Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 18 of 113
Found at i:6212578 original size:9 final size:9
Alignment explanation
Indices: 6212566--6212613 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
6212556 TTTCAAAGAT
6212566 AAAAAGAAA
1 AAAAAGAAA
6212575 AAAAAG-AA
1 AAAAAGAAA
6212583 AAAAAGTAAA
1 AAAAAG-AAA
*
6212593 ACAAAG--A
1 AAAAAGAAA
6212600 AAAAAGAAA
1 AAAAAGAAA
6212609 AAAAA
1 AAAAA
6212614 TGAATGGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
7 6 0.18
8 8 0.24
9 12 0.36
10 7 0.21
ACGTcount: A:0.85, C:0.02, G:0.10, T:0.02
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:6212580 original size:17 final size:16
Alignment explanation
Indices: 6212560--6212613 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 16
6212550 AAAAGGTTTC
6212560 AAAGATAAAAAGAAAAA
1 AAAGA-AAAAAGAAAAA
*
6212577 AAAGAAAAAAAGTAAAAC
1 AAAG-AAAAAAG-AAAAA
6212595 AAAGAAAAAAGAAAAA
1 AAAGAAAAAAGAAAAA
6212611 AAA
1 AAA
6212614 TGAATGGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 7 0.21
17 17 0.52
18 9 0.27
ACGTcount: A:0.83, C:0.02, G:0.11, T:0.04
Consensus pattern (16 bp):
AAAGAAAAAAGAAAAA
Found at i:6213053 original size:22 final size:21
Alignment explanation
Indices: 6213012--6213053 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
6213002 AAAAATGGAT
*
6213012 AAAAAATAAAAATAAGAGAAA
1 AAAAAATAAAAATAAAAGAAA
6213033 AAAAAGATGAAAAA-AAAAGAA
1 AAAAA-AT-AAAAATAAAAGAA
6213054 GACTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 5 0.28
22 8 0.44
23 5 0.28
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (21 bp):
AAAAAATAAAAATAAAAGAAA
Found at i:6214494 original size:79 final size:78
Alignment explanation
Indices: 6214395--6214662 Score: 356
Period size: 79 Copynumber: 3.4 Consensus size: 78
6214385 TTTGAGTGTT
* * * * *
6214395 AAATGAGAATATTTAAATTTCAAAGGAGAATTTTTGAGGTGTGAAATCCAAAATTTATCGAATGT
1 AAATGAGAATTTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAA-CCAAAATTTGTCGAATGT
*
6214460 AAATCTTCGAATTC
65 GAATCTTCGAATTC
* *
6214474 AAATGATAATTTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACTCAAAATTTGTTGAATGT
1 AAATGAGAATTTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAAC-CAAAATTTGTCGAATGT
6214539 GAATCTTCGAATTC
65 GAATCTTCGAATTC
* * ** * * * *
6214553 AAATAAGAATCTTTGAATTTCAAAAAAAAATCTTTGAAGTTTAAAACCTAAAATTTGTCGAATGT
1 AAATGAGAATTTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACC-AAAATTTGTCGAATGT
6214618 GAATCTTCGAATTC
65 GAATCTTCGAATTC
*
6214632 AAATGAGAATTTTTTAATTTCAAATGAGAAT
1 AAATGAGAATTTTTGAATTTCAAATGAGAAT
6214663 TTTTAAAATT
Statistics
Matches: 163, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
78 2 0.01
79 161 0.99
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (78 bp):
AAATGAGAATTTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCAAAATTTGTCGAATGTG
AATCTTCGAATTC
Found at i:6214690 original size:122 final size:122
Alignment explanation
Indices: 6214550--6214790 Score: 338
Period size: 122 Copynumber: 2.0 Consensus size: 122
6214540 AATCTTCGAA
* * *
6214550 TTCAAATAAGAATCTTTGAATTTCAAAAAAAAATCTTTGAAGTTTAAAACCTAAAATTTGTCGAA
1 TTCAAATAAGAATCTTTGAATTTCAAAAAAAAATCTTTGAAGTGTAAAACCCAAAATTTATCGAA
** * * *
6214615 TGTGAATCTTCGAATTCAAATGAGAATTTTTTAATTTCAAATGAGAATTTTTAAAAT
66 TGTGAATCTTCGAATTCAAATGAGAAACTTTGAATTTCAAATGAAAATCTTTAAAAT
* * ** * * *
6214672 TTCAAATGAGAATTTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCCAAAATTTATCGAA
1 TTCAAATAAGAATCTTTGAATTTCAAAAAAAAATCTTTGAAGTGTAAAACCCAAAATTTATCGAA
*
6214737 TGTGAATCTTCGAATTTAAATGAGAAACTTTGAATTTCAAATGAAAATCTTTAA
66 TGTGAATCTTCGAATTCAAATGAGAAACTTTGAATTTCAAATGAAAATCTTTAA
6214791 GATGTGAAAC
Statistics
Matches: 103, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
122 103 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.37
Consensus pattern (122 bp):
TTCAAATAAGAATCTTTGAATTTCAAAAAAAAATCTTTGAAGTGTAAAACCCAAAATTTATCGAA
TGTGAATCTTCGAATTCAAATGAGAAACTTTGAATTTCAAATGAAAATCTTTAAAAT
Found at i:6214710 original size:21 final size:21
Alignment explanation
Indices: 6214178--6214711 Score: 240
Period size: 21 Copynumber: 25.9 Consensus size: 21
6214168 TTAAAAAATA
*
6214178 TTCAAATGAGAATCTTTGAGT
1 TTCAAATGAGAATCTTTGAAT
* * *
6214199 TTTAAATG-GAAATTTTTAAAAAAT
1 TTCAAATGAG-AATCTTT---GAAT
* *
6214223 CTTCAAATGAAAATCTTTGAGT
1 -TTCAAATGAGAATCTTTGAAT
6214245 GTT-AAATGAGAATCTTTGAAT
1 -TTCAAATGAGAATCTTTGAAT
* *
6214266 TTCAAATGAAAATTTTTGAAT
1 TTCAAATGAGAATCTTTGAAT
*
6214287 TTCAAACGAGAATCTTTGAAT
1 TTCAAATGAGAATCTTTGAAT
* *
6214308 ATCAAATGAGAATCTTTAAAT
1 TTCAAATGAGAATCTTTGAAT
* * * *
6214329 GTCAAATGTGAATCTTCGAAC
1 TTCAAATGAGAATCTTTGAAT
*
6214350 TT-AAATGAAAATCTTTGAAT
1 TTCAAATGAGAATCTTTGAAT
* * *
6214370 CCTCAAATAAGAATCTTTGAGT
1 -TTCAAATGAGAATCTTTGAAT
* *
6214392 GTT-AAATGAGAATATTTAAAT
1 -TTCAAATGAGAATCTTTGAAT
* * *
6214413 TTCAAAGGAGAATTTTTGAGGT
1 TTCAAATGAGAATCTTTGA-AT
* * * *
6214435 GTGAAATCCA-AA-ATTT--A-
1 TTCAAAT-GAGAATCTTTGAAT
* *
6214452 -TCGAATGTA-AATCTTCGAA-
1 TTCAAATG-AGAATCTTTGAAT
* *
6214471 TTCAAATGATAATTTTTGAAT
1 TTCAAATGAGAATCTTTGAAT
*
6214492 TTCAAATGAGAATCTTTGAGGT
1 TTCAAATGAGAATCTTTGA-AT
* * * *
6214514 GTGAAACTCA-AA-ATTTG---
1 TTCAAA-TGAGAATCTTTGAAT
* * *
6214531 TT-GAATGTGAATCTTCGAA-
1 TTCAAATGAGAATCTTTGAAT
*
6214550 TTCAAATAAGAATCTTTGAAT
1 TTCAAATGAGAATCTTTGAAT
** *
6214571 TTCAAAAAAAAATCTTTGAAGT
1 TTCAAATGAGAATCTTTGAA-T
* *
6214593 TTAAAACCT-A-AA-ATTTG---
1 TTCAAA--TGAGAATCTTTGAAT
* * *
6214610 -TCGAATGTGAATCTTCGAA-
1 TTCAAATGAGAATCTTTGAAT
* *
6214629 TTCAAATGAGAATTTTTTAAT
1 TTCAAATGAGAATCTTTGAAT
* *
6214650 TTCAAATGAGAATTTTTAAAAT
1 TTCAAATGAGAATCTTT-GAAT
*
6214672 TTCAAATGAGAATTTTTGAAT
1 TTCAAATGAGAATCTTTGAAT
6214693 TTCAAATGAGAATCTTTGA
1 TTCAAATGAGAATCTTTGA
6214712 GGTGTGAAAC
Statistics
Matches: 382, Mismatches: 93, Indels: 76
0.69 0.17 0.14
Matches are distributed among these distances:
14 1 0.00
15 1 0.00
16 16 0.04
17 9 0.02
19 4 0.01
20 60 0.16
21 210 0.55
22 62 0.16
23 4 0.01
24 2 0.01
25 13 0.03
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (21 bp):
TTCAAATGAGAATCTTTGAAT
Found at i:6214759 original size:79 final size:82
Alignment explanation
Indices: 6214669--6214827 Score: 225
Period size: 79 Copynumber: 2.0 Consensus size: 82
6214659 GAATTTTTAA
** * * *
6214669 AATTTCAAATGAGAATTTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAACCC-AAAATTTA-
1 AATTTCAAATGAGAAACTTTGAATTTCAAATGAAAATCTTTAAGATGTGAAACCCTAAAATTTAT
*
6214732 TCGAATGTGAATCTTCG
66 TAGAATGTGAATCTTCG
*
6214749 AATTT-AAATGAGAAACTTTGAATTTCAAATGAAAATCTTTAAGATGTGAAACCCTAAAGTTTAT
1 AATTTCAAATGAGAAACTTTGAATTTCAAATGAAAATCTTTAAGATGTGAAACCCTAAAATTTAT
*
6214813 TAGGATGTGAATCTT
66 TAGAATGTGAATCTT
6214828 TGAACTAGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
79 44 0.64
80 12 0.17
81 13 0.19
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (82 bp):
AATTTCAAATGAGAAACTTTGAATTTCAAATGAAAATCTTTAAGATGTGAAACCCTAAAATTTAT
TAGAATGTGAATCTTCG
Found at i:6214780 original size:21 final size:20
Alignment explanation
Indices: 6214741--6214788 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
6214731 ATCGAATGTG
*
6214741 AATCTTCGAATTTAAATGAGA
1 AATCTTTGAATTTAAATGA-A
6214762 AA-CTTTGAATTTCAAATGAA
1 AATCTTTGAATTT-AAATGAA
6214782 AATCTTT
1 AATCTTT
6214789 AAGATGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (20 bp):
AATCTTTGAATTTAAATGAA
Found at i:6215401 original size:44 final size:44
Alignment explanation
Indices: 6215330--6215487 Score: 133
Period size: 43 Copynumber: 3.6 Consensus size: 44
6215320 AGCCTTATTT
* * * *
6215330 ATTT-TTTATTTTTTTAAAAATCGTTGAGCCTCTGATTATAGGAG
1 ATTTATTTA-TTTTTTAAAAGTCATTGAGCCTCTGATTAAAAGAG
* * * * * *
6215374 TTTTATTTATTTTTTCAAACTCATTGAGCTTTTGATTAAATGAG
1 ATTTATTTATTTTTTAAAAGTCATTGAGCCTCTGATTAAAAGAG
** ** *
6215418 CCTT-GCTATTTTTTAAAAGTTATTGAGCCTCTGATTAAAAGA-
1 ATTTATTTATTTTTTAAAAGTCATTGAGCCTCTGATTAAAAGAG
* *
6215460 ATTTATTTATTTTTTCAAAGTCGTTGAG
1 ATTTATTTATTTTTTAAAAGTCATTGAG
6215488 TCTACTGCGA
Statistics
Matches: 87, Mismatches: 25, Indels: 5
0.74 0.21 0.04
Matches are distributed among these distances:
42 2 0.02
43 48 0.55
44 33 0.38
45 4 0.05
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (44 bp):
ATTTATTTATTTTTTAAAAGTCATTGAGCCTCTGATTAAAAGAG
Found at i:6217194 original size:23 final size:23
Alignment explanation
Indices: 6217164--6217211 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
6217154 TTATTAATTT
6217164 AAAATATTTATTAAATTAATAAA
1 AAAATATTTATTAAATTAATAAA
6217187 AAAATATTTATTAAATTAATAAA
1 AAAATATTTATTAAATTAATAAA
6217210 AA
1 AA
6217212 TGAAATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATATTTATTAAATTAATAAA
Found at i:6217428 original size:2 final size:2
Alignment explanation
Indices: 6217421--6217481 Score: 65
Period size: 2 Copynumber: 32.0 Consensus size: 2
6217411 AATCTCATAA
* * *
6217421 AT AT AT AT -T AA AT AT AT AT AA AT A- AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
6217461 AT AT AT AT AG AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
6217482 GTTCAGATGA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
1 3 0.06
2 45 0.94
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:6217469 original size:29 final size:29
Alignment explanation
Indices: 6217423--6217480 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
6217413 TCTCATAAAT
6217423 ATATATTAAATATATATAAATAATATATAG
1 ATATATTAAATATATA-AAATAATATATAG
* *
6217453 ATATA-TATATATATATAGATAATATATA
1 ATATATTAAATATATA-AAATAATATATA
6217481 TGTTCAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (29 bp):
ATATATTAAATATATAAAATAATATATAG
Found at i:6217489 original size:17 final size:18
Alignment explanation
Indices: 6217421--6217481 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 18
6217411 AATCTCATAA
* *
6217421 ATATATAT-TAAATATAT
1 ATATATATATATATAGAT
*
6217438 ATAAATA-ATATATAGAT
1 ATATATATATATATAGAT
6217455 ATATATATATATATAGAT
1 ATATATATATATATAGAT
6217473 A-ATATATAT
1 ATATATATAT
6217482 GTTCAGATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 27 0.71
18 11 0.29
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
ATATATATATATATAGAT
Found at i:6217735 original size:5 final size:5
Alignment explanation
Indices: 6217725--6217786 Score: 63
Period size: 5 Copynumber: 11.6 Consensus size: 5
6217715 TAGGTGTTTG
*
6217725 TTATT TTATT TTATT TTATT CTTATTTT TTATT TT-TG TTATT TTATTAT
1 TTATT TTATT TTATT TTATT -TTA--TT TTATT TTATT TTATT TTA-T-T
6217774 TTATT TTATT TTA
1 TTATT TTATT TTA
6217787 AGATATTAGC
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
4 3 0.06
5 32 0.65
6 5 0.10
7 7 0.14
8 2 0.04
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:6217756 original size:13 final size:14
Alignment explanation
Indices: 6217735--6217783 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
6217725 TTATTTTATT
6217735 TTATTTTATTCTTA
1 TTATTTTATTCTTA
* *
6217749 TT-TTTTATTTTTG
1 TTATTTTATTCTTA
*
6217762 TTATTTTATT-AT-
1 TTATTTTATTCTTA
6217774 TTATTTTATT
1 TTATTTTATT
6217784 TTAAGATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 10 0.32
13 12 0.39
14 9 0.29
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (14 bp):
TTATTTTATTCTTA
Found at i:6217768 original size:27 final size:27
Alignment explanation
Indices: 6217725--6217786 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
6217715 TAGGTGTTTG
* * *
6217725 TTATTTTATTTTATTTTATTCTTATTTT
1 TTATTTTATGTTATTTTATTATT-TATT
6217753 TTATTTT-TGTTATTTTATTATTTATT
1 TTATTTTATGTTATTTTATTATTTATT
6217779 TTATTTTA
1 TTATTTTA
6217787 AGATATTAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 10 0.33
27 13 0.43
28 7 0.23
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (27 bp):
TTATTTTATGTTATTTTATTATTTATT
Found at i:6217793 original size:27 final size:27
Alignment explanation
Indices: 6217736--6217793 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
6217726 TATTTTATTT
* * * *
6217736 TATTTTATTCTTATTTTTTATTTTTGT
1 TATTTTATTATTATATTTTATTTTAGA
6217763 TATTTTATTATT-TATTTTATTTTAAGA
1 TATTTTATTATTATATTTTATTTT-AGA
6217790 TATT
1 TATT
6217794 AGCAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.72
Consensus pattern (27 bp):
TATTTTATTATTATATTTTATTTTAGA
Found at i:6218074 original size:21 final size:22
Alignment explanation
Indices: 6218050--6218103 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
6218040 GATGCAATAA
6218050 TAGAATTTTTAAG-ATTTTTTT-
1 TAGAATTTTT-AGCATTTTTTTC
* *
6218071 TAGAATTGTTGGCATTTTTTTC
1 TAGAATTTTTAGCATTTTTTTC
6218093 TAGAAATTTTT
1 TAG-AATTTTT
6218104 TGAAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 17 0.63
22 3 0.11
23 6 0.22
ACGTcount: A:0.26, C:0.04, G:0.13, T:0.57
Consensus pattern (22 bp):
TAGAATTTTTAGCATTTTTTTC
Found at i:6218883 original size:52 final size:54
Alignment explanation
Indices: 6218808--6219030 Score: 256
Period size: 60 Copynumber: 4.0 Consensus size: 54
6218798 TTTTTTAAAA
* *
6218808 AAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTT-TTTAAAATAAAATTTT
1 AAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTT
* *
6218861 -CATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTTTT
1 AAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAA-ATTTT
* *
6218915 AAAAAATATATTTTTGA-AGAAAAGTTGAAAGTATTAATTTTTGTTGAAAATAAAAATTTCT
1 ----AA-ATATTTTTGAGA-AAAAGTTGAAAGTATCAATTTTTCTTGAAAAT-AAAATTT-T
6218976 AAAAGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAGA-AAAATTT
1 -AAA-TATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAA-ATAAAATTT
6219031 CCAAAAAAAA
Statistics
Matches: 146, Mismatches: 10, Indels: 24
0.81 0.06 0.13
Matches are distributed among these distances:
52 34 0.23
53 10 0.07
54 4 0.03
57 8 0.05
58 40 0.27
59 3 0.02
60 43 0.29
61 4 0.03
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.41
Consensus pattern (54 bp):
AAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTT
Found at i:6218955 original size:60 final size:59
Alignment explanation
Indices: 6218862--6219081 Score: 248
Period size: 58 Copynumber: 3.7 Consensus size: 59
6218852 TAAAATTTTC
*
6218862 ATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTTTTAAAAAA
1 ATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTTATAAAAAA
* * * *
6218921 TATATTTTTGA-AGAAAAGTTGAAAGTATTAATTTTTGTTGAAAATAAAAATTTCT--AAAA
1 -ATATTTTTGAGA-AAAAGTTGAAAGTATCAATTTTTCTTGAAAAT-AAATTTTATAAAAAA
* * * *
6218980 GTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAGAAAAATTTCCAAAAAAAAAA
1 ATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAA-ATAAATTT---TATAAAAAA
* * *
6219043 ACATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTG
1 ATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
6219082 TATAAAAGCA
Statistics
Matches: 135, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
58 42 0.31
59 7 0.05
60 40 0.30
61 7 0.05
63 39 0.29
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (59 bp):
ATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAATTTTATAAAAAA
Found at i:6219007 original size:118 final size:111
Alignment explanation
Indices: 6218790--6219077 Score: 355
Period size: 118 Copynumber: 2.5 Consensus size: 111
6218780 AAAAAAATAA
* * *
6218790 AAAATAATTTTTTTAAAAAAATATTTTTG-AGAAAAAATTGAAAGTATCAATTTTTTTTAAAATA
1 AAAATAAATTTTTTAAAAAAATATTTTTGAAG-AAAAGTTGAAAGTATCAATTTTTTTGAAAATA
*
6218854 AAATTTTCATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
65 AAATTTTAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
*
6218901 AAAATAAATTTTTTAAAAAATATATTTTTGAAGAAAAGTTGAAAGTATTAATTTTTGTTGAAAAT
1 AAAATAAATTTTTTAAAAAA-ATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTT-TTGAAAAT
6218966 AAAAATTTCTAAAAGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
64 -AAAATTT-T--AA-TATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
* *** *
6219019 AAAGAAAAATTTCCAAAAAAAAAAACATTTTT-AAGGAAAAGTTGAAAGTATCAATTTTT
1 AAA-ATAAATTT---TTTAAAAAAATATTTTTGAA-GAAAAGTTGAAAGTATCAATTTTT
6219078 CTTGTATAAA
Statistics
Matches: 153, Mismatches: 11, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
111 19 0.12
112 30 0.20
113 9 0.06
114 7 0.05
115 1 0.01
117 1 0.01
118 41 0.27
119 7 0.05
120 2 0.01
121 30 0.20
122 6 0.04
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (111 bp):
AAAATAAATTTTTTAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTTTGAAAATAA
AATTTTAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
Found at i:6221945 original size:21 final size:21
Alignment explanation
Indices: 6221903--6221947 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
6221893 AAACAAACAC
* *
6221903 ATAAATAAAATACTAAATAAA
1 ATAAATAAAAAACCAAATAAA
6221924 ATAAATAAAAAAACCAAA-AAA
1 ATAAAT-AAAAAACCAAATAAA
6221945 ATA
1 ATA
6221948 GAATTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.18
Consensus pattern (21 bp):
ATAAATAAAAAACCAAATAAA
Found at i:6223331 original size:61 final size:65
Alignment explanation
Indices: 6223200--6223340 Score: 159
Period size: 61 Copynumber: 2.2 Consensus size: 65
6223190 CGTGTATTTA
* *
6223200 TGTTTTATTTTATATAAAAATTATATCTTATAATTTATATAAATATAATAATATAAAAATATATT
1 TGTTTTATTTTATATAAAAATTATATATAATAATTTATATAAATATAATAATATAAAAATATATT
* * * **
6223265 T-TTTTATTTTAT-T-AAATTTATATATAATAA-TTAT-TAAAATATTATATTAT-ATTATATAT
1 TGTTTTATTTTATATAAAAATTATATATAATAATTTATAT-AAATATAATAATATAAAAATATAT
6223324 T
65 T
6223325 TGTTTTATTTTCATAT
1 TGTTTTATTTT-ATAT
6223341 TTTATTTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
60 10 0.15
61 25 0.38
62 16 0.25
63 2 0.03
64 11 0.17
65 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (65 bp):
TGTTTTATTTTATATAAAAATTATATATAATAATTTATATAAATATAATAATATAAAAATATATT
Found at i:6230040 original size:20 final size:21
Alignment explanation
Indices: 6230015--6230053 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
6230005 CAGCATTTTG
6230015 GGTAGGAAT-GAACTGAAAAA
1 GGTAGGAATCGAACTGAAAAA
*
6230035 GGTAGGAATCGAATTGAAA
1 GGTAGGAATCGAACTGAAA
6230054 TAATCGGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.46, C:0.05, G:0.31, T:0.18
Consensus pattern (21 bp):
GGTAGGAATCGAACTGAAAAA
Found at i:6231529 original size:2 final size:2
Alignment explanation
Indices: 6231522--6231554 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
6231512 TTTGTAGGTT
6231522 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6231555 AAATACAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6231692 original size:15 final size:16
Alignment explanation
Indices: 6231672--6231701 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6231662 GCATATTAGA
6231672 TTTTATAGAT-TTTCG
1 TTTTATAGATGTTTCG
6231687 TTTTATAGATGTTTC
1 TTTTATAGATGTTTC
6231702 TATATACTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (16 bp):
TTTTATAGATGTTTCG
Found at i:6236997 original size:26 final size:25
Alignment explanation
Indices: 6236935--6236997 Score: 58
Period size: 26 Copynumber: 2.5 Consensus size: 25
6236925 TTGATGCATG
* *
6236935 TATT-TTATTTTATTTTTTAGAAAT
1 TATTATTATTTTATTTATTACAAAT
*
6236959 T-TTATTGATTTTTATTTATTACATTAT
1 TATTATT-A-TTTTATTTATTACA-AAT
6236986 TATTATTATTTT
1 TATTATTATTTT
6236998 GAAGAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
23 2 0.06
24 3 0.10
25 1 0.03
26 16 0.52
27 4 0.13
28 5 0.16
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (25 bp):
TATTATTATTTTATTTATTACAAAT
Found at i:6237200 original size:14 final size:14
Alignment explanation
Indices: 6237181--6237211 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6237171 TTATTCTTAA
6237181 TTTATTAGTTAATT
1 TTTATTAGTTAATT
*
6237195 TTTATTATTTAATT
1 TTTATTAGTTAATT
6237209 TTT
1 TTT
6237212 TACCAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTATTAGTTAATT
Found at i:6238690 original size:48 final size:48
Alignment explanation
Indices: 6238638--6239002 Score: 383
Period size: 48 Copynumber: 7.7 Consensus size: 48
6238628 CTTCAATCAA
*
6238638 AGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTCATCTAAGTAG
1 AGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTCATCTAAGCAG
* * * * * *
6238686 AGGCTTAATAACTTT-AAAATCCATATTAAAAAAGCTTC-TTTAAGCAG
1 AGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGC-TCATCTAAGCAG
* * * * *
6238733 ATGCTCAATAATTTTAAAAA-TCTATCTTAAAAAAGCTCTTCTAAG-A-
1 AGGCTCAACAACTTTAAAAATTC-ATCTTGAAAAAGCTCATCTAAGCAG
* * * *
6238779 A-GCTCAATAACTTTAAAAA-TCTATCTTGAAAAAGCTCTTATAAGCAA
1 AGGCTCAACAACTTTAAAAATTC-ATCTTGAAAAAGCTCATCTAAGCAG
*
6238826 AGGCTCAACAACTTTAAAAATTCATCTTG-AAAAGCTCCTCTAAGCAG
1 AGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTCATCTAAGCAG
* * * * *
6238873 AGGCTCTACAACTTTAAAAATCTCATCTT-ATAAAGACACCTCTTAGCAG
1 AGGCTCAACAACTTTAAAAAT-TCATCTTGAAAAAG-CTCATCTAAGCAG
*
6238922 AGGCTCTACAACTTTAAAAATT-ATCTTGAGAAAAGCTCATCTAAGCAG
1 AGGCTCAACAACTTTAAAAATTCATCTTGA-AAAAGCTCATCTAAGCAG
*
6238970 AGGCTCAACAACTTTTAAAATT-ATCTTGAAAAA
1 AGGCTCAACAACTTTAAAAATTCATCTTGAAAAA
6239003 ATTCATCTTG
Statistics
Matches: 274, Mismatches: 30, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
45 40 0.15
46 2 0.01
47 85 0.31
48 109 0.40
49 38 0.14
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (48 bp):
AGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTCATCTAAGCAG
Found at i:6239005 original size:14 final size:15
Alignment explanation
Indices: 6238986--6239017 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
6238976 AACAACTTTT
6238986 AAAATT-ATCTTGAA
1 AAAATTCATCTTGAA
6239000 AAAATTCATCTTGAA
1 AAAATTCATCTTGAA
6239015 AAA
1 AAA
6239018 GCTCTTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.31
Consensus pattern (15 bp):
AAAATTCATCTTGAA
Found at i:6239020 original size:62 final size:63
Alignment explanation
Indices: 6238937--6239066 Score: 210
Period size: 62 Copynumber: 2.1 Consensus size: 63
6238927 CTACAACTTT
*
6238937 AAAAATTATCTTGAGAAAAGCTCATCTAAGCAGAGGCTCAACAACTTTTAAAA-TTATCTTGA
1 AAAAATTATCTTGAGAAAAGCTCATCTAAGCAGAGGCTCAACAACTTTAAAAATTTATCTTGA
* *
6238999 AAAAATTCATCTTGA-AAAAGCTCTTCTAAGCAGAGGCTCAATAACTTTAAAAATTTATCTTGA
1 AAAAATT-ATCTTGAGAAAAGCTCATCTAAGCAGAGGCTCAACAACTTTAAAAATTTATCTTGA
6239062 AAAAA
1 AAAAA
6239067 AGCTCATCTA
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
62 42 0.67
63 21 0.33
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (63 bp):
AAAAATTATCTTGAGAAAAGCTCATCTAAGCAGAGGCTCAACAACTTTAAAAATTTATCTTGA
Found at i:6239052 original size:48 final size:48
Alignment explanation
Indices: 6238999--6239494 Score: 435
Period size: 47 Copynumber: 10.1 Consensus size: 48
6238989 ATTATCTTGA
* * *
6238999 AAAAATTCATCTTGAAAAAGCTCTTCTAAGCAGAGGCTCAATAACTTT
1 AAAAATTCATCTTGAAAAAGCTCCTCTAAGCAGAAGCTCAACAACTTT
* * * *
6239047 AAAAATTTATCTTGAAAAAAAGCTCATCTAAACAAAAGCTCAACAACTTT
1 AAAAATTCATCTTG--AAAAAGCTCCTCTAAGCAGAAGCTCAACAACTTT
* * * * * *
6239097 AAAAATTTAGCTTGAAAAAAAGCTCCTATAAGCAGAGGCTCTATAACTTT
1 AAAAATTCATCTTG--AAAAAGCTCCTCTAAGCAGAAGCTCAACAACTTT
* *
6239147 AAAAA-TCATATTGAAAAAGCTCCTCTAAGCA-AAGGCTCAATAACTTT
1 AAAAATTCATCTTGAAAAAGCTCCTCTAAGCAGAA-GCTCAACAACTTT
* * **
6239194 AAAAATTTATCTTGAAAAAGCTCCTATCGGCAG-AGACTCAACAACTTT
1 AAAAATTCATCTTGAAAAAGCTCCTCTAAGCAGAAG-CTCAACAACTTT
* * * *
6239242 AAAAA-TCATCTTGAAAAAGCTCTTATAAGTAGAAGCTCTACAACTTT
1 AAAAATTCATCTTGAAAAAGCTCCTCTAAGCAGAAGCTCAACAACTTT
* * * *
6239289 TAAAATTCATCTTGAAAAAGCTCATTTAAGCAAAAGCTCAACAA-TTT
1 AAAAATTCATCTTGAAAAAGCTCCTCTAAGCAGAAGCTCAACAACTTT
* * * * * *
6239336 TAAAATTCATATTGAAAAAACTCATCTCAGCAGAAGTTCAACAACTTT
1 AAAAATTCATCTTGAAAAAGCTCCTCTAAGCAGAAGCTCAACAACTTT
* * * *
6239384 AAAAATTCATCTTAAAAAAGCTCCTATGAGCTCCTTTTAGCAGAAGCTTAACAATTTT
1 AAAAATTCATCTTGAAAAAGCT-C------CT-C--TAAGCAGAAGCTCAACAACTTT
* * * *
6239442 AAAAATCTTATATTGGAAAAGCTCCTCTAAACAGAAGCTCAACAACTTT
1 AAAAAT-TCATCTTGAAAAAGCTCCTCTAAGCAGAAGCTCAACAACTTT
6239491 AAAA
1 AAAA
6239495 TTAAACTGTT
Statistics
Matches: 367, Mismatches: 61, Indels: 39
0.79 0.13 0.08
Matches are distributed among these distances:
46 1 0.00
47 113 0.31
48 107 0.29
49 28 0.08
50 76 0.21
51 1 0.00
52 2 0.01
55 1 0.00
56 1 0.00
58 25 0.07
59 12 0.03
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (48 bp):
AAAAATTCATCTTGAAAAAGCTCCTCTAAGCAGAAGCTCAACAACTTT
Found at i:6239261 original size:95 final size:95
Alignment explanation
Indices: 6238999--6239494 Score: 456
Period size: 95 Copynumber: 5.0 Consensus size: 95
6238989 ATTATCTTGA
* * * * * *
6238999 AAAAATTCATCTTGAAAAAGCTCTTCTAAGCAGAGGCTCAATAACTTTAAAAATTTATCTTGAAA
1 AAAAATTCATCTTGAAAAAGCTCCTATAAGCAGAGACTCAACAACTTTAAAAA-TCATATTG--A
* *
6239064 AAAAGCTCATCTAAACAAAAGCTCAACAACTTT
63 AAAAGCTCATCTAAGCAGAAGCTCAACAACTTT
* * * * *
6239097 AAAAATTTAGCTTGAAAAAAAGCTCCTATAAGCAGAGGCTCTATAACTTTAAAAATCATATTGAA
1 AAAAATTCATCTTG--AAAAAGCTCCTATAAGCAGAGACTCAACAACTTTAAAAATCATATTGAA
* *
6239162 AAAGCTCCTCTAAGCA-AAGGCTCAATAACTTT
64 AAAGCTCATCTAAGCAGAA-GCTCAACAACTTT
* ** *
6239194 AAAAATTTATCTTGAAAAAGCTCCTATCGGCAGAGACTCAACAACTTTAAAAATCATCTTGAAAA
1 AAAAATTCATCTTGAAAAAGCTCCTATAAGCAGAGACTCAACAACTTTAAAAATCATATTGAAAA
* * * *
6239259 AGCTCTTATAAGTAGAAGCTCTACAACTTT
66 AGCTCATCTAAGCAGAAGCTCAACAACTTT
* * * * * *
6239289 TAAAATTCATCTTGAAAAAGCTCATTTAAGCA-AAAGCTCAACAATTTTAAAATTCATATTGAAA
1 AAAAATTCATCTTGAAAAAGCTCCTATAAGCAGAGA-CTCAACAACTTTAAAAATCATATTGAAA
* * *
6239353 AAACTCATCTCAGCAGAAGTTCAACAACTTT
65 AAGCTCATCTAAGCAGAAGCTCAACAACTTT
* * * *
6239384 AAAAATTCATCTTAAAAAAGCTCCTATGAGCTCCTTTTAGCAGAAGCTTAACAATTTTAAAAATC
1 AAAAATTCATCTTGAAAAAGCTCCTATAAG---C----AG-AG-A-CTCAACAACTTTAAAAATC
* * *
6239449 TTATATTGGAAAAGCTCCTCTAAACAGAAGCTCAACAACTTT
56 --ATATTGAAAAAGCTCATCTAAGCAGAAGCTCAACAACTTT
6239491 AAAA
1 AAAA
6239495 TTAAACTGTT
Statistics
Matches: 328, Mismatches: 53, Indels: 25
0.81 0.13 0.06
Matches are distributed among these distances:
94 2 0.01
95 167 0.51
96 4 0.01
97 41 0.12
98 13 0.04
99 6 0.02
100 36 0.11
102 1 0.00
104 1 0.00
105 19 0.06
107 38 0.12
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (95 bp):
AAAAATTCATCTTGAAAAAGCTCCTATAAGCAGAGACTCAACAACTTTAAAAATCATATTGAAAA
AGCTCATCTAAGCAGAAGCTCAACAACTTT
Found at i:6239509 original size:107 final size:105
Alignment explanation
Indices: 6239307--6239510 Score: 248
Period size: 107 Copynumber: 1.9 Consensus size: 105
6239297 ATCTTGAAAA
* *
6239307 AGCTCATTTAAGCAAAAGCTCAACAATTTTAAAATTCATATTGAAAAAACTCATCTCAGCAGAAG
1 AGCTCATTTAAGCAAAAGCTCAACAATTTTAAAATTCATATTGAAAAAACTCATCTAAACAGAAG
* * *
6239372 TTCAACAACTTTAAAAATTCATCTTAAAAAAGCTCCTATG
66 CTCAACAACTTTAAAAATTAAACTTAAAAAAGCTCCTATG
* * * * * * * *
6239412 AGCTCCTTTTAGCAGAAGCTTAACAATTTTAAAAATCTTATATTGGAAAAGCTCCTCTAAACAGA
1 AGCTCATTTAAGCAAAAGCTCAACAATTTT-AAAAT-TCATATTGAAAAAACTCATCTAAACAGA
6239477 AGCTCAACAACTTT-AAAATTAAACTGTTAAAAAA
64 AGCTCAACAACTTTAAAAATTAAAC--TTAAAAAA
6239511 TAACTTTGAA
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
105 26 0.32
106 13 0.16
107 35 0.43
108 8 0.10
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (105 bp):
AGCTCATTTAAGCAAAAGCTCAACAATTTTAAAATTCATATTGAAAAAACTCATCTAAACAGAAG
CTCAACAACTTTAAAAATTAAACTTAAAAAAGCTCCTATG
Found at i:6239803 original size:75 final size:75
Alignment explanation
Indices: 6239716--6240074 Score: 429
Period size: 75 Copynumber: 4.8 Consensus size: 75
6239706 TCAAGCTTTA
*
6239716 ACACTC-GAATATCACCACTGAGAATATGCAAATGACTTTGGATATCACCATCGAAAAAATGCAA
1 ACACTCAG-ATATCACCACTGAGAATATGCAAATGACTTCGGATATCACCATCGAAAAAATGCAA
*
6239780 TTCAAACCTTA
65 TTCAAACCTTG
* * *
6239791 ACACTTAGATATCACCACTGAGAATATGCAAATGACTTCGAATATCGCCATCGAAAAAATAG-AA
1 ACACTCAGATATCACCACTGAGAATATGCAAATGACTTCGGATATCACCATCGAAAAAAT-GCAA
* *
6239855 TTTAAACTTTG
65 TTCAAACCTTG
* * * * * *
6239866 ACACTCGGATATCACTACTGAGAATATGTAAATGACTTCGAATATCACCATCGAGAAAATGTAAT
1 ACACTCAGATATCACCACTGAGAATATGCAAATGACTTCGGATATCACCATCGAAAAAATGCAAT
*
6239931 TTAAACCTTG
66 TCAAACCTTG
* * * ** *
6239941 ACACTTAGATATCACCA-TCGAGAA-AAGATAAATGACTTCGGATATCACCATAAAAAAAATACA
1 ACACTCAGATATCACCACT-GAGAATATG-CAAATGACTTCGGATATCACCATCGAAAAAATGCA
6240004 ATTCAAACCTTG
64 ATTCAAACCTTG
* * * * *
6240016 ACACTCAAATATCACCACTGAGAAAAGGCAAATGACTTTGGATATCACCATCGAGAAAA
1 ACACTCAGATATCACCACTGAGAATATGCAAATGACTTCGGATATCACCATCGAAAAAA
6240075 GAGAAAAGAC
Statistics
Matches: 244, Mismatches: 33, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
74 4 0.02
75 235 0.96
76 5 0.02
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.24
Consensus pattern (75 bp):
ACACTCAGATATCACCACTGAGAATATGCAAATGACTTCGGATATCACCATCGAAAAAATGCAAT
TCAAACCTTG
Found at i:6239953 original size:150 final size:150
Alignment explanation
Indices: 6239704--6240074 Score: 503
Period size: 150 Copynumber: 2.5 Consensus size: 150
6239694 AGAAAATATT
* *
6239704 ATTCAAGCTTTAACACTCGAATATCACCACTGAGAATATGCAAATGACTTTGGATATCACCATCG
1 ATTCAAACTTTGACACTCGAATATCACCACTGAGAATATGCAAATGACTTTGGATATCACCATCG
* *
6239769 AAAAAATGCAATTCAAACCTTAACACTTAGATATCACCA-CTGAGAATATG-CAAATGACTTCGA
66 AGAAAATGCAATTCAAACCTTAACACTTAGATATCACCATC-GAGAA-AAGACAAATGACTTCGA
* ** *
6239832 ATATCGCCATCGAAAAAATAGA
129 ATATCACCATAAAAAAAATACA
* * * * * *
6239854 ATTTAAACTTTGACACTCGGATATCACTACTGAGAATATGTAAATGACTTCGAATATCACCATCG
1 ATTCAAACTTTGACACTCGAATATCACCACTGAGAATATGCAAATGACTTTGGATATCACCATCG
* * * * *
6239919 AGAAAATGTAATTTAAACCTTGACACTTAGATATCACCATCGAGAAAAGATAAATGACTTCGGAT
66 AGAAAATGCAATTCAAACCTTAACACTTAGATATCACCATCGAGAAAAGACAAATGACTTCGAAT
6239984 ATCACCATAAAAAAAATACA
131 ATCACCATAAAAAAAATACA
* * * *
6240004 ATTCAAACCTTGACACTCAAATATCACCACTGAGAAAAGGCAAATGACTTTGGATATCACCATCG
1 ATTCAAACTTTGACACTCGAATATCACCACTGAGAATATGCAAATGACTTTGGATATCACCATCG
6240069 AGAAAA
66 AGAAAA
6240075 GAGAAAAGAC
Statistics
Matches: 190, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
149 2 0.01
150 187 0.98
151 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (150 bp):
ATTCAAACTTTGACACTCGAATATCACCACTGAGAATATGCAAATGACTTTGGATATCACCATCG
AGAAAATGCAATTCAAACCTTAACACTTAGATATCACCATCGAGAAAAGACAAATGACTTCGAAT
ATCACCATAAAAAAAATACA
Found at i:6240090 original size:40 final size:40
Alignment explanation
Indices: 6240035--6240154 Score: 163
Period size: 40 Copynumber: 3.0 Consensus size: 40
6240025 TATCACCACT
* *
6240035 GAGAAAAGGCAAATGACTTTGGATATCACCATCGAGAAAA
1 GAGAAAAGACAAATGACTTCGGATATCACCATCGAGAAAA
* * *
6240075 GAGAAAAGACAAATGACTTCGGATATCGCTA-CTAAGAAAA
1 GAGAAAAGACAAATGACTTCGGATATCACCATC-GAGAAAA
6240115 GAGAAAA-AGCAAATGACTTCGGATATCACCATCGAGAAAA
1 GAGAAAAGA-CAAATGACTTCGGATATCACCATCGAGAAAA
6240155 TGTAATTAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
39 2 0.03
40 66 0.96
41 1 0.01
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.17
Consensus pattern (40 bp):
GAGAAAAGACAAATGACTTCGGATATCACCATCGAGAAAA
Found at i:6240184 original size:42 final size:42
Alignment explanation
Indices: 6240137--6240314 Score: 196
Period size: 42 Copynumber: 4.2 Consensus size: 42
6240127 ATGACTTCGG
* *
6240137 ATATCACCATCGAGAAAATGTAATTAAAACCTTGACACTCGA
1 ATATCACCACCGAGAAAATGTAATTCAAACCTTGACACTCGA
* * * * * *
6240179 ATATCACCACCAAGAAAATGCAATTCATACCTTGATACTTGG
1 ATATCACCACCGAGAAAATGTAATTCAAACCTTGACACTCGA
* * * * * *
6240221 ATATCACCACTGAGAATATGTAAATGATACTTTGACACTCGA
1 ATATCACCACCGAGAAAATGTAATTCAAACCTTGACACTCGA
* *
6240263 ATATCACTACCGA-AAAGATGTAATTCAAACCTTGACACTCGG
1 ATATCACCACCGAGAAA-ATGTAATTCAAACCTTGACACTCGA
6240305 ATATCACCAC
1 ATATCACCAC
6240315 TAAAAAAATG
Statistics
Matches: 108, Mismatches: 27, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
41 2 0.02
42 106 0.98
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.25
Consensus pattern (42 bp):
ATATCACCACCGAGAAAATGTAATTCAAACCTTGACACTCGA
Found at i:6240330 original size:84 final size:84
Alignment explanation
Indices: 6240133--6240332 Score: 251
Period size: 84 Copynumber: 2.4 Consensus size: 84
6240123 GCAAATGACT
* * *
6240133 TCGGATATCACCA-TCGAGAAAATGTAATTAAAACCTTGACACTCGAATATCACCACCAAGAAAA
1 TCGGATATCACCACT-GAGAAAATGTAAATGATACCTTGACACTCGAATATCACCACCAAGAAAA
* *
6240197 TGCAATTCATACCTTGATAC
65 TGCAATTCAAACCTTGACAC
* * * * *
6240217 TTGGATATCACCACTGAGAATATGTAAATGATACTTTGACACTCGAATATCACTACCGAA-AAGA
1 TCGGATATCACCACTGAGAAAATGTAAATGATACCTTGACACTCGAATATCACCACC-AAGAAAA
*
6240281 TGTAATTCAAACCTTGACAC
65 TGCAATTCAAACCTTGACAC
* *
6240301 TCGGATATCACCACTAAAAAAATGTAAATGAT
1 TCGGATATCACCACTGAGAAAATGTAAATGAT
6240333 TTTTTTAAGT
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
84 96 0.97
85 3 0.03
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.26
Consensus pattern (84 bp):
TCGGATATCACCACTGAGAAAATGTAAATGATACCTTGACACTCGAATATCACCACCAAGAAAAT
GCAATTCAAACCTTGACAC
Found at i:6240786 original size:35 final size:35
Alignment explanation
Indices: 6240699--6240788 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 35
6240689 TATGAGGTAA
** * * *
6240699 ATGAAATGCAAGGTTCTTTT-TTTAAATGATGCTT
1 ATGAAATGCAAATTTCTTTTCTTAAAAAGATGCTC
* *
6240733 ATGAGATGCAAATGTCTTTTCTTAAAAAGATG-TAC
1 ATGAAATGCAAATTTCTTTTCTTAAAAAGATGCT-C
6240768 ATGAAATGCAAATTTCTTTTC
1 ATGAAATGCAAATTTCTTTTC
6240789 CAAAAATACT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
34 17 0.38
35 28 0.62
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (35 bp):
ATGAAATGCAAATTTCTTTTCTTAAAAAGATGCTC
Found at i:6246517 original size:23 final size:24
Alignment explanation
Indices: 6246491--6246541 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
6246481 CATGTATTTT
*
6246491 TTTTTTTTTA-GAAATT-TTATTGA
1 TTTTTATTTATGAAATTATTATT-A
*
6246514 TTTTTATTTATTAAATTATTATTA
1 TTTTTATTTATGAAATTATTATTA
6246538 TTTT
1 TTTT
6246542 GAAGAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.38
24 10 0.42
25 5 0.21
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (24 bp):
TTTTTATTTATGAAATTATTATTA
Found at i:6246737 original size:14 final size:14
Alignment explanation
Indices: 6246718--6246748 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6246708 TTATTCTTAA
6246718 TTTATTAGTTAATT
1 TTTATTAGTTAATT
*
6246732 TTTATTATTTAATT
1 TTTATTAGTTAATT
6246746 TTT
1 TTT
6246749 TACCAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTATTAGTTAATT
Found at i:6255679 original size:39 final size:39
Alignment explanation
Indices: 6255625--6255742 Score: 209
Period size: 39 Copynumber: 3.0 Consensus size: 39
6255615 CTGATTCTCA
*
6255625 ATTGCTTCATTACACGTAAATGGTATAAACACAATAAGT
1 ATTGCTTCATTACACGTCAATGGTATAAACACAATAAGT
6255664 ATTGCTTCATTACACGTCAATGGTATAAACACAATAAGT
1 ATTGCTTCATTACACGTCAATGGTATAAACACAATAAGT
* *
6255703 ACTGCTTCATTACACGTCAATGGTATGAACACAATAAGT
1 ATTGCTTCATTACACGTCAATGGTATAAACACAATAAGT
6255742 A
1 A
6255743 ATAATTTTAT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 76 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (39 bp):
ATTGCTTCATTACACGTCAATGGTATAAACACAATAAGT
Found at i:6257471 original size:27 final size:26
Alignment explanation
Indices: 6257433--6257483 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 26
6257423 AATAAAAAAA
*
6257433 TTAAAAATTATTTAAAATGATTTTTATT
1 TTAAAAATTA-TTAAAA-AATTTTTATT
6257461 TTAAAAA-TATTAAAAAATTTTTA
1 TTAAAAATTATTAAAAAATTTTTA
6257484 AGGAATTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 6 0.27
27 2 0.09
28 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (26 bp):
TTAAAAATTATTAAAAAATTTTTATT
Found at i:6257615 original size:58 final size:58
Alignment explanation
Indices: 6257531--6257987 Score: 192
Period size: 63 Copynumber: 7.4 Consensus size: 58
6257521 TTTATTTTTT
6257531 AATG-AAGATTATTTAAGATATTTTTTAACAAAAAATGTCTTAAATAATTTCTTTTAAAA
1 AATGAAAGATTATTTAAGATATTTTTTAACAAAAAA-G-CTTAAATAATTTCTTTTAAAA
* * ** * * * *
6257590 AAT-ATA-ATTATTTAAGACATTTTTTATTGAAAAACACCTTAAATAATCTCCATATAAAA
1 AATGAAAGATTATTTAAGATATTTTTTA-ACAAAAA-AGCTTAAATAAT-TTCTTTTAAAA
*
6257649 AATGAAAGGGATTATTTAAGATATTTTTTAACCAAAAAAGCTTTAAATAATCTT-TTTAAAAA
1 AATGAAA--GATTATTTAAGATATTTTTTAA-CAAAAAAGC-TTAAATAAT-TTCTTTTAAAA
* * * * ** ** * *
6257711 AAT-ATTAGGGATTATTTAAGGTATTTATGATTTAAAAATTCTTTAAATAATCCTTTTTATTTTT
1 AATGA--A-AGATTATTTAAGATATTTTTTA-ACAAAAAAGC-TTAAATAA-----TTTCTTTTA
**
6257775 TTA
56 AAA
* * *
6257778 AATG--AGATTATTTAAGGTATTTTTCAACCAAAAATA-CTTTAAATAATTTCATTTAACAAA
1 AATGAAAGATTATTTAAGATATTTTTTAA-CAAAAA-AGC-TTAAATAATTTC-TTTTA-AAA
* * ** ** *
6257838 AATAAGAAGACTATTTAAGATATTTTTTAACAAAAAAAATTAAATAATCCCCTTATAAAAA
1 AATGA-AAGATTATTTAAGATATTTTTTAACAAAAAAGCTTAAATAAT-TTCTT-TTAAAA
* * * * * * *
6257899 AATAAAGAGAATTATTTAAGGTGTTTTCTAACAAAAAATATCTTAAATAATTCCTTTAAAAA
1 AATGAA-AG-ATTATTTAAGATATTTTTTAAC-AAAAA-AGCTTAAATAATTTCTTTTAAAA
* * *
6257961 ATATTAAAAATTATTTAAAATATTTTT
1 A-ATGAAAGATTATTTAAGATATTTTT
6257988 GGTTTGAAAA
Statistics
Matches: 302, Mismatches: 60, Indels: 70
0.70 0.14 0.16
Matches are distributed among these distances:
58 32 0.11
59 23 0.08
60 8 0.03
61 37 0.12
62 79 0.26
63 103 0.34
64 10 0.03
66 2 0.01
67 8 0.03
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (58 bp):
AATGAAAGATTATTTAAGATATTTTTTAACAAAAAAGCTTAAATAATTTCTTTTAAAA
Found at i:6257935 original size:61 final size:61
Alignment explanation
Indices: 6257784--6257986 Score: 159
Period size: 61 Copynumber: 3.3 Consensus size: 61
6257774 TTTAAATGAG
* * * *
6257784 ATTATTTAAGGTATTTT-TCAAC-CAAAAATACTTTAAATAATTTCATTTAACAAAA-ATAAGAA
1 ATTATTTAAGATATTTTCT-AACAAAAAAATAC-TTAAATAA-TCCCTTTAA-AAAATATAA-AA
*
6257846 G
61 A
* *
6257847 ACTATTTAAGATATTTTTTAACAAAAAAA-A-TTAAATAATCCCCTTATAAAAAA-ATAAAGAGA
1 ATTATTTAAGATATTTTCTAACAAAAAAATACTTAAATAAT-CCCTT-TAAAAAATATAAA-A-A
* * * *
6257909 ATTATTTAAGGTGTTTTCTAAC-AAAAAATATCTTAAATAATTCCTTTAAAAAATATTAAAA
1 ATTATTTAAGATATTTTCTAACAAAAAAATA-CTTAAATAATCCCTTTAAAAAATATAAAAA
*
6257970 ATTATTTAAAATATTTT
1 ATTATTTAAGATATTTT
6257987 TGGTTTGAAA
Statistics
Matches: 115, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
60 2 0.02
61 41 0.36
62 30 0.26
63 27 0.23
64 15 0.13
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.37
Consensus pattern (61 bp):
ATTATTTAAGATATTTTCTAACAAAAAAATACTTAAATAATCCCTTTAAAAAATATAAAAA
Found at i:6263230 original size:21 final size:21
Alignment explanation
Indices: 6263206--6263246 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6263196 TGATTATCTA
6263206 AAAATTATATCAAAATTTATT
1 AAAATTATATCAAAATTTATT
* * *
6263227 AAAATTTTTTCAAATTTTAT
1 AAAATTATATCAAAATTTAT
6263247 ACACTTAATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATTATATCAAAATTTATT
Found at i:6264626 original size:13 final size:13
Alignment explanation
Indices: 6264608--6264649 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
6264598 TAAAAAGTTT
6264608 TAATTTAATTAAA
1 TAATTTAATTAAA
6264621 TAATTTAA-TAAA
1 TAATTTAATTAAA
* *
6264633 -AATATAATCAAA
1 TAATTTAATTAAA
6264645 TAATT
1 TAATT
6264650 AATCAATCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 6 0.25
12 7 0.29
13 11 0.46
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATTTAATTAAA
Found at i:6265725 original size:19 final size:19
Alignment explanation
Indices: 6265701--6265743 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
6265691 TATATTCATA
*
6265701 TATTTAATAA-ATTAATTTT
1 TATTTAATAATA-TAAATTT
6265720 TATTTAATAATATAAATTT
1 TATTTAATAATATAAATTT
6265739 TATTT
1 TATTT
6265744 TAGATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTAATAATATAAATTT
Found at i:6266703 original size:16 final size:16
Alignment explanation
Indices: 6266669--6266706 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
6266659 CATTCTATTT
6266669 TTTTAA-TTTTTTAAG
1 TTTTAATTTTTTTAAG
6266684 TTTTAATTTGTTTTAA-
1 TTTTAATTT-TTTTAAG
6266700 TTTTAAT
1 TTTTAAT
6266707 ATTTATCTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 9 0.43
17 6 0.29
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (16 bp):
TTTTAATTTTTTTAAG
Found at i:6268278 original size:25 final size:26
Alignment explanation
Indices: 6268241--6268299 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
6268231 CAAAATTTAT
* * *
6268241 ATTTGATATATTATTAATATATCAAA
1 ATTTGATACATTATCAATAAATCAAA
6268267 ATTT-ATACATTATCAATAAATC-AA
1 ATTTGATACATTATCAATAAATCAAA
6268291 ATTATGATA
1 ATT-TGATA
6268300 ACTCATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 5 0.18
25 16 0.57
26 7 0.25
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (26 bp):
ATTTGATACATTATCAATAAATCAAA
Found at i:6282412 original size:3 final size:3
Alignment explanation
Indices: 6282404--6282434 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
6282394 TGTCTTTCCA
6282404 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
6282435 CCTTTCTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:6290439 original size:23 final size:23
Alignment explanation
Indices: 6290406--6290451 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
6290396 AATAGACTTA
6290406 CCAACTATTTTCACCATTATATT
1 CCAACTATTTTCACCATTATATT
* *
6290429 CCAACTGTTTTCACCTTTATATT
1 CCAACTATTTTCACCATTATATT
6290452 ATAAAGCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.46
Consensus pattern (23 bp):
CCAACTATTTTCACCATTATATT
Found at i:6291677 original size:34 final size:35
Alignment explanation
Indices: 6291637--6291702 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
6291627 ATATGACTCA
* *
6291637 AAAATTTT-AAATCTTTTACCTACCATTAAGCCTC
1 AAAATTTTAAAATATTTTACCTACCATCAAGCCTC
6291671 AAAATTTTAAAATATTTTACCTACCATCAAGC
1 AAAATTTTAAAATATTTTACCTACCATCAAGC
6291703 AAAGTTAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 8 0.28
35 21 0.72
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.36
Consensus pattern (35 bp):
AAAATTTTAAAATATTTTACCTACCATCAAGCCTC
Found at i:6292139 original size:31 final size:33
Alignment explanation
Indices: 6292098--6292166 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
6292088 TAAATTATGC
6292098 AAAA-TAAACAAT-AAATC-ATCA-AATTATAAT
1 AAAATTAAACAATCAAATCAATCATAA-TATAAT
*
6292128 ATAATTAAACAATCAAATCAATCATAATATAAT
1 AAAATTAAACAATCAAATCAATCATAATATAAT
6292161 AAAATT
1 AAAATT
6292167 TGAATACAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 3 0.09
31 8 0.24
32 5 0.15
33 15 0.45
34 2 0.06
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (33 bp):
AAAATTAAACAATCAAATCAATCATAATATAAT
Found at i:6296280 original size:148 final size:149
Alignment explanation
Indices: 6296011--6296281 Score: 336
Period size: 148 Copynumber: 1.8 Consensus size: 149
6296001 AGGGGACTCA
* *
6296011 GGTGGACTGCCTCAGCTGCAGCACACCAGCTGCCCGACTGGCCACAGGGGCCTAGCAGCGTGCCT
1 GGTGGACTGCCTCAGCTGCAGCACACCA-C-GCCCGACTGGCCACAAGAGCCTAGCAGCGTGCCT
* ** *
6296076 GCCTGCTAGCCTGCGCATCCTCTCGGCTCAATGGCATCCCTCCTACATGCATACCATCGCGTGGT
64 GCCTGCTAGCCCGCGCATCCTCTCGGCTCAATGGCATCCCTCCTACATAAACACCATCGCGTGGT
6296141 CCATTCCCGCAAGGGTCCTTG
129 CCATTCCCGCAAGGGTCCTTG
* * *
6296162 GGTGGACTGCC-CTAGTTGCAGCCCACCA-GCCCGACTGGCCACAAGAGTCTAGCAGCGTGGCC-
1 GGTGGACTGCCTC-AGCTGCAGCACACCACGCCCGACTGGCCACAAGAGCCTAGCAGCGT-GCCT
* * * *
6296224 G-CTAGCTAGCCCGCGCATCC-CTTTGGCTCGATGGTATCCCTCCTACGTAAACACCATC
64 GCCT-GCTAGCCCGCGCATCCTC-TCGGCTCAATGGCATCCCTCCTACATAAACACCATC
6296282 ACCTGATCCT
Statistics
Matches: 103, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
147 3 0.03
148 72 0.70
149 3 0.03
150 1 0.01
151 24 0.23
ACGTcount: A:0.17, C:0.37, G:0.26, T:0.20
Consensus pattern (149 bp):
GGTGGACTGCCTCAGCTGCAGCACACCACGCCCGACTGGCCACAAGAGCCTAGCAGCGTGCCTGC
CTGCTAGCCCGCGCATCCTCTCGGCTCAATGGCATCCCTCCTACATAAACACCATCGCGTGGTCC
ATTCCCGCAAGGGTCCTTG
Found at i:6299311 original size:253 final size:253
Alignment explanation
Indices: 6298863--6299371 Score: 1018
Period size: 253 Copynumber: 2.0 Consensus size: 253
6298853 ACAAAATTTC
6298863 TAACCATTGAAATTGTAAGAGATACTTTCAACGATGACAAAACTGTGAATTTCTTAGGATTTCAA
1 TAACCATTGAAATTGTAAGAGATACTTTCAACGATGACAAAACTGTGAATTTCTTAGGATTTCAA
6298928 GATGCAGAATTAGAACTTTTCAAACTCATTGAACACTCTGCCTTTCAAACCCTCACCCCTTCCCC
66 GATGCAGAATTAGAACTTTTCAAACTCATTGAACACTCTGCCTTTCAAACCCTCACCCCTTCCCC
6298993 TTCACAATAGTTTCACATCTATATGATAGCAAAGAAACAAAAACCACCAGAACACATAATTCAGT
131 TTCACAATAGTTTCACATCTATATGATAGCAAAGAAACAAAAACCACCAGAACACATAATTCAGT
6299058 TCTCTTGTAACTCCAGGTCTAGGAGCTGCTGGACACATTCTTCGTTTCAGCAAACGAT
196 TCTCTTGTAACTCCAGGTCTAGGAGCTGCTGGACACATTCTTCGTTTCAGCAAACGAT
6299116 TAACCATTGAAATTGTAAGAGATACTTTCAACGATGACAAAACTGTGAATTTCTTAGGATTTCAA
1 TAACCATTGAAATTGTAAGAGATACTTTCAACGATGACAAAACTGTGAATTTCTTAGGATTTCAA
6299181 GATGCAGAATTAGAACTTTTCAAACTCATTGAACACTCTGCCTTTCAAACCCTCACCCCTTCCCC
66 GATGCAGAATTAGAACTTTTCAAACTCATTGAACACTCTGCCTTTCAAACCCTCACCCCTTCCCC
6299246 TTCACAATAGTTTCACATCTATATGATAGCAAAGAAACAAAAACCACCAGAACACATAATTCAGT
131 TTCACAATAGTTTCACATCTATATGATAGCAAAGAAACAAAAACCACCAGAACACATAATTCAGT
6299311 TCTCTTGTAACTCCAGGTCTAGGAGCTGCTGGACACATTCTTCGTTTCAGCAAACGAT
196 TCTCTTGTAACTCCAGGTCTAGGAGCTGCTGGACACATTCTTCGTTTCAGCAAACGAT
6299369 TAA
1 TAA
6299372 TCAAAGATGA
Statistics
Matches: 256, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
253 256 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.28
Consensus pattern (253 bp):
TAACCATTGAAATTGTAAGAGATACTTTCAACGATGACAAAACTGTGAATTTCTTAGGATTTCAA
GATGCAGAATTAGAACTTTTCAAACTCATTGAACACTCTGCCTTTCAAACCCTCACCCCTTCCCC
TTCACAATAGTTTCACATCTATATGATAGCAAAGAAACAAAAACCACCAGAACACATAATTCAGT
TCTCTTGTAACTCCAGGTCTAGGAGCTGCTGGACACATTCTTCGTTTCAGCAAACGAT
Found at i:6311015 original size:12 final size:12
Alignment explanation
Indices: 6310995--6311053 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
6310985 GATTTAGGTG
6310995 TATATATATAAA
1 TATATATATAAA
*
6311007 TATAAATATAAA
1 TATATATATAAA
* *
6311019 CATATATATATA
1 TATATATATAAA
* *
6311031 TACATAGATAAA
1 TATATATATAAA
*
6311043 -ATTTATATAAA
1 TATATATATAAA
6311054 ATTTTTAAAG
Statistics
Matches: 36, Mismatches: 11, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
11 8 0.22
12 28 0.78
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (12 bp):
TATATATATAAA
Found at i:6311079 original size:23 final size:25
Alignment explanation
Indices: 6311040--6311085 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
6311030 ATACATAGAT
6311040 AAAATTTATATAAAATTTTTAAAGG
1 AAAATTTATATAAAATTTTTAAAGG
6311065 AAAATTT-T-TAAAATTTTTAAA
1 AAAATTTATATAAAATTTTTAAA
6311086 ATAATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.62
24 1 0.05
25 7 0.33
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
AAAATTTATATAAAATTTTTAAAGG
Found at i:6330807 original size:30 final size:30
Alignment explanation
Indices: 6330765--6330829 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
6330755 AAAATATATC
6330765 AATAAGAATTATATATATTAATAGATAAAT
1 AATAAGAATTATATATATTAATAGATAAAT
6330795 AATAA-AATTTATATATATTAATAGATAAAT
1 AATAAGAA-TTATATATATTAATAGATAAAT
*
6330825 GATAA
1 AATAA
6330830 TATATATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 2 0.06
30 31 0.94
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (30 bp):
AATAAGAATTATATATATTAATAGATAAAT
Found at i:6330837 original size:24 final size:23
Alignment explanation
Indices: 6330742--6330869 Score: 82
Period size: 23 Copynumber: 5.3 Consensus size: 23
6330732 AAATGAATAG
* *
6330742 ATAAATAATAAATAAAATATATCA
1 ATAAATAAT-AATAATATATATTA
* * *
6330766 AT-AAGAATTAT-ATATATTAATA
1 ATAAATAATAATAATATA-TATTA
*
6330788 GATAAATAATAAAATTTATATATATTA
1 -ATAAATAAT--AA-TAATATATATTA
* *
6330815 ATAGATAAATGATAATATATATTA
1 ATAAAT-AATAATAATATATATTA
*
6330839 ATAAATAATAATAATAGTA-ATAA
1 ATAAATAATAATAATA-TATATTA
6330862 ATAAATAA
1 ATAAATAA
6330870 GATATAAAAT
Statistics
Matches: 81, Mismatches: 14, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
21 4 0.05
22 5 0.06
23 27 0.33
24 25 0.31
25 1 0.01
26 6 0.07
27 8 0.10
28 5 0.06
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (23 bp):
ATAAATAATAATAATATATATTA
Found at i:6330864 original size:23 final size:21
Alignment explanation
Indices: 6330807--6330888 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 21
6330797 TAAAATTTAT
* *
6330807 ATATATTAATAGATAAATGATA
1 ATATA-TAATAAATAAATAATA
*
6330829 ATATAT-ATTAATAAATAATA
1 ATATATAATAAATAAATAATA
*
6330849 ATAATAGTAATAAATAAATAA-G
1 AT-ATA-TAATAAATAAATAATA
*
6330871 ATATAAAATAAAATAAAT
1 ATATATAAT-AAATAAAT
6330889 TTAACTATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 16 0.32
21 15 0.30
22 8 0.16
23 11 0.22
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
ATATATAATAAATAAATAATA
Found at i:6330877 original size:54 final size:54
Alignment explanation
Indices: 6330775--6330877 Score: 118
Period size: 54 Copynumber: 1.9 Consensus size: 54
6330765 AATAAGAATT
* * * * * *
6330775 ATATATATTAATAGATAAATAATAAAATTTATATATATTAATAGATAAATGATA
1 ATATATATTAATAAATAAATAATAAAAGTAATAAATAATAAGAGATAAATGATA
* *
6330829 ATATATATTAATAAAT-AATAATAATAGTAATAAATAAATAAGATATAAA
1 ATATATATTAATAAATAAATAATAAAAGTAATAAAT-AATAAGAGATAAA
6330878 ATAAAATAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
53 15 0.38
54 25 0.62
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (54 bp):
ATATATATTAATAAATAAATAATAAAAGTAATAAATAATAAGAGATAAATGATA
Found at i:6338810 original size:18 final size:18
Alignment explanation
Indices: 6338783--6338834 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 18
6338773 TTAACGAAAT
*
6338783 TAAAAATAATAATTAAAA
1 TAAAATTAATAATTAAAA
*
6338801 TAAAATTAATTATT---A
1 TAAAATTAATAATTAAAA
6338816 TAAAATTAATAA-TAAAA
1 TAAAATTAATAATTAAAA
6338833 TA
1 TA
6338835 TGTATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 1 0.04
15 12 0.43
17 3 0.11
18 12 0.43
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATTAATAATTAAAA
Found at i:6338947 original size:10 final size:10
Alignment explanation
Indices: 6338920--6338952 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
6338910 ATAATAATAA
6338920 ATTATTTATAT
1 ATTATTTA-AT
6338931 ATT-TTTAAT
1 ATTATTTAAT
6338940 ATTATTTAAT
1 ATTATTTAAT
6338950 ATT
1 ATT
6338953 TAAAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.24
10 13 0.62
11 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTATTTAAT
Found at i:6338963 original size:19 final size:20
Alignment explanation
Indices: 6338920--6338964 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
6338910 ATAATAATAA
**
6338920 ATTATTTATATATTTTTAAT
1 ATTATTTATATATTTAAAAT
6338940 ATTATTTA-ATATTTAAAAT
1 ATTATTTATATATTTAAAAT
*
6338959 TTTATT
1 ATTATT
6338965 GAAACATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTATTTATATATTTAAAAT
Found at i:6339731 original size:30 final size:29
Alignment explanation
Indices: 6339686--6339756 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 29
6339676 TAAATATAAT
*
6339686 TTTTATTTGATTTGATTTGATTCGAATCGAA
1 TTTTA-TTAATTTGATTTGATTCG-ATCGAA
*
6339717 TTTTATTAATTTGATTTGATTCGATCTAA
1 TTTTATTAATTTGATTTGATTCGATCGAA
6339746 -TTTATTAATTT
1 TTTTATTAATTT
6339757 TTAAATTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 11 0.29
29 5 0.13
30 17 0.45
31 5 0.13
ACGTcount: A:0.27, C:0.06, G:0.11, T:0.56
Consensus pattern (29 bp):
TTTTATTAATTTGATTTGATTCGATCGAA
Found at i:6343941 original size:221 final size:222
Alignment explanation
Indices: 6343513--6343951 Score: 684
Period size: 221 Copynumber: 2.0 Consensus size: 222
6343503 AGCAGAGTTA
*
6343513 TTTACACATGGAATCTTTATTCATATGTTGACAACCTTTTCTAAAGGACGTAAATTTGTTGGATT
1 TTTACACATGGAATATTTATTCATATGTTGACAACCTTTTCTAAAGGACGTAAATTTGTTGGATT
* * *
6343578 TTATATCTTGCAATTGAAAATTGATATCCTGTATTTGCAAGAGTGCCCCATAAAAGTATCTCTAT
66 TTATATCCTACAATTGAAAATTGATATCCTGTATGTGCAAGAGTGCCCCATAAAAGTATCTCTAT
* *
6343643 GCTTTCTCTCAGTGACTTGTACTATATTTTGACATGTAATGTTTTTCAGCTTAAAAACTATAGAG
131 GCTTTCTCTCAGTGACTTGTACTATATTTTGAAATGTAATATTTTTCAGCTTAAAAACTATAGAG
*
6343708 AAGCTATAGTCAACTCTTATCTTAGTG
196 AAGCTATAGTCAACTCTGATCTTAGTG
* * * *
6343735 TTTACGCATGGAATATTTATTCATATGTTGACTATCTTTTCTAAAGGAGGTAAATTTGTTGGA-T
1 TTTACACATGGAATATTTATTCATATGTTGACAACCTTTTCTAAAGGACGTAAATTTGTTGGATT
* * *
6343799 TTATATCCTACTATTGAAAATTGATATCCTGTATGTGCAAGAGTGCCCCATGAAAGTATCTGTAT
66 TTATATCCTACAATTGAAAATTGATATCCTGTATGTGCAAGAGTGCCCCATAAAAGTATCTCTAT
** *
6343864 GC-TTCTCTCAGTGACTTGTACTATATTTTGAAATGTAATATTTTTCAGCTTAAAGGCTATGGAG
131 GCTTTCTCTCAGTGACTTGTACTATATTTTGAAATGTAATATTTTTCAGCTTAAAAACTATAGAG
* *
6343928 AAAGCTGTAGTCAATTCTGATCTT
196 -AAGCTATAGTCAACTCTGATCTT
6343952 GGTATGACTC
Statistics
Matches: 197, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
220 57 0.29
221 82 0.42
222 58 0.29
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (222 bp):
TTTACACATGGAATATTTATTCATATGTTGACAACCTTTTCTAAAGGACGTAAATTTGTTGGATT
TTATATCCTACAATTGAAAATTGATATCCTGTATGTGCAAGAGTGCCCCATAAAAGTATCTCTAT
GCTTTCTCTCAGTGACTTGTACTATATTTTGAAATGTAATATTTTTCAGCTTAAAAACTATAGAG
AAGCTATAGTCAACTCTGATCTTAGTG
Found at i:6360948 original size:8 final size:8
Alignment explanation
Indices: 6360916--6360946 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
6360906 TTGCAAGTTA
6360916 TCCAGAAC
1 TCCAGAAC
6360924 TCCAGAAC
1 TCCAGAAC
*
6360932 TCCAGAAT
1 TCCAGAAC
6360940 TCCAGAA
1 TCCAGAA
6360947 TTTAGAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.39, C:0.32, G:0.13, T:0.16
Consensus pattern (8 bp):
TCCAGAAC
Found at i:6361874 original size:2 final size:2
Alignment explanation
Indices: 6361867--6361898 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6361857 CAATCAATCT
6361867 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6361899 ATGGATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6366231 original size:2 final size:2
Alignment explanation
Indices: 6366219--6366258 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
6366209 CTTCTTCCAT
*
6366219 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6366259 AGAAAATCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6368195 original size:18 final size:18
Alignment explanation
Indices: 6368174--6368213 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
6368164 CAAGATTTCT
6368174 TTTTTC-ATTTTCATTTTA
1 TTTTTCGATTTTCA-TTTA
6368192 TTTTTCGATTTTCATTTA
1 TTTTTCGATTTTCATTTA
6368210 TTTT
1 TTTT
6368214 CATGTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.15, C:0.10, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTTCGATTTTCATTTA
Found at i:6369145 original size:39 final size:39
Alignment explanation
Indices: 6369092--6369172 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
6369082 TAAATTTGAG
* *
6369092 ATTTTTTTTAATTGCTCGTACTTGCTTAATTATTTATTT
1 ATTTCTTTTAATTGCTCATACTTGCTTAATTATTTATTT
* *
6369131 ATTTCTTTTCATTGCTTATACTTGCTTAATTATTTATTT
1 ATTTCTTTTAATTGCTCATACTTGCTTAATTATTTATTT
6369170 ATT
1 ATT
6369173 GTATCTGTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.21, C:0.11, G:0.06, T:0.62
Consensus pattern (39 bp):
ATTTCTTTTAATTGCTCATACTTGCTTAATTATTTATTT
Found at i:6372181 original size:193 final size:193
Alignment explanation
Indices: 6371852--6372239 Score: 686
Period size: 193 Copynumber: 2.0 Consensus size: 193
6371842 AAGAAGAAGC
* * *
6371852 ATGTTGAACCAGAAGAGATTCCAAAGAAAGACACTTTAAAGTCTGTGTCAGAAAAGAAGGCTTAT
1 ATGTTGAACCAGAAGAGATTCAAAAAAAAGACACTTTAAAATCTGTGTCAGAAAAGAAGGCTTAT
*
6371917 GAGTTTTTAACGCTAGTAAAGCATAGTAAATACTTTGTAGTGGAGTAATTAAATAAGATACCAGC
66 GAGTTTTTAACGCTAGTAAAGCATAGTAAATACTCTGTAGTGGAGTAATTAAATAAGATACCAGC
*
6371982 CAAAATCTCTTCTTTGTCACTTTTTTTGAACTCAAAACCACATTGTAATTTCTTATTAAAAGT
131 CAAAATCTCTTCTTTGTCACTTCTTTTGAACTCAAAACCACATTGTAATTTCTTATTAAAAGT
* * *
6372045 ATGTTGAACCAGAAGAGATTTAAAAAAAAGACACTTTAAAATTTGTGTCAGAAAAGGAGGCTTAT
1 ATGTTGAACCAGAAGAGATTCAAAAAAAAGACACTTTAAAATCTGTGTCAGAAAAGAAGGCTTAT
6372110 GAGTTTTTAACGCTAGTAAAGCATAGTAAATACTCTGTAGTGGAGTAATTAAATAAGATACCAGC
66 GAGTTTTTAACGCTAGTAAAGCATAGTAAATACTCTGTAGTGGAGTAATTAAATAAGATACCAGC
* *
6372175 CAAAATCTTTTCTTTGTCACTTCTTTTGAACTCAAAATCACATTGTAATTTCTTATTAAAAGT
131 CAAAATCTCTTCTTTGTCACTTCTTTTGAACTCAAAACCACATTGTAATTTCTTATTAAAAGT
6372238 AT
1 AT
6372240 TAAATCAAGT
Statistics
Matches: 185, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
193 185 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (193 bp):
ATGTTGAACCAGAAGAGATTCAAAAAAAAGACACTTTAAAATCTGTGTCAGAAAAGAAGGCTTAT
GAGTTTTTAACGCTAGTAAAGCATAGTAAATACTCTGTAGTGGAGTAATTAAATAAGATACCAGC
CAAAATCTCTTCTTTGTCACTTCTTTTGAACTCAAAACCACATTGTAATTTCTTATTAAAAGT
Found at i:6377257 original size:22 final size:22
Alignment explanation
Indices: 6377229--6377312 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 22
6377219 ATAAGTTCAA
6377229 AAATAAAATAAATAAAATAGAT
1 AAATAAAATAAATAAAATAGAT
*
6377251 AAATAAAATTAAAAAAAATCAAAGAT
1 AAATAAAA-TAAATAAAAT---AGAT
*
6377277 AAAACTAAAA-AATATAAAATAAAT
1 -AAA-TAAAATAA-ATAAAATAGAT
6377301 AAAT-AAATAAAT
1 AAATAAAATAAAT
6377313 GGAAAGGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 17
0.72 0.04 0.24
Matches are distributed among these distances:
21 5 0.10
22 11 0.22
23 12 0.24
24 3 0.06
26 6 0.12
27 9 0.18
28 5 0.10
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (22 bp):
AAATAAAATAAATAAAATAGAT
Found at i:6377293 original size:15 final size:15
Alignment explanation
Indices: 6377231--6377305 Score: 68
Period size: 15 Copynumber: 5.1 Consensus size: 15
6377221 AAGTTCAAAA
6377231 ATAAAATAAATAAA-
1 ATAAAATAAATAAAT
*
6377245 AT-AGATAAATAAA-
1 ATAAAATAAATAAAT
* *
6377258 ATTAAAAAAAATCAAAG
1 A-TAAAATAAAT-AAAT
6377275 ATAAAACTAAA-AAAT
1 ATAAAA-TAAATAAAT
6377290 ATAAAATAAATAAAT
1 ATAAAATAAATAAAT
6377305 A
1 A
6377306 AATAAATGGA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
13 11 0.22
14 7 0.14
15 20 0.40
16 8 0.16
17 4 0.08
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (15 bp):
ATAAAATAAATAAAT
Found at i:6378246 original size:21 final size:21
Alignment explanation
Indices: 6378220--6378479 Score: 157
Period size: 21 Copynumber: 12.1 Consensus size: 21
6378210 TTCACACTTT
6378220 AAAGATTCTCATTTGAAATTC
1 AAAGATTCTCATTTGAAATTC
6378241 AAAGATTCTCATTT-AAGATTC
1 AAAGATTCTCATTTGAA-ATTC
6378262 AAAGATTCTCATTTGAAAATGTC
1 AAAGATTCTCATTTG-AAAT-TC
* *
6378285 TTAAAGATTTTTATTTGAAAATGTC
1 --AAAGATTCTCATTTG-AAAT-TC
*
6378310 TTAAAGATTCTCATTT-AAGACTC
1 --AAAGATTCTCATTTGAA-ATTC
6378333 AAAGATTCTCATTTGAAAATGTC
1 AAAGATTCTCATTTG-AAAT-TC
* * *
6378356 TTAAAAATTTTCATTT-AAGACTC
1 --AAAGATTCTCATTTGAA-ATTC
6378379 AAAGATTCTCATTTG------
1 AAAGATTCTCATTTGAAATTC
* * * *
6378394 -AGGATTTCTTATTTAAAACTC
1 AAAGA-TTCTCATTTGAAATTC
* *
6378415 AAATATTCTCATTTGACACTT-
1 AAAGATTCTCATTTGA-AATTC
* *
6378436 AAAGATTTTCATTTAAAATTC
1 AAAGATTCTCATTTGAAATTC
6378457 AAAGATTCTCATTTG-AATTC
1 AAAGATTCTCATTTGAAATTC
6378477 AAA
1 AAA
6378480 TTTTCATCAA
Statistics
Matches: 189, Mismatches: 26, Indels: 49
0.72 0.10 0.19
Matches are distributed among these distances:
14 3 0.02
15 8 0.04
20 13 0.07
21 93 0.49
22 7 0.04
23 16 0.08
24 2 0.01
25 47 0.25
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (21 bp):
AAAGATTCTCATTTGAAATTC
Found at i:6378300 original size:25 final size:25
Alignment explanation
Indices: 6378218--6378394 Score: 161
Period size: 21 Copynumber: 7.7 Consensus size: 25
6378208 GTTTCACACT
6378218 TTAAAGATTCTCATTTG-AAAT-TC
1 TTAAAGATTCTCATTTGAAAATGTC
*
6378241 --AAAGATTCTCATTT-AAGAT-TC
1 TTAAAGATTCTCATTTGAAAATGTC
6378262 --AAAGATTCTCATTTGAAAATGTC
1 TTAAAGATTCTCATTTGAAAATGTC
* *
6378285 TTAAAGATTTTTATTTGAAAATGTC
1 TTAAAGATTCTCATTTGAAAATGTC
*
6378310 TTAAAGATTCTCATTT---AA-GAC
1 TTAAAGATTCTCATTTGAAAATGTC
*
6378331 TCAAAGATTCTCATTTGAAAATGTC
1 TTAAAGATTCTCATTTGAAAATGTC
* * *
6378356 TTAAAAATTTTCATTT---AA-GAC
1 TTAAAGATTCTCATTTGAAAATGTC
*
6378377 TCAAAGATTCTCATTTGA
1 TTAAAGATTCTCATTTGA
6378395 GGATTTCTTA
Statistics
Matches: 127, Mismatches: 16, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
21 65 0.51
22 8 0.06
23 2 0.02
24 2 0.02
25 50 0.39
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.40
Consensus pattern (25 bp):
TTAAAGATTCTCATTTGAAAATGTC
Found at i:6378328 original size:71 final size:67
Alignment explanation
Indices: 6378218--6378392 Score: 253
Period size: 71 Copynumber: 2.6 Consensus size: 67
6378208 GTTTCACACT
* *
6378218 TTAAAGATTCTCATTTGAAATTCAAAGATTCTCATTTAAGATTCAAAGATTCTCATTTGAAAATG
1 TTAAAGATTTTCATTTGAAATTCAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATG
6378283 TC
66 TC
*
6378285 TTAAAGATTTTTATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAA
1 TTAAAGATTTTCATTTG-AAAT-TC--AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAA
6378350 AATGTC
62 AATGTC
* *
6378356 TTAAAAATTTTCATTT-AAGACTCAAAGATTCTCATTT
1 TTAAAGATTTTCATTTGAA-ATTCAAAGATTCTCATTT
6378393 GAGGATTTCT
Statistics
Matches: 97, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
67 29 0.30
68 4 0.04
69 6 0.06
70 1 0.01
71 57 0.59
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (67 bp):
TTAAAGATTTTCATTTGAAATTCAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATG
TC
Found at i:6378338 original size:46 final size:47
Alignment explanation
Indices: 6378218--6378394 Score: 197
Period size: 46 Copynumber: 3.9 Consensus size: 47
6378208 GTTTCACACT
* * *
6378218 TTAAAGATTCTCATTTGAA-ATTCAAAGATTCTCATTT-AAGAT-TC
1 TTAAAGATTCTCATTTAAAGACTCAAAGATTCTCATTTGAAAATGTC
* * * *
6378262 --AAAGATTCTCATTTGAAAATGTCTTAAAGATTTTTATTTGAAAATGTC
1 TTAAAGATTCTCATTT--AAA-GACTCAAAGATTCTCATTTGAAAATGTC
6378310 TTAAAGATTCTCATTT-AAGACTCAAAGATTCTCATTTGAAAATGTC
1 TTAAAGATTCTCATTTAAAGACTCAAAGATTCTCATTTGAAAATGTC
* *
6378356 TTAAAAATTTTCATTT-AAGACTCAAAGATTCTCATTTGA
1 TTAAAGATTCTCATTTAAAGACTCAAAGATTCTCATTTGA
6378395 GGATTTCTTA
Statistics
Matches: 112, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
42 14 0.12
44 2 0.02
46 74 0.66
47 6 0.05
48 2 0.02
50 14 0.12
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.40
Consensus pattern (47 bp):
TTAAAGATTCTCATTTAAAGACTCAAAGATTCTCATTTGAAAATGTC
Found at i:6378461 original size:78 final size:80
Alignment explanation
Indices: 6378317--6378472 Score: 217
Period size: 78 Copynumber: 1.9 Consensus size: 80
6378307 GTCTTAAAGA
* *
6378317 TTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTTAAAAATTTTCATTTAAGACTCAAA
1 TTCTCATTTAAAACTCAAAGATTCTCATTTGAAAA--TCTTAAAAATTTTCATTTAAAACTCAAA
6378382 GATTCTCATTTGAGGAT
64 GATTCTCATTTGAGGAT
* * * * *
6378399 TTCTTATTTAAAACTCAAATATTCTCATTTG-ACA-CTTAAAGATTTTCATTTAAAATTCAAAGA
1 TTCTCATTTAAAACTCAAAGATTCTCATTTGAAAATCTTAAAAATTTTCATTTAAAACTCAAAGA
6378462 TTCTCATTTGA
66 TTCTCATTTGA
6378473 ATTCAAATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
78 37 0.55
81 2 0.03
82 28 0.42
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (80 bp):
TTCTCATTTAAAACTCAAAGATTCTCATTTGAAAATCTTAAAAATTTTCATTTAAAACTCAAAGA
TTCTCATTTGAGGAT
Found at i:6379737 original size:21 final size:21
Alignment explanation
Indices: 6379712--6379759 Score: 73
Period size: 19 Copynumber: 2.3 Consensus size: 21
6379702 CCTCATTTTC
6379712 TTTCTTTTCCATTTTTCTC-TT
1 TTTCTTTT-CATTTTTCTCTTT
6379733 TTTC-TTTCATTTTTCTCTTT
1 TTTCTTTTCATTTTTCTCTTT
6379753 TTTCTTT
1 TTTCTTT
6379760 CCTTCATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.40
20 9 0.36
21 6 0.24
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTCTTTTCATTTTTCTCTTT
Found at i:6386694 original size:11 final size:10
Alignment explanation
Indices: 6386669--6386693 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6386659 TCGAATTCTG
6386669 AAAAATTTTC
1 AAAAATTTTC
6386679 AAAAATTTTC
1 AAAAATTTTC
6386689 AAAAA
1 AAAAA
6386694 AAAAAACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAAATTTTC
Found at i:6390378 original size:12 final size:12
Alignment explanation
Indices: 6390361--6390493 Score: 84
Period size: 12 Copynumber: 11.3 Consensus size: 12
6390351 TACAATATAA
6390361 TATTATTAGTAT
1 TATTATTAGTAT
6390373 TATTA-TAGTA-
1 TATTATTAGTAT
*
6390383 TAGTATATAGTA-
1 TATTAT-TAGTAT
*
6390395 TAATACCTTA-TAT
1 TATTA--TTAGTAT
6390408 TATATATTA-TAT
1 TAT-TATTAGTAT
6390420 TA-TATTA-TCAT
1 TATTATTAGT-AT
* * * *
6390431 CATCATCATTAT
1 TATTATTAGTAT
*
6390443 TATTATTATTAT
1 TATTATTAGTAT
*
6390455 TATTATTATTAT
1 TATTATTAGTAT
6390467 TATTATT-GTAT
1 TATTATTAGTAT
*
6390478 TATTATTATTAT
1 TATTATTAGTAT
6390490 TATT
1 TATT
6390494 TTATTTTATT
Statistics
Matches: 100, Mismatches: 11, Indels: 20
0.76 0.08 0.15
Matches are distributed among these distances:
10 10 0.10
11 18 0.18
12 64 0.64
13 5 0.05
14 3 0.03
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (12 bp):
TATTATTAGTAT
Found at i:6390444 original size:3 final size:3
Alignment explanation
Indices: 6390405--6390513 Score: 111
Period size: 3 Copynumber: 37.3 Consensus size: 3
6390395 TAATACCTTA
* * * *
6390405 TAT TAT ATAT TA- TAT TA- TAT TAT CAT CAT CAT CAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
6390449 TAT TAT TAT TAT TAT TAT TAT TAT T-G TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
6390495 TAT T-T TATT TAT TGT TAT T
1 TAT TAT TA-T TAT TAT TAT T
6390514 TATTTACTTT
Statistics
Matches: 93, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
2 9 0.10
3 78 0.84
4 6 0.06
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:6390519 original size:23 final size:24
Alignment explanation
Indices: 6390438--6390524 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 24
6390428 CATCATCATC
6390438 ATTATTATTATTATTA-TTATTA-TT
1 ATTATTATTATT-TTACTT-TTATTT
*
6390462 ATTATTATTATTGTA---TTA-TT
1 ATTATTATTATTTTACTTTTATTT
6390482 ATTATTATTATTTTA-TTTTATTT
1 ATTATTATTATTTTACTTTTATTT
*
6390505 ATTGTTATT-TATTTACTTTT
1 ATTATTATTAT-TTTACTTTT
6390525 TTTTCATGTT
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
20 19 0.35
22 4 0.07
23 16 0.29
24 16 0.29
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.69
Consensus pattern (24 bp):
ATTATTATTATTTTACTTTTATTT
Found at i:6391332 original size:19 final size:18
Alignment explanation
Indices: 6391310--6391390 Score: 64
Period size: 18 Copynumber: 4.6 Consensus size: 18
6391300 TCCTTTTTCT
6391310 TTTTCATTTTATTTTTTGA
1 TTTTCATTTTATTTTTT-A
* *
6391329 TTTTCA-TTTATTTTCATG
1 TTTTCATTTTATTTT-TTA
*
6391347 TTTTAAGTTTTA--TTTTA
1 TTTTCA-TTTTATTTTTTA
*
6391364 TTTTCATTTT-TTTATTA
1 TTTTCATTTTATTTTTTA
6391381 TTTT-ATTTTA
1 TTTTCATTTTA
6391391 CTAGTTTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
16 9 0.18
17 14 0.29
18 15 0.31
19 7 0.14
20 4 0.08
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.73
Consensus pattern (18 bp):
TTTTCATTTTATTTTTTA
Found at i:6391350 original size:18 final size:19
Alignment explanation
Indices: 6391310--6391390 Score: 61
Period size: 17 Copynumber: 4.6 Consensus size: 19
6391300 TCCTTTTTCT
*
6391310 TTTTCATTTTATTTTTTGA
1 TTTTCATTTTATTTTATGA
6391329 TTTTCA-TTTATTTTCATG-
1 TTTTCATTTTATTTT-ATGA
*
6391347 TTTTAAGTTTTA-TTT-T-A
1 TTTTCA-TTTTATTTTATGA
*
6391364 TTTTCA-TTT-TTTTATTA
1 TTTTCATTTTATTTTATGA
6391381 TTTT-ATTTTA
1 TTTTCATTTTA
6391391 CTAGTTTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 19
0.69 0.04 0.26
Matches are distributed among these distances:
15 6 0.12
16 2 0.04
17 14 0.28
18 13 0.26
19 11 0.22
20 4 0.08
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.73
Consensus pattern (19 bp):
TTTTCATTTTATTTTATGA
Found at i:6391350 original size:25 final size:25
Alignment explanation
Indices: 6391310--6391375 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
6391300 TCCTTTTTCT
*
6391310 TTTTCATTTT-ATTTTTTGA-TTTTCA
1 TTTT-ATTTTCATTTTTTAAGTTTT-A
*
6391335 -TTTATTTTCATGTTTTAAGTTTTA
1 TTTTATTTTCATTTTTTAAGTTTTA
6391359 TTTTATTTTCATTTTTT
1 TTTTATTTTCATTTTTT
6391376 TATTATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
23 5 0.14
24 11 0.31
25 19 0.54
ACGTcount: A:0.17, C:0.06, G:0.05, T:0.73
Consensus pattern (25 bp):
TTTTATTTTCATTTTTTAAGTTTTA
Found at i:6391384 original size:22 final size:23
Alignment explanation
Indices: 6391354--6391406 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
6391344 ATGTTTTAAG
*
6391354 TTTTATTTTATTTT-C-ATTTTT
1 TTTTATTTTATTTTACTAGTTTT
6391375 TTATTATTTTATTTTACTAGTTTT
1 TT-TTATTTTATTTTACTAGTTTT
6391399 TTTTATTT
1 TTTTATTT
6391407 CATATAGCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 2 0.07
22 12 0.43
23 7 0.25
24 7 0.25
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTTATTTTATTTTACTAGTTTT
Found at i:6396546 original size:5 final size:5
Alignment explanation
Indices: 6396537--6396571 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
6396527 TTTGTTTATC
*
6396537 ATAAT CTAAT ATAAT ATAAT ATAAT ATAAT -TAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
6396572 AACAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:6396721 original size:29 final size:30
Alignment explanation
Indices: 6396682--6396753 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
6396672 AAATAATTAT
6396682 TTAAACTTTTATTAT-TTTATTATAATCAA
1 TTAAACTTTTATTATATTTATTATAATCAA
* * *
6396711 TTAAA-TCTTTA-AATATTTATTTTCATCAA
1 TTAAACT-TTTATTATATTTATTATAATCAA
6396740 TTAAACTTTTATTA
1 TTAAACTTTTATTA
6396754 GATTAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
28 3 0.09
29 30 0.86
30 2 0.06
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (30 bp):
TTAAACTTTTATTATATTTATTATAATCAA
Found at i:6396846 original size:30 final size:31
Alignment explanation
Indices: 6396794--6396867 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
6396784 TTCCCTGCAG
*
6396794 TAAAAATTTAATTGGAATAAAAATAGATGTT
1 TAAAAATTTAATTGGAATAAAAATAGATATT
* *
6396825 TAAAACTTTAATT-GTATAAAAATAGATATT
1 TAAAAATTTAATTGGAATAAAAATAGATATT
* *
6396855 GAAAATTTTAATT
1 TAAAAATTTAATT
6396868 AATCTAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 26 0.68
31 12 0.32
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.39
Consensus pattern (31 bp):
TAAAAATTTAATTGGAATAAAAATAGATATT
Found at i:6399005 original size:22 final size:22
Alignment explanation
Indices: 6398977--6399018 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
6398967 ATGACGTGAT
6398977 ATTATATGTAAA-AAAAAATACC
1 ATTATATG-AAATAAAAAATACC
6398999 ATTATATGAAATAAAAAATA
1 ATTATATGAAATAAAAAATA
6399019 TCATGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (22 bp):
ATTATATGAAATAAAAAATACC
Found at i:6404814 original size:17 final size:17
Alignment explanation
Indices: 6404781--6404814 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
6404771 CAAAATATGG
6404781 CTTATGATGAGATAAGA
1 CTTATGATGAGATAAGA
6404798 CTTATTGATGAGA-AAGA
1 CTTA-TGATGAGATAAGA
6404815 AAATCAGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (17 bp):
CTTATGATGAGATAAGA
Found at i:6406256 original size:51 final size:51
Alignment explanation
Indices: 6406170--6406271 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
6406160 ACTATCGACA
* * *
6406170 CCCATTTGTGTTCAGGCCCAATTAAGCCTACTTGTGTCCA-GCCCAATTAGG
1 CCCATCTGTGTCCAAGCCCAATTAAGCCTACTTGTGT-CAGGCCCAATTAGG
*
6406221 CCCATCTGTGTCCAAGCCCAATT-AGACCTATTTGTGTCAGGGCCCAATTAG
1 CCCATCTGTGTCCAAGCCCAATTAAG-CCTACTTGTGTCA-GGCCCAATTAG
6406272 ACAGTTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
50 4 0.09
51 30 0.68
52 10 0.23
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (51 bp):
CCCATCTGTGTCCAAGCCCAATTAAGCCTACTTGTGTCAGGCCCAATTAGG
Found at i:6406272 original size:26 final size:26
Alignment explanation
Indices: 6406173--6406273 Score: 109
Period size: 26 Copynumber: 3.9 Consensus size: 26
6406163 ATCGACACCC
*
6406173 ATTTGTGTTCAGGCCCAATTA-AGCCT
1 ATTTGTGTCCAGGCCCAATTAGA-CCT
* * *
6406199 ACTTGTGTCCA-GCCCAATTAGGCCC
1 ATTTGTGTCCAGGCCCAATTAGACCT
* *
6406224 ATCTGTGTCCAAGCCCAATTAGACCT
1 ATTTGTGTCCAGGCCCAATTAGACCT
6406250 ATTTGTGT-CAGGGCCCAATTAGAC
1 ATTTGTGTCCA-GGCCCAATTAGAC
6406274 AGTTTTTTAT
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
25 22 0.35
26 40 0.65
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (26 bp):
ATTTGTGTCCAGGCCCAATTAGACCT
Found at i:6406337 original size:25 final size:25
Alignment explanation
Indices: 6406289--6406337 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
6406279 TTTATGAATT
* * *
6406289 ATTATTATATTACATTGTTGTTATC
1 ATTATTATATCACATTATTATTATC
*
6406314 ATTATTATATCATATTATTATTAT
1 ATTATTATATCACATTATTATTAT
6406338 TATTTTTTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (25 bp):
ATTATTATATCACATTATTATTATC
Found at i:6407206 original size:19 final size:19
Alignment explanation
Indices: 6407182--6407225 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
6407172 CTCGATCGCA
*
6407182 AATTTTCCTTTTTTGATTT
1 AATTTTCATTTTTTGATTT
*
6407201 AATTTTTATTTTTTGATTT
1 AATTTTCATTTTTTGATTT
*
6407220 TATTTT
1 AATTTT
6407226 ATATTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.73
Consensus pattern (19 bp):
AATTTTCATTTTTTGATTT
Found at i:6407213 original size:20 final size:20
Alignment explanation
Indices: 6407190--6407232 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
6407180 CAAATTTTCC
6407190 TTTTTTGATTTAATTTT-TA
1 TTTTTTGATTTAATTTTATA
*
6407209 TTTTTTGATTTTATTTTATA
1 TTTTTTGATTTAATTTTATA
6407229 TTTT
1 TTTT
6407233 AATCCATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTTTTGATTTAATTTTATA
Found at i:6407449 original size:17 final size:18
Alignment explanation
Indices: 6407415--6407450 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6407405 AAAAAGATAT
*
6407415 AAAAAAATCTTTTTCAAA
1 AAAAAAATCTTTTACAAA
6407433 AAAAAAATC-TTTACAAA
1 AAAAAAATCTTTTACAAA
6407450 A
1 A
6407451 TAAATTTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAAAATCTTTTACAAA
Found at i:6407836 original size:20 final size:20
Alignment explanation
Indices: 6407811--6407850 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
6407801 ATCAATTGGG
6407811 TGAGCATTGTAAGAGTGCTA
1 TGAGCATTGTAAGAGTGCTA
6407831 TGAGCATTGTAAGAGTGCTA
1 TGAGCATTGTAAGAGTGCTA
6407851 CAACCTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (20 bp):
TGAGCATTGTAAGAGTGCTA
Found at i:6409088 original size:2 final size:2
Alignment explanation
Indices: 6409081--6409114 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6409071 ATGTATGTGC
6409081 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6409115 GTATGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6410635 original size:2 final size:2
Alignment explanation
Indices: 6410630--6410662 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
6410620 AAAAAATGGA
*
6410630 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6410663 GGAAAGAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:6411904 original size:27 final size:27
Alignment explanation
Indices: 6411874--6411925 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
6411864 AGAAAGGATA
* *
6411874 GAGAAGAAGGGGGAGGAGGAGAGGACG
1 GAGAAGAAGGCGGAGGAGAAGAGGACG
* *
6411901 GAGAAGGAGGCGGAGGTGAAGAGGA
1 GAGAAGAAGGCGGAGGAGAAGAGGA
6411926 ATTGAGTGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.58, T:0.02
Consensus pattern (27 bp):
GAGAAGAAGGCGGAGGAGAAGAGGACG
Found at i:6413080 original size:32 final size:32
Alignment explanation
Indices: 6413041--6413104 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
6413031 TATCAAGGTT
6413041 TTGTCAACCATATTTCATTTCTTTTATTCTTA
1 TTGTCAACCATATTTCATTTCTTTTATTCTTA
6413073 TTGTCAACCATATTTCATTTCTTTTATTCTTA
1 TTGTCAACCATATTTCATTTCTTTTATTCTTA
6413105 CTTCCTGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.19, G:0.03, T:0.56
Consensus pattern (32 bp):
TTGTCAACCATATTTCATTTCTTTTATTCTTA
Found at i:6416370 original size:26 final size:25
Alignment explanation
Indices: 6416338--6416393 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
6416328 AAAAATTTGT
*
6416338 AAATTTTT-TATTAAAAAATTTAATA
1 AAATTTTTAAATTAAAAAA-TTAATA
*
6416363 AAATTTTTAAATTAATAAATTAATA
1 AAATTTTTAAATTAAAAAATTAATA
6416388 AAATTT
1 AAATTT
6416394 AATGTAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 20 0.71
26 8 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATTTTTAAATTAAAAAATTAATA
Found at i:6430206 original size:21 final size:21
Alignment explanation
Indices: 6430182--6430222 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6430172 ATCTTCCTCA
* * *
6430182 TCATCGGATTTGCTCTCACTC
1 TCATCCGATTCGCTATCACTC
6430203 TCATCCGATTCGCTATCACT
1 TCATCCGATTCGCTATCACT
6430223 GTAGGACGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.34, G:0.12, T:0.37
Consensus pattern (21 bp):
TCATCCGATTCGCTATCACTC
Found at i:6434258 original size:120 final size:116
Alignment explanation
Indices: 6434085--6434457 Score: 263
Period size: 117 Copynumber: 3.2 Consensus size: 116
6434075 TGAAGTAAGG
* * * * *
6434085 AAGGAGTTC-AAGCGGAAGCGTGGGAGACCACCCAAGCTGCTGACAAATGGTGGGAATAGTGGA-
1 AAGGAG-TCAAAGCGTAAGCGTGGCAGACCA-CCAAGGTGCAGACAAATAGTGGG--T--TGGAG
* *
6434148 AAGAAAGCAGGTAAGATGGAAGCAGGAGAGATTGATCACTTTGATGGTGATGTG-AGA
60 AAGAAAGCAGGTAAGATGGAAGCAGGAGAGAGTGATCACTCTGATGGTGATG-GCAGA
* *** * *
6434205 AAGGAGTCAAAGCGTAAGCGTGGTAGACCACCAAAGGTGCAGGGGAATAGTGGGTTTGAGAAGAC
1 AAGGAGTCAAAGCGTAAGCGTGGCAGACCACC-AAGGTGCAGACAAATAGTGGGTTGGAGAAGAA
* * * * * *
6434270 AGCAGTTAAGGTGGAAGTAGGAGAGAGTGATCAGTCTGATGGTGGTGGCAGT
65 AGCAGGTAAGATGGAAGCAGGAGAGAGTGATCACTCTGATGGTGATGGCAGA
* * * * ** * *
6434322 AAGAAGTCAAAGCATAAACGTGGCAGACCAACCAAGGTGCACAGGAATCA-AGGGTTTGAGAAGA
1 AAGGAGTCAAAGCGTAAGCGTGGCAGACC-ACCAAGGTGCAGACAAAT-AGTGGGTTGGAGAAGA
* * * ** * * *
6434386 AAGCAGATGAGGTTAAAGC-GAGAGAGAGTTATCACTCTGATGTTGA-GGCAGGG
64 AAGCAGGTAAGATGGAAGCAG-GAGAGAGTGATCACTCTGATGGTGATGGCA-GA
* *
6434439 AAGGAGGCAAACCGTAAGC
1 AAGGAGTCAAAGCGTAAGC
6434458 ATGGAATACC
Statistics
Matches: 204, Mismatches: 41, Indels: 19
0.77 0.16 0.07
Matches are distributed among these distances:
116 9 0.04
117 146 0.72
118 5 0.02
119 4 0.02
120 40 0.20
ACGTcount: A:0.35, C:0.13, G:0.35, T:0.17
Consensus pattern (116 bp):
AAGGAGTCAAAGCGTAAGCGTGGCAGACCACCAAGGTGCAGACAAATAGTGGGTTGGAGAAGAAA
GCAGGTAAGATGGAAGCAGGAGAGAGTGATCACTCTGATGGTGATGGCAGA
Found at i:6434313 original size:117 final size:117
Alignment explanation
Indices: 6434148--6434436 Score: 300
Period size: 117 Copynumber: 2.5 Consensus size: 117
6434138 GAATAGTGGA
* * *
6434148 AAGAAAGCAGGTAAGATGGAAGCAGGAGAGATTGATCACTTTGATGGTGATGTG-AGAAAGGAGT
1 AAGAAAGCAGGTAAGATGGAAGCAGGAGAGAGTGATCACTCTGATGGTGATG-GCAGAAAGAAGT
* * * ** *
6434212 CAAAGCGTAAGCGTGGTAGACC-ACCAAAGGTGCAGGGGAAT-AGTGGGTTTGAG
65 CAAAGCATAAACGTGGCAGACCAACC-AAGGTGCACAGGAATCA-AGGGTTTGAG
* * * * * * *
6434265 AAGACAGCAGTTAAGGTGGAAGTAGGAGAGAGTGATCAGTCTGATGGTGGTGGCAGTAAGAAGTC
1 AAGAAAGCAGGTAAGATGGAAGCAGGAGAGAGTGATCACTCTGATGGTGATGGCAGAAAGAAGTC
6434330 AAAGCATAAACGTGGCAGACCAACCAAGGTGCACAGGAATCAAGGGTTTGAG
66 AAAGCATAAACGTGGCAGACCAACCAAGGTGCACAGGAATCAAGGGTTTGAG
* * * ** * *
6434382 AAGAAAGCAGATGAGGTTAAAGC-GAGAGAGAGTTATCACTCTGATGTTGA-GGCAG
1 AAGAAAGCAGGTAAGATGGAAGCAG-GAGAGAGTGATCACTCTGATGGTGATGGCAG
6434437 GGAAGGAGGC
Statistics
Matches: 142, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
116 7 0.05
117 131 0.92
118 4 0.03
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.18
Consensus pattern (117 bp):
AAGAAAGCAGGTAAGATGGAAGCAGGAGAGAGTGATCACTCTGATGGTGATGGCAGAAAGAAGTC
AAAGCATAAACGTGGCAGACCAACCAAGGTGCACAGGAATCAAGGGTTTGAG
Found at i:6441952 original size:25 final size:25
Alignment explanation
Indices: 6441922--6441972 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
6441912 GAAGAAAGCA
*
6441922 TTATACTAGGAAATTATATTACATT
1 TTATACGAGGAAATTATATTACATT
*
6441947 TTATACGAGGAAATTATATTGCATT
1 TTATACGAGGAAATTATATTACATT
6441972 T
1 T
6441973 GTGTTTGATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (25 bp):
TTATACGAGGAAATTATATTACATT
Found at i:6448217 original size:20 final size:21
Alignment explanation
Indices: 6448192--6448244 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
6448182 GATATTTTTA
6448192 AATATTTATATTTT-AAAAAT
1 AATATTTATATTTTAAAAAAT
6448212 AATATTTTATATTTTAAAAAAT
1 AATA-TTTATATTTTAAAAAAT
6448234 AATATTT-TATT
1 AATATTTATATT
6448245 AATTTCAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 8 0.26
21 13 0.42
22 10 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AATATTTATATTTTAAAAAAT
Found at i:6448222 original size:21 final size:22
Alignment explanation
Indices: 6448192--6448243 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
6448182 GATATTTTTA
6448192 AATA-TTTATATTTT-AAAAAT
1 AATATTTTATATTTTAAAAAAT
6448212 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
6448234 AATATTTTAT
1 AATATTTTAT
6448244 TAATTTCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 10 0.33
22 16 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:6448567 original size:2 final size:2
Alignment explanation
Indices: 6448560--6448604 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
6448550 ATCAATTGGA
6448560 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6448602 AT A
1 AT A
6448605 GACACACAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6454148 original size:29 final size:29
Alignment explanation
Indices: 6454106--6454163 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
6454096 CTGAGTTTAT
* *
6454106 CTAAATAATTCATTTAAGATCCAATTTGA
1 CTAAACAATTCATTTAAAATCCAATTTGA
6454135 CTAAACAATTCATTTAAAATCCAATTTGA
1 CTAAACAATTCATTTAAAATCCAATTTGA
6454164 TATGATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (29 bp):
CTAAACAATTCATTTAAAATCCAATTTGA
Found at i:6454399 original size:25 final size:26
Alignment explanation
Indices: 6454370--6454425 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
6454360 GTTTTACAAG
*
6454370 TTAATAAAAATGTAA-TTT-AAATAAC
1 TTAAT-AAAATATAATTTTAAAATAAC
6454395 TTAATAAAATATAATTTTAAAATAAC
1 TTAATAAAATATAATTTTAAAATAAC
6454421 TTAAT
1 TTAAT
6454426 TACTGTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 8 0.29
25 8 0.29
26 12 0.43
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (26 bp):
TTAATAAAATATAATTTTAAAATAAC
Found at i:6454700 original size:55 final size:56
Alignment explanation
Indices: 6454615--6454722 Score: 164
Period size: 55 Copynumber: 1.9 Consensus size: 56
6454605 GTCAATCCCC
* * *
6454615 AAATGATCTGAATTCAACCCGAACAAATAACCT-CAATCTGATATGATTTGAATAG
1 AAATGACCTGAATCCAACCCGAACAAATAACCTCCAATCTGATATGATATGAATAG
* *
6454670 AAATGACCTGAATCCAACCCGAACAGATAACCTCCGATCTGATATGATATGAA
1 AAATGACCTGAATCCAACCCGAACAAATAACCTCCAATCTGATATGATATGAA
6454723 CCAAAAGATC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 30 0.64
56 17 0.36
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (56 bp):
AAATGACCTGAATCCAACCCGAACAAATAACCTCCAATCTGATATGATATGAATAG
Found at i:6458077 original size:6 final size:6
Alignment explanation
Indices: 6458066--6458095 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
6458056 CTTTTATGGG
6458066 TCCGAC TCCGAC TCCGAC TCCGAC TCCGAC
1 TCCGAC TCCGAC TCCGAC TCCGAC TCCGAC
6458096 GTTAGCTGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.50, G:0.17, T:0.17
Consensus pattern (6 bp):
TCCGAC
Found at i:6458635 original size:16 final size:16
Alignment explanation
Indices: 6458610--6458642 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
6458600 AATCGAATAA
6458610 TAAATATA-TTTAAAT
1 TAAATATATTTTAAAT
6458625 TAAATTATATTTTAAAT
1 TAAA-TATATTTTAAAT
6458642 T
1 T
6458643 CTTAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 4 0.25
17 8 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAATATATTTTAAAT
Found at i:6459553 original size:17 final size:17
Alignment explanation
Indices: 6459506--6459554 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
6459496 AATACATAAA
* *
6459506 ATAAATTTTAAATTTTT
1 ATAAAATTTAATTTTTT
*
6459523 ATAAAATATAAATTTTTT
1 ATAAAAT-TTAATTTTTT
*
6459541 ATATAATTTAATTT
1 ATAAAATTTAATTT
6459555 AAAATTTACA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATAAAATTTAATTTTTT
Done.