATGATA
* * * *
158381 GCTTCAATCTGCCTCATGATCGGGGTAAGAGATTGGTATGTCTTCAATCTGCCTTC-TAATTAAG
1 GCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG-ATG-CTTCAATCTGCC-CCATGATTAGG
158445 GTAAAAGATTGGAT-
63 GTAAAAGATTGGATG
* ** *
158459 GCTTCAATCTACCCCATGATCAAGGTAAGAGATTGGATGGTTACAATCTGCCCCATGATTAGGGT
1 GCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGCTT-CAATCTGCCCCATGATTAGGGT
*
158524 CAAAGATTGGATG
65 AAAAGATTGGATG
* * * * *
158537 GCTGCAATTTGCCCCATGATCGGGGTAAGAGATTGGATGCTTCAATCTGCCCTATG-GTCGAGGT
1 GCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGCTTCAATCTGCCCCATGATTAG-GGT
*
158601 AAGAGATTGGATG
65 AAAAGATTGGATG
* ** * * * * *
158614 GTATTCAATCTGCCCTC-TGATTAGGATAAAAGATTGGATGCATCAATTTGCCCCATGA-TCGGA
1 G-CTTCAATCTGCCC-CATGATCGGGGTAAGAGATTGGATGCTTCAATCTGCCCCATGATTAGG-
*
158677 ATAAAAGATTGGATG
63 GTAAAAGATTGGATG
* * * *
158692 GTCTTCAATCTGCCCTATGGTC-GGGTAAGAGATTGGATGATCTTCAATCTGTCCTC-TAATTAG
1 G-CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATG--CTTCAATCTG-CCCCATGATTAG
158755 GGTAAAAGATTGGAT-
62 GGTAAAAGATTGGATG
** * * * * *
158770 GCTTCAATCTGCCCCATGATTAGGGTAAAAGACTAGATTCTTCAATTTGCCCCA
1 GCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGCTTCAATCTGCCCCA
158824 CCATAACTTA
Statistics
Matches: 297, Mismatches: 53, Indels: 32
0.78 0.14 0.08
Matches are distributed among these distances:
75 3 0.01
76 14 0.05
77 92 0.31
78 158 0.53
79 24 0.08
80 6 0.02
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (77 bp):
GCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGCTTCAATCTGCCCCATGATTAGGGTA
AAAGATTGGATG
Found at i:158727 original size:194 final size:195
Alignment explanation
Indices: 158381--158789 Score: 487
Period size: 194 Copynumber: 2.1 Consensus size: 195
158371 TAAGATGATA
* * *
158381 GCTTCAATCTG-CCTCATGATCGGGGTAAGAGATTGGTATGTCTTCAATCTGCCTTCTAATTAAG
1 GCTTCAATCTGCCCTCATGATCGAGGTAAGAGATTGGTATGTATTCAATCTGCCCTCTAATTAAG
* *
158445 GTAAAAGATTGGATGCTTCAATCTACCCCATGATCAAGGTAAGAGATTGGATGGTTACAATCTGC
66 GTAAAAGATTGGATGCATCAATCTACCCCATGATCAA-GTAAAAGATTGGATGGTTACAATCTGC
* * * * *
158510 CCCATGATTAGGGTCAAAGATTGGATG-GCTGCAATTTG-CCCCATGATCGGGGTAAGAGATTGG
130 CCCATGAGTAGGGTCAAAGATTGGATGAGCTGCAATCTGTCCCC-TAATCAGGGTAAAAGATTGG
158573 AT
194 AT
* *
158575 GCTTCAATCTGCCCT-ATGGTCGAGGTAAGAGATTGG-ATGGTATTCAATCTGCCCTCTGATT-A
1 GCTTCAATCTGCCCTCATGATCGAGGTAAGAGATTGGTAT-GTATTCAATCTGCCCTCTAATTAA
* * *
158637 GGATAAAAGATTGGATGCATCAATTTGCCCCATGATCGGAA-TAAAAGATTGGATGGTCTTCAAT
65 GG-TAAAAGATTGGATGCATCAATCTACCCCATGATC--AAGTAAAAGATTGGATGGT-TACAAT
* * * * * *
158701 CTGCCCTATG-GTCGGGT-AAGAGATTGGATGATCTTCAATCTGTCCTCTAATTAGGGTAAAAGA
126 CTGCCCCATGAGTAGGGTCAA-AGATTGGATGAGCTGCAATCTGTCCCCTAATCAGGGTAAAAGA
158764 TTGGAT
190 TTGGAT
158770 GCTTCAATCTGCCC-CATGAT
1 GCTTCAATCTGCCCTCATGAT
158790 TAGGGTAAAA
Statistics
Matches: 183, Mismatches: 22, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
193 7 0.04
194 110 0.60
195 61 0.33
196 5 0.03
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (195 bp):
GCTTCAATCTGCCCTCATGATCGAGGTAAGAGATTGGTATGTATTCAATCTGCCCTCTAATTAAG
GTAAAAGATTGGATGCATCAATCTACCCCATGATCAAGTAAAAGATTGGATGGTTACAATCTGCC
CCATGAGTAGGGTCAAAGATTGGATGAGCTGCAATCTGTCCCCTAATCAGGGTAAAAGATTGGAT
Found at i:158799 original size:117 final size:113
Alignment explanation
Indices: 158383--158821 Score: 468
Period size: 117 Copynumber: 3.8 Consensus size: 113
158373 AGATGATAGC
** * * * *
158383 TTCAATCTGCCTCATGATCGGGGTAAGAGATTGGTATGTCTTCAATCTGCCTTC-TAATTAAGGT
1 TTCAATCTGCCTC-TGATTAGGGTAAAAGATTGG-ATG-CTTCAATCTGCC-CCATGATTAGGGT
* * * *
158447 AAAAGATTGGATGCTTCAATCTACCCCATGATCAAGGTAAGAGATTGGATGGT
62 AAAAGATTGGATGCTTCAATCTGCCCTATGGTC-GGGTAAGAGATTGGATGGT
* * * * * **
158500 TACAATCTGCCCCATGATTAGGGTCAAAGATTGGATGGCTGCAATTTGCCCCATGATCGGGGTAA
1 TTCAATCTGCCTC-TGATTAGGGTAAAAGATTGGAT-GCTTCAATCTGCCCCATGATTAGGGTAA
*
158565 GAGATTGGATGCTTCAATCTGCCCTATGGTCGAGGTAAGAGATTGGATGGT
64 AAGATTGGATGCTTCAATCTGCCCTATGGTCG-GGTAAGAGATTGGATGGT
* * * * *
158616 ATTCAATCTGCCCTCTGATTAGGATAAAAGATTGGATGCATCAATTTGCCCCATGA-TCGGAATA
1 -TTCAATCTG-CCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATTAGG-GTA
*
158680 AAAGATTGGATGGTCTTCAATCTGCCCTATGGTCGGGTAAGAGATTGGATGAT
63 AAAGATTGGAT-G-CTTCAATCTGCCCTATGGTCGGGTAAGAGATTGGATGGT
*
158733 CTTCAATCTGTCCTCTAATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATTAGGGTAA
1 -TTCAATCTG-CCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATTAGGGTAA
* * * *
158798 AAGACTAGATTCTTCAATTTGCCC
64 AAGATTGGATGCTTCAATCTGCCC
158822 CACCATAACT
Statistics
Matches: 272, Mismatches: 41, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
115 15 0.06
116 94 0.35
117 136 0.50
118 27 0.10
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (113 bp):
TTCAATCTGCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATTAGGGTAAAA
GATTGGATGCTTCAATCTGCCCTATGGTCGGGTAAGAGATTGGATGGT
Found at i:162200 original size:123 final size:123
Alignment explanation
Indices: 161981--162231 Score: 412
Period size: 123 Copynumber: 2.0 Consensus size: 123
161971 CAAAATATTA
161981 GATCACATTTCTCGATTAATTGTGAAATAAATCTTGCGATATAATTCAATCTCCCTAAGAAACCT
1 GATCACATTTCTCGATTAATTGTGAAATAAATCTTGCGATATAATTCAATCTCCCTAAGAAACCT
* *
162046 CGAACTTCTTTCTGATAGCATGGCGATGGTAACACTTGTATGGCTTTTACTTTGTCTG
66 CAAACTTCTTTCTGATAGCATGGCGATGGTAACACTTGTATGGCTTTGACTTTGTCTG
* * * * *
162104 GATCACATTTCTCGGTTAATTGTGAAATAAATCTTGTGTTATAATTCAATCTCCCTAAGATACGT
1 GATCACATTTCTCGATTAATTGTGAAATAAATCTTGCGATATAATTCAATCTCCCTAAGAAACCT
* * *
162169 CAAACTTCTTTCTGATAGCGTGGCGGTGGTAACACTTGTATGGCTTTGACTTTGTTTG
66 CAAACTTCTTTCTGATAGCATGGCGATGGTAACACTTGTATGGCTTTGACTTTGTCTG
162227 GATCA
1 GATCA
162232 ATCTCGATAC
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
123 118 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (123 bp):
GATCACATTTCTCGATTAATTGTGAAATAAATCTTGCGATATAATTCAATCTCCCTAAGAAACCT
CAAACTTCTTTCTGATAGCATGGCGATGGTAACACTTGTATGGCTTTGACTTTGTCTG
Found at i:163268 original size:53 final size:53
Alignment explanation
Indices: 163210--163315 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
163200 AGAAGACCTG
* *
163210 TTAGAGGGATAATAATAGATCTAAAGAACAATTGAATTTAAGAATGATTGATT
1 TTAGAGGGATAAGAAGAGATCTAAAGAACAATTGAATTTAAGAATGATTGATT
163263 TTAGAGGGATAAGAAGAGATCTAAAGAACAATTGAATTTAAGAATGATTGATT
1 TTAGAGGGATAAGAAGAGATCTAAAGAACAATTGAATTTAAGAATGATTGATT
163316 ATATGGTATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.30
Consensus pattern (53 bp):
TTAGAGGGATAAGAAGAGATCTAAAGAACAATTGAATTTAAGAATGATTGATT
Found at i:169754 original size:29 final size:29
Alignment explanation
Indices: 169706--169991 Score: 197
Period size: 29 Copynumber: 9.8 Consensus size: 29
169696 TTTAGGGGTA
*
169706 AAAATGTAATTTT-GGAAAAGTTTAAGGTC
1 AAAATGTGATTTTAGG-AAAGTTTAAGGTC
*
169735 AAAATGTGATTTTAGGAAAGTTT-AGGGC
1 AAAATGTGATTTTAGGAAAGTTTAAGGTC
* * *
169763 TAAAATGTTATTTTTGAAAAGTTT-AGTGTC
1 -AAAATGTGATTTTAGGAAAGTTTAAG-GTC
* ** *
169793 AAAATGTAATTTTAAAAAAGTTTAAAGGTT
1 AAAATGTGATTTTAGGAAAGTTT-AAGGTC
* ** *
169823 AAAATATGATTTTAAAAAAGTTTAAGGTA
1 AAAATGTGATTTTAGGAAAGTTTAAGGTC
* *
169852 AAAATGCGATTTT-GGAAAAGTTTGGAGGTC
1 AAAATGTGATTTTAGG-AAAGTTT-AAGGTC
* * * *
169882 AAAATGTGACTTT-GGGAAGTTTGAGGTA
1 AAAATGTGATTTTAGGAAAGTTTAAGGTC
* * * *
169910 AAAATGTAATTTTTGAAAAGTTTGAGGATC
1 AAAATGTGATTTTAGGAAAGTTTAAGG-TC
* * * *
169940 AAAATGTAATTTTA-GTAATTTTAAGGGTT
1 AAAATGTGATTTTAGGAAAGTTTAA-GGTC
* *
169969 AAAATATGATTTTGGGAAAGTTT
1 AAAATGTGATTTTAGGAAAGTTT
169992 GAGGGCCTTT
Statistics
Matches: 207, Mismatches: 39, Indels: 21
0.78 0.15 0.08
Matches are distributed among these distances:
28 20 0.10
29 119 0.57
30 66 0.32
31 2 0.01
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (29 bp):
AAAATGTGATTTTAGGAAAGTTTAAGGTC
Found at i:169944 original size:117 final size:117
Alignment explanation
Indices: 169677--169997 Score: 267
Period size: 117 Copynumber: 2.7 Consensus size: 117
169667 ATTTGGGGAC
* * ** * * ** * *
169677 AATGTAATTTTGGAAAAATTTTAGGGGTAAAAATGTAATTTTGGAAAAGTTTAAGGTCAAAATGT
1 AATGTAATTTT-AAAAAAGTTTAAAGGTCAAAATATAATTTTAAAAAAGTTTAAGGTAAAAATGC
* * *
169742 GATTTTAGGAAAGTTTAGGGCTAAAATGTTATTTTTGAAAAGTTTAGTGTCAA
65 GATTTTAGGAAAGTTTAGGGCTAAAATGTGATCTTTGAAAAGTTTAGTGTAAA
* *
169795 AATGTAATTTTAAAAAAGTTTAAAGGTTAAAATATGATTTTAAAAAAGTTTAAGGTAAAAATGCG
1 AATGTAATTTTAAAAAAGTTTAAAGGTCAAAATATAATTTTAAAAAAGTTTAAGGTAAAAATGCG
* **
169860 ATTTT-GGAAAAGTTT-GGAGGTCAAAATGTGA-CTTTGGGAAGTTTGAG-GTAAA
66 ATTTTAGG-AAAGTTTAGG-GCT-AAAATGTGATCTTTGAAAAGTTT-AGTGTAAA
** * * ** * * *
169912 AATGTAATTTTTGAAAAGTTT-GAGGATCAAAATGTAATTTT-AGTAATTTTAAGGGTTAAAATA
1 AATGTAATTTTAAAAAAGTTTAAAGG-TCAAAATATAATTTTAAAAAAGTTTAA-GGTAAAAATG
* *
169975 TGATTTTGGGAAAGTTTGAGGGC
64 CGATTTTAGGAAAGTTT-AGGGC
169998 CTTTTTACGC
Statistics
Matches: 164, Mismatches: 30, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
116 15 0.09
117 123 0.75
118 24 0.15
119 2 0.01
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.36
Consensus pattern (117 bp):
AATGTAATTTTAAAAAAGTTTAAAGGTCAAAATATAATTTTAAAAAAGTTTAAGGTAAAAATGCG
ATTTTAGGAAAGTTTAGGGCTAAAATGTGATCTTTGAAAAGTTTAGTGTAAA
Found at i:171856 original size:19 final size:19
Alignment explanation
Indices: 171817--171857 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
171807 GTAATTTTCA
*
171817 TTAAAAATAAAATTTGATT
1 TTAAAAATAAAATCTGATT
*
171836 TTAAAAATAAAATCTGTTT
1 TTAAAAATAAAATCTGATT
171855 TTA
1 TTA
171858 GTCGTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (19 bp):
TTAAAAATAAAATCTGATT
Found at i:171905 original size:20 final size:21
Alignment explanation
Indices: 171862--171908 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
171852 TTTTTAGTCG
171862 TTTTAAAGAAAATGTTTAAAT
1 TTTTAAAGAAAATGTTTAAAT
* **
171883 TTTTAAATAAAAT-TTTATTT
1 TTTTAAAGAAAATGTTTAAAT
171903 TTTTAA
1 TTTTAA
171909 CTATTTCGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTAAAGAAAATGTTTAAAT
Found at i:185362 original size:30 final size:30
Alignment explanation
Indices: 185311--185371 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
185301 GATGGGAAGA
* *
185311 GAGTAAAAATTTTAGGAGGAAAATAGAAAG
1 GAGTAAAAATTTTAAGAGGAAAATAAAAAG
*
185341 GAGTAAAAAATTTTAAG-GGAAACTAAAAAG
1 GAGT-AAAAATTTTAAGAGGAAAATAAAAAG
185371 G
1 G
185372 TTCGAAGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.54, C:0.02, G:0.25, T:0.20
Consensus pattern (30 bp):
GAGTAAAAATTTTAAGAGGAAAATAAAAAG
Found at i:185465 original size:160 final size:160
Alignment explanation
Indices: 185294--185610 Score: 571
Period size: 160 Copynumber: 2.0 Consensus size: 160
185284 GAGTAGATGA
185294 GAAGTGAGATGGGAAGAGAGTAAAAATTTTAGGAGGAAAATAGAAAGGAGTAAAAAATTTTAAGG
1 GAAGTGAGATGGGAAGAGAGTAAAAATTTTAGGAGGAAAATAGAAAGGAGTAAAAAATTTTAAGG
*
185359 GAAACTAAAAAGGTTCGAAGGTTTGGGATAAAAATGTCAAATATTATAGCTTAATATTCGGTTAT
66 GAAACTAAAAAGGTCCGAAGGTTTGGGATAAAAATGTCAAATATTATAGCTTAATATTCGGTTAT
*
185424 TCGAATTTGAAAACTAAACTCGATTCATGG
131 TCGAATTTAAAAACTAAACTCGATTCATGG
* *
185454 GAAGTGAGATGGGAAGATAGTAAAAATTTTAGGAGGAAAGTAGAAAGGAGTAAAAAATTTTAAGG
1 GAAGTGAGATGGGAAGAGAGTAAAAATTTTAGGAGGAAAATAGAAAGGAGTAAAAAATTTTAAGG
* *
185519 GAAACTAAAAAGGTCCGAAGGTTTGGGATAAAAATGTCAAATATTATAGTTTAATATTCTGTTAT
66 GAAACTAAAAAGGTCCGAAGGTTTGGGATAAAAATGTCAAATATTATAGCTTAATATTCGGTTAT
*
185584 TCGAATTTAAAAACTAAACTTGATTCA
131 TCGAATTTAAAAACTAAACTCGATTCA
185611 AACTCGAAAA
Statistics
Matches: 150, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
160 150 1.00
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.28
Consensus pattern (160 bp):
GAAGTGAGATGGGAAGAGAGTAAAAATTTTAGGAGGAAAATAGAAAGGAGTAAAAAATTTTAAGG
GAAACTAAAAAGGTCCGAAGGTTTGGGATAAAAATGTCAAATATTATAGCTTAATATTCGGTTAT
TCGAATTTAAAAACTAAACTCGATTCATGG
Found at i:185808 original size:16 final size:15
Alignment explanation
Indices: 185763--185806 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
185753 ACAAATAATT
**
185763 TAAAAATTGTAAAAA
1 TAAAAATTCAAAAAA
*
185778 -AAATATTCAAAAAA
1 TAAAAATTCAAAAAA
185792 TAAAAATTCAAAAAA
1 TAAAAATTCAAAAAA
185807 ATTATAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (15 bp):
TAAAAATTCAAAAAA
Found at i:187328 original size:22 final size:22
Alignment explanation
Indices: 187231--187328 Score: 89
Period size: 21 Copynumber: 4.7 Consensus size: 22
187221 AGGTTGTTTT
*
187231 TATTTT-AATT-AGGTTTAGTG
1 TATTTTAAATTAAGGTTTAGGG
* *
187251 T-TTTTAAATTAGGGTTTAGGT
1 TATTTTAAATTAAGGTTTAGGG
* *
187272 TA-TTAAAATTAAGGTTT-TGG
1 TATTTTAAATTAAGGTTTAGGG
* * *
187292 TATTTTATATAAAGGTGTAGGG
1 TATTTTAAATTAAGGTTTAGGG
187314 TATTTTAAATTAAGG
1 TATTTTAAATTAAGG
187329 GTTATGGAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
19 4 0.07
20 8 0.14
21 32 0.54
22 15 0.25
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (22 bp):
TATTTTAAATTAAGGTTTAGGG
Found at i:188505 original size:51 final size:50
Alignment explanation
Indices: 188450--188666 Score: 122
Period size: 51 Copynumber: 4.3 Consensus size: 50
188440 AAATAAAATA
188450 TTTTTTAATCATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAATTTTGAT
1 TTTTTTAA-CATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAATTTTGAT
* * * ** * **
188501 TTTTTTAACTATTTCGAAA-TAAAAGTTTGAATTTTTAAGTAAAGTGGTGAT
1 TTTTTTAAC-ATTT-TAAAGAAAAAGTTTAAATTTTTAAACAAAATTTTGAT
* **** * * * *
188552 TTTCATTAA-AAAAAAAATAAGAAAGTTTAGATTTTTAAAAAATAAAAATTTG--
1 TTT-TTTAACATTTTAAAGAA-AAAGTTTAAATTTTT---AAACAAAATTTTGAT
* * *
188604 CTTTTTAGTCATTTTAAAG-AAAAGTTTAAAATTTTAAACAAAATTTTGA-
1 TTTTTTA-ACATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAATTTTGAT
188653 TTTTTTAACTATTT
1 TTTTTTAAC-ATTT
188667 CGAAATAAAA
Statistics
Matches: 119, Mismatches: 35, Indels: 26
0.66 0.19 0.14
Matches are distributed among these distances:
48 12 0.10
49 13 0.11
50 3 0.03
51 69 0.58
52 10 0.08
53 4 0.03
54 8 0.07
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (50 bp):
TTTTTTAACATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAATTTTGAT
Found at i:189871 original size:28 final size:28
Alignment explanation
Indices: 189825--189879 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
189815 TGGTAACAGA
* * *
189825 CATGACCTTTGGGTTAACAGGGAGTAAG
1 CATGACCTTTAGGTCAACAAGGAGTAAG
189853 CATGACCTTTAGGTCAACAAGGAGTAA
1 CATGACCTTTAGGTCAACAAGGAGTAA
189880 ATCGGATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (28 bp):
CATGACCTTTAGGTCAACAAGGAGTAAG
Found at i:191639 original size:10 final size:11
Alignment explanation
Indices: 191610--191642 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
191600 ATTTTTTTCA
*
191610 CTCAAATCTCT
1 CTCAACTCTCT
191621 CTCAACTCTCT
1 CTCAACTCTCT
191632 CT-AACTCTCT
1 CTCAACTCTCT
191642 C
1 C
191643 AAATACACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.36
Consensus pattern (11 bp):
CTCAACTCTCT
Found at i:197239 original size:14 final size:16
Alignment explanation
Indices: 197200--197239 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
197190 TTTTTTATGT
*
197200 ATTATATATTTTAAAAA
1 ATTATATA-TATAAAAA
197217 ATTATATATATAAAAA
1 ATTATATATATAAAAA
*
197233 ATAATAT
1 ATTATAT
197240 GGGCGGGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTATATATATAAAAA
Found at i:198356 original size:11 final size:12
Alignment explanation
Indices: 198330--198357 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
198320 TAAATAACCC
198330 TTTTGTTTATAT
1 TTTTGTTTATAT
198342 TTTTGTTTATAT
1 TTTTGTTTATAT
198354 TTTT
1 TTTT
198358 AAGGAGTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTGTTTATAT
Found at i:198423 original size:15 final size:15
Alignment explanation
Indices: 198403--198446 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
198393 AAAATAATAG
*
198403 AAAATATAAATTTTA
1 AAAATATAAATTATA
198418 AAAATATAATATTATA
1 AAAATATAA-ATTATA
198434 AAATTATATAAAT
1 AAA--ATATAAAT
198447 ACTTTAGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 9 0.36
16 8 0.32
17 2 0.08
18 6 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATATAAATTATA
Found at i:200434 original size:17 final size:17
Alignment explanation
Indices: 200414--200449 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
200404 GTAGACCATA
*
200414 TGGGGCACACGACCGTG
1 TGGGGCACACGACCCTG
*
200431 TGGGGCACATGACCCTG
1 TGGGGCACACGACCCTG
200448 TG
1 TG
200450 TGATTTTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.28, G:0.39, T:0.17
Consensus pattern (17 bp):
TGGGGCACACGACCCTG
Found at i:201135 original size:20 final size:20
Alignment explanation
Indices: 201110--201179 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
201100 AGGGTAGGAC
*
201110 ATGATATGATTCATTGTGAT
1 ATGATATGATTCATTATGAT
*
201130 ATGATATGATTCCTTATGAT
1 ATGATATGATTCATTATGAT
* * *
201150 ATGATAAGATTCGTTATGTT
1 ATGATATGATTCATTATGAT
201170 ATGATATGAT
1 ATGATATGAT
201180 ATGACACGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (20 bp):
ATGATATGATTCATTATGAT
Found at i:203852 original size:10 final size:10
Alignment explanation
Indices: 203834--203875 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
203824 CTACATCAAC
203834 AAATGATTTT
1 AAATGATTTT
*
203844 AAATTATTTT
1 AAATGATTTT
* *
203854 AAATTA-TTA
1 AAATGATTTT
203863 AAATGATTTT
1 AAATGATTTT
203873 AAA
1 AAA
203876 ATCATCATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.26
10 20 0.74
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (10 bp):
AAATGATTTT
Found at i:208598 original size:23 final size:23
Alignment explanation
Indices: 208572--208627 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
208562 AACATTAATT
**
208572 TTATTTTTGTAACTCTTTAGCCA
1 TTATTTTTGTAACTCTCCAGCCA
208595 TTATTTTTGTAACTCTCCAGCCA
1 TTATTTTTGTAACTCTCCAGCCA
*
208618 TTATATTTGT
1 TTATTTTTGT
208628 TTTAAATTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.52
Consensus pattern (23 bp):
TTATTTTTGTAACTCTCCAGCCA
Found at i:215504 original size:22 final size:22
Alignment explanation
Indices: 215476--215526 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
215466 TTAATTTTAT
* *
215476 TTTTGTAATTCTTCAGCCATTA
1 TTTTGTAACTCTCCAGCCATTA
215498 TTTTGTAACTCTCCAGCCATTA
1 TTTTGTAACTCTCCAGCCATTA
215520 TATTTGT
1 T-TTTGT
215527 TTTAAATTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (22 bp):
TTTTGTAACTCTCCAGCCATTA
Found at i:237180 original size:10 final size:11
Alignment explanation
Indices: 237154--237179 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
237144 TAAAGCTAGG
237154 TTTTTCTTTTT
1 TTTTTCTTTTT
237165 TTTTTCTTTTT
1 TTTTTCTTTTT
237176 TTTT
1 TTTT
237180 CCTTCCTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:237387 original size:20 final size:20
Alignment explanation
Indices: 237355--237404 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
237345 TTTTTTTCGG
* *
237355 TTGTTT-TCCTATTTTGTTA
1 TTGTTTATCTTATTTTATTA
*
237374 TTGTTTATCTTATTTTATTT
1 TTGTTTATCTTATTTTATTA
*
237394 TTGTCTATCTT
1 TTGTTTATCTT
237405 CTTATTAGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.12, C:0.10, G:0.08, T:0.70
Consensus pattern (20 bp):
TTGTTTATCTTATTTTATTA
Found at i:239398 original size:98 final size:98
Alignment explanation
Indices: 239223--239400 Score: 241
Period size: 98 Copynumber: 1.8 Consensus size: 98
239213 ATTTTTTTCT
* * *
239223 CTTAAGAATATATTGGCCCTTTTGACACGAAATGGAACGACAACCTAAGCACCCAATCTCGGTTA
1 CTTAAGAATATATTGGCCCTTTTGACACGAAATGAAACGACAACCCAAGCACCCAATCCCGGTTA
**
239288 CTCGGCCCAACACACTCCCAATCATTCTTTTTA
66 CTCAACCCAACACACTCCCAATCATTCTTTTTA
* * * *
239321 CTTAAGAATGTATTGGTCCTTTTGACGCGAAATGAAATGACAACCCAAGCACTCC-ATCCCGGTT
1 CTTAAGAATATATTGGCCCTTTTGACACGAAATGAAACGACAACCCAAGCAC-CCAATCCCGGTT
* *
239385 ACTCAATCTAACACAC
65 ACTCAACCCAACACAC
239401 CCCTAATTTA
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
98 66 0.97
99 2 0.03
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (98 bp):
CTTAAGAATATATTGGCCCTTTTGACACGAAATGAAACGACAACCCAAGCACCCAATCCCGGTTA
CTCAACCCAACACACTCCCAATCATTCTTTTTA
Found at i:244961 original size:13 final size:13
Alignment explanation
Indices: 244945--245002 Score: 57
Period size: 13 Copynumber: 4.4 Consensus size: 13
244935 GTATAAATAC
244945 TTCATATAA-TCAT
1 TTCATATAACT-AT
*
244958 TTCATATATCTACT
1 TTCATATAACTA-T
244972 TTCATAATAAC-AT
1 TTCAT-ATAACTAT
*
244985 TTCATGTAACTAT
1 TTCATATAACTAT
244998 TTCAT
1 TTCAT
245003 CTGAGGAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 4 0.11
13 22 0.58
14 8 0.21
15 4 0.11
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.47
Consensus pattern (13 bp):
TTCATATAACTAT
Found at i:244985 original size:27 final size:26
Alignment explanation
Indices: 244936--245002 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
244926 TAATATTACG
* *
244936 TATAAATACTTCATATAATCATTTCA
1 TATAACTATTTCATATAATCATTTCA
*
244962 TATATCTACTTTCATAATAA-CATTTCA
1 TATAACTA-TTTCAT-ATAATCATTTCA
*
244989 TGTAACTATTTCAT
1 TATAACTATTTCAT
245003 CTGAGGAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
26 12 0.35
27 18 0.53
28 4 0.12
ACGTcount: A:0.37, C:0.16, G:0.01, T:0.45
Consensus pattern (26 bp):
TATAACTATTTCATATAATCATTTCA
Found at i:249523 original size:35 final size:35
Alignment explanation
Indices: 249431--249524 Score: 127
Period size: 35 Copynumber: 2.7 Consensus size: 35
249421 TGGTAACAGG
249431 AATGACCTTTGGGTCAACAGGGAGAATATAAGCAT
1 AATGACCTTTGGGTCAACAGGGAGAATATAAGCAT
* * *
249466 AATGACCGTTAGGTCAACAGGGAGAA-AGTGAGCAT
1 AATGACCTTTGGGTCAACAGGGAGAATA-TAAGCAT
* *
249501 AATGACCTTTGGGTTAAGAGGGAG
1 AATGACCTTTGGGTCAACAGGGAG
249525 TAAACGAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
34 1 0.02
35 50 0.98
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.21
Consensus pattern (35 bp):
AATGACCTTTGGGTCAACAGGGAGAATATAAGCAT
Found at i:255409 original size:17 final size:17
Alignment explanation
Indices: 255387--255433 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
255377 AATTAGAAGG
255387 ACCAAATGAATAAATTA
1 ACCAAATGAATAAATTA
255404 ACCAAATGAATAAATTA
1 ACCAAATGAATAAATTA
*
255421 ACCAAATGTATAA
1 ACCAAATGAATAA
255434 TAGTGGGTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.57, C:0.13, G:0.06, T:0.23
Consensus pattern (17 bp):
ACCAAATGAATAAATTA
Found at i:262853 original size:35 final size:35
Alignment explanation
Indices: 262797--262889 Score: 102
Period size: 35 Copynumber: 2.7 Consensus size: 35
262787 GGTAACAAGC
*
262797 ATGACCTTTGTGG-CAACAGGGAGAAAATG-AGCATA
1 ATGACATTTG-GGTCAACAGGGAGAAAATGTA-CATA
* *
262832 ATGGACA-TTGGGTCAATAGGGAGAAAGTGTACATA
1 AT-GACATTTGGGTCAACAGGGAGAAAATGTACATA
*
262867 GTGACATTTGGGTCAACAGGGAG
1 ATGACATTTGGGTCAACAGGGAG
262890 TAAACGAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
34 6 0.12
35 39 0.80
36 4 0.08
ACGTcount: A:0.34, C:0.12, G:0.32, T:0.22
Consensus pattern (35 bp):
ATGACATTTGGGTCAACAGGGAGAAAATGTACATA
Found at i:274252 original size:20 final size:20
Alignment explanation
Indices: 274227--274265 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
274217 AATAAAAATA
274227 AAACTTACTATTTCATTTTT
1 AAACTTACTATTTCATTTTT
274247 AAACTTACTATTTCATTTT
1 AAACTTACTATTTCATTTT
274266 ATAGGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (20 bp):
AAACTTACTATTTCATTTTT
Found at i:278603 original size:26 final size:26
Alignment explanation
Indices: 278574--278697 Score: 107
Period size: 26 Copynumber: 5.0 Consensus size: 26
278564 TTTACTATAT
*
278574 TTAATTAAATGCAAATAAAAAC---A
1 TTAATTAAATACAAATAAAAACATAA
* *
278597 -TAATTAAAT--AAATACAAACATAT
1 TTAATTAAATACAAATAAAAACATAA
* * * *
278620 TTAAATAAATACAAACATAAACATAT
1 TTAATTAAATACAAATAAAAACATAA
*
278646 TTAATTAAATATAAATAAAAACATAA
1 TTAATTAAATACAAATAAAAACATAA
* * *
278672 TTAAATAAATACAAACATAAACATAA
1 TTAATTAAATACAAATAAAAACATAA
278698 ACTGAGTTTG
Statistics
Matches: 81, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
20 9 0.11
22 9 0.11
24 8 0.10
26 55 0.68
ACGTcount: A:0.63, C:0.09, G:0.01, T:0.27
Consensus pattern (26 bp):
TTAATTAAATACAAATAAAAACATAA
Found at i:278615 original size:20 final size:20
Alignment explanation
Indices: 278575--278639 Score: 94
Period size: 20 Copynumber: 3.1 Consensus size: 20
278565 TTACTATATT
*
278575 TAATTAAATGCAAATAAAAACA
1 TAATTAAAT--AAATACAAACA
278597 TAATTAAATAAATACAAACA
1 TAATTAAATAAATACAAACA
*
278617 TATTTAAATAAATACAAACA
1 TAATTAAATAAATACAAACA
278637 TAA
1 TAA
278640 ACATATTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 31 0.77
22 9 0.22
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (20 bp):
TAATTAAATAAATACAAACA
Found at i:278668 original size:52 final size:50
Alignment explanation
Indices: 278597--278696 Score: 164
Period size: 52 Copynumber: 2.0 Consensus size: 50
278587 AATAAAAACA
* *
278597 TAATTAAATAAATACAAACATATTTAAATAAATACAAACATAAACATATT
1 TAATTAAATAAATAAAAACATAATTAAATAAATACAAACATAAACATATT
278647 TAATTAAATATAAATAAAAACATAATTAAATAAATACAAACATAAACATA
1 TAATT-AA-ATAAATAAAAACATAATTAAATAAATACAAACATAAACATA
278697 AACTGAGTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 5 0.11
51 2 0.04
52 39 0.85
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (50 bp):
TAATTAAATAAATAAAAACATAATTAAATAAATACAAACATAAACATATT
Found at i:279181 original size:27 final size:26
Alignment explanation
Indices: 279120--279183 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 26
279110 CCGAGAAAAT
*
279120 CCGAATGATATCCGTGGCCTGACCAG
1 CCGAATGATATCCATGGCCTGACCAG
* *
279146 CTTGGATGATATCCATGGCCTGACCAG
1 C-CGAATGATATCCATGGCCTGACCAG
279173 ACCGAATGATA
1 -CCGAATGATA
279184 AGACTCGAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 1 0.03
27 29 0.94
28 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.22
Consensus pattern (26 bp):
CCGAATGATATCCATGGCCTGACCAG
Found at i:281784 original size:31 final size:31
Alignment explanation
Indices: 281746--281807 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
281736 GACTATGGTA
281746 GAAGTACAGAGCAAAATATATTTTAGCTACT
1 GAAGTACAGAGCAAAATATATTTTAGCTACT
281777 GAAGTACAGAGCAAAATATATTTTAGCTACT
1 GAAGTACAGAGCAAAATATATTTTAGCTACT
281808 AACTTCTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (31 bp):
GAAGTACAGAGCAAAATATATTTTAGCTACT
Found at i:282990 original size:46 final size:46
Alignment explanation
Indices: 282937--283030 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
282927 AAGGCCTACC
282937 CATGATTTACAATTCACCTACAAAAATTCTTAATTTTAATCTTAAA
1 CATGATTTACAATTCACCTACAAAAATTCTTAATTTTAATCTTAAA
282983 CATGATTTACAATTCACCTACAAAAATTCTTAATTTTAATCTTAAA
1 CATGATTTACAATTCACCTACAAAAATTCTTAATTTTAATCTTAAA
283029 CA
1 CA
283031 AAGTCCTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.41, C:0.18, G:0.02, T:0.38
Consensus pattern (46 bp):
CATGATTTACAATTCACCTACAAAAATTCTTAATTTTAATCTTAAA
Found at i:289558 original size:3 final size:3
Alignment explanation
Indices: 289552--289598 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
289542 AAAAAATAAT
*
289552 AAG AAG AAT AAG AAG AAG AAG AAG AAG AAG AA- AAG AA- AAG AA- AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
289597 AA
1 AA
289599 AGAAAAGGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 6 0.15
3 33 0.85
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:289602 original size:4 final size:5
Alignment explanation
Indices: 289555--289605 Score: 59
Period size: 6 Copynumber: 9.6 Consensus size: 5
289545 AAATAATAAG
289555 AAGAA TAAGAA GAAGAA GAAGAA GAAGAA AAGAA AAGAA AAG-A AAGAA
1 AAGAA -AAGAA -AAGAA -AAGAA -AAGAA AAGAA AAGAA AAGAA AAGAA
289603 AAG
1 AAG
289606 GTCAAGATGA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
4 4 0.09
5 17 0.40
6 22 0.51
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:289679 original size:21 final size:21
Alignment explanation
Indices: 289653--289701 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
289643 GAAAAATAGA
289653 AAAAGAAAAGAAAA-GAAAAG
1 AAAAGAAAAGAAAAGGAAAAG
289673 AAGAAGAAAAGAAAAGGAAAA-
1 AA-AAGAAAAGAAAAGGAAAAG
289694 AAAAGAAA
1 AAAAGAAA
289702 GTCATGATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.30
21 14 0.52
22 5 0.19
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAGAAAAGGAAAAG
Found at i:289702 original size:4 final size:5
Alignment explanation
Indices: 289653--289701 Score: 73
Period size: 5 Copynumber: 9.6 Consensus size: 5
289643 GAAAAATAGA
289653 AAAAG AAAAG AAAAG AAAAG AAGAAG AAAAG AAAAGG AAAA- AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG AAAA-G AAAAG AAAAG AAA
289702 GTCATGATGA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.10
5 27 0.66
6 10 0.24
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:291844 original size:148 final size:148
Alignment explanation
Indices: 291681--292303 Score: 662
Period size: 148 Copynumber: 4.2 Consensus size: 148
291671 CCGGTTCCAT
* * * *
291681 GAAGACATGAAGGGAAAGATTTAAGTCGCAACAGTGAATCTAGTACCACGAAGATATAGAGGGAA
1 GAAGATATGGAGGGAAAGATTTAAGTCGCAACAGCGAATCTAGTACCACGAAGATATGGAGGGAA
* * *
291746 AGGTTTAAGTCGCAACGGTGAACCTTGTACCTCAGAAGACATGAAGGGAAAGACTTAAGCTGAAA
66 AGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGACATGAAGGGAAAGATTTAAGCTGAAA
*
291811 CGGTGAATCTAGTACCAC
131 CGATGAATCTAGTACCAC
** * * *
291829 GAAGATATGGAGGGAAAGATTTAAACCGTAACAGCGAATCTAGTACCACAAAGATATGGAAGGAA
1 GAAGATATGGAGGGAAAGATTTAAGTCGCAACAGCGAATCTAGTACCACGAAGATATGGAGGGAA
* ** * * *
291894 AGGTTTAAGTCGCAACGATGAACCTTGTACTTCAAAAGACATGAAGGGAAAGATTTAAGC-CACA
66 AGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGACATGAAGGGAAAGATTTAAGCTGA-A
* *
291958 ACGATGAATCAAGTACCAT
130 ACGATGAATCTAGTACCAC
* * * * * * * *
291977 GAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGGACCTTGTACCTCAGAAGACATGAAGGGA
1 GAAGATATGGAGGGAAAGATTTAAGTCGCAACAGCGAATCTAGTACCAC-GAAGATATGGAGGGA
* * ** * * **
292042 AAGATTTAAGCCGCAACGGCGAATCTAATA-C-CATGAAGATAT-AGAGGGAAAGGTTTAAATTG
65 AAGATTTAAGTCGCAACGGCGAACCTTGTACCTCA-GAAGACATGA-AGGGAAAGATTTAAGCTG
* * ** * * *
292104 CAATGACAAACCTTGTACCTC
128 AAACGATGAATCTAGTACCAC
* ** *
292125 AGAAGACATTAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGA
1 -GAAGATATGGAGGGAAAGATTTAAGTCGCAACAGCGAATCTAGTACCACGAAGATATGGAGGGA
* * * * *
292190 AAGATTTAAGTTGCAACGGCGAACCTTGTACCTCAGAAGACATGAAAGGAAATATTTAAGCCGCA
65 AAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGACATGAAGGGAAAGATTTAAGCTGAA
*
292255 ACGGTGAATCTAGTACCAC
130 ACGATGAATCTAGTACCAC
*
292274 GAAGATATTGAGGGAAATG-TTTAAGTCGCA
1 GAAGATATGGAGGGAAA-GATTTAAGTCGCA
292304 GCGACGAACC
Statistics
Matches: 381, Mismatches: 84, Indels: 20
0.79 0.17 0.04
Matches are distributed among these distances:
147 4 0.01
148 264 0.69
149 110 0.29
150 3 0.01
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (148 bp):
GAAGATATGGAGGGAAAGATTTAAGTCGCAACAGCGAATCTAGTACCACGAAGATATGGAGGGAA
AGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGACATGAAGGGAAAGATTTAAGCTGAAA
CGATGAATCTAGTACCAC
Found at i:292363 original size:99 final size:99
Alignment explanation
Indices: 291661--292328 Score: 689
Period size: 99 Copynumber: 6.8 Consensus size: 99
291651 TTGAGACCGT
** * * * * * * * *
291661 AACGGCGAATCCGGTTCCATGAAGACATGAAGGGAAAGATTTAAGTCGCAAC-AGTGAATCTAGT
1 AACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGA-CGAACCTTGT
* * * *
291725 ACCAC-GAAGATAT-AGAGGGAAAGGTTTAAGTCGC
65 ACCTCAGAAGACATGA-AGGGAAAGATTTAAGCCGC
* * * * * * ** * ** * *
291759 AACGGTGAACCTTGTACCTCAGAAGACATGAAGGGAAAGACTTAAG-CTGAAACGGTGAATCTAG
1 AACGGCGAATCTAGTACCAC-GAAGATATGGAGGGAAAGGTTTAAGTC-GCAACGACGAACCTTG
* * * * *
291823 TACCAC-GAAGATATGGAGGGAAAGATTTAAACCGT
64 TACCTCAGAAGACATGAAGGGAAAGATTTAAGCCGC
* * * *
291858 AACAGCGAATCTAGTACCACAAAGATATGGAAGGAAAGGTTTAAGTCGCAACGATGAACCTTGTA
1 AACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTA
* * *
291923 CTTCAAAAGACATGAAGGGAAAGATTTAAGCCAC
66 CCTCAGAAGACATGAAGGGAAAGATTTAAGCCGC
** * * * *
291957 AACGATGAATCAAGTACCATGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGGACCTTGTA
1 AACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTA
292022 CCTCAGAAGACATGAAGGGAAAGATTTAAGCCGC
66 CCTCAGAAGACATGAAGGGAAAGATTTAAGCCGC
* * * * * * *
292056 AACGGCGAATCTAATACCATGAAGATATAGAGGGAAAGGTTTAAATTGCAATGACAAACCTTGTA
1 AACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTA
* *
292121 CCTCAGAAGACATTAAGGGAAAGATTTAAGTCGC
66 CCTCAGAAGACATGAAGGGAAAGATTTAAGCCGC
* * *
292155 AACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGATTTAAGTTGCAACGGCGAACCTTGTA
1 AACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTA
* *
292220 CCTCAGAAGACATGAAAGGAAATATTTAAGCCGC
66 CCTCAGAAGACATGAAGGGAAAGATTTAAGCCGC
* * * * *
292254 AACGGTGAATCTAGTACCACGAAGATATTGAGGGAAATGTTTAAGTCGCAGCGACGAACCTTATA
1 AACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTA
292319 CCTCAGAAGA
66 CCTCAGAAGA
292329 TATTATAGGA
Statistics
Matches: 480, Mismatches: 84, Indels: 11
0.83 0.15 0.02
Matches are distributed among these distances:
98 49 0.10
99 431 0.90
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (99 bp):
AACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTA
CCTCAGAAGACATGAAGGGAAAGATTTAAGCCGC
Found at i:296214 original size:20 final size:21
Alignment explanation
Indices: 296191--296230 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
296181 TTAAAAAAAG
*
296191 TTAAA-ATTTTGTTTAAAATT
1 TTAAACATTTTCTTTAAAATT
*
296211 TTAAACTTTTTCTTTAAAAT
1 TTAAACATTTTCTTTAAAAT
296231 CACTAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (21 bp):
TTAAACATTTTCTTTAAAATT
Found at i:296853 original size:7 final size:7
Alignment explanation
Indices: 296841--296866 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
296831 ACGTGATGCC
296841 TCTAGCG
1 TCTAGCG
296848 TCTAGCG
1 TCTAGCG
296855 TCTAGCG
1 TCTAGCG
296862 TCTAG
1 TCTAG
296867 TCTCATCGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.31
Consensus pattern (7 bp):
TCTAGCG
Found at i:299791 original size:11 final size:11
Alignment explanation
Indices: 299775--299799 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
299765 AAAAAAAATT
299775 AATAAACTGAA
1 AATAAACTGAA
299786 AATAAACTGAA
1 AATAAACTGAA
299797 AAT
1 AAT
299800 TTTAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.20
Consensus pattern (11 bp):
AATAAACTGAA
Found at i:301773 original size:10 final size:10
Alignment explanation
Indices: 301758--301786 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
301748 GGTTGGTCGA
301758 ATATTACATC
1 ATATTACATC
301768 ATATTACATC
1 ATATTACATC
301778 ATATTACAT
1 ATATTACAT
301787 TCTAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATTACATC
Found at i:306689 original size:21 final size:19
Alignment explanation
Indices: 306665--306703 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
306655 TCAGCTTACA
306665 AATTTTCTTTACCAAAATATT
1 AATTTT-TTT-CCAAAATATT
*
306686 AATTTTTTTTCAAAATAT
1 AATTTTTTTCCAAAATAT
306704 CAAAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTTTTTTCCAAAATATT
Found at i:310829 original size:21 final size:21
Alignment explanation
Indices: 310800--310843 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
310790 ATGAAATTTA
* *
310800 AACATGTAAAGACATCATATT
1 AACACGTAAAGACATCAAATT
*
310821 AACACGTAAATACATCAAATT
1 AACACGTAAAGACATCAAATT
310842 AA
1 AA
310844 ATTAAGTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.16, G:0.07, T:0.25
Consensus pattern (21 bp):
AACACGTAAAGACATCAAATT
Found at i:312714 original size:17 final size:17
Alignment explanation
Indices: 312692--312724 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
312682 AAATTTTTCA
*
312692 TTTAAATATTTTAAAAC
1 TTTAAAAATTTTAAAAC
312709 TTTAAAAATTTTAAAA
1 TTTAAAAATTTTAAAA
312725 ATGTAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTAAAAATTTTAAAAC
Found at i:312731 original size:17 final size:17
Alignment explanation
Indices: 312694--312732 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
312684 ATTTTTCATT
* * *
312694 TAAATATTTTAAAACTT
1 TAAAAATTTTAAAAATG
312711 TAAAAATTTTAAAAATG
1 TAAAAATTTTAAAAATG
312728 TAAAA
1 TAAAA
312733 TTGCATTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAAAATTTTAAAAATG
Found at i:313597 original size:51 final size:51
Alignment explanation
Indices: 313517--313618 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
313507 AAAAAATAGA
313517 TTACTATTTTAGAATTTCCAAAATCTAGTATTTACCTATTACAATATGAGT
1 TTACTATTTTAGAATTTCCAAAATCTAGTATTTACCTATTACAATATGAGT
* *
313568 TTACTATTTTAGAATTTCCAAAATTTAGTATTTACCTATTATAATATGAGT
1 TTACTATTTTAGAATTTCCAAAATCTAGTATTTACCTATTACAATATGAGT
313619 ATTGATGAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (51 bp):
TTACTATTTTAGAATTTCCAAAATCTAGTATTTACCTATTACAATATGAGT
Found at i:319109 original size:14 final size:13
Alignment explanation
Indices: 319090--319129 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
319080 GAAAAGTAAT
319090 TCATTTTTCAGAAA
1 TCATTTTT-AGAAA
319104 TCATTTTTTAGAAA
1 TCA-TTTTTAGAAA
*
319118 TAATTTTTAGAA
1 TCATTTTTAGAA
319130 GCTATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 9 0.38
14 10 0.42
15 5 0.21
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (13 bp):
TCATTTTTAGAAA
Found at i:319124 original size:13 final size:14
Alignment explanation
Indices: 319092--319129 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
319082 AAAGTAATTC
319092 ATTTTTCAGAAATCA
1 ATTTTT-AGAAATCA
*
319107 TTTTTTAGAAAT-A
1 ATTTTTAGAAATCA
319120 ATTTTTAGAA
1 ATTTTTAGAA
319130 GCTATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 10 0.48
14 6 0.29
15 5 0.24
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (14 bp):
ATTTTTAGAAATCA
Found at i:322119 original size:58 final size:57
Alignment explanation
Indices: 321997--322370 Score: 284
Period size: 59 Copynumber: 6.4 Consensus size: 57
321987 TAAACATCCG
* *
321997 GGGGTAAAATGGTAATTTTTGAAAGAATCAAG-GTCAAAAATGAAATTTTTGGAAGTTC-
1 GGGGTAAAATGGTAATTTTTGAAAAAAT--AGTGTCAAAAATGGAA-TTTTGGAAGTTCA
* * * *
322055 GAGGGTAAGATGGTAATTTTTGAAAAAATCGTATCAAAAATGGGATTTTGGAAAGTTCA
1 G-GGGTAAAATGGTAATTTTTGAAAAAATAGTGTCAAAAATGGAATTTTGG-AAGTTCA
* * *
322114 GGGGTAAAAAT-GTAATTTTTGGAAAAATTAG-GTTAAAAATAGAATTTTGGGAAG-TC-
1 GGGGT-AAAATGGTAATTTTT-GAAAAAATAGTGTCAAAAATGGAATTTT-GGAAGTTCA
* * * * *
322170 GACGGTAAAATGGTAATTTTTTAAAAAAATAGTGGTAAAAAATGAAATTGTTGGAAGTTTA
1 G-GGGTAAAATGGTAA-TTTTTGAAAAAATAGT-GTCAAAAATGGAATT-TTGGAAGTTCA
* *
322231 GGGGTAAAATGGTAATTTTCATAAAAAAATTAGGGTCAAAAATGGAATTTTGGAAAGTTC-
1 GGGGTAAAATGGTAATTTT--TGAAAAAA-TAGTGTCAAAAATGGAATTTTGG-AAGTTCA
* * * * *
322291 GAGGGAAAAAT-GTAATTTTTATAAAAAATTGAG-GT-AAAAATAGAATTTGGGAAAGTTTA
1 G-GGGTAAAATGGTAATTTTT-GAAAAAA-T-AGTGTCAAAAATGGAATTTTGG-AAGTTCA
322350 GGGGTAAAAAT-GTAATTTTTG
1 GGGGT-AAAATGGTAATTTTTG
322371 GACAGTTTAA
Statistics
Matches: 260, Mismatches: 32, Indels: 48
0.76 0.09 0.14
Matches are distributed among these distances:
56 6 0.02
57 24 0.09
58 75 0.29
59 86 0.33
60 31 0.12
61 35 0.13
62 3 0.01
ACGTcount: A:0.42, C:0.03, G:0.24, T:0.32
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTTGAAAAAATAGTGTCAAAAATGGAATTTTGGAAGTTCA
Found at i:322136 original size:30 final size:29
Alignment explanation
Indices: 322100--322377 Score: 96
Period size: 30 Copynumber: 9.4 Consensus size: 29
322090 AAAAATGGGA
322100 TTTTGGAAAGTTCAGGGGTAAAAATGTAAT
1 TTTTGGAAAGTT-AGGGGTAAAAATGTAAT
* *
322130 TTTTGGAAAAATTA-GGTTAAAAATAG-AA-
1 TTTTGG-AAAGTTAGGGGTAAAAAT-GTAAT
* * *
322158 TTTTGGGAAG-TCGACGGT-AAAATGGTAATT
1 TTTTGGAAAGTTAG-GGGTAAAAAT-GTAA-T
** ** * *
322188 TTTTAAAAAAATAGTGGTAAAAAATGAAAT
1 TTTTGGAAAGTTAGGGGT-AAAAATGTAAT
*
322218 TGTTGG-AAGTTTAGGGGT-AAAATGGTAAT
1 TTTTGGAAAG-TTAGGGGTAAAAAT-GTAAT
** * *
322247 TTTCATAAAAAAATTA-GGGTCAAAAATGGAA-
1 TTT--T-GGAAAGTTAGGGGT-AAAAATGTAAT
*
322278 TTTTGGAAAGTTCGAGGG-AAAAATGTAATT
1 TTTTGGAAAGTTAG-GGGTAAAAATGTAA-T
** * *
322308 TTTATAAAAAATT-GAGGTAAAAATAG-AA-
1 TTT-TGGAAAGTTAGGGGTAAAAAT-GTAAT
*
322336 TTTGGGAAAGTTTAGGGGTAAAAATGTAAT
1 TTTTGGAAAG-TTAGGGGTAAAAATGTAAT
*
322366 TTTTGGACAGTT
1 TTTTGGAAAGTT
322378 TAAGGACATT
Statistics
Matches: 176, Mismatches: 43, Indels: 59
0.63 0.15 0.21
Matches are distributed among these distances:
26 1 0.01
27 11 0.06
28 35 0.20
29 36 0.20
30 50 0.28
31 25 0.14
32 11 0.06
33 7 0.04
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.32
Consensus pattern (29 bp):
TTTTGGAAAGTTAGGGGTAAAAATGTAAT
Found at i:322365 original size:59 final size:58
Alignment explanation
Indices: 322090--322369 Score: 247
Period size: 58 Copynumber: 4.8 Consensus size: 58
322080 AAATCGTATC
* * * **
322090 AAAAATGGGATTTTGGAAAGTTCAGGGGTAAAAATGTAA-TTTTTGGAAAAATTAGGTT
1 AAAAATAGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTTAAAAAAATTAGG-T
* ** *
322148 AAAAATAGAATTTTGGGAAGTCGA-CGGT-AAAATGGTAATTTTTTAAAAAAA-TAGTGGT
1 AAAAATAGAATTTTGGAAAGTTTAGGGGTAAAAAT-GTAATTTTTTAAAAAAATTA--GGT
*
322206 AAAAA-ATGAAATTGTTGG-AAGTTTAGGGGT-AAAATGGTAATTTTCATAAAAAAATTAGGGT
1 AAAAATA-G-AATT-TTGGAAAGTTTAGGGGTAAAAAT-GTAATTTT-TTAAAAAAATTA-GGT
* *
322267 CAAAAATGGAATTTTGGAAAG-TTCGAGGG-AAAAATGTAA-TTTTTATAAAAAATTGAGGT
1 -AAAAATAGAATTTTGGAAAGTTTAG-GGGTAAAAATGTAATTTTTTA-AAAAAATT-AGGT
*
322326 AAAAATAGAATTTGGGAAAGTTTAGGGGTAAAAATGTAATTTTT
1 AAAAATAGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTT
322370 GGACAGTTTA
Statistics
Matches: 183, Mismatches: 19, Indels: 38
0.76 0.08 0.16
Matches are distributed among these distances:
56 5 0.03
57 10 0.05
58 59 0.32
59 38 0.21
60 37 0.20
61 26 0.14
62 8 0.04
ACGTcount: A:0.43, C:0.02, G:0.23, T:0.32
Consensus pattern (58 bp):
AAAAATAGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTTAAAAAAATTAGGT
Found at i:323435 original size:19 final size:18
Alignment explanation
Indices: 323400--323439 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
323390 ATTATTACCG
*
323400 TTATTAATATTATATTTA
1 TTATTAAAATTATATTTA
323418 TTATTAAAATTAATATTTA
1 TTATTAAAATT-ATATTTA
323437 TTA
1 TTA
323440 AAGTTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATTAAAATTATATTTA
Found at i:324277 original size:6 final size:6
Alignment explanation
Indices: 324250--324348 Score: 70
Period size: 6 Copynumber: 17.2 Consensus size: 6
324240 ACTTTTATTT
* *
324250 ATTTAA ATTTATA A--TAA TTTTAA ATTTAA ACTTAA A-TTAA ATTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
324296 ATTTTAGA A--TAA ATTTAA ATTTAA A-ATAA ATTT-A ATCTTAA A-ATAA
1 A-TTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA
324342 ATTTAA A
1 ATTTAA A
324349 ATGAGTTGAG
Statistics
Matches: 74, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
4 3 0.04
5 20 0.27
6 41 0.55
7 8 0.11
8 2 0.03
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:324277 original size:23 final size:23
Alignment explanation
Indices: 324251--324320 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 23
324241 CTTTTATTTA
* *
324251 TTTAAATTTATAA-TAATTTTAAA
1 TTTAAACTTA-AATTAAATTTAAA
324274 TTTAAACTTAAATTAAATTTAAA
1 TTTAAACTTAAATTAAATTTAAA
324297 TTTTAGAA--TAAATTTAAATTTAAA
1 -TTTA-AACTTAAA-TTAAATTTAAA
324321 ATAAATTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 2 0.05
23 22 0.54
24 15 0.37
25 2 0.05
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (23 bp):
TTTAAACTTAAATTAAATTTAAA
Found at i:324286 original size:12 final size:12
Alignment explanation
Indices: 324250--324348 Score: 70
Period size: 11 Copynumber: 8.6 Consensus size: 12
324240 ACTTTTATTT
324250 ATTTAAATTTATA
1 ATTTAAATTTA-A
*
324263 A--TAATTTTAA
1 ATTTAAATTTAA
*
324273 ATTTAAACTTAA
1 ATTTAAATTTAA
324285 A-TTAAATTTAA
1 ATTTAAATTTAA
324296 ATTTTAGAA--TAA
1 A-TTTA-AATTTAA
324308 ATTTAAATTTAA
1 ATTTAAATTTAA
*
324320 A-ATAAATTT-A
1 ATTTAAATTTAA
*
324330 ATCTTAAA-ATAA
1 AT-TTAAATTTAA
324342 ATTTAAA
1 ATTTAAA
324349 ATGAGTTGAG
Statistics
Matches: 69, Mismatches: 7, Indels: 22
0.70 0.07 0.22
Matches are distributed among these distances:
10 6 0.09
11 34 0.49
12 23 0.33
13 4 0.06
14 2 0.03
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (12 bp):
ATTTAAATTTAA
Found at i:324289 original size:17 final size:17
Alignment explanation
Indices: 324270--324348 Score: 104
Period size: 17 Copynumber: 4.6 Consensus size: 17
324260 ATAATAATTT
*
324270 TAAATTTAAACTTAAAT
1 TAAATTTAAACTTAAAA
* *
324287 TAAATTTAAATTTTAGAA
1 TAAATTTAAA-CTTAAAA
*
324305 TAAATTTAAATTTAAAA
1 TAAATTTAAACTTAAAA
*
324322 TAAATTTAATCTTAAAA
1 TAAATTTAAACTTAAAA
324339 TAAATTTAAA
1 TAAATTTAAA
324349 ATGAGTTGAG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
17 40 0.74
18 14 0.26
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:324325 original size:29 final size:29
Alignment explanation
Indices: 324250--324350 Score: 86
Period size: 29 Copynumber: 3.5 Consensus size: 29
324240 ACTTTTATTT
*
324250 ATTTAAATTTATAAT-AATTTTAAATTTAA
1 ATTTAAATTTAAAATAAATTTTAAA-TTAA
* *
324279 ACTTAAA-TTAAATTTAAATTTTAGAA-TAA
1 ATTTAAATTTAAA-ATAAATTTTA-AATTAA
*
324308 ATTTAAATTTAAAATAAA-TTTAATCTTAA
1 ATTTAAATTTAAAATAAATTTTAA-ATTAA
*
324337 A-ATAAATTTAAAAT
1 ATTTAAATTTAAAAT
324351 GAGTTGAGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
27 1 0.02
28 20 0.34
29 24 0.41
30 12 0.20
31 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (29 bp):
ATTTAAATTTAAAATAAATTTTAAATTAA
Found at i:325133 original size:50 final size:50
Alignment explanation
Indices: 325077--325173 Score: 167
Period size: 50 Copynumber: 1.9 Consensus size: 50
325067 CACACAGACA
*
325077 TGTGCCAAAACGTGTGAGTATGCTGTTTTGCTATTAAAGATGCAGTGACG
1 TGTGCCAAAACATGTGAGTATGCTGTTTTGCTATTAAAGATGCAGTGACG
* *
325127 TGTGCCAGAACATGTGAGTATGTTGTTTTGCTATTAAAGATGCAGTG
1 TGTGCCAAAACATGTGAGTATGCTGTTTTGCTATTAAAGATGCAGTG
325174 GTTACACGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (50 bp):
TGTGCCAAAACATGTGAGTATGCTGTTTTGCTATTAAAGATGCAGTGACG
Found at i:328219 original size:29 final size:30
Alignment explanation
Indices: 328162--328249 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 30
328152 AGATGAAAAC
* *
328162 GTAATTTTTTAGGA-ATTTGAGGGTCAAAATT
1 GTAAATTTTT-GGATATTCGAGGG-CAAAATT
*
328193 G-AAATTTTTGGATGTTCGAGGGCAAAA-T
1 GTAAATTTTTGGATATTCGAGGGCAAAATT
** *
328221 GTATTTTTTTGGATATTCGAGAGCAAAAT
1 GTAAATTTTTGGATATTCGAGGGCAAAAT
328250 CATAATTTTG
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
28 2 0.04
29 30 0.64
30 14 0.30
31 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.39
Consensus pattern (30 bp):
GTAAATTTTTGGATATTCGAGGGCAAAATT
Found at i:328258 original size:29 final size:28
Alignment explanation
Indices: 328195--328258 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
328185 TCAAAATTGA
* * *
328195 AATTTTTGGATGTTCGAGGGCAAAATGT
1 AATTTTTGGATATTCGAGAGCAAAATAT
*
328223 ATTTTTTTGGATATTCGAGAGCAAAATCAT
1 A-ATTTTTGGATATTCGAGAGCAAAAT-AT
328253 AATTTT
1 AATTTT
328259 GGAGAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 1 0.03
29 26 0.90
30 2 0.07
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (28 bp):
AATTTTTGGATATTCGAGAGCAAAATAT
Found at i:328403 original size:56 final size:57
Alignment explanation
Indices: 328269--328426 Score: 201
Period size: 56 Copynumber: 2.7 Consensus size: 57
328259 GGAGAAATTT
* *
328269 GGGTCAAAATGTAATTTTGGAGAAGTTTAGGGGGTCAAAATGTAATTTTGGAAAAGTTTGA
1 GGGTTAAAATGTAATTTTGGAGAAGTTTA--GGGTCAAAATGTAA--TTAGAAAAGTTTGA
* * * *
328330 GGGTTAAAATGTGATTTTGGAAAAGTTTAGGGTTAAATTGTAA-TAGAAAAGTTTGA
1 GGGTTAAAATGTAATTTTGGAGAAGTTTAGGGTCAAAATGTAATTAGAAAAGTTTGA
*
328386 GGGTTAAAATGCAATTTTGGAGAAGTTTAGGAGTCAAAATG
1 GGGTTAAAATGTAATTTTGGAGAAGTTTAGG-GTCAAAATG
328427 AGATTTTTAA
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
56 40 0.47
57 7 0.08
59 12 0.14
61 26 0.31
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (57 bp):
GGGTTAAAATGTAATTTTGGAGAAGTTTAGGGTCAAAATGTAATTAGAAAAGTTTGA
Found at i:328433 original size:30 final size:29
Alignment explanation
Indices: 328252--328426 Score: 180
Period size: 30 Copynumber: 6.0 Consensus size: 29
328242 AGCAAAATCA
328252 TAATTTTGGAGAAA-TTT-GGGTCAAAATG
1 TAATTTTGGA-AAAGTTTAGGGTCAAAATG
*
328280 TAATTTTGGAGAAGTTTAGGGGGTCAAAATG
1 TAATTTTGGAAAAGTTTA--GGGTCAAAATG
*
328311 TAATTTTGGAAAAGTTTGAGGGTTAAAATG
1 TAATTTTGGAAAAGTTT-AGGGTCAAAATG
* * *
328341 TGATTTTGGAAAAGTTTAGGGTTAAATTG
1 TAATTTTGGAAAAGTTTAGGGTCAAAATG
* *
328370 TAA---TAGAAAAGTTTGAGGGTTAAAATG
1 TAATTTTGGAAAAGTTT-AGGGTCAAAATG
* *
328397 CAATTTTGGAGAAGTTTAGGAGTCAAAATG
1 TAATTTTGGAAAAGTTTAGG-GTCAAAATG
328427 AGATTTTTAA
Statistics
Matches: 125, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
26 10 0.08
27 15 0.12
28 13 0.10
29 16 0.13
30 43 0.34
31 27 0.22
32 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.34
Consensus pattern (29 bp):
TAATTTTGGAAAAGTTTAGGGTCAAAATG
Found at i:329498 original size:3 final size:3
Alignment explanation
Indices: 329490--329565 Score: 125
Period size: 3 Copynumber: 25.0 Consensus size: 3
329480 CCCTTTAACC
329490 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
329538 TTA TTA TTA TTA TTTA ATA TTA TAA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA
329566 ATATGCATTA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
3 65 0.96
4 3 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:331747 original size:14 final size:15
Alignment explanation
Indices: 331720--331749 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
331710 AAAAATTCAA
331720 AAAATTATTTTAAAT
1 AAAATTATTTTAAAT
*
331735 AAAATTATTTAAAAT
1 AAAATTATTTTAAAT
331750 GTATAAAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTATTTTAAAT
Found at i:337476 original size:4 final size:4
Alignment explanation
Indices: 337469--337503 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
337459 ATATATATAT
337469 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
337504 TAGTGATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:341188 original size:22 final size:22
Alignment explanation
Indices: 341154--341198 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
341144 CTTTCCCATA
341154 ATTTTTTACTCCCCAAAACTTTTT
1 ATTTTTTA-T-CCCAAAACTTTTT
*
341178 ATTTTTT-TCCCTAAACTTTTT
1 ATTTTTTATCCCAAAACTTTTT
341199 CTTCTCACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 12 0.60
22 1 0.05
24 7 0.35
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTTTTATCCCAAAACTTTTT
Found at i:344247 original size:19 final size:18
Alignment explanation
Indices: 344223--344285 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
344213 ATTCCAAAAA
344223 TAATATTATTTTAATAGTT
1 TAATATTATTTTAATA-TT
*
344242 TAATATTAAATTT-A-ATT
1 TAATATT-ATTTTAATATT
* *
344259 TAATAGTATTTTATTAATT
1 TAATATTATTTTAAT-ATT
344278 TAATATTA
1 TAATATTA
344286 AAGTGATTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 4 0.11
17 8 0.23
18 1 0.03
19 18 0.51
20 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TAATATTATTTTAATATT
Found at i:344257 original size:20 final size:20
Alignment explanation
Indices: 344223--344309 Score: 58
Period size: 20 Copynumber: 4.6 Consensus size: 20
344213 ATTCCAAAAA
*
344223 TAATATT-ATTTTAATAGTT
1 TAATATTAAATTTAATAGTT
344242 TAATATTAAATTT-A-A-TT
1 TAATATTAAATTTAATAGTT
* * * *
344259 TAATAGT-ATTTTATTAATT
1 TAATATTAAATTTAATAGTT
* * * *
344278 TAATATTAAAGTGATTAGCT
1 TAATATTAAATTTAATAGTT
344298 TAATATTAAATT
1 TAATATTAAATT
344310 ATATTTAATG
Statistics
Matches: 52, Mismatches: 11, Indels: 9
0.72 0.15 0.12
Matches are distributed among these distances:
16 4 0.08
17 8 0.15
18 2 0.04
19 16 0.31
20 22 0.42
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (20 bp):
TAATATTAAATTTAATAGTT
Found at i:344260 original size:25 final size:24
Alignment explanation
Indices: 344223--344294 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 24
344213 ATTCCAAAAA
*
344223 TAATATTATTTTAATAGT-TTAATAT
1 TAAT-TTAATTTAATAGTATT-ATAT
*
344248 TAAATTTAATTTAATAGTATTTTAT
1 T-AATTTAATTTAATAGTATTATAT
344273 TAATTTAATATTAA-AGTGATTA
1 TAATTTAAT-TTAATAGT-ATTA
344295 GCTTAATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 11 0.28
25 24 0.60
26 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (24 bp):
TAATTTAATTTAATAGTATTATAT
Found at i:347019 original size:18 final size:18
Alignment explanation
Indices: 346996--347030 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
346986 CCCTCGTCCT
* *
346996 CTAAGGGGAAACAGAAAG
1 CTAAGGGAAAAAAGAAAG
347014 CTAAGGGAAAAAAGAAA
1 CTAAGGGAAAAAAGAAA
347031 CTGATTAAGT
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:0.57, C:0.09, G:0.29, T:0.06
Consensus pattern (18 bp):
CTAAGGGAAAAAAGAAAG
Found at i:355532 original size:15 final size:14
Alignment explanation
Indices: 355495--355533 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
355485 TTTTGAAAAT
*
355495 TTTAATTTAAAGAC
1 TTTAATTTTAAGAC
*
355509 TTTACTTTTAAGAC
1 TTTAATTTTAAGAC
355523 TTGTAATTTTA
1 TT-TAATTTTA
355534 GATAATTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (14 bp):
TTTAATTTTAAGAC
Done.