Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold31
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: 2401195
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 123915 characters in sequence are not A, C, G, or T
File 8 of 16
Found at i:1089162 original size:57 final size:57
Alignment explanation
Indices: 1089087--1089200 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 57
1089077 CAAATATCAC
1089087 GAGCAGAATTGGTTAATTAAGCTAACATAACAGAATGCAGATAACAACAAAGTTGAT
1 GAGCAGAATTGGTTAATTAAGCTAACATAACAGAATGCAGATAACAACAAAGTTGAT
* *
1089144 GAGCGGAATTGGTTAATTAAGCTAACATAACAGAATGCAGATAACAACATAGTTGAT
1 GAGCAGAATTGGTTAATTAAGCTAACATAACAGAATGCAGATAACAACAAAGTTGAT
1089201 CTTAGATCAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (57 bp):
GAGCAGAATTGGTTAATTAAGCTAACATAACAGAATGCAGATAACAACAAAGTTGAT
Found at i:1089342 original size:65 final size:65
Alignment explanation
Indices: 1089261--1089391 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
1089251 AAGATAATTT
* * *
1089261 CCAGCATTTGCTTGACCTAATATGTTCGTAAGACCTCATGAAATTCTAAAAAACACACAATTGCA
1 CCAGCATTTGCTTGACCTAATATGTGCGCAAGACCTAATGAAATTCTAAAAAACACACAATTGCA
1089326 CCAGCATTTGCTTGACCTAATATGTGCGCAAGACCTAATGAAATTCTAAAAAACACACAATTGCA
1 CCAGCATTTGCTTGACCTAATATGTGCGCAAGACCTAATGAAATTCTAAAAAACACACAATTGCA
1089391 C
1 C
1089392 TTAGTGCTCA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (65 bp):
CCAGCATTTGCTTGACCTAATATGTGCGCAAGACCTAATGAAATTCTAAAAAACACACAATTGCA
Found at i:1089855 original size:23 final size:22
Alignment explanation
Indices: 1089825--1089868 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
1089815 ATCAATGAAG
1089825 TTTTATAAAATGCAACAGAAAAA
1 TTTTATAAAATGCAACA-AAAAA
1089848 TTTTATAAAATGCAACAAAAA
1 TTTTATAAAATGCAACAAAAA
1089869 CAGTGAAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.27
Consensus pattern (22 bp):
TTTTATAAAATGCAACAAAAAA
Found at i:1091458 original size:22 final size:21
Alignment explanation
Indices: 1091379--1091458 Score: 58
Period size: 22 Copynumber: 3.8 Consensus size: 21
1091369 TTTAAAAAAA
1091379 AAAAATTATTATTTATT-A-AT
1 AAAAA-TATTATTTATTAATAT
*
1091399 AAAAATATT-TTAATTTAATTAT
1 AAAAATATTATTTA-TTAA-TAT
* **
1091421 AAAAATATAAAATATTAATAT
1 AAAAATATTATTTATTAATAT
*
1091442 AAAAATTATTTTTTATT
1 AAAAA-TATTATTTATT
1091459 TTATTTAATT
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
18 3 0.07
19 6 0.13
20 6 0.13
21 8 0.18
22 21 0.47
23 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAAATATTATTTATTAATAT
Found at i:1093853 original size:4 final size:4
Alignment explanation
Indices: 1093846--1093922 Score: 73
Period size: 4 Copynumber: 19.2 Consensus size: 4
1093836 ACATACATGC
* * * ** * *
1093846 ATAT ATAT ATAT ATAC ATAC ATAC ATAT ATAT ATAT ATGC ATAC ATAC
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* *
1093894 ATAT ATAT ATAT ATAT ATAC ATAC ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
1093923 GAGGGGTGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 65 1.00
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.39
Consensus pattern (4 bp):
ATAT
Found at i:1093872 original size:24 final size:24
Alignment explanation
Indices: 1093836--1093922 Score: 147
Period size: 24 Copynumber: 3.6 Consensus size: 24
1093826 AGCTTCCTGC
*
1093836 ACATACATGCATATATATATATAT
1 ACATACATACATATATATATATAT
1093860 ACATACATACATATATATATATAT
1 ACATACATACATATATATATATAT
*
1093884 GCATACATACATATATATATATAT
1 ACATACATACATATATATATATAT
*
1093908 ATATACATACATATA
1 ACATACATACATATA
1093923 GAGGGGTGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (24 bp):
ACATACATACATATATATATATAT
Found at i:1093877 original size:28 final size:28
Alignment explanation
Indices: 1093837--1093920 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
1093827 GCTTCCTGCA
** *
1093837 CATACATGCATATATATATATATACATA
1 CATACATATATATATATATACATACATA
*
1093865 CATACATATATATATATATGCATACATA
1 CATACATATATATATATATACATACATA
*
1093893 CATATATATATATATATATACATACATA
1 CATACATATATATATATATACATACATA
1093921 TAGAGGGGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (28 bp):
CATACATATATATATATATACATACATA
Found at i:1093913 original size:20 final size:20
Alignment explanation
Indices: 1093838--1093922 Score: 89
Period size: 20 Copynumber: 4.0 Consensus size: 20
1093828 CTTCCTGCAC
* *
1093838 ATACATGCATATATATATAT
1 ATACATACATACATATATAT
1093858 ATACATACATACATATATATAT
1 ATACATACATAC--ATATATAT
1093880 ATATGCATACATACATATATAT
1 ATA--CATACATACATATATAT
* * *
1093902 ATATATATATACATACATAT
1 ATACATACATACATATATAT
1093922 A
1 A
1093923 GAGGGGTGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
20 25 0.45
22 22 0.39
24 9 0.16
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (20 bp):
ATACATACATACATATATAT
Found at i:1094723 original size:34 final size:34
Alignment explanation
Indices: 1094644--1094723 Score: 142
Period size: 34 Copynumber: 2.4 Consensus size: 34
1094634 TCTTTGTTAA
*
1094644 GTGTGTTAGGTAGTATGTTAGGTAAACATATTAG
1 GTGTGTTAGGTGGTATGTTAGGTAAACATATTAG
*
1094678 ATGTGTTAGGTGGTATGTTAGGTAAACATATTAG
1 GTGTGTTAGGTGGTATGTTAGGTAAACATATTAG
1094712 GTGTGTTAGGTG
1 GTGTGTTAGGTG
1094724 AGCATATTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.26, C:0.03, G:0.33, T:0.39
Consensus pattern (34 bp):
GTGTGTTAGGTGGTATGTTAGGTAAACATATTAG
Found at i:1094745 original size:22 final size:22
Alignment explanation
Indices: 1094693--1094746 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
1094683 TTAGGTGGTA
* *
1094693 TGTTAGGTAAACATATTAGGTG
1 TGTTAGGTGAACATATTAAGTG
*
1094715 TGTTAGGTGAGCATATTAAGTG
1 TGTTAGGTGAACATATTAAGTG
1094737 TGTTAGGTGA
1 TGTTAGGTGA
1094747 TCTGTTAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.28, C:0.04, G:0.31, T:0.37
Consensus pattern (22 bp):
TGTTAGGTGAACATATTAAGTG
Found at i:1101360 original size:2 final size:2
Alignment explanation
Indices: 1101353--1101382 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1101343 CTTAATTTAG
1101353 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
1101383 TGAATAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1102388 original size:2 final size:2
Alignment explanation
Indices: 1102381--1102405 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1102371 TGGTCACCGC
1102381 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1102406 GTATTGGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1102557 original size:27 final size:28
Alignment explanation
Indices: 1102527--1102582 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
1102517 CATTGGATAT
1102527 ATATTCAAATATATAAAAAAA-TTTAAA
1 ATATTCAAATATATAAAAAAATTTTAAA
*
1102554 ATATTTAAATATATAAAAAAATTTTAAA
1 ATATTCAAATATATAAAAAAATTTTAAA
1102582 A
1 A
1102583 AATTAACACA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (28 bp):
ATATTCAAATATATAAAAAAATTTTAAA
Found at i:1102588 original size:27 final size:27
Alignment explanation
Indices: 1102533--1102588 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
1102523 ATATATATTC
*
1102533 AAATATATAAAAAAATTTAAAATATTT
1 AAATATATAAAAAAATTTAAAATAATT
1102560 AAATATATAAAAAAATTTTAAAA-AATT
1 AAATATATAAAAAAA-TTTAAAATAATT
1102587 AA
1 AA
1102589 CACACTTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
AAATATATAAAAAAATTTAAAATAATT
Found at i:1106080 original size:69 final size:69
Alignment explanation
Indices: 1105990--1106143 Score: 256
Period size: 69 Copynumber: 2.2 Consensus size: 69
1105980 TCAGAGGAAT
1105990 GAGGTTGGAGTATCCCTGACAATGATAATTTGGACAAAATAAGACTTAAATTTTGATGAGTTTAA
1 GAGGTTGGAGTATCCCTGACAATGATAATTTGGACAAAATAAGACTTAAATTTTGATGAGTTTAA
1106055 AAAC
66 AAAC
* * *
1106059 GGGGTTGGAGTAT-CATCGACAATGATAATTTGGACAAAATAAGATTTAAATTTTGATGAGTTTA
1 GAGGTTGGAGTATCCCT-GACAATGATAATTTGGACAAAATAAGACTTAAATTTTGATGAGTTTA
1106123 AAAAC
65 AAAAC
*
1106128 GAGGTTGGATTATCCC
1 GAGGTTGGAGTATCCC
1106144 CTCGGAGGAA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
68 2 0.03
69 74 0.96
70 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (69 bp):
GAGGTTGGAGTATCCCTGACAATGATAATTTGGACAAAATAAGACTTAAATTTTGATGAGTTTAA
AAAC
Found at i:1112457 original size:9 final size:9
Alignment explanation
Indices: 1112443--1112473 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1112433 CCATTTCATA
1112443 TTTTTTTTC
1 TTTTTTTTC
1112452 TTTTTTTTC
1 TTTTTTTTC
1112461 TTTTTCTTTC
1 TTTTT-TTTC
1112471 TTT
1 TTT
1112474 CTTCTTCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.67
10 7 0.33
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1112466 original size:15 final size:17
Alignment explanation
Indices: 1112446--1112496 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 17
1112436 TTTCATATTT
1112446 TTTTTCTTT-TTT-TTC
1 TTTTTCTTTCTTTCTTC
1112461 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
1112478 TTCATCTTCTTTCTTTCTT
1 TT--T-TTCTTTCTTTCTT
1112497 TCTTACTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.29
16 3 0.10
17 5 0.16
19 1 0.03
20 13 0.42
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:1113686 original size:45 final size:48
Alignment explanation
Indices: 1113594--1113686 Score: 120
Period size: 45 Copynumber: 2.0 Consensus size: 48
1113584 TCAAGGTTAA
*
1113594 CGACATTGGGCTAAGGGAAAAGTGGACCAATGTGCTGACTCAAGGCCAG
1 CGACATTGGGCTAA-GGAAAAGTGGACCAATATGCTGACTCAAGGCCAG
* * *
1113643 CGACATTGGGCTTA-GAAAAGT-G-CCAATATGCTGATTCAGGGCCA
1 CGACATTGGGCTAAGGAAAAGTGGACCAATATGCTGACTCAAGGCCA
1113687 ACGATATCGA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
45 19 0.47
46 1 0.03
47 7 0.17
49 13 0.32
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.19
Consensus pattern (48 bp):
CGACATTGGGCTAAGGAAAAGTGGACCAATATGCTGACTCAAGGCCAG
Found at i:1113850 original size:28 final size:28
Alignment explanation
Indices: 1113808--1115219 Score: 1137
Period size: 28 Copynumber: 50.4 Consensus size: 28
1113798 CACCGGCTTG
* *
1113808 TGTGGGTTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1113836 TGTGGGCTTTGAAAGGATGCCACTGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1113864 TGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * * *
1113893 TATGGTCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
1113922 TGTAGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1113950 TGTGGGATTTGAAAAGAGTGCCATTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
1113979 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1114007 TGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1114036 TGTGGGCTTTGAAAGGATGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1114064 CGTGGGCTTTAAAAGGATGCCACTGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1114092 TATGGGCTTTGAAAAGTTGCCACCGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * ** *
1114120 TGTGGGCTTTAAAAAGACGCCACTGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1114148 TGTGGGCTTTGAAAGGTTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1114176 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
1114204 CGTGGGCTTTAAAAGGATGCCACTAATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1114232 TGTGGACTTTGAAAGGTTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1114260 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * *
1114289 TGTGGGCTTTGAAAAGTTGCCACCGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** * * * *
1114317 CATGGGCTTTAAAAGGATGCCATTGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1114345 TGTGGGCTTTGAAAGGCTGCCACT-AAT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1114372 TCGTGGGCTTTAAAAAGAGTGCCACTGACT
1 T-GTGGGCTTT-GAAAGGGTGCCACTGACT
* *
1114402 TGTGGGCTTTGAAAGGATG-AACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1114429 TGTGGGCTTTGAAAAGATGCCACTGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1114457 TGTGGGCTTTGAAAGGTTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1114485 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1114514 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* **
1114542 TATGGGCTTTGAAAAAAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * * *
1114571 TGTGGACTTTGAAAAGATGCCACTGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1114599 TATGGGCTTTGAAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1114627 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* **
1114655 TCTGGGCTTTGAAAAAAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1114684 CGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1114712 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1114741 TGTGAGCTCTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1114769 TGCGGGCTTTGAAAAGAGTGCCACTGAGC-
1 TGTGGGCTTTG-AAAGGGTGCCACTGA-CT
* * *
1114798 TATGGGCTTTGAAAGGATGCCA-TGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACT-GACT
* * * * *
1114826 TGTGTGGAC-TTAAAAAGATGCCACAGAGT
1 TGTG-GG-CTTTGAAAGGGTGCCACTGACT
* * * * **
1114855 TGTGGAC-TTAAAAGGATGCCACAGTGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
1114882 TGTGGACTTTAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* ** * * *
1114910 TGTGGAC-TAAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * * **
1114937 TATGGACTTTAAAAGGATGCCACAGTGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1114965 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * * *
1114992 GGTGGACTTTAAAAGAGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
1115020 TATGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1115047 TGTGGACTTT-AGAGGGTGCCAC-GACGT
1 TGTGGGCTTTGAAAGGGTGCCACTGAC-T
* *
1115074 TGTGGAC-TTAAAAGGGTGCCAC-GACGT
1 TGTGGGCTTTGAAAGGGTGCCACTGAC-T
* * * *
1115101 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1115128 TGTGGAC-TTAAAAGGGTGCCACGGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* ** * *
1115155 TGTGGACTTACAAA-GGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
1115182 TGTGGACTTTAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1115210 TGTGGACTTT
1 TGTGGGCTTT
1115220 AAAAAGAAAT
Statistics
Matches: 1167, Mismatches: 189, Indels: 56
0.83 0.13 0.04
Matches are distributed among these distances:
26 4 0.00
27 240 0.21
28 634 0.54
29 284 0.24
30 5 0.00
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:1113886 original size:57 final size:57
Alignment explanation
Indices: 1113808--1115252 Score: 1269
Period size: 57 Copynumber: 25.7 Consensus size: 57
1113798 CACCGGCTTG
* * *
1113808 TGTGGG-TTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
1113864 TGTGGGCTTTGAAAAGAGTGCCACTGATTTATGGTCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACT
* * * * *
1113922 TGTAGGCTTTG-AAAGGGTGCCACTGACTTGTGGGATTTGAAAAGAGTGCCATTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACT
* * * *
1113979 TGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACT
* * * * *
1114036 TGTGGGCTTTGAAAGGA-TGCCATTGACTCGTGGGCTTTAAAAGGATGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * * *
1114092 TATGGGCTTTGAAAAG-TTGCCACCGACTTGTGGGCTTTAAAAAGACGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
*
1114148 TGTGGGCTTTG-AAAG-GTTGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * *
1114204 CGTGGGCTTT-AAAAG-GATGCCACTAATTTGTGGACTTTGAAAGGTTGCCACTAACT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1114260 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGTTGCCACCGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
** * * * *
1114317 CATGGGCTTT-AAAAG-GATGCCATTGATTTGTGGGCTTTGAAAGGCTGCCACT-AAT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* *
1114372 TCGTGGGCTTTAAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATG-AACTGACT
1 T-GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1114429 TGTGGGCTTTGAAAAGA-TGCCACTGATTTGTGGGCTTTGAAAGGTTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
*
1114485 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
1114542 TATGGGCTTTGAAAAAAGTGCCACTGACTTGTGGACTTTGAAAAGATGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
*
1114599 TATGGGCTTTG-AAAG-GTTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1114655 TCTGGGCTTTGAAAAAAGTGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1114712 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGAGCTCTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1114769 TGCGGGCTTTGAAAAGAGTGCCACTGAGC-TATGGGCTTTGAAAGGATGCCA-TGGAGT
1 TGTGGGCTTTGAAAAGAGTGCCACTGA-CTTGTGGGCTTTGAAAGGATGCCACT-GACT
* * * * * * **
1114826 TGTGTGGAC-TTAAAAAGA-TGCCACAGAGTTGTGGAC-TTAAAAGGATGCCACAGTGT
1 TGTG-GG-CTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *** * *
1114882 TGTGGACTTT-AAAAGAGTGCCACGGAGTTGTGGACTAAAAAAGG-TGCCACGGAGT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * ** * * * * *
1114937 TATGGACTTT-AAAAG-GATGCCACAGTGTTGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * * * * * *
1114992 GGTGGACTTT-AAAAGAGTGCCACAGAGTTATGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * *
1115047 TGTGGACTTT--AGAGGGTGCCAC-GACGTTGTGGAC-TTAAAAGGGTGCCAC-GACGT
1 TGTGGGCTTTGAAAAGAGTGCCACTGAC-TTGTGGGCTTTGAAAGGATGCCACTGAC-T
* * * * * * * * *
1115101 TGTGGAC-TT-AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * * *
1115155 TGTGGAC-TT-ACAAAG-GTGCCACGGAGTTGTGGACTTT-AAAAGAGTGCCACGGAGT
1 TGTGGGCTTTGA-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACT
* * * * * *
1115210 TGTGGACTTTAAAAAGAAATGCCACTGAATCGTGGACTTTGAA
1 TGTGGGCTTTGAAAAG-AGTGCCACTGACTTGTGGGCTTTGAA
1115253 GAGGTCACAG
Statistics
Matches: 1205, Mismatches: 141, Indels: 83
0.84 0.10 0.06
Matches are distributed among these distances:
53 6 0.00
54 122 0.10
55 191 0.16
56 333 0.28
57 494 0.41
58 56 0.05
59 3 0.00
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (57 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:1114069 original size:85 final size:85
Alignment explanation
Indices: 1113808--1115252 Score: 1148
Period size: 85 Copynumber: 17.2 Consensus size: 85
1113798 CACCGGCTTG
* * * *
1113808 TGTGGGTTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGATTTGTGGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
*
1113872 TTGAAAAGAGTGCCACTGATT
66 TTGAAAAGA-TGCCACTGACT
* * * * * * *
1113893 TATGGTCTTTGAAAAGAGTGCCACTGATTTGTAGGCTTTG-AAAGGGTGCCACTGACTTGTGGGA
1 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
*
1113957 TTTGAAAAGAGTGCCATTGACT
65 TTTGAAAAGA-TGCCACTGACT
* *
1113979 TGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
* *
1114044 TTGAAAGGATGCCATTGACT
66 TTGAAAAGATGCCACTGACT
* * * * * * *
1114064 CGTGGGCTTTAAAAGGATGCCACTGATTTATGGGCTTTGAAAAG-TTGCCACCGACTTGTGGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
* * *
1114128 TTAAAAAGACGCCACTGATT
66 TTGAAAAGATGCCACTGACT
* * * *
1114148 TGTGGGCTTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAGGA-TGCCACTGACTCGTGGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
* *
1114212 TT-AAAAGGATGCCACTAATT
66 TTGAAAA-GATGCCACTGACT
* * *
1114232 TGTGGACTTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
* *
1114297 TTGAAAAGTTGCCACCGACT
66 TTGAAAAGATGCCACTGACT
** * * * * *
1114317 CATGGGCTTTAAAAGGATGCCATTGATTTGTGGGCTTTG-AAAG-GCTGCCACT-AATTCGTGGG
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGACTT-GTGGG
*
1114379 CTTTAAAAAGAGTGCCACTGACT
64 CTTTGAAAAGA-TGCCACTGACT
* * *
1114402 TGTGGGCTTTGAAAGGATG-AACTGACTTGTGGGCTTTGAAAAGA-TGCCACTGATTTGTGGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
* * *
1114465 TTGAAAGGTTGCCACTAACT
66 TTGAAAAGATGCCACTGACT
* * * *
1114485 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTAACTTATGGGC
1 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
*
1114549 TTTGAAAAAAGTGCCACTGACT
65 TTTGAAAAGA-TGCCACTGACT
* * * * *
1114571 TGTGGACTTTGAAAAGATGCCACTGATTTATGGGCTTTG-AAAG-GTTGCCACTGACTTGTGGGC
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGC
*
1114634 TTTGAAAGGATGCCACTGACT
65 TTTGAAAAGATGCCACTGACT
* ** * *
1114655 TCTGGGCTTTGAAAAAAGTGCCACTGACTCGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGC
1 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
1114719 TTTGAAAAGAGTGCCACTGACT
65 TTTGAAAAGA-TGCCACTGACT
* * * *
1114741 TGTGAGCTCTGAAAGGGTGCCACTGACTTGCGGGCTTTGAAAAGAGTGCCACTGAGC-TATGGGC
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGA-CTTGTGGGC
* *
1114805 TTTGAAAGGATGCCA-TGGAGT
65 TTTGAAAAGATGCCACT-GACT
* * * * * * * **
1114826 TGTGTGGAC-TTAAAAAGATGCCACAGAGTTGTGGAC-TT-AAAAG-GATGCCACAGTGTTGTGG
1 TGTG-GG-CTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGG
* * *
1114887 ACTTT-AAAAGAGTGCCACGGAGT
63 GCTTTGAAAAGA-TGCCACTGACT
* ** * * * * * * ** *
1114910 TGTGGAC-TAAAAAAGGTGCCACGGAGTTATGGACTTT-AAAAG-GATGCCACAGTGTTGTGGAC
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGC
* * *
1114972 -TT-AAAAGGGTGCCACGGAGT
65 TTTGAAAA-GATGCCACTGACT
* * * * * * * * * * * *
1114992 GGTGGACTTTAAAAGAGTGCCACAGAGTTATGGAC-TT-AAAAGGGTGCCACGGAGTTGTGGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
* * *
1115055 TT-AGAGGGTGCCAC-GACGT
66 TTGAAAAGATGCCACTGAC-T
* * * * * * *
1115074 TGTGGAC-TTAAAAGGGTGCCAC-GACGTTGTGGAC-TT-AAAAGGGTGCCACGGAGTTGTGGAC
1 TGTGGGCTTTGAAAGGGTGCCACTGAC-TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
1115135 -TT-AAAAGGGTGCCACGGATT
65 TTTGAAAA-GATGCCACTGACT
* ** * * * * * *
1115155 TGTGGACTTACAAA-GGTGCCACGGAGTTGTGGACTTT-AAAAGAGTGCCACGGAGTTGTGGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
* *
1115218 TTAAAAAGAAATGCCACTGAAT
66 TTGAAAAG--ATGCCACTGACT
* *
1115240 CGTGGACTTTGAA
1 TGTGGGCTTTGAA
1115253 GAGGTCACAG
Statistics
Matches: 1144, Mismatches: 169, Indels: 94
0.81 0.12 0.07
Matches are distributed among these distances:
80 6 0.01
81 82 0.07
82 119 0.10
83 95 0.08
84 270 0.24
85 380 0.33
86 190 0.17
87 2 0.00
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (85 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
TTGAAAAGATGCCACTGACT
Found at i:1114866 original size:27 final size:27
Alignment explanation
Indices: 1114809--1115223 Score: 512
Period size: 27 Copynumber: 15.1 Consensus size: 27
1114799 ATGGGCTTTG
* *
1114809 AAAGGATGCCATGGAGTTGTGTGGACTTA
1 AAAGGGTGCCACGGAG-T-TGTGGACTTA
* * *
1114838 AAAAGATGCCACAGAGTTGTGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* * *
1114865 AAAGGATGCCACAGTGTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
* *
1114893 AAAGAGTGCCACGGAGTTGTGGACTAA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* *
1114920 AAAAGGTGCCACGGAGTTATGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
* * *
1114948 AAAGGATGCCACAGTGTTGTGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
*
1114975 AAAGGGTGCCACGGAGTGGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
* * *
1115003 AAAGAGTGCCACAGAGTTATGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
*
1115030 AAAGGGTGCCACGGAGTTGTGGACTTT
1 AAAGGGTGCCACGGAGTTGTGGACTTA
*
1115057 AGAGGGTGCCAC-GACGTTGTGGACTTA
1 AAAGGGTGCCACGGA-GTTGTGGACTTA
1115084 AAAGGGTGCCAC-GACGTTGTGGACTTA
1 AAAGGGTGCCACGGA-GTTGTGGACTTA
1115111 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
*
1115138 AAAGGGTGCCACGGATTTGTGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
1115165 CAAA-GGTGCCACGGAGTTGTGGACTTTA
1 -AAAGGGTGCCACGGAGTTGTGGAC-TTA
*
1115193 AAAGAGTGCCACGGAGTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
1115221 AAA
1 AAA
1115224 AGAAATGCCA
Statistics
Matches: 341, Mismatches: 37, Indels: 17
0.86 0.09 0.04
Matches are distributed among these distances:
26 2 0.01
27 224 0.66
28 102 0.30
29 13 0.04
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (27 bp):
AAAGGGTGCCACGGAGTTGTGGACTTA
Found at i:1116275 original size:1 final size:1
Alignment explanation
Indices: 1116269--1116299 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
1116259 GGTGAAAAGG
1116269 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1116300 AAGATTGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1121053 original size:52 final size:52
Alignment explanation
Indices: 1120975--1121102 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
1120965 CGAAATATGA
* *
1120975 AAATTTGCTTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
1121027 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1121079 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1121103 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
51 21 0.29
52 47 0.64
53 5 0.07
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:1121115 original size:51 final size:50
Alignment explanation
Indices: 1120975--1121122 Score: 185
Period size: 52 Copynumber: 2.9 Consensus size: 50
1120965 CGAAATATGA
* *
1120975 AAATTTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGC
1121027 AAATTTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGGGC
1121079 AAA-TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
1121123 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 2, Indels: 13
0.85 0.02 0.13
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 33 0.38
52 46 0.52
53 1 0.01
54 4 0.05
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (50 bp):
AAATTTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGC
Found at i:1121129 original size:13 final size:13
Alignment explanation
Indices: 1121111--1121135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1121101 CAAAGATCAG
1121111 TGTATCGATACAA
1 TGTATCGATACAA
1121124 TGTATCGATACA
1 TGTATCGATACA
1121136 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1121217 original size:13 final size:13
Alignment explanation
Indices: 1121199--1121223 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1121189 AAAAAAAATA
1121199 TGTATCGATACAT
1 TGTATCGATACAT
1121212 TGTATCGATACA
1 TGTATCGATACA
1121224 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1121322 original size:21 final size:21
Alignment explanation
Indices: 1121281--1121322 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1121271 GTTGGGACCT
*
1121281 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
1121302 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
1121323 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:1122290 original size:49 final size:49
Alignment explanation
Indices: 1122173--1122794 Score: 821
Period size: 49 Copynumber: 12.7 Consensus size: 49
1122163 AAAAGGATGT
* *
1122173 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
* *
1122225 CGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
1122274 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
1122323 CAATATGCTGATTCAAGGCCAGCTATA-TGGACTTAATGGTGCAA-GTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG-AAGGTGC
* ** * *
1122371 CAATGTGCTGAGTCAAGGCCAGCTACGTTGGACTTAAAGATAAAAGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
1122420 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
1122469 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * * *
1122518 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
1122567 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
*
1122619 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
1122662 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1122710 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
1122759 CAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTA
1122795 GAAGGGTTGC
Statistics
Matches: 497, Mismatches: 60, Indels: 29
0.85 0.10 0.05
Matches are distributed among these distances:
43 40 0.08
48 87 0.18
49 292 0.59
50 1 0.00
51 1 0.00
52 76 0.15
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
Found at i:1122500 original size:98 final size:98
Alignment explanation
Indices: 1122173--1122794 Score: 929
Period size: 98 Copynumber: 6.4 Consensus size: 98
1122163 AAAAGGATGT
* * *
1122173 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATT
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT--AAAA-GTGCCAATATGCTGATT
* *
1122238 CAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
63 CAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
*
1122274 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAGTGCCAATATGCTGATTCAA
1122339 GGCCAGCTATA-TGGACTTAATGGTGCAA-GTGC
66 GGCCAGCTATATTGGACTTAATGGTG-AAGGTGC
*
1122371 CAATGTGCTGAGTCAAGGCCAGCTACGTTGGACTTAAAGATAAAAGTGCCAATATGCTGATTCAA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAGTGCCAATATGCTGATTCAA
1122436 GGCCAGCTATATTGGACTTAATGGTGAAGGTGC
66 GGCCAGCTATATTGGACTTAATGGTGAAGGTGC
*
1122469 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAGTGCCAATATGCTGATTCAA
*
1122534 GGCCAGCTATATTGGGCTTAATGGTGAAGGTGC
66 GGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1122567 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT--AAAA-GTGCCAATATGCTGATT
1122632 CAAGGCCAGCTATATTGGACTT-A-----AAGGTGC
63 CAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
* * * * *
1122662 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGT-GAGGTGCCAATGTGCTGATTCAA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAGTGCCAATATGCTGATTCAA
* *
1122726 GGCCAGCTATATTGGACTTAAAGATGAAGGTGC
66 GGCCAGCTATATTGGACTTAATGGTGAAGGTGC
* * * * *
1122759 CAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
1122795 GAAGGGTTGC
Statistics
Matches: 487, Mismatches: 22, Indels: 28
0.91 0.04 0.05
Matches are distributed among these distances:
91 38 0.08
92 2 0.00
95 46 0.09
97 131 0.27
98 186 0.38
99 3 0.01
100 4 0.01
101 77 0.16
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (98 bp):
CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAATGGTGAAGGTGC
Found at i:1122508 original size:195 final size:196
Alignment explanation
Indices: 1122173--1122794 Score: 974
Period size: 195 Copynumber: 3.2 Consensus size: 196
1122163 AAAAGGATGT
* * *
1122173 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATT
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAAAGGTGCCAATATGCTGATT
1122238 CAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATT
65 CAAGGCCAGCTATATTGGACTT-AAG-TGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATT
1122303 GGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA-TGGACTTAATGGTGCAA
128 GGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTG-AA
1122367 -GTGC
192 GGTGC
*
1122371 CAATGTGCTGAGTCAAGGCCAGCTACGTTGGACTTAAAGAT-AAAA-GTGCCAATATGCTGATTC
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAGGTGCCAATATGCTGATTC
1122434 AAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTG
66 AAGGCCAGCTATATTGGACTTAA--GTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTG
*
1122499 GACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAATGGTGAAGG
129 GACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGG
1122564 TGC
194 TGC
1122567 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAAAGGTGCCAATATGCTGATT
*
1122632 CAAGGCCAGCTATATTGGACTT-A---AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
65 CAAGGCCAGCTATATTGGACTTAAGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGG
* * * * *
1122693 ACTTAAAGGT-GAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGT
130 ACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGT
1122757 GC
195 GC
* * * * *
1122759 CAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
1122795 GAAGGGTTGC
Statistics
Matches: 399, Mismatches: 18, Indels: 20
0.91 0.04 0.05
Matches are distributed among these distances:
192 82 0.21
193 46 0.12
194 2 0.01
195 125 0.31
196 62 0.16
198 43 0.11
199 39 0.10
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (196 bp):
CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAGGTGCCAATATGCTGATTC
AAGGCCAGCTATATTGGACTTAAGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
CTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTG
C
Found at i:1122672 original size:43 final size:44
Alignment explanation
Indices: 1122610--1122799 Score: 238
Period size: 43 Copynumber: 4.1 Consensus size: 44
1122600 TTAAAGATGG
1122610 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
1122654 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
1122697 AAAGGTGAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAA----AGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
1122745 AAAGATGAAGGTGCCAATATGCTGATTCAGGGCCAGCTATATTGGGCTT
1 --A-A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
1122794 AGAAGG
1 AAAAGG
1122800 GTTGCCACCG
Statistics
Matches: 129, Mismatches: 7, Indels: 20
0.83 0.04 0.13
Matches are distributed among these distances:
43 41 0.32
44 6 0.05
47 1 0.01
48 40 0.31
49 38 0.29
50 1 0.01
51 1 0.01
53 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.26
Consensus pattern (44 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:1122838 original size:33 final size:33
Alignment explanation
Indices: 1122794--1122998 Score: 301
Period size: 33 Copynumber: 6.2 Consensus size: 33
1122784 TATTGGGCTT
*
1122794 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
1122827 AGAATGGTTGCCACCAACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
1122859 GGAAGGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
1122891 GGAAGGGATTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
1122925 AGGAA-GGTTGCCACCGACTTGTGTGGGCTTTAG
1 A-GAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1122958 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
1122992 A-AAGGGT
1 AGAAGGGT
1122999 GAAAGATGCC
Statistics
Matches: 158, Mismatches: 9, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
32 40 0.25
33 85 0.54
34 30 0.19
35 3 0.02
ACGTcount: A:0.19, C:0.18, G:0.36, T:0.28
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:1122871 original size:65 final size:66
Alignment explanation
Indices: 1122795--1122998 Score: 306
Period size: 65 Copynumber: 3.1 Consensus size: 66
1122785 ATTGGGCTTA
* *
1122795 GAAGGGTTGCCACCGACTTGTGTGGGCTTTAAAGAATGG-TTGCCACCAACTTGTGTGGGCTTTG
1 GAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGATTGCCACCAACTTGTGTGGGCTTTG
1122859 G
66 G
*
1122860 GAAGGGTTGCCACCGACTTGTGTGGGCTTT-GGGAAGGGATTGCCACCAACTTGTGTGGGCTTTA
1 GAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGATTGCCACCAACTTGTGTGGGCTTT-
1122924 GAG
65 G-G
* * *
1122927 GAA-GGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCGACTTGTGTGGGCTTTA
1 GAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGATTGCCACCAACTTGTGTGGGCTTTG
1122991 G
66 G
*
1122992 AAAGGGT
1 GAAGGGT
1122999 GAAAGATGCC
Statistics
Matches: 126, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
64 5 0.04
65 57 0.45
66 30 0.24
67 34 0.27
ACGTcount: A:0.19, C:0.18, G:0.36, T:0.28
Consensus pattern (66 bp):
GAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGATTGCCACCAACTTGTGTGGGCTTTG
G
Found at i:1123110 original size:34 final size:34
Alignment explanation
Indices: 1123000--1123407 Score: 444
Period size: 34 Copynumber: 12.1 Consensus size: 34
1122990 AGAAAGGGTG
* * *
1123000 AAAGA-TGCCACGAAGTTGTGGACTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
1123033 CAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGGAAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAA-GG-AA
*
1123069 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
1123103 AAAGAGTGCCACGAAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
1123137 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
1123171 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
1123204 AAAGAGTGCCACGTAGTTGTGGGCTTTAAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* * * *
1123237 AAAGAGTGCCATGTAGTCGTGGACTTAAAA-G--
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
1123268 ---G-GTGCCACGGAGTTGTGGGCTGTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCT-TAAAAGGAA
1123299 AAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAA-GG-AA
** *
1123336 AAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * * *
1123371 AAAGTGTGCCACAGAGTTGTGGGCTTTAAAGAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
1123405 AAA
1 AAA
1123408 TGCAACTGAG
Statistics
Matches: 330, Mismatches: 28, Indels: 33
0.84 0.07 0.08
Matches are distributed among these distances:
27 16 0.05
28 6 0.02
29 1 0.00
32 1 0.00
33 76 0.23
34 137 0.42
35 32 0.10
36 12 0.04
37 29 0.09
38 20 0.06
ACGTcount: A:0.35, C:0.12, G:0.34, T:0.20
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:1123285 original size:27 final size:28
Alignment explanation
Indices: 1123236--1123294 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
1123226 GCTTTAAAGG
* *
1123236 AAAAGAGTGCCATGTAGTCGTGGACT-T
1 AAAAGAGTGCCACGGAGTCGTGGACTGT
* * *
1123263 AAAAGGGTGCCACGGAGTTGTGGGCTGT
1 AAAAGAGTGCCACGGAGTCGTGGACTGT
1123291 AAAA
1 AAAA
1123295 AGAAAAAGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.22
Consensus pattern (28 bp):
AAAAGAGTGCCACGGAGTCGTGGACTGT
Found at i:1123380 original size:35 final size:34
Alignment explanation
Indices: 1123263--1123400 Score: 177
Period size: 35 Copynumber: 3.9 Consensus size: 34
1123253 TCGTGGACTT
* * *
1123263 AAAAGGGTGCCACGGAGTTGTGGGCTGTAAAAAG
1 AAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAAG
* *
1123297 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
1 AAAAAGGTGCCACAGAGTTGTGGGCTTT-AAAA-AG
*
1123333 AAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAG
1 -AAAAAG-GTGCCACAGAGTTGTGGGCTTTAAAAAG
1123369 AAAAAGTGTGCCACAGAGTTGTGGGCTTTAAA
1 AAAAAG-GTGCCACAGAGTTGTGGGCTTTAAA
1123401 GAAAAAATGC
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
34 26 0.28
35 34 0.37
36 2 0.02
37 10 0.11
38 20 0.22
ACGTcount: A:0.36, C:0.12, G:0.33, T:0.20
Consensus pattern (34 bp):
AAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAAG
Found at i:1128420 original size:10 final size:10
Alignment explanation
Indices: 1128405--1128436 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1128395 CCATTTCATA
1128405 TTTTTTTTCT
1 TTTTTTTTCT
1128415 TTTTTTTTCT
1 TTTTTTTTCT
*
1128425 TTTTCTTTCT
1 TTTTTTTTCT
1128435 TT
1 TT
1128437 CTTCTTCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:1128433 original size:20 final size:20
Alignment explanation
Indices: 1128405--1128459 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1128395 CCATTTCATA
* *
1128405 TTTTT-TTTCTTTTTTTTTC
1 TTTTTCTTTCTTTCTTCTTC
1128424 TTTTTCTTTCTTTCTTCTTC
1 TTTTTCTTTCTTTCTTCTTC
* *
1128444 ATCTTCTTTCTTTCTT
1 TTTTTCTTTCTTTCTT
1128460 TCTTACTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 5 0.16
20 26 0.84
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTCTTTCTTTCTTCTTC
Found at i:1129929 original size:13 final size:13
Alignment explanation
Indices: 1129911--1129935 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1129901 CAAAGATCAG
1129911 TGTATCGATACAA
1 TGTATCGATACAA
1129924 TGTATCGATACA
1 TGTATCGATACA
1129936 TTTTAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1129998 original size:13 final size:13
Alignment explanation
Indices: 1129980--1130031 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
1129970 AGCTTCGTAG
1129980 CGATACATTGTAT
1 CGATACATTGTAT
1129993 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1130012 CGATACATTGTAT
1 CGATACATTGTAT
1130025 CGATACA
1 CGATACA
1130032 ACACTTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1130012 original size:19 final size:18
Alignment explanation
Indices: 1129988--1130050 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
1129978 AGCGATACAT
1129988 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1130007 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1130020 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
1130039 TATATCGATACA
1 TGTATCGATACA
1130051 TTGTATCAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
16 2 0.05
18 1 0.03
19 22 0.59
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1130021 original size:32 final size:32
Alignment explanation
Indices: 1129980--1130065 Score: 145
Period size: 32 Copynumber: 2.7 Consensus size: 32
1129970 AGCTTCGTAG
*
1129980 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATATAT
*
1130012 CGATACATTGTATCGATACAACACTTATATAT
1 CGATACATTGTATCGATACAAAACTTATATAT
*
1130044 CGATACATTGTATCAATACAAA
1 CGATACATTGTATCGATACAAA
1130066 TCGTTGAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATATAT
Found at i:1130184 original size:21 final size:21
Alignment explanation
Indices: 1130101--1130177 Score: 145
Period size: 21 Copynumber: 3.7 Consensus size: 21
1130091 GTTGGGACCT
1130101 TGTATCGATACATTCTAACAA
1 TGTATCGATACATTCTAACAA
*
1130122 TGTATCGATACATTCTAATAA
1 TGTATCGATACATTCTAACAA
1130143 TGTATCGATACATTCTAACAA
1 TGTATCGATACATTCTAACAA
1130164 TGTATCGATACATT
1 TGTATCGATACATT
1130178 TGGACAAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTCTAACAA
Found at i:1130954 original size:52 final size:52
Alignment explanation
Indices: 1130736--1132284 Score: 1054
Period size: 52 Copynumber: 31.8 Consensus size: 52
1130726 GTGATAAAAA
* * *
1130736 TGCCAATATGCTGATTCATGGCCAGCGACATTGGACTTGAAGA--A-GAA--
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* ** * * * * * *** *
1130783 TGCCAATGTGCTGAGACTAAGGTCAGTGACATTGGGCTT-AGGAATGTTAAAGT
1 TGCCAATATGCTGATTC-AAGGCCAGCGATATTGGACTTAAAG-ATGACGAAGG
* * * * * *
1130836 TGCCAATACGTTGATTCAAGGTCAACAATATTGGACTT-AAG--GATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* * * ** * *
1130885 TGTCAATGTACTGATTCAAGGCCAATGACATTGG-TTTGAAAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAAGATGACGAAGG
* *
1130937 CGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGAT---GAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* * * *
1130986 TGACAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
*
1131038 TGCTAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
*
1131090 TGCCTAATATACTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
1 TGCC-AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
1131143 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* * * * * *
1131186 TGCCAATGTGCTGATTCAAAGCCAGCGACATTGG-TTTTAA-A-GACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* *
1131235 TGCCAATATGCTAATTCAAGGCCAACGATATTGGAC-T-----T-A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* * * * * **
1131278 TGCCGATGTGCTGATTCAAGGCCAGCGACATTAGTCTTAAAGATGAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
1131330 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* * * * * * *
1131373 TGCCATTGTGCTAATTCAGGGCCAGCGACATTGGTCTTAAAGAT-A--AAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
1131422 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* * * * **
1131465 TGCCAATGTGCTGATTCAAGACCAGCGACATTGGTCTTAAAGATGAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
*
1131517 TACCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* * * **
1131560 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* ** *
1131612 TGCCAATATGCTGATTTAATACCAACGATATTGGAC-T-----T-A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* * * * * **
1131655 TGCCAATGTGCTGATTCAAGGCTAGCGACATTAGTCTTAAAGATGAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
1131707 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* * * * **
1131750 TGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* * **
1131802 TGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTAGAAG--GTTG-AGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGATGACGAAGG
* * * * * * * * **
1131852 TGTCGATGTACTGATTCAAGGCCAACGACATTAGTCTTAAAGATGAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* **
1131904 TGCCAATATGCTGATTTAATACCAGCGATATTGGAC-T-----T-A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* * * * * **
1131947 TGCCAATGTGCTGATTCAAGGCTAGCGACATTAGTCTTAAAGATGAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
1131999 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* * * * **
1132042 TGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* * **
1132094 TGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTAGAAG--GTTG-AGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGATGACGAAGG
* * * * * ** *
1132144 TGCCGATGTACTGATTCAAGGCCAACGACATCAGTCTTAAAGAT-A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* *
1132193 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
* *
1132242 TGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTCAAAG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAAG
1132285 GGTTGCCACC
Statistics
Matches: 1192, Mismatches: 206, Indels: 205
0.74 0.13 0.13
Matches are distributed among these distances:
43 311 0.26
44 8 0.01
45 8 0.01
46 7 0.01
47 17 0.01
48 21 0.02
49 235 0.20
50 80 0.07
51 12 0.01
52 422 0.35
53 71 0.06
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGG
Found at i:1131200 original size:43 final size:44
Alignment explanation
Indices: 1131139--1132285 Score: 674
Period size: 43 Copynumber: 24.1 Consensus size: 44
1131129 AAAGATGACG
1131139 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
* * * **
1131182 AAGGTGCCAATGTGCTGATTCAAAGCCAGCGACATTGGTTTTAAAGACA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-A
* *
1131231 AAGGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTT-A
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
* * * * *
1131274 AAGGTGCCGATGTGCTGATTCAAGGCCAGCGACATTAGTCTTAAAGATGAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T--AA
1131326 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
* * * * * *
1131369 AAGGTGCCATTGTGCTAATTCAGGGCCAGCGACATTGGTCTTAAAGATA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-A
*
1131418 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
* * * *
1131461 AAGGTGCCAATGTGCTGATTCAAGACCAGCGACATTGGTCTTAAAGATGAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T--AA
*
1131513 AAGGTACCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
* * *
1131556 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T--AA
* ** *
1131608 AAGGTGCCAATATGCTGATTTAATACCAACGATATTGGACTT-A
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
* * * * *
1131651 AAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGTCTTAAAGATGAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T--AA
1131703 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
* * * *
1131746 AAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T--AA
* *
1131798 AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTAGA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-A
* * * * * * * *
1131843 AGGTTGAGGTGTCGATGTACTGATTCAAGGCCAACGACATTAGTCTTAAAGATGAAA
1 A-----AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T--AA
* **
1131900 AAGGTGCCAATATGCTGATTTAATACCAGCGATATTGGACTT-A
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
* * * * *
1131943 AAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGTCTTAAAGATGAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T--AA
1131995 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
* * * *
1132038 AAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T--AA
* *
1132090 AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTAGA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-A
* * * * * ** *
1132135 AGGTTGAGGTGCCGATGTACTGATTCAAGGCCAACGACATCAGTCTTAAAGATA
1 A-----AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-A
* *
1132189 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-A
* * *
1132238 AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTCA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
1132282 AAGG
1 AAGG
1132286 GTTGCCACCG
Statistics
Matches: 861, Mismatches: 144, Indels: 197
0.72 0.12 0.16
Matches are distributed among these distances:
43 320 0.37
44 14 0.02
45 4 0.00
46 8 0.01
49 159 0.18
50 62 0.07
51 9 0.01
52 278 0.32
54 3 0.00
56 1 0.00
57 2 0.00
58 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (44 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
Found at i:1131340 original size:292 final size:286
Alignment explanation
Indices: 1130736--1132267 Score: 1857
Period size: 292 Copynumber: 5.2 Consensus size: 286
1130726 GTGATAAAAA
* * * **
1130736 TGCCAATATGCTGATTCATGGCCAGCGACATTGGACTTGAAGAAGAATGCCAATGTGCTGAGACT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-AAG-GTGCCAATGTGCTGATTC-
* * * * ** * * * * * *
1130801 AAGGTCAGTGACATTGGGCTT-AGGAATGTTAAAGTTGCCAATACGTTGATTCAAGGTCAACAAT
61 AAGGCCAGCGACATTGGTCTTAAAG-ATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGAT
* * **
1130865 ATTGGACTTAAGGATGAAGGTGTCAATGTACTGATTCAAGGCCAATGACATTGGT-TTGAAAGAT
125 ATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AAAGAT
** * * * *
1130929 GACGAAGGCGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGACAATG
183 GAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-A--AAGGTGCCGATG
* * * **
1130994 TGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACGAAGG
243 TGCTGATTCAAGGCCAGCGACATTAGTCTTAAAGATGAAAAAGG
* * *
1131038 TGCTAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGGTGCCTAATATACT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-A--AAGGTGCC-AATGTGCT
* * **
1131103 GATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGGTGCCAATATGCTGATTCAAGGCCAG
56 GATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAG
* * *
1131168 CGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAAGCCAGCGACATTGGT-TTTAA-A-GAC
121 CGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAA
* *
1131230 AAAGGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTT-AAAGGTGCCGATGTGCTGATT
186 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGGTGCCGATGTGCTGATT
1131294 CAAGGCCAGCGACATTAGTCTTAAAGATGAAAAAGG
251 CAAGGCCAGCGACATTAGTCTTAAAGATGAAAAAGG
* * *
1131330 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCATTGTGCTAATTCAGGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGC
*
1131395 CAGCGACATTGGTCTTAAAGAT---AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
66 CAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
* *
1131457 CTTAAAGGTGCCAATGTGCTGATTCAAGACCAGCGACATTGGTCTTAAAGATGAAAAAGGTACCA
131 CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCA
*
1131522 ATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAAGGTGCCAATGTGCTGATTCAAGGCCAGC
196 ATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGGTGCCGATGTGCTGATTCAAGGCCAGC
*
1131586 GACATTGGTCTTAAAGATGAAAAAGG
261 GACATTAGTCTTAAAGATGAAAAAGG
* ** *
1131612 TGCCAATATGCTGATTTAATACCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGC
* *
1131677 TAGCGACATTAGTCTTAAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
66 CAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
*
1131742 CTTAAAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCA
131 CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCA
* * * *
1131807 ATATGCTGATTCAAGGCCAGCAATATTGGGCTTAGAAGGTTGAGGTGTCGATGTACTGATTCAAG
196 ATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AA-----AGGTGCCGATGTGCTGATTCAAG
*
1131872 GCCAACGACATTAGTCTTAAAGATGAAAAAGG
255 GCCAGCGACATTAGTCTTAAAGATGAAAAAGG
* **
1131904 TGCCAATATGCTGATTTAATACCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGC
* *
1131969 TAGCGACATTAGTCTTAAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
66 CAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
*
1132034 CTTAAAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCA
131 CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCA
* * *
1132099 ATATGCTGATTCAAGGCCAGCAATATTGGGCTTAGAAGGTTGAGGTGCCGATGTACTGATTCAAG
196 ATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AA-----AGGTGCCGATGTGCTGATTCAAG
* *
1132164 GCCAACGACATCAGTCTTAAAGAT---AAAGG
255 GCCAGCGACATTAGTCTTAAAGATGAAAAAGG
* * *
1132193 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TAAAGGTGCCAATGTGCTGATT
1132258 CAAGGCCAGC
60 CAAGGCCAGC
1132268 AATATTGGGC
Statistics
Matches: 1114, Mismatches: 88, Indels: 63
0.88 0.07 0.05
Matches are distributed among these distances:
279 79 0.07
280 4 0.00
281 1 0.00
282 208 0.19
283 8 0.01
285 133 0.12
286 1 0.00
287 2 0.00
289 36 0.03
290 1 0.00
291 1 0.00
292 415 0.37
294 1 0.00
295 30 0.03
298 43 0.04
299 1 0.00
300 2 0.00
301 36 0.03
302 33 0.03
303 2 0.00
307 61 0.05
308 16 0.01
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (286 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGC
CAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCA
ATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGGTGCCGATGTGCTGATTCAAGGCCAGC
GACATTAGTCTTAAAGATGAAAAAGG
Found at i:1131373 original size:95 final size:95
Alignment explanation
Indices: 1131086--1132267 Score: 1671
Period size: 95 Copynumber: 12.3 Consensus size: 95
1131076 AAAGATGACG
* * * * **
1131086 AAGGTGCCTAATATACTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGGTGCCAATA
1 AAGGTGCC-AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATA
1131151 TGCTGATTCAAGGCCAGCGATATTGGACTTA
65 TGCTGATTCAAGGCCAGCGATATTGGACTTA
* * *
1131182 AAGGTGCCAATGTGCTGATTCAAAGCCAGCGACATTGGT-TTTAA-A-GACAAAGGTGCCAATAT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATAT
* *
1131244 GCTAATTCAAGGCCAACGATATTGGACTTA
66 GCTGATTCAAGGCCAGCGATATTGGACTTA
* *
1131274 AAGGTGCCGATGTGCTGATTCAAGGCCAGCGACATTAGTCTTAAAGATGAAAAAGGTGCCAATAT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATAT
1131339 GCTGATTCAAGGCCAGCGATATTGGACTTA
66 GCTGATTCAAGGCCAGCGATATTGGACTTA
* * * *
1131369 AAGGTGCCATTGTGCTAATTCAGGGCCAGCGACATTGGTCTTAAAGAT---AAAGATGCCAATAT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATAT
1131431 GCTGATTCAAGGCCAGCGATATTGGACTTA
66 GCTGATTCAAGGCCAGCGATATTGGACTTA
* *
1131461 AAGGTGCCAATGTGCTGATTCAAGACCAGCGACATTGGTCTTAAAGATGAAAAAGGTACCAATAT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATAT
1131526 GCTGATTCAAGGCCAGCGATATTGGACTTA
66 GCTGATTCAAGGCCAGCGATATTGGACTTA
1131556 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATAT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATAT
* ** *
1131621 GCTGATTTAATACCAACGATATTGGACTTA
66 GCTGATTCAAGGCCAGCGATATTGGACTTA
* *
1131651 AAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGTCTTAAAGATGAAAAAGGTGCCAATAT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATAT
1131716 GCTGATTCAAGGCCAGCGATATTGGACTTA
66 GCTGATTCAAGGCCAGCGATATTGGACTTA
*
1131746 AAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATAT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATAT
* *
1131811 GCTGATTCAAGGCCAGCAATATTGGGCTTAGA
66 GCTGATTCAAGGCCAGCGATATTGGACTT--A
* * * * *
1131843 AGGTTGAGGTGTCGATGTACTGATTCAAGGCCAACGACATTAGTCTTAAAGATGAAAAAGGTGCC
1 A-----AGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCC
* **
1131908 AATATGCTGATTTAATACCAGCGATATTGGACTTA
61 AATATGCTGATTCAAGGCCAGCGATATTGGACTTA
* *
1131943 AAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGTCTTAAAGATGAAAAAGGTGCCAATAT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATAT
1132008 GCTGATTCAAGGCCAGCGATATTGGACTTA
66 GCTGATTCAAGGCCAGCGATATTGGACTTA
*
1132038 AAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATAT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATAT
* *
1132103 GCTGATTCAAGGCCAGCAATATTGGGCTTAGA
66 GCTGATTCAAGGCCAGCGATATTGGACTT--A
* * * **
1132135 AGGTTGAGGTGCCGATGTACTGATTCAAGGCCAACGACATCAGTCTTAAAGAT---AAAGGTGCC
1 A-----AGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCC
* *
1132197 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATA
61 AATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TA
*
1132238 AAGGTGCCAATATGCTGATTCAAGGCCAGC
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGC
1132268 AATATTGGGC
Statistics
Matches: 977, Mismatches: 83, Indels: 50
0.88 0.07 0.05
Matches are distributed among these distances:
92 167 0.17
93 5 0.01
94 5 0.01
95 597 0.61
96 8 0.01
97 4 0.00
98 25 0.03
99 37 0.04
100 3 0.00
102 123 0.13
103 2 0.00
105 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (95 bp):
AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAAAGGTGCCAATAT
GCTGATTCAAGGCCAGCGATATTGGACTTA
Found at i:1132334 original size:32 final size:29
Alignment explanation
Indices: 1132273--1132361 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 29
1132263 CCAGCAATAT
* * *
1132273 TGGGCTTCAAAGGGTTGCCACCGACTTGTG
1 TGGGCTTAAAAGGG-TGCCACAGAGTTGTG
*
1132303 TGGGCTTTAGAAGGGAGTGCCACAGAG-T-TG
1 TGGGC-TTA-AAAGG-GTGCCACAGAGTTGTG
*
1132333 TGGGCTTAAAAGGGTGCCACGGAGTTGTG
1 TGGGCTTAAAAGGGTGCCACAGAGTTGTG
1132362 GACTTTAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
27 10 0.21
28 5 0.10
29 5 0.10
30 12 0.25
31 3 0.06
32 12 0.25
33 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.38, T:0.25
Consensus pattern (29 bp):
TGGGCTTAAAAGGGTGCCACAGAGTTGTG
Found at i:1132357 original size:27 final size:27
Alignment explanation
Indices: 1132273--1132372 Score: 83
Period size: 27 Copynumber: 3.5 Consensus size: 27
1132263 CCAGCAATAT
* * *
1132273 TGGGCTTCAAAGGGTTGCCACCGACTTGTG
1 TGGGCTTAAAAGGG-TGCCACAGA-GT-TG
*
1132303 TGGGCTTTAGAAGGGAGTGCCACAGAGTTG
1 TGGGC-TTA-AAAGG-GTGCCACAGAGTTG
*
1132333 TGGGCTTAAAAGGGTGCCACGGAGTTG
1 TGGGCTTAAAAGGGTGCCACAGAGTTG
* *
1132360 TGGACTTTAAAGG
1 TGGGCTTAAAAGG
1132373 AAAAAGAGTG
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
27 24 0.41
28 4 0.07
29 3 0.05
30 12 0.20
31 3 0.05
32 12 0.20
33 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.37, T:0.25
Consensus pattern (27 bp):
TGGGCTTAAAAGGGTGCCACAGAGTTG
Found at i:1132522 original size:69 final size:69
Alignment explanation
Indices: 1132340--1132577 Score: 271
Period size: 69 Copynumber: 3.5 Consensus size: 69
1132330 TTGTGGGCTT
* * *
1132340 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC-TTAAA
1 AAAAGGGTGCCACGAAGTTGTGGACTTTAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
*
1132404 AGGA
66 AAGA
1132408 AAAA-GGTGCCAC-AGAGTTGTGGAC-TTAAAAGGGAAAAAGGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGA-AGTTGTGGACTTTAAAA--GAAAAA-GAGTGCCACGGAGTTGTGGGCTT
1132470 TAAAAAGA
62 TAAAAAGA
* *
1132478 AAAAGGGTGCCACGAAATTGTGGGCTTTGAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTT--
1 AAAAGGGTGCCACGAAGTTGTGGACTTT-AAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
1132540 GAAG-
65 AAAGA
*
1132544 AAAA-GATGCCACTG-AGTTGTGGACTTTGAAAAGA
1 AAAAGGGTGCCAC-GAAGTTGTGGACTTT-AAAAGA
1132578 GATTGCCACT
Statistics
Matches: 150, Mismatches: 10, Indels: 23
0.82 0.05 0.13
Matches are distributed among these distances:
65 25 0.17
66 10 0.07
67 21 0.14
68 10 0.07
69 42 0.28
70 13 0.09
71 22 0.15
72 3 0.02
73 4 0.03
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (69 bp):
AAAAGGGTGCCACGAAGTTGTGGACTTTAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
AAGA
Found at i:1132554 original size:31 final size:31
Alignment explanation
Indices: 1132347--1132792 Score: 305
Period size: 31 Copynumber: 13.9 Consensus size: 31
1132337 CTTAAAAGGG
* *
1132347 TGCCACGGAGTTGTGGACTTTAAAGGAAAAAGA
1 TGCCACTGAGTTGTGGACTTTGAA-G-AAAAGA
* ** *
1132380 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGG
1 -TGCCACTGAGTTGTGGACTTTGAA-G-AAAAGA
* **
1132414 TGCCACAGAGTTGTGGACTTAAAAGGGAAAAAGGA
1 TGCCACTGAGTTGTGGACTTTGAA--G-AAAA-GA
* * * *
1132449 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGG
1 -TGCCACTGAGTTGTGGACTTT--GAAG-AAAA-GA
* * *
1132485 TGCCAC-GAAATTGTGGGCTTTGAAAAGAAAAAGG
1 TGCCACTG-AGTTGTGGACTTTG--AAG-AAAAGA
* *
1132519 TGCCACGGAGTTGTGGGCTTTGAAGAAAAGA
1 TGCCACTGAGTTGTGGACTTTGAAGAAAAGA
*
1132550 TGCCACTGAGTTGTGGACTTTGAA-AAGAGA
1 TGCCACTGAGTTGTGGACTTTGAAGAAAAGA
1132580 TTGCCACTGAGTTGTGGACTTTGAAGAAAAGA
1 -TGCCACTGAGTTGTGGACTTTGAAGAAAAGA
*
1132612 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGA
1 TGCCACTGAGTTGTGGACTTTGAAGAAAA-GA
* * *
1132644 TGCCACTAAGTCGTGGACTTTG-GGATAAA-A
1 TGCCACTGAGTTGTGGACTTTGAAGA-AAAGA
* * *
1132674 TGCCACTGAGTCGTGGGCTTTG-AGAAGAGA
1 TGCCACTGAGTTGTGGACTTTGAAGAAAAGA
* * *
1132704 TTGCCACTAAATCGTGGACTTTGAAGAAAAGAA
1 -TGCCACTGAGTTGTGGACTTTGAAGAAAAG-A
* * **
1132737 TGCCTCTAAGTCATGGACTTTG-AGACAAA-A
1 TGCCACTGAGTTGTGGACTTTGAAGA-AAAGA
* *
1132767 TGCCACTGAGTCGTGGGCTTT-AAGAA
1 TGCCACTGAGTTGTGGACTTTGAAGAA
1132793 GGTATTTGAA
Statistics
Matches: 359, Mismatches: 34, Indels: 43
0.82 0.08 0.10
Matches are distributed among these distances:
29 3 0.01
30 50 0.14
31 103 0.29
32 62 0.17
33 24 0.07
34 60 0.17
35 28 0.08
36 26 0.07
38 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (31 bp):
TGCCACTGAGTTGTGGACTTTGAAGAAAAGA
Found at i:1134029 original size:15 final size:15
Alignment explanation
Indices: 1134006--1134075 Score: 56
Period size: 15 Copynumber: 4.8 Consensus size: 15
1133996 TGCCTTTGCA
* *
1134006 TTTTCTTGTGTGTGT
1 TTTTTTTGTTTGTGT
*
1134021 TTTTTTTGTTTTTGT
1 TTTTTTTGTTTGTGT
1134036 TTTTGTTT-TTTGTGT
1 TTTT-TTTGTTTGTGT
* *
1134051 TGTTGTTG-TTGT-T
1 TTTTTTTGTTTGTGT
*
1134064 GTTTTTTGTTTG
1 TTTTTTTGTTTG
1134076 CACTTTTGAG
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
13 6 0.14
14 9 0.21
15 25 0.58
16 3 0.07
ACGTcount: A:0.00, C:0.01, G:0.23, T:0.76
Consensus pattern (15 bp):
TTTTTTTGTTTGTGT
Found at i:1134033 original size:24 final size:23
Alignment explanation
Indices: 1134006--1134074 Score: 72
Period size: 21 Copynumber: 3.1 Consensus size: 23
1133996 TGCCTTTGCA
*
1134006 TTTTCTTGTGTGTGTTTTTTTTGT
1 TTTTGTTGT-TGTGTTTTTTTTGT
*
1134030 TTTTGTT-TT-TGTTTTTTGTGT
1 TTTTGTTGTTGTGTTTTTTTTGT
* *
1134051 TGTTGTTGTTGT-TGTTTTTTGT
1 TTTTGTTGTTGTGTTTTTTTTGT
1134073 TT
1 TT
1134075 GCACTTTTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 17 0.46
22 12 0.32
23 2 0.05
24 6 0.16
ACGTcount: A:0.00, C:0.01, G:0.22, T:0.77
Consensus pattern (23 bp):
TTTTGTTGTTGTGTTTTTTTTGT
Found at i:1134034 original size:6 final size:6
Alignment explanation
Indices: 1134023--1134074 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
1134013 GTGTGTGTTT
* * *
1134023 TTTTTG TTTTTG TTTTTG TTTTT- TGTGTTG TTGTTG TTGTTG TTTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG T-TTTTG TTTTTG TTTTTG -TTTTTG
1134072 TTT
1 TTT
1134075 GCACTTTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 1 0.02
6 34 0.83
7 6 0.15
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (6 bp):
TTTTTG
Found at i:1134060 original size:30 final size:31
Alignment explanation
Indices: 1134016--1134074 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1134006 TTTTCTTGTG
* * *
1134016 TGTGTTTTTTTTGTTTTTG-TTTTTGTTTTT
1 TGTGTTGTTGTTGTTGTTGTTTTTTGTTTTT
1134046 TGTGTTGTTGTTGTTGTTGTTTTTTGTTT
1 TGTGTTGTTGTTGTTGTTGTTTTTTGTTT
1134075 GCACTTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (31 bp):
TGTGTTGTTGTTGTTGTTGTTTTTTGTTTTT
Found at i:1144658 original size:20 final size:19
Alignment explanation
Indices: 1144633--1144683 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
1144623 TTTACACCCC
1144633 AAAAAAAACAAAAAACAAAT
1 AAAAAAAACAAAAAA-AAAT
*
1144653 AAAAAAAACCAAGAAAAAAT
1 AAAAAAAA-CAAAAAAAAAT
1144673 AGCAAAAAAAC
1 A--AAAAAAAC
1144684 TAGAAAGAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 13 0.48
21 7 0.26
22 7 0.26
ACGTcount: A:0.80, C:0.12, G:0.04, T:0.04
Consensus pattern (19 bp):
AAAAAAAACAAAAAAAAAT
Found at i:1145938 original size:28 final size:28
Alignment explanation
Indices: 1145902--1146634 Score: 830
Period size: 28 Copynumber: 25.5 Consensus size: 28
1145892 CGTTCATCTC
1145902 TTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
*
1145930 TTCAAAGCCCACAAGTCAGTGGCACTATT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CT
* *
1145959 TTCAAAGCCCATAAGTTAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CT
* *
1145987 TTCAAAGCCCATAAGTCAGTGGCACTATT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CT
* * *
1146016 TTCAAAGCTCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
*
1146044 TTCAAAGCCCATAAGTCAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1146072 TTCAAAGCCCACAAGTTAGTAGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1146100 TTTAAAGCCCACAAG-CTAGTAGCACTCCT
1 TTCAAAGCCCACAAGTC-AGTGGCACT-CT
1146129 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CT
* *
1146157 TTTAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1146185 TTCAAAGCCCATAAATCAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
*
1146213 TGTCAAAGCCCACAAGTCAGTGGCACCCT
1 T-TCAAAGCCCACAAGTCAGTGGCACTCT
* *
1146242 TTCAAAGCCCAAAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTC-T
*
1146271 TTCAAAGCCCACAAGTTAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CT
* * * *
1146299 TTCAAAGCCTAGAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
*
1146327 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
*
1146355 TTCAAAGCTCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTC-T
* * *
1146384 TTTAAAGCCCACAAGTTAGTGGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGG-CACTC-T
* *
1146414 TTCAAAGCCCACACTGATTCGGTGGCAACTCTT
1 TTCAAAGCCCACA---AGTCAGTGGC-ACTC-T
*
1146447 TTCAAAGCCCACAAGTTAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CT
*
1146475 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
1146503 TTCAAAGCCAACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
*
1146531 TTCAAAGCCCACAAGTCAGTGGCACACTT
1 TTCAAAGCCCACAAGTCAGTGGCACTC-T
*
1146560 TTCAAAGCCCACAAG-CTAGTGGTAACTCTT
1 TTCAAAGCCCACAAGTC-AGTGG-CACTC-T
*
1146590 TTCAAAGCCCACACGAGTCGGTGGCAACTCTT
1 TTCAAAGCCCACA--AGTCAGTGGC-ACTC-T
1146622 TTCAAAGCCCACA
1 TTCAAAGCCCACA
1146635 GCAAGTTAAT
Statistics
Matches: 610, Mismatches: 70, Indels: 46
0.84 0.10 0.06
Matches are distributed among these distances:
28 353 0.58
29 162 0.27
30 44 0.07
32 25 0.04
33 26 0.04
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:1145990 original size:57 final size:57
Alignment explanation
Indices: 1145902--1146634 Score: 799
Period size: 57 Copynumber: 12.7 Consensus size: 57
1145892 CGTTCATCTC
**
1145902 TTCAAAGCCCACAAGTCAGTGGCA-CTCTTTCAAAGCCCACAAGTCAGTGGCACTATT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * **
1145959 TTCAAAGCCCATAAGTTAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGGCACTATT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * *
1146016 TTCAAAGCTCACAAGTTAGTGGCACCCTTTCAAAGCCCATAAGTCAGTGGCACT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * *
1146072 TTCAAAGCCCACAAGTTAGTAGCA-CTCTTTTAAAGCCCACAAG-CTAGTAGCACTCCT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CTTTCAAAGCCCACAAGTC-AGTGGCACTCCT
*
1146129 TTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* *
1146185 TTCAAAGCCCATAAATCAGTGGCA-CTCTTGTCAAAGCCCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CTT-TCAAAGCCCACAAGTCAGTGGCACTCCT
* * * *
1146242 TTCAAAGCCCAAAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * *
1146299 TTCAAAGCCTAGAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * * * *
1146355 TTCAAAGCTCACAAGTCAGTGGCACTCTTTTTAAAGCCCACAAGTTAGTGGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGG-CACTCCT
* * * *
1146414 TTCAAAGCCCACACTGATTCGGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA-TCCT
1 TTCAAAGCCCACA---AGTCAGTGGC-A-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * *
1146475 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCAACAAGTTAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* *
1146531 TTCAAAGCCCACAAGTCAGTGGCA-CACTTTTCAAAGCCCACAAG-CTAGTGGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCATC-C-TTTCAAAGCCCACAAGTC-AGTGG-CACTCCT
* *
1146590 TTCAAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACA
1 TTCAAAGCCCACA--AGTCAGTGGC-A-TCCTTTCAAAGCCCACA
1146635 GCAAGTTAAT
Statistics
Matches: 589, Mismatches: 57, Indels: 55
0.84 0.08 0.08
Matches are distributed among these distances:
55 4 0.01
56 175 0.30
57 286 0.49
58 17 0.03
59 30 0.05
61 25 0.04
62 24 0.04
63 27 0.05
64 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (57 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
Found at i:1146047 original size:85 final size:86
Alignment explanation
Indices: 1145902--1146634 Score: 860
Period size: 85 Copynumber: 8.5 Consensus size: 86
1145892 CGTTCATCTC
**
1145902 TTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACTATTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
* *
1145966 CCCATAAGTTAGTGGCATCCT
66 CCCACAAGTCAGTGGCATCCT
* * * *
1145987 TTCAAAGCCCATAAGTCAGTGGCACTATTTTCAAAGCTCACAAGTTAGTGGCAC-CCTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
*
1146051 CCCATAAGTCAGTGGCA-CTCT
66 CCCACAAGTCAGTGGCATC-CT
* * *
1146072 TTCAAAGCCCACAAGTTAGTAGCACTCTTTT-AAAGCCCACAAG-CTAGTAGCACTCCTTTCAAA
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTC-AGTGGCACTCCTTTCAAA
1146135 GCCCACAAGTCAGTGGCATCCT
65 GCCCACAAGTCAGTGGCATCCT
* * * *
1146157 TTTAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCATAAATCAGTGGCACT-CTTGTCAAA
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTT-TCAAA
*
1146220 GCCCACAAGTCAGTGGCACCCT
65 GCCCACAAGTCAGTGGCATCCT
* * *
1146242 TTCAAAGCCCAAAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
* * * *
1146306 CCTAGAAGTCAATGGCACCCT
66 CCCACAAGTCAGTGGCATCCT
* * * *
1146327 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCTCACAAGTCAGTGGCACTCTTTTTAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
* * *
1146391 CCCACAAGTTAGTGGTAACTCTT
66 CCCACAAGTCAGTGG-CA-TCCT
* * *
1146414 TTCAAAGCCCACACTGATTCGGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA-TCCTTTC
1 TTCAAAGCCCACA---AGTCAGTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
*
1146478 AAAGCCCACAAGTCAGTGGCACCCT
62 AAAGCCCACAAGTCAGTGGCATCCT
* * * * *
1146503 TTCAAAGCCAACAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACACTTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
* *
1146567 CCCACAAG-CTAGTGGTAACTCTT
66 CCCACAAGTC-AGTGG-CA-TCCT
*
1146590 TTCAAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACA
1 TTCAAAGCCCACA--AGTCAGTGGC-ACTCTTTTCAAAGCCCACA
1146635 GCAAGTTAAT
Statistics
Matches: 549, Mismatches: 73, Indels: 46
0.82 0.11 0.07
Matches are distributed among these distances:
84 76 0.14
85 286 0.52
86 61 0.11
87 29 0.05
89 22 0.04
90 11 0.02
91 40 0.07
92 24 0.04
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (86 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
CCCACAAGTCAGTGGCATCCT
Found at i:1150785 original size:12 final size:12
Alignment explanation
Indices: 1150762--1150795 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1150752 GATAGCTTGG
1150762 AAAATGGAAAAAT
1 AAAAT-GAAAAAT
1150775 AAAATGAAAAAT
1 AAAATGAAAAAT
1150787 AAAA-GAAAA
1 AAAATGAAAA
1150796 TGGAGAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.24
12 11 0.52
13 5 0.24
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (12 bp):
AAAATGAAAAAT
Found at i:1151293 original size:6 final size:6
Alignment explanation
Indices: 1151282--1151309 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1151272 TATGAACTTT
1151282 TTTTTC TTTTTC TTTTTC TTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTT
1151310 CTTATTTAGG
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:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:1157481 original size:21 final size:20
Alignment explanation
Indices: 1157457--1157519 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 20
1157447 TCAAAAAGTC
1157457 AGAAAGCAAAAAAAAAAAAAA
1 AGAAAG-AAAAAAAAAAAAAA
*
1157478 AGAAAGAAAAAGTAAAAAAAA
1 AGAAAGAAAAA-AAAAAAAAA
1157499 AGAAAGAACAAAAGAAAAAAA
1 AGAAAGAA-AAAA-AAAAAAA
1157520 TAGCTTAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
20 5 0.14
21 22 0.59
22 10 0.27
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.02
Consensus pattern (20 bp):
AGAAAGAAAAAAAAAAAAAA
Found at i:1158237 original size:20 final size:20
Alignment explanation
Indices: 1158212--1158303 Score: 59
Period size: 20 Copynumber: 4.8 Consensus size: 20
1158202 GACTTAAGTC
*
1158212 TTTTTATATTATTTT-ATGCA
1 TTTTTATATCATTTTAAT-CA
*
1158232 TTTTTATGTCATTTTAATCA
1 TTTTTATATCATTTTAATCA
** **
1158252 TTTTT-TAT-AACTTAAAGA
1 TTTTTATATCATTTTAATCA
1158270 -TTTTATATCATTTT-ATACA
1 TTTTTATATCATTTTAAT-CA
* *
1158289 TATTTATGTCATTTT
1 TTTTTATATCATTTT
1158304 TATGACTTAA
Statistics
Matches: 54, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
17 4 0.07
18 10 0.19
19 6 0.11
20 32 0.59
21 2 0.04
ACGTcount: A:0.28, C:0.08, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTTTATATCATTTTAATCA
Found at i:1158844 original size:21 final size:21
Alignment explanation
Indices: 1158805--1158844 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1158795 GTTTTAAAAA
*
1158805 TTTATTTTATTATTTGATATT
1 TTTATTTAATTATTTGATATT
1158826 TTTATTTAATT-TTTAGATA
1 TTTATTTAATTATTT-GATA
1158845 ATATATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTATTTAATTATTTGATATT
Found at i:1161255 original size:2 final size:2
Alignment explanation
Indices: 1161248--1161276 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1161238 AATACATAAT
1161248 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 T
1161277 TCCTTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1161368 original size:15 final size:15
Alignment explanation
Indices: 1161348--1161396 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
1161338 ATTTATTTTA
1161348 TATTTTATCATAATT
1 TATTTTATCATAATT
1161363 TATTTTATCATAATT
1 TATTTTATCATAATT
* *
1161378 TATTTTTTTATAATT
1 TATTTTATCATAATT
1161393 TATT
1 TATT
1161397 GTATAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTTATCATAATT
Found at i:1161403 original size:12 final size:12
Alignment explanation
Indices: 1161386--1161419 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1161376 TTTATTTTTT
1161386 TATAATTTATTG
1 TATAATTTATTG
1161398 TATAATTTATTG
1 TATAATTTATTG
*
1161410 TATCATTTAT
1 TATAATTTAT
1161420 ATTTATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (12 bp):
TATAATTTATTG
Found at i:1163807 original size:13 final size:13
Alignment explanation
Indices: 1163789--1163814 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1163779 CAATTTTTTG
1163789 TGTATCGATACAT
1 TGTATCGATACAT
1163802 TGTATCGATACAT
1 TGTATCGATACAT
1163815 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1163879 original size:21 final size:21
Alignment explanation
Indices: 1163853--1163928 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1163843 CTGCCAAGAA
*
1163853 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1163874 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1163894 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1163915 ATGTATCGATACAT
1 ATGTATCGATACAT
1163929 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1163899 original size:20 final size:20
Alignment explanation
Indices: 1163874--1163946 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1163864 CATCTTTTTT
1163874 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1163894 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1163915 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1163935 ATGTATCGATAC
1 ATGTATCGATAC
1163947 TTTGAATTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1163910 original size:41 final size:41
Alignment explanation
Indices: 1163853--1163946 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1163843 CTGCCAAGAA
*
1163853 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1163894 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1163935 ATGTATCGATAC
1 ATGTATCGATAC
1163947 TTTGAATTGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1166380 original size:13 final size:13
Alignment explanation
Indices: 1166362--1166399 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1166352 ATAATCACCC
1166362 TGTATCGATACAG
1 TGTATCGATACAG
*
1166375 TGTATCGATACAT
1 TGTATCGATACAG
1166388 TGTATCGATACA
1 TGTATCGATACA
1166400 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1166413 original size:20 final size:20
Alignment explanation
Indices: 1166388--1166464 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
1166378 ATCGATACAT
1166388 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
* *
1166408 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACAAAGAA-----AAA
* *
1166433 TGTATCGATACACAGAAACA
1 TGTATCGATACAAAGAAAAA
1166453 TGTATCGATACA
1 TGTATCGATACA
1166465 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 30 0.62
25 18 0.38
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:1168505 original size:16 final size:15
Alignment explanation
Indices: 1168476--1168506 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1168466 ATTTCGTTTG
1168476 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
*
1168491 GAGCTTCCTCAATTT
1 GAGCTTCCTCATTTT
1168506 G
1 G
1168507 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.26, G:0.16, T:0.42
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1170339 original size:21 final size:21
Alignment explanation
Indices: 1170310--1170354 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1170300 AAGTTTTCAT
*
1170310 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1170330 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1170352 TTT
1 TTT
1170355 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1172585 original size:13 final size:13
Alignment explanation
Indices: 1172567--1172592 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1172557 CAATTTTTTG
1172567 TGTATCGATACAT
1 TGTATCGATACAT
1172580 TGTATCGATACAT
1 TGTATCGATACAT
1172593 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1172657 original size:21 final size:21
Alignment explanation
Indices: 1172631--1172706 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1172621 CTGCCAAGAA
*
1172631 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1172652 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1172672 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1172693 ATGTATCGATACAT
1 ATGTATCGATACAT
1172707 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1172677 original size:20 final size:20
Alignment explanation
Indices: 1172652--1172724 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1172642 CATCTTTTTT
1172652 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1172672 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1172693 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1172713 ATGTATCGATAC
1 ATGTATCGATAC
1172725 TTTGAATTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1172688 original size:41 final size:41
Alignment explanation
Indices: 1172631--1172724 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1172621 CTGCCAAGAA
*
1172631 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1172672 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1172713 ATGTATCGATAC
1 ATGTATCGATAC
1172725 TTTGAATTGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1174186 original size:21 final size:21
Alignment explanation
Indices: 1174156--1174197 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1174146 ATATTGATTT
1174156 AATATTAAAATTCT-TTTAAA
1 AATATTAAAATTCTATTTAAA
*
1174176 AATATTTAAAATTTTATTTAAA
1 AATA-TTAAAATTCTATTTAAA
1174198 TTAATGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
AATATTAAAATTCTATTTAAA
Found at i:1174420 original size:5 final size:5
Alignment explanation
Indices: 1174410--1174462 Score: 61
Period size: 5 Copynumber: 10.6 Consensus size: 5
1174400 AGTTTTTTAA
* * * * *
1174410 AAAAT AAAAT AAAAT TAAAT TAAAT TAAAT AAAAT TAAAT AAAAT TAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1174460 AAA
1 AAA
1174463 TACAAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (5 bp):
AAAAT
Found at i:1174429 original size:10 final size:10
Alignment explanation
Indices: 1174410--1174462 Score: 88
Period size: 10 Copynumber: 5.3 Consensus size: 10
1174400 AGTTTTTTAA
*
1174410 AAAATAAAAT
1 AAAATTAAAT
1174420 AAAATTAAAT
1 AAAATTAAAT
*
1174430 TAAATTAAAT
1 AAAATTAAAT
1174440 AAAATTAAAT
1 AAAATTAAAT
1174450 AAAATTAAAT
1 AAAATTAAAT
1174460 AAA
1 AAA
1174463 TACAAATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 40 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAATTAAAT
Found at i:1174788 original size:15 final size:16
Alignment explanation
Indices: 1174770--1174799 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1174760 TTAATTAATT
1174770 TTAAATTA-AATTTTA
1 TTAAATTATAATTTTA
1174785 TTAAATTATAATTTT
1 TTAAATTATAATTTT
1174800 TTTATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAAATTATAATTTTA
Found at i:1176979 original size:21 final size:20
Alignment explanation
Indices: 1176912--1176985 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 20
1176902 TAACATGATG
** *
1176912 TATCGATATAGGAAAATATT
1 TATCGATATATTATAATATT
1176932 GTATCGATATAATTCATAATA--
1 -TATCGATAT-ATT-ATAATATT
1176953 TATCGATATATTATAATATTT
1 TATCGATATATTATAATA-TT
1176974 TATCGATATATT
1 TATCGATATATT
1176986 TAAAGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 6 0.13
19 3 0.07
20 9 0.20
21 21 0.47
22 1 0.02
23 5 0.11
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (20 bp):
TATCGATATATTATAATATT
Found at i:1176994 original size:21 final size:21
Alignment explanation
Indices: 1176953--1176996 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1176943 ATTCATAATA
*
1176953 TATCGATATATTATAATATTT
1 TATCGATATATTATAAGATTT
1176974 TATCGATATATT-TAAAGATTT
1 TATCGATATATTAT-AAGATTT
1176995 TA
1 TA
1176997 AGTTTGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (21 bp):
TATCGATATATTATAAGATTT
Found at i:1177839 original size:15 final size:16
Alignment explanation
Indices: 1177819--1177848 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1177809 ATAATTAATT
1177819 TTAAATTA-AATTTTA
1 TTAAATTATAATTTTA
1177834 TTAAATTATAATTTT
1 TTAAATTATAATTTT
1177849 TATTTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAAATTATAATTTTA
Found at i:1178436 original size:20 final size:21
Alignment explanation
Indices: 1178396--1178436 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1178386 CCCTAAAACT
*
1178396 TTTAAAAATAATTTTTTAATC
1 TTTAAAAATAATTTATTAATC
*
1178417 TTTACAAATAA-TTATTAATC
1 TTTAAAAATAATTTATTAATC
1178437 ATCATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAAAAATAATTTATTAATC
Found at i:1179163 original size:2 final size:2
Alignment explanation
Indices: 1179156--1179182 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1179146 TTGTATAGTG
1179156 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 T
1179183 TTCGTTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1180810 original size:20 final size:20
Alignment explanation
Indices: 1180785--1180830 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1180775 GACTTAAAGA
*
1180785 TTTTATATTATTCTATGCAT
1 TTTTATATCATTCTATGCAT
* *
1180805 TTTTATATCATTTTATGTAT
1 TTTTATATCATTCTATGCAT
1180825 TTTTAT
1 TTTTAT
1180831 GACTTAGGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTTATATCATTCTATGCAT
Found at i:1180827 original size:57 final size:56
Alignment explanation
Indices: 1180728--1180836 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 56
1180718 ACTTGAGGTT
*
1180728 TTTTATATTATTTCATGCATTTTTATGTCATTTTAATCATTTTCCATGACTTAAAGA
1 TTTTATATTATTTCATGCATTTTTATATCATTTTAATCATTTT-CATGACTTAAAGA
* *
1180785 TTTTATATTA-TTCTATGCATTTTTATATCATTTT-ATGTATTTTTATGACTTA
1 TTTTATATTATTTC-ATGCATTTTTATATCATTTTAAT-CATTTTCATGACTTA
1180837 GGGACTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
56 13 0.28
57 34 0.72
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.57
Consensus pattern (56 bp):
TTTTATATTATTTCATGCATTTTTATATCATTTTAATCATTTTCATGACTTAAAGA
Found at i:1182544 original size:21 final size:21
Alignment explanation
Indices: 1182520--1182579 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
1182510 TATTAAAAGT
*
1182520 TGCATTTTTTCATCCAAAAAA
1 TGCATTATTTCATCCAAAAAA
* **
1182541 TGCATTCTTTCATCCAACCAA
1 TGCATTATTTCATCCAAAAAA
*
1182562 TGCATCATTTCATCCAAA
1 TGCATTATTTCATCCAAA
1182580 GATACCTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (21 bp):
TGCATTATTTCATCCAAAAAA
Found at i:1183436 original size:13 final size:13
Alignment explanation
Indices: 1183418--1183443 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1183408 TACAGCAAGT
1183418 ATGTATCGATACA
1 ATGTATCGATACA
1183431 ATGTATCGATACA
1 ATGTATCGATACA
1183444 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1185694 original size:21 final size:21
Alignment explanation
Indices: 1185661--1185705 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1185651 TTGCAAGTTG
*
1185661 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1185683 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1185703 AAA
1 AAA
1185706 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1187528 original size:15 final size:15
Alignment explanation
Indices: 1187508--1187538 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1187498 TAAAAATGTC
*
1187508 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1187523 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1187538 C
1 C
1187539 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1189626 original size:20 final size:20
Alignment explanation
Indices: 1189547--1189626 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1189537 AATGTCCAAA
*
1189547 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1189567 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1189592 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1189612 TTGTATCGATACATT
1 ATGTATCGATACATT
1189627 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1189630 original size:13 final size:13
Alignment explanation
Indices: 1189612--1189650 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1189602 ACATTTTTCT
1189612 TTGTATCGATACA
1 TTGTATCGATACA
1189625 TTGTATCGATACA
1 TTGTATCGATACA
*
1189638 CTGTATCGATACA
1 TTGTATCGATACA
1189651 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1189795 original size:21 final size:21
Alignment explanation
Indices: 1189771--1189817 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1189761 AAATCTTTTG
1189771 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
1189792 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
1189812 CAAAAT
1 CAAAAT
1189818 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:1189814 original size:20 final size:19
Alignment explanation
Indices: 1189773--1189815 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1189763 ATCTTTTGCA
1189773 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
1189793 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1189813 AAA
1 AAA
1189816 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:1192211 original size:13 final size:13
Alignment explanation
Indices: 1192193--1192218 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1192183 TACAGCAAGT
1192193 ATGTATCGATACA
1 ATGTATCGATACA
1192206 ATGTATCGATACA
1 ATGTATCGATACA
1192219 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1195711 original size:5 final size:5
Alignment explanation
Indices: 1195701--1195748 Score: 64
Period size: 5 Copynumber: 10.0 Consensus size: 5
1195691 AAATGATTTA
* *
1195701 GAATG GAATG GAATG G-GTG GAATG GAATG GAATG G-GTG GAATG GAATG
1 GAATG GAATG GAATG GAATG GAATG GAATG GAATG GAATG GAATG GAATG
1195749 AAAATTTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 6 0.16
5 31 0.84
ACGTcount: A:0.33, C:0.00, G:0.46, T:0.21
Consensus pattern (5 bp):
GAATG
Found at i:1195725 original size:19 final size:19
Alignment explanation
Indices: 1195701--1195748 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
1195691 AAATGATTTA
1195701 GAATGGAATGGAATGGGTG
1 GAATGGAATGGAATGGGTG
1195720 GAATGGAATGGAATGGGTG
1 GAATGGAATGGAATGGGTG
1195739 GAATGGAATG
1 GAATGGAATG
1195749 AAAATTTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.46, T:0.21
Consensus pattern (19 bp):
GAATGGAATGGAATGGGTG
Found at i:1195748 original size:14 final size:14
Alignment explanation
Indices: 1195704--1195730 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1195694 TGATTTAGAA
1195704 TGGAATGGAATGGG
1 TGGAATGGAATGGG
1195718 TGGAATGGAATGG
1 TGGAATGGAATGG
1195731 AATGGGTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.48, T:0.22
Consensus pattern (14 bp):
TGGAATGGAATGGG
Found at i:1195890 original size:21 final size:21
Alignment explanation
Indices: 1195866--1195923 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
1195856 TTAAAAGTTA
*
1195866 CATTTTTTCATCCAAAAAATG
1 CATTATTTCATCCAAAAAATG
* **
1195887 CATTCTTTCATCCAACCAATG
1 CATTATTTCATCCAAAAAATG
*
1195908 CATCATTTCATCCAAA
1 CATTATTTCATCCAAA
1195924 GATATCTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (21 bp):
CATTATTTCATCCAAAAAATG
Found at i:1199802 original size:11 final size:11
Alignment explanation
Indices: 1199783--1199818 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1199773 AATATATATT
*
1199783 TTTACTATTAA
1 TTTAATATTAA
*
1199794 TTTAATATTTA
1 TTTAATATTAA
1199805 TTTAATATTAA
1 TTTAATATTAA
1199816 TTT
1 TTT
1199819 TTTTAAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTAATATTAA
Found at i:1203368 original size:52 final size:52
Alignment explanation
Indices: 1203278--1203402 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
1203268 ATATGAAAAG
* * *
1203278 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTACCGATACATCTGGGCAAAT
*
1203330 TTGCCTGCATGTATCGATACATTTTATAATGTACCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTACCGATACATCTGGGCAAAT
1203382 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1203403 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTACCGATACATCTGGGCAAAT
Found at i:1203420 original size:52 final size:51
Alignment explanation
Indices: 1203278--1203422 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
1203268 ATATGAAAAG
*
1203278 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* * *
1203330 TTGCCTGCATGTATCGATACATTTTATAATGTACCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
1203382 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1203423 ATGTATTGAT
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 81 0.98
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1203513 original size:33 final size:33
Alignment explanation
Indices: 1203476--1203542 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1203466 AGTAGCTTAA
1203476 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1203509 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1203542 A
1 A
1203543 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1203516 original size:13 final size:13
Alignment explanation
Indices: 1203498--1203522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1203488 CAAAAAAATA
1203498 TGTATCGATACAT
1 TGTATCGATACAT
1203511 TGTATCGATACA
1 TGTATCGATACA
1203523 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1204685 original size:17 final size:18
Alignment explanation
Indices: 1204657--1204690 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1204647 CTACTAATCA
*
1204657 TTTTTAATTTCTCTAAAT
1 TTTTTAATTTCTATAAAT
1204675 TTTTTAA-TTCTATAAA
1 TTTTTAATTTCTATAAA
1204691 CAAAACTAAT
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:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTAATTTCTATAAAT
Found at i:1206016 original size:52 final size:52
Alignment explanation
Indices: 1205954--1206290 Score: 185
Period size: 52 Copynumber: 6.4 Consensus size: 52
1205944 AAATAACGAG
*
1205954 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * ** * *
1206006 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCGG-
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* * * * * *
1206057 GATTGGAGTATCCCCGATTGTGGAGAAATTAGTGTTTTAGCG--ATAAAACCGGG
1 G-TTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
* **** * * *
1206110 GTTGGAGTATCCCC--TCG-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
1206165 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * * *
1206219 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
*
1206270 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
1206291 GAGAATTGAG
Statistics
Matches: 215, Mismatches: 43, Indels: 54
0.69 0.14 0.17
Matches are distributed among these distances:
48 3 0.01
49 2 0.01
50 2 0.01
51 36 0.17
52 82 0.38
53 31 0.14
54 28 0.13
55 19 0.09
56 2 0.01
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:1206169 original size:27 final size:28
Alignment explanation
Indices: 1206106--1206181 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
1206096 GCGATAAAAC
***
1206106 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
1206134 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1206161 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1206182 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1206195 original size:212 final size:212
Alignment explanation
Indices: 1205889--1206295 Score: 631
Period size: 212 Copynumber: 1.9 Consensus size: 212
1205879 GAAGAAAAAA
* * *
1205889 AAAATCGGGATTGGAGTATCCCCTCGGAAGTAATGGGGTTGGAGTATCCCCAATGAAATAACGAG
1 AAAACCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAG
* *
1205954 GTTGGAGTATCCTCGATTGTGAAAAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCC
66 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTATCC
* *
1206018 CCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGG-GATTGGAGTATCCCCGATTGTGGAG
131 CCGATTAAA-GAAAATTAGCGTTTTGAAAATAAAACCGGAG-TTGGAATATCCCCGATTGTGGAG
1206082 AAATTAGTGTTTTAGCGAT
194 AAATTAGTGTTTTAGCGAT
* * * *
1206101 AAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGG
1 AAAACCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAG
*
1206165 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATC
66 GTTGGAGTATCCCCGATTGTGAA-AAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTATC
* * *
1206230 CCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGAGA
130 CCCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAGA
1206295 A
195 A
1206296 TTGAGAAACT
Statistics
Matches: 177, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 29 0.16
212 108 0.61
213 40 0.23
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (212 bp):
AAAACCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAG
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTATCC
CCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAGAA
ATTAGTGTTTTAGCGAT
Found at i:1206265 original size:51 final size:53
Alignment explanation
Indices: 1206169--1206287 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
1206159 AACGGGGTTG
* * *
1206169 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
1206223 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
1206274 GAATATCCCCGATT
1 GAGTATCCCCGATT
1206288 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:1208651 original size:13 final size:13
Alignment explanation
Indices: 1208633--1208658 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1208623 ACAAAGATCC
1208633 ATGTATCGATACA
1 ATGTATCGATACA
1208646 ATGTATCGATACA
1 ATGTATCGATACA
1208659 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1208654 original size:33 final size:33
Alignment explanation
Indices: 1208612--1208678 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1208602 AAAATTTCCA
***
1208612 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1208645 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1208678 A
1 A
1208679 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1209718 original size:26 final size:26
Alignment explanation
Indices: 1209689--1209778 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
1209679 GTGTGGGCTT
1209689 TGAAAGGTGTCCTGCTCTTTGGGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** ***
1209715 TGAAAAATG-CCATTAACTTGTGTGGG-C
1 TGAAAGGTGTCC-TGCTCTT-TG-GGGAC
*
1209742 TTCGAAAGGGGTCCTGCTCTTTGGGGAC
1 -T-GAAAGGTGTCCTGCTCTTTGGGGAC
1209770 TGAAAGGTG
1 TGAAAGGTG
1209779 CCACCAACTT
Statistics
Matches: 45, Mismatches: 12, Indels: 14
0.63 0.17 0.20
Matches are distributed among these distances:
25 2 0.04
26 18 0.40
27 7 0.16
28 7 0.16
29 9 0.20
30 2 0.04
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:1209891 original size:59 final size:58
Alignment explanation
Indices: 1209533--1210124 Score: 621
Period size: 55 Copynumber: 10.3 Consensus size: 58
1209523 ATAAAGTGTA
* * * * *
1209533 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTT----GAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGCG
*
1209588 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG--AGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGCG
* * *
1209643 TCCTGCTCTTTGAGGACTGGAAAATGCCACTAACTTGTGTGGGCTTT----GAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGCG
* * ** * *
1209698 TCCTGCTCTTTGGGGACTGAAAAATGCCATTAACTTGTGTGGGC-TT---CGAAAGGGG
1 TCCTGCTCTTTGAGGACTG-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGCG
* * *
1209753 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTT-AAAAG-AAAGGCG
* * *
1209814 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG-AAAGGCG
* * *
1209873 TCCCGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTATGGGCTTTAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG-AAAGGCG
* *
1209932 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG-AAAGGCG
* * * *
1209991 TCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGACTTTAAAAGGGGAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAA--GAAAGGCG
* * *
1210052 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCATCTTGTGTGGGCTTT---A-AAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGCG
1210107 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
1210125 AAAAAGCGGA
Statistics
Matches: 475, Mismatches: 44, Indels: 36
0.86 0.08 0.06
Matches are distributed among these distances:
53 1 0.00
54 9 0.02
55 194 0.41
56 6 0.01
57 1 0.00
58 1 0.00
59 138 0.29
60 52 0.11
61 72 0.15
62 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (58 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAGGCG
Found at i:1211101 original size:1 final size:1
Alignment explanation
Indices: 1211091--1211163 Score: 56
Period size: 1 Copynumber: 73.0 Consensus size: 1
1211081 CTTAAGCAGA
* * * * * * * * *
1211091 TTTTTCTTTTTTTTTTTGTTTGTTTTGTTTGTTTTGTTTTTTTTTTGTTTTTTTTTGTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
1211156 TCTTTTTT
1 TTTTTTTT
1211164 GAAAAAGAAT
Statistics
Matches: 52, Mismatches: 20, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.86
Consensus pattern (1 bp):
T
Found at i:1211116 original size:9 final size:9
Alignment explanation
Indices: 1211104--1211141 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
1211094 TTCTTTTTTT
1211104 TTTTGTTTG
1 TTTTGTTTG
1211113 TTTTGTTTG
1 TTTTGTTTG
1211122 TTTTGTTT-
1 TTTTGTTTG
1211130 TTTT-TTTG
1 TTTTGTTTG
1211138 TTTT
1 TTTT
1211142 TTTTTGTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 3 0.11
8 8 0.29
9 17 0.61
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (9 bp):
TTTTGTTTG
Done.