Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 3 of 211
Found at i:994237 original size:10 final size:11
Alignment explanation
Indices: 994219--994251 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
994209 CGAATCGAGT
994219 TTAATTTATAA
1 TTAATTTATAA
994230 TT-ATTTATAA
1 TTAATTTATAA
994240 TTAATTT-TAA
1 TTAATTTATAA
994250 TT
1 TT
994252 TAAGATGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 15 0.71
11 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTAATTTATAA
Found at i:995280 original size:17 final size:17
Alignment explanation
Indices: 995240--995296 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 17
995230 AGATCTAAAC
995240 AATTATAAAAT-AAAATA
1 AATTA-AAAATCAAAATA
995257 AATTAAATATAAATCACAAATA
1 AATT--A-A-AAATCA-AAATA
995279 AATTAAAAATCAAAATA
1 AATTAAAAATCAAAATA
995296 A
1 A
995297 TCCAAACTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 10 0.29
18 6 0.17
19 4 0.11
20 5 0.14
21 1 0.03
22 9 0.26
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
AATTAAAAATCAAAATA
Found at i:999219 original size:2 final size:2
Alignment explanation
Indices: 999212--999239 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
999202 AGTGAATCAT
999212 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
999240 AATAGGGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1016061 original size:95 final size:95
Alignment explanation
Indices: 1015874--1016244 Score: 471
Period size: 89 Copynumber: 4.0 Consensus size: 95
1015864 AAAAAACCAT
* * * * *
1015874 ACATATACATATACATATACATGTGCAAATAGTAATCATCATATAAAAAAA-ATCAAACTAGCAT
1 ACATACACATATTCATATACATATACATATAGTAATCATCATATAAAAAAACATCAAACTAGCAT
*
1015938 ATAGTATTGATCATAGATTCAATGAACTAA
66 ATAGTATTGATCATAGATTCAATAAACTAA
1015968 ACATACACATATTCATATACATATACATATAGTAATCATCATATAAAAAAACATCAAACTAGCAT
1 ACATACACATATTCATATACATATACATATAGTAATCATCATATAAAAAAACATCAAACTAGCAT
*
1016033 ATAGTATTGATCATAGATTCAATAAACTAT
66 ATAGTATTGATCATAGATTCAATAAACTAA
*
1016063 ACATACACATA--C----ACATATACATATAGTAATCATCATATAAAAGAACATCAAACTAGCAT
1 ACATACACATATTCATATACATATACATATAGTAATCATCATATAAAAAAACATCAAACTAGCAT
*
1016122 ATAGTATTGATCATAGATTCAATAAACTAT
66 ATAGTATTGATCATAGATTCAATAAACTAA
* * * * *
1016152 ACATACACATACAT-ATATACATAT--ATAGTAGTTATTAT-ATAGAAAAACAACATCAAAATA-
1 ACATACACATA-TTCATATACATATACATA-TAGTAATCATCATATAAAAA-AACATCAAACTAG
* * *
1016212 -ATATAGCACTGATCAAAGATTCAATAAACTAA
63 CATATAGTATTGATCATAGATTCAATAAACTAA
1016244 A
1 A
1016245 TAGATGTGCA
Statistics
Matches: 250, Mismatches: 17, Indels: 22
0.87 0.06 0.08
Matches are distributed among these distances:
89 87 0.35
92 29 0.12
93 11 0.04
94 65 0.26
95 58 0.23
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.29
Consensus pattern (95 bp):
ACATACACATATTCATATACATATACATATAGTAATCATCATATAAAAAAACATCAAACTAGCAT
ATAGTATTGATCATAGATTCAATAAACTAA
Found at i:1017336 original size:3 final size:3
Alignment explanation
Indices: 1017330--1017360 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1017320 TCACCACCGT
*
1017330 CTC CTC CTC CTC CTC CTC CTC CTC CAC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1017361 GCCACTGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.68, G:0.00, T:0.29
Consensus pattern (3 bp):
CTC
Found at i:1018983 original size:66 final size:66
Alignment explanation
Indices: 1018909--1019039 Score: 210
Period size: 66 Copynumber: 2.0 Consensus size: 66
1018899 GTTTTATACA
* * *
1018909 ATGCTTATAACTATACATAG-TGTCTCCCCAACCCTTAAATAAGAGAATAATGGGCTTCAGTGCA
1 ATGCTTATAACTATACATAGCT-CCTCCCCAACCCTTAAATAAGAGAATAATGCGCTTCAGCGCA
1018973 CG
65 CG
*
1018975 ATGCTTATAACTATACATAGCTCCTCCCCAACCCTTAAATAAGAGGATAATGCGCTTCAGCGCAC
1 ATGCTTATAACTATACATAGCTCCTCCCCAACCCTTAAATAAGAGAATAATGCGCTTCAGCGCAC
1019040 TTGAACCCAC
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
66 59 0.98
67 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (66 bp):
ATGCTTATAACTATACATAGCTCCTCCCCAACCCTTAAATAAGAGAATAATGCGCTTCAGCGCAC
G
Found at i:1019463 original size:21 final size:20
Alignment explanation
Indices: 1019438--1019478 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
1019428 TAATATTTTA
*
1019438 TTAATTTATATATTTTAATTT
1 TTAATATATATA-TTTAATTT
1019459 TTAATATATATATTTAATTT
1 TTAATATATATATTTAATTT
1019479 CATAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTAATATATATATTTAATTT
Found at i:1019465 original size:17 final size:18
Alignment explanation
Indices: 1019424--1019478 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 18
1019414 GCTGTAAAAT
*
1019424 TTTTTAATATTTTATTAA
1 TTTTTAATATATTATTAA
1019442 --TTT-ATATATT-TTAA
1 TTTTTAATATATTATTAA
1019456 TTTTTAATATATATATTTAA
1 TTTTTAATATAT-TA-TTAA
1019476 TTT
1 TTT
1019479 CATAATAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
14 4 0.13
15 6 0.20
16 6 0.20
17 6 0.20
18 1 0.03
20 7 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTAATATATTATTAA
Found at i:1019484 original size:21 final size:19
Alignment explanation
Indices: 1019444--1019485 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
1019434 TTTATTAATT
*
1019444 TATATATTTTAATTTTTAA
1 TATATATTTTAATTTATAA
1019463 TATATATATTTAATTTCATAA
1 TATATAT-TTTAATTT-ATAA
1019484 TA
1 TA
1019486 ATAATATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 8 0.40
21 5 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATATTTTAATTTATAA
Found at i:1020888 original size:4 final size:4
Alignment explanation
Indices: 1020879--1020923 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
1020869 GATATTTTAG
* *
1020879 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT- ATTA GTTT ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA AT
1020924 ATTTTAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 3 0.08
4 33 0.92
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (4 bp):
ATTA
Found at i:1023344 original size:30 final size:29
Alignment explanation
Indices: 1023287--1023344 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
1023277 TGCGCAGTTG
*
1023287 TATACATGAATTTTGATTTTGTGCAATTT
1 TATACATGAATTTTGATTTTGTCCAATTT
1023316 TATACATGAAATTTTGA-TTTGATCCAATT
1 TATACATG-AATTTTGATTTTG-TCCAATT
1023345 CTTGTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (29 bp):
TATACATGAATTTTGATTTTGTCCAATTT
Found at i:1024516 original size:19 final size:21
Alignment explanation
Indices: 1024483--1024523 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
1024473 TCCTAATTCT
*
1024483 AAAAATTAAAGAAATATATAA
1 AAAAATTAAAGAAATACATAA
1024504 AAAAATT-AA-AAATACATAA
1 AAAAATTAAAGAAATACATAA
1024523 A
1 A
1024524 TATTTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 2 0.11
21 7 0.37
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (21 bp):
AAAAATTAAAGAAATACATAA
Found at i:1028355 original size:21 final size:21
Alignment explanation
Indices: 1028331--1028376 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1028321 AAATAAATAG
1028331 ATAATTCATGAAGTTAAA-AAA
1 ATAATTC-TGAAGTTAAAGAAA
* *
1028352 ATAATTCTTAATTTAAAGAAA
1 ATAATTCTGAAGTTAAAGAAA
1028373 ATAA
1 ATAA
1028377 ATGTAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.33
Consensus pattern (21 bp):
ATAATTCTGAAGTTAAAGAAA
Found at i:1032008 original size:23 final size:22
Alignment explanation
Indices: 1031974--1032017 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1031964 ATGCTTTATG
1031974 TTTTTTATTATTCAAGATTAGT
1 TTTTTTATTATTCAAGATTAGT
* *
1031996 TTTTCTTATTATTTATGATTAG
1 TTTT-TTATTATTCAAGATTAG
1032018 AATTTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTTTTATTATTCAAGATTAGT
Found at i:1041543 original size:29 final size:32
Alignment explanation
Indices: 1041505--1041568 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
1041495 CTACATAAAA
*
1041505 TTTGATTAAAATATGTAAT-TAGTCCCT-TAT
1 TTTGATTAAAATATGCAATATAGTCCCTATAT
* *
1041535 TTTGA-TAAAGTTTGCAATATAGTCCCTATAT
1 TTTGATTAAAATATGCAATATAGTCCCTATAT
1041566 TTT
1 TTT
1041569 AAAAGTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 10 0.34
30 13 0.45
31 6 0.21
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (32 bp):
TTTGATTAAAATATGCAATATAGTCCCTATAT
Found at i:1043581 original size:21 final size:21
Alignment explanation
Indices: 1043557--1043599 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1043547 AATATAAAAC
*
1043557 TATCTTAAAGATAAATAATAT
1 TATCATAAAGATAAATAATAT
* *
1043578 TATCATAAATATAAATATTAT
1 TATCATAAAGATAAATAATAT
1043599 T
1 T
1043600 TAATTATCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (21 bp):
TATCATAAAGATAAATAATAT
Found at i:1043605 original size:26 final size:26
Alignment explanation
Indices: 1043576--1043627 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1043566 GATAAATAAT
*
1043576 ATTATCATAAATATAAATATTATTTA
1 ATTATCATAAAGATAAATATTATTTA
*
1043602 ATTATCATTAAGATAAATATTATTTA
1 ATTATCATAAAGATAAATATTATTTA
1043628 TCTTAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTATCATAAAGATAAATATTATTTA
Found at i:1044045 original size:2 final size:2
Alignment explanation
Indices: 1044032--1044065 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1044022 AAATAAATTA
*
1044032 AT AT AT AC 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
1044066 GAATCTCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1044744 original size:8 final size:8
Alignment explanation
Indices: 1044719--1044754 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
1044709 AAAAAAATTA
1044719 ATAATTTAT
1 ATAATTT-T
*
1044728 ATAACTTT
1 ATAATTTT
1044736 ATAATTTT
1 ATAATTTT
1044744 ATAATTTT
1 ATAATTTT
1044752 ATA
1 ATA
1044755 CCAATTCCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 19 0.76
9 6 0.24
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (8 bp):
ATAATTTT
Found at i:1047487 original size:173 final size:173
Alignment explanation
Indices: 1047198--1047543 Score: 620
Period size: 173 Copynumber: 2.0 Consensus size: 173
1047188 CACGTTTGAA
* *
1047198 TTCATATCATTCTAATTGTTGCTAGAACAACGGTGCCAATTGCGTTAAGGCTTAATATATAGTAT
1 TTCATATCATTCTAATTGTTGCTAGAACAACGGTGCCAACTACGTTAAGGCTTAATATATAGTAT
* * *
1047263 TTGGATGCGGAAATTGAGGGCATCGCTTTATGCAGTGATTTCCAAATTACAACATTGTAAGAAGG
66 TAGGATGCGAAAATTGAGGGCATCGCTTTATGCAATGATTTCCAAATTACAACATTGTAAGAAGG
*
1047328 ATCTTTCCATGACGAGGGCAACACTTAGGGGAGAGCAAATTTC
131 ATCTTTCCATGACAAGGGCAACACTTAGGGGAGAGCAAATTTC
1047371 TTCATATCATTCTAATTGTTGCTAGAACAACGGTGCCAACTACGTTAAGGCTTAATATATAGTAT
1 TTCATATCATTCTAATTGTTGCTAGAACAACGGTGCCAACTACGTTAAGGCTTAATATATAGTAT
* *
1047436 TAGGATGTGAAAATTGAGGGCATCGCTTTATGCAATGATTTCCAAATTACAACATTGTAAGATGG
66 TAGGATGCGAAAATTGAGGGCATCGCTTTATGCAATGATTTCCAAATTACAACATTGTAAGAAGG
1047501 ATCTTTCCATGACAAGGGCAACACTTAGGGGAGAGCAAATTTC
131 ATCTTTCCATGACAAGGGCAACACTTAGGGGAGAGCAAATTTC
1047544 GGTTAAAACT
Statistics
Matches: 165, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
173 165 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (173 bp):
TTCATATCATTCTAATTGTTGCTAGAACAACGGTGCCAACTACGTTAAGGCTTAATATATAGTAT
TAGGATGCGAAAATTGAGGGCATCGCTTTATGCAATGATTTCCAAATTACAACATTGTAAGAAGG
ATCTTTCCATGACAAGGGCAACACTTAGGGGAGAGCAAATTTC
Found at i:1057085 original size:31 final size:31
Alignment explanation
Indices: 1057004--1057089 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
1056994 ATGGGCTCAG
* *
1057004 GTGACTAATTTGTCACTTTCCGAAAACATTA
1 GTGACTGATTTGTCACTTTTCGAAAACATTA
** *
1057035 GTGACTGATTTGTTGCTTTTCGTAAACATTA
1 GTGACTGATTTGTCACTTTTCGAAAACATTA
* *
1057066 TTTACTGATTTGTCACTTTT-GAAA
1 GTGACTGATTTGTCACTTTTCGAAA
1057090 GTTTAGTGAC
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
30 3 0.07
31 42 0.93
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (31 bp):
GTGACTGATTTGTCACTTTTCGAAAACATTA
Found at i:1063768 original size:12 final size:11
Alignment explanation
Indices: 1063701--1063770 Score: 60
Period size: 11 Copynumber: 6.6 Consensus size: 11
1063691 ATTTTTTTAA
1063701 TTTTAAAATAT
1 TTTTAAAATAT
1063712 TTTTAAAATACT
1 TTTTAAAATA-T
* *
1063724 TTTT-TATTAT
1 TTTTAAAATAT
*
1063734 TTTT----TAA
1 TTTTAAAATAT
1063741 TTTTAAAATAT
1 TTTTAAAATAT
1063752 TTTTAAAATACT
1 TTTTAAAATA-T
1063764 TTTTAAA
1 TTTTAAA
1063771 TTTTTTTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
7 6 0.12
10 5 0.10
11 25 0.51
12 13 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:1063771 original size:11 final size:10
Alignment explanation
Indices: 1063684--1063796 Score: 58
Period size: 10 Copynumber: 11.5 Consensus size: 10
1063674 ATATATTTAT
1063684 TTTTTAAAT-
1 TTTTTAAATA
*
1063693 TTTTT-TA-A
1 TTTTTAAATA
*
1063701 TTTTAAAATA
1 TTTTTAAATA
1063711 TTTTTAAAATA
1 TTTTT-AAATA
* *
1063722 CTTTTTTATTA
1 -TTTTTAAATA
*
1063733 TTTTT-TA-A
1 TTTTTAAATA
*
1063741 TTTTAAAATA
1 TTTTTAAATA
1063751 TTTTTAAAATA
1 TTTTT-AAATA
*
1063762 CTTTTTAAATT
1 -TTTTTAAATA
**
1063773 TTTTTTTA-A
1 TTTTTAAATA
*
1063782 TTTTAAAATA
1 TTTTTAAATA
1063792 TTTTT
1 TTTTT
1063797 TTAATTTTTA
Statistics
Matches: 75, Mismatches: 19, Indels: 19
0.66 0.17 0.17
Matches are distributed among these distances:
8 10 0.13
9 12 0.16
10 26 0.35
11 17 0.23
12 10 0.13
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:1063778 original size:41 final size:41
Alignment explanation
Indices: 1063684--1063796 Score: 187
Period size: 40 Copynumber: 2.8 Consensus size: 41
1063674 ATATATTTAT
1063684 TTTTTAAA--TTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTAAATTTTTTTTTAATTTTAAAATATTTTTAAAATAC
* *
1063723 TTTTT-TATTATTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTAAATTTTTTTTTAATTTTAAAATATTTTTAAAATAC
1063763 TTTTTAAATTTTTTTTTAATTTTAAAATATTTTT
1 TTTTTAAATTTTTTTTTAATTTTAAAATATTTTT
1063797 TTAATTTTTA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
38 1 0.01
39 5 0.07
40 35 0.52
41 26 0.39
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (41 bp):
TTTTTAAATTTTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:1063817 original size:19 final size:19
Alignment explanation
Indices: 1063776--1063817 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1063766 TTAAATTTTT
**
1063776 TTTTAATTTTAAAATATTT
1 TTTTAATTTTAAAATATAA
1063795 TTTTAATTTTTAAAATA-AA
1 TTTTAA-TTTTAAAATATAA
1063814 TTTT
1 TTTT
1063818 TGGTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAATTTTAAAATATAA
Found at i:1063817 original size:20 final size:19
Alignment explanation
Indices: 1063775--1063818 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1063765 TTTAAATTTT
**
1063775 TTTTTAATTTTAAAATATT
1 TTTTTAATTTTAAAATAAA
1063794 TTTTTAATTTTTAAAATAAA
1 TTTTTAA-TTTTAAAATAAA
1063814 TTTTT
1 TTTTT
1063819 GGTATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTAATTTTAAAATAAA
Found at i:1063818 original size:41 final size:40
Alignment explanation
Indices: 1063690--1063818 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
1063680 TTATTTTTTA
**
1063690 AATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAT
1 AATTTTTTTAATTTTAAAATATTTTTAAAATA-TTTTAAAT
*
1063731 TA-TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAAAT
1 AATTTTTTTAATTTTAAAATATTTTTAAAATA--TTTTAAAT
* **
1063772 -TTTTTTTTAATTTTAAAATATTTTTTTAAT-TTTTAAAAT
1 AATTTTTTTAATTTTAAAATATTTTTAAAATATTTT-AAAT
*
1063811 AAATTTTT
1 AATTTTTT
1063819 GGTATTTATT
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
38 4 0.05
39 4 0.05
40 34 0.45
41 33 0.44
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (40 bp):
AATTTTTTTAATTTTAAAATATTTTTAAAATATTTTAAAT
Found at i:1067049 original size:35 final size:33
Alignment explanation
Indices: 1067002--1067071 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 33
1066992 GTGATAATTG
1067002 GACACATGTTTTGTATTAACTTAATTACA-ACAT
1 GACACATGTTTTGTATTAACTTAATTA-AGACAT
* *
1067035 GACACAATGGTTTTGTGTTAAGTTAATTAAGACAT
1 GACAC-AT-GTTTTGTATTAACTTAATTAAGACAT
1067070 GA
1 GA
1067072 TTTGACATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 5 0.16
34 3 0.09
35 24 0.75
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (33 bp):
GACACATGTTTTGTATTAACTTAATTAAGACAT
Found at i:1069943 original size:27 final size:27
Alignment explanation
Indices: 1069900--1069969 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
1069890 TAGTCGAGGG
* *
1069900 ACTGCCACAGACGGCACTAAAGGTGCC
1 ACTGCCACAGGCGGCACCAAAGGTGCC
* * *
1069927 AGTGGCAGAGGCGGCACCAAAGGTGCC
1 ACTGCCACAGGCGGCACCAAAGGTGCC
1069954 ACTGCCACAGGCGGCA
1 ACTGCCACAGGCGGCA
1069970 AGAAGAAGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.27, C:0.31, G:0.33, T:0.09
Consensus pattern (27 bp):
ACTGCCACAGGCGGCACCAAAGGTGCC
Found at i:1072255 original size:14 final size:14
Alignment explanation
Indices: 1072223--1072256 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1072213 AAATATATAC
1072223 ATATATGTATGTGT
1 ATATATGTATGTGT
* *
1072237 GTATATGTGTGTGT
1 ATATATGTATGTGT
1072251 ATATAT
1 ATATAT
1072257 ATAAACACTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (14 bp):
ATATATGTATGTGT
Found at i:1075986 original size:8 final size:7
Alignment explanation
Indices: 1075958--1075984 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1075948 ATCTTTACCA
1075958 AAAAAAT
1 AAAAAAT
1075965 AAAAAAT
1 AAAAAAT
1075972 AAAAAAT
1 AAAAAAT
1075979 AAAAAA
1 AAAAAA
1075985 ATCATAGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:1083062 original size:41 final size:40
Alignment explanation
Indices: 1083036--1083114 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
1083026 AATATACCAT
*
1083036 ATAATATTAGATATATATATATAGTATAAAAAATATAACTA
1 ATAATATTA-AAATATATATATAGTATAAAAAATATAACTA
*
1083077 ATAATATTAAAATATATAATAATA-TATATAAAATATAA
1 ATAATATTAAAATATAT-AT-ATAGTATAAAAAATATAA
1083115 TATTAAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 7 0.21
41 24 0.71
42 3 0.09
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (40 bp):
ATAATATTAAAATATATATATAGTATAAAAAATATAACTA
Found at i:1083092 original size:34 final size:34
Alignment explanation
Indices: 1083052--1083122 Score: 81
Period size: 34 Copynumber: 2.0 Consensus size: 34
1083042 TTAGATATAT
*
1083052 ATATATAGTATAAAAAATAT-AACTAATAATATTAAA
1 ATATATA--ATAAAAAATATAAAAT-ATAATATTAAA
* *
1083088 ATATATAATAATATATATAAAATATAATATTAAA
1 ATATATAATAAAAAATATAAAATATAATATTAAA
1083122 A
1 A
1083123 ACTTATATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
34 21 0.68
35 3 0.10
36 7 0.23
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (34 bp):
ATATATAATAAAAAATATAAAATATAATATTAAA
Found at i:1083099 original size:21 final size:21
Alignment explanation
Indices: 1083004--1083113 Score: 77
Period size: 21 Copynumber: 5.2 Consensus size: 21
1082994 ATAAATATAT
* *
1083004 ATATATAAATAACAGTATTAGAA
1 ATATAT-AATAATAATATTA-AA
** *
1083027 ATATACCAT-ATAATATT-AG
1 ATATATAATAATAATATTAAA
*
1083046 ATATAT-ATATATAGTA-TAAA
1 ATATATAATA-ATAATATTAAA
*
1083066 AAATATAACTAATAATATTAAA
1 ATATATAA-TAATAATATTAAA
1083088 ATATATAATAAT-ATATATAAA
1 ATATATAATAATAATAT-TAAA
1083109 ATATA
1 ATATA
1083114 ATATTAAAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
18 2 0.03
19 7 0.10
20 15 0.22
21 25 0.36
22 15 0.22
23 5 0.07
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (21 bp):
ATATATAATAATAATATTAAA
Found at i:1083420 original size:21 final size:23
Alignment explanation
Indices: 1083396--1083443 Score: 73
Period size: 21 Copynumber: 2.1 Consensus size: 23
1083386 AATAATACTT
1083396 TAAAAATAAT-TAAT-ATATTAA
1 TAAAAATAATATAATAATATTAA
1083417 TAAAAATAATAGTAATAATATTAA
1 TAAAAATAATA-TAATAATATTAA
1083441 TAA
1 TAA
1083444 TATGTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 10 0.42
23 4 0.17
24 10 0.42
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAAAATAATATAATAATATTAA
Found at i:1083445 original size:21 final size:21
Alignment explanation
Indices: 1083382--1083445 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 21
1083372 TAATCATTAG
*
1083382 TAGTAATAATACTTTAAAAATAA
1 TAGTAATAATA--TTAATAATAA
1083405 T--TAAT-ATATTAATAAAAATAA
1 TAGTAATAATATTAAT---AATAA
1083426 TAGTAATAATATTAATAATA
1 TAGTAATAATATTAATAATA
1083446 TGTAAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 14
0.69 0.02 0.29
Matches are distributed among these distances:
18 4 0.12
20 3 0.09
21 14 0.41
23 5 0.15
24 8 0.24
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (21 bp):
TAGTAATAATATTAATAATAA
Found at i:1085010 original size:159 final size:158
Alignment explanation
Indices: 1084798--1085088 Score: 539
Period size: 160 Copynumber: 1.8 Consensus size: 158
1084788 AACAGAAATG
*
1084798 GAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACAC
1 GAAAATACCTCGGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACAC
1084863 -AAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTACAATATGAGCTGATTT
66 AAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTACAATATGAGCTGATTT
1084927 TGGAAACAGAATTTGCCAAACAGATTTT
131 TGGAAACAGAATTTGCCAAACAGATTTT
1084955 GAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAAC
1 GAAAATACCTCGG--TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAAC
*
1085020 ACAAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGAT
64 ACAAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTACAATATGAGCTGAT
1085085 TTTG
129 TTTG
1085089 AAAAAGTAGA
Statistics
Matches: 129, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
157 13 0.10
159 51 0.40
160 65 0.50
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (158 bp):
GAAAATACCTCGGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACAC
AAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTACAATATGAGCTGATTT
TGGAAACAGAATTTGCCAAACAGATTTT
Found at i:1085327 original size:72 final size:72
Alignment explanation
Indices: 1085110--1085512 Score: 488
Period size: 72 Copynumber: 5.5 Consensus size: 72
1085100 ATTAAAAGGT
* ** * * * *
1085110 TCAACCCACCTCTCGCAATATGAGTTGATTTTTTTG-AAAGTAGAATTTGAAAATACCTCGGCGT
1 TCAACTCACCTCTCGCAATATGAGTTGA---TTTTGAAAAACAAAAATTGAAATTACCTCAGCGT
1085174 G-CCTTGAGGC
63 GTCC-TGAGGC
** *
1085184 TCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTGAAATTACCTCAGCGTG
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTG-AAAAACAAAAATTGAAATTACCTCAGCGTG
1085249 TCCTGAGGC
64 TCCTGAGGC
1085258 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTGAAATTACCTCAGCGTGTC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTGAAATTACCTCAGCGTGTC
1085323 CTGAGGC
66 CTGAGGC
* ** * * *
1085330 TCAACCCAGTTCTCGCAACATGAGTTGAAATTTGGAAAACAAAAATTGAAATTACCTCAGCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTG-ATTTTGAAAAACAAAAATTGAAATTACCTCAGCGTGT
1085395 CCTGAGGC
65 CCTGAGGC
** * * *
1085403 TCAACTCACCTCTCGCAATATGAGTTGAAATT-AAAACACAAAAATTAAAAATACCTCAGCGTGC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAA-ACAAAAATTGAAATTACCTCAGCGTGT
*
1085467 CCCGAGGC
65 CCTGAGGC
* * *
1085475 TCAACTCACCTCTTGCAATATGAGCTGATTTTGGAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAA
1085513 GTAGAATTTG
Statistics
Matches: 291, Mismatches: 32, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
71 3 0.01
72 131 0.45
73 74 0.25
74 81 0.28
75 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (72 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTGAAATTACCTCAGCGTGTC
CTGAGGC
Found at i:1085403 original size:145 final size:145
Alignment explanation
Indices: 1085110--1085479 Score: 494
Period size: 145 Copynumber: 2.5 Consensus size: 145
1085100 ATTAAAAGGT
* ** * * *
1085110 TCAACCCACCTCTCGCAATATGAGTTGATTTTTTTG-AAAGTAGAATTTGAAAATACCTCGGCGT
1 TCAACTCACCTCTCGCAATATGAGTTGA---TTTTGAAAAACAAAAATTGAAAATACCTCAGCGT
* * * ** *
1085174 GCCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTGAAATTA
63 GCC-TGAGGCTCAACCCAGTTCTCGCAACATGAGTTGAAATTTGAAAAAACAAAAATTGAAATTA
1085239 CCTCAGCGTGTCCTGAGGC
127 CCTCAGCGTGTCCTGAGGC
*
1085258 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTGAAATTACCTCAGCGTGTC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTGAAAATACCTCAGCGTG-C
*
1085323 CTGAGGCTCAACCCAGTTCTCGCAACATGAGTTGAAATTTG-GAAAACAAAAATTGAAATTACCT
65 CTGAGGCTCAACCCAGTTCTCGCAACATGAGTTGAAATTTGAAAAAACAAAAATTGAAATTACCT
1085387 CAGCGTGTCCTGAGGC
130 CAGCGTGTCCTGAGGC
** *
1085403 TCAACTCACCTCTCGCAATATGAGTTGAAATT-AAAACACAAAAATTAAAAATACCTCAGCGTGC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAA-ACAAAAATTGAAAATACCTCAGCGTG-
*
1085467 CCCGAGGCTCAAC
64 CCTGAGGCTCAAC
1085480 TCACCTCTTG
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
144 4 0.02
145 108 0.54
146 58 0.29
147 2 0.01
148 27 0.14
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (145 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTGAAAATACCTCAGCGTGCC
TGAGGCTCAACCCAGTTCTCGCAACATGAGTTGAAATTTGAAAAAACAAAAATTGAAATTACCTC
AGCGTGTCCTGAGGC
Found at i:1085498 original size:145 final size:145
Alignment explanation
Indices: 1085159--1085512 Score: 505
Period size: 145 Copynumber: 2.4 Consensus size: 145
1085149 GTAGAATTTG
* * * * *
1085159 AAAATACCTCGGCGTGCCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAAAA
1 AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGAATTTTG-GAAAA
* **
1085224 CAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
65 CAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAAT
*
1085289 TGAAAAACAAAAATTG
130 TGAAAAACAAAAATTA
* * * * * *
1085305 AAATTACCTCAGCGTGTCCTGAGGCTCAACCCAGTTCTCGCAACATGAGTTGAAATTTGGAAAAC
1 AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGAATTTTGGAAAAC
1085370 AAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATT
66 AAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATT
1085435 -AAAACACAAAAATTA
131 GAAAA-ACAAAAATTA
* * * *
1085450 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTG-ATTTTGGAAAA
1 AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGAATTTTGGAAAA
1085513 GTAGAATTTG
Statistics
Matches: 183, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
144 14 0.08
145 119 0.65
146 50 0.27
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (145 bp):
AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGAATTTTGGAAAAC
AAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATT
GAAAAACAAAAATTA
Found at i:1085749 original size:72 final size:73
Alignment explanation
Indices: 1085548--1085754 Score: 240
Period size: 72 Copynumber: 2.8 Consensus size: 73
1085538 AAAAACGAAA
1085548 AATTGAAAATACCTCAGCGTGCGAGCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AATTGAAAATACCTCAGCGT--GA-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----
1085612 TTTTTTGAAAAGCA-G
59 TTTTTTGAAAA-CATG
* * * ** *
1085627 AACTTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTT
1 AA-TTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1085692 GAAAACATG
65 GAAAACATG
**
1085701 AATT-AAAATACCTCAGCGTGACCTGAGGCTTGACTCACCTCTCGCAATATGAGT
1 AATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1085755 CAATTTTCCT
Statistics
Matches: 111, Mismatches: 14, Indels: 13
0.80 0.10 0.09
Matches are distributed among these distances:
72 42 0.38
73 4 0.04
74 14 0.13
77 1 0.01
78 31 0.28
79 2 0.02
80 17 0.15
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (73 bp):
AATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG
AAAACATG
Found at i:1085761 original size:72 final size:73
Alignment explanation
Indices: 1085548--1085784 Score: 219
Period size: 72 Copynumber: 3.1 Consensus size: 73
1085538 AAAAACGAAA
* *
1085548 AATTGAAAATACCTCAGCGTGCGAGCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AATTGAAAATACCTCAGCGT--GA-CCTGAGGCTCAACTCACCTCTCGCAATATGAG-TCA---A
1085612 TTTTTTGAAAAGCA-G
59 TTTTTTGAAAA-CATG
* * * ** * **
1085627 AACTTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTT
1 AA-TTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTCAATTTTTT
1085692 GAAAACATG
65 GAAAACATG
**
1085701 AATT-AAAATACCTCAGCGTGACCTGAGGCTTGACTCACCTCTCGCAATATGAGTCAATTTTCCT
1 AATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTCAATTTT--T
*
1085765 TGGAAAGCATG
64 T-GAAAACATG
*
1085776 AATTAAAAA
1 AATTGAAAA
1085785 CATCAAAATA
Statistics
Matches: 131, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
72 47 0.36
73 4 0.03
74 16 0.12
75 12 0.09
76 4 0.03
77 2 0.02
78 27 0.21
79 2 0.02
80 17 0.13
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (73 bp):
AATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTCAATTTTTTG
AAAACATG
Found at i:1097079 original size:41 final size:41
Alignment explanation
Indices: 1097014--1097123 Score: 116
Period size: 41 Copynumber: 2.7 Consensus size: 41
1097004 ATATAAATAT
* * * * *
1097014 ATATATAATAACAGTATTAGAAATAT-ACCATATAATATTAGAT
1 ATATATAATAATA-TATAAAAAATATAACTA-ATAATATTA-AA
*
1097057 ATATATAATAGTATA-AAAAAATATAACTAATAATATTAAA
1 ATATATAATAATATATAAAAAATATAACTAATAATATTAAA
*
1097097 ATATATAATAATATATATAAAATATAA
1 ATATATAATAATATATAAAAAATATAA
1097124 TATTAAAAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
40 15 0.26
41 26 0.46
42 5 0.09
43 11 0.19
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (41 bp):
ATATATAATAATATATAAAAAATATAACTAATAATATTAAA
Found at i:1097081 original size:22 final size:19
Alignment explanation
Indices: 1097059--1097125 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 19
1097049 TATTAGATAT
*
1097059 ATATAATAGTATA-AAAAA
1 ATATAATAATATATAAAAA
*
1097077 ATATAACTAATAATATTAAAAT
1 ATATAA-TAAT-ATA-TAAAAA
*
1097099 ATATAATAATATATATAAA
1 ATATAATAATATATAAAAA
1097118 ATATAATA
1 ATATAATA
1097126 TTAAAAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 6 0.15
19 15 0.37
20 6 0.15
21 4 0.10
22 10 0.24
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (19 bp):
ATATAATAATATATAAAAA
Found at i:1097444 original size:18 final size:20
Alignment explanation
Indices: 1097423--1097472 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 20
1097413 ATTAATATAT
1097423 TAATAAAAATAATA-GT-AA
1 TAATAAAAATAATATGTAAA
*
1097441 TAAT-ATAATAATATGTAAAA
1 TAATAAAAATAATATGT-AAA
*
1097461 AAATAAAAATAA
1 TAATAAAAATAA
1097473 ACGAAAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 8 0.32
18 6 0.24
20 5 0.20
21 6 0.24
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (20 bp):
TAATAAAAATAATATGTAAA
Found at i:1103801 original size:3 final size:3
Alignment explanation
Indices: 1103793--1103863 Score: 83
Period size: 3 Copynumber: 23.7 Consensus size: 3
1103783 TTGTTATTTC
* *
1103793 TAT TAT TAT TA- AAT TAGT T-T TAT TAC TAT TAT TAT TAT TAT TATT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TA-T
*
1103838 TAT TAT TAT TAT TAT TAT CAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1103864 GTTTTATTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
2 3 0.05
3 50 0.86
4 5 0.09
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1103843 original size:19 final size:19
Alignment explanation
Indices: 1103819--1103855 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1103809 GTTTTATTAC
1103819 TATTATTATTATTATTATT
1 TATTATTATTATTATTATT
1103838 TATTATTATTATTATTAT
1 TATTATTATTATTATTAT
1103856 CATTATTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTATTATTATTATTATT
Found at i:1104126 original size:27 final size:27
Alignment explanation
Indices: 1104096--1104151 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1104086 GTTTTCCTAT
*
1104096 ATATATACATACATACGAT-TTTTTTTA
1 ATATATACATACATAC-ATATTGTTTTA
* *
1104123 ATATATATATACGTACATATTGTTTTA
1 ATATATACATACATACATATTGTTTTA
1104150 AT
1 AT
1104152 TTTTATGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (27 bp):
ATATATACATACATACATATTGTTTTA
Found at i:1104417 original size:31 final size:31
Alignment explanation
Indices: 1104351--1104417 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
1104341 GTTTTCATAC
* *
1104351 TTTATAATTTATATATATATCTTTTATATTT
1 TTTATAATTTATACATATATCTTTTATATTA
* * *
1104382 TTTATAGTTTATACAT-TTTCTTTGTTTATTA
1 TTTATAATTTATACATATATCTTT-TATATTA
1104413 TTTAT
1 TTTAT
1104418 TTCATTTTCG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.66
Consensus pattern (31 bp):
TTTATAATTTATACATATATCTTTTATATTA
Found at i:1111764 original size:4 final size:4
Alignment explanation
Indices: 1111755--1111808 Score: 99
Period size: 4 Copynumber: 13.5 Consensus size: 4
1111745 ATTGAAAAGC
*
1111755 TGTA TGTA TGTA TGTA TGTA TATA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1111803 TGTA TG
1 TGTA TG
1111809 AATTTGTATG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:1115813 original size:32 final size:31
Alignment explanation
Indices: 1115768--1115877 Score: 98
Period size: 31 Copynumber: 3.5 Consensus size: 31
1115758 TTGGTCGCTC
* * * *
1115768 AAATATTTGAAAATTCTAACTAGGTCCCTTCA
1 AAATTTTTAAAAATTCTAAATA-GACCCTTCA
*
1115800 AAATTTTTAAAAATTCTAAATA-AACCTTCA
1 AAATTTTTAAAAATTCTAAATAGACCCTTCA
* * *
1115830 AATAGTTTTAAAAATTTTAATTAGACCC-TCA
1 AA-ATTTTTAAAAATTCTAAATAGACCCTTCA
* *
1115861 AATTTTTTGAAAATTCT
1 AAATTTTTAAAAATTCT
1115878 CATTAATCCT
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
30 19 0.30
31 22 0.35
32 22 0.35
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (31 bp):
AAATTTTTAAAAATTCTAAATAGACCCTTCA
Found at i:1115830 original size:30 final size:30
Alignment explanation
Indices: 1115794--1115896 Score: 107
Period size: 31 Copynumber: 3.4 Consensus size: 30
1115784 TAACTAGGTC
*
1115794 CCTTCAAAATTTTTAAAAATTCTAAATAAA
1 CCTTCAAAATTTTTAAAAATTCTAATTAAA
* * *
1115824 CCTTCAAATAGTTTTAAAAATTTTAATTAGA
1 CCTTCAAA-ATTTTTAAAAATTCTAATTAAA
* * * * *
1115855 CCCTCAAATTTTTTGAAAATTCTCATTAAT
1 CCTTCAAAATTTTTAAAAATTCTAATTAAA
1115885 CCTCTCAAAATT
1 CCT-TCAAAATT
1115897 GTAACATTTT
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
30 25 0.44
31 32 0.56
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.40
Consensus pattern (30 bp):
CCTTCAAAATTTTTAAAAATTCTAATTAAA
Found at i:1118923 original size:27 final size:28
Alignment explanation
Indices: 1118863--1118924 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
1118853 TGTATATATA
* *
1118863 ATTATATATAATTATTTAAATATTATTT
1 ATTATATATAATTATTTAAAAAATATTT
*
1118891 ATTATATTTAATT-TTTAAAAAATA-TT
1 ATTATATATAATTATTTAAAAAATATTT
1118917 -TTATATAT
1 ATTATATAT
1118925 CATCAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 7 0.23
26 2 0.07
27 9 0.30
28 12 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTATATATAATTATTTAAAAAATATTT
Found at i:1120870 original size:9 final size:9
Alignment explanation
Indices: 1120827--1120880 Score: 63
Period size: 9 Copynumber: 5.8 Consensus size: 9
1120817 ACATAATAAA
1120827 AATATATACT
1 AATA-ATACT
*
1120837 AATACATAAT
1 AATA-ATACT
1120847 AATAATACT
1 AATAATACT
**
1120856 GGTAATACT
1 AATAATACT
1120865 AATAATACT
1 AATAATACT
1120874 AATAATA
1 AATAATA
1120881 TAAAAATAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
9 25 0.68
10 12 0.32
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (9 bp):
AATAATACT
Found at i:1121369 original size:11 final size:12
Alignment explanation
Indices: 1121355--1121390 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
1121345 AAGAAAAAAA
1121355 GAAGAGAG-AGG
1 GAAGAGAGAAGG
1121366 GAAGAGAGAAGG
1 GAAGAGAGAAGG
1121378 G-AGAGAGAAGG
1 GAAGAGAGAAGG
1121389 GA
1 GA
1121391 GGGGGAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:1121506 original size:11 final size:12
Alignment explanation
Indices: 1121493--1121544 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
1121483 AAAAAAAATT
1121493 TATTTTTTATT-
1 TATTTTTTATTA
*
1121504 TATTTTTTATTTC
1 TATTTTTTA-TTA
1121517 TATTATTTTATTA
1 TATT-TTTTATTA
*
1121530 TATTTTTTAATA
1 TATTTTTTATTA
1121542 TAT
1 TAT
1121545 ATATGTGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
11 9 0.25
12 12 0.33
13 10 0.28
14 5 0.14
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (12 bp):
TATTTTTTATTA
Found at i:1121530 original size:17 final size:17
Alignment explanation
Indices: 1121491--1121530 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1121481 GAAAAAAAAA
1121491 TTTATT-TTTTATTTAT
1 TTTATTATTTTATTTAT
1121507 TTT-TTATTTCTA-TTAT
1 TTTATTATTT-TATTTAT
1121523 TTTATTAT
1 TTTATTAT
1121531 ATTTTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.10
16 13 0.62
17 6 0.29
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTATTTTATTTAT
Found at i:1123131 original size:57 final size:58
Alignment explanation
Indices: 1123031--1123145 Score: 153
Period size: 57 Copynumber: 2.0 Consensus size: 58
1123021 ATAGAAATGG
* *
1123031 TGAAAATGGAGAAATGAGAAAATTTTGGAAATGATGATGATTTTATCCAAAATGAAAA
1 TGAAAATGGAGAAATGAGAAAATTTTGGAAATGATGATAATTTTATCCAAAAAGAAAA
* * * *
1123089 TGAAAATGGAGAAATGA-AATCA-TTTGGAAATGATTATAATTTTCTCTAAAAAGAAAA
1 TGAAAATGGAGAAATGAGAA-AATTTTGGAAATGATGATAATTTTATCCAAAAAGAAAA
1123146 AAATGAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
57 32 0.64
58 18 0.36
ACGTcount: A:0.49, C:0.04, G:0.18, T:0.29
Consensus pattern (58 bp):
TGAAAATGGAGAAATGAGAAAATTTTGGAAATGATGATAATTTTATCCAAAAAGAAAA
Found at i:1124651 original size:30 final size:30
Alignment explanation
Indices: 1124617--1124696 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 30
1124607 TTAAATTGTG
*
1124617 TACAATTGAATAAAATCAAAGTTTCATGTA
1 TACAATTGAATCAAATCAAAGTTTCATGTA
* *
1124647 TACAATTAAATCAAATTAAAGTTTCATGTA
1 TACAATTGAATCAAATCAAAGTTTCATGTA
* *
1124677 TATAATTGCATCAAATCAAA
1 TACAATTGAATCAAATCAAA
1124697 TCAATAAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.34
Consensus pattern (30 bp):
TACAATTGAATCAAATCAAAGTTTCATGTA
Found at i:1127289 original size:2 final size:2
Alignment explanation
Indices: 1127282--1127308 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1127272 AACTCGATTA
1127282 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1127309 AACTGAATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1127524 original size:48 final size:48
Alignment explanation
Indices: 1127442--1127535 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
1127432 TTTCTTGGCT
* *
1127442 TAAAAACGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
1127490 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
1127536 AGAATTCCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 4 0.10
48 38 0.90
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:1132873 original size:30 final size:31
Alignment explanation
Indices: 1132838--1132920 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
1132828 AAAAAAGATT
* * * *
1132838 AAGTACCAAATTAGGTATAAGTATCAAGTTC
1 AAGTACCAAATTAAGAAAAAATATCAAGTTC
*
1132869 -AGTACCAAACTAAGAAAAAATATCAAGTTC
1 AAGTACCAAATTAAGAAAAAATATCAAGTTC
*
1132899 AAGTACCAAATTGAACAAAAAA
1 AAGTACCAAATT-AAGAAAAAA
1132921 GTCTAGGTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 25 0.58
31 10 0.23
32 8 0.19
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.22
Consensus pattern (31 bp):
AAGTACCAAATTAAGAAAAAATATCAAGTTC
Found at i:1137872 original size:12 final size:13
Alignment explanation
Indices: 1137855--1137891 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1137845 GAACCGGACA
1137855 CGAACCGAA-CTC
1 CGAACCGAAGCTC
1137867 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
1137879 CGAACCGTAGCTC
1 CGAACCGAAGCTC
1137892 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:1139906 original size:16 final size:17
Alignment explanation
Indices: 1139885--1139917 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1139875 AAATTTTATA
1139885 TAAATAT-TTATAATTT
1 TAAATATATTATAATTT
1139901 TAAATATGATTATAATT
1 TAAATAT-ATTATAATT
1139918 AGATGAGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TAAATATATTATAATTT
Found at i:1140461 original size:21 final size:19
Alignment explanation
Indices: 1140437--1140484 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
1140427 TAGGATTCGT
*
1140437 GGTTCAAGGTTCGAGGTTTGA
1 GGTTCAAGATTC-AGGTTT-A
*
1140458 GGTTCAAGATTCAGGTTTT
1 GGTTCAAGATTCAGGTTTA
1140477 GGTTCAAG
1 GGTTCAAG
1140485 TTGATTCGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.32
20 6 0.24
21 11 0.44
ACGTcount: A:0.21, C:0.10, G:0.33, T:0.35
Consensus pattern (19 bp):
GGTTCAAGATTCAGGTTTA
Found at i:1145545 original size:54 final size:54
Alignment explanation
Indices: 1145463--1145573 Score: 222
Period size: 54 Copynumber: 2.1 Consensus size: 54
1145453 CCGGTGGAAG
1145463 ACGAAATGTTAGAGTTCTACAAGATAACAACCGAGAATCCAGAACAGAAAGGCA
1 ACGAAATGTTAGAGTTCTACAAGATAACAACCGAGAATCCAGAACAGAAAGGCA
1145517 ACGAAATGTTAGAGTTCTACAAGATAACAACCGAGAATCCAGAACAGAAAGGCA
1 ACGAAATGTTAGAGTTCTACAAGATAACAACCGAGAATCCAGAACAGAAAGGCA
1145571 ACG
1 ACG
1145574 GGATCGCGTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (54 bp):
ACGAAATGTTAGAGTTCTACAAGATAACAACCGAGAATCCAGAACAGAAAGGCA
Found at i:1146493 original size:21 final size:21
Alignment explanation
Indices: 1146469--1146510 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1146459 TATTTAATGG
1146469 TTATATTTAA-ATATTTAAAAT
1 TTATATTTAATATA-TTAAAAT
*
1146490 TTATATTTCATATATTAAAAT
1 TTATATTTAATATATTAAAAT
1146511 ATTAACAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATATTTAATATATTAAAAT
Found at i:1146723 original size:13 final size:13
Alignment explanation
Indices: 1146685--1146724 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1146675 TTTAAACCAA
*
1146685 ACTTTTCAAAAGC
1 ACTTTTCAAAAGT
1146698 ACTTCTT-AAAAGT
1 ACTT-TTCAAAAGT
1146711 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
1146724 A
1 A
1146725 ATGAAGAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 2 0.08
13 20 0.83
14 2 0.08
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.35
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:1150450 original size:162 final size:162
Alignment explanation
Indices: 1150266--1150626 Score: 530
Period size: 162 Copynumber: 2.2 Consensus size: 162
1150256 TGAAGAAAAT
** *
1150266 GGTGAAGATGCATATTTTGATGATTGGAGGTCTAAGCTTAGTAGCAACCAAGGATTTGTTGAAGA
1 GGTGAAGATGCATATTTTGATGATTGGAGGTCTAAGCTTAGTAGCAACCAAGGAAATGGTGAAGA
*
1150331 T-AATTATGTTGATGATTGGAGGTCTAAGCTTAGTAGCAACCATGGAAATGAAGAACTTGATGAT
66 TGAA-TATGTTGATGACTGGAGGTCTAAGCTTAGTAGCAACCATGGAAATGAAGAACTTGATGAT
*
1150395 TGG-GACCATGATTTTAGTGGCAGCCATGGAAAC
130 TGGAG-CCATGATTTTAGTGGCAGCCAGGGAAAC
* * * *
1150428 GGTGAAGATTCATATTTTGATGATTGGAGGTCTAAGCTTAGTGGTAACCATGGAAATGGTGAAGA
1 GGTGAAGATGCATATTTTGATGATTGGAGGTCTAAGCTTAGTAGCAACCAAGGAAATGGTGAAGA
* * *
1150493 TGCATATTTTGATGACTGGAGGTCTAAGCTTAGTAGCAACCATGGAAATGAAGAATTTGATGATT
66 TGAATATGTTGATGACTGGAGGTCTAAGCTTAGTAGCAACCATGGAAATGAAGAACTTGATGATT
*
1150558 GGAGCCATGATTTTAGTGGCAGCCAGGGAAAT
131 GGAGCCATGATTTTAGTGGCAGCCAGGGAAAC
* * *
1150590 AGTGAAGATGAATATTTTGAT-ACTTGGAGATCTAAGC
1 GGTGAAGATGCATATTTTGATGA-TTGGAGGTCTAAGC
1150627 CCAGTTCCAA
Statistics
Matches: 179, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
161 1 0.01
162 176 0.98
163 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.30
Consensus pattern (162 bp):
GGTGAAGATGCATATTTTGATGATTGGAGGTCTAAGCTTAGTAGCAACCAAGGAAATGGTGAAGA
TGAATATGTTGATGACTGGAGGTCTAAGCTTAGTAGCAACCATGGAAATGAAGAACTTGATGATT
GGAGCCATGATTTTAGTGGCAGCCAGGGAAAC
Found at i:1150541 original size:57 final size:57
Alignment explanation
Indices: 1150408--1150542 Score: 216
Period size: 57 Copynumber: 2.4 Consensus size: 57
1150398 GACCATGATT
* * * *
1150408 TTAGTGGCAGCCATGGAAACGGTGAAGATTCATATTTTGATGATTGGAGGTCTAAGC
1 TTAGTGGCAACCATGGAAATGGTGAAGATGCATATTTTGATGACTGGAGGTCTAAGC
*
1150465 TTAGTGGTAACCATGGAAATGGTGAAGATGCATATTTTGATGACTGGAGGTCTAAGC
1 TTAGTGGCAACCATGGAAATGGTGAAGATGCATATTTTGATGACTGGAGGTCTAAGC
*
1150522 TTAGTAGCAACCATGGAAATG
1 TTAGTGGCAACCATGGAAATG
1150543 AAGAATTTGA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 71 1.00
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.29
Consensus pattern (57 bp):
TTAGTGGCAACCATGGAAATGGTGAAGATGCATATTTTGATGACTGGAGGTCTAAGC
Found at i:1150552 original size:105 final size:105
Alignment explanation
Indices: 1150443--1150661 Score: 253
Period size: 105 Copynumber: 2.1 Consensus size: 105
1150433 AGATTCATAT
* * * * *
1150443 TTTGATGATTGGAGGTC-TAAGCTTAGTGGTAACCATGGAAATGGTGAAGATGCATATTTTGATG
1 TTTGATGATTGGA-GCCATAAGCTTAGTGGCAACCAGGGAAATAGTGAAGATGAATATTTTGAT-
* ** * * *
1150507 AC-TGGAGGTCTAAGCTTAGTAGCAACCATGGAAATGAAGAA
64 ACTTGGAGATCTAAGCCCAGTACCAACAATGGAAACGAAGAA
* ** *
1150548 TTTGATGATTGGAGCCATGATTTTAGTGGCAGCCAGGGAAATAGTGAAGATGAATATTTTGATAC
1 TTTGATGATTGGAGCCATAAGCTTAGTGGCAACCAGGGAAATAGTGAAGATGAATATTTTGATAC
* *
1150613 TTGGAGATCTAAGCCCAGTTCCAACAATGGAAACGGAGAA
66 TTGGAGATCTAAGCCCAGTACCAACAATGGAAACGAAGAA
1150653 TTTGATGAT
1 TTTGATGAT
1150662 CGGGACCATG
Statistics
Matches: 95, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
104 4 0.04
105 91 0.96
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.29
Consensus pattern (105 bp):
TTTGATGATTGGAGCCATAAGCTTAGTGGCAACCAGGGAAATAGTGAAGATGAATATTTTGATAC
TTGGAGATCTAAGCCCAGTACCAACAATGGAAACGAAGAA
Found at i:1150694 original size:105 final size:105
Alignment explanation
Indices: 1150465--1150680 Score: 274
Period size: 105 Copynumber: 2.1 Consensus size: 105
1150455 AGGTCTAAGC
* * * * * ** *
1150465 TTAGTGGTAACCATGGAAATGGTGAAGATGCATATTTTGATGACTGGAGGTCTAAGCTTAGTAGC
1 TTAGTGGCAGCCATGGAAATAGTGAAGATGAATATTTTGATGACTGGAGATCTAAGCCCAGTACC
* * *
1150530 AACCATGGAAATGAAGAATTTGATGATTGGAGCCATGATT
66 AACAATGGAAACGAAGAATTTGATGATGGGAGCCATGATT
* *
1150570 TTAGTGGCAGCCAGGGAAATAGTGAAGATGAATATTTTGAT-ACTTGGAGATCTAAGCCCAGTTC
1 TTAGTGGCAGCCATGGAAATAGTGAAGATGAATATTTTGATGAC-TGGAGATCTAAGCCCAGTAC
*
1150634 CAACAATGGAAACGGAGAATTTGATGATCGGGA-CCATGATT
65 CAACAATGGAAACGAAGAATTTGATGAT-GGGAGCCATGATT
1150675 TTAGTG
1 TTAGTG
1150681 CTCGTCATGG
Statistics
Matches: 95, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
104 2 0.02
105 90 0.95
106 3 0.03
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.28
Consensus pattern (105 bp):
TTAGTGGCAGCCATGGAAATAGTGAAGATGAATATTTTGATGACTGGAGATCTAAGCCCAGTACC
AACAATGGAAACGAAGAATTTGATGATGGGAGCCATGATT
Found at i:1152125 original size:25 final size:24
Alignment explanation
Indices: 1152097--1152146 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
1152087 TTTCACCTCC
1152097 AAACTCCAAAGTAAATCTAATAAAA
1 AAACTCCAAAGTAAATCTAA-AAAA
** *
1152122 AAACTCCACCGTGAATCTAAAAAA
1 AAACTCCAAAGTAAATCTAAAAAA
1152146 A
1 A
1152147 TCAACATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.56, C:0.20, G:0.06, T:0.18
Consensus pattern (24 bp):
AAACTCCAAAGTAAATCTAAAAAA
Found at i:1153449 original size:22 final size:22
Alignment explanation
Indices: 1153392--1153453 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
1153382 CCCAAAACCC
1153392 AACTAACCTAGCCCAATACCCTAA
1 AACT-ACCTAGCCCAATA-CCTAA
* *
1153416 ACCAACCTAGCCCAAT-CCTAA
1 AACTACCTAGCCCAATACCTAA
1153437 AACTACCTGAGCCCAAT
1 AACTACCT-AGCCCAAT
1153454 TTACAAACCC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 11 0.33
22 8 0.24
23 12 0.36
24 2 0.06
ACGTcount: A:0.39, C:0.39, G:0.06, T:0.16
Consensus pattern (22 bp):
AACTACCTAGCCCAATACCTAA
Found at i:1156393 original size:132 final size:134
Alignment explanation
Indices: 1156245--1156499 Score: 399
Period size: 132 Copynumber: 1.9 Consensus size: 134
1156235 ATGTACAAAT
*
1156245 ATATATTATTTGTTCTCAAAAGTCAACTATAAAAT-GGACAAGGTTAAAAGCAACATCTTTTACA
1 ATATATTATTTATTCTCAAAAGTCAACTATAAAATGGGA-AAGGTTAAAAGCAACATCTTTTACA
* ** *
1156309 ACAACAAAGTAGAAT-TTTTT-TTACAAGAGAGGTCAAACATTATTTTATAAGAAAAAAGAAAAA
65 AAAACAAAGTAGAATATTTTTCCAACAACAGAGGTCAAACATTATTTTATAAGAAAAAAGAAAAA
1156372 GAAAC
130 GAAAC
* * *
1156377 ATATATTATTTATTCTCAAAAGTCAACTATAAAATGGGAAATGTTAAAGGCAACATCTTTTGCAA
1 ATATATTATTTATTCTCAAAAGTCAACTATAAAATGGGAAAGGTTAAAAGCAACATCTTTTACAA
*
1156442 AAACAAAGTAGAATATTTTTCCAACAACAGAGGTCAAACATTATTTTATAGGAAAAAA
66 AAACAAAGTAGAATATTTTTCCAACAACAGAGGTCAAACATTATTTTATAAGAAAAAA
1156500 AAATTCTAAA
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
132 70 0.63
133 8 0.07
134 33 0.30
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (134 bp):
ATATATTATTTATTCTCAAAAGTCAACTATAAAATGGGAAAGGTTAAAAGCAACATCTTTTACAA
AAACAAAGTAGAATATTTTTCCAACAACAGAGGTCAAACATTATTTTATAAGAAAAAAGAAAAAG
AAAC
Found at i:1159038 original size:227 final size:227
Alignment explanation
Indices: 1158643--1159809 Score: 1385
Period size: 227 Copynumber: 5.2 Consensus size: 227
1158633 CCAATGCTGG
* * *
1158643 CTACCAGGCAGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTTATTTCCATTATA
1 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTTCATTATA
* * *
1158708 TGTATATATGTTAATGTTTAGGTTTTCGAGAACAGAACTCAACTGCT-TAAGCCAAATTAACTAA
66 TGTATATATATTAATGTTTAGGTTTTCGAGAATAAAACTCAACTG-TATAAGCCAAATTAACTAA
* * *
1158772 ACTTTAACATTTAAAATTTGGGTTTAAATGCTTTCAGACTATTCAGGTAATGGTACTGGACCATC
130 GCTTTAACATTTAAATTTTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATC
*
1158837 TAAGGAATTTAGTGCTCCAACCTCTCTAGGAGC
195 TAAGGAATTTAGTGCTCCAAGCTCTCTAGGAGC
1158870 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTTCATTATA
1 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTTCATTATA
* * **
1158935 TGTATATATATTAATATTTAGGTTTTTGAGAATAAAACTCAGTTGTATAAGCCAAATTAACTAAG
66 TGTATATATATTAATGTTTAGGTTTTCGAGAATAAAACTCAACTGTATAAGCCAAATTAACTAAG
*
1159000 CTTTAACATTTAAAATTTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCT
131 CTTTAACATTTAAATTTTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCT
*
1159065 AAGGAATTTAGTGCTCCAACCTCTCTAGGAGC
196 AAGGAATTTAGTGCTCCAAGCTCTCTAGGAGC
*
1159097 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTTC-TTTTA
1 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTTCATTATA
* * * * *** * * ** * *
1159161 GGT-TTTCGAGAATAAAACTCA-ATTGTTTAAGCCAA-ATTAACT-AAGCT-T-TAA--C-ATTT
66 TGTATAT--ATATTAATGTTTAGGTT-TTCGAG--AATA-AAACTCAA-CTGTATAAGCCAAATT
***
1159217 AA--AA--TTT-GGGTTTAAA-------------TGTTTTCAGACTATTCAGGTAATGGTACTGG
124 AACTAAGCTTTAACATTTAAATTTTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGG
*
1159264 ACCATCTAAGGAATTTAGTGCTCCAAGCTCTCTAGGTGC
189 ACCATCTAAGGAATTTAGTGCTCCAAGCTCTCTAGGAGC
*
1159303 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGA-TTTCTACTAT
1 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTTC-ATTAT
* * *
1159367 ATGTATATATGTTAATGTTTAGGTTTTCGAGAATAAAACTCAACTGT-TCGAGCCAAATTAACAA
65 ATGTATATATATTAATGTTTAGGTTTTCGAGAATAAAACTCAACTGTAT-AAGCCAAATTAACTA
* * * * * *
1159431 AGTTTTAACATTTAAATTTTGGGTCTAAATGTCTTCAGACTATTCAGGCAA-GAATACTAGACCA
129 AGCTTTAACATTTAAATTTTGGGTTTAAATGTTTTCAGACTATTCAGGTAATG-GTACTGGACCA
*
1159495 TCTAAGGAATTTAGTGCTCCAAGCTCTCTAGGTGC
193 TCTAAGGAATTTAGTGCTCCAAGCTCTCTAGGAGC
* * *
1159530 CTATCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTCCATTACA
1 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTTCATTATA
* * *
1159595 TGTATATATATGTTAATGTTTAGATTTTCGAAAATAAAACTCAACTGTATAAGCTAAATTAACTA
66 TGTATATATA--TTAATGTTTAGGTTTTCGAGAATAAAACTCAACTGTATAAGCCAAATTAACTA
* * * * **
1159660 AGCTTTAACATTTAAATTTTGAGTCTAAATATTTTCAGACTATTCAGGTAATAGTACTACACCAT
129 AGCTTTAACATTTAAATTTTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCAT
* * *
1159725 CTAAAGAATTTAGTACTCTAAGCTCTCTAGGTA-C
194 CTAAGGAATTTAGTGCTCCAAGCTCTCTAGG-AGC
** * *
1159759 CTACCAGGCCAGAAGTTATGAAAATAAACAATCAATCTC-AGGTAAATCATT
1 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATC-CAAGGTAAATCATT
1159810 ATGCCTACAT
Statistics
Matches: 813, Mismatches: 82, Indels: 88
0.83 0.08 0.09
Matches are distributed among these distances:
204 8 0.01
205 9 0.01
206 133 0.16
207 7 0.01
208 3 0.00
209 5 0.01
211 2 0.00
213 3 0.00
214 6 0.01
219 6 0.01
220 3 0.00
222 2 0.00
224 5 0.01
225 3 0.00
226 10 0.01
227 418 0.51
228 6 0.01
229 182 0.22
230 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (227 bp):
CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTTCATTATA
TGTATATATATTAATGTTTAGGTTTTCGAGAATAAAACTCAACTGTATAAGCCAAATTAACTAAG
CTTTAACATTTAAATTTTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCT
AAGGAATTTAGTGCTCCAAGCTCTCTAGGAGC
Found at i:1159307 original size:206 final size:206
Alignment explanation
Indices: 1158951--1159359 Score: 773
Period size: 206 Copynumber: 2.0 Consensus size: 206
1158941 TATATTAATA
* *
1158951 TTTAGGTTTTTGAGAATAAAACTCAGTTGTATAAGCCAAATTAACTAAGCTTTAACATTTAAAAT
1 TTTAGGTTTTCGAGAATAAAACTCAATTGTATAAGCCAAATTAACTAAGCTTTAACATTTAAAAT
1159016 TTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATTTAGTGCTC
66 TTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATTTAGTGCTC
1159081 CAACCTCTCTAGGAGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
131 CAACCTCTCTAGGAGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
1159146 TTTGATTTTCT
196 TTTGATTTTCT
*
1159157 TTTAGGTTTTCGAGAATAAAACTCAATTGTTTAAGCCAAATTAACTAAGCTTTAACATTTAAAAT
1 TTTAGGTTTTCGAGAATAAAACTCAATTGTATAAGCCAAATTAACTAAGCTTTAACATTTAAAAT
1159222 TTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATTTAGTGCTC
66 TTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATTTAGTGCTC
* *
1159287 CAAGCTCTCTAGGTGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
131 CAACCTCTCTAGGAGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
1159352 TTTGATTT
196 TTTGATTT
1159360 CTACTATATG
Statistics
Matches: 198, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
206 198 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (206 bp):
TTTAGGTTTTCGAGAATAAAACTCAATTGTATAAGCCAAATTAACTAAGCTTTAACATTTAAAAT
TTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATTTAGTGCTC
CAACCTCTCTAGGAGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
TTTGATTTTCT
Found at i:1159540 original size:433 final size:438
Alignment explanation
Indices: 1158724--1159809 Score: 1515
Period size: 433 Copynumber: 2.4 Consensus size: 438
1158714 TATGTTAATG
* * * *
1158724 TTTAGGTTTTCGAGAACAGAACTCAACTGCTTAAGCCAAATTAACTAAACTTTAACATTTAAAAT
1 TTTAGGTTTTCGAGAATAAAACTCAACTGTTTAAGCCAAATTAACTAAGCTTTAACATTTAAAAT
*
1158789 TTGGGTTTAAATGCTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATTTAGTGCTC
66 TTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATTTAGTGCTC
* *
1158854 CAACCTCTCTAGGAGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
131 CAAGCTCTCTAGGTGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
* * **
1158919 TTTGATTTTCATTATATGTATATATATTAATATTTAGGTTTTTGAGAATAAAACTCAGTTGTATA
196 TTTGATTTTCACTATATGTATATATATTAATATTTAGGTTTTCGAGAATAAAACTCAACTGTATA
* * * *
1158984 AGCCAAATTAACTAAGCTTTAACATTTAAAATTTGGGTTTAAATGTTTTCAGACTATTCAGGTAA
261 AGCCAAATTAACAAAGCTTTAACATTTAAAATTTGGGTCTAAATGTCTTCAGACTATTCAGGCAA
* *
1159049 TGGTACTGGACCATCTAAGGAATTTAGTGCTCCAACCTCTCTAGGAGCCTACCAGGCTGGAAGTT
326 TGATACTAGACCATCTAAGGAATTTAGTGCTCCAACCTCTCTAGGAGCCTACCAGGCTGGAAGTT
1159114 ATGGAAATGAACAATCAATCCAAGGTAAATCATTTGA-TT-TT-C-T-
391 ATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTCTTACATA
*
1159157 TTTAGGTTTTCGAGAATAAAACTCAATTGTTTAAGCCAAATTAACTAAGCTTTAACATTTAAAAT
1 TTTAGGTTTTCGAGAATAAAACTCAACTGTTTAAGCCAAATTAACTAAGCTTTAACATTTAAAAT
1159222 TTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATTTAGTGCTC
66 TTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATTTAGTGCTC
1159287 CAAGCTCTCTAGGTGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
131 CAAGCTCTCTAGGTGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
* *
1159352 TTTGA-TTTCTACTATATGTATATATGTTAATGTTTAGGTTTTCGAGAATAAAACTCAACTGT-T
196 TTTGATTTTC-ACTATATGTATATATATTAATATTTAGGTTTTCGAGAATAAAACTCAACTGTAT
* * *
1159415 CGAGCCAAATTAACAAAGTTTTAACATTTAAATTTTGGGTCTAAATGTCTTCAGACTATTCAGGC
260 -AAGCCAAATTAACAAAGCTTTAACATTTAAAATTTGGGTCTAAATGTCTTCAGACTATTCAGGC
* * *
1159480 AA-GAATACTAGACCATCTAAGGAATTTAGTGCTCCAAGCTCTCTAGGTGCCTATCAGGCTGGAA
324 AATG-ATACTAGACCATCTAAGGAATTTAGTGCTCCAACCTCTCTAGGAGCCTACCAGGCTGGAA
1159544 GTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTCCATTACATGTATATATA
388 GTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTT-C-TTAC--------ATA
* * *
1159605 TGTTAATGTTTAGATTTTCGAAAATAAAACTCAACTGTATAAGCTAAATTAACTAAGCTTTAACA
1 T-TT-A-G----G-TTTTCGAGAATAAAACTCAACTGTTTAAGCCAAATTAACTAAGCTTTAACA
* * * * * ** *
1159670 TTTAAATTTTGAGTCTAAATATTTTCAGACTATTCAGGTAATAGTACTACACCATCTAAAGAATT
58 TTTAAAATTTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATT
* * * ** * *
1159735 TAGTACTCTAAGCTCTCTAGGTACCTACCAGGCCAGAAGTTATGAAAATAAACAATCAATCTC-A
123 TAGTGCTCCAAGCTCTCTAGGTGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATC-CAA
1159799 GGTAAATCATT
187 GGTAAATCATT
1159810 ATGCCTACAT
Statistics
Matches: 581, Mismatches: 45, Indels: 31
0.88 0.07 0.05
Matches are distributed among these distances:
432 6 0.01
433 392 0.67
434 2 0.00
437 2 0.00
438 1 0.00
447 1 0.00
448 1 0.00
449 2 0.00
450 1 0.00
451 1 0.00
455 1 0.00
456 170 0.29
457 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (438 bp):
TTTAGGTTTTCGAGAATAAAACTCAACTGTTTAAGCCAAATTAACTAAGCTTTAACATTTAAAAT
TTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATTTAGTGCTC
CAAGCTCTCTAGGTGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
TTTGATTTTCACTATATGTATATATATTAATATTTAGGTTTTCGAGAATAAAACTCAACTGTATA
AGCCAAATTAACAAAGCTTTAACATTTAAAATTTGGGTCTAAATGTCTTCAGACTATTCAGGCAA
TGATACTAGACCATCTAAGGAATTTAGTGCTCCAACCTCTCTAGGAGCCTACCAGGCTGGAAGTT
ATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTCTTACATA
Found at i:1171106 original size:24 final size:22
Alignment explanation
Indices: 1171089--1171132 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1171079 ATTTTTACTA
1171089 ATTATAAATTTATGATTTATAC
1 ATTATAAATTTATGATTTATAC
1171111 ATTATAAAATATTAT-ATTTATA
1 ATTAT-AAAT-TTATGATTTATA
1171133 TTTTTTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 11 0.55
24 4 0.20
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTATAAATTTATGATTTATAC
Found at i:1176848 original size:7 final size:7
Alignment explanation
Indices: 1176834--1176862 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1176824 CTCAGTTTTC
1176834 TTTT-TT
1 TTTTCTT
1176840 TTTTCTT
1 TTTTCTT
1176847 TTTTCTT
1 TTTTCTT
1176854 TTTTCTT
1 TTTTCTT
1176861 TT
1 TT
1176863 CTAAGTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTCTT
Found at i:1176852 original size:18 final size:19
Alignment explanation
Indices: 1176829--1176864 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1176819 ACAAACTCAG
1176829 TTTTCTTTTTT-TTTTCTT
1 TTTTCTTTTTTCTTTTCTT
1176847 TTTTCTTTTTTCTTTTCT
1 TTTTCTTTTTTCTTTTCT
1176865 AAGTTTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTTCTTTTTTCTTTTCTT
Found at i:1178758 original size:17 final size:17
Alignment explanation
Indices: 1178730--1178769 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1178720 ATTTTAATAA
*
1178730 TTTAATAATTATTTATT
1 TTTAATAATTATATATT
1178747 TATTAA-AATTATATATT
1 T-TTAATAATTATATATT
1178764 TTTAAT
1 TTTAAT
1178770 TATTTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 4 0.20
17 12 0.60
18 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTAATAATTATATATT
Found at i:1180626 original size:30 final size:30
Alignment explanation
Indices: 1180590--1180660 Score: 124
Period size: 30 Copynumber: 2.3 Consensus size: 30
1180580 GGAGGTATGG
1180590 GATAGGTTCTACCTCGGACAACAACTCTAC
1 GATAGGTTCTACCTCGGACAACAACTCTAC
1180620 GATAGGTTCTACCTCGGACAACAACTCTAC
1 GATAGGTTCTACCTCGGACAACAACTCTAC
*
1180650 GTTAGTGTTCT
1 GATAG-GTTCT
1180661 TTCTCCGAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 34 0.87
31 5 0.13
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (30 bp):
GATAGGTTCTACCTCGGACAACAACTCTAC
Found at i:1183799 original size:93 final size:93
Alignment explanation
Indices: 1183612--1183812 Score: 219
Period size: 93 Copynumber: 2.2 Consensus size: 93
1183602 GGTTCTGACC
* * * *
1183612 ACCGAATCGTTGGTTTTAGTAACAGGATTGGGTGCTAAAGCAGGGGACATTGCCGGAGCTGGTGA
1 ACCGAATCATTGGTTTTAGTAACAGGATTGGGTGCTAAAGCAGGGGACATAGCCGGAGCTAGCGA
* ** *
1183677 AGACTTGCTTTCTTCACCGGATTTAACA
66 AGACTCGAATCCTTCACCGGATTTAACA
* *
1183705 ACCGAATCATTGGTTTTAGTAACCGGATTGGGTGCTACAA-CAGGGGACATAGCTGGAGCTAGCG
1 ACCGAATCATTGGTTTTAGTAACAGGATTGGGTGCTA-AAGCAGGGGACATAGCCGGAGCTAGCG
* * *
1183769 AAGAAAC-CGAATCCTT-ACTGGTTTTTACA
65 AAG--ACTCGAATCCTTCACCGGATTTAACA
* *
1183798 ACAGAAGCATTGGTT
1 ACCGAATCATTGGTT
1183813 GCTAAAACAG
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
93 81 0.90
94 7 0.08
95 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (93 bp):
ACCGAATCATTGGTTTTAGTAACAGGATTGGGTGCTAAAGCAGGGGACATAGCCGGAGCTAGCGA
AGACTCGAATCCTTCACCGGATTTAACA
Found at i:1183954 original size:75 final size:75
Alignment explanation
Indices: 1183731--1183962 Score: 295
Period size: 75 Copynumber: 3.1 Consensus size: 75
1183721 TAGTAACCGG
* * * * * ** * *
1183731 ATTGGGTGCTACAACAGGGGACATAGCTGGAGCTAGCGAAGAAACCGAATCCTTACTGGTTTTTA
1 ATTGGTTGCTAAAACAGGGGACATTGCCGGAACCGGCGAAGAAACCGAATCCTCACCGGTTTTTA
* *
1183796 CAACAGAAGC
66 CAACGGAATC
1183806 ATTGGTTGCTAAAACAGGGGACATTGCCGGAACCGGCGAAGAAACCGAATCCTCACCGGTTTTTA
1 ATTGGTTGCTAAAACAGGGGACATTGCCGGAACCGGCGAAGAAACCGAATCCTCACCGGTTTTTA
1183871 CAACGGAATC
66 CAACGGAATC
** * *
1183881 ATTGGTTGCTAATGCAGGGGGA-ATTGCCGGAGCCGGCGAAGAAACCGAATCCTCACCGGTTTTA
1 ATTGGTTGCTAAAACA-GGGGACATTGCCGGAACCGGCGAAGAAACCGAATCCTCACCGGTTTTT
*
1183945 ACAATGGAATC
65 ACAACGGAATC
*
1183956 ATCGGTT
1 ATTGGTT
1183963 TCAGTAATGG
Statistics
Matches: 139, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
75 134 0.96
76 5 0.04
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.22
Consensus pattern (75 bp):
ATTGGTTGCTAAAACAGGGGACATTGCCGGAACCGGCGAAGAAACCGAATCCTCACCGGTTTTTA
CAACGGAATC
Found at i:1187879 original size:18 final size:18
Alignment explanation
Indices: 1187856--1187894 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1187846 TTAGGATAAT
*
1187856 TAATTACGGTACTTATAG
1 TAATTACGGTAATTATAG
*
1187874 TAATTATGGTAATTATAG
1 TAATTACGGTAATTATAG
1187892 TAA
1 TAA
1187895 AGGTTATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.41
Consensus pattern (18 bp):
TAATTACGGTAATTATAG
Found at i:1192961 original size:20 final size:21
Alignment explanation
Indices: 1192936--1192984 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1192926 GCTTGGCTCG
1192936 GATACCCTTAAC-AAAGTATC
1 GATACCCTTAACAAAAGTATC
* **
1192956 GATACCTTTTTCAAAAGTATC
1 GATACCCTTAACAAAAGTATC
*
1192977 GACACCCT
1 GATACCCT
1192985 GCTTGAGAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.29
Consensus pattern (21 bp):
GATACCCTTAACAAAAGTATC
Found at i:1195056 original size:29 final size:29
Alignment explanation
Indices: 1195014--1195080 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
1195004 ATAGGGATTT
*
1195014 GATCAAATTAGT-CCTTCAACTATTAAATA
1 GATCAAATTAGTCCCTT-AACTATTAAAAA
* *
1195043 GATCAATTTAGTCCCTTTACTATTAAAAA
1 GATCAAATTAGTCCCTTAACTATTAAAAA
1195072 GAATCAAAT
1 G-ATCAAAT
1195081 AAGACCAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.34
Consensus pattern (29 bp):
GATCAAATTAGTCCCTTAACTATTAAAAA
Found at i:1197995 original size:14 final size:14
Alignment explanation
Indices: 1197976--1198002 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1197966 ACATGACTTT
1197976 GTAGGATTACAATG
1 GTAGGATTACAATG
1197990 GTAGGATTACAAT
1 GTAGGATTACAAT
1198003 TGACTAGATT
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:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (14 bp):
GTAGGATTACAATG
Found at i:1198183 original size:20 final size:21
Alignment explanation
Indices: 1198158--1198206 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1198148 GCCTGGCTCA
1198158 GATACCCTTAAC-AAAGTATC
1 GATACCCTTAACAAAAGTATC
**
1198178 GATACCCTTCCCAAAAGTATC
1 GATACCCTTAACAAAAGTATC
*
1198199 GACACCCT
1 GATACCCT
1198207 GCTTGAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.35, C:0.33, G:0.10, T:0.22
Consensus pattern (21 bp):
GATACCCTTAACAAAAGTATC
Found at i:1198659 original size:24 final size:24
Alignment explanation
Indices: 1198614--1198659 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1198604 TTCAATTTGT
** *
1198614 ATTAAATATTTTAATTATTTAAGC
1 ATTAAATATTTTAACAAATTAAGC
*
1198638 ATTAAATATTTTACCAAATTAA
1 ATTAAATATTTTAACAAATTAA
1198660 TATTTAAATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (24 bp):
ATTAAATATTTTAACAAATTAAGC
Found at i:1198746 original size:20 final size:23
Alignment explanation
Indices: 1198700--1198748 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
1198690 AAATTAAACT
*
1198700 AAAAATATTATTAAATTTATCAT
1 AAAAATATTATTAAATTTATCAA
*
1198723 AAAAAT-TTA-TAATTTTAT-AA
1 AAAAATATTATTAAATTTATCAA
1198743 AAAAAT
1 AAAAAT
1198749 CAAGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.29
21 8 0.33
22 3 0.12
23 6 0.25
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAAATATTATTAAATTTATCAA
Found at i:1199326 original size:51 final size:51
Alignment explanation
Indices: 1199264--1199463 Score: 188
Period size: 51 Copynumber: 3.9 Consensus size: 51
1199254 CCCTTATGAT
* * * *
1199264 CAATGCTATCCGGTATACATAGTAGCCTACACTTAGTACTACACATATGAC
1 CAATACTATCCGGTACACATAGTAGCCTACACATAGTACTACACATGTGAC
* * * * *
1199315 CAATACCATCCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGAC
1 CAATACTATCCGGTACACATAGTAGCCTACACATAGTACTACACATGTGAC
* * * * * * *
1199366 CGAA-GCTATCCAGTACACATAGTAGCCTGCACTTAATATTACATATGTGAC
1 C-AATACTATCCGGTACACATAGTAGCCTACACATAGTACTACACATGTGAC
*** *
1199417 C-ATAACTATCTTATACTCATAGTAGCCTACACATAGTACTACACATG
1 CAAT-ACTATCCGGTACACATAGTAGCCTACACATAGTACTACACATG
1199464 ATTTCTCATG
Statistics
Matches: 117, Mismatches: 29, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
49 1 0.01
51 114 0.97
52 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.26
Consensus pattern (51 bp):
CAATACTATCCGGTACACATAGTAGCCTACACATAGTACTACACATGTGAC
Found at i:1201559 original size:21 final size:20
Alignment explanation
Indices: 1201530--1201568 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1201520 AAGTCATCGT
*
1201530 GTGGATAAAAAGATAGAGAGA
1 GTGGAT-AAAAGAAAGAGAGA
*
1201551 GTGGTTAAAAGAAAGAGA
1 GTGGATAAAAGAAAGAGA
1201569 AAGAAAGTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.51, C:0.00, G:0.33, T:0.15
Consensus pattern (20 bp):
GTGGATAAAAGAAAGAGAGA
Found at i:1201691 original size:67 final size:67
Alignment explanation
Indices: 1201583--1201717 Score: 234
Period size: 67 Copynumber: 2.0 Consensus size: 67
1201573 AAGTAGGAAA
* * * *
1201583 AATGTTCTCTTGTATTGTTTTTATAGTCTCTTCCGTGCAATGATAAGTCGTATATATGACATCTC
1 AATGTTCTCTTGTATTGTTTTTATAGTCTCTTCAGTACAATGATAAATCATATATATGACATCTC
1201648 AC
66 AC
1201650 AATGTTCTCTTGTATTGTTTTTATAGTCTCTTCAGTACAATGATAAATCATATATATGACATCTC
1 AATGTTCTCTTGTATTGTTTTTATAGTCTCTTCAGTACAATGATAAATCATATATATGACATCTC
1201715 AC
66 AC
1201717 A
1 A
1201718 TGTCATGACA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (67 bp):
AATGTTCTCTTGTATTGTTTTTATAGTCTCTTCAGTACAATGATAAATCATATATATGACATCTC
AC
Found at i:1202960 original size:29 final size:29
Alignment explanation
Indices: 1202918--1202984 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
1202908 ATAGGGATTT
*
1202918 GATCAAATTAGT-CCTTCAACTATTAAATA
1 GATCAAATTAGTCCCTT-AACTATTAAAAA
* *
1202947 GATCAATTTAGTCCCTTTACTATTAAAAA
1 GATCAAATTAGTCCCTTAACTATTAAAAA
1202976 GAATCAAAT
1 G-ATCAAAT
1202985 AAGACCAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.34
Consensus pattern (29 bp):
GATCAAATTAGTCCCTTAACTATTAAAAA
Found at i:1213208 original size:4 final size:4
Alignment explanation
Indices: 1213193--1213228 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
1213183 TTTTTGTGTC
1213193 TAAT TAA- T-AT TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TA
1213229 TAAGCTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 2 0.07
4 27 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:1214526 original size:20 final size:20
Alignment explanation
Indices: 1214490--1214527 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1214480 TTATTTAGAA
*
1214490 TAAGGTAAAATTTTAAAAAT
1 TAAGGTAAAATTGTAAAAAT
1214510 TAAGGATAAAA-TGTAAAA
1 TAAGG-TAAAATTGTAAAA
1214528 TATATTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (20 bp):
TAAGGTAAAATTGTAAAAAT
Found at i:1215256 original size:31 final size:31
Alignment explanation
Indices: 1215179--1215262 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
1215169 AGAAAACAAA
* *
1215179 TGTATAACTGAATCAAAATTAAAGTTTTATG
1 TGTATAACTGAATCAAAATTAAAGTTTCATC
** *
1215210 T-TCATATGTGAATCAAAATTTAAGTTTCATC
1 TGT-ATAACTGAATCAAAATTAAAGTTTCATC
*
1215241 TGTATAACTGCATC-AAATTAAA
1 TGTATAACTGAATCAAAATTAAA
1215263 ATTCATATAC
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
30 8 0.19
31 33 0.79
32 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (31 bp):
TGTATAACTGAATCAAAATTAAAGTTTCATC
Found at i:1215569 original size:6 final size:6
Alignment explanation
Indices: 1215558--1215589 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1215548 TTTGCTTACA
*
1215558 AGTCGC AGTCGC AGTCGC AGTCGG AGTCGC AG
1 AGTCGC AGTCGC AGTCGC AGTCGC AGTCGC AG
1215590 CAGCAGCAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.28, G:0.38, T:0.16
Consensus pattern (6 bp):
AGTCGC
Found at i:1220468 original size:29 final size:30
Alignment explanation
Indices: 1220402--1220476 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
1220392 ATTATACTCA
* * *
1220402 TGGTCACTCAATTATCAGTAAATTTATATTT
1 TGGTCACTCAATTAT-AGAAAAGTTATAATT
* *
1220433 TGATCACTAAATTAT-GAAAAGTTATAATT
1 TGGTCACTCAATTATAGAAAAGTTATAATT
1220462 TGGTCACTCAATTAT
1 TGGTCACTCAATTAT
1220477 TTGAAATAGA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
29 24 0.65
31 13 0.35
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (30 bp):
TGGTCACTCAATTATAGAAAAGTTATAATT
Found at i:1223049 original size:18 final size:18
Alignment explanation
Indices: 1223028--1223066 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1223018 TGTATACTGC
*
1223028 ATTAACCGAATTAATCGA
1 ATTAACCGAATTAATCAA
*
1223046 ATTACCCGAATTAATCAA
1 ATTAACCGAATTAATCAA
1223064 ATT
1 ATT
1223067 GAATCACTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.31
Consensus pattern (18 bp):
ATTAACCGAATTAATCAA
Found at i:1227610 original size:20 final size:20
Alignment explanation
Indices: 1227596--1227667 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1227586 AAATATTTTC
1227596 AAAAATATAATAATAAATTT
1 AAAAATATAATAATAAATTT
*
1227616 AAAAATAT-ATAAAAAATGTT
1 AAAAATATAATAATAAAT-TT
*
1227636 GAAAATAATAATATATAAAATTT
1 AAAAAT-ATAATA-AT-AAATTT
*
1227659 TAAAATATA
1 AAAAATATA
1227668 TAAGAATTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 8 0.19
20 15 0.35
21 2 0.05
22 6 0.14
23 8 0.19
24 4 0.09
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAAATATAATAATAAATTT
Found at i:1227649 original size:24 final size:24
Alignment explanation
Indices: 1227622--1227670 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1227612 ATTTAAAAAT
1227622 ATATAAAAAATGTTGAAAATA-ATA
1 ATATAAAAAAT-TTGAAAATATATA
* *
1227646 ATATATAAAATTTTAAAATATATA
1 ATATAAAAAATTTGAAAATATATA
1227670 A
1 A
1227671 GAATTAGGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (24 bp):
ATATAAAAAATTTGAAAATATATA
Found at i:1229375 original size:13 final size:13
Alignment explanation
Indices: 1229357--1229384 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1229347 TAAATGCTGG
1229357 AGATGTCTGAACT
1 AGATGTCTGAACT
1229370 AGATGTCTGAACT
1 AGATGTCTGAACT
1229383 AG
1 AG
1229385 TATATCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (13 bp):
AGATGTCTGAACT
Found at i:1230448 original size:15 final size:15
Alignment explanation
Indices: 1230428--1230463 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1230418 TGTAACGAGG
*
1230428 AAGAAATAGAGTGTA
1 AAGAAATACAGTGTA
1230443 AAGAAATACAGTGTA
1 AAGAAATACAGTGTA
*
1230458 AGGAAA
1 AAGAAA
1230464 GGAATAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.03, G:0.25, T:0.17
Consensus pattern (15 bp):
AAGAAATACAGTGTA
Found at i:1230720 original size:21 final size:20
Alignment explanation
Indices: 1230673--1230714 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1230663 AAATGTAGTG
*
1230673 TATTTTTAAAATAAAAAATA
1 TATTTTAAAAATAAAAAATA
1230693 TATTTTAAAAATAAAAAA-A
1 TATTTTAAAAATAAAAAATA
1230712 TAT
1 TAT
1230715 GGTTTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TATTTTAAAAATAAAAAATA
Found at i:1231337 original size:13 final size:13
Alignment explanation
Indices: 1231319--1231343 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1231309 GAAGTTTTGA
1231319 AATTTAAAAAATT
1 AATTTAAAAAATT
1231332 AATTTAAAAAAT
1 AATTTAAAAAAT
1231344 ATAGAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTTAAAAAATT
Found at i:1240123 original size:22 final size:22
Alignment explanation
Indices: 1240095--1240141 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1240085 GAGGAACTAT
1240095 TTTGATCCGGTCCCTATAGTAC
1 TTTGATCCGGTCCCTATAGTAC
1240117 TTTGATCCGGTCCCTATAGTAC
1 TTTGATCCGGTCCCTATAGTAC
1240139 TTT
1 TTT
1240142 AACCATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (22 bp):
TTTGATCCGGTCCCTATAGTAC
Found at i:1248569 original size:31 final size:31
Alignment explanation
Indices: 1248520--1248582 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
1248510 GTTACAAAAT
*
1248520 AGTCACCGAGCTACTTGAACA-TTTTCATTTA
1 AGTCACCGAACTACTTGAA-AGTTTTCATTTA
* * *
1248551 AGTCATCGAACTATTTGAAAGTTTTTATTTA
1 AGTCACCGAACTACTTGAAAGTTTTCATTTA
1248582 A
1 A
1248583 ATTATTGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (31 bp):
AGTCACCGAACTACTTGAAAGTTTTCATTTA
Found at i:1253089 original size:15 final size:15
Alignment explanation
Indices: 1253065--1253094 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1253055 ATTCGACTAT
1253065 TTGGTCTTAAGAATG
1 TTGGTCTTAAGAATG
*
1253080 TTGGTTTTAAGAATG
1 TTGGTCTTAAGAATG
1253095 AGTGACTGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.27, T:0.43
Consensus pattern (15 bp):
TTGGTCTTAAGAATG
Found at i:1265031 original size:29 final size:31
Alignment explanation
Indices: 1264995--1265055 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
1264985 AAACCTTTTT
* *
1264995 ACTTTTCCCTCAAAACTTTTACTCCT-TCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
1265025 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
1265056 CTCCCAACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.36
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
Found at i:1265196 original size:30 final size:31
Alignment explanation
Indices: 1265160--1265219 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
1265150 AAAAATTTAG
*
1265160 TTTCCCCCAAAATTTTTACTCCC-TCCCATT
1 TTTCCCCCAAAACTTTTACTCCCTTCCCATT
* *
1265190 TTTCCCCTAAAACTTTTATTCCCTTCCCAT
1 TTTCCCCCAAAACTTTTACTCCCTTCCCAT
1265220 CTCACCTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTCCCCCAAAACTTTTACTCCCTTCCCATT
Found at i:1269534 original size:15 final size:14
Alignment explanation
Indices: 1269504--1269543 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
1269494 AAGAAAAAAT
*
1269504 AAATTAATTTAAATG
1 AAATTAATTT-TATG
1269519 AAATTTAATTTTATG
1 AAA-TTAATTTTATG
1269534 AAATTAATTT
1 AAATTAATTT
1269544 AAGTGTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.30
15 9 0.39
16 7 0.30
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (14 bp):
AAATTAATTTTATG
Found at i:1271530 original size:22 final size:23
Alignment explanation
Indices: 1271504--1271550 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1271494 TATCCAGATT
*
1271504 TATTTCGA-TATAAATTTAAATA
1 TATTTCGATTATAAATCTAAATA
*
1271526 TATTTCGATTATCAATCTAAATA
1 TATTTCGATTATAAATCTAAATA
1271549 TA
1 TA
1271551 CGTTTTAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (23 bp):
TATTTCGATTATAAATCTAAATA
Found at i:1272706 original size:23 final size:22
Alignment explanation
Indices: 1272670--1272757 Score: 68
Period size: 23 Copynumber: 3.7 Consensus size: 22
1272660 CTACCTTGTC
*
1272670 TGGACAGCTCTTATACATCAATT
1 TGGACAGCT-TTATACACCAATT
* *
1272693 TGGACAGCATTTATATACCAAAT
1 TGGACAGC-TTTATACACCAATT
** *
1272716 TAAACAACATTTATACACCAAAATT
1 TGGACAGC-TTTATACACC--AATT
1272741 TGGACAGCTTATATACA
1 TGGACAGCTT-TATACA
1272758 ACAAATGGGC
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
23 33 0.66
24 3 0.06
25 14 0.28
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (22 bp):
TGGACAGCTTTATACACCAATT
Found at i:1272775 original size:22 final size:23
Alignment explanation
Indices: 1272745--1272913 Score: 105
Period size: 24 Copynumber: 7.4 Consensus size: 23
1272735 AAAATTTGGA
* *
1272745 CAGCTTATATACAACAAA-TGGG
1 CAGCATATATACAACAAATTGAG
* * * *
1272767 CAGCATATACATACCAAATTTAG
1 CAGCATATATACAACAAATTGAG
* * * * *
1272790 CAGCATTTTTACACCAAAATTTAA
1 CAGCATATATACAAC-AAATTGAG
*
1272814 CAGCATATATACAACAAA-TGGG
1 CAGCATATATACAACAAATTGAG
1272836 CAGCATATACGTAC--CAAATTGAG
1 CAGCATATA--TACAACAAATTGAG
* * * * * *
1272859 CAACATTTTTACACCAAAATTTAA
1 CAGCATATATACAAC-AAATTGAG
1272883 CAGCATATATACAACAAATTG-G
1 CAGCATATATACAACAAATTGAG
1272905 CAGCATATA
1 CAGCATATA
1272914 CATAGTACAT
Statistics
Matches: 110, Mismatches: 29, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
21 3 0.03
22 37 0.34
23 31 0.28
24 39 0.35
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.25
Consensus pattern (23 bp):
CAGCATATATACAACAAATTGAG
Found at i:1272826 original size:24 final size:23
Alignment explanation
Indices: 1272696--1272902 Score: 103
Period size: 23 Copynumber: 8.9 Consensus size: 23
1272686 ATCAATTTGG
* * *
1272696 ACAGCATTTATATACCAAATTAA
1 ACAGCATATATACACCAAATTTA
* * *
1272719 ACAACATTTATACACCAAAATTTGG
1 ACAGCATATATACACC-AAATTT-A
* * **
1272744 ACAGCTTATATACAACAAA-TGG
1 ACAGCATATATACACCAAATTTA
* * *
1272766 GCAGCATATACATACCAAATTTA
1 ACAGCATATATACACCAAATTTA
* * *
1272789 GCAGCATTTTTACACCAAAATTTA
1 ACAGCATATATACACC-AAATTTA
* **
1272813 ACAGCATATATACAACAAA-TGG
1 ACAGCATATATACACCAAATTTA
* *** *
1272835 GCAGCATATACGTACCAAATTGA
1 ACAGCATATATACACCAAATTTA
* * * *
1272858 GCAACATTTTTACACCAAAATTTA
1 ACAGCATATATACACC-AAATTTA
*
1272882 ACAGCATATATACAACAAATT
1 ACAGCATATATACACCAAATT
1272903 GGCAGCATAT
Statistics
Matches: 134, Mismatches: 44, Indels: 12
0.71 0.23 0.06
Matches are distributed among these distances:
22 30 0.22
23 48 0.36
24 44 0.33
25 12 0.09
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (23 bp):
ACAGCATATATACACCAAATTTA
Found at i:1272842 original size:69 final size:69
Alignment explanation
Indices: 1272697--1272917 Score: 334
Period size: 69 Copynumber: 3.2 Consensus size: 69
1272687 TCAATTTGGA
* * * * * *
1272697 CAGCATTTATATACCAAATTAAACAACATTTATACACCAAAATTTGGACAGCTTATATACAACAA
1 CAGCATATACATACCAAATTAAGCAACATTTTTACACCAAAATTT-AACAGCATATATACAACAA
1272762 ATGGG
65 ATGGG
* *
1272767 CAGCATATACATACCAAATTTAGCAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAA
1 CAGCATATACATACCAAATTAAGCAACATTTTTACACCAAAATTTAACAGCATATATACAACAAA
1272832 TGGG
66 TGGG
* *
1272836 CAGCATATACGTACCAAATTGAGCAACATTTTTACACCAAAATTTAACAGCATATATACAACAAA
1 CAGCATATACATACCAAATTAAGCAACATTTTTACACCAAAATTTAACAGCATATATACAACAAA
*
1272901 TTGG
66 TGGG
1272905 CAGCATATACATA
1 CAGCATATACATA
1272918 GTACATCATA
Statistics
Matches: 138, Mismatches: 13, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
69 99 0.72
70 39 0.28
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.26
Consensus pattern (69 bp):
CAGCATATACATACCAAATTAAGCAACATTTTTACACCAAAATTTAACAGCATATATACAACAAA
TGGG
Found at i:1274487 original size:69 final size:69
Alignment explanation
Indices: 1274401--1274597 Score: 304
Period size: 69 Copynumber: 2.8 Consensus size: 69
1274391 TTTGTACTAA
*
1274401 CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTCAATTTGGTACGTATAT
1 CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTAAATTTGGTACGTATAT
1274466 GCTG
66 GCTG
* * *
1274470 CCCATTTGTTGTGTATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTAAATTTGGTATGTATAT
1 CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTAAATTTGGTACGTATAT
1274535 GCTG
66 GCTG
* * * * *
1274539 CCCATTTGTTGTATATAAGCTGTCCAAATTTTGGTGTATAAATGTTGTTTAATTTGGTA
1 CCCATTTGTTGTATATATGCTGT-TAAATTTTGGTGTAAAAATGTTGCTAAATTTGGTA
1274598 TATAAATGCT
Statistics
Matches: 116, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
69 86 0.74
70 30 0.26
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (69 bp):
CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTAAATTTGGTACGTATAT
GCTG
Done.