Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 12 of 210
Found at i:4513733 original size:42 final size:42
Alignment explanation
Indices: 4513687--4513822 Score: 155
Period size: 42 Copynumber: 3.2 Consensus size: 42
4513677 AGGCCGCACA
* * *
4513687 GAAGCACATAAGTGCTAAACAGAAACCCATAAAGGTTGAACG
1 GAAGCTCATAAGAGCTAAACAGAAACCCATAAAGGTTAAACG
* * * *
4513729 GAAGCTCATAAGAGCTTAACGGAAACCCATAAAGCTTAAACT
1 GAAGCTCATAAGAGCTAAACAGAAACCCATAAAGGTTAAACG
* * * * *
4513771 GAAGCTCAAAAGAGCCAAACAGTAACCCATTAGGGTTAAACG
1 GAAGCTCATAAGAGCTAAACAGAAACCCATAAAGGTTAAACG
*
4513813 GAAACTCATA
1 GAAGCTCATA
4513823 TGAGTTAACT
Statistics
Matches: 76, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAACAGAAACCCATAAAGGTTAAACG
Found at i:4513738 original size:21 final size:20
Alignment explanation
Indices: 4513714--4513782 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
4513704 AACAGAAACC
*
4513714 CATAAAGGTTGAACGGAAGCT
1 CATAAAGCTT-AACGGAAGCT
* *
4513735 CATAAGAGCTTAACGGAAACC
1 CATAA-AGCTTAACGGAAGCT
*
4513756 CATAAAGCTTAAACTGAAGCT
1 CATAAAGCTT-AACGGAAGCT
4513777 CA-AAAG
1 CATAAAG
4513783 AGCCAAACAG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 9 0.22
21 27 0.68
22 4 0.10
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.17
Consensus pattern (20 bp):
CATAAAGCTTAACGGAAGCT
Found at i:4515996 original size:15 final size:15
Alignment explanation
Indices: 4515976--4516005 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4515966 TTTAATTTAT
4515976 GGGCCAAAACTTTTG
1 GGGCCAAAACTTTTG
4515991 GGGCCAAAACTTTTG
1 GGGCCAAAACTTTTG
4516006 CTTACCCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (15 bp):
GGGCCAAAACTTTTG
Found at i:4518814 original size:2 final size:2
Alignment explanation
Indices: 4518807--4518838 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4518797 GTGTTAAAAC
4518807 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4518839 TTGCATATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4520303 original size:3 final size:3
Alignment explanation
Indices: 4520295--4520322 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4520285 GAACCCAACA
4520295 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4520323 TCTTCTAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:4521435 original size:23 final size:22
Alignment explanation
Indices: 4521392--4521435 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
4521382 TGCTTAAAAT
* *
4521392 TTAAAGTATTTTAATTTAATTC
1 TTAAAATATTTTAATTCAATTC
*
4521414 TTAAAATATTTTTATATCAATT
1 TTAAAATATTTTAAT-TCAATT
4521436 AAGTCCTTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (22 bp):
TTAAAATATTTTAATTCAATTC
Found at i:4522562 original size:17 final size:18
Alignment explanation
Indices: 4522528--4522565 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4522518 CTGGTTAGAG
* *
4522528 TTTTAGCCATCTTTTCTT
1 TTTTAACCATCTTCTCTT
4522546 TTTTAACCATC-TCTCTT
1 TTTTAACCATCTTCTCTT
4522563 TTT
1 TTT
4522566 GATTCTCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.13, C:0.24, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTAACCATCTTCTCTT
Found at i:4531755 original size:2 final size:2
Alignment explanation
Indices: 4531748--4531773 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4531738 TTTTGCTAAT
4531748 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
4531774 ATAGTTAGTG
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):
TA
Found at i:4541227 original size:119 final size:119
Alignment explanation
Indices: 4541016--4541254 Score: 469
Period size: 119 Copynumber: 2.0 Consensus size: 119
4541006 TTGATGCTCA
*
4541016 TCAAAGTGCGGAGTTGTAGAAAACTTCTACAGTTGTCGAGTTGTATCAAGTGCTAGCTAAGACTA
1 TCAAAGTACGGAGTTGTAGAAAACTTCTACAGTTGTCGAGTTGTATCAAGTGCTAGCTAAGACTA
4541081 ATAAGTCAAGTATTTATTCTCTTCTTGATAGAATTATTCGTCTTGTGCTAACTC
66 ATAAGTCAAGTATTTATTCTCTTCTTGATAGAATTATTCGTCTTGTGCTAACTC
4541135 TCAAAGTACGGAGTTGTAGAAAACTTCTACAGTTGTCGAGTTGTATCAAGTGCTAGCTAAGACTA
1 TCAAAGTACGGAGTTGTAGAAAACTTCTACAGTTGTCGAGTTGTATCAAGTGCTAGCTAAGACTA
4541200 ATAAGTCAAGTATTTATTCTCTTCTTGATAGAATTATTCGTCTTGTGCTAACTC
66 ATAAGTCAAGTATTTATTCTCTTCTTGATAGAATTATTCGTCTTGTGCTAACTC
4541254 T
1 T
4541255 TCCCGTGTCT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (119 bp):
TCAAAGTACGGAGTTGTAGAAAACTTCTACAGTTGTCGAGTTGTATCAAGTGCTAGCTAAGACTA
ATAAGTCAAGTATTTATTCTCTTCTTGATAGAATTATTCGTCTTGTGCTAACTC
Found at i:4542203 original size:14 final size:15
Alignment explanation
Indices: 4542175--4542204 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4542165 CACATATGAA
4542175 ACTTCTATGTATTTC
1 ACTTCTATGTATTTC
4542190 ACTTCTAT-TATTTC
1 ACTTCTATGTATTTC
4542204 A
1 A
4542205 TCCACATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.23, C:0.20, G:0.03, T:0.53
Consensus pattern (15 bp):
ACTTCTATGTATTTC
Found at i:4545074 original size:24 final size:24
Alignment explanation
Indices: 4545010--4545082 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
4545000 GTGCTTCCTG
*
4545010 ATTAATTGCTCTTCGGAGTTACCC
1 ATTAATTGCTCTTCGGAGCTACCC
* * *
4545034 GTTAACTACTCTTCGGAGCTACCC
1 ATTAATTGCTCTTCGGAGCTACCC
* *
4545058 ATTAATTGCTATCCGGAGCTACCC
1 ATTAATTGCTCTTCGGAGCTACCC
4545082 A
1 A
4545083 ATATAGGCTC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (24 bp):
ATTAATTGCTCTTCGGAGCTACCC
Found at i:4547445 original size:2 final size:2
Alignment explanation
Indices: 4547438--4547473 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4547428 AAAATATTAA
* *
4547438 AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4547474 TTACAAACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4551496 original size:22 final size:23
Alignment explanation
Indices: 4551471--4551514 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
4551461 AAATTTTATA
*
4551471 AATAATTTAA-AAGAATAAATTC
1 AATAATATAAGAAGAATAAATTC
4551493 AATAATATAATGAAGAATAAAT
1 AATAATATAA-GAAGAATAAAT
4551515 GTTATACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
24 10 0.53
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (23 bp):
AATAATATAAGAAGAATAAATTC
Found at i:4552795 original size:12 final size:12
Alignment explanation
Indices: 4552778--4552810 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4552768 GTTCGCAAAT
4552778 AAAAACATAAAG
1 AAAAACATAAAG
4552790 AAAAACAT-AAG
1 AAAAACATAAAG
4552801 -AAAACATAAA
1 AAAAACATAAA
4552811 AACAACTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.35
11 5 0.25
12 8 0.40
ACGTcount: A:0.76, C:0.09, G:0.06, T:0.09
Consensus pattern (12 bp):
AAAAACATAAAG
Found at i:4555459 original size:21 final size:21
Alignment explanation
Indices: 4555429--4555488 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
4555419 GGTGGATTAG
4555429 CTCTCACGAGCTTCTGTTCAA
1 CTCTCACGAGCTTCTGTTCAA
* * *
4555450 CTCTCGCGAGCTTTTGTTCAG
1 CTCTCACGAGCTTCTGTTCAA
* * *
4555471 CTCTTATGAACTTCTGTT
1 CTCTCACGAGCTTCTGTT
4555489 AATGATGTAC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.15, C:0.28, G:0.17, T:0.40
Consensus pattern (21 bp):
CTCTCACGAGCTTCTGTTCAA
Found at i:4559340 original size:17 final size:18
Alignment explanation
Indices: 4559307--4559342 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
4559297 TGCTTCCAAT
4559307 AAGCACTTTTGGGACAAA
1 AAGCACTTTTGGGACAAA
4559325 AAGCACTTTT-GGACAAA
1 AAGCACTTTTGGGACAAA
4559342 A
1 A
4559343 TCATTCCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (18 bp):
AAGCACTTTTGGGACAAA
Found at i:4582679 original size:2 final size:2
Alignment explanation
Indices: 4582672--4582706 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4582662 TTGAATGCTT
*
4582672 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4582707 GTAACAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4588266 original size:45 final size:44
Alignment explanation
Indices: 4588168--4588297 Score: 170
Period size: 45 Copynumber: 2.9 Consensus size: 44
4588158 GCTATATGCC
*
4588168 TAAAATGAGTAAGACCATAATTGAAAGATGTTATGGCATCATGA
1 TAAAATGAGTAAGACCATAGTTGAAAGATGTTATGGCATCATGA
* *
4588212 TAAGGATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGA
1 TAA-AATGAGTAAGACCATAGTTGAAAGATGTTATGGCATCATGA
* * * * *
4588257 TATAAATGAGTAGGATCATGGTTGAAAGACGTTATGACATC
1 TA-AAATGAGTAAGACCATAGTTGAAAGATGTTATGGCATC
4588298 CTTTGACAGC
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
44 3 0.04
45 70 0.95
46 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (44 bp):
TAAAATGAGTAAGACCATAGTTGAAAGATGTTATGGCATCATGA
Found at i:4588370 original size:27 final size:27
Alignment explanation
Indices: 4588305--4588441 Score: 112
Period size: 27 Copynumber: 5.1 Consensus size: 27
4588295 ATCCTTTGAC
* * *
4588305 AGCCCGACGGGACGTTAAACACAGGAT
1 AGCCCGACGAGACATTAAACACGGGAT
** * * *
4588332 AATCCAATGAGACATTAAACATGGGAT
1 AGCCCGACGAGACATTAAACACGGGAT
* * *
4588359 AGCCCGACGAGACGTTAAATACGAGAT
1 AGCCCGACGAGACATTAAACACGGGAT
** * * *
4588386 AGTTCGACAAGACGTTAAACATGGGAT
1 AGCCCGACGAGACATTAAACACGGGAT
* *
4588413 AACCCGACGGGACATTAAACACGGGAT
1 AGCCCGACGAGACATTAAACACGGGAT
4588440 AG
1 AG
4588442 TTCAACGGGA
Statistics
Matches: 80, Mismatches: 30, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
27 80 1.00
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (27 bp):
AGCCCGACGAGACATTAAACACGGGAT
Found at i:4588449 original size:27 final size:27
Alignment explanation
Indices: 4588419--4588577 Score: 156
Period size: 27 Copynumber: 5.9 Consensus size: 27
4588409 GGATAACCCG
*
4588419 ACGGGACATTAAACACGGGATAGTTCA
1 ACGGGACATTAAACACGAGATAGTTCA
* * **
4588446 ACGGGATATTAAACACAAGATAGTTTG
1 ACGGGACATTAAACACGAGATAGTTCA
* * *
4588473 ATGGGACATTAAACATGAGATATTTCA
1 ACGGGACATTAAACACGAGATAGTTCA
* **
4588500 ATGGGACATTAAACATAAGATAGTTCA
1 ACGGGACATTAAACACGAGATAGTTCA
** *
4588527 ATAGGACATTAAACACGAGATATTTCA
1 ACGGGACATTAAACACGAGATAGTTCA
** * *
4588554 ACAAGACATTAAACATGAGTTAGT
1 ACGGGACATTAAACACGAGATAGT
4588578 CCGTCGGGAC
Statistics
Matches: 109, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 109 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.25
Consensus pattern (27 bp):
ACGGGACATTAAACACGAGATAGTTCA
Found at i:4588458 original size:54 final size:54
Alignment explanation
Indices: 4588307--4588460 Score: 182
Period size: 54 Copynumber: 2.9 Consensus size: 54
4588297 CCTTTGACAG
* * * * *
4588307 CCCGACGGGACGTTAAACACAGGATAATCCAATGAGACATTAAACATGGGATAG
1 CCCGACGGGACGTTAAACACGGGATAGTTCAACGAGACATTAAACATGGGATAA
* * * * * *
4588361 CCCGACGAGACGTTAAATACGAGATAGTTCGACAAGACGTTAAACATGGGATAA
1 CCCGACGGGACGTTAAACACGGGATAGTTCAACGAGACATTAAACATGGGATAA
* * *
4588415 CCCGACGGGACATTAAACACGGGATAGTTCAACGGGATATTAAACA
1 CCCGACGGGACGTTAAACACGGGATAGTTCAACGAGACATTAAACA
4588461 CAAGATAGTT
Statistics
Matches: 80, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
54 80 1.00
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (54 bp):
CCCGACGGGACGTTAAACACGGGATAGTTCAACGAGACATTAAACATGGGATAA
Found at i:4588458 original size:81 final size:81
Alignment explanation
Indices: 4588373--4588572 Score: 211
Period size: 81 Copynumber: 2.5 Consensus size: 81
4588363 CGACGAGACG
* * * * **
4588373 TTAAATACGAGATAGTTCGACAAGACGTTAAACATGGGATAACCCGACGGGACATTAAACACGGG
1 TTAAACACGAGATAGTTCGACAAGACATTAAACATGAGATAACCCAACGGGACATTAAACACAAG
* *
4588438 ATAGTTCAACGGGATA
66 ATAGTTCAACAGGACA
* * *** *** * *
4588454 TTAAACACAAGATAGTTTGATGGGACATTAAACATGAGATATTTCAATGGGACATTAAACATAAG
1 TTAAACACGAGATAGTTCGACAAGACATTAAACATGAGATAACCCAACGGGACATTAAACACAAG
*
4588519 ATAGTTCAATAGGACA
66 ATAGTTCAACAGGACA
* *
4588535 TTAAACACGAGATATTTCAACAAGACATTAAACATGAG
1 TTAAACACGAGATAGTTCGACAAGACATTAAACATGAG
4588573 TTAGTCCGTC
Statistics
Matches: 93, Mismatches: 26, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
81 93 1.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.23
Consensus pattern (81 bp):
TTAAACACGAGATAGTTCGACAAGACATTAAACATGAGATAACCCAACGGGACATTAAACACAAG
ATAGTTCAACAGGACA
Found at i:4588569 original size:54 final size:54
Alignment explanation
Indices: 4588422--4588569 Score: 197
Period size: 54 Copynumber: 2.7 Consensus size: 54
4588412 TAACCCGACG
* * * * ** *
4588422 GGACATTAAACACGGGATAGTTCAACGGGATATTAAACACAAGATAGTTTGATG
1 GGACATTAAACACGAGATATTTCAACGGGACATTAAACATAAGATAGTTCAATA
* *
4588476 GGACATTAAACATGAGATATTTCAATGGGACATTAAACATAAGATAGTTCAATA
1 GGACATTAAACACGAGATATTTCAACGGGACATTAAACATAAGATAGTTCAATA
**
4588530 GGACATTAAACACGAGATATTTCAACAAGACATTAAACAT
1 GGACATTAAACACGAGATATTTCAACGGGACATTAAACAT
4588570 GAGTTAGTCC
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 81 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (54 bp):
GGACATTAAACACGAGATATTTCAACGGGACATTAAACATAAGATAGTTCAATA
Found at i:4588588 original size:54 final size:54
Alignment explanation
Indices: 4588341--4588588 Score: 185
Period size: 54 Copynumber: 4.6 Consensus size: 54
4588331 TAATCCAATG
* * * * * * *
4588341 AGACATTAAACATGGGATAGCCCGACGAGACGTTAAATACGAGATAGTTCGACA
1 AGACATTAAACATGAGATAGTCCGTCGGGACATTAAACACGAGATAGTTCAACA
* * ** * * *
4588395 AGACGTTAAACATGGGATAACCCGACGGGACATTAAACACGGGATAGTTCAACG
1 AGACATTAAACATGAGATAGTCCGTCGGGACATTAAACACGAGATAGTTCAACA
* * ** ** * * **
4588449 GGATATTAAACACAAGATAGTTTGAT-GGGACATTAAACATGAGATATTTCAATG
1 AGACATTAAACATGAGATAGTCCG-TCGGGACATTAAACACGAGATAGTTCAACA
* * ** * *
4588503 GGACATTAAACATAAGATAGTTCAAT-AGGACATTAAACACGAGATATTTCAACA
1 AGACATTAAACATGAGATAG-TCCGTCGGGACATTAAACACGAGATAGTTCAACA
*
4588557 AGACATTAAACATGAGTTAGTCCGTCGGGACA
1 AGACATTAAACATGAGATAGTCCGTCGGGACA
4588589 CTCAACATGG
Statistics
Matches: 153, Mismatches: 38, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
53 3 0.02
54 149 0.97
55 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (54 bp):
AGACATTAAACATGAGATAGTCCGTCGGGACATTAAACACGAGATAGTTCAACA
Found at i:4590662 original size:7 final size:6
Alignment explanation
Indices: 4590634--4590661 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
4590624 TTTTCAAAAT
4590634 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
4590662 TACATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:4596115 original size:17 final size:16
Alignment explanation
Indices: 4596093--4596124 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
4596083 TGACAATCTA
4596093 TTTTAATATTTATTTAT
1 TTTTAATA-TTATTTAT
4596110 TTTTAATATTATTTA
1 TTTTAATATTATTTA
4596125 GTTAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTAATATTATTTAT
Found at i:4597211 original size:21 final size:21
Alignment explanation
Indices: 4597172--4597212 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4597162 GTGAGAAAGC
* * *
4597172 AGTAAAAAATAATAGTAAAAT
1 AGTAAAAAACAACAATAAAAT
4597193 AGTAAAAAACAACAATAAAA
1 AGTAAAAAACAACAATAAAA
4597213 AATAGCAATT
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:0.71, C:0.05, G:0.07, T:0.17
Consensus pattern (21 bp):
AGTAAAAAACAACAATAAAAT
Found at i:4605709 original size:30 final size:30
Alignment explanation
Indices: 4605673--4605730 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
4605663 TTAACAAGCC
*
4605673 AATGCCTCTAAAATAGTAACAAAATTAACA
1 AATGCCTCTAAAATAATAACAAAATTAACA
4605703 AATGCCTCTAAAATAATAACAAAATTAA
1 AATGCCTCTAAAATAATAACAAAATTAA
4605731 TAATAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.24
Consensus pattern (30 bp):
AATGCCTCTAAAATAATAACAAAATTAACA
Found at i:4611583 original size:50 final size:50
Alignment explanation
Indices: 4611525--4611656 Score: 158
Period size: 50 Copynumber: 2.6 Consensus size: 50
4611515 CATTGAGATT
* *
4611525 ATGAGAGGTCCCATATAAGACCATGTCTGGGACATGACGTTGGCACCAAG
1 ATGAGAGGTCCCATATAAGACCATGTCTGGGACATGACATGGGCACCAAG
* * * *
4611575 ATGAGAGGTCCGC-CATAAGACCATGTCTGAGACATGACATGGGCACCGAT
1 ATGAGAGGTCC-CATATAAGACCATGTCTGGGACATGACATGGGCACCAAG
** * *
4611625 ATGAGAACTCGCATATAAGACCATATCTGGGA
1 ATGAGAGGTCCCATATAAGACCATGTCTGGGA
4611657 TATGGAATTG
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
49 1 0.01
50 66 0.97
51 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (50 bp):
ATGAGAGGTCCCATATAAGACCATGTCTGGGACATGACATGGGCACCAAG
Found at i:4613777 original size:40 final size:39
Alignment explanation
Indices: 4613733--4613818 Score: 120
Period size: 38 Copynumber: 2.2 Consensus size: 39
4613723 ACATGTGTCA
* **
4613733 TATATTACCCCAAGGATCCATGACAAGGGCTAGACCTCAT
1 TATATTACCCCAAGAATCCACAACAA-GGCTAGACCTCAT
*
4613773 TATATTA-CCCAAGAATCCACAACAAGGCTAGATCTCAT
1 TATATTACCCCAAGAATCCACAACAAGGCTAGACCTCAT
4613811 TATATTAC
1 TATATTAC
4613819 TCGAGAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
38 19 0.46
39 15 0.37
40 7 0.17
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (39 bp):
TATATTACCCCAAGAATCCACAACAAGGCTAGACCTCAT
Found at i:4613811 original size:38 final size:38
Alignment explanation
Indices: 4613733--4613859 Score: 137
Period size: 39 Copynumber: 3.3 Consensus size: 38
4613723 ACATGTGTCA
* * *
4613733 TATATTACCCCAAGGATCCATGACAAGGGCTAGACCTCAT
1 TATATTA-CCCAAGAATCCATAACAA-GGCTAGATCTCAT
*
4613773 TATATTACCCAAGAATCCACAACAAGGCTAGATCTCAT
1 TATATTACCCAAGAATCCATAACAAGGCTAGATCTCAT
* * ** * *
4613811 TATATTACTCGAGAATCTGTAACAAATGCTAGATCTCGT
1 TATATTACCCAAGAATCCATAAC-AAGGCTAGATCTCAT
4613850 TATATTACCC
1 TATATTACCC
4613860 GATAATTTGT
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
38 30 0.41
39 37 0.50
40 7 0.09
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (38 bp):
TATATTACCCAAGAATCCATAACAAGGCTAGATCTCAT
Found at i:4613871 original size:39 final size:39
Alignment explanation
Indices: 4613761--4613892 Score: 140
Period size: 39 Copynumber: 3.4 Consensus size: 39
4613751 CATGACAAGG
* * * *** *
4613761 GCTAGACCTCATTATATTACCCAAGAATCCACAAC-AAG
1 GCTAGATCTCGTTATATTACCCGAGAATCTGTAACAAAT
* *
4613799 GCTAGATCTCATTATATTACTCGAGAATCTGTAACAAAT
1 GCTAGATCTCGTTATATTACCCGAGAATCTGTAACAAAT
* *
4613838 GCTAGATCTCGTTATATTACCCGATAATTTGTAACAAAT
1 GCTAGATCTCGTTATATTACCCGAGAATCTGTAACAAAT
* *
4613877 TCTAGATCTTGTTATA
1 GCTAGATCTCGTTATA
4613893 ACCTGTGCAA
Statistics
Matches: 80, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
38 29 0.36
39 51 0.64
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (39 bp):
GCTAGATCTCGTTATATTACCCGAGAATCTGTAACAAAT
Found at i:4615961 original size:41 final size:41
Alignment explanation
Indices: 4615916--4615997 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
4615906 AAAATATGGG
4615916 ATAAAATTGAGGGATAATAGGTATTTTTTTAGGTGTAATGA
1 ATAAAATTGAGGGATAATAGGTATTTTTTTAGGTGTAATGA
4615957 ATAAAATTGAGGGATAATAGGTATTTTTTTAGGTGTAATGA
1 ATAAAATTGAGGGATAATAGGTATTTTTTTAGGTGTAATGA
4615998 CTTATTTAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (41 bp):
ATAAAATTGAGGGATAATAGGTATTTTTTTAGGTGTAATGA
Found at i:4623730 original size:28 final size:28
Alignment explanation
Indices: 4623665--4623730 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 28
4623655 TTTATAATGT
* *
4623665 TTTCCTTAAAATAAATTAAATATCAAAG
1 TTTCTTTAAAATAAATTAAATATCAAAA
* * *
4623693 TTT-TTCAAAATAAAATTTAGTA-CAAAA
1 TTTCTTTAAAAT-AAATTAAATATCAAAA
4623720 TTTCTTTAAAA
1 TTTCTTTAAAA
4623731 AATCCATTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
27 13 0.43
28 17 0.57
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.39
Consensus pattern (28 bp):
TTTCTTTAAAATAAATTAAATATCAAAA
Found at i:4625057 original size:17 final size:17
Alignment explanation
Indices: 4625037--4625072 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
4625027 TTCTAAATAA
4625037 TTTTTATTTTAAAATTT
1 TTTTTATTTTAAAATTT
*
4625054 TTTTTATTTTCAAATTT
1 TTTTTATTTTAAAATTT
4625071 TT
1 TT
4625073 AAAAATCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTATTTTAAAATTT
Found at i:4630471 original size:17 final size:17
Alignment explanation
Indices: 4630449--4630482 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4630439 GTCTATATTT
* *
4630449 AAAATTTTAATAAAATA
1 AAAATTCTAAAAAAATA
4630466 AAAATTCTAAAAAAATA
1 AAAATTCTAAAAAAATA
4630483 TATATGCTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATTCTAAAAAAATA
Found at i:4631866 original size:13 final size:13
Alignment explanation
Indices: 4631827--4631866 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
4631817 AGTTCTTCAT
4631827 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
4631840 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
4631853 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
4631866 T
1 T
4631867 TTAGTTTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.28, C:0.07, G:0.30, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:4642682 original size:16 final size:16
Alignment explanation
Indices: 4642663--4642704 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
4642653 TAAAATTATT
4642663 AAATATTAAAATAAAA
1 AAATATTAAAATAAAA
*
4642679 AAATA-TAAATATTAAA
1 AAATATTAAA-ATAAAA
4642695 AAA-ATTAAAA
1 AAATATTAAAA
4642705 ATAATATGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATATTAAAATAAAA
Found at i:4642706 original size:18 final size:17
Alignment explanation
Indices: 4642674--4642707 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4642664 AATATTAAAA
*
4642674 TAAAAAAATATAAATAT
1 TAAAAAAATAAAAATAT
4642691 TAAAAAAATTAAAAATA
1 TAAAAAAA-TAAAAATA
4642708 ATATGGACAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAAAATAAAAATAT
Found at i:4661859 original size:21 final size:22
Alignment explanation
Indices: 4661834--4661874 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4661824 ATAACTTTGT
4661834 TTAAATAT-AAACCCTAAACGC
1 TTAAATATGAAACCCTAAACGC
* *
4661855 TTAAATTTGAGACCCTAAAC
1 TTAAATATGAAACCCTAAAC
4661875 TCGATATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.27
Consensus pattern (22 bp):
TTAAATATGAAACCCTAAACGC
Found at i:4666864 original size:9 final size:9
Alignment explanation
Indices: 4666850--4666925 Score: 73
Period size: 9 Copynumber: 8.4 Consensus size: 9
4666840 GTAGTGATTC
4666850 AATTCGGTT
1 AATTCGGTT
*
4666859 AATTCGGAT
1 AATTCGGTT
*
4666868 AATTCGATT
1 AATTCGGTT
* *
4666877 AATTTGGGT
1 AATTCGGTT
*
4666886 AATTCAGTT
1 AATTCGGTT
4666895 AATTCGAG-T
1 AATTCG-GTT
**
4666904 AATTTAGTT
1 AATTCGGTT
4666913 AATTCGGTT
1 AATTCGGTT
4666922 AATT
1 AATT
4666926 TTTAACCAAA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
8 1 0.02
9 49 0.96
10 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:4666888 original size:27 final size:27
Alignment explanation
Indices: 4666858--4666925 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
4666848 TCAATTCGGT
* * *
4666858 TAATTCGGATAATTCGATTAATTTGGG
1 TAATTCGGTTAATTCGAGTAATTTAGG
* *
4666885 TAATTCAGTTAATTCGAGTAATTTAGT
1 TAATTCGGTTAATTCGAGTAATTTAGG
4666912 TAATTCGGTTAATT
1 TAATTCGGTTAATT
4666926 TTTAACCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (27 bp):
TAATTCGGTTAATTCGAGTAATTTAGG
Found at i:4668992 original size:5 final size:5
Alignment explanation
Indices: 4668982--4669048 Score: 55
Period size: 5 Copynumber: 12.6 Consensus size: 5
4668972 AGCTACCCCA
* * *
4668982 TTTAT TTTAT TTTAT TATTATTT TTTAT ATTAT TTAAT TTTAT TTTCT
1 TTTAT TTTAT TTTAT T-TTA--T TTTAT TTTAT TTTAT TTTAT TTTAT
4669030 TAATT-T TTTAT TTTAT TTT
1 T--TTAT TTTAT TTTAT TTT
4669049 TTCATTATTC
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
4 2 0.04
5 37 0.73
6 5 0.10
7 5 0.10
8 2 0.04
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:4669008 original size:23 final size:22
Alignment explanation
Indices: 4668982--4669050 Score: 88
Period size: 23 Copynumber: 3.1 Consensus size: 22
4668972 AGCTACCCCA
*
4668982 TTTATTTTATTTTATTATTATTT
1 TTTATATTATTTTATT-TTATTT
*
4669005 TTTATATTATTTAATTTTATTT
1 TTTATATTATTTTATTTTATTT
4669027 TCTTA-ATT-TTTTATTTTATTT
1 T-TTATATTATTTTATTTTATTT
4669048 TTT
1 TTT
4669051 CATTATTCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.05
21 13 0.31
22 10 0.24
23 17 0.40
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTATATTATTTTATTTTATTT
Found at i:4669062 original size:22 final size:21
Alignment explanation
Indices: 4668988--4669062 Score: 89
Period size: 21 Copynumber: 3.4 Consensus size: 21
4668978 CCCATTTATT
4668988 TTATTTTATTATTATTTTTTATA
1 TTATTTTATT-TTATTTTTTA-A
*
4669011 TTATTTAATTTTATTTTCTTAA
1 TTATTTTATTTTATTTT-TTAA
*
4669033 TT-TTTTATTTTATTTTTTCA
1 TTATTTTATTTTATTTTTTAA
4669053 TTATTCTTAT
1 TTATT-TTAT
4669063 ACTTAGATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
20 5 0.11
21 15 0.33
22 14 0.30
23 12 0.26
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (21 bp):
TTATTTTATTTTATTTTTTAA
Found at i:4669183 original size:12 final size:11
Alignment explanation
Indices: 4669158--4669232 Score: 51
Period size: 12 Copynumber: 6.4 Consensus size: 11
4669148 TATCATTGAG
4669158 TTTACTTTTTTT
1 TTTA-TTTTTTT
*
4669170 TTTGTTTTTGTT
1 TTTATTTTT-TT
4669182 TTTATTTTTTAT
1 TTTATTTTTT-T
* *
4669194 TTTACTTTCTTA
1 TTTA-TTTTTTT
*
4669206 TTTATCTTTCTT
1 TTTAT-TTTTTT
* *
4669218 TTTAATTTTGT
1 TTTATTTTTTT
4669229 TTTA
1 TTTA
4669233 GTTGCTTAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
11 15 0.31
12 29 0.59
13 5 0.10
ACGTcount: A:0.12, C:0.07, G:0.04, T:0.77
Consensus pattern (11 bp):
TTTATTTTTTT
Found at i:4673935 original size:10 final size:10
Alignment explanation
Indices: 4673880--4673945 Score: 57
Period size: 10 Copynumber: 6.7 Consensus size: 10
4673870 GTTTTATAAT
4673880 TAAAATCATT-
1 TAAAAT-ATTA
4673890 TAAAAT-TTA
1 TAAAATATTA
*
4673899 TTAAA-ATTA
1 TAAAATATTA
* *
4673908 TAGAAGACTTA
1 TAAAATA-TTA
*
4673919 TAGAATATTA
1 TAAAATATTA
4673929 TAAAATATTA
1 TAAAATATTA
4673939 TAAAATA
1 TAAAATA
4673946 AAAATATTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
8 2 0.04
9 10 0.21
10 26 0.55
11 9 0.19
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (10 bp):
TAAAATATTA
Found at i:4673951 original size:16 final size:16
Alignment explanation
Indices: 4673930--4673973 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
4673920 AGAATATTAT
4673930 AAAATATTATAAAATA
1 AAAATATTATAAAATA
*
4673946 AAAATATTATAAATTA
1 AAAATATTATAAAATA
*
4673962 TAAATATATATA
1 AAAATAT-TATA
4673974 TATATAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATATTATAAAATA
Found at i:4674551 original size:21 final size:20
Alignment explanation
Indices: 4674521--4674570 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
4674511 TACAATATTT
*
4674521 TAATTCATATAACTTTTT-TAA
1 TAATTTATATAA-TTTTTGT-A
4674542 TAATTTATATAATTTTTGTA
1 TAATTTATATAATTTTTGTA
4674562 TAATTTATA
1 TAATTTATA
4674571 ATAAATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (20 bp):
TAATTTATATAATTTTTGTA
Found at i:4674564 original size:20 final size:21
Alignment explanation
Indices: 4674521--4674579 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
4674511 TACAATATTT
*
4674521 TAATTCATATAACTTTTTTAA
1 TAATTTATATAACTTTTTTAA
4674542 TAATTTATATAA-TTTTTGT-A
1 TAATTTATATAACTTTTT-TAA
*
4674562 TAATTTATAATAAATTTT
1 TAATTTAT-ATAACTTTT
4674580 ATAAATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 14 0.41
21 16 0.47
22 4 0.12
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (21 bp):
TAATTTATATAACTTTTTTAA
Found at i:4674573 original size:30 final size:29
Alignment explanation
Indices: 4674539--4674618 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
4674529 ATAACTTTTT
4674539 TAATAATTTATATAATTTTTGTA-TAATTTA
1 TAATAATTT-TATAATTTTT-TAGTAATTTA
* *
4674569 TAATAAATTTTATAAATTTTTAGTCATTTA
1 TAAT-AATTTTATAATTTTTTAGTAATTTA
*
4674599 TAATATTTTTATAATTTTTT
1 TAATAATTTTATAATTTTTT
4674619 GCACTTTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 16 0.36
30 23 0.52
31 5 0.11
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.59
Consensus pattern (29 bp):
TAATAATTTTATAATTTTTTAGTAATTTA
Found at i:4674586 original size:20 final size:20
Alignment explanation
Indices: 4674521--4674587 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 20
4674511 TACAATATTT
* * *
4674521 TAATTCATATAACTTTTTTAA
1 TAATTTATATAAATTTTAT-A
* *
4674542 TAATTTATATAATTTTTGTA
1 TAATTTATATAAATTTTATA
4674562 TAATTTATAATAAATTTTATA
1 TAATTTAT-ATAAATTTTATA
4674583 -AATTT
1 TAATTT
4674588 TTAGTCATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.55
Consensus pattern (20 bp):
TAATTTATATAAATTTTATA
Found at i:4674616 original size:9 final size:9
Alignment explanation
Indices: 4674535--4674617 Score: 51
Period size: 10 Copynumber: 8.6 Consensus size: 9
4674525 TCATATAACT
4674535 TTTTTAATAA
1 TTTTT-ATAA
*
4674545 TTTATATAA
1 TTTTTATAA
4674554 TTTTTGTATAA
1 -TTTT-TATAA
*
4674565 TTTATAATAA
1 TTT-TTATAA
*
4674575 ATTTTATAAA
1 TTTTTAT-AA
*
4674585 TTTTTAGTCA
1 TTTTTA-TAA
*
4674595 TTTATA-ATA
1 TTTTTATA-A
4674604 TTTTTATAA
1 TTTTTATAA
4674613 TTTTT
1 TTTTT
4674618 TGCACTTTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
9 19 0.34
10 30 0.54
11 7 0.12
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:4674651 original size:30 final size:29
Alignment explanation
Indices: 4674595--4674665 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
4674585 TTTTTAGTCA
*
4674595 TTTATAATATTTTTATAATTTTTTGC-ACT
1 TTTAT-ATATTTTTACAATTTTTTGCAACT
4674624 TTTATATATTTTTACATATTCTTTTGCAACT
1 TTTATATATTTTTACA-ATT-TTTTGCAACT
4674655 TTTA-ATATTTT
1 TTTATATATTTT
4674666 AATTATTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
28 10 0.26
29 8 0.21
30 13 0.34
31 7 0.18
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (29 bp):
TTTATATATTTTTACAATTTTTTGCAACT
Found at i:4677165 original size:37 final size:37
Alignment explanation
Indices: 4677131--4677209 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 37
4677121 TGTTGTAACT
4677131 ATGT-ATTTTTAAATTAAAAATTATATTAAATGTAAAAA
1 ATGTGATTTTT-AA-TAAAAATTATATTAAATGTAAAAA
* *
4677169 ATGTGATTTTTAATAAAAATTATTTTAAA-G-ATAAA
1 ATGTGATTTTTAATAAAAATTATATTAAATGTAAAAA
4677204 ATGTGA
1 ATGTGA
4677210 AATTGATACC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
35 10 0.26
36 1 0.03
37 15 0.39
38 6 0.16
39 6 0.16
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (37 bp):
ATGTGATTTTTAATAAAAATTATATTAAATGTAAAAA
Found at i:4688794 original size:14 final size:14
Alignment explanation
Indices: 4688775--4688821 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
4688765 TTAGCTTACC
4688775 ATTTTAGTTTATAT
1 ATTTTAGTTTATAT
*
4688789 ATTTTAATTTGATAT
1 ATTTTAGTTT-ATAT
* *
4688804 -TTTTTGTTTTTAT
1 ATTTTAGTTTATAT
4688817 ATTTT
1 ATTTT
4688822 TAAAATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 3 0.11
14 20 0.74
15 4 0.15
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.70
Consensus pattern (14 bp):
ATTTTAGTTTATAT
Found at i:4691332 original size:23 final size:23
Alignment explanation
Indices: 4691283--4691416 Score: 184
Period size: 23 Copynumber: 6.0 Consensus size: 23
4691273 CCTGATCAGT
*
4691283 ATACGACACAT-AAGTGTCTG--
1 ATACGACACATAAAGTGCCTGAA
* *
4691303 ATACGACACACAAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
** *
4691326 ATACGACACACGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
*
4691349 ATACGACACATAAAGTGCCTGAT
1 ATACGACACATAAAGTGCCTGAA
4691372 ATACGACACATAAAGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
4691395 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
4691417 TCGGCATAGC
Statistics
Matches: 102, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
20 10 0.10
21 7 0.07
23 85 0.83
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:4697573 original size:47 final size:46
Alignment explanation
Indices: 4697522--4697669 Score: 172
Period size: 45 Copynumber: 3.2 Consensus size: 46
4697512 CAACTGACAC
* *
4697522 AAAAATCAAGCAAGCTAAAAAAATCCCCAATTTCATATGAACCCTAA
1 AAAAAT-ATGCAAACTAAAAAAATCCCCAATTTCATATGAACCCTAA
** * * * *
4697569 AAAAAT-TGCAAACTAAAAAAATCTACAATTTTATATAAATCTTAA
1 AAAAATATGCAAACTAAAAAAATCCCCAATTTCATATGAACCCTAA
*
4697614 AACAATATTGCAAACTAAAAAAAATCCCCAATTTCATATGAACCCTAA
1 AAAAATA-TGCAAACT-AAAAAAATCCCCAATTTCATATGAACCCTAA
*
4697662 AACAATAT
1 AAAAATAT
4697670 TGTTAAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
45 36 0.43
47 15 0.18
48 32 0.39
ACGTcount: A:0.53, C:0.19, G:0.04, T:0.24
Consensus pattern (46 bp):
AAAAATATGCAAACTAAAAAAATCCCCAATTTCATATGAACCCTAA
Found at i:4697663 original size:48 final size:47
Alignment explanation
Indices: 4697531--4697671 Score: 196
Period size: 48 Copynumber: 3.0 Consensus size: 47
4697521 CAAAAATCAA
*
4697531 GCAAGCTAAAAAAATCCCCAATTTCATATGAACCCTAAAA-AA-ATT
1 GCAAACTAAAAAAATCCCCAATTTCATATGAACCCTAAAACAATATT
** * * * *
4697576 GCAAACTAAAAAAATCTACAATTTTATATAAATCTTAAAACAATATT
1 GCAAACTAAAAAAATCCCCAATTTCATATGAACCCTAAAACAATATT
4697623 GCAAACTAAAAAAAATCCCCAATTTCATATGAACCCTAAAACAATATT
1 GCAAACT-AAAAAAATCCCCAATTTCATATGAACCCTAAAACAATATT
4697671 G
1 G
4697672 TTAAATATAT
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
45 33 0.41
46 2 0.03
47 10 0.12
48 35 0.44
ACGTcount: A:0.50, C:0.19, G:0.05, T:0.26
Consensus pattern (47 bp):
GCAAACTAAAAAAATCCCCAATTTCATATGAACCCTAAAACAATATT
Found at i:4698935 original size:13 final size:14
Alignment explanation
Indices: 4698919--4698957 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
4698909 ATAATTTATG
4698919 TATTTCATTTTCA-
1 TATTTCATTTTCAC
*
4698932 TATTTCA-ATTCAC
1 TATTTCATTTTCAC
4698945 TATTTCATTTTCA
1 TATTTCATTTTCA
4698958 ATTCACATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 4 0.18
13 14 0.64
14 4 0.18
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTTCATTTTCAC
Found at i:4699117 original size:40 final size:40
Alignment explanation
Indices: 4699062--4699196 Score: 118
Period size: 37 Copynumber: 3.4 Consensus size: 40
4699052 ACCAGTTTGG
*
4699062 CACCCAGTGCCTCATCGGATAATTCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGGATAATCCGAAGTAGTAAATTGA
* * *
4699102 CACCCAGTGTCTCATCGG-TTATACCG-A--AGTAAATTGG
1 CACCCAGTGCCTCATCGGATAAT-CCGAAGTAGTAAATTGA
* * * *
4699139 CATCCAGTGCCTCATC-AAGTAAATCCGAAGTAATAAATTTA
1 CACCCAGTGCCTCATCGGA-T-AATCCGAAGTAGTAAATTGA
* *
4699180 CACCCAATGTCTCATCG
1 CACCCAGTGCCTCATCG
4699197 ACTTGAAGTT
Statistics
Matches: 73, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
37 23 0.32
38 4 0.05
39 7 0.10
40 19 0.26
41 20 0.27
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGGATAATCCGAAGTAGTAAATTGA
Found at i:4699377 original size:2 final size:2
Alignment explanation
Indices: 4699370--4699413 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4699360 TACATTCATA
4699370 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4699412 AT
1 AT
4699414 CAATTCAGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4700175 original size:2 final size:2
Alignment explanation
Indices: 4700160--4700201 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
4700150 ACTTCTTTTA
4700160 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AGT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
4700201 A
1 A
4700202 CTTAAACATT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 33 0.89
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4700253 original size:34 final size:34
Alignment explanation
Indices: 4700185--4700253 Score: 79
Period size: 34 Copynumber: 2.0 Consensus size: 34
4700175 TATATATATA
* *
4700185 TATAGTATATATATATACTTAAACATTAAGATTT
1 TATAGTATATATATATACATAAACATTAACATTT
*
4700219 TATATTATAATATATATA-ATAAAC-TTACACATTT
1 TATAGTAT-ATATATATACATAAACATTA-ACATTT
4700253 T
1 T
4700254 TTAACCTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
33 3 0.10
34 18 0.60
35 9 0.30
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (34 bp):
TATAGTATATATATATACATAAACATTAACATTT
Found at i:4701380 original size:6 final size:6
Alignment explanation
Indices: 4701369--4701397 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4701359 AATTTTATTT
4701369 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
4701398 AGAACCCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:4703169 original size:18 final size:19
Alignment explanation
Indices: 4703146--4703190 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
4703136 AAATTCATAT
4703146 CTAAATTATACTTTATT-C
1 CTAAATTATACTTTATTAC
*
4703164 CTAAATTATATTTTATTAC
1 CTAAATTATACTTTATTAC
4703183 CTAAATTA
1 CTAAATTA
4703191 CCTAACTCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (19 bp):
CTAAATTATACTTTATTAC
Found at i:4704485 original size:2 final size:2
Alignment explanation
Indices: 4704478--4704514 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
4704468 GCAGGAAGAG
* *
4704478 TA TA TA TA TA TA TA TA TA TA TA TA TA CA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4704515 TCTGTTCACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:4708188 original size:27 final size:28
Alignment explanation
Indices: 4708152--4708207 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
4708142 ACCAAAATGT
4708152 TATAACTTTTTTTATTTACCAAAAAATA
1 TATAACTTTTTTTATTTACCAAAAAATA
*
4708180 TATAA-TTTTTTTATTTACCAAAATATA
1 TATAACTTTTTTTATTTACCAAAAAATA
4708207 T
1 T
4708208 TAAAAAAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (28 bp):
TATAACTTTTTTTATTTACCAAAAAATA
Found at i:4708291 original size:27 final size:27
Alignment explanation
Indices: 4708258--4708331 Score: 116
Period size: 27 Copynumber: 2.7 Consensus size: 27
4708248 CCTTGGTCAC
4708258 GCCAATGGCATTGGCGGCACCAATGGT
1 GCCAATGGCATTGGCGGCACCAATGGT
4708285 GCCAATGGCATTGGCGGCACCAATGGT
1 GCCAATGGCATTGGCGGCACCAATGGT
4708312 GCCATACT-G-ATTGGCGGCAC
1 GCCA-A-TGGCATTGGCGGCAC
4708332 TATTCGTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
27 42 0.93
28 2 0.04
29 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.32, T:0.19
Consensus pattern (27 bp):
GCCAATGGCATTGGCGGCACCAATGGT
Found at i:4708577 original size:3 final size:3
Alignment explanation
Indices: 4708571--4708602 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
4708561 ATTATTATTA
*
4708571 TTG TTG TTG TTG TTG TTG TTG TTG TTA TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
4708603 AGTATTAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.28, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:4711841 original size:21 final size:22
Alignment explanation
Indices: 4711801--4711842 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
4711791 GTGAAATGGT
*
4711801 AGCAAAACAGTGGGAAAACAAC
1 AGCAAAACAGTGGAAAAACAAC
*
4711823 AGCAAAATA-TGGAAAAACAA
1 AGCAAAACAGTGGAAAAACAA
4711843 AAAAAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.60, C:0.14, G:0.19, T:0.07
Consensus pattern (22 bp):
AGCAAAACAGTGGAAAAACAAC
Found at i:4717947 original size:32 final size:35
Alignment explanation
Indices: 4717898--4717976 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 35
4717888 AAGTACAAAA
*
4717898 TATATACATGTACATAT-A-TATAAAAAA-ATAAT
1 TATATACATATACATATAATTATAAAAAAGATAAT
*
4717930 TATATACATATATATATAGATTATAAAAAAGATAAT
1 TATATACATATACATATA-ATTATAAAAAAGATAAT
* *
4717966 TACATATATAT
1 TATATACATAT
4717977 GTAAAAACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 15 0.38
34 1 0.03
35 9 0.23
36 14 0.36
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (35 bp):
TATATACATATACATATAATTATAAAAAAGATAAT
Found at i:4718113 original size:2 final size:2
Alignment explanation
Indices: 4718108--4718140 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4718098 AAAATAAAAG
4718108 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4718141 GCATATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4718185 original size:17 final size:17
Alignment explanation
Indices: 4718163--4718206 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
4718153 TAGGAAATAA
4718163 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
*
4718180 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
4718197 -ATATGTATAT
1 AAAATGTATAT
4718207 AAAAGTTACG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:4718340 original size:3 final size:3
Alignment explanation
Indices: 4718332--4718367 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
4718322 ATATATATAG
* *
4718332 TAA TAA TAA TAA TAA TAA TAA CAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4718368 AACTAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:4720525 original size:20 final size:20
Alignment explanation
Indices: 4720468--4720541 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
4720458 AAAATATATA
* *
4720468 TATTTTTAAATTTTTATAAA-
1 TATTTTGAATTTTTTA-AAAT
*
4720488 TATTTTGAA-TTTTAAAAAT
1 TATTTTGAATTTTTTAAAAT
4720507 TATTTTGAATTTTTTAAAAT
1 TATTTTGAATTTTTTAAAAT
4720527 TATTTTGAATTTTTT
1 TATTTTGAATTTTTT
4720542 TGTTGAGAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
18 3 0.06
19 14 0.29
20 32 0.65
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (20 bp):
TATTTTGAATTTTTTAAAAT
Found at i:4720527 original size:10 final size:9
Alignment explanation
Indices: 4720470--4720541 Score: 54
Period size: 9 Copynumber: 7.6 Consensus size: 9
4720460 AATATATATA
4720470 TTTTTAAAT
1 TTTTTAAAT
4720479 TTTTATAAAT
1 TTTT-TAAAT
* *
4720489 ATTTTGAAT
1 TTTTTAAAT
**
4720498 TTTAAAAAT
1 TTTTTAAAT
*
4720507 TATTTTGAAT
1 T-TTTTAAAT
4720517 TTTTTAAAAT
1 TTTTT-AAAT
*
4720527 TATTTTGAAT
1 T-TTTTAAAT
4720537 TTTTT
1 TTTTT
4720542 TGTTGAGAGA
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
9 22 0.46
10 22 0.46
11 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:4730247 original size:18 final size:18
Alignment explanation
Indices: 4730224--4730261 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
4730214 CCAGCAACAG
*
4730224 CAACAGCAACTACTGCAA
1 CAACAGCAACTACAGCAA
*
4730242 CAACAGCAGCTACAGCAA
1 CAACAGCAACTACAGCAA
4730260 CA
1 CA
4730262 TGCTCAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.34, G:0.13, T:0.08
Consensus pattern (18 bp):
CAACAGCAACTACAGCAA
Found at i:4730251 original size:27 final size:27
Alignment explanation
Indices: 4730221--4730273 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
4730211 ACACCAGCAA
4730221 CAGCAACAGCAAC-TACTGCAACAACAG
1 CAGCAACAGCAACATACT-CAACAACAG
* *
4730248 CAGCTACAGCAACATGCTCAACAACA
1 CAGCAACAGCAACATACTCAACAACA
4730274 ATTACAACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.43, C:0.34, G:0.13, T:0.09
Consensus pattern (27 bp):
CAGCAACAGCAACATACTCAACAACAG
Found at i:4730260 original size:15 final size:15
Alignment explanation
Indices: 4730197--4730261 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 15
4730187 TCCTCAAATG
*
4730197 CAGCAGCCACAGCAA
1 CAGCAGCTACAGCAA
* *
4730212 CACCAGCAACAGCAA
1 CAGCAGCTACAGCAA
* *
4730227 CAGCAACTACTGCAACAA
1 CAGCAGCTA---CAGCAA
4730245 CAGCAGCTACAGCAA
1 CAGCAGCTACAGCAA
4730260 CA
1 CA
4730262 TGCTCAACAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
15 26 0.67
18 13 0.33
ACGTcount: A:0.43, C:0.37, G:0.15, T:0.05
Consensus pattern (15 bp):
CAGCAGCTACAGCAA
Found at i:4734787 original size:37 final size:37
Alignment explanation
Indices: 4734746--4734857 Score: 98
Period size: 31 Copynumber: 3.2 Consensus size: 37
4734736 TATGGGACTC
4734746 AAATATATTATTTAATCATGCTTTATTCTTAACGTGA
1 AAATATATTATTTAATCATGCTTTATTCTTAACGTGA
* * *
4734783 AAATATCGAAT-TTTAA--AT--TAATATT-TTAA---AA
1 AAATAT--ATTATTTAATCATGCT-TTATTCTTAACGTGA
4734814 AAATGATATTATTTAATCATGCTTTATTCTTAACGTGA
1 AAAT-ATATTATTTAATCATGCTTTATTCTTAACGTGA
4734852 AAATAT
1 AAATAT
4734858 CGAATTTTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 26
0.64 0.07 0.30
Matches are distributed among these distances:
30 2 0.04
31 10 0.18
32 2 0.04
33 2 0.04
34 9 0.16
35 9 0.16
36 2 0.04
37 8 0.14
38 10 0.18
39 2 0.04
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (37 bp):
AAATATATTATTTAATCATGCTTTATTCTTAACGTGA
Found at i:4734861 original size:69 final size:68
Alignment explanation
Indices: 4734746--4734886 Score: 273
Period size: 69 Copynumber: 2.1 Consensus size: 68
4734736 TATGGGACTC
4734746 AAATATATTATTTAATCATGCTTTATTCTTAACGTGAAAATATCGAATTTTAAATTAATATTTTA
1 AAATATATTATTTAATCATGCTTTATTCTTAACGTGAAAATATCGAATTTTAAATTAATATTTTA
4734811 AAA
66 AAA
4734814 AAATGATATTATTTAATCATGCTTTATTCTTAACGTGAAAATATCGAATTTTAAATTAATATTTT
1 AAAT-ATATTATTTAATCATGCTTTATTCTTAACGTGAAAATATCGAATTTTAAATTAATATTTT
4734879 AAAA
65 AAAA
4734883 AAAT
1 AAAT
4734887 TACTCTTGTA
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
68 4 0.06
69 68 0.94
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (68 bp):
AAATATATTATTTAATCATGCTTTATTCTTAACGTGAAAATATCGAATTTTAAATTAATATTTTA
AAA
Found at i:4738660 original size:3 final size:3
Alignment explanation
Indices: 4738654--4738686 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
4738644 GTGGTGCTGT
4738654 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
4738687 ATTAGCTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:4743132 original size:29 final size:30
Alignment explanation
Indices: 4743081--4743144 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 30
4743071 AGTATTTATG
4743081 TTAAGTAATAATTAAGACATATTAAAAATATA
1 TTAAGTAATAA-TAAGACATATTAAAAATA-A
* *
4743113 TTAAGTAATAA-AA-ATATATTAAAACTAA
1 TTAAGTAATAATAAGACATATTAAAAATAA
4743141 TTAA
1 TTAA
4743145 ATAAATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.17
29 12 0.40
30 2 0.07
32 11 0.37
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (30 bp):
TTAAGTAATAATAAGACATATTAAAAATAA
Found at i:4749328 original size:3 final size:3
Alignment explanation
Indices: 4749322--4749375 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
4749312 TTTATTTTTC
* * *
4749322 TAT TAT T-T TAT TGT CAT TA- TAT TAT TA- TAT TAC TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4749366 TAT TAT TAT T
1 TAT TAT TAT T
4749376 TAAATATCTG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
2 8 0.20
3 33 0.80
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4749372 original size:11 final size:11
Alignment explanation
Indices: 4749313--4749372 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
4749303 AATTTTTTTT
4749313 TTATTTT-TCTA
1 TTATTTTAT-TA
*
4749324 TTATTTTATTG
1 TTATTTTATTA
* *
4749335 TCATTATATTA
1 TTATTTTATTA
* *
4749346 TTATATTACTA
1 TTATTTTATTA
4749357 TTATTTTATTA
1 TTATTTTATTA
4749368 TTATT
1 TTATT
4749373 ATTTAAATAT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
11 37 0.97
12 1 0.03
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:4750875 original size:17 final size:18
Alignment explanation
Indices: 4750848--4750884 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
4750838 ATTCGCACCC
4750848 AATTGAAACTTTGCCGTT
1 AATTGAAACTTTGCCGTT
*
4750866 AATT-AAACTTTTCCGTT
1 AATTGAAACTTTGCCGTT
4750883 AA
1 AA
4750885 CGAAATCCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (18 bp):
AATTGAAACTTTGCCGTT
Found at i:4753097 original size:5 final size:5
Alignment explanation
Indices: 4753087--4753114 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
4753077 TGTGAAATTG
4753087 ATTAT ATTAT ATTAT ATTAT ATTAT ATT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATT
4753115 TGCTGGTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTAT
Found at i:4754087 original size:18 final size:18
Alignment explanation
Indices: 4754064--4754100 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4754054 CATAAAAGAT
4754064 AGAAACGAAGAGGCGTCA
1 AGAAACGAAGAGGCGTCA
4754082 AGAAACGAAGAGGCGTCA
1 AGAAACGAAGAGGCGTCA
4754100 A
1 A
4754101 CGTCGTGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.16, G:0.32, T:0.05
Consensus pattern (18 bp):
AGAAACGAAGAGGCGTCA
Found at i:4759267 original size:13 final size:13
Alignment explanation
Indices: 4759251--4759275 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4759241 AATTATAAAA
4759251 AAATTAAAATTAT
1 AAATTAAAATTAT
4759264 AAATTAAAATTA
1 AAATTAAAATTA
4759276 CATATAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATTAAAATTAT
Found at i:4759456 original size:9 final size:9
Alignment explanation
Indices: 4759444--4759473 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
4759434 TTTTATTAAT
*
4759444 TTTTTAAAA
1 TTTTAAAAA
4759453 TTTTAAAAA
1 TTTTAAAAA
4759462 TTTTAAAAA
1 TTTTAAAAA
4759471 TTT
1 TTT
4759474 AATAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:4759467 original size:17 final size:18
Alignment explanation
Indices: 4759445--4759481 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
4759435 TTTATTAATT
*
4759445 TTTTAAAATTTTAA-AAA
1 TTTTAAAAATTTAATAAA
4759462 TTTTAAAAATTTAATAAA
1 TTTTAAAAATTTAATAAA
4759480 TT
1 TT
4759482 ATTTGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTAAAAATTTAATAAA
Found at i:4760702 original size:19 final size:19
Alignment explanation
Indices: 4760678--4760743 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
4760668 NNNNNNTTTT
4760678 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
4760697 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
*
4760715 TTACATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
4760734 TTAAATTAAA
1 TTAAATTAAA
4760744 CTATTTTAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:4761090 original size:27 final size:27
Alignment explanation
Indices: 4761060--4761128 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
4761050 CTTTGGGACA
4761060 ATTGGTGCCGCCAATCACATTGGCACC
1 ATTGGTGCCGCCAATCACATTGGCACC
* *
4761087 ATTGGTGCCGCCAATCTCTTTGGCACC
1 ATTGGTGCCGCCAATCACATTGGCACC
*
4761114 TTTGGTGCCGCCAAT
1 ATTGGTGCCGCCAAT
4761129 GTGATTGACC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.17, C:0.32, G:0.23, T:0.28
Consensus pattern (27 bp):
ATTGGTGCCGCCAATCACATTGGCACC
Found at i:4761209 original size:28 final size:28
Alignment explanation
Indices: 4761176--4761250 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 28
4761166 CTGTTTTTTT
4761176 ATTTTTTAT-ATATTTTGGTAAATAAAA
1 ATTTTTTATAATATTTTGGTAAATAAAA
4761203 ATTTTTTATAATATTTTGGTAAATAAAA
1 ATTTTTTATAATATTTTGGTAAATAAAA
****
4761231 AAAAGTTATAATATTTTGGT
1 ATTTTTTATAATATTTTGGT
4761251 TATTTTTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 9 0.21
28 34 0.79
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.49
Consensus pattern (28 bp):
ATTTTTTATAATATTTTGGTAAATAAAA
Found at i:4777330 original size:30 final size:30
Alignment explanation
Indices: 4777289--4777350 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
4777279 GTCTTCTTAA
* *
4777289 TCCCAAACTCCTGAACG-CAATATCGAGTCT
1 TCCCAAACTCCTAAACGAC-ATATCGAATCT
*
4777319 TCCCAAGCTCCTAAACGACATATCGAATCT
1 TCCCAAACTCCTAAACGACATATCGAATCT
4777349 TC
1 TC
4777351 TCAATCTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.31, C:0.34, G:0.11, T:0.24
Consensus pattern (30 bp):
TCCCAAACTCCTAAACGACATATCGAATCT
Found at i:4777496 original size:3 final size:3
Alignment explanation
Indices: 4777488--4777518 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4777478 TTGCCCCTAG
4777488 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
4777519 TACTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:4780803 original size:24 final size:25
Alignment explanation
Indices: 4780759--4780805 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
4780749 ATCATATTTG
*
4780759 AATTGAAAATTTATAATAAAATTAA
1 AATTGAAAATTTATAACAAAATTAA
4780784 AATT-AAAATTGTAT-ACAAAATT
1 AATTGAAAATT-TATAACAAAATT
4780806 CATGCGGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.36
Consensus pattern (25 bp):
AATTGAAAATTTATAACAAAATTAA
Found at i:4781823 original size:12 final size:12
Alignment explanation
Indices: 4781808--4781861 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
4781798 TGGATTTTAT
*
4781808 TTTCTGTTTTTG
1 TTTCTGTGTTTG
*
4781820 TTTCTGGGTTTG
1 TTTCTGTGTTTG
*
4781832 TTTCTGTTTTTG
1 TTTCTGTGTTTG
*
4781844 TTTCTGTGTCTG
1 TTTCTGTGTTTG
4781856 TTTCTG
1 TTTCTG
4781862 GATTCGCATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.00, C:0.11, G:0.22, T:0.67
Consensus pattern (12 bp):
TTTCTGTGTTTG
Found at i:4781835 original size:24 final size:24
Alignment explanation
Indices: 4781808--4781861 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
4781798 TGGATTTTAT
*
4781808 TTTCTGTTTTTGTTTCTGGGTTTG
1 TTTCTGTTTTTGTTTCTGGGTCTG
*
4781832 TTTCTGTTTTTGTTTCTGTGTCTG
1 TTTCTGTTTTTGTTTCTGGGTCTG
4781856 TTTCTG
1 TTTCTG
4781862 GATTCGCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.00, C:0.11, G:0.22, T:0.67
Consensus pattern (24 bp):
TTTCTGTTTTTGTTTCTGGGTCTG
Found at i:4781839 original size:6 final size:6
Alignment explanation
Indices: 4781808--4781861 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
4781798 TGGATTTTAT
* * * *
4781808 TTTCTG TTTTTG TTTCTGG GTT-TG TTTCTG TTTTTG TTTCTG TGTCTG
1 TTTCTG TTTCTG TTTCT-G TTTCTG TTTCTG TTTCTG TTTCTG TTTCTG
4781856 TTTCTG
1 TTTCTG
4781862 GATTCGCATA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
5 3 0.08
6 32 0.84
7 3 0.08
ACGTcount: A:0.00, C:0.11, G:0.22, T:0.67
Consensus pattern (6 bp):
TTTCTG
Found at i:4786449 original size:27 final size:27
Alignment explanation
Indices: 4786384--4786453 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
4786374 CAGATTTTAG
* *
4786384 ATTGTTGGATTTTGATATATGTCTTGA
1 ATTGTTGGATATTGATATATGTCTTAA
* *
4786411 ATTGGTTAGATATTGAT-TATGTTTTAA
1 ATT-GTTGGATATTGATATATGTCTTAA
4786438 CATTGTTGGATATTGA
1 -ATTGTTGGATATTGA
4786454 ATTGATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (27 bp):
ATTGTTGGATATTGATATATGTCTTAA
Found at i:4786458 original size:32 final size:33
Alignment explanation
Indices: 4786422--4786489 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 33
4786412 TTGGTTAGAT
*
4786422 ATTG-ATTATGTTTTAA-CATTGTTGGATATTGA
1 ATTGTATTATGTTTTAAGC-TTGTTAGATATTGA
4786454 ATTGATTATTATGTTTTAAGCTTGTTAGATATTGA
1 ATTG--TATTATGTTTTAAGCTTGTTAGATATTGA
4786489 A
1 A
4786490 ATTATTGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 4 0.13
35 26 0.84
36 1 0.03
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (33 bp):
ATTGTATTATGTTTTAAGCTTGTTAGATATTGA
Found at i:4787918 original size:14 final size:14
Alignment explanation
Indices: 4787895--4787934 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
4787885 ACAGAAAAGT
*
4787895 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
4787909 AAATCATTTTACGG
1 AAAACATTTTACAG
4787923 AAAACATTTTAC
1 AAAACATTTTAC
4787935 TGCCAATATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:4787920 original size:34 final size:35
Alignment explanation
Indices: 4787860--4787926 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
4787850 CAAACACCAG
* *
4787860 AAAATATTTTCCAGTAAGTCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
4787895 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
4787927 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:4796187 original size:18 final size:18
Alignment explanation
Indices: 4796164--4796199 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4796154 TACATGGATT
4796164 TTTTAATATCTATTTAAA
1 TTTTAATATCTATTTAAA
4796182 TTTTAATATCTATTTAAA
1 TTTTAATATCTATTTAAA
4796200 ATTGGCGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAATATCTATTTAAA
Found at i:4799007 original size:37 final size:37
Alignment explanation
Indices: 4798966--4799057 Score: 134
Period size: 37 Copynumber: 2.5 Consensus size: 37
4798956 CTTACATTTC
4798966 AATTATGT-GTTAATTTC-AAGACTTATGTAATGTTTTT
1 AATTATGTAG-TAA-TTCAAAGACTTATGTAATGTTTTT
*
4799003 AATTATGTAGTGATTCAAAGACTTATGTAATGTTTTT
1 AATTATGTAGTAATTCAAAGACTTATGTAATGTTTTT
*
4799040 AATTATGTAGTGATTCAA
1 AATTATGTAGTAATTCAA
4799058 TTCGGGTAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
36 3 0.06
37 48 0.92
38 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (37 bp):
AATTATGTAGTAATTCAAAGACTTATGTAATGTTTTT
Found at i:4799008 original size:17 final size:17
Alignment explanation
Indices: 4798988--4799048 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
4798978 ATTTCAAGAC
4798988 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
4799005 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
4799024 CTTATGTAATGTTTTTAA
1 -TTATGTAATGTTTTTAA
4799042 TTATGTA
1 TTATGTA
4799049 GTGATTCAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 16 0.48
18 4 0.12
19 4 0.12
20 9 0.27
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:4799070 original size:9 final size:9
Alignment explanation
Indices: 4799056--4799086 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
4799046 GTAGTGATTC
*
4799056 AATTCGGGT
1 AATTCGGTT
4799065 AATTCGGTT
1 AATTCGGTT
4799074 AATTCGGTT
1 AATTCGGTT
4799083 AATT
1 AATT
4799087 TTTAATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:4800119 original size:13 final size:13
Alignment explanation
Indices: 4800101--4800153 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
4800091 AGTTTAGCAT
* *
4800101 TGTTTTTGAGAAG
1 TGTTTTTAAAAAG
4800114 TGTTTTTAAAAAG
1 TGTTTTTAAAAAG
* *
4800127 TGATTTTAAGAAG
1 TGTTTTTAAAAAG
* *
4800140 TATTTTTGAAAAG
1 TGTTTTTAAAAAG
4800153 T
1 T
4800154 TTGGTTTAAG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (13 bp):
TGTTTTTAAAAAG
Found at i:4800133 original size:26 final size:26
Alignment explanation
Indices: 4800104--4800153 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
4800094 TTAGCATTGT
* *
4800104 TTTTGAGAAGTGTTTTTAAAAAGTGA
1 TTTTAAGAAGTATTTTTAAAAAGTGA
*
4800130 TTTTAAGAAGTATTTTTGAAAAGT
1 TTTTAAGAAGTATTTTTAAAAAGT
4800154 TTGGTTTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (26 bp):
TTTTAAGAAGTATTTTTAAAAAGTGA
Found at i:4813813 original size:10 final size:9
Alignment explanation
Indices: 4813799--4813835 Score: 51
Period size: 10 Copynumber: 4.2 Consensus size: 9
4813789 AATTAATTTT
4813799 TAAAAATTA
1 TAAAAATTA
4813808 TAAAAA-T-
1 TAAAAATTA
4813815 TAAAAATTA
1 TAAAAATTA
4813824 TTAAAAATTA
1 -TAAAAATTA
4813834 TA
1 TA
4813836 TTTTTTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
7 6 0.24
8 2 0.08
9 8 0.32
10 9 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:4813819 original size:16 final size:17
Alignment explanation
Indices: 4813798--4813833 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
4813788 TAATTAATTT
4813798 TTAAAAATTA-TAAAAA
1 TTAAAAATTATTAAAAA
4813814 TTAAAAATTATTAAAAA
1 TTAAAAATTATTAAAAA
4813831 TTA
1 TTA
4813834 TATTTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAAATTATTAAAAA
Found at i:4820245 original size:22 final size:22
Alignment explanation
Indices: 4820220--4820263 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
4820210 AAAATCAATC
* * *
4820220 AAAGTCAAAAATAAGAGAAAAA
1 AAAGACAAAAAGAAAAGAAAAA
*
4820242 AAAGAGAAAAAGAAAAGAAAAA
1 AAAGACAAAAAGAAAAGAAAAA
4820264 GGAGAGGTCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (22 bp):
AAAGACAAAAAGAAAAGAAAAA
Found at i:4820246 original size:11 final size:11
Alignment explanation
Indices: 4820226--4820263 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4820216 AATCAAAGTC
*
4820226 AAAAATAAGAG
1 AAAAAAAAGAG
4820237 AAAAAAAAGAG
1 AAAAAAAAGAG
4820248 AAAAAGAAA-AG
1 AAAAA-AAAGAG
4820259 AAAAA
1 AAAAA
4820264 GGAGAGGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 22 0.88
12 3 0.12
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:4820264 original size:11 final size:12
Alignment explanation
Indices: 4820232--4820264 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4820222 AGTCAAAAAT
4820232 AAGAGAAAAA-A
1 AAGAGAAAAAGA
4820243 AAGAGAAAAAGA
1 AAGAGAAAAAGA
4820255 AA-AGAAAAAG
1 AAGAGAAAAAG
4820265 GAGAGGTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 18 0.86
12 3 0.14
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAGAGAAAAAGA
Found at i:4822261 original size:50 final size:50
Alignment explanation
Indices: 4822150--4822392 Score: 396
Period size: 50 Copynumber: 4.8 Consensus size: 50
4822140 AATAATAACA
* * * **
4822150 TGCCAAAGCCATGCCCCAGACATAGTCTTACATGGGATGTTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
4822201 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
4822251 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
4822301 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
4822351 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
4822393 TTACCCAAAT
Statistics
Matches: 179, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
50 148 0.83
51 31 0.17
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:4822780 original size:29 final size:30
Alignment explanation
Indices: 4822730--4822786 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
4822720 CCTTGACTCT
* *
4822730 AACTTTTTCAAAATTATGATTTTGCCCCTA
1 AACTTTTACAAAATTATCATTTTGCCCCTA
* *
4822760 AACTTTTACATAATTA-CATTTTTCCCC
1 AACTTTTACAAAATTATCATTTTGCCCC
4822787 AAGGCTTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 9 0.39
30 14 0.61
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.44
Consensus pattern (30 bp):
AACTTTTACAAAATTATCATTTTGCCCCTA
Found at i:4823882 original size:8 final size:7
Alignment explanation
Indices: 4823865--4823918 Score: 67
Period size: 7 Copynumber: 7.6 Consensus size: 7
4823855 AATGATGATG
4823865 AATG-AA
1 AATGAAA
4823871 AATGAAAA
1 AATG-AAA
4823879 AATG-AA
1 AATGAAA
4823885 AATGAAA
1 AATGAAA
4823892 AATGAAA
1 AATGAAA
4823899 AATGAAAAA
1 AATG--AAA
4823908 AATGAAA
1 AATGAAA
4823915 AATG
1 AATG
4823919 GAGAGGCTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
6 10 0.23
7 20 0.47
8 6 0.14
9 7 0.16
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
AATGAAA
Found at i:4823884 original size:14 final size:14
Alignment explanation
Indices: 4823865--4823915 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
4823855 AATGATGATG
4823865 AATGAAAATGAAAA
1 AATGAAAATGAAAA
4823879 AATGAAAATG-AAA
1 AATGAAAATGAAAA
4823892 AATGAAAAATGAAAAA
1 AATG-AAAATG-AAAA
4823908 AATGAAAA
1 AATGAAAA
4823916 ATGGAGAGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
13 7 0.21
14 16 0.47
15 4 0.12
16 7 0.21
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATGAAAATGAAAA
Done.