Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold273
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: 1282806
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 4 of 9
Found at i:475454 original size:16 final size:16
Alignment explanation
Indices: 475429--475459 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
475419 GATTAAATTT
475429 AAAAGCTCAATCCTCA
1 AAAAGCTCAATCCTCA
*
475445 AAAAGTTCAATCCTC
1 AAAAGCTCAATCCTC
475460 TTTATTATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.29, G:0.06, T:0.23
Consensus pattern (16 bp):
AAAAGCTCAATCCTCA
Found at i:476817 original size:74 final size:74
Alignment explanation
Indices: 476696--476844 Score: 271
Period size: 74 Copynumber: 2.0 Consensus size: 74
476686 TTATTCCTAA
* *
476696 TTTGTATATAATTTTCAAATGGACTTCGTAGCTATCTTTGATCATGACACAACTTCTCATGTGTA
1 TTTGTATATAATTTTCAAATGGACTTCGCAGCTATCTTTGATCATGACACAACTTCTCATGTGCA
476761 TAGATTTTC
66 TAGATTTTC
*
476770 TTTGTATATAATTTTCAAATGGACTTCGCAGCTATCTTTGATCATGACATAACTTCTCATGTGCA
1 TTTGTATATAATTTTCAAATGGACTTCGCAGCTATCTTTGATCATGACACAACTTCTCATGTGCA
476835 TAGATTTTC
66 TAGATTTTC
476844 T
1 T
476845 CTTTCTCTTC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (74 bp):
TTTGTATATAATTTTCAAATGGACTTCGCAGCTATCTTTGATCATGACACAACTTCTCATGTGCA
TAGATTTTC
Found at i:478357 original size:19 final size:21
Alignment explanation
Indices: 478322--478368 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
478312 CTATTTTATA
*
478322 TTATA-ATTCTAT-TTAAATT
1 TTATATATTCTATATAAAATT
478341 TTATATATT-TATATAAAATT
1 TTATATATTCTATATAAAATT
478361 TTAT-TATT
1 TTATATATT
478369 ATAATATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATATATTCTATATAAAATT
Found at i:478470 original size:37 final size:37
Alignment explanation
Indices: 478400--478470 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
478390 ATTTTAATAT
* * *
478400 ATTATATATTTATATTATCTTTCTATTTTTTTATCAA
1 ATTATATATTTATATTATATTTCTAATTATTTATCAA
*
478437 ATTATAT-TTTATATTATATATTTTAATTATTTAT
1 ATTATATATTTATATTATAT-TTCTAATTATTTAT
478471 TAGGGTATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 11 0.38
37 18 0.62
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.63
Consensus pattern (37 bp):
ATTATATATTTATATTATATTTCTAATTATTTATCAA
Found at i:478471 original size:13 final size:14
Alignment explanation
Indices: 478439--478471 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
478429 TTTATCAAAT
478439 TATATTTTATATTA
1 TATATTTTATATTA
478453 TATATTTTA-ATTA
1 TATATTTTATATTA
*
478466 TTTATT
1 TATATT
478472 AGGGTATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATATTTTATATTA
Found at i:478836 original size:25 final size:27
Alignment explanation
Indices: 478787--478838 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
478777 AATTTTAAAT
* *
478787 TATTATTTAAATATTTAATTAAATATA
1 TATTATTTAAATATTAAAATAAATATA
478814 TATTATTTAAAT-TTAAAAT-AATATA
1 TATTATTTAAATATTAAAATAAATATA
478839 AAATTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 5 0.22
27 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TATTATTTAAATATTAAAATAAATATA
Found at i:478993 original size:8 final size:9
Alignment explanation
Indices: 478959--478990 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
478949 CATTTAAAAT
478959 TAAAATTAA
1 TAAAATTAA
478968 -AAAATTAA
1 TAAAATTAA
478976 TAAAATTAA
1 TAAAATTAA
478985 TAAAAT
1 TAAAAT
478991 AATTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAAATTAA
Found at i:479109 original size:26 final size:26
Alignment explanation
Indices: 479080--479138 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
479070 ATAAATTATT
*
479080 TAAAAAAGCAAA-AAAAATATTAAAAC
1 TAAAAAACCAAATAAAAA-ATTAAAAC
* * *
479106 TAAAAACCCAAATTAAAAATTAAAAT
1 TAAAAAACCAAATAAAAAATTAAAAC
479132 TAAAAAA
1 TAAAAAA
479139 AATATAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.19
Consensus pattern (26 bp):
TAAAAAACCAAATAAAAAATTAAAAC
Found at i:479141 original size:16 final size:16
Alignment explanation
Indices: 479120--479152 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
479110 AACCCAAATT
479120 AAAAAT-TAAAATTAAA
1 AAAAATATAAAA-TAAA
479136 AAAAATATAAAATAAA
1 AAAAATATAAAATAAA
479152 A
1 A
479153 TCCATCACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATATAAAATAAA
Found at i:480625 original size:13 final size:14
Alignment explanation
Indices: 480606--480638 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
480596 CGTCAATATA
480606 GTTTTTTTTCAATT
1 GTTTTTTTTCAATT
480620 -TTTTTTTTCAATT
1 GTTTTTTTTCAATT
480633 GTTTTT
1 GTTTTT
480639 GTTTTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (14 bp):
GTTTTTTTTCAATT
Found at i:480659 original size:25 final size:25
Alignment explanation
Indices: 480641--480702 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 25
480631 TTGTTTTTGT
480641 TTTTTTTATAGTTTTTTGTTTTCTTA
1 TTTTTTTA-AGTTTTTTGTTTTCTTA
* *
480667 GTTTTTTTAAGTTTTTT-TTAT-ATA
1 -TTTTTTTAAGTTTTTTGTTTTCTTA
480691 TTTTTTTAAGTT
1 TTTTTTTAAGTT
480703 ATAGTATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 12 0.36
24 2 0.06
25 3 0.09
26 8 0.24
27 8 0.24
ACGTcount: A:0.16, C:0.02, G:0.08, T:0.74
Consensus pattern (25 bp):
TTTTTTTAAGTTTTTTGTTTTCTTA
Found at i:484375 original size:89 final size:89
Alignment explanation
Indices: 484102--484375 Score: 313
Period size: 89 Copynumber: 3.1 Consensus size: 89
484092 TAAAGACTAA
* * * * * *
484102 TTTCAAGAAATTTATTAGG-AATTGTCAAATATTTTCTATTGTGTTAGAAAGAATTTGATACCCA
1 TTTCAAGAAATTTATTAGGCAATAGTCAAATATTTTCTGTTGTGTCAAAAAGAATATGATACCTA
* * * *
484166 CATGCATTTATCACA-TCTTCTAAG
66 CATGCATCTGTCACATTTTTC-AGG
* * * *
484190 TTTCAAGAAATTTATTAGGCATTAGTTAAATATTTTCTGTTGTGTCAAAAGGAATCTGATATCCT
1 TTTCAAGAAATTTATTAGGCAATAGTCAAATATTTTCTGTTGTGTCAAAAAGAATATGATA-CCT
* * *
484255 -CATTCATCTGTCATATCTTTT-GGG
65 ACATGCATCTGTCACAT-TTTTCAGG
* *
484279 TTTCAAGAAATTTATTAGGCAATAGTCAAATATTTTCTGTCGTGTCAAAAAGAATATGATACGTA
1 TTTCAAGAAATTTATTAGGCAATAGTCAAATATTTTCTGTTGTGTCAAAAAGAATATGATACCTA
484344 CATGCATCTGTCACATTTTTCAGG
66 CATGCATCTGTCACATTTTTCAGG
*
484368 TTCCAAGA
1 TTTCAAGA
484376 TTAATTTTAT
Statistics
Matches: 154, Mismatches: 26, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
88 25 0.16
89 124 0.81
90 2 0.01
91 3 0.02
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (89 bp):
TTTCAAGAAATTTATTAGGCAATAGTCAAATATTTTCTGTTGTGTCAAAAAGAATATGATACCTA
CATGCATCTGTCACATTTTTCAGG
Found at i:487744 original size:52 final size:52
Alignment explanation
Indices: 487599--487724 Score: 216
Period size: 52 Copynumber: 2.4 Consensus size: 52
487589 AATATGAAAT
* *
487599 TTTGCCTGCATATATCGATACATTTCATAGTATATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
* *
487651 TTTGCCTGTAAGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
487703 TTTGCCTGCATGTATCGATACA
1 TTTGCCTGCATGTATCGATACA
487725 AAGATCAGTG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
Found at i:487834 original size:19 final size:19
Alignment explanation
Indices: 487810--487874 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
487800 AGCGATACAT
487810 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
487829 TGTATCAATAC---A--T-
1 TGTATCGATACAAAACTTA
*
487842 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
487861 TGTATCGATACAAA
1 TGTATCGATACAAA
487875 TCGTTGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
13 10 0.27
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.62
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:487845 original size:32 final size:32
Alignment explanation
Indices: 487804--487872 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
487794 CTTCGTAGCG
487804 ATACATTGTATCGATACAAAACTTATGTATCA
1 ATACATTGTATCGATACAAAACTTATGTATCA
* *
487836 ATACATTGTATCGATACAACACTTATGTATCG
1 ATACATTGTATCGATACAAAACTTATGTATCA
487868 ATACA
1 ATACA
487873 AATCGTTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.33
Consensus pattern (32 bp):
ATACATTGTATCGATACAAAACTTATGTATCA
Found at i:488822 original size:55 final size:52
Alignment explanation
Indices: 488731--489535 Score: 592
Period size: 43 Copynumber: 17.1 Consensus size: 52
488721 GAAGGTGAGA
* * * * * * *
488731 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTT
1 AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * *
488782 AAAGATGAAAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTT
1 AAAGATG--AAAAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
488837 AAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T
1 AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
488888 -----T---AAAGGTGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * *
488932 -AA-A-GAAGAAGGTGCCAATATGCTAATTCAAGGACAGCTATATTTGAC-T
1 AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
488980 -----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
489024 -AA-A-GAAGAAGGTGTCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T
1 AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
489072 -----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
489116 AAAGATG---AAGGTGCCAATATGTTGATTCAAGGCCAGCTATATTGGGC-T
1 AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
489164 -----T---AAAGGTGCCAATGTGCTGATTTAAGGCCAGCTACATTGGACTT
1 AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
489208 AAAGATG---AAGGTACCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T
1 AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * * *
489256 -----T---AAAGGTACCAATGTGCTAATTCAAGGCTAGCTACATTGGACTT
1 AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
489300 AAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T
1 AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
489348 -----T---AAAGGTACCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
489392 AAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T
1 AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
489440 -----T---AAAGGTGCCAATGTGCTGATTCAAGGCCACCTACATTGGACTT
1 AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
489484 AAAGATG--AAA-GTGCCAATATGCTGGTTCAAGGCCAGCTATATTGAACTT
1 AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
489533 AAA
1 AAA
489536 AGGGTTGCCA
Statistics
Matches: 619, Mismatches: 76, Indels: 120
0.76 0.09 0.15
Matches are distributed among these distances:
43 259 0.42
44 7 0.01
46 1 0.00
48 6 0.01
49 257 0.42
50 3 0.00
51 5 0.01
52 34 0.05
53 6 0.01
54 5 0.01
55 36 0.06
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (52 bp):
AAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:488983 original size:92 final size:92
Alignment explanation
Indices: 488793--489535 Score: 1261
Period size: 92 Copynumber: 8.0 Consensus size: 92
488783 AAGATGAAAA
* *
488793 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAAT
488858 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
488889 AAAGGTGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* * *
488954 TAATTCAAGGACAGCTATATTTGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* *
488981 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGTCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
489046 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
489073 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
489138 TGATTCAAGGCCAGCTATATTGGGCTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* *
489165 AAAGGTGCCAATGTGCTGATTTAAGGCCAGCTACATTGGACTTAAAGATGAAGGTACCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
489230 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* * *
489257 AAAGGTACCAATGTGCTAATTCAAGGCTAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
489322 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
489349 AAAGGTACCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
489414 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* *
489441 AAAGGTGCCAATGTGCTGATTCAAGGCCACCTACATTGGACTTAAAGATGAAAGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
489506 TGGTTCAAGGCCAGCTATATTGAACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
489533 AAA
1 AAA
489536 AGGGTTGCCA
Statistics
Matches: 617, Mismatches: 30, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
92 569 0.92
94 1 0.00
95 42 0.07
96 5 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:489719 original size:57 final size:56
Alignment explanation
Indices: 489533--489824 Score: 334
Period size: 57 Copynumber: 5.0 Consensus size: 56
489523 TATTGAACTT
* * *
489533 AAAAGGGTTGCCACCGACTTATGTGAGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAAGGG-TGCCACTGA-TT-TGTGGGCTTTG-AAGGTTGCCACTGACTTGTGGGCTTTG
* * **
489593 AAAAGGGTTGCCACCGACTCGTGTGGGCTTTGAAAATAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGG-TGCCACTGA-T-TTGTGGGCTTTGAAGGT--TGCCACTGACTTGTGGGCTTTG
* *
489654 AAAA-GGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGATTTGTGGGCTTCG
1 AAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTG
* *
489709 AAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGATTTATGGGCTTTGG
1 -AAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTT-G
* *
489767 AAAAGGGTGCCACTGATTTGTGGGCTTCGGAAAAGGGTGCCACTGACTTGTGGGCTTT
1 AAAAGGGTGCCACTGATTTGTGGGCTT-TG--AAGGTTGCCACTGACTTGTGGGCTTT
489825 TGCAGAAAAG
Statistics
Matches: 206, Mismatches: 17, Indels: 18
0.85 0.07 0.07
Matches are distributed among these distances:
55 20 0.10
56 4 0.02
57 89 0.43
58 3 0.01
59 10 0.05
60 54 0.26
61 26 0.13
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (56 bp):
AAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTG
Found at i:489723 original size:30 final size:29
Alignment explanation
Indices: 489533--489824 Score: 326
Period size: 30 Copynumber: 10.0 Consensus size: 29
489523 TATTGAACTT
* *
489533 AAAAGGGTTGCCACCGACTTATGTGAGCTTTG
1 AAAAGGG-TGCCACTGA-TT-TGTGGGCTTTG
* *
489565 -AAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGATTTGTGGGCTTTG
* *
489593 AAAAGGGTTGCCACCGACTCGTGTGGGCTTTG
1 AAAAGGG-TGCCACTGA-T-TTGTGGGCTTTG
** *
489625 AAAATAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGATTTGTGGGCTTTG
489654 AAAA-GGTGCCACTGATTTGTGGGCTTTG
1 AAAAGGGTGCCACTGATTTGTGGGCTTTG
* *
489682 --AAGGTTGCCACTGATTTGTGGGCTTCG
1 AAAAGGGTGCCACTGATTTGTGGGCTTTG
489709 AAAAAGGGTGCCACTGATTTGTGGGCTTTG
1 -AAAAGGGTGCCACTGATTTGTGGGCTTTG
* *
489739 --AAGGTTGCCACTGATTTATGGGCTTTGG
1 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
*
489767 AAAAGGGTGCCACTGATTTGTGGGCTTCGG
1 AAAAGGGTGCCACTGATTTGTGGGCTT-TG
*
489797 AAAAGGGTGCCACTGACTTGTGGGCTTT
1 AAAAGGGTGCCACTGATTTGTGGGCTTT
489825 TGCAGAAAAG
Statistics
Matches: 222, Mismatches: 26, Indels: 27
0.81 0.09 0.10
Matches are distributed among these distances:
26 2 0.01
27 46 0.21
28 33 0.15
29 21 0.09
30 91 0.41
31 13 0.06
32 16 0.07
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (29 bp):
AAAAGGGTGCCACTGATTTGTGGGCTTTG
Found at i:489801 original size:87 final size:86
Alignment explanation
Indices: 489533--489824 Score: 358
Period size: 87 Copynumber: 3.3 Consensus size: 86
489523 TATTGAACTT
* * *
489533 AAAAGGGTTGCCACCGACTTATGTGAGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAG
1 AAAAGGG-TGCCACTGAC-T-TGTGGGCTTTGAAAGG-TGCCACTGATTTGTGGGCTTTGAAAAG
* * *
489598 GGTTGCCACCGACTCGTGTGGGCTT-TG
62 GG-TGCCACTGA-T-TTGTGGGCTTCGG
** *
489625 AAAATAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGATTTGTGGGCTTTG--AAGGTT
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGTGCCACTGATTTGTGGGCTTTGAAAAGGGT
*
489688 GCCACTGATTTGTGGGCTTCGA
65 GCCACTGATTTGTGGGCTTCGG
* *
489710 AAAAGGGTGCCACTGATTTGTGGGCTTTG-AAGGTTGCCACTGATTTATGGGCTTTGGAAAAGGG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG-TGCCACTGATTTGTGGGCTTT-GAAAAGGG
489774 TGCCACTGATTTGTGGGCTTCGG
64 TGCCACTGATTTGTGGGCTTCGG
489797 AAAAGGGTGCCACTGACTTGTGGGCTTT
1 AAAAGGGTGCCACTGACTTGTGGGCTTT
489825 TGCAGAAAAG
Statistics
Matches: 177, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
83 4 0.02
84 29 0.16
85 28 0.16
86 8 0.05
87 57 0.32
89 31 0.18
90 6 0.03
91 9 0.05
92 5 0.03
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (86 bp):
AAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGTGCCACTGATTTGTGGGCTTTGAAAAGGGTG
CCACTGATTTGTGGGCTTCGG
Found at i:489872 original size:30 final size:31
Alignment explanation
Indices: 489804--489924 Score: 120
Period size: 31 Copynumber: 3.9 Consensus size: 31
489794 CGGAAAAGGG
* * * * *
489804 TGCCACTGACTTGTGGGCTTTTGCAGAAAAGGA
1 TGCCACTGAGTCGTGGAC-TTTG-AGAAGAGAA
*
489837 TGCCACTAAGTCGTGGACTTTGAGATA-A-AA
1 TGCCACTGAGTCGTGGACTTTGAGA-AGAGAA
* *
489867 TGCCACTGAGTCGTGGGCTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAA
*
489898 TGCCACTGAGTCGTGGACTTTAAGAAG
1 TGCCACTGAGTCGTGGACTTTGAGAAG
489925 GTATTTGAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
29 1 0.01
30 25 0.33
31 30 0.40
32 5 0.07
33 14 0.19
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTGAGAAGAGAA
Found at i:498252 original size:52 final size:52
Alignment explanation
Indices: 498177--498302 Score: 225
Period size: 52 Copynumber: 2.4 Consensus size: 52
498167 AATATGAAAT
*
498177 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCTATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
* *
498229 TTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGTAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
498281 TTTGCCTGCATGTATCGATACA
1 TTTGCCTGCATGTATCGATACA
498303 AAGATCAGTA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
Found at i:498422 original size:32 final size:32
Alignment explanation
Indices: 498380--498482 Score: 161
Period size: 32 Copynumber: 3.2 Consensus size: 32
498370 AGCTTCGTAG
*
498380 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
* * *
498412 CGATATATTGTATCAATACAACACTTATATAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
498444 CAATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
498476 CGATACA
1 CGATACA
498483 AATCGTTGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:498984 original size:15 final size:15
Alignment explanation
Indices: 498958--498995 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
498948 TTCTTCCTAA
498958 ATGGCTTCTTCTT-G
1 ATGGCTTCTTCTTGG
498972 AGTGGCTTCTTCTTGG
1 A-TGGCTTCTTCTTGG
498988 ATGGCTTC
1 ATGGCTTC
498996 ATCTGCAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 19 0.86
16 2 0.09
ACGTcount: A:0.08, C:0.21, G:0.26, T:0.45
Consensus pattern (15 bp):
ATGGCTTCTTCTTGG
Found at i:501062 original size:21 final size:21
Alignment explanation
Indices: 501038--501082 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
501028 TTTATCGTAC
* *
501038 TAAAATTAAACTTAGTTATAA
1 TAAAATTAAACTTAATAATAA
*
501059 TAAAATTAAATTTAATAATAA
1 TAAAATTAAACTTAATAATAA
501080 TAA
1 TAA
501083 TAAATTACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAAATTAAACTTAATAATAA
Found at i:501197 original size:23 final size:21
Alignment explanation
Indices: 501151--501200 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
501141 TCATAAGAAT
*
501151 AAAAAAAAAAAAAAACATATC
1 AAAAAAAAAAAAAAACATAGC
501172 AAAACAAAAAAAAAAACACTAGC
1 AAAA-AAAAAAAAAAACA-TAGC
501195 AAAAAA
1 AAAAAA
501201 TTACATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 4 0.15
22 15 0.58
23 7 0.27
ACGTcount: A:0.80, C:0.12, G:0.02, T:0.06
Consensus pattern (21 bp):
AAAAAAAAAAAAAAACATAGC
Found at i:501281 original size:13 final size:12
Alignment explanation
Indices: 501239--501272 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
501229 ACAATAAAAT
*
501239 TAAATTTAATTA
1 TAAAATTAATTA
501251 TAATAATTAATTA
1 TAA-AATTAATTA
501264 TAAAATTAA
1 TAAAATTAA
501273 ATTTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAATTAATTA
Found at i:502041 original size:16 final size:16
Alignment explanation
Indices: 502020--502050 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
502010 AATTATAAAC
*
502020 AAAAAACATTTTATGA
1 AAAAAAAATTTTATGA
502036 AAAAAAAATTTTATG
1 AAAAAAAATTTTATG
502051 TTGGGTGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.32
Consensus pattern (16 bp):
AAAAAAAATTTTATGA
Found at i:505895 original size:12 final size:12
Alignment explanation
Indices: 505861--505896 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
505851 ACTAAAAAAA
*
505861 TTAAAAAAACGTT
1 TTAAAAAAA-TTT
505874 TTAAAAAAATTT
1 TTAAAAAAATTT
505886 TTAAAAAAATT
1 TTAAAAAAATT
505897 ATAATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (12 bp):
TTAAAAAAATTT
Found at i:506432 original size:25 final size:27
Alignment explanation
Indices: 506402--506453 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
506392 CATATGCAAT
506402 AAAAATTATAATATTA-AAAAA-TTTA
1 AAAAATTATAATATTATAAAAAGTTTA
**
506427 AAAAATTATTTTATTATAAAAAGTTTA
1 AAAAATTATAATATTATAAAAAGTTTA
506454 TATATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 14 0.61
26 5 0.22
27 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
AAAAATTATAATATTATAAAAAGTTTA
Found at i:506477 original size:26 final size:26
Alignment explanation
Indices: 506431--506485 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
506421 AATTTAAAAA
*
506431 ATTATTTTATTATAAAAAGTTTATAT
1 ATTATTTTATTACAAAAAGTTTATAT
* *
506457 ATTATTTT-TTGACAAAGAGTTTATCT
1 ATTATTTTATT-ACAAAAAGTTTATAT
506483 ATT
1 ATT
506486 GTTAGTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (26 bp):
ATTATTTTATTACAAAAAGTTTATAT
Found at i:507790 original size:2 final size:2
Alignment explanation
Indices: 507783--507816 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
507773 CAAAAGCTAA
*
507783 AT AT AT AT TT 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
507817 TTTAAGTGAT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:508314 original size:11 final size:11
Alignment explanation
Indices: 508285--508326 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
508275 TTTTTAAGTA
508285 AAATATAAATAT
1 AAATAT-AATAT
508297 AAA-ATAATAT
1 AAATATAATAT
*
508307 AAATATAATTT
1 AAATATAATAT
508318 AAATA-AATA
1 AAATATAATA
508327 AATTTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 11 0.41
11 13 0.48
12 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATATAATAT
Found at i:508329 original size:19 final size:20
Alignment explanation
Indices: 508298--508337 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
508288 TATAAATATA
508298 AAATAATATAAATATAATTT
1 AAATAATATAAATATAATTT
*
508318 AAATAA-ATAAATTTAATTT
1 AAATAATATAAATATAATTT
508337 A
1 A
508338 TTATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATAATATAAATATAATTT
Found at i:510095 original size:13 final size:14
Alignment explanation
Indices: 510077--510110 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
510067 AAACAAACTC
510077 TTTTTTCTTTC-AT
1 TTTTTTCTTTCTAT
510090 TTTTTTCTTTCTAT
1 TTTTTTCTTTCTAT
510104 TTCTTTT
1 TT-TTTT
510111 ATTCCAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
14 4 0.21
15 4 0.21
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTCTTTCTAT
Found at i:512248 original size:20 final size:19
Alignment explanation
Indices: 512225--512269 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
512215 ATACAAAAAT
512225 AATATTAAAAAAATAATATA
1 AATATTAAAAAAAT-ATATA
* *
512245 AATATGATAAAAATATATA
1 AATATTAAAAAAATATATA
512264 AATATT
1 AATATT
512270 TCAAAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
AATATTAAAAAAATATATA
Found at i:512275 original size:19 final size:19
Alignment explanation
Indices: 512233--512281 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
512223 ATAATATTAA
512233 AAAAATAATATAAATATGAT
1 AAAAAT-ATATAAATATGAT
*
512253 AAAAATATATAAATAT-TT
1 AAAAATATATAAATATGAT
*
512271 CAAAATATATA
1 AAAAATATATA
512282 TGATAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 11 0.41
19 10 0.37
20 6 0.22
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAATATATAAATATGAT
Found at i:512282 original size:20 final size:20
Alignment explanation
Indices: 512234--512282 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
512224 TAATATTAAA
512234 AAAATA-ATATAAATATGAT
1 AAAATATATATAAATATGAT
*
512253 AAAA-ATATATAAATAT-TT
1 AAAATATATATAAATATGAT
512271 CAAAATATATAT
1 -AAAATATATAT
512283 GATAAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 18 0.69
20 6 0.23
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAATATATATAAATATGAT
Found at i:512323 original size:17 final size:17
Alignment explanation
Indices: 512284--512325 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
512274 AATATATATG
*
512284 ATAAAAATTATTAACAT
1 ATAAAATTTATTAACAT
512301 ATTAAAATTTATATAA-AT
1 A-TAAAATTTAT-TAACAT
512319 ATAAAAT
1 ATAAAAT
512326 ATTTTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 12 0.55
19 3 0.14
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAATTTATTAACAT
Found at i:516481 original size:20 final size:21
Alignment explanation
Indices: 516444--516482 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
516434 TTTGACATGT
516444 TAAAATGCATGGAACATGGCA
1 TAAAATGCATGGAACATGGCA
*
516465 TAAAATGCAT-TAACATGG
1 TAAAATGCATGGAACATGG
516483 GCTGTCAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.23
Consensus pattern (21 bp):
TAAAATGCATGGAACATGGCA
Found at i:518092 original size:16 final size:16
Alignment explanation
Indices: 518063--518098 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
518053 AAGCTAGGTA
*
518063 AACAGAGTGGTGGATG
1 AACAGAGTGATGGATG
*
518079 AACAGGGTGATGGATG
1 AACAGAGTGATGGATG
518095 AACA
1 AACA
518099 AGATCAGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.08, G:0.39, T:0.17
Consensus pattern (16 bp):
AACAGAGTGATGGATG
Found at i:519987 original size:22 final size:22
Alignment explanation
Indices: 519959--520006 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
519949 AATGCTCTGA
519959 AATATGTGCTTCCTACAAGTCC
1 AATATGTGCTTCCTACAAGTCC
519981 AATATGTGCTTCCTACAAGTCC
1 AATATGTGCTTCCTACAAGTCC
520003 AATA
1 AATA
520007 ACGAAGTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (22 bp):
AATATGTGCTTCCTACAAGTCC
Found at i:524294 original size:31 final size:31
Alignment explanation
Indices: 524259--524319 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
524249 AGATTAATTA
* * *
524259 TAAAATAATAATATTTTGATAAATTATTTTT
1 TAAAAAAATAATAATTTAATAAATTATTTTT
* *
524290 TAAAAAAATATTAATTTAATAATTTATTTT
1 TAAAAAAATAATAATTTAATAAATTATTTT
524320 AATTTTAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (31 bp):
TAAAAAAATAATAATTTAATAAATTATTTTT
Found at i:524975 original size:17 final size:16
Alignment explanation
Indices: 524936--525014 Score: 90
Period size: 16 Copynumber: 5.0 Consensus size: 16
524926 ATAAAAAATT
*
524936 AATAATTTAAAATT-A
1 AATAATTTAAATTTAA
* *
524951 ATTAATTTAGATTTAAA
1 AATAATTTAAATTT-AA
524968 AATAATTTAAATTTAA
1 AATAATTTAAATTTAA
*
524984 AATAATTTAAAATTAA
1 AATAATTTAAATTTAA
*
525000 ATTAA-TTAAATTTAA
1 AATAATTTAAATTTAA
525015 TTATCAGAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
15 20 0.37
16 21 0.39
17 13 0.24
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (16 bp):
AATAATTTAAATTTAA
Found at i:524977 original size:32 final size:31
Alignment explanation
Indices: 524911--525017 Score: 96
Period size: 32 Copynumber: 3.5 Consensus size: 31
524901 TTTAATTATG
**
524911 ATTTAAA-TTAATTTAATAAAAAATT--AATA
1 ATTTAAATTTAA-TTAATTTAAAATTAAAATA
* * *
524940 ATTTAAAATTAATTAATTTAGATTTAAAAATA
1 ATTTAAATTTAATTAATTTAAAATT-AAAATA
* *
524972 ATTTAAATTTAAAATAATTTAAAATTAAATTA
1 ATTTAAATTT-AATTAATTTAAAATTAAAATA
525004 A-TTAAATTTAATTA
1 ATTTAAATTTAATTA
525018 TCAGAATAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
29 16 0.25
30 8 0.13
31 8 0.13
32 19 0.30
33 12 0.19
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (31 bp):
ATTTAAATTTAATTAATTTAAAATTAAAATA
Found at i:525012 original size:37 final size:35
Alignment explanation
Indices: 524911--525014 Score: 90
Period size: 33 Copynumber: 3.0 Consensus size: 35
524901 TTTAATTATG
*
524911 ATTTAAATTAATTTAATAA-AAAATTAATAATTTAA
1 ATTTAAAATAATTTAA-AATAAAATTAATAATTTAA
* * * * *
524946 AATT-AATTAATTTAGATTTAAA--AATAATTTAA
1 ATTTAAAATAATTTAAAATAAAATTAATAATTTAA
*
524978 ATTTAAAATAATTTAAAATTAAATTAATTAAATTTAA
1 ATTTAAAATAATTTAAAATAAAATTAA-T-AATTTAA
525015 TTATCAGAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
32 13 0.24
33 16 0.29
34 13 0.24
35 5 0.09
36 1 0.02
37 7 0.13
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (35 bp):
ATTTAAAATAATTTAAAATAAAATTAATAATTTAA
Found at i:525014 original size:21 final size:20
Alignment explanation
Indices: 524916--524977 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 20
524906 TTATGATTTA
524916 AATTAATTTAATAAA-AAATT
1 AATTAATTTAA-AAATAAATT
*
524936 AA-TAATTT-AAAATTAATT
1 AATTAATTTAAAAATAAATT
*
524954 AATTTAGATTTAAAAATAATTT
1 AA-TTA-ATTTAAAAATAAATT
524976 AA
1 AA
524978 ATTTAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
17 3 0.09
18 7 0.21
19 6 0.18
20 4 0.12
21 4 0.12
22 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
AATTAATTTAAAAATAAATT
Found at i:525031 original size:53 final size:52
Alignment explanation
Indices: 524897--525052 Score: 130
Period size: 52 Copynumber: 3.0 Consensus size: 52
524887 CTTACTCATC
*
524897 TTAATTTAA-TTATGATTT-AAATTAATTT-AAT-AAAA-AA-TTAATAATTTAAAA
1 TTAA-TTAATTTA-GATTTAAAAATAATTTAAATCAAAATAATTTAA-AA-TT-AAA
*
524948 TTAATTAATTTAGATTTAAAAATAATTTAAATTTAAAATAATTTAAAATTAAA
1 TTAATTAATTTAGATTTAAAAATAATTTAAA-TCAAAATAATTTAAAATTAAA
* * * *
525001 TTAATTAAATTTA-ATTATCAGAATAA-TTAAATCAAAATTATTTAAATTTAAA
1 TTAATT-AATTTAGATT-TAAAAATAATTTAAATCAAAATAATTTAAAATTAAA
525053 ATATTCAAAT
Statistics
Matches: 90, Mismatches: 6, Indels: 17
0.80 0.05 0.15
Matches are distributed among these distances:
50 9 0.10
51 16 0.18
52 20 0.22
53 18 0.20
54 19 0.21
55 4 0.04
56 4 0.04
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (52 bp):
TTAATTAATTTAGATTTAAAAATAATTTAAATCAAAATAATTTAAAATTAAA
Found at i:525496 original size:26 final size:26
Alignment explanation
Indices: 525451--525506 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
525441 TATATAAATT
525451 AATTTAATTTTTTAAGAAAA-TATAA
1 AATTTAATTTTTTAAGAAAATTATAA
* *
525476 AATTTACA-TTTTTATATAAAATTTTAA
1 AATTTA-ATTTTTTA-AGAAAATTATAA
525503 AATT
1 AATT
525507 CTCACAGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 12 0.46
26 6 0.23
27 8 0.31
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
AATTTAATTTTTTAAGAAAATTATAA
Found at i:527358 original size:20 final size:19
Alignment explanation
Indices: 527315--527358 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
527305 TTAATATTTA
*
527315 AAATTATTTTAATTTAAGT
1 AAATTATTTTAATTAAAGT
* *
527334 CAATTAATTTTAATTAAATT
1 AAATT-ATTTTAATTAAAGT
527354 AAATT
1 AAATT
527359 TATTGAAGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
AAATTATTTTAATTAAAGT
Found at i:528720 original size:14 final size:14
Alignment explanation
Indices: 528701--528727 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
528691 AGATTTAGCT
528701 GACTTTATTGTTAA
1 GACTTTATTGTTAA
528715 GACTTTATTGTTA
1 GACTTTATTGTTA
528728 GAACGCTATA
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:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (14 bp):
GACTTTATTGTTAA
Found at i:530884 original size:2 final size:2
Alignment explanation
Indices: 530877--530912 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
530867 GATATGCAGC
530877 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
530913 CAAGGAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:531960 original size:2 final size:2
Alignment explanation
Indices: 531953--531981 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
531943 TGTTCCAACA
531953 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
531982 TTGGTTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:534263 original size:2 final size:2
Alignment explanation
Indices: 534258--534297 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
534248 TTTAGTACAT
*
534258 TA TA TA TA TA TA TA TA TA -A TA TG TA TA -A TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
534297 T
1 T
534298 CGATAAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:534284 original size:9 final size:9
Alignment explanation
Indices: 534258--534291 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
534248 TTTAGTACAT
534258 TATATATATA
1 TATATATA-A
534268 TATATATAA
1 TATATATAA
*
534277 TATGTATAA
1 TATATATAA
534286 TATATA
1 TATATA
534292 ATATATCGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (9 bp):
TATATATAA
Found at i:534290 original size:16 final size:17
Alignment explanation
Indices: 534259--534297 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
534249 TTAGTACATT
534259 ATATATATATATATATA
1 ATATATATATATATATA
*
534276 ATATGTATA-ATATATA
1 ATATATATATATATATA
534292 ATATAT
1 ATATAT
534298 CGATAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:534624 original size:22 final size:21
Alignment explanation
Indices: 534594--534634 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
534584 TATAAAGTTT
534594 GTTACATGTGAAAATTATATTAA
1 GTTACATGT-AAAATT-TATTAA
534617 GTTA-ATGTAAAATTTATT
1 GTTACATGTAAAATTTATT
534635 CTTTTCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 4 0.22
23 4 0.22
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.44
Consensus pattern (21 bp):
GTTACATGTAAAATTTATTAA
Found at i:537252 original size:20 final size:18
Alignment explanation
Indices: 537223--537268 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
537213 TGACACATTC
537223 AATTTATTATAAATTTATAT
1 AATTTATTATAAA-TTA-AT
* *
537243 AATTTTTTATATATTAAT
1 AATTTATTATAAATTAAT
537261 AATTTATT
1 AATTTATT
537269 TTATATAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 9 0.39
19 3 0.13
20 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTTATTATAAATTAAT
Found at i:538569 original size:32 final size:34
Alignment explanation
Indices: 538532--538604 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 34
538522 TTTAAAATAA
538532 ATATAATATT-AT-AAA-AAAT-ATTAATTTTAATT
1 ATATAATATTAATCAAATAAATAATTAA--TTAATT
538564 ATATAATATTAATCAAATAAATAATTAATTAATT
1 ATATAATATTAATCAAATAAATAATTAATTAATT
538598 ATA-AATA
1 ATATAATA
538605 GTTTAGTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
32 10 0.27
33 6 0.16
34 12 0.32
35 4 0.11
36 5 0.14
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (34 bp):
ATATAATATTAATCAAATAAATAATTAATTAATT
Found at i:538601 original size:18 final size:18
Alignment explanation
Indices: 538558--538604 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
538548 AATATTAATT
538558 TTAATTATATAAT-ATTAA
1 TTAATTATA-AATAATTAA
*
538576 TCAA--ATAAATAATTAA
1 TTAATTATAAATAATTAA
538592 TTAATTATAAATA
1 TTAATTATAAATA
538605 GTTTAGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.12
16 11 0.46
18 10 0.42
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAATTATAAATAATTAA
Found at i:539805 original size:17 final size:18
Alignment explanation
Indices: 539774--539820 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
539764 AATATTTATT
* *
539774 AAAATATATAGAT-AATA
1 AAAATATTTAAATAAATA
539791 AAAATATTTAAATAAATA
1 AAAATATTTAAATAAATA
*
539809 ATAATTATTTAA
1 A-AAATATTTAA
539821 TTTGAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 11 0.44
18 5 0.20
19 9 0.36
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAATATTTAAATAAATA
Found at i:540975 original size:16 final size:16
Alignment explanation
Indices: 540954--540996 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
540944 ATTAAAATTT
540954 TAAATATTAAATAAAA
1 TAAATATTAAATAAAA
* *
540970 TAAATAATAAATATAA
1 TAAATATTAAATAAAA
540986 TAAATAATTAA
1 TAAAT-ATTAA
540997 TTTAAGTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAATATTAAATAAAA
Found at i:542114 original size:4 final size:4
Alignment explanation
Indices: 542098--542132 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
542088 AATGAAAACA
*
542098 AAAT AAGT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
542133 CTATTACCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:542583 original size:16 final size:17
Alignment explanation
Indices: 542562--542594 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
542552 TATTATTTAA
542562 TTATTTAAAAT-TATTT
1 TTATTTAAAATATATTT
542578 TTATTTAAAATATATTT
1 TTATTTAAAATATATTT
542595 AAAAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTTAAAATATATTT
Found at i:543980 original size:16 final size:17
Alignment explanation
Indices: 543954--543985 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
543944 AAAATTTATG
543954 AATTAAAAATCAAATCA
1 AATTAAAAATCAAATCA
543971 AATT-AAAATCAAATC
1 AATTAAAAATCAAATC
543986 GAGCATTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (17 bp):
AATTAAAAATCAAATCA
Found at i:544553 original size:28 final size:29
Alignment explanation
Indices: 544504--544563 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
544494 AATATGTGAT
*
544504 TTATAATTTTATTTATGATA-TTAAAAAA
1 TTATAATTTAATTTATGATATTTAAAAAA
*
544532 TTATTATTTAATTATATG-TATTTTAAAAAA
1 TTATAATTTAATT-TATGATA-TTTAAAAAA
544562 TT
1 TT
544564 TTAAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 13 0.48
29 4 0.15
30 10 0.37
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (29 bp):
TTATAATTTAATTTATGATATTTAAAAAA
Found at i:545070 original size:51 final size:51
Alignment explanation
Indices: 544994--545254 Score: 372
Period size: 50 Copynumber: 5.2 Consensus size: 51
544984 AGTTGTTGTC
*
544994 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGACCATA
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGACCATA
*
545045 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGACCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGACCATA
* * *
545096 ATTGTTGACAATTCTTCACCAACCTTTGACAATAAAGGGAGGTGG-TCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGACCATA
* * *
545146 ATTGTTTACGATTCTTCACCAATCTTTGACAATAGA-AGGAGGT-GACCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGACCATA
*
545196 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGT-GACCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGACCATA
545246 ATTGTTGAC
1 ATTGTTGAC
545255 TCTAAGTATA
Statistics
Matches: 189, Mismatches: 15, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
49 1 0.01
50 100 0.53
51 86 0.46
52 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (51 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGACCATA
Found at i:545235 original size:100 final size:101
Alignment explanation
Indices: 544994--545254 Score: 427
Period size: 100 Copynumber: 2.6 Consensus size: 101
544984 AGTTGTTGTC
* *
544994 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGACCATAATTGTTGACGATT
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGGGAGGTGG-CCATAATTGTTGACGATT
545058 CTTCACCAACCTTTGACAATAGAAGGAGGTGGACCATA
64 CTTCACCAACCTTTGACAATAGAAGGAGGTGGACCATA
* * *
545096 ATTGTTGACAATTCTTCACCAACCTTTGACAATAAAGGGAGGTGGTCATAATTGTTTACGATTCT
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
*
545161 TCACCAATCTTTGACAATAGAAGGAGGT-GACCATA
66 TCACCAACCTTTGACAATAGAAGGAGGTGGACCATA
*
545196 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGACCATAATTGTTGAC
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGAC
545255 TCTAAGTATA
Statistics
Matches: 148, Mismatches: 10, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
100 62 0.42
101 45 0.30
102 39 0.26
103 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (101 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
TCACCAACCTTTGACAATAGAAGGAGGTGGACCATA
Found at i:546974 original size:158 final size:158
Alignment explanation
Indices: 546686--547002 Score: 616
Period size: 158 Copynumber: 2.0 Consensus size: 158
546676 AAATCTATTG
546686 TCTTTGGGACAATTAGATGATATCGGATGCAAGACTCATGTAGAGAATGGGGTCATGAAAATACT
1 TCTTTGGGACAATTAGATGATATCGGATGCAAGACTCATGTAGAGAATGGGGTCATGAAAATACT
546751 CAGAGGTGCATTGGTGGTGATGAAGGCAGAGAAAGTTGCTGCAAATCTATACATGCTTAAAGGAG
66 CAGAGGTGCATTGGTGGTGATGAAGGCAGAGAAAGTTGCTGCAAATCTATACATGCTTAAAGGAG
546816 AGACACTGCAGGAGGCAGACACATCTGT
131 AGACACTGCAGGAGGCAGACACATCTGT
546844 TCTTTGGGACAATTAGATGATATCGGATGCAAGACTCATGTAGAGAATGGGGTCATGAAAATACT
1 TCTTTGGGACAATTAGATGATATCGGATGCAAGACTCATGTAGAGAATGGGGTCATGAAAATACT
*
546909 CAGAGGTGCATTGGTGGTGATGAAGGCAGAGAAAGTTGCTGCAAATCTATGCATGCTTAAAGGAG
66 CAGAGGTGCATTGGTGGTGATGAAGGCAGAGAAAGTTGCTGCAAATCTATACATGCTTAAAGGAG
*
546974 AGACACTGCAGGAGGCAGACGCATCTGT
131 AGACACTGCAGGAGGCAGACACATCTGT
547002 T
1 T
547003 GCGACAACCA
Statistics
Matches: 157, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
158 157 1.00
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.24
Consensus pattern (158 bp):
TCTTTGGGACAATTAGATGATATCGGATGCAAGACTCATGTAGAGAATGGGGTCATGAAAATACT
CAGAGGTGCATTGGTGGTGATGAAGGCAGAGAAAGTTGCTGCAAATCTATACATGCTTAAAGGAG
AGACACTGCAGGAGGCAGACACATCTGT
Found at i:551191 original size:23 final size:22
Alignment explanation
Indices: 551144--551191 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
551134 ATATTTTTAT
*
551144 TATTATAATTAGTTATAATTTAA
1 TATTATAATTAG-TATAATTGAA
551167 TATTATAATATA-TATAATATGAA
1 TATTATAAT-TAGTATAAT-TGAA
551190 TA
1 TA
551192 AGTTAAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 6 0.27
23 14 0.64
24 2 0.09
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
TATTATAATTAGTATAATTGAA
Found at i:552718 original size:19 final size:19
Alignment explanation
Indices: 552691--552739 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
552681 TGATTGATTT
* *
552691 AATTTATATTT-ATAAATTA
1 AATTAATATTTAAT-AATAA
552710 AATTAATATTTAATAATAA
1 AATTAATATTTAATAATAA
*
552729 AAATAATATTT
1 AATTAATATTT
552740 TTATGTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 24 0.92
20 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTAATATTTAATAATAA
Found at i:554329 original size:6 final size:6
Alignment explanation
Indices: 554320--554354 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
554310 ATTTTTCAGG
554320 TTTGAT TTTGAT TTTG-- TTTGAT TTTGAT TTTGAT T
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT T
554355 AAATTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
6 23 0.85
ACGTcount: A:0.14, C:0.00, G:0.17, T:0.69
Consensus pattern (6 bp):
TTTGAT
Found at i:554340 original size:16 final size:16
Alignment explanation
Indices: 554319--554351 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
554309 TATTTTTCAG
554319 GTTTGATTTTGATTTT
1 GTTTGATTTTGATTTT
554335 GTTTGATTTTGATTTT
1 GTTTGATTTTGATTTT
554351 G
1 G
554352 ATTAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.21, T:0.67
Consensus pattern (16 bp):
GTTTGATTTTGATTTT
Found at i:556022 original size:29 final size:30
Alignment explanation
Indices: 555974--556031 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
555964 ATTTTATTTG
* *
555974 AAAAATTTATTTATTGTTTAAAATATATTA
1 AAAAATTTATGTATTATTTAAAATATATTA
* *
556004 AAAAATTTATGTA-TATTTATATTATATT
1 AAAAATTTATGTATTATTTAAAATATATT
556032 TTACAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
AAAAATTTATGTATTATTTAAAATATATTA
Found at i:557082 original size:13 final size:13
Alignment explanation
Indices: 557064--557101 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
557054 ATCATATCAT
557064 ATTTTA-TAGTATA
1 ATTTTATTA-TATA
557077 ATTTTATTATATA
1 ATTTTATTATATA
*
557090 ATTATATTATAT
1 ATTTTATTATAT
557102 TTAAAATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 21 0.91
14 2 0.09
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
ATTTTATTATATA
Found at i:557630 original size:21 final size:19
Alignment explanation
Indices: 557585--557652 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 19
557575 ATTAAATTTA
*
557585 AATAAAAAT-ATTTATATT
1 AATAAAAATCATTTAAATT
*
557603 GATTAAAAATCACTTTAAATT
1 -AATAAAAATCA-TTTAAATT
* *
557624 AAGTAAAACTTATTTAAATT
1 AA-TAAAAATCATTTAAATT
557644 -ATAAAAATC
1 AATAAAAATC
557653 TTACTTTAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
18 6 0.15
19 9 0.23
20 10 0.26
21 14 0.36
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (19 bp):
AATAAAAATCATTTAAATT
Found at i:557638 original size:41 final size:39
Alignment explanation
Indices: 557576--557664 Score: 99
Period size: 41 Copynumber: 2.2 Consensus size: 39
557566 ATTAGTATTA
*
557576 TTAAATTTAAATAAAAATATTTATATTGATTAAAAATC-ACT
1 TTAAA-TTAAATAAAAATATTTAAATT-A-TAAAAATCTACT
* *
557617 TTAAATTAAGTAAAACTTATTTAAATTATAAAAATCTTACT
1 TTAAATTAAATAAAA-ATATTTAAATTATAAAAATC-TACT
557658 TTAAATT
1 TTAAATT
557665 TAATCTAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
39 8 0.19
40 10 0.24
41 24 0.57
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (39 bp):
TTAAATTAAATAAAAATATTTAAATTATAAAAATCTACT
Found at i:557662 original size:21 final size:21
Alignment explanation
Indices: 557606--557664 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
557596 TTATATTGAT
557606 TAAAAATC--ACTTTAAATTA
1 TAAAAATCTTACTTTAAATTA
557625 -AGTAAAA-CTTA-TTTAAATTA
1 TA--AAAATCTTACTTTAAATTA
557645 TAAAAATCTTACTTTAAATT
1 TAAAAATCTTACTTTAAATT
557665 TAATCTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
18 1 0.03
19 5 0.15
20 17 0.52
21 10 0.30
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAAAATCTTACTTTAAATTA
Found at i:561169 original size:16 final size:16
Alignment explanation
Indices: 561123--561174 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
561113 ATATAATAAA
561123 TATTATTTAATAATT-T
1 TATTATTT-ATAATTAT
* * *
561139 TAATATTTTTTATTAT
1 TATTATTTATAATTAT
*
561155 TATTATTTATAATTAA
1 TATTATTTATAATTAT
561171 TATT
1 TATT
561175 TATTCTAATT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
15 4 0.14
16 24 0.86
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTATTTATAATTAT
Found at i:561185 original size:29 final size:29
Alignment explanation
Indices: 561118--561205 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
561108 ATACGATATA
* *
561118 ATAAATATTATTTAATAATTTTAATATTTTTT
1 ATAATTATTATTT-ATAA--TTAATATTTATT
*
561150 ATTATTATTATTTATAATTAATATTTATT
1 ATAATTATTATTTATAATTAATATTTATT
*
561179 CTAATTA--A-TTATAA-TAATATTTATT
1 ATAATTATTATTTATAATTAATATTTATT
561204 AT
1 AT
561206 GTTAACTGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
25 12 0.24
26 6 0.12
27 1 0.02
29 16 0.32
31 4 0.08
32 11 0.22
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (29 bp):
ATAATTATTATTTATAATTAATATTTATT
Found at i:564418 original size:3 final size:3
Alignment explanation
Indices: 564410--564444 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
564400 CACAATTGAC
564410 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
564445 CTTTGGGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:565744 original size:7 final size:7
Alignment explanation
Indices: 565732--565756 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
565722 ATGTATATTT
565732 TAAAAAA
1 TAAAAAA
565739 TAAAAAA
1 TAAAAAA
565746 TAAAAAA
1 TAAAAAA
565753 TAAA
1 TAAA
565757 TAAAAGATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:566515 original size:15 final size:15
Alignment explanation
Indices: 566497--566541 Score: 58
Period size: 14 Copynumber: 3.0 Consensus size: 15
566487 TAAAAATAAA
566497 AAAATTATAAATATT
1 AAAATTATAAATATT
566512 AAAATT-TAAA-ATTT
1 AAAATTATAAATA-TT
566526 AAAATTATTAAATATT
1 AAAATTA-TAAATATT
566542 CTTATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.04
14 12 0.46
15 6 0.23
16 6 0.23
17 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:568561 original size:19 final size:20
Alignment explanation
Indices: 568533--568577 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
568523 CTTTTTACTC
*
568533 AAAA-TATTTTTTA-ACTAT
1 AAAATTATTTTTAATACTAT
568551 AAAATTATTTTTAATACTAT
1 AAAATTATTTTTAATACTAT
568571 AAAATTA
1 AAAATTA
568578 AATTATATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 4 0.17
19 8 0.33
20 12 0.50
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATTATTTTTAATACTAT
Found at i:569182 original size:26 final size:27
Alignment explanation
Indices: 569135--569191 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 27
569125 TTTAATATGC
569135 ATTTGAATTGAATATAACTTAATA-ATA
1 ATTTGAATTGAATATAACTTAA-AGATA
*
569162 ATTT-AATTTAATAGTAA-TTAAAGATA
1 ATTTGAATTGAATA-TAACTTAAAGATA
569188 ATTT
1 ATTT
569192 TAAGATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 1 0.04
26 19 0.70
27 7 0.26
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (27 bp):
ATTTGAATTGAATATAACTTAAAGATA
Found at i:570114 original size:22 final size:22
Alignment explanation
Indices: 570072--570116 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
570062 GAAAAAAATT
*
570072 ATTTGAAAAATAATAAAATAAA
1 ATTTGAAAAAGAATAAAATAAA
570094 ATTTGAAAAAGAA-AAATATAAA
1 ATTTGAAAAAGAATAAA-ATAAA
570116 A
1 A
570117 AGAAAAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (22 bp):
ATTTGAAAAAGAATAAAATAAA
Found at i:570141 original size:19 final size:19
Alignment explanation
Indices: 570099--570141 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
570089 ATAAAATTTG
570099 AAAAAGAAAAATATAAAAA
1 AAAAAGAAAAATATAAAAA
* *
570118 GAAAAGATAAAT-TAAAATA
1 AAAAAGAAAAATATAAAA-A
570137 AAAAA
1 AAAAA
570142 AAATTCACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (19 bp):
AAAAAGAAAAATATAAAAA
Found at i:570960 original size:2 final size:2
Alignment explanation
Indices: 570953--570987 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
570943 TTTTAGAGTT
570953 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
570988 TAGTTTAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:572146 original size:22 final size:22
Alignment explanation
Indices: 572119--572166 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
572109 ATAATATTTT
*
572119 ATTTATAAT-AATAATAATAATA
1 ATTTATAATAAAT-ATAATAAAA
*
572141 ATTTATATTAAATATAATAAAA
1 ATTTATAATAAATATAATAAAA
572163 ATTT
1 ATTT
572167 TATTTATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTTATAATAAATATAATAAAA
Found at i:572449 original size:17 final size:15
Alignment explanation
Indices: 572429--572475 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 15
572419 ATAAAGTAAT
572429 ATATTATTTATTAAAAA
1 ATATT-TTT-TTAAAAA
572446 ATA-TTTTTTAAAAA
1 ATATTTTTTTAAAAA
572460 ATTATTTTTTTTAAAA
1 A-TA-TTTTTTTAAAA
572476 TAAAGAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.30
15 5 0.19
16 1 0.04
17 13 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTTTTTAAAAA
Found at i:572476 original size:15 final size:15
Alignment explanation
Indices: 572431--572469 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
572421 AAAGTAATAT
*
572431 ATTATTTATTAAAAA
1 ATTATTTTTTAAAAA
572446 A-TATTTTTTAAAAA
1 ATTATTTTTTAAAAA
572460 ATTATTTTTT
1 ATTATTTTTT
572470 TTAAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTATTTTTTAAAAA
Found at i:572612 original size:2 final size:2
Alignment explanation
Indices: 572605--572642 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
572595 TTAATTGTTT
572605 TA TA 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
572643 GCGTGAGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:572911 original size:23 final size:22
Alignment explanation
Indices: 572885--572946 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
572875 TAATTTTTTA
572885 TTATAAATTATATTAATTTAAAT
1 TTATAAATTATATTAATTT-AAT
*
572908 TTATAATTTA-ATTTAA-TTAAT
1 TTATAAATTATA-TTAATTTAAT
572929 TTATATAATTATATTAAT
1 TTATA-AATTATATTAAT
572947 ATTTAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
21 8 0.24
22 11 0.33
23 14 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATAAATTATATTAATTTAAT
Found at i:577981 original size:20 final size:19
Alignment explanation
Indices: 577952--578022 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
577942 TCGCAATTTA
577952 TATC-ATACATTATTCATTG
1 TATCGATACATT-TTCATTG
* *
577971 TATCGATACATTGCTCATTA
1 TATCGATACATT-TTCATTG
*
577991 TATCGATACATTTTACAATG
1 TATCGATACATTTT-CATTG
578011 TATCGATACATT
1 TATCGATACATT
578023 CAGGCATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 5 0.11
20 39 0.89
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.42
Consensus pattern (19 bp):
TATCGATACATTTTCATTG
Found at i:578457 original size:21 final size:21
Alignment explanation
Indices: 578433--578486 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
578423 TCTTTTTTTT
578433 GGAGGAGAAAACAATTTTCCA
1 GGAGGAGAAAACAATTTTCCA
578454 GGAGGAGAAAACAATTTTCCA
1 GGAGGAGAAAACAATTTTCCA
* *
578475 GCAGTAGAAAAC
1 GGAGGAGAAAAC
578487 CCTTAGGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.17
Consensus pattern (21 bp):
GGAGGAGAAAACAATTTTCCA
Found at i:580501 original size:51 final size:50
Alignment explanation
Indices: 580427--580688 Score: 325
Period size: 51 Copynumber: 5.2 Consensus size: 50
580417 TTATTTCCGA
* * *
580427 GGGGATACTCCAA-TCCTGGTTTTATTTCTAAAACACCAATTTTCCACAATC
1 GGGGATACTCTAACTCC-GATTTTATTTCTAAAACACCAATTTT-CATAATC
* * *
580478 GGGGATACTCTAACTCCGATTTTATTTCCAAAACATCAATTTTTCTTAATC
1 GGGGATACTCTAACTCCGATTTTATTTCTAAAACACCAA-TTTTCATAATC
* *
580529 GGGGATACTCCAACTCCGATTTTATTTCTAAAACACCCATTTTCTATAATC
1 GGGGATACTCTAACTCCGATTTTATTTCTAAAACACCAATTTTC-ATAATC
* *
580580 GGAGATACTCTAACTCCGATTTTATTTCTAAAACACCGACTTTTCATAATC
1 GGGGATACTCTAACTCCGATTTTATTTCTAAAACACC-AATTTTCATAATC
* * *
580631 GGGGATACTCTAAC-CCTGGTTTTATTTCTAAAACATCAATTTT--TCATC
1 GGGGATACTCTAACTCC-GATTTTATTTCTAAAACACCAATTTTCATAATC
580679 GGGGATACTC
1 GGGGATACTC
580689 CAACCCCGTT
Statistics
Matches: 186, Mismatches: 20, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
48 14 0.08
50 12 0.06
51 148 0.80
52 12 0.06
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (50 bp):
GGGGATACTCTAACTCCGATTTTATTTCTAAAACACCAATTTTCATAATC
Found at i:580603 original size:102 final size:103
Alignment explanation
Indices: 580427--580673 Score: 365
Period size: 102 Copynumber: 2.4 Consensus size: 103
580417 TTATTTCCGA
*
580427 GGGGATACTCCAA-TCCTGGTTTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCTAA
1 GGGGATACTCCAACTCCTGGTTTTATTTCTAAAACACCAATTTTCCACAATCGGAGATACTCTAA
* * *
580491 CTCCGATTTTATTTCCAAAACATCAATTTTTCTTAATC
66 CTCCGATTTTATTTCCAAAACACCAACTTTTCATAATC
* * * *
580529 GGGGATACTCCAACTCC-GATTTTATTTCTAAAACACCCATTTTCTATAATCGGAGATACTCTAA
1 GGGGATACTCCAACTCCTGGTTTTATTTCTAAAACACCAATTTTCCACAATCGGAGATACTCTAA
* *
580593 CTCCGATTTTATTTCTAAAACACCGACTTTTCATAATC
66 CTCCGATTTTATTTCCAAAACACCAACTTTTCATAATC
* *
580631 GGGGATACTCTAAC-CCTGGTTTTATTTCTAAAACATCAATTTT
1 GGGGATACTCCAACTCCTGGTTTTATTTCTAAAACACCAATTTT
580674 TCATCGGGGA
Statistics
Matches: 129, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
101 2 0.02
102 124 0.96
103 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (103 bp):
GGGGATACTCCAACTCCTGGTTTTATTTCTAAAACACCAATTTTCCACAATCGGAGATACTCTAA
CTCCGATTTTATTTCCAAAACACCAACTTTTCATAATC
Found at i:580757 original size:76 final size:76
Alignment explanation
Indices: 580631--580958 Score: 417
Period size: 76 Copynumber: 4.2 Consensus size: 76
580621 TTTCATAATC
* *
580631 GGGGATACTCTAACCCTGGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
580696 GTTATTTTCAA
66 GTTATTTTCAA
* *
580707 GGGGATACCCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCG
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
*
580772 GTTATTTAT-GA
66 GTTATTT-TCAA
* * *
580783 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAACTTCTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAA-TT-T-TTCATCGGGGATACTCCAAC
* *
580848 CTCGTTA-TTTCTGA
63 CCCGTTATTTTC-AA
* * * * * * *
580862 GGGGATACTCTAATCCCGATTTTATTTCGAAATCATCGATTTTTCACTATCCGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTT--C-ATCGGGGATACTCCAAC
580927 CCCGTTATTTTCAA
63 CCCGTTATTTTCAA
580941 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
580959 TTATTATCTC
Statistics
Matches: 217, Mismatches: 25, Indels: 17
0.84 0.10 0.07
Matches are distributed among these distances:
76 107 0.49
77 5 0.02
78 5 0.02
79 96 0.44
80 4 0.02
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (76 bp):
GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
GTTATTTTCAA
Found at i:586381 original size:50 final size:51
Alignment explanation
Indices: 586284--586429 Score: 188
Period size: 51 Copynumber: 2.9 Consensus size: 51
586274 AAAAGTTACA
* * *
586284 TTTTTA-CTCAGATGTATCGATACATTTTTCAACGTATTGATAAATTCTATC
1 TTTTTACCT-AGATGTATCGATACATTTTTCAATGTATCGATACATTCTATC
* * * * *
586335 -TTTTACCTAGATGTATCAATACATGTATAAATGTATCGATACATTCTGTC
1 TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATC
*
586385 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
1 TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACAT
586430 ATAGTTAAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
50 39 0.49
51 41 0.51
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.42
Consensus pattern (51 bp):
TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATC
Found at i:586408 original size:51 final size:51
Alignment explanation
Indices: 586284--586429 Score: 195
Period size: 50 Copynumber: 2.9 Consensus size: 51
586274 AAAAGTTACA
* * * *
586284 TTTTTACTCAGATGTATCGATACATTTTTCAACGTATTGATAAATTCTATC
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATC
* * * * * *
586335 -TTTTACCTAGATGTATCAATACATGTATAAATGTATCGATACATTCTGTC
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATC
586385 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
586430 ATAGTTAAAA
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
50 40 0.51
51 39 0.49
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.42
Consensus pattern (51 bp):
TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATC
Found at i:591316 original size:3 final size:3
Alignment explanation
Indices: 591302--591331 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
591292 CGATCAGGGT
*
591302 ATA ATA AGA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
591332 TAAATAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:592233 original size:9 final size:10
Alignment explanation
Indices: 592210--592235 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
592200 CATCTTTTCC
592210 TTTTTTATTA
1 TTTTTTATTA
592220 TTTTTTATTA
1 TTTTTTATTA
592230 TTTTTT
1 TTTTTT
592236 CATTTCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:592567 original size:27 final size:28
Alignment explanation
Indices: 592537--592616 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 28
592527 AATTATATAT
*
592537 TCATATGT-A-AATTTTAATTTTAAAAAC
1 TCATATGTGAGAATTTTAA-TTGAAAAAC
*
592564 TCATATGTGAGAATTTTAATTGAAAATC
1 TCATATGTGAGAATTTTAATTGAAAAAC
*
592592 TCATATATGAGAA-TTTAATT-AAAAA
1 TCATATGTGAGAATTTTAATTGAAAAA
592617 TTTTATATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 4 0.09
27 15 0.32
28 20 0.43
29 8 0.17
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (28 bp):
TCATATGTGAGAATTTTAATTGAAAAAC
Found at i:592602 original size:28 final size:27
Alignment explanation
Indices: 592546--592644 Score: 92
Period size: 27 Copynumber: 3.6 Consensus size: 27
592536 TTCATATGTA
* *
592546 AATTTTAATTTTAAAAACTCATATGTGAG
1 AATTTTAA--TTAAAATCTCATATATGAG
592575 AATTTTAATTGAAAATCTCATATATGAG
1 AATTTTAATT-AAAATCTCATATATGAG
* * * *
592603 AA-TTTAATTAAAAATTTTATATATAAA
1 AATTTTAATT-AAAATCTCATATATGAG
*
592630 AAATTTAATTAAAAT
1 AATTTTAATTAAAAT
592645 TTTTACATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
27 29 0.48
28 24 0.39
29 8 0.13
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.41
Consensus pattern (27 bp):
AATTTTAATTAAAATCTCATATATGAG
Found at i:592617 original size:27 final size:27
Alignment explanation
Indices: 592556--592643 Score: 97
Period size: 28 Copynumber: 3.2 Consensus size: 27
592546 AATTTTAATT
*
592556 TTAAAAA-CTCATATGTGAGAATTTTAA
1 TTAAAAATCTCATATATGAGAA-TTTAA
*
592583 TTGAAAATCTCATATATGAGAATTTAA
1 TTAAAAATCTCATATATGAGAATTTAA
* * * *
592610 TTAAAAATTTTATATATAAAAAATTTAA
1 TTAAAAATCTCATATAT-GAGAATTTAA
592638 TTAAAA
1 TTAAAA
592644 TTTTTACATA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 25 0.48
28 27 0.52
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.39
Consensus pattern (27 bp):
TTAAAAATCTCATATATGAGAATTTAA
Found at i:592649 original size:13 final size:13
Alignment explanation
Indices: 592605--592649 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
592595 TATATGAGAA
592605 TTTAATTAAAAAT
1 TTTAATTAAAAAT
*
592618 TTTATATATAAAAAA
1 TTTA-AT-TAAAAAT
*
592633 TTTAATTAAAATT
1 TTTAATTAAAAAT
592646 TTTA
1 TTTA
592650 CATATGAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 13 0.48
14 4 0.15
15 10 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTTAATTAAAAAT
Found at i:592666 original size:27 final size:28
Alignment explanation
Indices: 592603--592675 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
592593 CATATATGAG
* * *
592603 AATTTAATTAAAAATTTTATATATAAAA
1 AATTAAATTAAAATTTTTACATATAAAA
* *
592631 AATTTAATTAAAATTTTTACATAT-GAA
1 AATTAAATTAAAATTTTTACATATAAAA
*
592658 GATTAAATTGAAAATTTT
1 AATTAAATT-AAAATTTT
592676 AAAGTTTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.23
28 30 0.77
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (28 bp):
AATTAAATTAAAATTTTTACATATAAAA
Found at i:592676 original size:27 final size:27
Alignment explanation
Indices: 592578--592676 Score: 94
Period size: 27 Copynumber: 3.6 Consensus size: 27
592568 ATGTGAGAAT
* *
592578 TTTAATTGAAAATCTCATATATG-AGAA
1 TTTAATTGAAAATTTTATATATGAAG-A
* * *
592605 TTTAATTAAAAATTTTATATATAAAAAA
1 TTTAATTGAAAATTTTATATAT-GAAGA
*
592633 TTTAATT-AAAATTTTTACATATGAAGA
1 TTTAATTGAAAA-TTTTATATATGAAGA
*
592660 TTAAATTGAAAATTTTA
1 TTTAATTGAAAATTTTA
592677 AAGTTTAATT
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
27 37 0.63
28 21 0.36
29 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (27 bp):
TTTAATTGAAAATTTTATATATGAAGA
Found at i:594260 original size:26 final size:26
Alignment explanation
Indices: 594229--594278 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
594219 GTAGTAAGGC
594229 GAACATGAAACATTATTCCATGTAAT
1 GAACATGAAACATTATTCCATGTAAT
594255 GAACATGAAACATTATTCCATGTA
1 GAACATGAAACATTATTCCATGTA
594279 CCCATTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (26 bp):
GAACATGAAACATTATTCCATGTAAT
Found at i:594779 original size:12 final size:12
Alignment explanation
Indices: 594750--594794 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
594740 AAAATTTTTA
594750 TTTAAAT-TTAAT
1 TTTAAATATT-AT
*
594762 TATAAATATTAT
1 TTTAAATATTAT
594774 TTTAAAATATTAT
1 TTT-AAATATTAT
594787 TTTAAATA
1 TTTAAATA
594795 ATAAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 15 0.52
13 14 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTAAATATTAT
Found at i:594783 original size:13 final size:13
Alignment explanation
Indices: 594765--594792 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
594755 ATTTAATTAT
594765 AAATATTATTTTA
1 AAATATTATTTTA
594778 AAATATTATTTTA
1 AAATATTATTTTA
594791 AA
1 AA
594793 TAATAAAATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATATTATTTTA
Found at i:595525 original size:25 final size:26
Alignment explanation
Indices: 595487--595536 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
595477 ACATTATTAT
595487 TTATAATAAATAAT-ATTATATTAAA
1 TTATAATAAATAATAATTATATTAAA
* *
595512 TTATAATAATTAATAATTTTATTAA
1 TTATAATAAATAATAATTATATTAA
595537 TATTTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTATAATAAATAATAATTATATTAAA
Found at i:597732 original size:24 final size:26
Alignment explanation
Indices: 597696--597743 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
597686 ATTTTTTAGA
* *
597696 TAATCTTTAAAAATTGACATATTTAT
1 TAATCTTTAAAAATTAAAATATTTAT
597722 TAAT-TTT-AAAATTAAAATATTT
1 TAATCTTTAAAAATTAAAATATTT
597744 TATCTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 3 0.15
26 4 0.20
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (26 bp):
TAATCTTTAAAAATTAAAATATTTAT
Found at i:598419 original size:18 final size:17
Alignment explanation
Indices: 598398--598431 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
598388 TATCTCACTT
*
598398 TTTGTTATTTATATATGA
1 TTTGTCATTTAT-TATGA
598416 TTTGTCATTTATTATG
1 TTTGTCATTTATTATG
598432 GAATTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.03, G:0.12, T:0.62
Consensus pattern (17 bp):
TTTGTCATTTATTATGA
Found at i:598493 original size:32 final size:30
Alignment explanation
Indices: 598436--598494 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
598426 ATTATGGAAT
*
598436 TATATTTTTTTATAATTAATCAATTTTTAA
1 TATATTTTTTTATAATCAATCAATTTTTAA
*
598466 TATATTATTATTTATAATCAATTAATTTT
1 TATATT-TT-TTTATAATCAATCAATTTT
598495 AATTGATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 2 0.08
32 17 0.68
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (30 bp):
TATATTTTTTTATAATCAATCAATTTTTAA
Found at i:599328 original size:24 final size:24
Alignment explanation
Indices: 599295--599341 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
599285 ATATATAAAA
*
599295 TTTTAATTATTAAAATAATAATAT
1 TTTTAATTATTAAAATAAAAATAT
* *
599319 TTTTACTTATTAAAGTAAAAATA
1 TTTTAATTATTAAAATAAAAATA
599342 AAATTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTTAATTATTAAAATAAAAATAT
Found at i:599461 original size:24 final size:23
Alignment explanation
Indices: 599414--599481 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
599404 AATATTATTA
*
599414 ATATAAATTATATTTTTTTAATAT
1 ATATATATTATA-TTTTTTAATAT
* *
599438 TTTTATATTATATTTTTTACATAT
1 ATATATATTATATTTTTTA-ATAT
*
599462 ATATATATATATATATTTTA
1 ATATATAT-TATATTTTTTA
599482 TAGGCGTTGC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 7 0.19
24 19 0.53
25 10 0.28
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (23 bp):
ATATATATTATATTTTTTAATAT
Found at i:599740 original size:6 final size:6
Alignment explanation
Indices: 599729--599757 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
599719 TCTGGTGCTG
599729 TGCTTC TGCTTC TGCTTC TGCTTC TGCTT
1 TGCTTC TGCTTC TGCTTC TGCTTC TGCTT
599758 TTTCCAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.17, T:0.52
Consensus pattern (6 bp):
TGCTTC
Found at i:604009 original size:2 final size:2
Alignment explanation
Indices: 604002--604033 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
603992 AAGAGTTGTC
604002 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
604034 CACACACACA
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:606822 original size:20 final size:20
Alignment explanation
Indices: 606797--606837 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
606787 GGTTATGTTT
606797 TTTAATCGCGCTAAATATGA
1 TTTAATCGCGCTAAATATGA
* *
606817 TTTAATCGTGTTAAATATGA
1 TTTAATCGCGCTAAATATGA
606837 T
1 T
606838 GCAATACGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (20 bp):
TTTAATCGCGCTAAATATGA
Done.