Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014995.1 Kokia drynarioides strain JFW-HI SEQ_130039, 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: 341517
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 255 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:634 original size:28 final size:28
Alignment explanation
Indices: 581--638 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
571 AATATATTTA
* **
581 TTGAATAATAAATCATCACTTTTTAAAT
1 TTGAATAATAAATCATCAATAATTAAAT
609 TTGAATAAGT-AATCATCAATAATTAAAT
1 TTGAATAA-TAAATCATCAATAATTAAAT
637 TT
1 TT
639 ACAATCTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (28 bp):
TTGAATAATAAATCATCAATAATTAAAT
Found at i:1299 original size:14 final size:14
Alignment explanation
Indices: 1265--1299 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1255 CTACTTCTCT
* *
1265 TAAAAAATTGAAGA
1 TAAAAATTTAAAGA
1279 TAAAAATTTAAAGA
1 TAAAAATTTAAAGA
1293 TAAAAAT
1 TAAAAAT
1300 AATGATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (14 bp):
TAAAAATTTAAAGA
Found at i:1484 original size:21 final size:22
Alignment explanation
Indices: 1460--1501 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1450 TTTTTTTTAA
*
1460 TTTCTAATTT-TTTTAATTTTT
1 TTTCTAATTTATTATAATTTTT
1481 TTTCTAATTTATTATAATTTT
1 TTTCTAATTTATTATAATTTT
1502 ATATTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTCTAATTTATTATAATTTTT
Found at i:1501 original size:28 final size:28
Alignment explanation
Indices: 1447--1502 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1437 GGTTTAAATG
* * **
1447 ATTTTTTTTTTAATTTCTAATTTTTTTA
1 ATTTTTTTTCTAATTTATAATAATTTTA
*
1475 ATTTTTTTTCTAATTTATTATAATTTTA
1 ATTTTTTTTCTAATTTATAATAATTTTA
1503 TATTATTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (28 bp):
ATTTTTTTTCTAATTTATAATAATTTTA
Found at i:1649 original size:23 final size:24
Alignment explanation
Indices: 1623--1675 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
1613 AATTTTATAA
1623 ATTTATATCAAT-TTTAATATTTT
1 ATTTATATCAATATTTAATATTTT
* *
1646 ATTT-TTTTAATATTTAATATTTT
1 ATTTATATCAATATTTAATATTTT
*
1669 TTTTATA
1 ATTTATA
1676 ATCTTTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 5 0.21
23 18 0.75
24 1 0.04
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
ATTTATATCAATATTTAATATTTT
Found at i:1655 original size:16 final size:17
Alignment explanation
Indices: 1634--1671 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 17
1624 TTTATATCAA
1634 TTTTAATATTT-TATTT
1 TTTTAATATTTATATTT
1650 TTTTAATATTTAATATTT
1 TTTTAATATTT-ATATTT
1668 TTTT
1 TTTT
1672 TATAATCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.55
18 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTAATATTTATATTT
Found at i:4765 original size:60 final size:60
Alignment explanation
Indices: 4646--4758 Score: 199
Period size: 60 Copynumber: 1.9 Consensus size: 60
4636 AGGTATGTTC
*
4646 ACTTTCCAAGATTTCCATGTATTTAGCGGGTCTTTAGAAGATCATAACCCCATACCCATT
1 ACTTTCCAAGATTTCCATGTATTTAGCGGGTCTTTAGAAGAACATAACCCCATACCCATT
* *
4706 ACTTTCCAAGGTTTCCATGTATTTAGCGGGTCTTTGGAAGAACATAACCCCAT
1 ACTTTCCAAGATTTCCATGTATTTAGCGGGTCTTTAGAAGAACATAACCCCAT
4759 TTCCATTTCT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (60 bp):
ACTTTCCAAGATTTCCATGTATTTAGCGGGTCTTTAGAAGAACATAACCCCATACCCATT
Found at i:8192 original size:71 final size:71
Alignment explanation
Indices: 8076--8219 Score: 216
Period size: 71 Copynumber: 2.0 Consensus size: 71
8066 TGAGTAGGTT
*
8076 AAGAATGAAAGGTTATTGAAATGACGAAAACCGAGTCATGTCAGTCACTAGTGTTCAATCCAATG
1 AAGAATGAAAGGTTATTGAAATGACGAAAACCGAGTCATGTCAGTCACTAGCGTTCAATCCAATG
*
8141 GTGAAG
66 GTAAAG
* * * * **
8147 AAGAATGAAGGGTTATTGAAATGGCGAAAATCGAGTCATTTCAGTCGTTAGCGTTCAATCCAATG
1 AAGAATGAAAGGTTATTGAAATGACGAAAACCGAGTCATGTCAGTCACTAGCGTTCAATCCAATG
8212 GTAAAG
66 GTAAAG
8218 AA
1 AA
8220 TCGACGTATC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (71 bp):
AAGAATGAAAGGTTATTGAAATGACGAAAACCGAGTCATGTCAGTCACTAGCGTTCAATCCAATG
GTAAAG
Found at i:8840 original size:31 final size:29
Alignment explanation
Indices: 8802--8867 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
8792 TGAGGTTAAA
*
8802 TTATGATTATATGTAGTTTTTTTTATAATAT
1 TTATGATTATAGGT--TTTTTTTTATAATAT
* *
8833 TTATGATTTTAGGTTTTTTTTTTTAATAT
1 TTATGATTATAGGTTTTTTTTTATAATAT
8862 TTATGA
1 TTATGA
8868 GAATTAATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 20 0.62
31 12 0.38
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.64
Consensus pattern (29 bp):
TTATGATTATAGGTTTTTTTTTATAATAT
Found at i:9271 original size:18 final size:16
Alignment explanation
Indices: 9237--9267 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9227 CATCAATTAA
9237 TTCTTTTGATATAATT
1 TTCTTTTGATATAATT
*
9253 TTCTTTTTATATAAT
1 TTCTTTTGATATAAT
9268 ATTTATATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (16 bp):
TTCTTTTGATATAATT
Found at i:9386 original size:18 final size:18
Alignment explanation
Indices: 9342--9377 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
9332 AAATTAACTA
*
9342 ATTATTTCAAATGTCATT
1 ATTATTTCAAATATCATT
9360 ATTATTTCAAATATCATT
1 ATTATTTCAAATATCATT
9378 GTTTTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.50
Consensus pattern (18 bp):
ATTATTTCAAATATCATT
Found at i:12347 original size:19 final size:21
Alignment explanation
Indices: 12304--12348 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
12294 GTATTTATAT
12304 TTTTTGTTAATTTAATCTTTA
1 TTTTTGTTAATTTAATCTTTA
12325 TTTTT-TTAA-TTAAT-TTTA
1 TTTTTGTTAATTTAATCTTTA
12343 GTTTTT
1 -TTTTT
12349 AATTTTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.17
19 10 0.43
20 4 0.17
21 5 0.22
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTTTGTTAATTTAATCTTTA
Found at i:12554 original size:21 final size:21
Alignment explanation
Indices: 12514--12554 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12504 TCAAAAATTA
*
12514 TAAAAATAAAAAAATCAAAAT
1 TAAAAATAAAAAAATAAAAAT
* *
12535 TAAAATTAAAAATATAAAAA
1 TAAAAATAAAAAAATAAAAA
12555 ATTCATAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAAAATAAAAAAATAAAAAT
Found at i:13571 original size:22 final size:22
Alignment explanation
Indices: 13543--13586 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
13533 ACATTAGAGC
*
13543 ATTCATCTCTAATTTCATCATG
1 ATTCATCTCTAATTTCAACATG
13565 ATTCATCTCTAATTTCAACATG
1 ATTCATCTCTAATTTCAACATG
13587 GTATCAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.43
Consensus pattern (22 bp):
ATTCATCTCTAATTTCAACATG
Found at i:15017 original size:22 final size:22
Alignment explanation
Indices: 14992--15033 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
14982 AATACATTAG
14992 ATTATTCATCTATAATTTCATC
1 ATTATTCATCTATAATTTCATC
*
15014 ATTATTCATCTCTAATTTCA
1 ATTATTCATCTATAATTTCA
15034 ATAGTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTATTCATCTATAATTTCATC
Found at i:31558 original size:22 final size:23
Alignment explanation
Indices: 31515--31566 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
31505 CGTTGATTTC
* * *
31515 TTCTCGTCGGGACGTTGGCTCT-
1 TTCTCGTCAGGACGTCGACTCTA
*
31537 TTCTCGTCATGACGTCGACTCTA
1 TTCTCGTCAGGACGTCGACTCTA
31560 TT-TCGTC
1 TTCTCGTC
31567 CAAAATGCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.10, C:0.29, G:0.23, T:0.38
Consensus pattern (23 bp):
TTCTCGTCAGGACGTCGACTCTA
Found at i:35158 original size:16 final size:17
Alignment explanation
Indices: 35131--35163 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
35121 AAATTTAACC
35131 ATTTTGTTTTAGATCTA
1 ATTTTGTTTTAGATCTA
35148 ATTTT-TTTTAGATCTA
1 ATTTTGTTTTAGATCTA
35164 GTTGGTCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.61
Consensus pattern (17 bp):
ATTTTGTTTTAGATCTA
Found at i:35210 original size:32 final size:32
Alignment explanation
Indices: 35165--35234 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
35155 TTAGATCTAG
* *
35165 TTGGTCCCCGAACTTGTATCCCGTCCATTAGA
1 TTGGTCCCCGAACTTGTATCCCATCAATTAGA
* * * *
35197 TTGGTTCCTGAACTTGTATTCCATCAATTAGG
1 TTGGTCCCCGAACTTGTATCCCATCAATTAGA
35229 TTGGTC
1 TTGGTC
35235 TCTCCACATT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (32 bp):
TTGGTCCCCGAACTTGTATCCCATCAATTAGA
Found at i:36005 original size:52 final size:52
Alignment explanation
Indices: 35948--36057 Score: 168
Period size: 52 Copynumber: 2.1 Consensus size: 52
35938 CTAAACCTAT
* * *
35948 TTTAAATTTATTTTAAGATTGAATTTA-TTTTAAATTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAGATTCAATTTATTTTTAAATTTAAAATTATTAT-AAA
*
36000 TTTAAATTTATTTTAAGTTTCAATTTATTTTTAAATTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAGATTCAATTTATTTTTAAATTTAAAATTATTATAAA
36052 TTTAAA
1 TTTAAA
36058 AGTCTAGAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 34 0.64
53 19 0.36
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (52 bp):
TTTAAATTTATTTTAAGATTCAATTTATTTTTAAATTTAAAATTATTATAAA
Found at i:36015 original size:35 final size:35
Alignment explanation
Indices: 35948--36057 Score: 150
Period size: 35 Copynumber: 3.2 Consensus size: 35
35938 CTAAACCTAT
* *
35948 TTTAAATTTATTTTAAGA-TTGAATTTATTTTAAA
1 TTTAAATTTATTTTAAAATTTAAATTTATTTTAAA
*
35982 TTTAAATTTATTTTAAAATTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAAATTTAAATTTATTTTAAA
* * * *
36017 TTTCAATTTATTTTTAAATTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAAATTTAAATTTATTTTAAA
36052 TTTAAA
1 TTTAAA
36058 AGTCTAGAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
34 17 0.26
35 49 0.74
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (35 bp):
TTTAAATTTATTTTAAAATTTAAATTTATTTTAAA
Found at i:36058 original size:17 final size:17
Alignment explanation
Indices: 35948--36057 Score: 141
Period size: 17 Copynumber: 6.4 Consensus size: 17
35938 CTAAACCTAT
35948 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
35966 -TTGAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
35982 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
*
36000 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
*
36017 TTTCAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
36035 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
36052 TTTAAA
1 TTTAAA
36058 AGTCTAGAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
16 1 0.01
17 49 0.60
18 31 0.38
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:36787 original size:3 final size:3
Alignment explanation
Indices: 36779--36827 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
36769 ATGAATATTA
36779 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
36827 A
1 A
36828 GTAGTAGATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39928 original size:3 final size:3
Alignment explanation
Indices: 39920--39956 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
39910 ATGCATATTA
39920 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
39957 GTAGTAGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:41378 original size:59 final size:57
Alignment explanation
Indices: 41095--41579 Score: 312
Period size: 58 Copynumber: 8.3 Consensus size: 57
41085 AAACTCTCTG
* * *
41095 AAAATTACATTTTTACCCAC-AAACTTT-TGAAAATTCCATTTTTGATCTCGATTTTTCC-
1 AAAATTACA-TTTTACCC-CTAAA-TTTCT-AAAATTCCATTTTTGACCCCAATTTTTCCA
* * * * * * *
41153 AAAATCACATTTTTTCCCCTGAACTTCTCAAAATTCCATATTTGACCCC---TTTTACT
1 AAAATTACA-TTTTACCCCTAAATTTCT-AAAATTCCATTTTTGACCCCAATTTTTCCA
* * * * * * * *
41209 AAAATTACAATTTTACCCCCGAACTTTCCAAAATTCTATTTTTGACCTCGATTTCTCTA
1 AAAATTAC-ATTTTA-CCCCTAAATTTCTAAAATTCCATTTTTGACCCCAATTTTTCCA
* * * **
41268 AGAATTACCATTTTACCCC-AAACTTCCAAAATTCCCATTTTT-ACCATAATTTTTCCAA
1 AAAATTA-CATTTTACCCCTAAATTTCTAAAATT-CCATTTTTGACCCCAATTTTTCC-A
*
41326 AAAATTACATTTTTACCCCTAAATTTCTAAAATTCCATTTTTGACCCCAATTTTTCCC
1 AAAATTACA-TTTTACCCCTAAATTTCTAAAATTCCATTTTTGACCCCAATTTTTCCA
* * * *
41384 AAAATTACAATTTTACCCCTAATCTTTC-AAAATTCCATTTTTTATCCCAATTTTTTCA
1 AAAATTAC-ATTTTACCCCTAA-ATTTCTAAAATTCCATTTTTGACCCCAATTTTTCCA
* * * * * * *
41442 AAAACTACCATTTTACCCCCGAACTTCCAAATAATT-CATTTTTGACCCCGATTCTTCCA
1 AAAATTA-CATTTTA-CCCCTAAATTTCTAA-AATTCCATTTTTGACCCCAATTTTTCCA
* ** *
41501 AAAAGTACCATTTTACCCCCGAATGTT-TAAAAATTCCATTTTTGAACCCCCAA-CTTTCTC-
1 AAAATTA-CATTTTACCCCTAAAT-TTCT-AAAATTCCATTTTTG-A-CCCCAATTTTTC-CA
41561 AAAATTACCATTTTACCCC
1 AAAATTA-CATTTTACCCC
41580 CGAGTATCCA
Statistics
Matches: 340, Mismatches: 61, Indels: 50
0.75 0.14 0.11
Matches are distributed among these distances:
55 5 0.01
56 28 0.08
57 35 0.10
58 143 0.42
59 96 0.28
60 27 0.08
61 6 0.02
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.38
Consensus pattern (57 bp):
AAAATTACATTTTACCCCTAAATTTCTAAAATTCCATTTTTGACCCCAATTTTTCCA
Found at i:41521 original size:30 final size:28
Alignment explanation
Indices: 41440--41582 Score: 96
Period size: 29 Copynumber: 4.8 Consensus size: 28
41430 CCAATTTTTT
41440 CAAAAACTACCATTTTACCCCCGAACTTC
1 CAAAAA-TACCATTTTACCCCCGAACTTC
* *
41469 CAAATAAT-TCATTTTTGA-CCCCGATTCTTC
1 CAAA-AATACCA-TTTT-ACCCCCGA-ACTTC
*
41499 CAAAAAGTACCATTTTACCCCCGAA-TGTT
1 CAAAAA-TACCATTTTACCCCCGAACT-TC
* *
41528 TAAAAATTCCATTTTTGAACCCCC-AACTTTC
1 CAAAAATACCA-TTTT--ACCCCCGAAC-TTC
*
41559 TCAAAATTACCATTTTACCCCCGA
1 -CAAAAATACCATTTTACCCCCGA
41583 GTATCCAAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 29
0.69 0.09 0.23
Matches are distributed among these distances:
28 7 0.08
29 34 0.39
30 25 0.28
31 13 0.15
32 9 0.10
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.31
Consensus pattern (28 bp):
CAAAAATACCATTTTACCCCCGAACTTC
Found at i:41936 original size:97 final size:98
Alignment explanation
Indices: 41796--41990 Score: 245
Period size: 97 Copynumber: 2.0 Consensus size: 98
41786 AAAAACTTTA
* * * * *
41796 AAATCGAGGCAATACTCTTTTATTTCGAGTTTTGAAAATTTGTGCCTTAACTGATTAGGTG-TAA
1 AAATCGAGGCAATACTCTTTTATCTCGAGTTCTGAAAATTTGTGCCTTAACTCACTAGGTGCGAA
*
41860 TTTTTCCTCAAATCGAAATAATCGAATA-CCCTT
66 -TTTTCCTCAAATCGAAATAATCAAATATCCCTT
* *
41893 AAATCGAGGCAAT-GTCTCTTTATCTCTGA-TTCTGAAAATTTGTGCCTTAACTCACTATGTGCG
1 AAATCGAGGCAATACTCT-TTTATCTC-GAGTTCTGAAAATTTGTGCCTTAACTCACTAGGTGCG
* *
41956 AATTTTCTTCAAATCGAGATAATCAAATATCCCTT
64 AATTTTCCTCAAATCGAAATAATCAAATATCCCTT
41991 TCCAAAGTTT
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
96 3 0.04
97 72 0.86
98 9 0.11
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.37
Consensus pattern (98 bp):
AAATCGAGGCAATACTCTTTTATCTCGAGTTCTGAAAATTTGTGCCTTAACTCACTAGGTGCGAA
TTTTCCTCAAATCGAAATAATCAAATATCCCTT
Found at i:42721 original size:15 final size:16
Alignment explanation
Indices: 42701--42731 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
42691 ATATTGAAAT
42701 TAAAATTTA-ATATAG
1 TAAAATTTATATATAG
42716 TAAAATTTATATATAG
1 TAAAATTTATATATAG
42732 ACAGTCACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
TAAAATTTATATATAG
Found at i:50266 original size:16 final size:16
Alignment explanation
Indices: 50245--50277 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
50235 GAACTACGAA
50245 TAATGTAAAATAAAAT
1 TAATGTAAAATAAAAT
*
50261 TAATGTTAAATAAAAT
1 TAATGTAAAATAAAAT
50277 T
1 T
50278 TATTCATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (16 bp):
TAATGTAAAATAAAAT
Found at i:51065 original size:29 final size:30
Alignment explanation
Indices: 51033--51091 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
51023 TATAATATAA
*
51033 TGTGTAATTGTATATAT-AAACTTTGATTT
1 TGTGTAATTGTATATATGAAAATTTGATTT
* *
51062 TGTGTAATTTTATATTTGAAAATTTGATTT
1 TGTGTAATTGTATATATGAAAATTTGATTT
51092 GATTCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.54
Consensus pattern (30 bp):
TGTGTAATTGTATATATGAAAATTTGATTT
Found at i:55577 original size:19 final size:19
Alignment explanation
Indices: 55553--55591 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
55543 AAGTTGTAAG
55553 TAAACTAAAAACATCAAAC
1 TAAACTAAAAACATCAAAC
55572 TAAACTAAAAACATCAAAC
1 TAAACTAAAAACATCAAAC
55591 T
1 T
55592 CGAAGTCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.18
Consensus pattern (19 bp):
TAAACTAAAAACATCAAAC
Found at i:58342 original size:20 final size:21
Alignment explanation
Indices: 58319--58367 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
58309 ATTTGCAATT
58319 TATATTTTAATAT-TTTAAAA
1 TATATTTTAATATATTTAAAA
* *
58339 TATAGTTT-ATATATTTAAAT
1 TATATTTTAATATATTTAAAA
*
58359 TAAATTTTA
1 TATATTTTA
58368 CAAATAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TATATTTTAATATATTTAAAA
Found at i:58757 original size:25 final size:25
Alignment explanation
Indices: 58723--58791 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 25
58713 TGAACTTGAC
*
58723 ACTTTTTTTTTAATTTGGTATCTAA
1 ACTTTTTTTTTAATTTGGTACCTAA
58748 ACTTTTTTTTGACTCAATTTGGTACCTAA
1 ACTTTTTTTT---T-AATTTGGTACCTAA
* *
58777 ACTTTATTTTAAATT
1 ACTTTTTTTTTAATT
58792 CAGTTTGGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
25 14 0.38
28 1 0.03
29 22 0.59
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.55
Consensus pattern (25 bp):
ACTTTTTTTTTAATTTGGTACCTAA
Found at i:58801 original size:30 final size:30
Alignment explanation
Indices: 58734--58813 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
58724 CTTTTTTTTT
* **
58734 AATTTGGTATCTAAACTTT-TTTTTGACTC
1 AATTTGGTACCTAAACTTTATTTTAAACTC
*
58763 AATTTGGTACCTAAACTTTATTTTAAATTC
1 AATTTGGTACCTAAACTTTATTTTAAACTC
*
58793 AGTTTGGTACCTAAA-TTTATT
1 AATTTGGTACCTAAACTTTATT
58814 AAATATTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
29 24 0.53
30 21 0.47
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (30 bp):
AATTTGGTACCTAAACTTTATTTTAAACTC
Found at i:59070 original size:31 final size:33
Alignment explanation
Indices: 59009--59077 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 33
58999 GGACCCCAAA
*
59009 AAGTTTAAGTACCAACTTTAAAGAAAAAGTGTC
1 AAGTTTAAGTACCAACATTAAAGAAAAAGTGTC
* * *
59042 AAGTTTTAGTACCAA-ATTAGA-AAAAAGTGTT
1 AAGTTTAAGTACCAACATTAAAGAAAAAGTGTC
59073 AAGTT
1 AAGTT
59078 CAGGTACGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 14 0.44
32 4 0.12
33 14 0.44
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (33 bp):
AAGTTTAAGTACCAACATTAAAGAAAAAGTGTC
Found at i:59567 original size:23 final size:23
Alignment explanation
Indices: 59541--59586 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
59531 GTTAACATTA
*
59541 TATATATATATATATTGATAATG
1 TATAGATATATATATTGATAATG
* * *
59564 TATAGATTTATTTATTTATAATG
1 TATAGATATATATATTGATAATG
59587 CTTTCATTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (23 bp):
TATAGATATATATATTGATAATG
Found at i:65684 original size:21 final size:21
Alignment explanation
Indices: 65658--65697 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
65648 TTTATCTTCA
* *
65658 ACTTCCTATAATATATTATCT
1 ACTTCCTAAAATAAATTATCT
65679 ACTTCCTAAAATAAATTAT
1 ACTTCCTAAAATAAATTAT
65698 TCAATAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.42
Consensus pattern (21 bp):
ACTTCCTAAAATAAATTATCT
Found at i:70984 original size:29 final size:30
Alignment explanation
Indices: 70947--71243 Score: 159
Period size: 29 Copynumber: 10.1 Consensus size: 30
70937 TAGACATCCA
*
70947 AGGG-AAAAATGGTAA-TTTTGGAAATTTTG
1 AGGGTAAAAATGGTAATTTTTGGAAA-TTCG
* *
70976 AGGTTAAAAATGG-AATTTTTGGATATTCG
1 AGGGTAAAAATGGTAATTTTTGGAAATTCG
* * **
71005 AGGGT-AAAATTGTAATTTTTGGAAGTTAA
1 AGGGTAAAAATGGTAATTTTTGGAAATTCG
71034 AGGGGTAAAAAT-GTAA-TTTTGGAAAGTTC-
1 A-GGGTAAAAATGGTAATTTTTGGAAA-TTCG
** *** *
71063 AGGGGTAAAAA-CATAAATTTTCAAAAACTCG
1 A-GGGTAAAAATGGT-AATTTTTGGAAATTCG
* *
71094 A-GGTCAAAAATAG-AA-TTTTGGAAAGTTTG
1 AGGGT-AAAAATGGTAATTTTTGGAAA-TTCG
71123 -GGGTTAAAAAT-GTAATTTTTGGAAAATTCG
1 AGGG-TAAAAATGGTAATTTTTGG-AAATTCG
*
71153 A-GGTCAAAAATGG-AA-TTTTGGAAAGTTCA
1 AGGGT-AAAAATGGTAATTTTTGGAAA-TTCG
71182 AGGGT-AAAAT-GTAACTTTTTGGAAAATTCG
1 AGGGTAAAAATGGTAA-TTTTTGG-AAATTCG
*
71212 -GAGTCAAAAATGG-AA-TTTTGGAAAGTTCG
1 AGGGT-AAAAATGGTAATTTTTGGAAA-TTCG
71241 AGG
1 AGG
71244 ACCTCCTTGG
Statistics
Matches: 208, Mismatches: 28, Indels: 63
0.70 0.09 0.21
Matches are distributed among these distances:
27 1 0.00
28 26 0.12
29 86 0.41
30 68 0.33
31 26 0.12
32 1 0.00
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.32
Consensus pattern (30 bp):
AGGGTAAAAATGGTAATTTTTGGAAATTCG
Found at i:71069 original size:59 final size:59
Alignment explanation
Indices: 70951--71239 Score: 270
Period size: 59 Copynumber: 4.9 Consensus size: 59
70941 CATCCAAGGG
* * * *
70951 AAAAATGGTAA-TTTTGGAAATTTTGAGGTTAAAAATGGAATTTTTGGATA-TTC-GAGGGT
1 AAAAAT-GTAATTTTTGGAAAATTAGAGGTCAAAAATGGAA-TTTTGGAAAGTTCAG-GGGT
* * * *
71010 AAAATTGTAATTTTTGG-AAGTTAAAGGGGT-AAAAATGTAATTTTGGAAAGTTCAGGGGT
1 AAAAATGTAATTTTTGGAAAATT--AGAGGTCAAAAATGGAATTTTGGAAAGTTCAGGGGT
** * ** * * * *
71069 AAAAACATAAATTTTCAAAAACTCGAGGTCAAAAATAGAATTTTGGAAAGTT-TGGGGTT
1 AAAAATGTAATTTTTGGAAAATTAGAGGTCAAAAATGGAATTTTGGAAAGTTCAGGGG-T
* *
71128 AAAAATGTAATTTTTGGAAAATTCGAGGTCAAAAATGGAATTTTGGAAAGTTCAAGGGT
1 AAAAATGTAATTTTTGGAAAATTAGAGGTCAAAAATGGAATTTTGGAAAGTTCAGGGGT
*
71187 -AAAATGTAACTTTTTGGAAAATTCG-GAGTCAAAAATGGAATTTTGGAAAGTTC
1 AAAAATGTAA-TTTTTGGAAAATTAGAG-GTCAAAAATGGAATTTTGGAAAGTTC
71240 GAGGACCTCC
Statistics
Matches: 191, Mismatches: 28, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
58 34 0.18
59 146 0.76
60 11 0.06
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (59 bp):
AAAAATGTAATTTTTGGAAAATTAGAGGTCAAAAATGGAATTTTGGAAAGTTCAGGGGT
Found at i:72107 original size:62 final size:62
Alignment explanation
Indices: 72037--72159 Score: 237
Period size: 62 Copynumber: 2.0 Consensus size: 62
72027 TCAAAAAAAG
72037 ATCTTTATTTCCTTATATTTTTGTTAAATATGCTTAGTGATTGCTTGGTAATTCTGGAAATT
1 ATCTTTATTTCCTTATATTTTTGTTAAATATGCTTAGTGATTGCTTGGTAATTCTGGAAATT
*
72099 ATCTTTATTTCCTTATATTTTTGTTAAATCTGCTTAGTGATTGCTTGGTAATTCTGGAAAT
1 ATCTTTATTTCCTTATATTTTTGTTAAATATGCTTAGTGATTGCTTGGTAATTCTGGAAAT
72160 GAGTCTCTTC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.51
Consensus pattern (62 bp):
ATCTTTATTTCCTTATATTTTTGTTAAATATGCTTAGTGATTGCTTGGTAATTCTGGAAATT
Found at i:73097 original size:17 final size:17
Alignment explanation
Indices: 73070--73139 Score: 88
Period size: 17 Copynumber: 4.2 Consensus size: 17
73060 ATTCGACATT
73070 ATTT-AAATAAATTTAA
1 ATTTAAAATAAATTTAA
**
73086 ATTTCCAATAAATTTAA
1 ATTTAAAATAAATTTAA
**
73103 ATTTAAAATAAACATAA
1 ATTTAAAATAAATTTAA
*
73120 TTTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
73137 ATT
1 ATT
73140 ATGTTAGGCC
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
16 4 0.09
17 40 0.91
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:73634 original size:49 final size:47
Alignment explanation
Indices: 73527--74001 Score: 360
Period size: 49 Copynumber: 9.7 Consensus size: 47
73517 ATGGTACTAA
* * * * * *
73527 ATTCGCCGTTGCGGCTTAAA-TTTTCCTTTCATGTTTTTGAGGTATAAG
1 ATTCGCCATTGCGACTTAAACCTTTCCCTTCATG-TCTTAAGGTAT-AG
* ** * *
73575 CTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTAATGATACTGG
1 ATTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTAA-GGTA-TAG
* * ** * *
73624 ATTCACCATTGCGGCTTAAGTCTTTCCCTTCTTGTCTCTAAGGTATAA
1 ATTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCT-TAAGGTATAG
* * * * *
73672 AGTTTGTCATTACGACTTAAACCTTTCCCTTCGTGTCTTCATGGTACTAG
1 A-TTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTT-AAGGTA-TAG
* * * * *
73722 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGCTATAAG
1 ATTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCT-TAAGGTAT-AG
* * *
73771 GTTCGCCATTGCGACTTAAACCTTTCCCTTCGTGTCTTCATGGTACTAG
1 ATTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTT-AAGGTA-TAG
* * * * * *
73820 ATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAA
1 ATTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCT-TAAGGTATAG
** * * * *
73868 AGTTCATCATTGCGACTTAAACTTTTCCCTTCATTTCTTCATGGTACTGG
1 A-TTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTT-AAGGTA-TAG
* *
73918 ATTCGCCATTGCGGCTTAAATCTTTCCCTTCATG-CTTCCAAGGTATAGG
1 ATTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTT--AAGGTATA-G
*
73967 GTTCGCCATTGCGACTTAAACCTTTCCCTTCATGT
1 ATTCGCCATTGCGACTTAAACCTTTCCCTTCATGT
74002 TTCGCGGTAC
Statistics
Matches: 330, Mismatches: 79, Indels: 34
0.74 0.18 0.08
Matches are distributed among these distances:
48 34 0.10
49 284 0.86
50 12 0.04
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (47 bp):
ATTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTAAGGTATAG
Found at i:73999 original size:98 final size:98
Alignment explanation
Indices: 73516--73997 Score: 662
Period size: 98 Copynumber: 4.9 Consensus size: 98
73506 CTTCAATCCG
* * * * *
73516 CATGGTACTAAATTCGCCGTTGCGGCTTAAAT-TTTCCTTTCATGTTTTTGAGGTATAAGCTTCG
1 CATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCG
*
73580 CCATTGCGACTTAAACCTTTCCCTTTGTGTCTT
66 CCATTGCGACTTAAACCTTTCCCTTCGTGTCTT
* * * * * * * * * *
73613 AATGATACTGGATTCACCATTGCGGCTTAAGTCTTTCCCTTCTTGTCTCTAAGGTATAAAGTTTG
1 CATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCG
* *
73678 TCATTACGACTTAAACCTTTCCCTTCGTGTCTT
66 CCATTGCGACTTAAACCTTTCCCTTCGTGTCTT
*
73711 CATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGCTATAAGGTTCG
1 CATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCG
73776 CCATTGCGACTTAAACCTTTCCCTTCGTGTCTT
66 CCATTGCGACTTAAACCTTTCCCTTCGTGTCTT
* * *
73809 CATGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAAGTTCA
1 CATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCG
* * * *
73874 TCATTGCGACTTAAACTTTTCCCTTCATTTCTT
66 CCATTGCGACTTAAACCTTTCCCTTCGTGTCTT
* * ** *
73907 CATGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATG-CTTCCAAGGTATAGGGTTC
1 CATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTATAAGGTTC
73971 GCCATTGCGACTTAAACCTTTCCCTTC
65 GCCATTGCGACTTAAACCTTTCCCTTC
73998 ATGTTTCGCG
Statistics
Matches: 334, Mismatches: 49, Indels: 3
0.87 0.13 0.01
Matches are distributed among these distances:
97 26 0.08
98 308 0.92
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (98 bp):
CATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCG
CCATTGCGACTTAAACCTTTCCCTTCGTGTCTT
Found at i:79770 original size:15 final size:16
Alignment explanation
Indices: 79745--79774 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
79735 GTAACAAGGT
79745 TTACATCTTCTTTGGA
1 TTACATCTTCTTTGGA
79761 TTAC-TCTTCTTTGG
1 TTACATCTTCTTTGG
79775 GCGTTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.13, C:0.20, G:0.13, T:0.53
Consensus pattern (16 bp):
TTACATCTTCTTTGGA
Found at i:84698 original size:39 final size:39
Alignment explanation
Indices: 84655--85321 Score: 201
Period size: 39 Copynumber: 17.2 Consensus size: 39
84645 AACGACTGCA
* *
84655 ATCTGCCCTAGGCTCGAGGTAAGAGATTGGTTGATGATG
1 ATCTGCCCTAAGCTCGAGGTAAGAGATTGGCTGATGATG
* * * *
84694 ATCTGCCCT-AGACTCGGGGTAAGAGA-T--CAGAAGGCTG
1 ATCTGCCCTAAG-CTCGAGGTAAGAGATTGGCTG-ATGATG
* * * *
84731 CAATCTACCCTAAGCTCGAGGTAAAAGATTGGTTGATGGTG
1 --ATCTGCCCTAAGCTCGAGGTAAGAGATTGGCTGATGATG
* * * * *
84772 ATCTG-CCTCAAGATCGAGGTAAGAGATTAGACGGTTG-TA
1 ATCTGCCCT-AAGCTCGAGGTAAGAGATT-GGCTGATGATG
*
84811 ATCTGCCCTAAGCTCGGGGTAAGAGATTGGCTGATGATG
1 ATCTGCCCTAAGCTCGAGGTAAGAGATTGGCTGATGATG
* * * * ** **
84850 GTTTGCCCTAGGCT--ATGGATAAGAGATCGAATGACT-ACA
1 ATCTGCCCTAAGCTCGA-GG-TAAGAGATTGGCTGA-TGATG
* *
84889 ATCTGCCCTAAGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCTAAGCTCGAGGTAAGAGATTGGCTGATGATG
* * * * ** **
84928 ATCTGCCCTAAGCTTGGGGAAAGAGATCGAATGA-GTACA
1 ATCTGCCCTAAGCTCGAGGTAAGAGATTGGCTGATG-ATG
* * * *
84967 ATCTGCCCCAAGCTC-AGGGTAGGAGATTGGCTTATGGTG
1 ATCTGCCCTAAGCTCGA-GGTAAGAGATTGGCTGATGATG
* * * * * * **
85006 ATCTACCCCAAGCTTG-GGTAAAAGATCGGGC-GATTACA
1 ATCTGCCCTAAGCTCGAGGTAAGAGAT-TGGCTGATGATG
* * * * * * *
85044 ATTTACCCCAAGCTCGGGGTAAGAGATCGAAC-GATTG-TA
1 ATCTGCCCTAAGCTCGAGGTAAGAGATTG-GCTGA-TGATG
* * ** *
85083 ATCTGCCCCAAGCTC-AGGGTAAGAGATCGAATG--GTTG
1 ATCTGCCCTAAGCTCGA-GGTAAGAGATTGGCTGATGATG
* * * *
85120 CAATCTGCCCCAGGCTC--GGTAAGAGATTGACTGATGGTG
1 --ATCTGCCCTAAGCTCGAGGTAAGAGATTGGCTGATGATG
* * * * ** *
85159 ATCTGCACC-AAACTCGAGCTAAAAGATCGAATGATTG-TA
1 ATCTGC-CCTAAGCTCGAGGTAAGAGATTGGCTGA-TGATG
* * * *
85198 ATCT-ACCTCAAGCTCGGGGTAAGAGATTAGCTGATGGTG
1 ATCTGCCCT-AAGCTCGAGGTAAGAGATTGGCTGATGATG
* * * * * ** ** **
85237 ATCTACCCCAAACTCGGGGTAAGAGATCGAATGACAACA
1 ATCTGCCCTAAGCTCGAGGTAAGAGATTGGCTGATGATG
* * * *
85276 ATCTGCTCTAGGCTCGAGGTAAGAGATTGGTTGATGGTG
1 ATCTGCCCTAAGCTCGAGGTAAGAGATTGGCTGATGATG
85315 ATCTGCC
1 ATCTGCC
85322 TCAGGCTCAG
Statistics
Matches: 451, Mismatches: 136, Indels: 82
0.67 0.20 0.12
Matches are distributed among these distances:
36 2 0.00
37 31 0.07
38 44 0.10
39 350 0.78
40 19 0.04
41 4 0.01
42 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (39 bp):
ATCTGCCCTAAGCTCGAGGTAAGAGATTGGCTGATGATG
Found at i:84710 original size:78 final size:78
Alignment explanation
Indices: 84621--85425 Score: 689
Period size: 78 Copynumber: 10.4 Consensus size: 78
84611 CTGCAATTTA
* * * * *
84621 CCCCAGGCTCGGGGTAAGAGATCGAACGACTGCAATCTGCCCTAGGCTCGAGGTAAGAGATTGGT
1 CCCCAGACTCGGGGTAAGAGATCGAATGACTGCAATCTGCCCTAAGCTCGGGGTAAGAGATTGGC
*
84686 TGATGATGATCTG
66 TGATGGTGATCTG
* * * * *
84699 CCCTAGACTCGGGGTAAGAGATCAGAA-GGCTGCAATCTACCCTAAGCTCGAGGTAAAAGATTGG
1 CCCCAGACTCGGGGTAAGAGATC-GAATGACTGCAATCTGCCCTAAGCTCGGGGTAAGAGATTGG
*
84763 TTGATGGTGATCTG
65 CTGATGGTGATCTG
* * * * ** *
84777 CCTCAAGA-TCGAGGTAAGAGAT-TAGACGGTTGTAATCTGCCCTAAGCTCGGGGTAAGAGATTG
1 CC-CCAGACTCGGGGTAAGAGATCGA-ATGACTGCAATCTGCCCTAAGCTCGGGGTAAGAGATTG
* * *
84840 GCTGATGATGGTTTG
64 GCTGATGGTGATCTG
* * ** * *
84855 CCCTAGGCTATGGATAAGAGATCGAATGACTACAATCTGCCCTAAGCTCGGGGTAAGAGATTGGC
1 CCCCAGACTCGGGGTAAGAGATCGAATGACTGCAATCTGCCCTAAGCTCGGGGTAAGAGATTGGC
84920 TGATGGTGATCTG
66 TGATGGTGATCTG
* * * * * * * *
84933 CCCTA-AGCTTGGGGAAAGAGATCGAATGAGTACAATCTGCCCCAAGCTCAGGGTAGGAGATTGG
1 CCCCAGA-CTCGGGGTAAGAGATCGAATGACTGCAATCTGCCCTAAGCTCGGGGTAAGAGATTGG
* *
84997 CTTATGGTGATCTA
65 CTGATGGTGATCTG
* * *** * * * * * *
85011 CCCCA-AGCT-TGGGTAAAAGATCGGGCGATTACAATTTACCCCAAGCTCGGGGTAAGAGATCGA
1 CCCCAGA-CTCGGGGTAAGAGATCGAATGACTGCAATCTGCCCTAAGCTCGGGGTAAGAGATTG-
* * *
85074 AC-GATTGTAATCTG
64 GCTGATGGTGATCTG
* ** * * *
85088 CCCCA-AGCTCAGGGTAAGAGATCGAATGGTTGCAATCTGCCCCAGGCTC--GGTAAGAGATTGA
1 CCCCAGA-CTCGGGGTAAGAGATCGAATGACTGCAATCTGCCCTAAGCTCGGGGTAAGAGATTGG
85150 CTGATGGTGATCTG
65 CTGATGGTGATCTG
* * * * * * * * *
85164 CACCAAACTCGAGCTAAAAGATCGAATGATTGTAATCT-ACCTCAAGCTCGGGGTAAGAGATTAG
1 CCCCAGACTCGGGGTAAGAGATCGAATGACTGCAATCTGCCCT-AAGCTCGGGGTAAGAGATTGG
*
85228 CTGATGGTGATCTA
65 CTGATGGTGATCTG
* ** * * * *
85242 CCCCAAACTCGGGGTAAGAGATCGAATGACAACAATCTGCTCTAGGCTCGAGGTAAGAGATTGGT
1 CCCCAGACTCGGGGTAAGAGATCGAATGACTGCAATCTGCCCTAAGCTCGGGGTAAGAGATTGGC
85307 TGATGGTGATCTG
66 TGATGGTGATCTG
* * * * * * *
85320 CCTCAGGCTCAGGGTAAGAGATCGAATGGCTGCAATCT-ACCTCATGCTTGGGGTAAGAGATTGG
1 CCCCAGACTCGGGGTAAGAGATCGAATGACTGCAATCTGCCCT-AAGCTCGGGGTAAGAGATTGG
*
85384 CTAATGGTGATCTG
65 CTGATGGTGATCTG
*
85398 CCCCAGACTCGGGGTAAAAGATCGAATG
1 CCCCAGACTCGGGGTAAGAGATCGAATG
85426 GTTGCCCTTC
Statistics
Matches: 589, Mismatches: 122, Indels: 32
0.79 0.16 0.04
Matches are distributed among these distances:
75 4 0.01
76 56 0.10
77 65 0.11
78 454 0.77
79 10 0.02
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (78 bp):
CCCCAGACTCGGGGTAAGAGATCGAATGACTGCAATCTGCCCTAAGCTCGGGGTAAGAGATTGGC
TGATGGTGATCTG
Found at i:84776 original size:117 final size:117
Alignment explanation
Indices: 84558--84799 Score: 272
Period size: 117 Copynumber: 2.1 Consensus size: 117
84548 AATATCACAC
* * * *
84558 AAGAGATTGACTGATGGTGATCTGCCCTAGATTCGGGATAAAAGATCAGACGGCTGCAATTTACC
1 AAGAGATTGACTGATGATGATCTGCCCTAGACTCGGGATAAAAGATCAGAAGGCTGCAATCTACC
* * * * *
84623 CCAGGCTCGGGGTAAGAGATCGAACGACTGCAATCTGCC-CTAGGCTCGAGGT
66 CCAAGCTCGAGGTAAAAGATCGAACGACTGCAATCTGCCTC-AAGATCGAGGT
** * *
84675 AAGAGATTGGTTGATGATGATCTGCCCTAGACTCGGGGTAAGAGATCAGAAGGCTGCAATCTACC
1 AAGAGATTGACTGATGATGATCTGCCCTAGACTCGGGATAAAAGATCAGAAGGCTGCAATCTACC
* * *** **
84740 CTAAGCTCGAGGTAAAAGATTGGTTGA-TGGTGATCTGCCTCAAGATCGAGGT
66 CCAAGCTCGAGGTAAAAGATCGAACGACT-GCAATCTGCCTCAAGATCGAGGT
84792 AAGAGATT
1 AAGAGATT
84800 AGACGGTTGT
Statistics
Matches: 103, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
116 1 0.01
117 101 0.98
118 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (117 bp):
AAGAGATTGACTGATGATGATCTGCCCTAGACTCGGGATAAAAGATCAGAAGGCTGCAATCTACC
CCAAGCTCGAGGTAAAAGATCGAACGACTGCAATCTGCCTCAAGATCGAGGT
Found at i:85328 original size:39 final size:39
Alignment explanation
Indices: 84655--85419 Score: 176
Period size: 39 Copynumber: 19.7 Consensus size: 39
84645 AACGACTGCA
* * *
84655 ATCTGCC-CTAGGCTCGAGGTAAGAGATTGGTTGATGATG
1 ATCTGCCTC-AGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * *
84694 ATCTGCC-CTAGACTCGGGGTAAGAGA-T--CAGAAGGCTG
1 ATCTGCCTC-AGGCTCGGGGTAAGAGATTGGCTGATGG-TG
* * * * *
84731 CAATCTACC-CTAAGCTCGAGGTAAAAGATTGGTTGATGGTG
1 --ATCTGCCTC-AGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * * * *
84772 ATCTGCCTCAAGATCGAGGTAAGAGATTAGAC-GGTTGTA
1 ATCTGCCTCAGGCTCGGGGTAAGAGATT-GGCTGATGGTG
* *
84811 ATCTGCC-CTAAGCTCGGGGTAAGAGATTGGCTGATGATG
1 ATCTGCCTC-AGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * ** * * ** ***
84850 GTTTGCC-CTAGGCTATGGATAAGAGATCGAATGACT-ACA
1 ATCTGCCTC-AGGCTCGGGGTAAGAGATTGGCTGA-TGGTG
*
84889 ATCTGCC-CTAAGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCTC-AGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * ** *
84928 ATCTGCC-CTAAGCTTGGGGAAAGAGATCGAATGA--GTACA
1 ATCTGCCTC-AGGCTCGGGGTAAGAGATTGGCTGATGGT--G
* * * * *
84967 ATCTGCCCCAAGCTCAGGGTAGGAGATTGGCTTATGGTG
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * * * ****
85006 ATCTACCCCAAGCT-TGGGTAAAAGATCGGGC-GATTACA
1 ATCTGCCTCAGGCTCGGGGTAAGAGAT-TGGCTGATGGTG
* * * * * * * *
85044 ATTTACCCCAAGCTCGGGGTAAGAGATCGAAC-GATTGTA
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTG-GCTGATGGTG
* * * * ** * * **
85083 ATCTGCCCCAAGCTCAGGGTAAGAGATCGAATGGTTGCA
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* *
85122 ATCTGCCCCAGGCTC--GGTAAGAGATTGACTGATGGTG
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
** * * * * ** * *
85159 ATCTGCAC-CAAACTCGAGCTAAAAGATCGAATGATTGTA
1 ATCTGC-CTCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * *
85198 ATCTACCTCAAGCTCGGGGTAAGAGATTAGCTGATGGTG
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * ** * ** *****
85237 ATCTACCCCAAACTCGGGGTAAGAGATCGAATGACAACA
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* *
85276 ATCTG-CTCTAGGCTCGAGGTAAGAGATTGGTTGATGGTG
1 ATCTGCCTC-AGGCTCGGGGTAAGAGATTGGCTGATGGTG
*
85315 ATCTGCCTCAGGCTCAGGGTAAGAGA-T--C-GAATGGCTG
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTGGCTG-ATGG-TG
* * * *
85352 CAATCTACCTCATGCTTGGGGTAAGAGATTGGCTAATGGTG
1 --ATCTGCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * *
85393 ATCTGCCCCAGACTCGGGGTAAAAGAT
1 ATCTGCCTCAGGCTCGGGGTAAGAGAT
85420 CGAATGGTTG
Statistics
Matches: 537, Mismatches: 154, Indels: 70
0.71 0.20 0.09
Matches are distributed among these distances:
35 1 0.00
36 7 0.01
37 33 0.06
38 36 0.07
39 436 0.81
40 9 0.02
41 6 0.01
42 9 0.02
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (39 bp):
ATCTGCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
Found at i:96990 original size:14 final size:14
Alignment explanation
Indices: 96958--97009 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
96948 CACGAACAAT
96958 TATACGAATGAATAAA
1 TATACGAA--AATAAA
*
96974 TATACGAAAATAGA
1 TATACGAAAATAAA
*
96988 TATAAGAAAAATAAA
1 TATACG-AAAATAAA
97003 -ATACGAA
1 TATACGAA
97010 TCATGAAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 2 0.06
14 14 0.45
15 7 0.23
16 8 0.26
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (14 bp):
TATACGAAAATAAA
Found at i:97108 original size:29 final size:29
Alignment explanation
Indices: 97032--97195 Score: 116
Period size: 28 Copynumber: 5.6 Consensus size: 29
97022 AGAGAATTTA
* * *
97032 GGGTTAAAATGTAATTTTGGAAAGTTTTAG
1 GGGTAAAAATGTAATTTTAGAAAATTTT-G
*
97062 GGGTAAAAAATGTCATTTTAGAAAATTTTG
1 GGGT-AAAAATGTAATTTTAGAAAATTTTG
* * * *
97092 GGGTAAAAATGTGATTTTTG-GAAGTTTG
1 GGGTAAAAATGTAATTTTAGAAAATTTTG
* * * **
97120 GGGTAAAAATGTAATTATGGAGAAGTTTCA
1 GGGTAAAAATGTAATTTTAGA-AAATTTTG
* * * * **
97150 AGGTAAAAATGT-ATTTTTGGAAGTTCAG
1 GGGTAAAAATGTAATTTTAGAAAATTTTG
97178 GGGTAAAAATGTAATTTT
1 GGGTAAAAATGTAATTTT
97196 TGGAAGTTCG
Statistics
Matches: 106, Mismatches: 24, Indels: 9
0.76 0.17 0.06
Matches are distributed among these distances:
28 39 0.37
29 24 0.23
30 23 0.22
31 20 0.19
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.37
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTAGAAAATTTTG
Found at i:97131 original size:88 final size:86
Alignment explanation
Indices: 97031--97321 Score: 325
Period size: 88 Copynumber: 3.3 Consensus size: 86
97021 CAGAGAATTT
* ** * * * *
97031 AGGGTTAAAATGTAATTTTGGAAAGTTTTAGGGGTAAAAAATGTCATTTTAGAAAATTTTGGGGT
1 AGGGTAAAAATGTAATTTTGGAAAG-TTTAAAGGT-AAAAATGT-ATTTTTGGAAGTTTAGGGGT
*
97096 AAAAATGTGATTTTTGGAAGTTTG
63 AAAAATGTAATTTTTGGAAGTTTG
* * *
97120 -GGGTAAAAATGTAATTATGGAGAAGTTTCAAGGTAAAAATGTATTTTTGGAAGTTCAGGGGTAA
1 AGGGTAAAAATGTAATTTTGGA-AAGTTTAAAGGTAAAAATGTATTTTTGGAAGTTTAGGGGTAA
*
97184 AAATGTAATTTTTGGAAGTTCG
65 AAATGTAATTTTTGGAAGTTTG
* * *
97206 AGGGCAAAAATGTAATTTTTGG-AAGTTCAAAAGGTTAAAATGTGATTTTTGGAAGTTTAGGGGT
1 AGGGTAAAAATGTAA-TTTTGGAAAGTT-TAAAGGTAAAAATGT-ATTTTTGGAAGTTTAGGGGT
* *
97270 AAAAGTGTAATTTTTAGAAGTTTG
63 AAAAATGTAATTTTTGGAAGTTTG
* **
97294 AGGGTCAAAATGTAATTTTTAAAAGTTT
1 AGGGTAAAAATGTAATTTTGGAAAGTTT
97322 GAGAGTCAAA
Statistics
Matches: 170, Mismatches: 26, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
86 42 0.25
87 37 0.22
88 88 0.52
89 3 0.02
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.36
Consensus pattern (86 bp):
AGGGTAAAAATGTAATTTTGGAAAGTTTAAAGGTAAAAATGTATTTTTGGAAGTTTAGGGGTAAA
AATGTAATTTTTGGAAGTTTG
Found at i:97196 original size:29 final size:29
Alignment explanation
Indices: 97032--97313 Score: 243
Period size: 29 Copynumber: 9.7 Consensus size: 29
97022 AGAGAATTTA
* *
97032 GGGTTAAAATGTAA-TTTTGGAAAGTTTTAG
1 GGGTAAAAATGTAATTTTTGG-AAG-TTCAG
* * * * **
97062 GGGTAAAAAATGTCATTTTAGAAAATTTTG
1 GGGT-AAAAATGTAATTTTTGGAAGTTCAG
* *
97092 GGGTAAAAATGTGATTTTTGGAAGTT-TG
1 GGGTAAAAATGTAATTTTTGGAAGTTCAG
* *
97120 GGGTAAAAATGTAATTATGGAGAAGTTTCA-
1 GGGTAAAAATGTAATTTTTG-GAAG-TTCAG
*
97150 AGGTAAAAATGT-ATTTTTGGAAGTTCAG
1 GGGTAAAAATGTAATTTTTGGAAGTTCAG
97178 GGGTAAAAATGTAATTTTTGGAAGTTC-G
1 GGGTAAAAATGTAATTTTTGGAAGTTCAG
* *
97206 AGGGCAAAAATGTAATTTTTGGAAGTTCAAA
1 -GGGTAAAAATGTAATTTTTGGAAGTTC-AG
* * * *
97237 AGGTTAAAATGTGATTTTTGGAAGTTTAG
1 GGGTAAAAATGTAATTTTTGGAAGTTCAG
* * *
97266 GGGTAAAAGTGTAATTTTTAGAAGTT-TG
1 GGGTAAAAATGTAATTTTTGGAAGTTCAG
*
97294 AGGGTCAAAATGTAATTTTT
1 -GGGTAAAAATGTAATTTTT
97314 AAAAGTTTGA
Statistics
Matches: 207, Mismatches: 34, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
27 4 0.02
28 36 0.17
29 106 0.51
30 47 0.23
31 10 0.05
32 4 0.02
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAGTTCAG
Found at i:97314 original size:29 final size:29
Alignment explanation
Indices: 97024--97350 Score: 231
Period size: 29 Copynumber: 11.2 Consensus size: 29
97014 GAAGTTTCAG
*
97024 AGAA-TTT-AGGGTTAAAATGTAA-TTTT
1 AGAAGTTTGAGGGTAAAAATGTAATTTTT
* * *
97050 GGAAAGTTTTAGGGGTAAAAAATGTCA-TTTT
1 AG-AAGTTTGA-GGGT-AAAAATGTAATTTTT
* *
97081 AGAAAATTTTG-GGGTAAAAATGTGATTTTT
1 AG--AAGTTTGAGGGTAAAAATGTAATTTTT
* **
97111 GGAAGTTTG-GGGTAAAAATGTAATTATGG
1 AGAAGTTTGAGGGTAAAAATGTAATT-TTT
* *
97140 AGAAGTTTCAAGGTAAAAATGT-ATTTTT
1 AGAAGTTTGAGGGTAAAAATGTAATTTTT
* *
97168 GGAAG-TTCAGGGGTAAAAATGTAATTTTT
1 AGAAGTTTGA-GGGTAAAAATGTAATTTTT
* * *
97197 GGAAGTTCGAGGGCAAAAATGTAATTTTT
1 AGAAGTTTGAGGGTAAAAATGTAATTTTT
* ** * * *
97226 GGAAGTTCAAAAGGTTAAAATGTGATTTTT
1 AGAAGTT-TGAGGGTAAAAATGTAATTTTT
* *
97256 GGAAGTTT-AGGGGTAAAAGTGTAATTTTT
1 AGAAGTTTGA-GGGTAAAAATGTAATTTTT
*
97285 AGAAGTTTGAGGGTCAAAATGTAATTTTT
1 AGAAGTTTGAGGGTAAAAATGTAATTTTT
* * * * *
97314 AAAAGTTTGAGAGTCAAAATATGATTTTT
1 AGAAGTTTGAGGGTAAAAATGTAATTTTT
97343 AGACAGTT
1 AGA-AGTT
97351 CAGGGACCTT
Statistics
Matches: 244, Mismatches: 41, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
26 1 0.00
27 6 0.02
28 41 0.17
29 123 0.50
30 54 0.22
31 13 0.05
32 6 0.02
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
AGAAGTTTGAGGGTAAAAATGTAATTTTT
Found at i:98280 original size:13 final size:13
Alignment explanation
Indices: 98262--98298 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
98252 TTTCGACTTT
98262 TTATTATTTATTA
1 TTATTATTTATTA
98275 TTATTATTTA-TA
1 TTATTATTTATTA
98287 -T-TTATTTATTA
1 TTATTATTTATTA
98298 T
1 T
98299 AACGCTTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.32
11 3 0.14
12 2 0.09
13 10 0.45
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTATTTATTA
Found at i:112606 original size:14 final size:15
Alignment explanation
Indices: 112578--112616 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
112568 CCCATCCCAT
112578 TTTTTTAAATAATTA
1 TTTTTTAAATAATTA
*
112593 TTTTTTCAAT-ATTA
1 TTTTTTAAATAATTA
112607 TTTTTATAAA
1 TTTTT-TAAA
112617 AAAATTCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTTAAATAATTA
Found at i:113715 original size:30 final size:30
Alignment explanation
Indices: 113680--113739 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
113670 TTTTGTTGAT
113680 AAAATGATTTTGAAATATTAATTTTATATA
1 AAAATGATTTTGAAATATTAATTTTATATA
113710 AAAATGATTTTGAAATATTAATTTTATATA
1 AAAATGATTTTGAAATATTAATTTTATATA
113740 TGATTATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (30 bp):
AAAATGATTTTGAAATATTAATTTTATATA
Found at i:114960 original size:29 final size:29
Alignment explanation
Indices: 114921--115019 Score: 117
Period size: 29 Copynumber: 3.4 Consensus size: 29
114911 GAAATAATAC
* * *
114921 AGATACAGTTACAGATACAATCATGTCAG
1 AGATACAGTTACAAATGCAGTCATGTCAG
* **
114950 AGATACAGTTACAAATGCAGCCAAATCAG
1 AGATACAGTTACAAATGCAGTCATGTCAG
* *
114979 AGATACAGTTACAAATGCAGTTATGTCAC
1 AGATACAGTTACAAATGCAGTCATGTCAG
*
115008 AGATATAGTTAC
1 AGATACAGTTAC
115020 GGATGCAGAC
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (29 bp):
AGATACAGTTACAAATGCAGTCATGTCAG
Found at i:115025 original size:29 final size:29
Alignment explanation
Indices: 114917--115065 Score: 99
Period size: 29 Copynumber: 5.1 Consensus size: 29
114907 TATAGAAATA
* *
114917 ATACAGATACAGTTACAGATACA-ATCATG
1 ATACAGATATAGTTACAGATGCAGA-CATG
* * * * *
114946 -TCAGAGATACAGTTACAAATGCAGCCA-A
1 AT-ACAGATATAGTTACAGATGCAGACATG
* * * **
114974 ATCAGAGATACAGTTACAAATGCAGTTATG
1 AT-ACAGATATAGTTACAGATGCAGACATG
*
115004 -TCACAGATATAGTTACGGATGCAGACATG
1 AT-ACAGATATAGTTACAGATGCAGACATG
* *
115033 ATATAGATATAGTTACAGATGTAGACATG
1 ATACAGATATAGTTACAGATGCAGACATG
115062 ATAC
1 ATAC
115066 CACCATCCGT
Statistics
Matches: 97, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
28 1 0.01
29 95 0.98
30 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (29 bp):
ATACAGATATAGTTACAGATGCAGACATG
Found at i:115041 original size:58 final size:58
Alignment explanation
Indices: 114921--115030 Score: 139
Period size: 58 Copynumber: 1.9 Consensus size: 58
114911 GAAATAATAC
* * *
114921 AGATACAGTTACAGATACAATCATGTCAGAGATACAGTTACAAATGCAGCCAAATCAG
1 AGATACAGTTACAAATACAATCATGTCACAGATACAGTTACAAATGCAGACAAATCAG
* * * * **
114979 AGATACAGTTACAAATGCAGTTATGTCACAGATATAGTTACGGATGCAGACA
1 AGATACAGTTACAAATACAATCATGTCACAGATACAGTTACAAATGCAGACA
115031 TGATATAGAT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
58 43 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (58 bp):
AGATACAGTTACAAATACAATCATGTCACAGATACAGTTACAAATGCAGACAAATCAG
Found at i:115791 original size:19 final size:19
Alignment explanation
Indices: 115767--115806 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
115757 AAACAATATA
115767 CACACACACCCTCGTGTGC
1 CACACACACCCTCGTGTGC
*
115786 CACACATACCCTCGTGTGC
1 CACACACACCCTCGTGTGC
115805 CA
1 CA
115807 GCTCGTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.15, T:0.17
Consensus pattern (19 bp):
CACACACACCCTCGTGTGC
Found at i:120487 original size:24 final size:24
Alignment explanation
Indices: 120442--120490 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
120432 AAATAAATTA
*
120442 TGTTTATTTATTTCAATTAAACTC
1 TGTTTATTTATTTCAATCAAACTC
* * *
120466 TGTTTATTTGTTTGAGTCAAACTC
1 TGTTTATTTATTTCAATCAAACTC
120490 T
1 T
120491 TATTAGTCTA
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:0.24, C:0.12, G:0.10, T:0.53
Consensus pattern (24 bp):
TGTTTATTTATTTCAATCAAACTC
Found at i:122447 original size:24 final size:24
Alignment explanation
Indices: 122420--122487 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
122410 ATCTTTTAGT
* *
122420 TAAACTTTATTTAATTGTTTCAAA
1 TAAACTCTATTTATTTGTTTCAAA
*
122444 TAAACTCTATTTATTTGTTTCAAT
1 TAAACTCTATTTATTTGTTTCAAA
*
122468 TAAACTCTGTTTATTTGTTT
1 TAAACTCTATTTATTTGTTT
122488 GTGTCAAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.54
Consensus pattern (24 bp):
TAAACTCTATTTATTTGTTTCAAA
Found at i:122482 original size:28 final size:26
Alignment explanation
Indices: 122424--122495 Score: 76
Period size: 24 Copynumber: 2.8 Consensus size: 26
122414 TTTAGTTAAA
*
122424 CTTTATTTAATTGTTTCAAATAAACT
1 CTTTATTTATTTGTTTCAAATAAACT
*
122450 C--TATTTATTTGTTTCAATTAAACT
1 CTTTATTTATTTGTTTCAAATAAACT
* *
122474 CTGTTTATTTGTTTGTGTCAAA
1 C--TTTATTTATTTGTTTCAAA
122496 CTTTTATTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
24 22 0.59
26 1 0.03
28 14 0.38
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (26 bp):
CTTTATTTATTTGTTTCAAATAAACT
Found at i:125871 original size:5 final size:5
Alignment explanation
Indices: 125861--125885 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
125851 CTTCATTAGA
125861 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
125886 GTTCAATCTT
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:126713 original size:45 final size:45
Alignment explanation
Indices: 126664--126755 Score: 141
Period size: 45 Copynumber: 2.0 Consensus size: 45
126654 TGTTATCATT
*
126664 AATTCATTTTCTTTT-ATTTTCCACACTAATTATATCCTACATGGC
1 AATTCATTCTCTTTTAATTTT-CACACTAATTATATCCTACATGGC
* *
126709 AATTCATTCTCTTTTAATTTTCATATTAATTATATCCTACATGGC
1 AATTCATTCTCTTTTAATTTTCACACTAATTATATCCTACATGGC
126754 AA
1 AA
126756 AGTAACATCC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 38 0.88
46 5 0.12
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (45 bp):
AATTCATTCTCTTTTAATTTTCACACTAATTATATCCTACATGGC
Found at i:126879 original size:16 final size:18
Alignment explanation
Indices: 126844--126881 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
126834 AACATTAATA
126844 TAATTTTATAATTAAAATG
1 TAATTTTAT-ATTAAAATG
126863 TAATTTTAT-TT-AAATG
1 TAATTTTATATTAAAATG
126879 TAA
1 TAA
126882 AACACAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 2 0.11
19 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TAATTTTATATTAAAATG
Found at i:129936 original size:7 final size:8
Alignment explanation
Indices: 129924--129971 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
129914 AAAAAAATTA
129924 TTTTT-AT
1 TTTTTAAT
129931 TTTTT-AT
1 TTTTTAAT
129938 TTTTTAAT
1 TTTTTAAT
129946 TTTTTAAT
1 TTTTTAAT
*
129954 TTTTGTTAT
1 TTTT-TAAT
129963 TTTTCTAAT
1 TTTT-TAAT
129972 CATCTTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
7 12 0.33
8 14 0.39
9 10 0.28
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTTTAAT
Found at i:129947 original size:15 final size:15
Alignment explanation
Indices: 129924--129971 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 15
129914 AAAAAAATTA
129924 TTTTTATTTTTT-AT
1 TTTTTATTTTTTAAT
129938 TTTTTAATTTTTTAATT
1 TTTTT-ATTTTTTAA-T
129955 TTTGTTATTTTTCTAAT
1 TTT-TTATTTTT-TAAT
129972 CATCTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.17
15 7 0.24
16 1 0.03
17 11 0.38
18 5 0.17
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTTTATTTTTTAAT
Found at i:129971 original size:18 final size:16
Alignment explanation
Indices: 129919--129971 Score: 63
Period size: 15 Copynumber: 3.2 Consensus size: 16
129909 TTTATAAAAA
129919 AATTATTTTTATTTTTT
1 AATT-TTTTTATTTTTT
*
129936 -ATTTTTTAATTTTTT
1 AATTTTTTTATTTTTT
129951 AATTTTTGTTATTTTTCT
1 AATTTTT-TTATTTTT-T
129969 AAT
1 AAT
129972 CATCTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 11 0.35
16 9 0.29
17 7 0.23
18 4 0.13
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (16 bp):
AATTTTTTTATTTTTT
Found at i:130438 original size:25 final size:25
Alignment explanation
Indices: 130396--130444 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
130386 ATATATCAAT
* *
130396 TTATTTTTATATTAAATAAATATAA
1 TTATTTATATATGAAATAAATATAA
* *
130421 TTATTTATATATGCAATATATATA
1 TTATTTATATATGAAATAAATATA
130445 CATAAAATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (25 bp):
TTATTTATATATGAAATAAATATAA
Found at i:150578 original size:12 final size:12
Alignment explanation
Indices: 150564--150629 Score: 80
Period size: 12 Copynumber: 5.6 Consensus size: 12
150554 CCAAACAATC
*
150564 AAAATAACAACC
1 AAAATAACAACA
*
150576 AAAATAGCAACA
1 AAAATAACAACA
**
150588 AAAATAAC-AGT
1 AAAATAACAACA
150599 AAAATAACAACA
1 AAAATAACAACA
*
150611 AAAATAACAATA
1 AAAATAACAACA
150623 AAAATAA
1 AAAATAA
150630 TACAAAAACA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
11 9 0.20
12 36 0.80
ACGTcount: A:0.71, C:0.14, G:0.03, T:0.12
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:150637 original size:23 final size:23
Alignment explanation
Indices: 150564--150625 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
150554 CCAAACAATC
* *
150564 AAAATAACAACCAAAATAGCAACA
1 AAAATAACAA-TAAAATAACAACA
*
150588 AAAATAACAGTAAAATAACAACA
1 AAAATAACAATAAAATAACAACA
150611 AAAATAACAATAAAA
1 AAAATAACAATAAAA
150626 ATAATACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 25 0.74
24 9 0.26
ACGTcount: A:0.71, C:0.15, G:0.03, T:0.11
Consensus pattern (23 bp):
AAAATAACAATAAAATAACAACA
Found at i:150648 original size:23 final size:24
Alignment explanation
Indices: 150576--150649 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 24
150566 AATAACAACC
* * **
150576 AAAATAGCAACAAAAATAAC-AGT
1 AAAATAACAACAAAAACAACAAAA
* *
150599 AAAATAACAACAAAAATAACAATA
1 AAAATAACAACAAAAACAACAAAA
* *
150623 AAAATAA-TACAAAAACAATAAAA
1 AAAATAACAACAAAAACAACAAAA
150646 AAAA
1 AAAA
150650 CCAAAACAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 35 0.81
24 8 0.19
ACGTcount: A:0.74, C:0.11, G:0.03, T:0.12
Consensus pattern (24 bp):
AAAATAACAACAAAAACAACAAAA
Found at i:150657 original size:18 final size:18
Alignment explanation
Indices: 150616--150685 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
150606 CAACAAAAAT
*
150616 AACAATAAAAATAATACAAA
1 AACAATAAAAA-AA-ACCAA
150636 AACAATAAAAAAAACCAA
1 AACAATAAAAAAAACCAA
*
150654 AACAGTAAAAAAAACCAA
1 AACAATAAAAAAAACCAA
* *
150672 AATAGTAAAAAAAA
1 AACAATAAAAAAAA
150686 AAATAGGCAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
18 34 0.72
19 2 0.04
20 11 0.23
ACGTcount: A:0.76, C:0.11, G:0.03, T:0.10
Consensus pattern (18 bp):
AACAATAAAAAAAACCAA
Found at i:152189 original size:22 final size:21
Alignment explanation
Indices: 152141--152189 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
152131 TTAGTAAAAC
* * *
152141 AAAAATAATATTTATTTTAAT
1 AAAAACAATATTTATTCTAAG
152162 AGAAAACAATATTCTATTCTAAG
1 A-AAAACAATATT-TATTCTAAG
152185 AAAAA
1 AAAAA
152190 TGGGATGGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 14 0.61
23 8 0.35
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (21 bp):
AAAAACAATATTTATTCTAAG
Found at i:155196 original size:26 final size:27
Alignment explanation
Indices: 155152--155231 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 27
155142 TTTGTTGCGC
* *
155152 ACTCT-AAAAGAATTGCCTTCGTGACA
1 ACTCTGAAAAGAACTACCTTCGTGACA
** * *
155178 ACTCTGAAAAGAA-TACCTTTATGGCGC
1 ACTCTGAAAAGAACTACCTTCGTGAC-A
*
155205 ACTCTG-AAAGAACGACCTTCGTGACA
1 ACTCTGAAAAGAACTACCTTCGTGACA
155231 A
1 A
155232 ATTTTGAATG
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
26 20 0.49
27 21 0.51
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (27 bp):
ACTCTGAAAAGAACTACCTTCGTGACA
Found at i:160588 original size:30 final size:29
Alignment explanation
Indices: 160554--160623 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
160544 TCAACCATTC
* * *
160554 AAAAATTTAAATGGAGTGAAAATTTTGATA
1 AAAAATTTAAATGAAGTGAAAAGTTTCA-A
* *
160584 AAAAA-TAAAATTAAGTGAAAAGTTTCAA
1 AAAAATTTAAATGAAGTGAAAAGTTTCAA
*
160612 TAAAATTTAAAT
1 AAAAATTTAAAT
160624 ATAATGGCTC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
28 5 0.16
29 22 0.69
30 5 0.16
ACGTcount: A:0.56, C:0.01, G:0.11, T:0.31
Consensus pattern (29 bp):
AAAAATTTAAATGAAGTGAAAAGTTTCAA
Found at i:160819 original size:15 final size:15
Alignment explanation
Indices: 160781--160829 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 15
160771 ACAAATTTAG
*
160781 AATTTAATTTTT-AT
1 AATTTAATTTTTAAA
* *
160795 ATTTTTATTTTTAAA
1 AATTTAATTTTTAAA
160810 AATTTAA-TTTTAAA
1 AATTTAATTTTTAAA
160824 AATTTA
1 AATTTA
160830 GTTAAATTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 23 0.79
15 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTTAATTTTTAAA
Found at i:164803 original size:140 final size:136
Alignment explanation
Indices: 164512--164821 Score: 320
Period size: 140 Copynumber: 2.2 Consensus size: 136
164502 CTGACTAAAT
** * *
164512 TAAGAACAACAACTATTTAGAGTGACTAACGTGAAAATGTAAATTAACTTTTCGTTACCATTTAA
1 TAAGAACAACCCCTATTTAGAGTGACTAACGTGAAAATGTAAATTAACATTCCGTTACCATTTAA
* * * * *
164577 TGACGGAGTGATCAATTTGATCAATTTTTTAAATGACCAAATTAATAACAAAAAAATTTATAGTG
66 TGACGAAGTGACCAATCTGATCAATTTTTTAAATAACCAAATT-ATAACAAAAAAATTTAGAGTG
164642 ATCAAAA
130 ATCAAAA
** * ** * *
164649 TAAGAATGACCCCTATTTAGAGTGACTAATGTGAAAATGTATTGTTAGCATTCCGTTACTATTTA
1 TAAGAACAACCCCTATTTAGAGTGACTAACGTGAAAATGTA-AATTAACATTCCGTTACCATTTA
* * * *
164714 ATGATGAAGTGACCAATCTGATCAAATTTTTTTTGGGAATAATC-AATT-TAACAAAAAAATTTG
65 ATGACGAAGTGACCAATCTGATC-AA--TTTTTT--AAATAACCAAATTATAACAAAAAAATTTA
164777 GAGTGA-CTAAAA
125 GAGTGATC-AAAA
* * *
164789 TAAGAGCAATCCCTATTTAGAGTGAGTAACGTG
1 TAAGAACAACCCCTATTTAGAGTGACTAACGTG
164822 TCCACATTCC
Statistics
Matches: 140, Mismatches: 26, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
137 36 0.26
138 36 0.26
139 3 0.02
140 50 0.36
141 6 0.04
142 4 0.03
143 5 0.04
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (136 bp):
TAAGAACAACCCCTATTTAGAGTGACTAACGTGAAAATGTAAATTAACATTCCGTTACCATTTAA
TGACGAAGTGACCAATCTGATCAATTTTTTAAATAACCAAATTATAACAAAAAAATTTAGAGTGA
TCAAAA
Found at i:167036 original size:26 final size:26
Alignment explanation
Indices: 167006--167057 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
166996 TTATAATTAT
167006 GTAAATATTATT-AAAATAAAATAATA
1 GTAAA-ATTATTGAAAATAAAATAATA
* *
167032 GTAAAATTATTGAATATCAAATAATA
1 GTAAAATTATTGAAAATAAAATAATA
167058 ATAATTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (26 bp):
GTAAAATTATTGAAAATAAAATAATA
Found at i:168432 original size:19 final size:19
Alignment explanation
Indices: 168410--168447 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
168400 ACAATAAAAC
*
168410 AATTGCAACATAATAGTGA
1 AATTGCAACAAAATAGTGA
*
168429 AATTGTAACAAAATAGTGA
1 AATTGCAACAAAATAGTGA
168448 GAAAATAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (19 bp):
AATTGCAACAAAATAGTGA
Found at i:168828 original size:22 final size:24
Alignment explanation
Indices: 168800--168843 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
168790 ATTTCTTATT
168800 TATATAATATAT-TCTT-TATATG
1 TATATAATATATATCTTATATATG
*
168822 TATATAATTTATATCTTATATA
1 TATATAATATATATCTTATATA
168844 ATAAGATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 4 0.21
24 4 0.21
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (24 bp):
TATATAATATATATCTTATATATG
Found at i:169926 original size:6 final size:6
Alignment explanation
Indices: 169917--169963 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
169907 GATTAGAACC
* *
169917 CAAGAA CAAGAA CAAGAA -ATGGGA -AAGAA CAAGAA CAAGAA CAAGAA
1 CAAGAA CAAGAA CAAGAA CA-AGAA CAAGAA CAAGAA CAAGAA CAAGAA
169964 ATCTTCAGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 3 0.09
6 32 0.91
ACGTcount: A:0.64, C:0.13, G:0.21, T:0.02
Consensus pattern (6 bp):
CAAGAA
Found at i:171077 original size:28 final size:25
Alignment explanation
Indices: 171029--171083 Score: 65
Period size: 28 Copynumber: 2.1 Consensus size: 25
171019 AAATTTAAAA
*
171029 TTTCAAAATTGAAAAAAAATATAAT
1 TTTCAAAATTGAAAAAAAATACAAT
*
171054 TTTCAGAAATGTGATAAACAAATACAAT
1 TTTCA-AAAT-TGA-AAAAAAATACAAT
171082 TT
1 TT
171084 GACAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.20
26 4 0.16
27 3 0.12
28 13 0.52
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (25 bp):
TTTCAAAATTGAAAAAAAATACAAT
Found at i:182477 original size:6 final size:6
Alignment explanation
Indices: 182467--182499 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
182457 CGCCCCTCCA
*
182467 AAAAAA AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
182500 GATCGTTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:183553 original size:3 final size:3
Alignment explanation
Indices: 183545--183581 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
183535 ACAATATATG
*
183545 TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
183582 GCCTGAAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:196486 original size:17 final size:17
Alignment explanation
Indices: 196464--196497 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
196454 TGTCGGATAT
196464 GCATATG-CTAAGAAAAA
1 GCATATGTC-AAGAAAAA
196481 GCATATGTCAAGAAAAA
1 GCATATGTCAAGAAAAA
196498 TTATTGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (17 bp):
GCATATGTCAAGAAAAA
Found at i:204674 original size:17 final size:18
Alignment explanation
Indices: 204652--204687 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
204642 TAAATTAGTT
204652 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
204669 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
204687 A
1 A
204688 TAGAAGTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:212943 original size:8 final size:8
Alignment explanation
Indices: 212930--212972 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
212920 CAAATAAATT
212930 ATTATAAA
1 ATTATAAA
212938 ATTATAAA
1 ATTATAAA
* *
212946 AATAAAAA
1 ATTATAAA
212954 TATTA-AAA
1 -ATTATAAA
212962 ATTATAAA
1 ATTATAAA
212970 ATT
1 ATT
212973 TAATTTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
7 4 0.13
8 23 0.77
9 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
ATTATAAA
Found at i:212948 original size:24 final size:24
Alignment explanation
Indices: 212921--212970 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
212911 AATTCAAATC
*
212921 AAAT-AAATTATTATAAAATTATAA
1 AAATAAAAATATTA-AAAATTATAA
212945 AAATAAAAATATTAAAAATTATAA
1 AAATAAAAATATTAAAAATTATAA
212969 AA
1 AA
212971 TTTAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATAAAAATATTAAAAATTATAA
Found at i:214247 original size:41 final size:41
Alignment explanation
Indices: 214200--214280 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
214190 AGTTGAATTG
*
214200 AATTTTACAATTTAAATAATTTAATTAATTTTTTAAGTTCA
1 AATTTTACAATTTAAATAATTTAAATAATTTTTTAAGTTCA
*
214241 AATTTTACAATTTAAATAATTTAAATAATTTTTTAGGTTC
1 AATTTTACAATTTAAATAATTTAAATAATTTTTTAAGTTC
214281 TTGATATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.51
Consensus pattern (41 bp):
AATTTTACAATTTAAATAATTTAAATAATTTTTTAAGTTCA
Found at i:214438 original size:30 final size:30
Alignment explanation
Indices: 214384--214445 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
214374 ATATTTTTTC
214384 AAATTTTTTTATAAATATATAAATAT-TAA
1 AAATTTTTTTATAAATATATAAATATATAA
214413 AAATTATTTTTA-AAATAT-TGAAAATATATAA
1 AAATT-TTTTTATAAATATAT--AAATATATAA
214444 AA
1 AA
214446 TACTAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
28 1 0.03
29 11 0.38
30 12 0.41
31 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (30 bp):
AAATTTTTTTATAAATATATAAATATATAA
Found at i:220538 original size:26 final size:28
Alignment explanation
Indices: 220485--220538 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
220475 AAAAGCTTGA
*
220485 AACATAATTAAAATAAAAAATCTTCAAAC
1 AACATAAATAAAATAAAAAATC-TCAAAC
220514 AACATAAATAAAA-AAAAAATC-CAAA
1 AACATAAATAAAATAAAAAATCTCAAA
220539 ATGTTGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
28 8 0.33
29 12 0.50
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.19
Consensus pattern (28 bp):
AACATAAATAAAATAAAAAATCTCAAAC
Found at i:221046 original size:27 final size:27
Alignment explanation
Indices: 220987--221049 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 27
220977 AAATATCCAT
220987 GAAAAAATATATTTAATAAATTTACCAA
1 GAAAAAATATATTTAATAAATTTACC-A
221015 GAAAAAATATATTTAATAAATTTACC-
1 GAAAAAATATATTTAATAAATTTACCA
221041 GTAAAAAAT
1 G-AAAAAAT
221050 CCATAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 1 0.03
27 7 0.21
28 26 0.76
ACGTcount: A:0.57, C:0.06, G:0.05, T:0.32
Consensus pattern (27 bp):
GAAAAAATATATTTAATAAATTTACCA
Found at i:221048 original size:28 final size:28
Alignment explanation
Indices: 220987--221040 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
220977 AAATATCCAT
220987 GAAAAAATATATTTAATAAATTTACCAA
1 GAAAAAATATATTTAATAAATTTACCAA
221015 GAAAAAATATATTTAATAAATTTACC
1 GAAAAAATATATTTAATAAATTTACC
221041 GTAAAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (28 bp):
GAAAAAATATATTTAATAAATTTACCAA
Found at i:242511 original size:23 final size:23
Alignment explanation
Indices: 242485--242540 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
242475 AATAAAATCA
*
242485 TATTTACATTTAAAAA-TTATATT
1 TATTTA-ATTAAAAAATTTATATT
242508 TATTTAATTAAAAAATTTATATT
1 TATTTAATTAAAAAATTTATATT
*
242531 TTTATTAATT
1 TAT-TTAATT
242541 TTAATTTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 8 0.28
23 15 0.52
24 6 0.21
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTTAATTAAAAAATTTATATT
Found at i:242719 original size:34 final size:34
Alignment explanation
Indices: 242640--242727 Score: 88
Period size: 34 Copynumber: 2.6 Consensus size: 34
242630 TACTGTCAGA
* * *
242640 TTAATAAATATTTAATTAATATTTTTTTATTATCAC
1 TTAAT-AATA-TTAATTAATATTATTTTAATATAAC
* * * *
242676 TTAAAAATATTAATAAATATTATTTTAATGTAAT
1 TTAATAATATTAATTAATATTATTTTAATATAAC
242710 TTAATAATA-TAATTAATA
1 TTAATAATATTAATTAATA
242728 ATAAATAATA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
33 8 0.19
34 27 0.63
35 4 0.09
36 4 0.09
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (34 bp):
TTAATAATATTAATTAATATTATTTTAATATAAC
Found at i:242984 original size:19 final size:19
Alignment explanation
Indices: 242948--242986 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
242938 TTACTATCAT
*
242948 AAAATATTAGTTTAAATTA
1 AAAATATTAATTTAAATTA
242967 AAAATGATTAATTT-AATTA
1 AAAAT-ATTAATTTAAATTA
242986 A
1 A
242987 GGTTTATTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
AAAATATTAATTTAAATTA
Found at i:243465 original size:21 final size:21
Alignment explanation
Indices: 243440--243486 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
243430 ATTTATATTA
*
243440 AATTTTAAGTTTTGGT-TTTTC
1 AATTTTAA-TTTTGGTGATTTC
243461 AATTTTTAATTTTGGTGATTTC
1 AA-TTTTAATTTTGGTGATTTC
243483 AATT
1 AATT
243487 CTCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.23, C:0.04, G:0.13, T:0.60
Consensus pattern (21 bp):
AATTTTAATTTTGGTGATTTC
Found at i:243469 original size:22 final size:22
Alignment explanation
Indices: 243442--243506 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 22
243432 TTATATTAAA
*
243442 TTTTAAGTTTTGGT-TTTTCAAT
1 TTTTAA-TTTTGGTGATTTCAAT
243464 TTTTAATTTTGGTGATTTCAAT
1 TTTTAATTTTGGTGATTTCAAT
*
243486 TCTCATTAATTTTGGTAATTT
1 T-T--TTAATTTTGGTGATTT
243507 TCGATTGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
21 7 0.19
22 14 0.38
23 1 0.03
25 15 0.41
ACGTcount: A:0.22, C:0.06, G:0.12, T:0.60
Consensus pattern (22 bp):
TTTTAATTTTGGTGATTTCAAT
Found at i:254699 original size:21 final size:23
Alignment explanation
Indices: 254673--254726 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 23
254663 ACTGTTATGT
*
254673 AGGTATCGATAATTT-TGA-AGG
1 AGGTATCGATAATTTCTCATAGG
*
254694 AGGTATCGATAGTTTCTCATAGG
1 AGGTATCGATAATTTCTCATAGG
254717 -GGTATCGATA
1 AGGTATCGATA
254727 CTGTTGGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 14 0.48
22 12 0.41
23 3 0.10
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.33
Consensus pattern (23 bp):
AGGTATCGATAATTTCTCATAGG
Found at i:256565 original size:20 final size:20
Alignment explanation
Indices: 256542--256589 Score: 51
Period size: 24 Copynumber: 2.2 Consensus size: 20
256532 TGAGAAATAA
256542 TATTCCAGTTAAACTCTGTT
1 TATTCCAGTTAAACTCTGTT
*
256562 TATTTGTTTCAGTTAAACTCTGTT
1 TA----TTCCAGTTAAACTCTGTT
256586 TATT
1 TATT
256590 TGTTTCAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 8
0.72 0.03 0.25
Matches are distributed among these distances:
20 4 0.17
24 19 0.83
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.52
Consensus pattern (20 bp):
TATTCCAGTTAAACTCTGTT
Found at i:256579 original size:24 final size:24
Alignment explanation
Indices: 256547--256606 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
256537 AATAATATTC
256547 CAGTTAAACTCTGTTTATTTGTTT
1 CAGTTAAACTCTGTTTATTTGTTT
256571 CAGTTAAACTCTGTTTATTTGTTT
1 CAGTTAAACTCTGTTTATTTGTTT
*
256595 CAGTCAAACTCT
1 CAGTTAAACTCT
256607 TATTAGTCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (24 bp):
CAGTTAAACTCTGTTTATTTGTTT
Found at i:258713 original size:15 final size:15
Alignment explanation
Indices: 258690--258719 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
258680 GTGCTTACAT
258690 TTTTAGGGTTTTTTG
1 TTTTAGGGTTTTTTG
*
258705 TTTTCGGGTTTTTTG
1 TTTTAGGGTTTTTTG
258720 GGATTTAGTT
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:0.03, C:0.03, G:0.27, T:0.67
Consensus pattern (15 bp):
TTTTAGGGTTTTTTG
Found at i:262151 original size:31 final size:35
Alignment explanation
Indices: 262114--262190 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
262104 AATATTAAAT
262114 TTAATTTAATACTTAT-TT-TA-ATA-ATATTTTA
1 TTAATTTAATACTTATCTTGTAGATATATATTTTA
**
262145 TTAATTTAATGTTTATCTTGTAGATATATATTTTA
1 TTAATTTAATACTTATCTTGTAGATATATATTTTA
*
262180 TTATTTTAATA
1 TTAATTTAATA
262191 AGATTTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 14 0.37
32 2 0.05
33 2 0.05
34 3 0.08
35 17 0.45
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (35 bp):
TTAATTTAATACTTATCTTGTAGATATATATTTTA
Found at i:265462 original size:22 final size:20
Alignment explanation
Indices: 265437--265486 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 20
265427 ATATTATAAA
265437 ATGTTATATCATATCATATAGT
1 ATGTTATAT-ATATCA-ATAGT
265459 ATG-TA-ATATATCAATAGT
1 ATGTTATATATATCAATAGT
*
265477 TTG-TATATAT
1 ATGTTATATAT
265487 GCATCAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 9 0.35
19 10 0.38
20 2 0.08
21 2 0.08
22 3 0.12
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (20 bp):
ATGTTATATATATCAATAGT
Found at i:265484 original size:17 final size:19
Alignment explanation
Indices: 265447--265486 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
265437 ATGTTATATC
265447 ATATCATATAGTATGTAAT
1 ATATCATATAGTATGTAAT
*
265466 ATATCA-ATAGTTTGT-AT
1 ATATCATATAGTATGTAAT
265483 ATAT
1 ATAT
265487 GCATCAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 8 0.40
19 6 0.30
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (19 bp):
ATATCATATAGTATGTAAT
Found at i:266888 original size:18 final size:18
Alignment explanation
Indices: 266848--266889 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
266838 CCACACTTAT
*
266848 AAATAT-TTTAATATAAT
1 AAATATATTTAATATAAA
* *
266865 ATATATATTTATTATAAA
1 AAATATATTTAATATAAA
266883 AAATATA
1 AAATATA
266890 GGAAAAATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATATATTTAATATAAA
Found at i:269282 original size:24 final size:24
Alignment explanation
Indices: 269249--269294 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
269239 TATCCTTTTT
269249 TCGAGAATTAAGTCAAATCATCTC
1 TCGAGAATTAAGTCAAATCATCTC
* * *
269273 TCGAGGATTAAGTTAGATCATC
1 TCGAGAATTAAGTCAAATCATC
269295 GGCCGGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (24 bp):
TCGAGAATTAAGTCAAATCATCTC
Found at i:272348 original size:50 final size:50
Alignment explanation
Indices: 272280--272398 Score: 211
Period size: 50 Copynumber: 2.4 Consensus size: 50
272270 GAACTCATGC
* **
272280 TTGTATCGGTAGAAGTATAGGGTAGGAGAGAGGTTGTTCACTGACTTGAG
1 TTGTTTCGGTAGTTGTATAGGGTAGGAGAGAGGTTGTTCACTGACTTGAG
272330 TTGTTTCGGTAGTTGTATAGGGTAGGAGAGAGGTTGTTCACTGACTTGAG
1 TTGTTTCGGTAGTTGTATAGGGTAGGAGAGAGGTTGTTCACTGACTTGAG
272380 TTGTTTCGGTAGTTGTATA
1 TTGTTTCGGTAGTTGTATA
272399 ACAAGTATCG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.22, C:0.08, G:0.34, T:0.36
Consensus pattern (50 bp):
TTGTTTCGGTAGTTGTATAGGGTAGGAGAGAGGTTGTTCACTGACTTGAG
Found at i:277795 original size:23 final size:24
Alignment explanation
Indices: 277769--277814 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
277759 AAATTATAAA
277769 ATATAATACT-ATAAAATAAAAAC
1 ATATAATACTAATAAAATAAAAAC
* *
277792 ATATACTAGTAATAAAATAAAAA
1 ATATAATACTAATAAAATAAAAA
277815 AATTTGAGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (24 bp):
ATATAATACTAATAAAATAAAAAC
Found at i:278160 original size:21 final size:22
Alignment explanation
Indices: 278135--278181 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
278125 AAAAGTTTAT
*
278135 TTTTTGAAAAAAATACA-AAAGA
1 TTTTAGAAAAAAATACATAAA-A
*
278157 TTTTATAAAAAAATACATAAAA
1 TTTTAGAAAAAAATACATAAAA
278179 TTT
1 TTT
278182 ATAAATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (22 bp):
TTTTAGAAAAAAATACATAAAA
Found at i:278182 original size:21 final size:22
Alignment explanation
Indices: 278141--278191 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
278131 TTATTTTTTG
278141 AAAAAAATACAAAAGATTTTAT
1 AAAAAAATACAAAAGATTTTAT
278163 AAAAAAATACATAAA-A-TTTAT
1 AAAAAAATACA-AAAGATTTTAT
*
278184 AAATAAAT
1 AAAAAAAT
278192 GAATACTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.44
22 12 0.44
23 3 0.11
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAAAATACAAAAGATTTTAT
Found at i:283157 original size:17 final size:17
Alignment explanation
Indices: 283135--283173 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
283125 TTCTGCAAAG
*
283135 TTTTTTT-AAAATGTGC
1 TTTTTTTCAAAATGTGA
*
283151 TTTTTTTCAAAATTTGA
1 TTTTTTTCAAAATGTGA
283168 TTTTTT
1 TTTTTT
283174 ATTTTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.64
Consensus pattern (17 bp):
TTTTTTTCAAAATGTGA
Found at i:284198 original size:70 final size:70
Alignment explanation
Indices: 284081--284230 Score: 246
Period size: 70 Copynumber: 2.1 Consensus size: 70
284071 CCTGGTCCTA
*
284081 TCTACCGATAAAACTAGAGTTCTACTGAAACAAATCAAGACAGTAGCCAAAGTTCAGCATCCCCT
1 TCTACCGATAAAACTAGAGTTCTACTGAAACAAATCAAGACAATAGCCAAAGTTCAGCATCCCCT
284146 GCACT
66 GCACT
* * * *
284151 TCTACCTATAAAACTAGAGTTCTACTGAAACAAGTCAAGACAATAGCCAAAGTTCATCATCCCTT
1 TCTACCGATAAAACTAGAGTTCTACTGAAACAAATCAAGACAATAGCCAAAGTTCAGCATCCCCT
284216 GCACT
66 GCACT
*
284221 TCTATCGATA
1 TCTACCGATA
284231 CTCTGATGGG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.25
Consensus pattern (70 bp):
TCTACCGATAAAACTAGAGTTCTACTGAAACAAATCAAGACAATAGCCAAAGTTCAGCATCCCCT
GCACT
Found at i:287707 original size:9 final size:9
Alignment explanation
Indices: 287693--287723 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
287683 TTATTAATTT
287693 AAAATTTTA
1 AAAATTTTA
287702 AAAATTTTA
1 AAAATTTTA
287711 AAAATTTTA
1 AAAATTTTA
287720 AAAA
1 AAAA
287724 AAATTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
AAAATTTTA
Found at i:288148 original size:16 final size:16
Alignment explanation
Indices: 288127--288168 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
288117 TTTGTTAATG
*
288127 GTTTTTAATAAATATA
1 GTTTTTAATAAAAATA
288143 GTTTTTAATAAAAATA
1 GTTTTTAATAAAAATA
* *
288159 ATGTTTAATA
1 GTTTTTAATA
288169 TATTAGTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (16 bp):
GTTTTTAATAAAAATA
Found at i:288164 original size:18 final size:18
Alignment explanation
Indices: 288122--288164 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
288112 TGTTTTTTGT
*
288122 TAATGGTTTTTAATAAATA
1 TAAT-GTTTTTAATAAAAA
288141 T-A-GTTTTTAATAAAAA
1 TAATGTTTTTAATAAAAA
288157 TAATGTTT
1 TAATGTTT
288165 AATATATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 14 0.67
17 1 0.05
18 5 0.24
19 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (18 bp):
TAATGTTTTTAATAAAAA
Found at i:291639 original size:21 final size:21
Alignment explanation
Indices: 291583--291645 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
291573 AAATATTAGC
291583 AATAAATAACATTAATAAGTATT
1 AATAAA-AACATTAATAA-TATT
* * *
291606 AATAAACATATTATTAATATT
1 AATAAAAACATTAATAATATT
291627 AATAAAAACATTAATAATA
1 AATAAAAACATTAATAATA
291646 ACAAAAGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 20 0.59
22 8 0.24
23 6 0.18
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (21 bp):
AATAAAAACATTAATAATATT
Found at i:292761 original size:30 final size:29
Alignment explanation
Indices: 292727--292927 Score: 130
Period size: 29 Copynumber: 6.9 Consensus size: 29
292717 CTTGGAGGTC
*
292727 CCAAAAATTCCATTTTTACCCCTCGAATTT
1 CCAAAAATTCCATTTTTA-CCCTCGAACTT
* *
292757 CCAAAAAAAATT--ATTTTTACCCCCAAACTT
1 CC---AAAAATTCCATTTTTACCCTCGAACTT
*
292787 CCAAAAATTCCATTTTTA-CCTTGAAACTT
1 CCAAAAATTCCATTTTTACCCTCG-AACTT
* *
292816 CCAAAAATTCCATTTTTACCCTTGGA-TGT
1 CCAAAAATTCCATTTTTACCCTCGAACT-T
* * *
292845 TCAAAAACTCCATTTTTGA-CCTCGAAATT
1 CCAAAAATTCCATTTTT-ACCCTCGAACTT
* ** *
292874 CTC-AAAATTACC-CTTTTATTCTCGAACCT
1 C-CAAAAATT-CCATTTTTACCCTCGAACTT
* *
292903 CCAAAATTTCCATTTTGA-CCTCGAA
1 CCAAAAATTCCATTTTTACCCTCGAA
292928 ATTACCATTT
Statistics
Matches: 135, Mismatches: 21, Indels: 32
0.72 0.11 0.17
Matches are distributed among these distances:
27 7 0.05
28 13 0.10
29 79 0.59
30 22 0.16
31 7 0.05
33 7 0.05
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (29 bp):
CCAAAAATTCCATTTTTACCCTCGAACTT
Found at i:292890 original size:29 final size:28
Alignment explanation
Indices: 292858--292930 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
292848 AAAACTCCAT
*
292858 TTTTGACCTCGAAATTCTCAAAATTACCC
1 TTTTGACCTCGAAATTC-CAAAATTACCA
* ** *
292887 TTTT-ATTCTCGAACCTCCAAAATTTCCA
1 TTTTGA-CCTCGAAATTCCAAAATTACCA
292915 TTTTGACCTCGAAATT
1 TTTTGACCTCGAAATT
292931 ACCATTTTGC
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.29, C:0.26, G:0.07, T:0.38
Consensus pattern (28 bp):
TTTTGACCTCGAAATTCCAAAATTACCA
Done.