Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 19 of 143
Found at i:5865990 original size:47 final size:47
Alignment explanation
Indices: 5865894--5865990 Score: 131
Period size: 47 Copynumber: 2.1 Consensus size: 47
5865884 CTGCGTTGCT
* * ***
5865894 TTTATTGTGTCGCTTGCACCCTTCGTGTTTCTCGATCCTGCGTTGCC
1 TTTATTGTGTCGCTTGCACCCTTCGTGTTTCTCGATACTGAGGCACC
* *
5865941 TTTATTGTGTCGCTTGCACCCTTTGTGTTTCTCGATAGTGAGGCACC
1 TTTATTGTGTCGCTTGCACCCTTCGTGTTTCTCGATACTGAGGCACC
5865988 TTT
1 TTT
5865991 GTGCAAGTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.09, C:0.26, G:0.22, T:0.43
Consensus pattern (47 bp):
TTTATTGTGTCGCTTGCACCCTTCGTGTTTCTCGATACTGAGGCACC
Found at i:5867140 original size:34 final size:34
Alignment explanation
Indices: 5867092--5867193 Score: 150
Period size: 34 Copynumber: 3.0 Consensus size: 34
5867082 GAAAGTGAGG
* *
5867092 CTGAGAGGTTAGCGTGTATTGGTCGATTAGTTAA
1 CTGAGAGGTAAGCGTGTATTGATCGATTAGTTAA
*
5867126 CTGAGAGGTAAGCGTGTATAGATCGATTAGTTAA
1 CTGAGAGGTAAGCGTGTATTGATCGATTAGTTAA
* * *
5867160 CCGAGAGGTAAGTGTGTATTGATCGATTAATTAA
1 CTGAGAGGTAAGCGTGTATTGATCGATTAGTTAA
5867194 TTAGTTAGAG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 61 1.00
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.32
Consensus pattern (34 bp):
CTGAGAGGTAAGCGTGTATTGATCGATTAGTTAA
Found at i:5869340 original size:22 final size:22
Alignment explanation
Indices: 5869299--5869339 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5869289 TTAGCCCACG
*
5869299 TCAAAATATAAAAATAAAAATT
1 TCAAAATAAAAAAATAAAAATT
5869321 TCAAAA-AAAAAAATAAAAA
1 TCAAAATAAAAAAATAAAAA
5869340 AATATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.20
Consensus pattern (22 bp):
TCAAAATAAAAAAATAAAAATT
Found at i:5869492 original size:19 final size:19
Alignment explanation
Indices: 5869445--5869532 Score: 70
Period size: 19 Copynumber: 4.4 Consensus size: 19
5869435 TATTCTAGAA
**
5869445 TTATAAAAATATAAAAAAAT
1 TTATAAAAATA-ATTAAAAT
* *
5869465 TATAAAAAAATAATTAAACT
1 T-TATAAAAATAATTAAAAT
*
5869485 TTATAAAAATTATTAGAAAT
1 TTATAAAAATAATTA-AAAT
*
5869505 TAATTAAAAATAA-TAAAATT
1 TTA-TAAAAATAATTAAAA-T
5869525 TTATAAAA
1 TTATAAAA
5869533 TTTATATGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
19 20 0.37
20 17 0.31
21 17 0.31
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (19 bp):
TTATAAAAATAATTAAAAT
Found at i:5869505 original size:40 final size:40
Alignment explanation
Indices: 5869461--5869537 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
5869451 AAATATAAAA
*
5869461 AAATT-ATAAAAAAATAATTAAACTTTATAAAAATTATTAG
1 AAATTAAT-AAAAAATAATAAAACTTTATAAAAATTATTAG
* * *
5869501 AAATTAATTAAAAATAATAAAATTTTATAAAATTTAT
1 AAATTAATAAAAAATAATAAAACTTTATAAAAATTAT
5869538 ATGAAATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 30 0.94
41 2 0.06
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (40 bp):
AAATTAATAAAAAATAATAAAACTTTATAAAAATTATTAG
Found at i:5869521 original size:30 final size:30
Alignment explanation
Indices: 5869448--5869532 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
5869438 TCTAGAATTA
*
5869448 TAAAAATATAAAAAAATTATAAAAAAATAAT
1 TAAAAATA-ATAAAAATTATAAAAAAATAAT
** * * * *
5869479 TAAACTTTATAAAAATTATTAGAAATTAAT
1 TAAAAATAATAAAAATTATAAAAAAATAAT
*
5869509 TAAAAATAATAAAATTTTATAAAA
1 TAAAAATAATAAAA-ATTATAAAA
5869533 TTTATATGAA
Statistics
Matches: 40, Mismatches: 13, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
30 29 0.73
31 11 0.28
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (30 bp):
TAAAAATAATAAAAATTATAAAAAAATAAT
Found at i:5871031 original size:2 final size:2
Alignment explanation
Indices: 5871024--5871066 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
5871014 GGCTCACATG
* *
5871024 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5871066 A
1 A
5871067 AAGATCTGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5874537 original size:18 final size:18
Alignment explanation
Indices: 5874514--5874548 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5874504 TTTATAATAC
*
5874514 TTTATATTATGTTATTTT
1 TTTATATTATGTAATTTT
5874532 TTTATATTATGTAATTT
1 TTTATATTATGTAATTT
5874549 CAAACATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTATATTATGTAATTTT
Found at i:5875474 original size:2 final size:2
Alignment explanation
Indices: 5875469--5875509 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
5875459 CAATATATTG
*
5875469 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5875510 ATTTTAATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5875476 original size:10 final size:9
Alignment explanation
Indices: 5875461--5875509 Score: 59
Period size: 8 Copynumber: 5.6 Consensus size: 9
5875451 TATATTACCA
5875461 ATATATTGAT
1 ATATATT-AT
5875471 ATATA-TAT
1 ATATATTAT
5875479 ATATA-TAT
1 ATATATTAT
5875487 ATATATATAT
1 ATATAT-TAT
5875497 ATATATT-T
1 ATATATTAT
5875505 ATATA
1 ATATA
5875510 ATTTTAATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
8 21 0.57
9 2 0.05
10 14 0.38
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (9 bp):
ATATATTAT
Found at i:5875515 original size:10 final size:12
Alignment explanation
Indices: 5875461--5875509 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
5875451 TATATTACCA
*
5875461 ATATATTGATAT
1 ATATATTTATAT
*
5875473 ATATATATATAT
1 ATATATTTATAT
*
5875485 ATATATATATAT
1 ATATATTTATAT
5875497 ATATATTTATAT
1 ATATATTTATAT
5875509 A
1 A
5875510 ATTTTAATCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
ATATATTTATAT
Found at i:5882337 original size:36 final size:36
Alignment explanation
Indices: 5882286--5882369 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 36
5882276 TAAATTAATA
* *
5882286 TATTACTAATGCATAAAATAATGTAATATAATA-TA-T
1 TATTACTATTACATAAAATAA--TAATATAATAGTATT
* *
5882322 TATTACTATTACATAATATAATAATATATTAGTATT
1 TATTACTATTACATAAAATAATAATATAATAGTATT
*
5882358 TATTAGTATTAC
1 TATTACTATTAC
5882370 TTATACATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 9 0.22
35 2 0.05
36 30 0.73
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (36 bp):
TATTACTATTACATAAAATAATAATATAATAGTATT
Found at i:5882384 original size:39 final size:41
Alignment explanation
Indices: 5882286--5882408 Score: 113
Period size: 39 Copynumber: 3.2 Consensus size: 41
5882276 TAAATTAATA
* *
5882286 TATTACTAATGCATAAAATAATGTAATATAATATATTATTAC
1 TATTACT-ATACATAAAATAATATAATATAATATATTATTAC
* * *
5882328 TATTAC-ATA-ATATAATAATAT-AT-TAGTAT-TTATTAG
1 TATTACTATACATAAAATAATATAATATAATATATTATTAC
5882364 TATTACTTATACATAAAATAATAT--TATAATATA-TA--AC
1 TATTAC-TATACATAAAATAATATAATATAATATATTATTAC
5882401 TATTACTA
1 TATTACTA
5882409 AAAATATTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
36 14 0.21
37 12 0.18
38 6 0.09
39 28 0.41
40 2 0.03
42 6 0.09
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (41 bp):
TATTACTATACATAAAATAATATAATATAATATATTATTAC
Found at i:5882530 original size:15 final size:16
Alignment explanation
Indices: 5882501--5882542 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
5882491 TCATTGATGC
*
5882501 ATATATATATATATATT
1 ATAT-TATATATATATA
5882518 ATATTATAT-TATATA
1 ATATTATATATATATA
*
5882533 ACATTATATA
1 ATATTATATA
5882543 ATAATGTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 13 0.59
16 5 0.23
17 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTATATATATATA
Found at i:5883410 original size:15 final size:15
Alignment explanation
Indices: 5883392--5883443 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
5883382 ATATAAAATG
*
5883392 AATTATTATATTTAA
1 AATTATAATATTTAA
*
5883407 AATTAAAATATTTATA
1 AATTATAATATTTA-A
* *
5883423 ACTTATAAAATTTAA
1 AATTATAATATTTAA
5883438 AATTAT
1 AATTAT
5883444 TTGAATCCGT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTATAATATTTAA
Found at i:5892369 original size:59 final size:59
Alignment explanation
Indices: 5892302--5892422 Score: 224
Period size: 59 Copynumber: 2.1 Consensus size: 59
5892292 CCTGACACTA
*
5892302 GCATGTCTTTGTAGCACGCCAAACAACCAAGTCTTGCCATATGCATAATCGAACCCCAC
1 GCATGTCTTCGTAGCACGCCAAACAACCAAGTCTTGCCATATGCATAATCGAACCCCAC
*
5892361 GCATGTCTTCGTAGCACGCCAAACAACCAAGTCTTGCCATATGCATAATCGGACCCCAC
1 GCATGTCTTCGTAGCACGCCAAACAACCAAGTCTTGCCATATGCATAATCGAACCCCAC
5892420 GCA
1 GCA
5892423 GCATTGGCGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.21
Consensus pattern (59 bp):
GCATGTCTTCGTAGCACGCCAAACAACCAAGTCTTGCCATATGCATAATCGAACCCCAC
Found at i:5893787 original size:3 final size:3
Alignment explanation
Indices: 5893781--5893844 Score: 83
Period size: 3 Copynumber: 21.3 Consensus size: 3
5893771 ACCACCATTA
* * * * *
5893781 TTG TTG TTG TTG TTG TTG TTG TTA TTG TTG TTG TCG TTA TTG TCG TTT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
5893829 TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG T
5893845 CCGTCTCTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.03, C:0.03, G:0.28, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:5900599 original size:32 final size:32
Alignment explanation
Indices: 5900545--5900606 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
5900535 CAAATATCTC
*
5900545 AATTTAATTTTATTCCAATCAAATTAATTTTT
1 AATTTAATTTAATTCCAATCAAATTAATTTTT
* * * *
5900577 AATTTGATTTAATTCTATTCAAATTGATTT
1 AATTTAATTTAATTCCAATCAAATTAATTT
5900607 AAAAGCTCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.53
Consensus pattern (32 bp):
AATTTAATTTAATTCCAATCAAATTAATTTTT
Found at i:5902015 original size:17 final size:17
Alignment explanation
Indices: 5901968--5902023 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
5901958 TTTAATTCAA
5901968 AGTTATTTTAGA-TTTAG
1 AGTTATTTTAGAGTTT-G
* *
5901985 AATT-TTTTTG-GTTTG
1 AGTTATTTTAGAGTTTG
*
5902000 AGTTATTTTAGAGTTTA
1 AGTTATTTTAGAGTTTG
5902017 AGTTATT
1 AGTTATT
5902024 CAGGTTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 4 0.13
16 13 0.42
17 14 0.45
ACGTcount: A:0.25, C:0.00, G:0.18, T:0.57
Consensus pattern (17 bp):
AGTTATTTTAGAGTTTG
Found at i:5902030 original size:32 final size:32
Alignment explanation
Indices: 5901968--5902032 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
5901958 TTTAATTCAA
* **
5901968 AGTTATTTTAGATTTAGAATTTTTTTGGTTTG
1 AGTTATTTTAGATTTAGAATTATTCAGGTTTG
*
5902000 AGTTATTTTAGAGTTTA-AGTTATTCAGGTTTG
1 AGTTATTTTAGA-TTTAGAATTATTCAGGTTTG
5902032 A
1 A
5902033 TGTTTAGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.25, C:0.02, G:0.20, T:0.54
Consensus pattern (32 bp):
AGTTATTTTAGATTTAGAATTATTCAGGTTTG
Found at i:5904608 original size:17 final size:18
Alignment explanation
Indices: 5904571--5904605 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5904561 ATAAATATTA
5904571 AATTTATATATTAATTTT
1 AATTTATATATTAATTTT
5904589 AATTTA-ATATGTAATTT
1 AATTTATATAT-TAATTT
5904606 AATACTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
AATTTATATATTAATTTT
Found at i:5905428 original size:23 final size:23
Alignment explanation
Indices: 5905359--5905428 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
5905349 TCGTTAACAT
5905359 TGTTCGTGAACATGTTCCATTATA
1 TGTTCGTGAACATGTTCCATTA-A
* * *
5905383 TGCTCATGAACATGTT-TATTTAA
1 TGTTCGTGAACATGTTCCA-TTAA
*
5905406 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCCATTAA
5905429 GTTAAATGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCCATTAA
Found at i:5907732 original size:21 final size:21
Alignment explanation
Indices: 5907708--5907753 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
5907698 TCGTGTGAAA
5907708 TTTTGAATTTTACTGCTGCTT
1 TTTTGAATTTTACTGCTGCTT
*
5907729 TTTTGGATTTTACTGCTGCTT
1 TTTTGAATTTTACTGCTGCTT
5907750 TTTT
1 TTTT
5907754 TTCTTGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.11, C:0.13, G:0.15, T:0.61
Consensus pattern (21 bp):
TTTTGAATTTTACTGCTGCTT
Found at i:5928387 original size:24 final size:26
Alignment explanation
Indices: 5928347--5928396 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 26
5928337 ACAATAATAA
5928347 AATATATTTGTTTCCA-C-AATTAGC
1 AATATATTTGTTTCCACCTAATTAGC
*
5928371 AATA-ATTTTTTTCCCACCTAATTAGC
1 AATATATTTGTTT-CCACCTAATTAGC
5928397 TAGATTAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 7 0.32
24 7 0.32
25 1 0.05
26 7 0.32
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (26 bp):
AATATATTTGTTTCCACCTAATTAGC
Found at i:5938838 original size:61 final size:62
Alignment explanation
Indices: 5938684--5938862 Score: 224
Period size: 62 Copynumber: 2.9 Consensus size: 62
5938674 TGGATGAAAA
* * * * *
5938684 TGATCATTGC-ATGGCCGACA-CTCTCTATTTTTCGAGAAAAAAATTTCAAATTTTTTTGGTGT
1 TGATCA-TGCAATGGCCGACACCCCCCT-TTTCTCGAGAAAAAAAATTCAAATTTTTTTGGTAT
* **
5938746 TGGTCATGCAATGGTTGACACCCCCCTTTTCTCGAGAAAAAAAATTCAAATTTTTTTGGTAT
1 TGATCATGCAATGGCCGACACCCCCCTTTTCTCGAGAAAAAAAATTCAAATTTTTTTGGTAT
5938808 TGATCAT-CAAATGGCCGACACCCCCC-TTTCTCGAG-AAAAAAATTCAAATTTTTTT
1 TGATCATGC-AATGGCCGACACCCCCCTTTTCTCGAGAAAAAAAATTCAAATTTTTTT
5938863 ATGGTCGACA
Statistics
Matches: 103, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
60 20 0.19
61 13 0.13
62 66 0.64
63 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (62 bp):
TGATCATGCAATGGCCGACACCCCCCTTTTCTCGAGAAAAAAAATTCAAATTTTTTTGGTAT
Found at i:5938894 original size:106 final size:106
Alignment explanation
Indices: 5938774--5938969 Score: 279
Period size: 106 Copynumber: 1.8 Consensus size: 106
5938764 CACCCCCCTT
* *
5938774 TTCTCGAGAAAAAAAATTCAAATTTTTTTGGTATTGATCATCAAATGGCCGACACCCCCCTTTCT
1 TTCTCGAGAAAAAAAATTCAAATTTTTTTGGTATGGACCATCAAATGGCCGACA-CCCCCTTTCT
5938839 CGAGA-AAAAAA-TTCAAATTTTTTTATGGTCGACATCCTCTG
65 CGA-ATAAAAAATTTCAAATTTTTTTATGGTCGACATCCTCTG
* * * * **
5938880 TTCTCGAGAAAAAAATTTTAAATTTTTTTGGTGTGGGCCATCAAATGGCCGACACCCTTTTTCTC
1 TTCTCGAGAAAAAAAATTCAAATTTTTTTGGTATGGACCATCAAATGGCCGACACCCCCTTTCTC
5938945 GAATAAAAAATTTTCAAATTTTTTT
66 GAATAAAAAA-TTTCAAATTTTTTT
5938970 TGTGTTGGCC
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
104 1 0.01
105 17 0.22
106 48 0.61
107 13 0.16
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (106 bp):
TTCTCGAGAAAAAAAATTCAAATTTTTTTGGTATGGACCATCAAATGGCCGACACCCCCTTTCTC
GAATAAAAAATTTCAAATTTTTTTATGGTCGACATCCTCTG
Found at i:5938967 original size:60 final size:60
Alignment explanation
Indices: 5938880--5938996 Score: 191
Period size: 61 Copynumber: 1.9 Consensus size: 60
5938870 ACATCCTCTG
5938880 TTCTCGAGAAAAAAATTTTAAATTTTTTTGGTGTGGGCCATCAAATGGCCGACACCCTTT
1 TTCTCGAGAAAAAAATTTTAAATTTTTTTGGTGTGGGCCATCAAATGGCCGACACCCTTT
* *
5938940 TTCTCGA-ATAAAAAATTTTCAAATTTTTTTTGTGTTGGCCATCAAATGGCCGACACC
1 TTCTCGAGA-AAAAAATTTT-AAATTTTTTTGGTGTGGGCCATCAAATGGCCGACACC
5938997 AACTTCTCAT
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
59 1 0.02
60 17 0.32
61 35 0.66
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (60 bp):
TTCTCGAGAAAAAAATTTTAAATTTTTTTGGTGTGGGCCATCAAATGGCCGACACCCTTT
Found at i:5942772 original size:12 final size:12
Alignment explanation
Indices: 5942730--5942777 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
5942720 ATTTGTGTAA
*
5942730 AAATTAATTTGA
1 AAATTAATTTGG
5942742 AAATTAATTTAAGTTG
1 AAATTAATTT--G--G
5942758 AAATTAATTTGG
1 AAATTAATTTGG
5942770 AAATTAAT
1 AAATTAAT
5942778 GAACATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (12 bp):
AAATTAATTTGG
Found at i:5943098 original size:83 final size:83
Alignment explanation
Indices: 5942908--5943432 Score: 824
Period size: 83 Copynumber: 6.3 Consensus size: 83
5942898 AAAAAGATAG
* * * * * *
5942908 TTATTATATTACAATTTATATCAAATATTGTATTAATTTGACAATACATTATTTATCAAATTTTC
1 TTATTATATTACAATTTTTATCATATAATGTATTGATTTGACAATACAATATTTAT-TAATTTT-
*
5942973 ATA--TTTAAAGTACAAA-TTA
64 ATATCTTTAAA-TA-AAATTTT
* *
5942992 TTATTATATTATAATTTTTATCATATAATGTATTGATTTAACAATACAATATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
5943057 ATCTTTAAATAAAATTTT
66 ATCTTTAAATAAAATTTT
* * *
5943075 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGATAATAGAATATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
5943140 ATCTTTAAATAAAATTTTT
66 ATCTTTAAATAAAA-TTTT
* *
5943159 TTATTATATTACAATTTTTATAATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
*
5943224 ATCTATAAATAAAA-TTT
66 ATCTTTAAATAAAATTTT
5943241 TTATTATATTACAATTTTTATCATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
*
5943306 ATCTTTAAATAAATTTTT
66 ATCTTTAAATAAAATTTT
*
5943324 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
5943389 ATCTTTAAATAAAATTTT
66 ATCTTTAAATAAAATTTT
5943407 TTATTATATTACAATTTTTATCATAT
1 TTATTATATTACAATTTTTATCATAT
5943433 TTTATATTTA
Statistics
Matches: 412, Mismatches: 24, Indels: 11
0.92 0.05 0.02
Matches are distributed among these distances:
82 84 0.20
83 194 0.47
84 134 0.33
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.52
Consensus pattern (83 bp):
TTATTATATTACAATTTTTATCATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
ATCTTTAAATAAAATTTT
Found at i:5943621 original size:19 final size:20
Alignment explanation
Indices: 5943597--5943651 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
5943587 TCTCGAGACT
*
5943597 GCCGTTGA-CTACTTTGTCC
1 GCCGTTGACCGACTTTGTCC
5943616 GCCGTTGACCGACTTTGTCC
1 GCCGTTGACCGACTTTGTCC
*
5943636 GCCGTTGATCGACTTT
1 GCCGTTGACCGACTTT
5943652 CATCCATCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 8 0.24
20 25 0.76
ACGTcount: A:0.11, C:0.31, G:0.24, T:0.35
Consensus pattern (20 bp):
GCCGTTGACCGACTTTGTCC
Found at i:5945913 original size:30 final size:30
Alignment explanation
Indices: 5945850--5945941 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 30
5945840 TCCCTTTACT
5945850 TTTTAAATTTAATTT-GTAATTTCGTT-T-TCA
1 TTTTAAATTTAATTTCG-AATTTC-TTGTAT-A
5945880 TTTTAAATTTAATTTCGAATTTCTTGTATA
1 TTTTAAATTTAATTTCGAATTTCTTGTATA
* ** * *
5945910 TTTTAATTTTTCTTTCTAATTTCATGTATA
1 TTTTAAATTTAATTTCGAATTTCTTGTATA
5945940 TT
1 TT
5945942 CTAATTATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
29 2 0.04
30 50 0.93
31 2 0.04
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (30 bp):
TTTTAAATTTAATTTCGAATTTCTTGTATA
Found at i:5947020 original size:121 final size:120
Alignment explanation
Indices: 5946795--5947140 Score: 534
Period size: 121 Copynumber: 2.9 Consensus size: 120
5946785 AAAAAATTGC
* *
5946795 AAAATTTGCTATTTTTTTCTCGAGAGCAGGGGGTGTCGGCCATTTGATGGCCAACACAAAAAAAA
1 AAAATTTG-AATTTTTTTCTCGAGAGCAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAAAAA
* *
5946860 TTGAATTTTTTTCTCGAGAACAGGGGGTGTCGACCATTTGATGGCCAACA-CTAAA
65 TTGAATTTTTTTCTCGAGAACAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAA
5946915 AAAATTTGAATTTTTTTTCTCGAGAGCAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAAAAA
1 AAAATTTGAA-TTTTTTTCTCGAGAGCAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAAAAA
*
5946980 TATAAATTTTTTTCTCGAGAACAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAA
65 T-TGAATTTTTTTCTCGAGAACAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAA
* ** *
5947037 AAAATTTGAATTTTTTTCTCGAGAACAAAGGGTGTCGGCCA-TTGCACGGCCAACACCAAAAAAA
1 AAAATTTGAATTTTTTTCTCGAGAGCAGGGGGTGTCGGCCATTTG-ATGGCCAACACCAAAAAAA
*
5947101 TTTGAATTTTTTTCTCGAGAAATAGGGGGTGTCGGCCATT
65 -TTGAATTTTTTTCTCGAG-AACAGGGGGTGTCGGCCATT
5947141 GCTTCTCGAG
Statistics
Matches: 209, Mismatches: 11, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
119 1 0.00
120 65 0.31
121 109 0.52
122 34 0.16
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (120 bp):
AAAATTTGAATTTTTTTCTCGAGAGCAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAAAAAT
TGAATTTTTTTCTCGAGAACAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAA
Found at i:5947142 original size:61 final size:60
Alignment explanation
Indices: 5946795--5947140 Score: 525
Period size: 61 Copynumber: 5.7 Consensus size: 60
5946785 AAAAAATTGC
* *
5946795 AAAATTTGCTATTTTTTTCTCGAGAGCAGGGGGTGTCGGCCATTTGATGGCCAACA-CAAA
1 AAAATTTG-AATTTTTTTCTCGAGAACAGGGGGTGTCGGCCATTTGATGGCCAACACCAAA
* * *
5946855 AAAAATTGAATTTTTTTCTCGAGAACAGGGGGTGTCGACCATTTGATGGCCAACACTAAA
1 AAAATTTGAATTTTTTTCTCGAGAACAGGGGGTGTCGGCCATTTGATGGCCAACACCAAA
*
5946915 AAAATTTGAATTTTTTTTCTCGAGAGCAGGGGGTGTCGGCCATTTGATGGCCAACACCAAA
1 AAAATTTGAA-TTTTTTTCTCGAGAACAGGGGGTGTCGGCCATTTGATGGCCAACACCAAA
* *
5946976 AAAATATAAATTTTTTTCTCGAGAACAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAA
1 AAAATTTGAATTTTTTTCTCGAGAACAGGGGGTGTCGGCCATTTGATGGCCAACACC-AAA
** *
5947037 AAAATTTGAATTTTTTTCTCGAGAACAAAGGGTGTCGGCCA-TTGCACGGCCAACACCAAA
1 AAAATTTGAATTTTTTTCTCGAGAACAGGGGGTGTCGGCCATTTG-ATGGCCAACACCAAA
*
5947097 AAAATTTGAATTTTTTTCTCGAGAAATAGGGGGTGTCGGCCATT
1 AAAATTTGAATTTTTTTCTCGAG-AACAGGGGGTGTCGGCCATT
5947141 GCTTCTCGAG
Statistics
Matches: 260, Mismatches: 20, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
59 44 0.17
60 94 0.36
61 121 0.47
62 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (60 bp):
AAAATTTGAATTTTTTTCTCGAGAACAGGGGGTGTCGGCCATTTGATGGCCAACACCAAA
Found at i:5947150 original size:31 final size:31
Alignment explanation
Indices: 5947112--5947170 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
5947102 TTGAATTTTT
5947112 TTCTCGAGAAATAGGGGGTGTCGGCCATTGC
1 TTCTCGAGAAATAGGGGGTGTCGGCCATTGC
5947143 TTCTCGAGAAATAGGGGGTGTCGGCCAT
1 TTCTCGAGAAATAGGGGGTGTCGGCCAT
5947171 GCAATGGCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.36, T:0.25
Consensus pattern (31 bp):
TTCTCGAGAAATAGGGGGTGTCGGCCATTGC
Found at i:5950050 original size:50 final size:50
Alignment explanation
Indices: 5949993--5950091 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
5949983 TTTAAGTCAC
* *
5949993 GTTAAATTTATACATGTATTATCTATTGAAGTTTGA-TTTTTAAATCAAAT
1 GTTAAATTTAAACATGTATTATCTATTGAAATTT-ATTTTTTAAATCAAAT
*
5950043 GTTAAATTTAAATATGTATTATCTATTGAAATTTATTTTTTAAATCAAA
1 GTTAAATTTAAACATGTATTATCTATTGAAATTTATTTTTTAAATCAAA
5950092 ATACTAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 1 0.02
50 44 0.98
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.48
Consensus pattern (50 bp):
GTTAAATTTAAACATGTATTATCTATTGAAATTTATTTTTTAAATCAAAT
Found at i:5951830 original size:36 final size:38
Alignment explanation
Indices: 5951740--5951830 Score: 97
Period size: 36 Copynumber: 2.5 Consensus size: 38
5951730 AAAAATCAAG
5951740 TTAAA-TCGAGTTTAATTTTCAATTTTAATTTAATACGA
1 TTAAATTCGAGTTT-ATTTTCAATTTTAATTTAATACGA
5951778 TTAAATTCGA--TTATTTT-AATTTCTAATTTAAT-CGA
1 TTAAATTCGAGTTTATTTTCAATTT-TAATTTAATACGA
*
5951813 TT-TATT-GAGTTTGATTTT
1 TTAAATTCGAGTTT-ATTTT
5951831 TAAATTTATA
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
33 2 0.04
34 3 0.06
35 12 0.26
36 19 0.40
37 2 0.04
38 5 0.11
39 4 0.09
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.53
Consensus pattern (38 bp):
TTAAATTCGAGTTTATTTTCAATTTTAATTTAATACGA
Found at i:5963524 original size:14 final size:16
Alignment explanation
Indices: 5963493--5963524 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5963483 TTACAAAGTA
5963493 AACCAATATTATATCT
1 AACCAATATTATATCT
5963509 AACCAAT-TTA-ATCT
1 AACCAATATTATATCT
5963523 AA
1 AA
5963525 AATAATTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (16 bp):
AACCAATATTATATCT
Found at i:5965475 original size:123 final size:122
Alignment explanation
Indices: 5965327--5965574 Score: 417
Period size: 123 Copynumber: 2.0 Consensus size: 122
5965317 TTTTCTTTTC
* * *
5965327 TTATTGTTTTACGATTTTTCTATTGTCATTATCGACGTTAGTTTTAACACAAATTAAAATTTT-A
1 TTATTATTTTACGATCTTTCTATTGTCATTATCGACGTTAATTTTAACACAAATT-AAATTTTAA
*
5965391 AAATAGTTAATATTAATTACTTATAATTATTTAAAATTTATATTTCATATATTAAAATA
65 AAATAGTTAATATTAATTACTTATAATTATAT-AAATTTATATTTCATATATTAAAATA
* *
5965450 TTATTATTTTGCGATCTTTCTATTGTCATTATTGACGTTAATTTTAACACAAATTAAATTTTAAA
1 TTATTATTTTACGATCTTTCTATTGTCATTATCGACGTTAATTTTAACACAAATTAAATTTTAAA
5965515 AATAGTTAATATTAATTACTTATAATTATATAAATTTATATTTCATATATTAAAATA
66 AATAGTTAATATTAATTACTTATAATTATATAAATTTATATTTCATATATTAAAATA
5965572 TTA
1 TTA
5965575 ATAATGAGTT
Statistics
Matches: 118, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
122 36 0.31
123 82 0.69
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (122 bp):
TTATTATTTTACGATCTTTCTATTGTCATTATCGACGTTAATTTTAACACAAATTAAATTTTAAA
AATAGTTAATATTAATTACTTATAATTATATAAATTTATATTTCATATATTAAAATA
Found at i:5965738 original size:13 final size:15
Alignment explanation
Indices: 5965713--5965744 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5965703 AACATTTAAG
5965713 TTTTAAAATAATAT-
1 TTTTAAAATAATATC
5965727 TTTTAAAA-AATATC
1 TTTTAAAATAATATC
5965741 TTTT
1 TTTT
5965745 CACCCATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTAAAATAATATC
Found at i:5966363 original size:29 final size:30
Alignment explanation
Indices: 5966326--5966385 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
5966316 TAACAACCTG
*
5966326 ATGACTTAAAT-AAAACTTTTGAATAGTTC
1 ATGACTTAAATGAAAACTTTTAAATAGTTC
*
5966355 ATGATTTAAATGAAAACTTTTAAATAGTTC
1 ATGACTTAAATGAAAACTTTTAAATAGTTC
5966385 A
1 A
5966386 ACGATAATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.38
Consensus pattern (30 bp):
ATGACTTAAATGAAAACTTTTAAATAGTTC
Found at i:5970300 original size:14 final size:13
Alignment explanation
Indices: 5970251--5970299 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
5970241 TTGAGAAATG
*
5970251 CTTTTTAAAAGTA
1 CTTTTGAAAAGTA
*
5970264 CTTTGGAAAAGTTA
1 CTTTTGAAAAG-TA
5970278 -TTTTGAAAAGTA
1 CTTTTGAAAAGTA
5970290 CTTTTGAAAA
1 CTTTTGAAAA
5970300 ATTTGGTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 2 0.06
13 27 0.87
14 2 0.06
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (13 bp):
CTTTTGAAAAGTA
Found at i:5972749 original size:2 final size:2
Alignment explanation
Indices: 5972704--5972729 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5972694 CTCAAAATCA
5972704 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5972730 TCTGTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5986201 original size:40 final size:40
Alignment explanation
Indices: 5986118--5986260 Score: 153
Period size: 40 Copynumber: 3.6 Consensus size: 40
5986108 AGTCTAGCGA
* * * *
5986118 TGTTTACAATGTCACGGCTAGTTCAGTAATAATATTG-ATG
1 TGTTTACAGTGTCACTGCCAGTTCAGTAATAATATCGCA-G
* *
5986158 TGTTTACAGTGTCACTGTCAGTTCAGTAGTAATATCGCAG
1 TGTTTACAGTGTCACTGCCAGTTCAGTAATAATATCGCAG
* * * * *
5986198 TGTTTATAGTATCACTGCCAATTCAGTAATATTATCACAG
1 TGTTTACAGTGTCACTGCCAGTTCAGTAATAATATCGCAG
* *
5986238 TGTTTACAGTGTTACTTCCAGTT
1 TGTTTACAGTGTCACTGCCAGTT
5986261 ATAAACATTC
Statistics
Matches: 84, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 83 0.99
41 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (40 bp):
TGTTTACAGTGTCACTGCCAGTTCAGTAATAATATCGCAG
Found at i:5993037 original size:17 final size:17
Alignment explanation
Indices: 5993005--5993046 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
5992995 AGGAAAAAGT
*
5993005 GGTTACAAGAATATGAAA
1 GGTTA-AAGAAAATGAAA
5993023 GGTTAAAGAAAATGAAA
1 GGTTAAAGAAAATGAAA
5993040 GGTTAAA
1 GGTTAAA
5993047 AGTCAAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.52, C:0.02, G:0.24, T:0.21
Consensus pattern (17 bp):
GGTTAAAGAAAATGAAA
Found at i:6009214 original size:21 final size:21
Alignment explanation
Indices: 6009184--6009234 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
6009174 GGATTATGTA
*
6009184 ATTTAAATTTATAAACTTTAT
1 ATTTAGATTTATAAACTTTAT
* *
6009205 GTTTAGATTTCTAAACTTTAT
1 ATTTAGATTTATAAACTTTAT
*
6009226 ATTTGGATT
1 ATTTAGATT
6009235 ATACTATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (21 bp):
ATTTAGATTTATAAACTTTAT
Found at i:6010958 original size:16 final size:14
Alignment explanation
Indices: 6010922--6010949 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6010912 CCGGCCTTCC
6010922 ATATTAATTTTTTA
1 ATATTAATTTTTTA
6010936 ATATTAATTTTTTA
1 ATATTAATTTTTTA
6010950 TAATTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATATTAATTTTTTA
Found at i:6012020 original size:32 final size:32
Alignment explanation
Indices: 6011961--6012032 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
6011951 TTTTTTTAAA
* *
6011961 TTTCGAGTTAATTGAATCAAATTATTCGGTTT
1 TTTCGAGTTAATTGAATCAAATAATTCGATTT
* *
6011993 TTTCGAGTTAACTTGAAT-GAGTAATTCGATTT
1 TTTCGAGTTAA-TTGAATCAAATAATTCGATTT
6012025 TTT-GAGTT
1 TTTCGAGTT
6012033 TGAGATGAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 5 0.14
32 24 0.69
33 6 0.17
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.47
Consensus pattern (32 bp):
TTTCGAGTTAATTGAATCAAATAATTCGATTT
Found at i:6012314 original size:65 final size:66
Alignment explanation
Indices: 6012241--6012365 Score: 234
Period size: 66 Copynumber: 1.9 Consensus size: 66
6012231 AAAATTCTAT
6012241 ACAAAATTCT-AAAAATATATAAAAGGGATAATTTAAAAAAAAATCAAAATTGTTATGAAAATTA
1 ACAAAATTCTAAAAAATATATAAAAGGGATAATTTAAAAAAAAATCAAAATTGTTATGAAAATTA
6012305 A
66 A
*
6012306 ACAAAATTCTAAAAAATATATAAAAGGGATAATTTTAAAAAAAATCAAAATTGTTATGAA
1 ACAAAATTCTAAAAAATATATAAAAGGGATAATTTAAAAAAAAATCAAAATTGTTATGAA
6012366 TATTTTATTA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
65 10 0.17
66 48 0.83
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (66 bp):
ACAAAATTCTAAAAAATATATAAAAGGGATAATTTAAAAAAAAATCAAAATTGTTATGAAAATTA
A
Found at i:6017787 original size:22 final size:22
Alignment explanation
Indices: 6017759--6017810 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
6017749 TTATTTCCTG
* *
6017759 CCATTTTGATATTATTTTGCTA
1 CCATTTTGATATTATATTACTA
*
6017781 CCATTTTGCTATTATATTACTA
1 CCATTTTGATATTATATTACTA
*
6017803 GCATTTTG
1 CCATTTTG
6017811 TTGTTACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.52
Consensus pattern (22 bp):
CCATTTTGATATTATATTACTA
Found at i:6020008 original size:97 final size:97
Alignment explanation
Indices: 6019836--6020026 Score: 294
Period size: 97 Copynumber: 2.0 Consensus size: 97
6019826 TTAGAAAAAT
* * * *
6019836 GGTATTTGATTATCTCGATTTGAAGAAAAGTCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAA
1 GGTATTCGATTATCTCGATTTGAAAAAAAATCGCGCCTAATAAGTTAAGGCACAAATTTTCAAAA
*
6019901 CCAGAGATAAAGAAATATTGCCTCGATTTAAG
66 CCAGAAATAAAGAAATATTGCCTCGATTTAAG
*
6019933 GGTATTCGATTATC-CAGGTTTGAAAAAAAATCGCGCCTAATAAGTTAAGGCACAAATTTTCAAA
1 GGTATTCGATTATCTC-GATTTGAAAAAAAATCGCGCCTAATAAGTTAAGGCACAAATTTTCAAA
* *
6019997 ACCCGAAATAAAGGAATATTGCCTCGATTT
65 ACCAGAAATAAAGAAATATTGCCTCGATTT
6020027 TAAATATTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
96 1 0.01
97 84 0.99
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (97 bp):
GGTATTCGATTATCTCGATTTGAAAAAAAATCGCGCCTAATAAGTTAAGGCACAAATTTTCAAAA
CCAGAAATAAAGAAATATTGCCTCGATTTAAG
Found at i:6020386 original size:59 final size:60
Alignment explanation
Indices: 6020316--6020438 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
6020306 GAAATGTTTT
* *
6020316 AGGGGTAAAAATGTTA-TTTT-GGAAAAATTCGGAG-TAAAAATATAATTCTTGGGAAGTTC
1 AGGGGTAAAAATGTAATTTTTAGG--AAATTCAGAGATAAAAATATAATTCTTGGGAAGTTC
* * * * *
6020375 AGGGGTCAAAATGTAATTTTTAGGAAGTTTAGAGATCAAAATATAATTTTTGGGAAGTTC
1 AGGGGTAAAAATGTAATTTTTAGGAAATTCAGAGATAAAAATATAATTCTTGGGAAGTTC
6020435 AGGG
1 AGGG
6020439 ACCTTTTAGG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
59 21 0.39
60 31 0.57
61 2 0.04
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (60 bp):
AGGGGTAAAAATGTAATTTTTAGGAAATTCAGAGATAAAAATATAATTCTTGGGAAGTTC
Found at i:6020392 original size:30 final size:30
Alignment explanation
Indices: 6020352--6020439 Score: 122
Period size: 30 Copynumber: 2.9 Consensus size: 30
6020342 ATTCGGAGTA
* *
6020352 AAAATATAATTCTTGGGAAGTTCAGGGGTC
1 AAAATATAATTTTTGGGAAGTTCAGGGATC
* * * *
6020382 AAAATGTAATTTTTAGGAAGTTTAGAGATC
1 AAAATATAATTTTTGGGAAGTTCAGGGATC
6020412 AAAATATAATTTTTGGGAAGTTCAGGGA
1 AAAATATAATTTTTGGGAAGTTCAGGGA
6020440 CCTTTTAGGA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.33
Consensus pattern (30 bp):
AAAATATAATTTTTGGGAAGTTCAGGGATC
Found at i:6021187 original size:17 final size:17
Alignment explanation
Indices: 6021165--6021250 Score: 100
Period size: 17 Copynumber: 5.1 Consensus size: 17
6021155 ACTTTTTAAT
*
6021165 TAAATTCAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
6021182 TAAATTTAAACTCAAAA
1 TAAATTTAAATTTAAAA
* *
6021199 TAGATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* *
6021216 TAAATATAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
6021233 TAAATTAAAATTTAAAA
1 TAAATTTAAATTTAAAA
6021250 T
1 T
6021251 TGAATTTAAG
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.36
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:6021210 original size:34 final size:34
Alignment explanation
Indices: 6021165--6021259 Score: 118
Period size: 34 Copynumber: 2.8 Consensus size: 34
6021155 ACTTTTTAAT
*
6021165 TAAATTCAAATTTAAAATAAATTTAAACTCAAAA
1 TAAATTAAAATTTAAAATAAATTTAAACTCAAAA
* * * * *
6021199 TAGATTTAAATTTATAATAAATATAAACTTAAAA
1 TAAATTAAAATTTAAAATAAATTTAAACTCAAAA
*
6021233 TAAATTAAAATTTAAAATTGAATTTAA
1 TAAATTAAAATTTAAAA-TAAATTTAA
6021260 GTACTGGACC
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
34 43 0.86
35 7 0.14
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (34 bp):
TAAATTAAAATTTAAAATAAATTTAAACTCAAAA
Found at i:6021702 original size:20 final size:21
Alignment explanation
Indices: 6021667--6021706 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
6021657 GTTTAAATTT
6021667 TATTTTTCACAATTTAATATA
1 TATTTTTCACAATTTAATATA
*
6021688 TATTTTTC-CATTTTAATAT
1 TATTTTTCACAATTTAATAT
6021707 CATACTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTTCACAATTTAATATA
Found at i:6022369 original size:2 final size:2
Alignment explanation
Indices: 6022356--6022392 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
6022346 CAATTCATAC
*
6022356 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
6022393 TGAAAAGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6024616 original size:6 final size:6
Alignment explanation
Indices: 6024602--6024631 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
6024592 ACATGGGATC
*
6024602 CCCAGT CCCACT CCCACT CCCACT CCCACT
1 CCCACT CCCACT CCCACT CCCACT CCCACT
6024632 GATGACATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.63, G:0.03, T:0.17
Consensus pattern (6 bp):
CCCACT
Found at i:6025808 original size:2 final size:2
Alignment explanation
Indices: 6025803--6025851 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
6025793 ATATATATAT
6025803 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6025845 AG AG AG A
1 AG AG AG A
6025852 TGATATTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6038535 original size:20 final size:20
Alignment explanation
Indices: 6038499--6038537 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6038489 CCATAATCCA
*
6038499 AAAGAAAATAAGTTTAAAAT
1 AAAGAAAATAAGATTAAAAT
6038519 AAAGAAAA-AAGAATTAAAA
1 AAAGAAAATAAG-ATTAAAA
6038538 ATGTAGTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (20 bp):
AAAGAAAATAAGATTAAAAT
Found at i:6043342 original size:16 final size:16
Alignment explanation
Indices: 6043321--6043351 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6043311 TTATGATTAA
6043321 TTATATTAATTTTATT
1 TTATATTAATTTTATT
*
6043337 TTATATTATTTTTAT
1 TTATATTAATTTTAT
6043352 GAGTTTTGAA
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATATTAATTTTATT
Found at i:6044053 original size:11 final size:11
Alignment explanation
Indices: 6044033--6044086 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
6044023 GTTTAAATGG
6044033 ATTTTAAATTT
1 ATTTTAAATTT
6044044 ATTTTAAATTT
1 ATTTTAAATTT
* *
6044055 AAATTT--ACTT
1 -ATTTTAAATTT
6044065 A-TTTAAATTT
1 ATTTTAAATTT
*
6044075 ACTTTAAATTT
1 ATTTTAAATTT
6044086 A
1 A
6044087 AGTTTAATCA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
8 3 0.08
9 1 0.03
10 7 0.19
11 21 0.58
12 4 0.11
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:6044055 original size:6 final size:6
Alignment explanation
Indices: 6044035--6044093 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
6044025 TTAAATGGAT
* * *
6044035 TTTAAA TTT-AT TTTAAA TTTAAA TTTACTTA TTTAAA TTT-AC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
*
6044083 TTTAAG TTTAA
1 TTTAAA TTTAA
6044094 TCAAATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:6044070 original size:14 final size:14
Alignment explanation
Indices: 6044051--6044078 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6044041 TTTATTTTAA
6044051 ATTTAAATTTACTT
1 ATTTAAATTTACTT
6044065 ATTTAAATTTACTT
1 ATTTAAATTTACTT
6044079 TAAATTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTAAATTTACTT
Found at i:6046188 original size:58 final size:57
Alignment explanation
Indices: 6046119--6046338 Score: 171
Period size: 58 Copynumber: 3.8 Consensus size: 57
6046109 AAAATTTTAG
* *
6046119 AAAATTACATTTTGACCTCGAAACTT-CCAAAAATTACCATTTTATCCCT-AAACTTTCT
1 AAAATTACATTTTAACCTCG--ACTTACCAAAAATTACCATTTTA-CCCTCAAACTTTCC
* * * *
6046177 TAAATTCCATTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCTCGAACTTTCC
1 AAAATTACATTTTAACCTCGACTT-ACCAAAAATTACCATTTTACCCTCAAACTTTCC
* * * * ** *
6046235 AAAATTTCATTTTAACCCCGATTTCAACAAAAATTATTATTTTA-CCTCCGAACTTTCC
1 AAAATTACATTTTAACCTCGACTT-ACCAAAAATTACCATTTTACCCT-CAAACTTTCC
* * * * *
6046293 AAAGTCT-CATTTTAATCTC-AATTTCACTAAAATTACCATTTTACCC
1 AAAAT-TACATTTTAACCTCGACTTAC-CAAAAATTACCATTTTACCC
6046339 CTCGAACCTT
Statistics
Matches: 134, Mismatches: 21, Indels: 14
0.79 0.12 0.08
Matches are distributed among these distances:
56 3 0.02
57 24 0.18
58 106 0.79
59 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.37
Consensus pattern (57 bp):
AAAATTACATTTTAACCTCGACTTACCAAAAATTACCATTTTACCCTCAAACTTTCC
Found at i:6046239 original size:29 final size:30
Alignment explanation
Indices: 6046119--6046354 Score: 114
Period size: 29 Copynumber: 8.1 Consensus size: 30
6046109 AAAATTTTAG
6046119 AAAATTA-CATTTTGA-CCTCGAAAC-TTCCA
1 AAAATTACCATTTT-ACCCTCG-AACTTTCCA
* *
6046148 AAAATTACCATTTTATCCCT-AAACTTT-CT
1 AAAATTACCATTTTA-CCCTCGAACTTTCCA
* *
6046177 TAAATT-CCATTTTAACCTCG-A-TTTCACCA
1 AAAATTACCATTTTACCCTCGAACTTT--CCA
6046206 AAAATTACCATTTTACCCTCGAACTTTCC-
1 AAAATTACCATTTTACCCTCGAACTTTCCA
*
6046235 AAAATT-TCATTTTAACCC-CG-A-TTTCAACA
1 AAAATTACCATTTT-ACCCTCGAACTTTC--CA
**
6046264 AAAATTATTATTTTA-CCTCCGAACTTTCC-
1 AAAATTACCATTTTACCCT-CGAACTTTCCA
* ** *
6046293 -AAAGT-CTCATTTTAATCTC-AA-TTTCACT
1 AAAATTAC-CATTTTACCCTCGAACTTTC-CA
* *
6046321 AAAATTACCATTTTACCCCTCGAACCTTCTA
1 AAAATTACCATTTTA-CCCTCGAACTTTCCA
6046352 AAA
1 AAA
6046355 TCCCCTTCTA
Statistics
Matches: 158, Mismatches: 20, Indels: 56
0.68 0.09 0.24
Matches are distributed among these distances:
26 11 0.07
27 8 0.05
28 30 0.19
29 53 0.34
30 36 0.23
31 10 0.06
32 10 0.06
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAATTACCATTTTACCCTCGAACTTTCCA
Found at i:6046345 original size:58 final size:58
Alignment explanation
Indices: 6046146--6046356 Score: 232
Period size: 58 Copynumber: 3.7 Consensus size: 58
6046136 TCGAAACTTC
* * **
6046146 CAAAAATTACCATTTTATCCCT-AAACTTTCTTAAAT-TCCATTTTAACCTCGATTTCA
1 CAAAAATTACCATTTTACCCCTCGAACTTTCCAAAATCT-CATTTTAACCTCGATTTCA
* *
6046203 CCAAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTTCATTTTAACCCCGATTTCAA
1 -CAAAAATTACCATTTTACCCCTCGAACTTTCCAAAATCTCATTTTAACCTCGATTTC-A
** * * * *
6046262 CAAAAATTATTATTTTACCTC-CGAACTTTCCAAAGTCTCATTTTAATCTCAATTTCA
1 CAAAAATTACCATTTTACCCCTCGAACTTTCCAAAATCTCATTTTAACCTCGATTTCA
* * *
6046319 CTAAAATTACCATTTTACCCCTCGAACCTTCTAAAATC
1 CAAAAATTACCATTTTACCCCTCGAACTTTCCAAAATC
6046357 CCCTTCTAAC
Statistics
Matches: 129, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
57 22 0.17
58 103 0.80
59 4 0.03
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.37
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCTCGAACTTTCCAAAATCTCATTTTAACCTCGATTTCA
Found at i:6058725 original size:76 final size:76
Alignment explanation
Indices: 6058599--6059664 Score: 1756
Period size: 76 Copynumber: 14.0 Consensus size: 76
6058589 ATCAACCAAC
* * *
6058599 ATCATTTCCTATCCTCTTGAAATTGAAATAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
6058664 GTAAGAGCAAG
66 GTAAGAGCAAG
*
6058675 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
*
6058740 GTAAGAGCCAG
66 GTAAGAGCAAG
* * *
6058751 ATCATTTCCTATCCTCTTGAAATTGAAATAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
6058816 GTAAGAGCAAG
66 GTAAGAGCAAG
* * * *
6058827 ATCATTTCCTATCCTCTTGAAATTGAAATAGAGTTGGATAACAAGTATTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
6058892 GTAAGAGCAAG
66 GTAAGAGCAAG
* *
6058903 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCCTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
*
6058968 GTAAGAGCAAA
66 GTAAGAGCAAG
* *
6058979 ATCATTTCCTATCCTATTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
6059044 GTAAGAGCAAG
66 GTAAGAGCAAG
* * *
6059055 ATCATTTCCTATCCTCTTGAAATTGAAATAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
6059120 GTAAGAGCAAG
66 GTAAGAGCAAG
* * *
6059131 ATCATTTCCTATCCTCTTGAAATTGAAATAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
6059196 GTAAGAGCAAG
66 GTAAGAGCAAG
* *
6059207 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCCTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
*
6059272 GTAAGAGCAAA
66 GTAAGAGCAAG
* *
6059283 ATCATTTCCTATCCTATTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
6059348 GTAAGAGCAAG
66 GTAAGAGCAAG
*
6059359 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
6059424 GTAAGAGCAAG
66 GTAAGAGCAAG
* * * *
6059435 ATCATTTTCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGGCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
6059500 GTAAGAGCAAG
66 GTAAGAGCAAG
* * * *
6059511 ATCATTTCCTATCCTCTTGAAATTGAAGCAAAGCTGGATATCAGGTCTGTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
6059576 GTAAGAGCAAG
66 GTAAGAGCAAG
* * *
6059587 ATCATTTTCTATCCTCTTGAAATTGAAGTAAAGCTTGATAACAAGTCTTTATCTCTGAAGTT-AT
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGA-
6059651 AGTAAGAGCAAG
65 AGTAAGAGCAAG
6059663 AT
1 AT
6059665 GAATTTTCAA
Statistics
Matches: 933, Mismatches: 56, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
75 1 0.00
76 932 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (76 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAG
Found at i:6060027 original size:11 final size:11
Alignment explanation
Indices: 6060013--6060082 Score: 52
Period size: 11 Copynumber: 6.0 Consensus size: 11
6060003 TTTAAATGGG
6060013 TTTTAAATTTA
1 TTTTAAATTTA
6060024 TTTTAAATTTAA
1 TTTTAAATTT-A
* *
6060036 ATTT-ATTTTAA
1 TTTTAAATTT-A
*
6060047 ATTTAAATTTA
1 TTTTAAATTTA
6060058 CTTATTTAAATTTA
1 --T-TTTAAATTTA
*
6060072 CTTTAAATTTA
1 TTTTAAATTTA
6060083 AGTTTAATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
11 31 0.63
12 8 0.16
14 10 0.20
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:6060034 original size:6 final size:6
Alignment explanation
Indices: 6060014--6060089 Score: 68
Period size: 6 Copynumber: 12.8 Consensus size: 6
6060004 TTAAATGGGT
* * *
6060014 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTACTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA
* *
6060062 TTTAAA TTT-AC TTTAAA TTTAAG TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
6060090 TCAAATTTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
5 12 0.21
6 39 0.70
8 5 0.09
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:6060034 original size:17 final size:17
Alignment explanation
Indices: 6060014--6060088 Score: 102
Period size: 17 Copynumber: 4.6 Consensus size: 17
6060004 TTAAATGGGT
6060014 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
6060031 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
6060048 TTTAAATTTA-CTT--A
1 TTTAAATTTATTTTAAA
*
6060062 TTTAAATTTACTTTAAA
1 TTTAAATTTATTTTAAA
*
6060079 TTTAAGTTTA
1 TTTAAATTTA
6060089 ATCAAATTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
14 11 0.21
15 2 0.04
16 2 0.04
17 37 0.71
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:6060066 original size:14 final size:14
Alignment explanation
Indices: 6060047--6060074 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6060037 TTTATTTTAA
6060047 ATTTAAATTTACTT
1 ATTTAAATTTACTT
6060061 ATTTAAATTTACTT
1 ATTTAAATTTACTT
6060075 TAAATTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTAAATTTACTT
Found at i:6060068 original size:31 final size:31
Alignment explanation
Indices: 6060030--6060088 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
6060020 TTTATTTTAA
*
6060030 ATTTAAATTTATTTTAAATTTAAATTTACTT
1 ATTTAAATTTACTTTAAATTTAAATTTACTT
*
6060061 ATTTAAATTTACTTTAAATTTAAGTTTA
1 ATTTAAATTTACTTTAAATTTAAATTTA
6060089 ATCAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (31 bp):
ATTTAAATTTACTTTAAATTTAAATTTACTT
Found at i:6062176 original size:29 final size:28
Alignment explanation
Indices: 6062122--6062284 Score: 104
Period size: 29 Copynumber: 5.6 Consensus size: 28
6062112 AAATTTTTAG
6062122 AAAATTA-CATTTTGA-CCTCGAAACTTCCA
1 AAAATTACCATTTT-ACCCTCG--ACTTCCA
* * *
6062151 AAAATTACCATTTTATCCCTAGACTTTCT
1 AAAATTACCATTTTA-CCCTCGACTTCCA
* * *
6062180 TAAATT-CCATTTTAACCTCGATTTCACCA
1 AAAATTACCATTTTACCCTCGACTT--CCA
6062209 AAAATTACCATTTTACCCTCGAACTTTCC-
1 AAAATTACCATTTTACCCTCG-AC-TTCCA
* *
6062238 AAAATT-TCATTTTAACCC-CGATTTCAACA
1 AAAATTACCATTTT-ACCCTCGACTTC--CA
*
6062267 AAAATTATCATTTTACCC
1 AAAATTACCATTTTACCC
6062285 CTGAACTTTC
Statistics
Matches: 107, Mismatches: 14, Indels: 26
0.73 0.10 0.18
Matches are distributed among these distances:
26 3 0.03
27 8 0.07
28 17 0.16
29 44 0.41
30 28 0.26
31 5 0.05
32 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (28 bp):
AAAATTACCATTTTACCCTCGACTTCCA
Found at i:6062191 original size:58 final size:57
Alignment explanation
Indices: 6062122--6062341 Score: 198
Period size: 58 Copynumber: 3.8 Consensus size: 57
6062112 AAATTTTTAG
* *
6062122 AAAATTACATTTTGACCTCGAAACTT-CCAAAAATTACCATTTTATCCCTAG-ACTTTCT
1 AAAATTACATTTTAACCTCG--ACTTACCAAAAATTACCATTTTA-CCCTAGAACTTTCC
* * * *
6062180 TAAATTCCATTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCTCGAACTTTCC
1 AAAATTACATTTTAACCTCGACTT-ACCAAAAATTACCATTTTACCCTAGAACTTTCC
* * * * *
6062238 AAAATTTCATTTTAACCCCGATTTCAACAAAAATTATCATTTTACCCCT-GAACTTTCC
1 AAAATTACATTTTAACCTCGACTT-ACCAAAAATTACCATTTTA-CCCTAGAACTTTCC
* * * *
6062296 AAAGTCT-CATTTTAACCTCGA-TTTCACTAAGATTACCATTTTACCC
1 AAAAT-TACATTTTAACCTCGACTTAC-CAAAAATTACCATTTTACCC
6062342 CTCGAACCTT
Statistics
Matches: 138, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
56 6 0.04
57 21 0.15
58 106 0.77
59 5 0.04
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (57 bp):
AAAATTACATTTTAACCTCGACTTACCAAAAATTACCATTTTACCCTAGAACTTTCC
Found at i:6062221 original size:30 final size:29
Alignment explanation
Indices: 6062181--6062281 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 29
6062171 AGACTTTCTT
6062181 AAATTCCATTTTAACCTCGATTTCACCAA
1 AAATTCCATTTTAACCTCGATTTCACCAA
*
6062210 AAATTACCATTTTACCCTCGAACTTT--CC-A
1 AAATT-CCATTTTAACCTCG-A-TTTCACCAA
* * *
6062239 AAATTTCATTTTAACCCCGATTTCAACAA
1 AAATTCCATTTTAACCTCGATTTCACCAA
*
6062268 AAATTATCATTTTA
1 AAATT-CCATTTTA
6062282 CCCCTGAACT
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
26 3 0.05
27 1 0.02
28 12 0.20
29 17 0.28
30 23 0.38
31 1 0.02
32 3 0.05
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.37
Consensus pattern (29 bp):
AAATTCCATTTTAACCTCGATTTCACCAA
Found at i:6062285 original size:29 final size:29
Alignment explanation
Indices: 6062187--6062342 Score: 105
Period size: 29 Copynumber: 5.4 Consensus size: 29
6062177 TCTTAAATTC
* *
6062187 CATTTTAACCTCGATTTCACCAAAAATTAC
1 CATTTTAACCCCGATTTCA-CAAAAATTAT
6062217 CATTTT-ACCCTCGAACTTTC-C-AAAATT-T
1 CATTTTAACCC-CG-A-TTTCACAAAAATTAT
6062245 CATTTTAACCCCGATTTCAACAAAAATTAT
1 CATTTTAACCCCGATTTC-ACAAAAATTAT
* *
6062275 CATTTT-ACCCCTGAACTTTC-C--AAAGTCT
1 CATTTTAACCCC-G-A-TTTCACAAAAATTAT
* * * *
6062303 CATTTTAACCTCGATTTCACTAAGATTAC
1 CATTTTAACCCCGATTTCACAAAAATTAT
6062332 CATTTT-ACCCC
1 CATTTTAACCCC
6062343 TCGAACCTTC
Statistics
Matches: 101, Mismatches: 10, Indels: 32
0.71 0.07 0.22
Matches are distributed among these distances:
26 8 0.08
27 3 0.03
28 25 0.25
29 37 0.37
30 18 0.18
31 2 0.02
32 8 0.08
ACGTcount: A:0.31, C:0.28, G:0.04, T:0.36
Consensus pattern (29 bp):
CATTTTAACCCCGATTTCACAAAAATTAT
Found at i:6062344 original size:116 final size:116
Alignment explanation
Indices: 6062149--6062358 Score: 300
Period size: 116 Copynumber: 1.8 Consensus size: 116
6062139 TCGAAACTTC
* * *
6062149 CAAAAATTACCATTTTATCCCTAGACTTTCTTAAATTCCATTTTAACCTCGATTTCACCAAAAAT
1 CAAAAATTACCATTTTACCCCTAGACTTTCTCAAAGTCCATTTTAACCTCGATTTCACCAAAAAT
*
6062214 TACCATTTTACCCTCGAACTTTCCAAAATTTCATTTTAACCCCGATTTCAA
66 TACCATTTTACCCTCGAACCTTCCAAAATTTCATTTTAACCCCGATTTCAA
* * *
6062265 CAAAAATTATCATTTTACCCCT-GAACTTTC-CAAAGTCTCATTTTAACCTCGATTTCA-CTAAG
1 CAAAAATTACCATTTTACCCCTAG-ACTTTCTCAAAGTC-CATTTTAACCTCGATTTCACCAAAA
*
6062327 ATTACCATTTTACCCCTCGAACCTTCTAAAAT
64 ATTACCATTTTA-CCCTCGAACCTTCCAAAAT
6062359 CCCCTTCTAA
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
115 21 0.25
116 62 0.75
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.36
Consensus pattern (116 bp):
CAAAAATTACCATTTTACCCCTAGACTTTCTCAAAGTCCATTTTAACCTCGATTTCACCAAAAAT
TACCATTTTACCCTCGAACCTTCCAAAATTTCATTTTAACCCCGATTTCAA
Found at i:6062370 original size:58 final size:58
Alignment explanation
Indices: 6062149--6062370 Score: 252
Period size: 58 Copynumber: 3.8 Consensus size: 58
6062139 TCGAAACTTC
* * ** *
6062149 CAAAAATTACCATTTTATCCCTAG-ACTTTCTTAAATTCCATTTTAACCTCGATTTCA
1 CAAAAATTACCATTTTACCCCTCGAACTTTCCAAAATCCCATTTTAACCTCGATTTCA
** *
6062206 CCAAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTTCATTTTAACCCCGATTTCAA
1 -CAAAAATTACCATTTTACCCCTCGAACTTTCCAAAATCCCATTTTAACCTCGATTTC-A
* * *
6062265 CAAAAATTATCATTTTACCCCT-GAACTTTCCAAAGTCTCATTTTAACCTCGATTTCA
1 CAAAAATTACCATTTTACCCCTCGAACTTTCCAAAATCCCATTTTAACCTCGATTTCA
* * * * * *
6062322 CTAAGATTACCATTTTACCCCTCGAACCTTCTAAAATCCCCTTCTAACC
1 CAAAAATTACCATTTTACCCCTCGAACTTTCCAAAATCCCATTTTAACC
6062371 CTAAAATTTC
Statistics
Matches: 142, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
57 25 0.18
58 112 0.79
59 5 0.04
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.36
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCTCGAACTTTCCAAAATCCCATTTTAACCTCGATTTCA
Found at i:6062387 original size:116 final size:113
Alignment explanation
Indices: 6062146--6062395 Score: 272
Period size: 116 Copynumber: 2.2 Consensus size: 113
6062136 ACCTCGAAAC
* * *
6062146 TTCCAAAAATTACCATTTTATCCCTAGACTTTCTTAAATTCCATTTTAACCTCGATTTCACCAAA
1 TTCCAAAAATTA-CATTTTACCCCTAGACTTTCTCAAAGTCCATTTTAACCTCGATTTCACCAAA
* ** * **
6062211 AATTACCATTTTACCCTCGAACTTTCCAAAATTTCATTTTAACCCCGAT
65 AATTACCATTTTACCCTCGAACCTTCCAAAATCCCATTCTAACCCAAAT
6062260 TTCAACAAAAATTATCATTTTACCCCT-GAACTTTC-CAAAGTCTCATTTTAACCTCGATTTCA-
1 TTC--CAAAAATTA-CATTTTACCCCTAG-ACTTTCTCAAAGTC-CATTTTAACCTCGATTTCAC
* * * *
6062322 CTAAGATTACCATTTTACCCCTCGAACCTTCTAAAATCCCCTTCTAACCCTAAAAT
61 CAAAAATTACCATTTTA-CCCTCGAACCTTCCAAAATCCCATTCTAACCC--AAAT
*
6062378 TTCCCAAAATTACATTTT
1 TTCCAAAAATTACATTTT
6062396 TGCCCTCAAA
Statistics
Matches: 114, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
114 3 0.03
115 27 0.24
116 79 0.69
118 5 0.04
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (113 bp):
TTCCAAAAATTACATTTTACCCCTAGACTTTCTCAAAGTCCATTTTAACCTCGATTTCACCAAAA
ATTACCATTTTACCCTCGAACCTTCCAAAATCCCATTCTAACCCAAAT
Found at i:6066043 original size:9 final size:9
Alignment explanation
Indices: 6066026--6066061 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
6066016 GCCGGTACCA
6066026 GATTCAAAG
1 GATTCAAAG
*
6066035 GATTTAAAG
1 GATTCAAAG
*
6066044 GATTCAAAA
1 GATTCAAAG
6066053 GATTCAAAG
1 GATTCAAAG
6066062 AAATTCATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.25
Consensus pattern (9 bp):
GATTCAAAG
Found at i:6068027 original size:26 final size:25
Alignment explanation
Indices: 6067981--6068031 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
6067971 TTCAAATATA
6067981 ATTACACTTACTAATTAATTTAATT
1 ATTACACTTACTAATTAATTTAATT
*
6068006 ATTACATTTGACTAAATT-ATTTAATT
1 ATTACACTT-ACT-AATTAATTTAATT
6068032 TTATATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 11 0.48
27 4 0.17
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (25 bp):
ATTACACTTACTAATTAATTTAATT
Found at i:6068075 original size:21 final size:21
Alignment explanation
Indices: 6068018--6068078 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
6068008 TACATTTGAC
* *
6068018 TAAATT-ATTTAATTT-TATA
1 TAAATTAAATTAATTTCTAAA
*
6068037 T-AATTAAA-TATTTCTCTAAA
1 TAAATTAAATTAATT-TCTAAA
6068057 TAAATTAAATTAATTTCTAAA
1 TAAATTAAATTAATTTCTAAA
6068078 T
1 T
6068079 TATTTATTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 8 0.24
19 3 0.09
20 4 0.12
21 14 0.42
22 4 0.12
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAATTAAATTAATTTCTAAA
Found at i:6068722 original size:17 final size:18
Alignment explanation
Indices: 6068685--6068723 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6068675 AATACTTTTT
* *
6068685 AAAAGTGCTTTTGAGTCA
1 AAAAGTACTTTTGAGTAA
6068703 AAAAGTACTTTTGAG-AA
1 AAAAGTACTTTTGAGTAA
6068720 AAAA
1 AAAA
6068724 CTAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (18 bp):
AAAAGTACTTTTGAGTAA
Found at i:6079758 original size:31 final size:31
Alignment explanation
Indices: 6079684--6079758 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
6079674 TTTAGTTTTT
*
6079684 AATTAAGATT-AAAATTTTATATATACATTTA
1 AATTAA-ATTAAAAATTTTATATATACAATTA
* * * *
6079715 AATCAAAATAAAAATTTTATGTATATAATTA
1 AATTAAATTAAAAATTTTATATATACAATTA
*
6079746 TATTAAATTAAAA
1 AATTAAATTAAAA
6079759 TTCATATATC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 2 0.06
31 33 0.94
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (31 bp):
AATTAAATTAAAAATTTTATATATACAATTA
Found at i:6081802 original size:15 final size:16
Alignment explanation
Indices: 6081778--6081818 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 16
6081768 ATGGGATGAG
6081778 AATAAAATTTTAATTA
1 AATAAAATTTTAATTA
6081794 AAT-AAA-TTTAATTA
1 AATAAAATTTTAATTA
*
6081808 ATTAAAATTTT
1 AATAAAATTTT
6081819 TAAACCCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 10 0.45
15 6 0.27
16 6 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATAAAATTTTAATTA
Found at i:6088095 original size:20 final size:21
Alignment explanation
Indices: 6088059--6088099 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
6088049 AGTTTTTAAG
6088059 TTTAAAATTCAAAAAATTATTT
1 TTTAAAATT-AAAAAATTATTT
6088081 TTTAAAATT-AAAAATTATT
1 TTTAAAATTAAAAAATTATT
6088100 AAAAAGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTAAAATTAAAAAATTATTT
Found at i:6088901 original size:29 final size:29
Alignment explanation
Indices: 6088864--6088927 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
6088854 TAAAAATTTT
* * * *
6088864 ATGTGTATGATTGCACTAAATCAAAGTTC
1 ATGTATATGATTGAACCAAATCAAAATTC
*
6088893 ATGTATATGATTGAACCAAATCAAAATTT
1 ATGTATATGATTGAACCAAATCAAAATTC
6088922 ATGTAT
1 ATGTAT
6088928 CAAATTACAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (29 bp):
ATGTATATGATTGAACCAAATCAAAATTC
Found at i:6090561 original size:14 final size:14
Alignment explanation
Indices: 6090542--6090574 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6090532 ATACATATTA
6090542 AAAAATATAAAA-AT
1 AAAAATA-AAAATAT
6090556 AAAAATAAAAATAT
1 AAAAATAAAAATAT
6090570 AAAAA
1 AAAAA
6090575 ATTAAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAAATAAAAATAT
Found at i:6090580 original size:8 final size:7
Alignment explanation
Indices: 6090540--6090582 Score: 52
Period size: 8 Copynumber: 5.9 Consensus size: 7
6090530 ATATACATAT
6090540 TAAAAAA
1 TAAAAAA
6090547 TATAAAAA
1 TA-AAAAA
6090555 T-AAAAA
1 TAAAAAA
6090561 TAAAAATA
1 TAAAAA-A
6090569 TAAAAAA
1 TAAAAAA
6090576 TTAAAAA
1 -TAAAAA
6090583 CATATATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.19
7 7 0.22
8 19 0.59
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAAAAA
Found at i:6090723 original size:22 final size:22
Alignment explanation
Indices: 6090695--6090752 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 22
6090685 CAAAAATGTA
6090695 AAAAATTGTAAAAA-AATGTTTT-
1 AAAAATT-TAAAAATAAT-TTTTC
6090717 AAAAATTTAAAAATAATTTTTC
1 AAAAATTTAAAAATAATTTTTC
6090739 ATAAAATTCTAAAA
1 A-AAAATT-TAAAA
6090753 TATATAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 10 0.31
22 11 0.34
23 6 0.19
24 5 0.16
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (22 bp):
AAAAATTTAAAAATAATTTTTC
Found at i:6090752 original size:23 final size:21
Alignment explanation
Indices: 6090695--6090768 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 21
6090685 CAAAAATGTA
*
6090695 AAAAATTGTAAAAAAATGTTTT
1 AAAAATT-TAAAATAATGTTTT
6090717 AAAAATTTAAAAATAAT-TTTT
1 AAAAATTT-AAAATAATGTTTT
*
6090738 CATAAAATTCTAAAATATATAATTTT
1 -A-AAAATT-TAAAATA-AT-GTTTT
6090764 AAAAA
1 AAAAA
6090769 GGTATTAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
21 5 0.11
22 15 0.34
23 12 0.27
24 7 0.16
25 1 0.02
26 4 0.09
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
AAAAATTTAAAATAATGTTTT
Found at i:6090768 original size:24 final size:21
Alignment explanation
Indices: 6090695--6090768 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 21
6090685 CAAAAATGTA
*
6090695 AAAAATTGTAAAAA-AATGTTTT
1 AAAAATT-TAAAAATAA-ATTTT
*
6090717 AAAAATTTAAAAATAATTTTT
1 AAAAATTTAAAAATAAATTTT
6090738 CATAAAATTCTAAAATATATAATTTT
1 -A-AAAATT-TAAAA-ATA-AATTTT
6090764 AAAAA
1 AAAAA
6090769 GGTATTAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
21 10 0.23
22 10 0.23
23 6 0.14
24 9 0.20
25 4 0.09
26 5 0.11
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
AAAAATTTAAAAATAAATTTT
Found at i:6093272 original size:17 final size:17
Alignment explanation
Indices: 6093242--6093292 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
6093232 TAAAAGTTTT
6093242 TAAAATTAGA-TAAATGA
1 TAAAATTA-ATTAAATGA
*
6093259 TAAAATTAATTAAATTGT
1 TAAAATTAATTAAA-TGA
*
6093277 TAATATTTAATTAAAT
1 TAA-AATTAATTAAAT
6093293 AAATTAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 1 0.03
17 12 0.41
18 6 0.21
19 10 0.34
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
TAAAATTAATTAAATGA
Found at i:6093421 original size:18 final size:18
Alignment explanation
Indices: 6093384--6093439 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 18
6093374 TTTTGTAGTT
6093384 ATAGA-ATATTGTTATGTAA
1 ATAGATATATTGTTA--TAA
6093403 ATAGATATATTGTTATAA
1 ATAGATATATTGTTATAA
*
6093421 ATTTAGATATGTTGTTATA
1 A--TAGATATATTGTTATA
6093440 TGCTATATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 4 0.12
19 5 0.15
20 24 0.73
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.46
Consensus pattern (18 bp):
ATAGATATATTGTTATAA
Found at i:6093654 original size:39 final size:40
Alignment explanation
Indices: 6093596--6093705 Score: 134
Period size: 39 Copynumber: 2.8 Consensus size: 40
6093586 TATTATTTAT
* *
6093596 ATTCTTATTGGAAATTCAATTTTGTATCAAAATACTC-AA
1 ATTCTTATTGGAAACTCAATTTTGTAACAAAATACTCAAA
* *
6093635 ATTCTTTTTGGAAACTCAATTTTGTAACCAAATACTCAAA
1 ATTCTTATTGGAAACTCAATTTTGTAACAAAATACTCAAA
* * * *
6093675 ATTC-TATTGAAAACACAAATTTATAACAAAA
1 ATTCTTATTGGAAACTCAATTTTGTAACAAAA
6093706 AAAAACCTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 54 0.90
40 6 0.10
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (40 bp):
ATTCTTATTGGAAACTCAATTTTGTAACAAAATACTCAAA
Found at i:6093807 original size:20 final size:22
Alignment explanation
Indices: 6093782--6093823 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
6093772 TGTAAAAACG
*
6093782 TTAATTG-AACATTA-TAAAAA
1 TTAATTGTAAAATTATTAAAAA
6093802 TTAATTGTAAAATTATTAAAAA
1 TTAATTGTAAAATTATTAAAAA
6093824 ATAAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 6 0.32
22 6 0.32
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (22 bp):
TTAATTGTAAAATTATTAAAAA
Found at i:6093908 original size:37 final size:38
Alignment explanation
Indices: 6093856--6093942 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
6093846 TATGTAAGCC
* *
6093856 TAAAATATAAAAATTA-AAGAATGAACTTAAAACTTAA
1 TAAATTATACAAATTATAAGAATGAACTTAAAACTTAA
* * **
6093893 TAAATTATACAAATTATTATAATGAGTTTAAAACTTAA
1 TAAATTATACAAATTATAAGAATGAACTTAAAACTTAA
6093931 TAAATTTATACA
1 TAAA-TTATACA
6093943 TATTTAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 14 0.33
38 21 0.50
39 7 0.17
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (38 bp):
TAAATTATACAAATTATAAGAATGAACTTAAAACTTAA
Found at i:6094787 original size:26 final size:24
Alignment explanation
Indices: 6094758--6094814 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 24
6094748 GGGCACAAAC
6094758 TATGTTCTTAATGTAGTGTTTGTTAT
1 TATGTT-TTAATGTAGTG-TTGTTAT
*
6094784 TATGATTTTAATTTAGTGTTGTTAT
1 TATG-TTTTAATGTAGTGTTGTTAT
*
6094809 TGTGTT
1 TATGTT
6094815 ATTTGTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 2 0.07
25 10 0.36
26 14 0.50
27 2 0.07
ACGTcount: A:0.19, C:0.02, G:0.19, T:0.60
Consensus pattern (24 bp):
TATGTTTTAATGTAGTGTTGTTAT
Found at i:6095493 original size:21 final size:20
Alignment explanation
Indices: 6095441--6095533 Score: 82
Period size: 19 Copynumber: 4.6 Consensus size: 20
6095431 TGCATATATT
***
6095441 ATTTTTATAATTTTCAGA-A
1 ATTTTTATAATTTTTTTATA
* *
6095460 ATTTTTA-ATTTTTTTTATC
1 ATTTTTATAATTTTTTTATA
6095479 ATTTTTATCAATTTTTTTTATAA
1 ATTTTTAT-AA-TTTTTTTAT-A
* *
6095502 ATTTTTAAAATATTTTTATA
1 ATTTTTATAATTTTTTTATA
6095522 ATTTTTATAATT
1 ATTTTTATAATT
6095534 ATTTAAGAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
18 6 0.10
19 14 0.24
20 11 0.19
21 9 0.16
22 11 0.19
23 7 0.12
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (20 bp):
ATTTTTATAATTTTTTTATA
Found at i:6095494 original size:22 final size:21
Alignment explanation
Indices: 6095461--6095533 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
6095451 TTTTCAGAAA
*
6095461 TTTT-TAATTTTTTTTATCAT
1 TTTTATAATTTTTTTTATAAT
6095481 TTTTATCAATTTTTTTTATAAAT
1 TTTTAT-AATTTTTTTTAT-AAT
* *
6095504 TTTTA-AAATATTTTTATAAT
1 TTTTATAATTTTTTTTATAAT
6095524 TTTTATAATT
1 TTTTATAATT
6095534 ATTTAAGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
20 12 0.27
21 14 0.31
22 12 0.27
23 7 0.16
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATAATTTTTTTTATAAT
Found at i:6095526 original size:8 final size:9
Alignment explanation
Indices: 6095441--6095538 Score: 52
Period size: 9 Copynumber: 9.8 Consensus size: 9
6095431 TGCATATATT
6095441 ATTTTTATA
1 ATTTTTATA
* *
6095450 ATTTTCAGAA
1 ATTTTTA-TA
*
6095460 ATTTTTAATT
1 ATTTTT-ATA
* *
6095470 TTTTTTATC
1 ATTTTTATA
6095479 ATTTTTATCA
1 ATTTTTAT-A
6095489 ATTTTTTTTATAA
1 A---TTTTTAT-A
*
6095502 ATTTTTAAAA
1 ATTTTT-ATA
6095512 TATTTTTATA
1 -ATTTTTATA
6095522 ATTTTTATA
1 ATTTTTATA
6095531 ATTATTTA
1 ATT-TTTA
6095539 AGAAACCATT
Statistics
Matches: 68, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
9 27 0.40
10 24 0.35
11 8 0.12
13 9 0.13
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:6095655 original size:9 final size:10
Alignment explanation
Indices: 6095636--6095721 Score: 71
Period size: 10 Copynumber: 9.4 Consensus size: 10
6095626 CTGGATTTTC
6095636 TTAAT-ATTT
1 TTAATAATTT
*
6095645 TTATTAATTT
1 TTAATAATTT
6095655 TTAATAA-TT
1 TTAATAATTT
6095664 TT-A-AATTT
1 TTAATAATTT
*
6095672 TT-ATAATTC
1 TTAATAATTT
*
6095681 TTAATAAATT
1 TTAATAATTT
6095691 TT-A-AATTT
1 TTAATAATTT
*
6095699 TT-ATAATTC
1 TTAATAATTT
*
6095708 TTAATAAATT
1 TTAATAATTT
6095718 TTAA
1 TTAA
6095722 ATAGTTCTCT
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
7 2 0.03
8 13 0.21
9 21 0.34
10 26 0.42
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
TTAATAATTT
Found at i:6095690 original size:27 final size:27
Alignment explanation
Indices: 6095636--6095723 Score: 142
Period size: 27 Copynumber: 3.2 Consensus size: 27
6095626 CTGGATTTTC
*
6095636 TTAATATTTTTATTAATTTTTAAT-AATT
1 TTAA-ATTTTTA-TAATTCTTAATAAATT
6095664 TTAAATTTTTATAATTCTTAATAAATT
1 TTAAATTTTTATAATTCTTAATAAATT
6095691 TTAAATTTTTATAATTCTTAATAAATT
1 TTAAATTTTTATAATTCTTAATAAATT
6095718 TTAAAT
1 TTAAAT
6095724 AGTTCTCTAT
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
26 10 0.17
27 44 0.76
28 4 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (27 bp):
TTAAATTTTTATAATTCTTAATAAATT
Found at i:6106479 original size:18 final size:19
Alignment explanation
Indices: 6106446--6106484 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
6106436 AAAATCTAAA
* *
6106446 ATAAAAATTTATAAAT-TT
1 ATAAAAATATAAAAATATT
6106464 ATAAAAATATAAAAATATT
1 ATAAAAATATAAAAATATT
6106483 AT
1 AT
6106485 TTGACACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAAAATATAAAAATATT
Found at i:6107911 original size:19 final size:19
Alignment explanation
Indices: 6107887--6107980 Score: 66
Period size: 19 Copynumber: 4.8 Consensus size: 19
6107877 AATTATAAAA
6107887 ATAAAAATCA-ATAAAATTT
1 ATAAAAAT-ATATAAAATTT
*
6107906 ATAAAAATATTTAAAATTT
1 ATAAAAATATATAAAATTT
* * **
6107925 ACTAAAAATTAGAAAAAAAAT
1 A-TAAAAA-TATATAAAATTT
* *
6107946 ATAAAAAAATTGTAAAATTTT
1 ATAAAAATA-TATAAAA-TTT
6107967 ATAAAAAT-TATAAA
1 ATAAAAATATATAAA
6107981 TAAATTATAA
Statistics
Matches: 56, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
18 1 0.02
19 23 0.41
20 16 0.29
21 16 0.29
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
ATAAAAATATATAAAATTT
Found at i:6107963 original size:30 final size:30
Alignment explanation
Indices: 6107929--6107993 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
6107919 AAATTTACTA
*
6107929 AAAATTAGAAAAAAAATATAAAAAAATTGT
1 AAAATTAGAAAAAAAATATAAAAAAATTAT
** * * *
6107959 AAAATTTTATAAAAATTATAAATAAATTAT
1 AAAATTAGAAAAAAAATATAAAAAAATTAT
6107989 AAAAT
1 AAAAT
6107994 GCATCAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (30 bp):
AAAATTAGAAAAAAAATATAAAAAAATTAT
Found at i:6107963 original size:41 final size:40
Alignment explanation
Indices: 6107905--6107992 Score: 115
Period size: 41 Copynumber: 2.2 Consensus size: 40
6107895 CAATAAAATT
*
6107905 TATAAAAATATTTAAAA-TTTACTAAAAATTAGAAAAAAAA
1 TATAAAAAAATTTAAAATTTTA-TAAAAATTAGAAAAAAAA
* * *
6107945 TATAAAAAAATTGTAAAATTTTATAAAAATTATAAATAAAT
1 TATAAAAAAATT-TAAAATTTTATAAAAATTAGAAAAAAAA
6107986 TATAAAA
1 TATAAAA
6107993 TGCATCAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
40 11 0.26
41 27 0.64
42 4 0.10
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (40 bp):
TATAAAAAAATTTAAAATTTTATAAAAATTAGAAAAAAAA
Found at i:6109692 original size:12 final size:12
Alignment explanation
Indices: 6109675--6109746 Score: 51
Period size: 12 Copynumber: 6.2 Consensus size: 12
6109665 CGTTTGTTTA
6109675 ATGTTCACGAAC
1 ATGTTCACGAAC
***
6109687 ATGTTCATTTA-
1 ATGTTCACGAAC
*
6109698 AT-TTAATCGAAC
1 ATGTTCA-CGAAC
6109710 ATGTTCACGAAC
1 ATGTTCACGAAC
**
6109722 AT-TAAACGAAC
1 ATGTTCACGAAC
*
6109733 ATGTTCATGAAC
1 ATGTTCACGAAC
6109745 AT
1 AT
6109747 ATAATTGAAC
Statistics
Matches: 43, Mismatches: 13, Indels: 8
0.67 0.20 0.12
Matches are distributed among these distances:
10 3 0.07
11 12 0.28
12 25 0.58
13 3 0.07
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (12 bp):
ATGTTCACGAAC
Found at i:6109726 original size:23 final size:23
Alignment explanation
Indices: 6109700--6109769 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
6109690 TTCATTTAAT
6109700 TTAATCGAACATGTTCACGAACA
1 TTAATCGAACATGTTCACGAACA
* *
6109723 TTAAACGAACATGTTCATGAACA
1 TTAATCGAACATGTTCACGAACA
* *
6109746 TATAATTGAACAGGTTCACGAACA
1 T-TAATCGAACATGTTCACGAACA
6109770 ATGTTAATGA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 22 0.55
24 18 0.45
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:6109767 original size:47 final size:46
Alignment explanation
Indices: 6109681--6109769 Score: 124
Period size: 47 Copynumber: 1.9 Consensus size: 46
6109671 TTTAATGTTC
** * *
6109681 ACGAACATGTTCATTTAATTTAATCGAACATGTTCACGAACATTAA
1 ACGAACATGTTCATGAAATATAATCGAACAGGTTCACGAACATTAA
*
6109727 ACGAACATGTTCATGAACATATAATTGAACAGGTTCACGAACA
1 ACGAACATGTTCATGAA-ATATAATCGAACAGGTTCACGAACA
6109770 ATGTTAATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
46 15 0.41
47 22 0.59
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.28
Consensus pattern (46 bp):
ACGAACATGTTCATGAAATATAATCGAACAGGTTCACGAACATTAA
Found at i:6121119 original size:16 final size:16
Alignment explanation
Indices: 6121096--6121167 Score: 108
Period size: 16 Copynumber: 4.5 Consensus size: 16
6121086 CGTTTGGTTC
*
6121096 GCTGTAATAGAATAGA
1 GCTGTAATGGAATAGA
*
6121112 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
6121128 ACTGTAATGGAATATA
1 GCTGTAATGGAATAGA
6121144 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
6121160 GCTGTAAT
1 GCTGTAAT
6121168 CAGTAATTCT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:6121240 original size:44 final size:46
Alignment explanation
Indices: 6121149--6121242 Score: 140
Period size: 44 Copynumber: 2.1 Consensus size: 46
6121139 ATATAGCTGT
* *
6121149 AATGGAATAGAGCTGTAATCAGTAATTCTATTGTTTGGTTGATTGG
1 AATGGAATAGAGCTGTAATCAATAATTCTATTGTTTGGTTGAATGG
6121195 AATGGAATAGAGCTGTAAT-AAT-ATTCT-TGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATCAATAATTCTAT-TGTTTGGTTGAATGG
6121239 AATG
1 AATG
6121243 ATGCTGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 2 0.04
46 19 0.42
ACGTcount: A:0.30, C:0.05, G:0.27, T:0.38
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAATCAATAATTCTATTGTTTGGTTGAATGG
Found at i:6121404 original size:58 final size:55
Alignment explanation
Indices: 6121337--6121482 Score: 177
Period size: 58 Copynumber: 2.5 Consensus size: 55
6121327 AATTTTAATG
*
6121337 ATTATTATTAAATATAATTGAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATT-AATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
*
6121395 ATTATTATTAAATATAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAA-TTAAT-AAA-AATATGTAATTTAATAATATTTTTAACATA
*
6121453 ATTATTATTAAAATATGAATTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTAATAAAAAT
6121483 TATAATATAT
Statistics
Matches: 79, Mismatches: 3, Indels: 13
0.83 0.03 0.14
Matches are distributed among these distances:
57 3 0.04
58 41 0.52
59 18 0.23
60 10 0.13
61 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.47
Consensus pattern (55 bp):
ATTATTATTAAATATAATTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:6127545 original size:25 final size:24
Alignment explanation
Indices: 6127500--6127546 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
6127490 GGTTTTTATG
**
6127500 TTATTTTATTCAATATTAATATAA
1 TTATTTTATTCAATAAAAATATAA
*
6127524 TTATATTTATTTAATAAAAATAT
1 TTAT-TTTATTCAATAAAAATAT
6127547 TAATATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TTATTTTATTCAATAAAAATATAA
Found at i:6139008 original size:29 final size:30
Alignment explanation
Indices: 6138971--6139170 Score: 129
Period size: 29 Copynumber: 6.8 Consensus size: 30
6138961 GGTTAAAATT
6138971 GGGTCAAAAAT-GAGATTTTGGAAAGTTCGA
1 GGGTCAAAAATGGA-ATTTTGGAAAGTTCGA
*
6139001 GGGT--AAAATGGTAATTTTTGGTAAA-ATCG-
1 GGGTCAAAAATGG-AA-TTTTGG-AAAGTTCGA
6139030 GGGTCAAAAATGGAATTTTGGAAAGTTCGA
1 GGGTCAAAAATGGAATTTTGGAAAGTTCGA
* **
6139060 GGGT--AAAATGGTAATTTTTGATAAAATCGA
1 GGGTCAAAAATGG-AATTTTGGA-AAGTTCGA
* * * *
6139090 -GGTAAAAAATGGAATTATGGAAAACTT-GG
1 GGGTCAAAAATGGAATTTTGG-AAAGTTCGA
* * *
6139119 GGGT-AAAAATGTAATTTTAGAAAGTTTTG-
1 GGGTCAAAAATGGAATTTTGGAAAG-TTCGA
6139148 GGGTCAAAATAT--AATTTTGGAAA
1 GGGTCAAAA-ATGGAATTTTGGAAA
6139171 AGTTTAGGGG
Statistics
Matches: 137, Mismatches: 15, Indels: 37
0.72 0.08 0.20
Matches are distributed among these distances:
28 18 0.13
29 56 0.41
30 43 0.31
31 20 0.15
ACGTcount: A:0.39, C:0.04, G:0.27, T:0.30
Consensus pattern (30 bp):
GGGTCAAAAATGGAATTTTGGAAAGTTCGA
Found at i:6139047 original size:30 final size:29
Alignment explanation
Indices: 6138943--6139136 Score: 124
Period size: 29 Copynumber: 6.7 Consensus size: 29
6138933 GGATACCCGA
*
6138943 GGGT-AAAATGGTAATTTTGGTTAAAAT-T
1 GGGTAAAAATGGTAATTTTGG-TAAAATCG
*
6138971 GGGTCAAAAAT-G-AGATTTTGG-AAAGTTCG
1 GGGT-AAAAATGGTA-ATTTTGGTAAA-ATCG
6139000 AGGGT-AAAATGGTAATTTTTGGTAAAATCG
1 -GGGTAAAAATGGTAA-TTTTGGTAAAATCG
*
6139030 GGGTCAAAAATGG-AATTTTGG-AAAGTTCG
1 GGGT-AAAAATGGTAATTTTGGTAAA-ATCG
*
6139059 AGGGT-AAAATGGTAATTTTTGATAAAATCG
1 -GGGTAAAAATGGTAA-TTTTGGTAAAATCG
* * *
6139089 AGGTAAAAAATGG-AATTATGG-AAAACTTGG
1 GGGT-AAAAATGGTAATTTTGGTAAAA--TCG
6139119 GGGTAAAAAT-GTAATTTT
1 GGGTAAAAATGGTAATTTT
6139137 AGAAAGTTTT
Statistics
Matches: 132, Mismatches: 12, Indels: 43
0.71 0.06 0.23
Matches are distributed among these distances:
27 3 0.02
28 26 0.20
29 43 0.33
30 40 0.30
31 20 0.15
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (29 bp):
GGGTAAAAATGGTAATTTTGGTAAAATCG
Found at i:6139049 original size:59 final size:59
Alignment explanation
Indices: 6138940--6139112 Score: 262
Period size: 59 Copynumber: 2.9 Consensus size: 59
6138930 TTTGGATACC
*
6138940 CGAGGGTAAAATGGTAA-TTTTGGTTAAAAT-TGGGTCAAAAAT-GAGATTTTGGAAAGTT
1 CGAGGGTAAAATGGTAATTTTTGG-TAAAATCGGGGTCAAAAATGGA-ATTTTGGAAAGTT
6138998 CGAGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGGAATTTTGGAAAGTT
1 CGAGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGGAATTTTGGAAAGTT
* * * *
6139057 CGAGGGTAAAATGGTAATTTTTGATAAAATCGAGGTAAAAAATGGAATTATGGAAA
1 CGAGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGGAATTTTGGAAA
6139113 ACTTGGGGGT
Statistics
Matches: 107, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
58 23 0.21
59 82 0.77
60 2 0.02
ACGTcount: A:0.39, C:0.04, G:0.27, T:0.30
Consensus pattern (59 bp):
CGAGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGGAATTTTGGAAAGTT
Found at i:6139133 original size:59 final size:59
Alignment explanation
Indices: 6138940--6139136 Score: 231
Period size: 59 Copynumber: 3.4 Consensus size: 59
6138930 TTTGGATACC
* * * * * *
6138940 CGAGGGTAAAATGGTAATTTTGGTTAAAATTG-GGTCAAAAAT-GAGATTTTGGAAAGTT
1 CGAGGGTAAAATGGTAATTTTTGATAAAATCGAGGTAAAAAATGGA-ATTATGGAAACTT
* * * * *
6138998 CGAGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGGAATTTTGGAAAGTT
1 CGAGGGTAAAATGGTAATTTTTGATAAAATCGAGGTAAAAAATGGAATTATGGAAACTT
6139057 CGAGGGTAAAATGGTAATTTTTGATAAAATCGAGGTAAAAAATGGAATTATGGAAAACTT
1 CGAGGGTAAAATGGTAATTTTTGATAAAATCGAGGTAAAAAATGGAATTATGG-AAACTT
*
6139117 -GGGGGTAAAAAT-GTAATTTT
1 CGAGGGT-AAAATGGTAATTTT
6139137 AGAAAGTTTT
Statistics
Matches: 126, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
58 29 0.23
59 85 0.67
60 12 0.10
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (59 bp):
CGAGGGTAAAATGGTAATTTTTGATAAAATCGAGGTAAAAAATGGAATTATGGAAACTT
Found at i:6139149 original size:30 final size:29
Alignment explanation
Indices: 6139095--6139217 Score: 106
Period size: 29 Copynumber: 4.2 Consensus size: 29
6139085 ATCGAGGTAA
* * * * * *
6139095 AAAATGGAATTATGGAAAACTTGGGGGTA
1 AAAATGTAATTTTAGAAAAGTTTGGGGTC
6139124 AAAATGTAATTTTAG-AAAGTTTTGGGGTC
1 AAAATGTAATTTTAGAAAAG-TTTGGGGTC
* *
6139153 AAAATATAATTTTGGAAAAGTTTAGGGGTC
1 AAAATGTAATTTTAGAAAAGTTT-GGGGTC
* *
6139183 AAAATGTAA-TTTACAAAAAGTTTTAGGGTC
1 AAAATGTAATTTTA-GAAAAG-TTTGGGGTC
6139213 AAAAT
1 AAAAT
6139218 AGCATTTTTG
Statistics
Matches: 77, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
28 3 0.04
29 38 0.49
30 33 0.43
31 3 0.04
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAAGTTTGGGGTC
Found at i:6139225 original size:60 final size:59
Alignment explanation
Indices: 6139118--6139239 Score: 156
Period size: 60 Copynumber: 2.1 Consensus size: 59
6139108 GGAAAACTTG
* * * *
6139118 GGGGTAAAAATGTAATTTTAGAAAGTTTTGGGGTCAAAATATAA-TTTTGGAAAAGTTTA
1 GGGGTAAAAATGTAATTTCAAAAAGTTTTAGGGTCAAAATAGAATTTTTGG-AAAGTTTA
* * *
6139177 GGGGTCAAAATGTAATTTACAAAAAGTTTTAGGGTCAAAATAGCATTTTTGGATAGTTTA
1 GGGGTAAAAATGTAATTT-CAAAAAGTTTTAGGGTCAAAATAGAATTTTTGGAAAGTTTA
6139237 GGG
1 GGG
6139240 ACTACCAAGG
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 17 0.31
60 31 0.57
61 6 0.11
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (59 bp):
GGGGTAAAAATGTAATTTCAAAAAGTTTTAGGGTCAAAATAGAATTTTTGGAAAGTTTA
Done.