Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold373
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: 3053563
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 20
Found at i:340760 original size:21 final size:22
Alignment explanation
Indices: 340719--340765 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
340709 GAATGAGTTG
* *
340719 AATTTTAATATTTTAATAA-TT
1 AATTTGAATAATTTAATAATTT
340740 AATTTGAATAATTT-ATAAATTT
1 AATTTGAATAATTTAAT-AATTT
340762 AATT
1 AATT
340766 AAAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 14 0.64
22 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
AATTTGAATAATTTAATAATTT
Found at i:341722 original size:19 final size:20
Alignment explanation
Indices: 341683--341733 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
341673 AATTTTATTT
341683 AAAT-TTAATTATAAAATATA
1 AAATATTAA-TATAAAATATA
341703 AAATATTAATATAAAA-ATA
1 AAATATTAATATAAAATATA
341722 AAA-ATTTAATAT
1 AAATA-TTAATAT
341734 TTTAATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.03
19 13 0.45
20 11 0.38
21 4 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATATTAATATAAAATATA
Found at i:343568 original size:32 final size:31
Alignment explanation
Indices: 343532--343613 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 31
343522 TAGTTATATC
*
343532 TTAAA-AATTTTTATTTAGATTTTTTTATAGTT
1 TTAAATAA-TTTTATTTA-ATTTTCTTATAGTT
343564 TTAAATTAATTTTATTTAATTTTCTTATA--T
1 TTAAA-TAATTTTATTTAATTTTCTTATAGTT
* *
343594 TTAAATTATATATATTTAAT
1 TTAAATAAT-TTTATTTAAT
343614 ATTTTTGTAC
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
29 3 0.07
30 15 0.34
32 15 0.34
33 9 0.20
34 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.61
Consensus pattern (31 bp):
TTAAATAATTTTATTTAATTTTCTTATAGTT
Found at i:343601 original size:30 final size:32
Alignment explanation
Indices: 343540--343601 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
343530 TCTTAAAAAT
*
343540 TTTTATTTAGATTTTTTTATAGTTTTAAATTAA
1 TTTTATTTAGATTTTCTTATAG-TTTAAATTAA
343573 TTTTATTTA-ATTTTCTTATA-TTTAAATTA
1 TTTTATTTAGATTTTCTTATAGTTTAAATTA
343602 TATATATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 9 0.32
32 10 0.36
33 9 0.32
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (32 bp):
TTTTATTTAGATTTTCTTATAGTTTAAATTAA
Found at i:343610 original size:30 final size:31
Alignment explanation
Indices: 343543--343613 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
343533 TAAAAATTTT
* *
343543 TATTTAGATTTTTTTATAGTTTTAAATTAATTT
1 TATTTA-ATTTTCTTATAG-TTTAAATTAATTA
343576 TATTTAATTTTCTTATA-TTTAAATT-ATATA
1 TATTTAATTTTCTTATAGTTTAAATTAAT-TA
343606 TATTTAAT
1 TATTTAAT
343614 ATTTTTGTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 2 0.06
30 17 0.49
32 10 0.29
33 6 0.17
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (31 bp):
TATTTAATTTTCTTATAGTTTAAATTAATTA
Found at i:345780 original size:18 final size:16
Alignment explanation
Indices: 345750--345798 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
345740 TTTCAATGTA
345750 ATTTTATTTATTTATATT
1 ATTTT-TTTATTTA-ATT
345768 ATTTTTTTAATTTAATT
1 ATTTTTTT-ATTTAATT
345785 -TTTTTATTATTTAA
1 ATTTTT-TTATTTAA
345799 ATAATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 11 0.38
17 8 0.28
18 10 0.34
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTTTATTTAATT
Found at i:345803 original size:25 final size:27
Alignment explanation
Indices: 345748--345809 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 27
345738 TTTTTCAATG
* ***
345748 TAATTTTATTTATTTATATTATTTTTT
1 TAATTTAATTTATTTATATTATTTAAA
345775 TAATTTAATTT-TTT-TATTATTTAAA
1 TAATTTAATTTATTTATATTATTTAAA
*
345800 TAATTAAATT
1 TAATTTAATT
345810 AATATTTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 17 0.57
26 3 0.10
27 10 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TAATTTAATTTATTTATATTATTTAAA
Found at i:346027 original size:17 final size:16
Alignment explanation
Indices: 345977--346047 Score: 63
Period size: 16 Copynumber: 4.4 Consensus size: 16
345967 ATATTTATTA
*
345977 TATTTTTATAATTTAAT
1 TATTTTTATAATAT-AT
* * *
345994 T-TTTTTAAAAAAAAT
1 TATTTTTATAATATAT
*
346009 TATTTTTATTATAATAT
1 TATTTTTATAAT-ATAT
346026 TATTTTTATAATATAT
1 TATTTTTATAATATAT
*
346042 AATTTT
1 TATTTT
346048 ATTCACACCT
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
15 3 0.07
16 24 0.57
17 15 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTTTATAATATAT
Found at i:346034 original size:14 final size:15
Alignment explanation
Indices: 346017--346049 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
346007 ATTATTTTTA
*
346017 TTATAATAT-TATTT
1 TTATAATATATAATT
346031 TTATAATATATAATT
1 TTATAATATATAATT
346046 TTAT
1 TTAT
346050 TCACACCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATAATATATAATT
Found at i:350424 original size:51 final size:51
Alignment explanation
Indices: 350367--350502 Score: 236
Period size: 51 Copynumber: 2.7 Consensus size: 51
350357 TTTTAACTAG
* *
350367 ATGTATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGATAGA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCCAGGTAAAAAGATAGA
* *
350418 ATGTATCGATACATTGAAGAATGTATCGATACATCTAGGTAAAAAGATATA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCCAGGTAAAAAGATAGA
350469 ATGTATCGATACATTGAAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAGAATGTATCGATACAT
350503 TCATACCATA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 81 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (51 bp):
ATGTATCGATACATTGAAGAATGTATCGATACATCCAGGTAAAAAGATAGA
Found at i:350440 original size:20 final size:20
Alignment explanation
Indices: 350415--350503 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
350405 GTAAAAAGAT
350415 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
350435 AGAATGTATCGATACATCTAGGTAAAA
1 AGAATGTATCGATACAT-T--G----A
350462 AGATATAATGTATCGATACATTGA
1 AG----AATGTATCGATACATTGA
350486 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
350504 CATACCATAC
Statistics
Matches: 58, Mismatches: 0, Indels: 22
0.73 0.00 0.28
Matches are distributed among these distances:
20 33 0.57
21 1 0.02
23 1 0.02
24 3 0.05
27 3 0.05
28 1 0.02
30 1 0.02
31 15 0.26
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:351105 original size:32 final size:30
Alignment explanation
Indices: 351065--351200 Score: 133
Period size: 28 Copynumber: 4.6 Consensus size: 30
351055 CACTAACTTG
351065 TGTGGGCTTTGAAAAGAGTTACCATCGACT
1 TGTGGGCTTTGAAAAGAGTTACCATCGACT
*
351095 CGTGTGGGCTTTGAAAAGAGTTACCA-CTGGCT
1 --TGTGGGCTTTGAAAAGAGTTACCATC-GACT
* * *
351127 TGTGGGCTTTG-AAAG-GGTGCCATTGACT
1 TGTGGGCTTTGAAAAGAGTTACCATCGACT
* *
351155 TGTGGGCTTTGAAAAG-G-TGCCA-CTGGCT
1 TGTGGGCTTTGAAAAGAGTTACCATC-GACT
351183 TGTGGGCTTTG-AAAGAGT
1 TGTGGGCTTTGAAAAGAGT
351201 GTCACTAACT
Statistics
Matches: 91, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
27 4 0.04
28 39 0.43
29 9 0.10
30 11 0.12
31 1 0.01
32 27 0.30
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.30
Consensus pattern (30 bp):
TGTGGGCTTTGAAAAGAGTTACCATCGACT
Found at i:351165 original size:28 final size:28
Alignment explanation
Indices: 351097--351821 Score: 731
Period size: 28 Copynumber: 25.6 Consensus size: 28
351087 CATCGACTCG
* * *
351097 TGTGGGCTTTGAAAAGAGTTACCACTGGCT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
*
351127 TGTGGGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
351155 TGTGGGCTTTGAAAAGGTGCCACTGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
351183 TGTGGGCTTTGAAAGAGTGTCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
**
351211 CATGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
351239 AGTGGGCATTGAAAAGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
351267 CGTGGGCTTTGAAAGGGTGGCACTGAC-
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
351294 TGATGGGCTTTGAAAGGGTGCTACTAAGT
1 TG-TGGGCTTTGAAAGGGTGCCACTGACT
*
351323 TGTGGGTTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** *
351351 CATGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
351379 CGTGGGCTTTGAAAGGGTACTACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * **
351407 TGTGGGCTTTAAAAAGAGTGTTACTGACT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACT
* *
351436 TGCGTGGGCTTTAAAAGGGTGCCACTAACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACT
* * *
351466 TGCGTGAGCTTTAAAAGGGTGTCACTGACTT
1 T--GTGGGCTTTGAAAGGGTGCCACTGAC-T
*
351497 GTGTGGGCTTTGAAAGGATGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
351526 TGTAGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
351554 TGTGGGC-TTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
351581 GGTGGGCTTTGAAATGGTGCTACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** * *
351609 CATGGGC-TTGAAAGTGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
351636 CGTGGGCTTTGAAAAGAGTGCCATTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * * *
351665 TGTAGGCTTTGAAAGAGTACCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
351693 CGTGGGC-TTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
351720 CGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
351749 TGTGAGCTTT-AACAGGGTGCCACTGACT
1 TGTGGGCTTTGAA-AGGGTGCCACTGACT
* **
351777 TGTGGGCTTTAAAAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
351805 TGTGGGCTTTGAAAGGG
1 TGTGGGCTTTGAAAGGG
351822 ATGAACGTTC
Statistics
Matches: 582, Mismatches: 99, Indels: 30
0.82 0.14 0.04
Matches are distributed among these distances:
27 73 0.13
28 354 0.61
29 71 0.12
30 73 0.13
31 10 0.02
32 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:353066 original size:1 final size:1
Alignment explanation
Indices: 353062--353117 Score: 58
Period size: 1 Copynumber: 56.0 Consensus size: 1
353052 TTTTTCTTGG
* * * * * *
353062 TTTTTTTGTTTTTTTGTTTTTTGTTTTTTGTTTTTTTGTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
353118 GGGTGTAAAG
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:353072 original size:8 final size:8
Alignment explanation
Indices: 353039--353116 Score: 81
Period size: 8 Copynumber: 9.9 Consensus size: 8
353029 CCCCTTTCTA
353039 TTTTTTTG
1 TTTTTTTG
* *
353047 CTATTTT-
1 TTTTTTTG
* *
353054 TTTCTTGG
1 TTTTTTTG
353062 TTTTTTTG
1 TTTTTTTG
353070 TTTTTTTG
1 TTTTTTTG
353078 -TTTTTTG
1 TTTTTTTG
353085 -TTTTTTG
1 TTTTTTTG
353092 TTTTTTTG
1 TTTTTTTG
353100 TTTTTTTTTG
1 --TTTTTTTG
353110 TTTTTTT
1 TTTTTTT
353117 TGGGTGTAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
7 17 0.29
8 33 0.57
10 8 0.14
ACGTcount: A:0.01, C:0.03, G:0.12, T:0.85
Consensus pattern (8 bp):
TTTTTTTG
Found at i:353075 original size:7 final size:7
Alignment explanation
Indices: 353063--353118 Score: 71
Period size: 7 Copynumber: 8.0 Consensus size: 7
353053 TTTTCTTGGT
353063 TTTTTTG
1 TTTTTTG
353070 TTTTTTTG
1 -TTTTTTG
353078 TTTTTTG
1 TTTTTTG
353085 TTTTTTG
1 TTTTTTG
353092 TTTTTTTG
1 -TTTTTTG
353100 TTTTTT-
1 TTTTTTG
*
353106 TTTGTT-
1 TTTTTTG
353112 TTTTTTG
1 TTTTTTG
353119 GGTGTAAAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
6 10 0.23
7 20 0.45
8 14 0.32
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTTTG
Found at i:353075 original size:22 final size:21
Alignment explanation
Indices: 353039--353117 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 21
353029 CCCCTTTCTA
*
353039 TTTTTTTGCTATTTTTTTCTTGG
1 TTTTTTTG-TTTTTTTTTCTT-G
353062 TTTTTTTGTTTTTTTGTT-TT-
1 TTTTTTTGTTTTTTT-TTCTTG
* *
353082 TTGTTTTT-TGTTTTTTTGTT-
1 TT-TTTTTGTTTTTTTTTCTTG
353102 TTTTTTTGTTTTTTTT
1 TTTTTTTGTTTTTTTT
353118 GGGTGTAAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
19 7 0.14
20 19 0.39
21 5 0.10
22 8 0.16
23 10 0.20
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.85
Consensus pattern (21 bp):
TTTTTTTGTTTTTTTTTCTTG
Found at i:353075 original size:30 final size:30
Alignment explanation
Indices: 353039--353115 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
353029 CCCCTTTCTA
353039 TTTTTTTGCTATTTTT-TTCTTGGTTTTTTTG
1 TTTTTTTG-T-TTTTTGTTCTTGGTTTTTTTG
* *
353070 TTTTTTTGTTTTTTGTTTTTTGTTTTTTTG
1 TTTTTTTGTTTTTTGTTCTTGGTTTTTTTG
353100 TTTTTTTTTGTTTTTT
1 --TTTTTTTGTTTTTT
353116 TTGGGTGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
29 5 0.12
30 14 0.34
31 8 0.20
32 14 0.34
ACGTcount: A:0.01, C:0.03, G:0.12, T:0.84
Consensus pattern (30 bp):
TTTTTTTGTTTTTTGTTCTTGGTTTTTTTG
Found at i:358524 original size:30 final size:28
Alignment explanation
Indices: 358490--358545 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
358480 TCGATGATTA
358490 GAAAATAAATCGAGATTGGAGTATCCCCTC
1 GAAAAT-AA-CGAGATTGGAGTATCCCCTC
* *
358520 GAAAATGACGGGATTGGAGTATCCCC
1 GAAAATAACGAGATTGGAGTATCCCC
358546 AATTATGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.71
29 1 0.04
30 6 0.25
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (28 bp):
GAAAATAACGAGATTGGAGTATCCCCTC
Found at i:358792 original size:52 final size:50
Alignment explanation
Indices: 358638--359026 Score: 200
Period size: 53 Copynumber: 7.3 Consensus size: 50
358628 GAAATAACGA
* * *
358638 GGTTGGAGTATCCTCGATTAT-GAAAAATTGGTAATTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTGGT--GTTTT-GAAATAAAACCG
* * *
358690 GAGTTGGAGTATCTCCGATTAAAGGGAAAATTGGTGTTTTGAAAATAAAACCAG
1 G-GTTGGAGTATCCCCGATT-ATGGAAAAATTGGTGTTTTG-AAATAAAACC-G
* *
358744 GGTTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGCAATAAAACCG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTGGTGTTTT-GAAATAAAACCG
* * * * * *
358795 AGGTTGGAGTATCCCC---T-CGGAAATAA-CGG-GGTTAGAGTATCCCCGATGATTAACGG
1 -GGTTGGAGTATCCCCGATTATGGAAA-AATTGGTGTTTTGA--A------AT-A-AAACCG
* * * *
358851 GGTTGGAGTATCCTCAATTGT-GAAGAAATTGGTGTTTTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTATGGAA-AAATTGGTG---TTTT-GAAATAAAACCG
* * *
358905 GAGTTGGAGTATCCCCGATTAAAGGGAAAATTGATGTTTTGAAAATAAAACCGG
1 G-GTTGGAGTATCCCCGATT-ATGGAAAAATTGGTGTTTTG-AAATAAAACC-G
* * * *
358959 GGTTGGAGTATCCCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACTG
1 GGTTGGAGTAT--CCCCGATTATGGAAAAATTGGTGTTTT-GAAATAAAACCG
359012 AGGTTGGAGTATCCC
1 -GGTTGGAGTATCCC
359027 TCGGAAATAA
Statistics
Matches: 258, Mismatches: 41, Indels: 76
0.69 0.11 0.20
Matches are distributed among these distances:
46 1 0.00
47 3 0.01
48 7 0.03
49 3 0.01
51 1 0.00
52 46 0.18
53 71 0.28
54 44 0.17
55 51 0.20
56 14 0.05
57 2 0.01
58 6 0.02
59 3 0.01
60 1 0.00
62 1 0.00
63 2 0.01
64 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTATGGAAAAATTGGTGTTTTGAAATAAAACCG
Found at i:358925 original size:215 final size:213
Alignment explanation
Indices: 358533--359078 Score: 792
Period size: 215 Copynumber: 2.5 Consensus size: 213
358523 AATGACGGGA
* * * * * * * * * *
358533 TTGGAGTATCCCCAATTAT-GAGAAATCAATATTTTGGGAATAAAGCCGGGGTTAGAGTATCCCC
1 TTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGCAATAAAACCGAGGTTGGAGTATCCCC
** * * *
358597 TC-GAAAGTAATAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTATGA
66 TCGGAAA-TAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCTCAATTATGA
* *
358661 AAAATTGGTAATTTTTGGAAATAAAATCGGAGTTGGAGTATCTCCGATTAAAGGGAAAATTGGTG
129 AAAATTGGTAATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAAAATTGATG
358726 TTTTGAAAATAAAACCAGGG
194 TTTTGAAAATAAAACCAGGG
358746 TTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGCAATAAAACCGAGGTTGGAGTATCCCC
1 TTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGCAATAAAACCGAGGTTGGAGTATCCCC
* *
358811 TCGGAAATAACGGGGTTAGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCTCAATTGTGAAG
66 TCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCTCAATTATGAA-
**
358876 AAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAAAATTGATG
130 AAATTGGT-AATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAAAATTGATG
*
358941 TTTTGAAAATAAAACCGGGG
194 TTTTGAAAATAAAACCAGGG
* *
358961 TTGGAGTATCCCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACTGAGGTTGGAGTAT-C
1 TTGGAGTAT--CCCCGATTATGGAAAAATTAGTGTTTTAGCAATAAAACCGAGGTTGGAGTATCC
*
359025 CCTCGGAAATAACGGGGTTGGATTATCCCCGATGATTAACGGGGTTGGAGTATC
64 CCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATC
359079 TCCGATGATT
Statistics
Matches: 301, Mismatches: 26, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
213 46 0.15
214 68 0.23
215 84 0.28
216 53 0.18
217 50 0.17
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (213 bp):
TTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGCAATAAAACCGAGGTTGGAGTATCCCC
TCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCTCAATTATGAAA
AATTGGTAATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAAAATTGATGTT
TTGAAAATAAAACCAGGG
Found at i:358986 original size:53 final size:54
Alignment explanation
Indices: 358888--359026 Score: 137
Period size: 54 Copynumber: 2.6 Consensus size: 54
358878 ATTGGTGTTT
* * *
358888 TTTTGGAAATAAAATCGGAGTTGGAGTAT--CCCCGATTAAAGGG-AAAATT-GATG
1 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCCCGATT--AGGGAAAAATTAG-TG
358941 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCCCGATT-GTGGAAAAATTAGTG
1 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCCCGATTAG-GGAAAAATTAGTG
* * *
358995 TTTT-AGCAATAAAACTGAGGTTGGAGTATCCC
1 TTTTGA-AAATAAAACCGGGGTTGGAGTATCCC
359027 TCGGAAATAA
Statistics
Matches: 74, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
52 1 0.01
53 29 0.39
54 35 0.47
55 9 0.12
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (54 bp):
TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCCCGATTAGGGAAAAATTAGTG
Found at i:359111 original size:27 final size:27
Alignment explanation
Indices: 359013--359111 Score: 123
Period size: 27 Copynumber: 3.7 Consensus size: 27
359003 ATAAAACTGA
*
359013 GGTTGGAGTATCCCTCG--GAAATAACGG
1 GGTTGGAGTAT-CCTCGATG-ATTAACGG
* *
359040 GGTTGGATTATCCCCGATGATTAACGG
1 GGTTGGAGTATCCTCGATGATTAACGG
359067 GGTTGGAGTAT-CTCCGATGATTAACGG
1 GGTTGGAGTATCCT-CGATGATTAACGG
359094 GGTTGGAGTATCCTCGAT
1 GGTTGGAGTATCCTCGAT
359112 TGTGAAGAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
26 5 0.08
27 55 0.87
28 3 0.05
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.28
Consensus pattern (27 bp):
GGTTGGAGTATCCTCGATGATTAACGG
Found at i:361602 original size:33 final size:33
Alignment explanation
Indices: 361560--361624 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
361550 AAAATTTCCA
***
361560 AATGTATCGATACAAAGATCCATGTATCGATAT
1 AATGTATCGATACAAAGAAAAATGTATCGATAT
*
361593 AATGTATCGATACACAGAAAAATGTATCGATA
1 AATGTATCGATACAAAGAAAAATGTATCGATA
361625 CATTTCCTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAT
Found at i:361670 original size:19 final size:18
Alignment explanation
Indices: 361646--361713 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
361636 CAGTAGCTAA
361646 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
361665 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
361680 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
361697 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
361714 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:361686 original size:13 final size:13
Alignment explanation
Indices: 361668--361692 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
361658 ACAATACTTA
361668 TGTATCGATACAT
1 TGTATCGATACAT
361681 TGTATCGATACA
1 TGTATCGATACA
361693 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:361690 original size:32 final size:32
Alignment explanation
Indices: 361649--361711 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
361639 TAGCTAATTA
*
361649 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
361681 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
361712 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:361793 original size:21 final size:21
Alignment explanation
Indices: 361769--361825 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
361759 CATTTGTAGG
361769 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
361790 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
361811 ATGTATCGATACATT
1 ATGTATCGATACATT
361826 TGGATAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:362663 original size:55 final size:55
Alignment explanation
Indices: 362579--363254 Score: 1030
Period size: 55 Copynumber: 12.3 Consensus size: 55
362569 AAAGTGTATT
* *
362579 CTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCT-TGTGGGCTTTGAAAGGCGTC
1 CTGCTCTTTGAGGACTGGAAAA-TGCCACCAACT-TGTGTGGGCTTTGAAAGGTGTC
*
362634 CTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTC
1 CTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTC
362689 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
*
362744 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAGAGGTGTC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
*
362799 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGCGTGGGCTTTGAAAGGTGTC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
* * *
362854 CTACTTTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGGC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
*
362909 CTGCTTTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
362964 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
*
363019 CTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
363074 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
* **
363129 CTGCTC-TTCAGGGACT-GAAGGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTC
1 CTGCTCTTTGA-GGACTGGAA-AATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTC
* * * * *
363184 CTTCTCTTTGAGGAC--CAAAAGGTTCCACCAACTTATGTGGGCTTT-AAGAGGTTTC
1 CTGCTCTTTGAGGACTGGAAAA--TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTC
363239 CTGCTCTTTGAGGACT
1 CTGCTCTTTGAGGACT
363255 AAAAAGCGGA
Statistics
Matches: 581, Mismatches: 28, Indels: 23
0.92 0.04 0.04
Matches are distributed among these distances:
54 13 0.02
55 559 0.96
56 9 0.02
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (55 bp):
CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
Found at i:362764 original size:27 final size:27
Alignment explanation
Indices: 362624--362764 Score: 65
Period size: 28 Copynumber: 5.1 Consensus size: 27
362614 TGTGGGCTTT
*
362624 GAAAGGCGTCCTGCTCTTTGAGGACT-
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
** * * * *
362650 GAAAGGTG-CCACCAACTTGTGTGGGCTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGACTG
*
362678 TAAGAGGTGTCCTGCTCTTTGAGGACTG
1 GAA-AGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
362706 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
362734 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
362761 GAAA
1 GAAA
362765 ATGCCACCAA
Statistics
Matches: 77, Mismatches: 28, Indels: 19
0.62 0.23 0.15
Matches are distributed among these distances:
25 6 0.08
26 15 0.19
27 17 0.22
28 20 0.26
29 13 0.17
30 6 0.08
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:362984 original size:27 final size:27
Alignment explanation
Indices: 362954--363094 Score: 65
Period size: 27 Copynumber: 5.1 Consensus size: 27
362944 TGTGGGCTTT
*
362954 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTCCTCTTTGAGGACTG
* * * * * *
362981 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTCC-TCTT-TGAGGAC-TG
*
363009 GAAAGGTGTCCTACTCTTTGAGGACTG
1 GAAAGGTGTCCTCCTCTTTGAGGACTG
* * * * * *
363036 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTCC-TCTT-TGAGGAC-TG
*
363064 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTCCTCTTTGAGGACTG
363091 GAAA
1 GAAA
363095 ATGCCACCAA
Statistics
Matches: 76, Mismatches: 28, Indels: 20
0.61 0.23 0.16
Matches are distributed among these distances:
25 6 0.08
26 10 0.13
27 24 0.32
28 20 0.26
29 10 0.13
30 6 0.08
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTCCTCTTTGAGGACTG
Found at i:364242 original size:1 final size:1
Alignment explanation
Indices: 364238--364314 Score: 55
Period size: 1 Copynumber: 77.0 Consensus size: 1
364228 CTTTTCTCTC
* * * * * * * ** *
364238 TTTTTCTTTGTTTTGTTTTTTTATTTTGTTTGTTTTTTTTTTCTTTTTTTTTGCTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
364303 CTTTTTTTTTTT
1 TTTTTTTTTTTT
364315 GAAGAGAATG
Statistics
Matches: 55, Mismatches: 21, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.01, C:0.06, G:0.06, T:0.86
Consensus pattern (1 bp):
T
Found at i:364266 original size:13 final size:12
Alignment explanation
Indices: 364248--364315 Score: 75
Period size: 13 Copynumber: 5.4 Consensus size: 12
364238 TTTTTCTTTG
364248 TTTTGTTTTTTT
1 TTTTGTTTTTTT
364260 ATTTTGTTTGTTTT
1 -TTTTGTTT-TTTT
364274 TTTT-TTCTTTTT
1 TTTTGTT-TTTTT
*
364286 TTTTGCTCTTTTT
1 TTTTG-TTTTTTT
*
364299 TTTTCTTTTTTT
1 TTTTGTTTTTTT
364311 TTTTG
1 TTTTG
364316 AAGAGAATGT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
12 20 0.43
13 22 0.47
14 5 0.11
ACGTcount: A:0.01, C:0.06, G:0.07, T:0.85
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:364269 original size:22 final size:21
Alignment explanation
Indices: 364239--364314 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 21
364229 TTTTCTCTCT
364239 TTTTCTTTGTTTTGTTTTTTTA
1 TTTTCTTTGTTTT-TTTTTTTA
*
364261 TTTTGTTTGTTTTTTTTTTCT-
1 TTTTCTTTGTTTTTTTTTT-TA
* * *
364282 TTTTTTTTGCTCTTTTTTTTTC
1 TTTTCTTTG-TTTTTTTTTTTA
364304 TTTT-TTT-TTTT
1 TTTTCTTTGTTTT
364315 GAAGAGAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
19 3 0.06
21 18 0.38
22 26 0.55
ACGTcount: A:0.01, C:0.07, G:0.07, T:0.86
Consensus pattern (21 bp):
TTTTCTTTGTTTTTTTTTTTA
Found at i:364309 original size:25 final size:24
Alignment explanation
Indices: 364223--364315 Score: 75
Period size: 25 Copynumber: 3.8 Consensus size: 24
364213 AAGCAGGTTC
*
364223 TTTTTCTTTTCTCTCTTTTTCTTTG-T
1 TTTTTCTTTT-T-T-TTTTTGTTTGTT
* *
364249 TTTGT-TTTTTTATTTTGTTTGTT
1 TTTTTCTTTTTTTTTTTGTTTGTT
*
364272 TTTTTTTTCTTTTTTTTTGCTCTT-TT
1 TTTTTCTT-TTTTTTTTTG-T-TTGTT
364298 TTTTTCTTTTTTTTTTTG
1 TTTTTCTTTTTTTTTTTG
364316 AAGAGAATGT
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
22 8 0.14
23 6 0.11
24 3 0.05
25 23 0.41
26 14 0.25
27 2 0.04
ACGTcount: A:0.01, C:0.10, G:0.06, T:0.83
Consensus pattern (24 bp):
TTTTTCTTTTTTTTTTTGTTTGTT
Found at i:376822 original size:30 final size:28
Alignment explanation
Indices: 376788--376843 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
376778 TTGATGATTA
376788 GAAAATAAATCGAGATTGGAGTATCCCCTC
1 GAAAAT-AA-CGAGATTGGAGTATCCCCTC
* *
376818 GAAAATGACGGGATTGGAGTATCCCC
1 GAAAATAACGAGATTGGAGTATCCCC
376844 AATTATGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.71
29 1 0.04
30 6 0.25
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (28 bp):
GAAAATAACGAGATTGGAGTATCCCCTC
Found at i:376997 original size:53 final size:51
Alignment explanation
Indices: 376937--377325 Score: 170
Period size: 53 Copynumber: 7.3 Consensus size: 51
376927 AAATAACGAG
* * * *
376937 GTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGG--TGTTTTGAAAACAAAACCGGA
* * *
376990 GTTGGAGTATCCCCGATTAAAGGGAAAATTGGTGTTTTGAAAACAAAACCGGG
1 GTTGGAGTATCCCCGATT--ATGAAAAATTGGTGTTTTGAAAACAAAACCGGA
* * * *
377043 GTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCAATAAAACC-GA
1 GTTGGAGTATCCCCGATTAT-GAAAAATTGGTGTTTTGA-AAACAAAACCGGA
* * * * * ** *
377094 GGTTAGAGTATCCCC--TT-GGAAATAA-CGG-GGTTAGAGTATCCCCGATGATTAA-CGGG
1 -GTTGGAGTATCCCCGATTATGAAA-AATTGGTGTTTTGA--A--AAC-A--A--AACCGGA
* * * *
377150 GTTGGAGTATCCTCGATTGTGAAGAAATTGGTGTTTTTCTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAA-AAATTGGTG--TTT-TGAAAACAAAACCGGA
* * *
377205 GTTGGAGTATCCCCGATTAAAGGGAAAATTGGTGTTTTGAAAATAAAACC-GA
1 GTTGGAGTATCCCCGATT--ATGAAAAATTGGTGTTTTGAAAACAAAACCGGA
* * * *
377257 GGTTGGAGTATCCCCCCGATTGTGGAAAAATTAGTGTTTT-AGTAATAAAACC-GA
1 -GTTGGAGTAT--CCCCGATTAT-GAAAAATTGGTGTTTTGA-AAACAAAACCGGA
377311 GGTTGGAGTATCCCC
1 -GTTGGAGTATCCCC
377326 TCGGAAATAA
Statistics
Matches: 257, Mismatches: 46, Indels: 67
0.69 0.12 0.18
Matches are distributed among these distances:
47 3 0.01
48 6 0.02
49 2 0.01
50 2 0.01
51 2 0.01
52 42 0.16
53 75 0.29
54 42 0.16
55 51 0.20
56 13 0.05
57 4 0.02
58 6 0.02
59 3 0.01
60 1 0.00
61 1 0.00
62 2 0.01
63 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAACAAAACCGGA
Found at i:377126 original size:28 final size:27
Alignment explanation
Indices: 377094--377166 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
377084 ATAAAACCGA
*
377094 GGTTAGAGTATCCCC-TTGGAAATAACGG
1 GGTTAGAGTATCCCCGAT-G-AATAACGG
*
377122 GGTTAGAGTATCCCCGATGATTAACGG
1 GGTTAGAGTATCCCCGATGAATAACGG
* *
377149 GGTTGGAGTATCCTCGAT
1 GGTTAGAGTATCCCCGAT
377167 TGTGAAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 23 0.57
28 16 0.40
29 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (27 bp):
GGTTAGAGTATCCCCGATGAATAACGG
Found at i:377155 original size:107 final size:106
Alignment explanation
Indices: 377039--377435 Score: 348
Period size: 107 Copynumber: 3.7 Consensus size: 106
377029 AAAACAAAAC
*
377039 CGGGGTTGGAGTATCCCCGATTGTGGAA-AAATTAGTG-TTTTAGCAATAAAACC-GAGGTTAGA
1 CGGGGTTGGAGTATCCCCGATTGT-GAAGAAATTAGTGTTTTTAGAAATAAAACCGGA-GTTAGA
377101 GTATCCCCTTGGAAATAACGGGGTTAGAGTATCCCCGATGATTAA
64 GTATCCCC-TGGAAATAACGGGGTT-GAGTATCCCCGATGATTAA
* * * * *
377146 CGGGGTTGGAGTATCCTCGATTGTGAAGAAATTGGTGTTTTTCTGAAAATAAAATCGGAGTTGGA
1 CGGGGTTGGAGTATCCCCGATTGTGAAGAAATTAGTGTTTTT-AG-AAATAAAACCGGAGTTAGA
* * * * *** ** *
377211 GTATCCCC--G-ATTAAAGGGAAAATTG-GTGT-TTTGAAAATAAAA
64 GTATCCCCTGGAAATAACGGG---GTTGAGTATCCCCGATGAT-TAA
* *
377253 CCGAGGTTGGAGTATCCCCCCGATTGTGGAA-AAATTAGTG-TTTTAGTAATAAAACC-GAGGTT
1 -CGGGGTTGGAGTAT--CCCCGATTGT-GAAGAAATTAGTGTTTTTAGAAATAAAACCGGA-GTT
*
377315 GGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAA
61 AGAGTATCCCCT-GGAAATAACGGGGTT-GAGTATCCCCGATGATTAA
* * *
377363 CGGGGTTGGAGTATCCTCGATTGTGAAGAAATTGGTGTTTTTTTAGAAATAAAATCGGAGTTAGA
1 CGGGGTTGGAGTATCCCCGATTGTGAAGAAATTAGTG--TTTTTAGAAATAAAACCGGAGTTAGA
377428 GTATCCCC
64 GTATCCCC
377436 GATTATAGAA
Statistics
Matches: 226, Mismatches: 38, Indels: 49
0.72 0.12 0.16
Matches are distributed among these distances:
106 19 0.08
107 76 0.34
108 21 0.09
109 21 0.09
110 71 0.31
111 18 0.08
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (106 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAGAAATTAGTGTTTTTAGAAATAAAACCGGAGTTAGAGT
ATCCCCTGGAAATAACGGGGTTGAGTATCCCCGATGATTAA
Found at i:377213 original size:55 final size:52
Alignment explanation
Indices: 377144--377498 Score: 187
Period size: 55 Copynumber: 6.6 Consensus size: 52
377134 CCCGATGATT
* *
377144 AACGGGGTTGGAGTATCCTCGATTGTGAAGAAATTGGTGTTTTTCTGAAAATAA
1 AACGGAGTTGGAGTATCCCCGATTGTGAAGAAATTGGTG-TTTT-TGAAAATAA
*
377198 AATCGGAGTTGGAGTATCCCCGA-T-TAAAGGGAAAATTGGTG-TTTTGAAAATAA
1 AA-CGGAGTTGGAGTATCCCCGATTGTGAA--G-AAATTGGTGTTTTTGAAAATAA
* * * *
377251 AACCGAGGTTGGAGTATCCCCCCGATTGTGGAA-AAATTAGTGTTTTAG-TAATAA
1 AACGGA-GTTGGAGTAT--CCCCGATTGT-GAAGAAATTGGTGTTTTTGAAAATAA
* * * *** ** *
377305 AACCGAGGTTGGAGTATCCCC--TCG-GAA-ATAACGGGGTTGGAGTATCCCCGATGAT-T
1 AACGGA-GTTGGAGTATCCCCGATTGTGAAGA-AA-----TTGGTGT-T-TTTGAAAATAA
* * *
377361 AACGGGGTTGGAGTATCCTCGATTGTGAAGAAATTGGTGTTTTTTTAGAAATAA
1 AACGGAGTTGGAGTATCCCCGATTGTGAAGAAATTGGTG-TTTTTGA-AAATAA
* * *
377415 AATCGGAGTTAGAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAA
1 AA-CGGAGTTGGAGTATCCCCGATTGTGAAG-AAATTGGTGTTTTTGAAAATAA
* *
377466 AATCGGAGTTGGAATATCCCCGATTGTGGAGAA
1 AA-CGGAGTTGGAGTATCCCCGATTGTGAAGAA
377499 TTGAGAAACT
Statistics
Matches: 233, Mismatches: 37, Indels: 64
0.70 0.11 0.19
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 2 0.01
51 30 0.13
52 15 0.06
53 36 0.15
54 52 0.22
55 63 0.27
56 15 0.06
57 6 0.03
58 7 0.03
59 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
AACGGAGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTGAAAATAA
Found at i:377232 original size:215 final size:214
Alignment explanation
Indices: 376869--377495 Score: 990
Period size: 217 Copynumber: 2.9 Consensus size: 214
376859 ATATTTTGGG
* * * ** *
376869 AATAAAGCCGGGGTTAGAGTATCCCCTTGGAAGTAATAGGGTTGGAGTATCCCCGATGAAATAAC
1 AATAAAACCGAGGTTAGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAAC
* * *
376934 GAGGTTGGAGTATCCTCGATTATGAA-AAATTGGTATTTTTTGAAAATAAAATCGGAGTTGGAGT
65 GGGGTTGGAGTATCCTCGATTGTGAAGAAATTGGTGTTTTTTGAAAATAAAATCGGAGTTGGAGT
*
376998 ATCCCCGATTAAAGGGAAAATTGGTGTTTTGAAAACAAAACCGGGGTTGGAGTATCCCCGATTGT
130 ATCCCCGATTAAAGGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGT
377063 GGAAAAATTAGTGTTTTAGC
195 GGAAAAATTAGTGTTTTAGC
*
377083 AATAAAACCGAGGTTAGAGTATCCCCTTGGAAATAACGGGGTTAGAGTATCCCCGATGATTAACG
1 AATAAAACCGAGGTTAGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACG
377148 GGGTTGGAGTATCCTCGATTGTGAAGAAATTGGTGTTTTTCTGAAAATAAAATCGGAGTTGGAGT
66 GGGTTGGAGTATCCTCGATTGTGAAGAAATTGGTGTTTTT-TGAAAATAAAATCGGAGTTGGAGT
*
377213 ATCCCCGATTAAAGGGAAAATTGGTGTTTTGAAAATAAAACCGAGGTTGGAGTATCCCCCCGATT
130 ATCCCCGATTAAAGGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTAT--CCCCGATT
*
377278 GTGGAAAAATTAGTGTTTTAGT
193 GTGGAAAAATTAGTGTTTTAGC
* *
377300 AATAAAACCGAGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACG
1 AATAAAACCGAGGTTAGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACG
* *
377365 GGGTTGGAGTATCCTCGATTGTGAAGAAATTGGTGTTTTTTTAGAAATAAAATCGGAGTTAGAGT
66 GGGTTGGAGTATCCTCGATTGTGAAGAAATTGGTGTTTTTTGA-AAATAAAATCGGAGTTGGAGT
* * * * *
377430 ATCCCCGATTATA--GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGT
130 ATCCCCGATTAAAGGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGT
377493 GGA
195 GGA
377496 GAATTGAGAA
Statistics
Matches: 384, Mismatches: 24, Indels: 11
0.92 0.06 0.03
Matches are distributed among these distances:
213 42 0.11
214 65 0.17
215 112 0.29
216 2 0.01
217 163 0.42
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (214 bp):
AATAAAACCGAGGTTAGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACG
GGGTTGGAGTATCCTCGATTGTGAAGAAATTGGTGTTTTTTGAAAATAAAATCGGAGTTGGAGTA
TCCCCGATTAAAGGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTG
GAAAAATTAGTGTTTTAGC
Found at i:377343 original size:28 final size:27
Alignment explanation
Indices: 377311--377378 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
377301 ATAAAACCGA
**
377311 GGTTGGAGTATCCCCTCGGAAATAACGG
1 GGTTGGAGTATCCCCGAGG-AATAACGG
* *
377339 GGTTGGAGTATCCCCGATGATTAACGG
1 GGTTGGAGTATCCCCGAGGAATAACGG
377366 GGTTGGAGTATCC
1 GGTTGGAGTATCC
377379 TCGATTGTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 20 0.56
28 16 0.44
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.25
Consensus pattern (27 bp):
GGTTGGAGTATCCCCGAGGAATAACGG
Found at i:379872 original size:13 final size:13
Alignment explanation
Indices: 379854--379879 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
379844 ACAAAGATCC
379854 ATGTATCGATACA
1 ATGTATCGATACA
379867 ATGTATCGATACA
1 ATGTATCGATACA
379880 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:379875 original size:33 final size:33
Alignment explanation
Indices: 379833--379899 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
379823 AAAATTTCCA
***
379833 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
379866 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
379899 A
1 A
379900 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:379943 original size:19 final size:18
Alignment explanation
Indices: 379919--379990 Score: 84
Period size: 19 Copynumber: 4.2 Consensus size: 18
379909 CAGTAGCTAA
379919 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
379938 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
379953 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
379970 TTATGTATCGATACAAA-
1 TTATGTATCGATACAAAC
379987 TTAT
1 TTAT
379991 TGAATTTCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.23
14 1 0.02
16 2 0.04
17 4 0.09
18 4 0.09
19 25 0.53
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:379959 original size:13 final size:13
Alignment explanation
Indices: 379941--379965 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
379931 ACAATACTTA
379941 TGTATCGATACAT
1 TGTATCGATACAT
379954 TGTATCGATACA
1 TGTATCGATACA
379966 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:379963 original size:32 final size:32
Alignment explanation
Indices: 379922--379984 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
379912 TAGCTAATTA
*
379922 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
379954 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
379985 AATTATTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:380066 original size:21 final size:21
Alignment explanation
Indices: 380042--380098 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
380032 CATTTGTAGG
380042 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
380063 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
380084 ATGTATCGATACATT
1 ATGTATCGATACATT
380099 TGGATAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:387905 original size:52 final size:52
Alignment explanation
Indices: 387760--387885 Score: 216
Period size: 52 Copynumber: 2.4 Consensus size: 52
387750 AATATGAAAT
*
387760 TTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
* * *
387812 TTTACCTGTATGTATCGATACATTTCATAGTGTATTGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
387864 TTTGCCTGCATGTATCGATACA
1 TTTGCCTGCATGTATCGATACA
387886 AAGATCAGTA
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:0.27, C:0.17, G:0.18, T:0.37
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
Found at i:387983 original size:19 final size:19
Alignment explanation
Indices: 387959--388025 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
387949 CAGTAGCTAA
387959 TTATGTATCGATACAACAC
1 TTATGTATCGATACAACAC
387978 TTATGTATCGAT---ACA-
1 TTATGTATCGATACAACAC
387993 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAACAC
388010 TTATGTATCGATACAA
1 TTATGTATCGATACAA
388026 ATCGTTGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 9 0.21
14 1 0.02
16 6 0.14
18 1 0.02
19 25 0.60
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (19 bp):
TTATGTATCGATACAACAC
Found at i:387999 original size:13 final size:13
Alignment explanation
Indices: 387981--388005 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
387971 ACAACACTTA
387981 TGTATCGATACAT
1 TGTATCGATACAT
387994 TGTATCGATACA
1 TGTATCGATACA
388006 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:388003 original size:32 final size:32
Alignment explanation
Indices: 387962--388024 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
387952 TAGCTAATTA
387962 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
387994 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
388025 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:388507 original size:170 final size:170
Alignment explanation
Indices: 388224--388560 Score: 602
Period size: 170 Copynumber: 2.0 Consensus size: 170
388214 GCCGGGCGCC
**
388224 AATTCGTCCCCACATATATCAAATCCTCCACCTACTAACTAGGCCTCAAATTGTCGAAAATTGGT
1 AATTCGTCCCCACATATATCAAATCCTCCACCTACTAACTAGGCCTCAAATTGTCGAAAATTGAC
388289 CCGGACAAAATGAGGTGTCTACAGCTTCCTTCAAACTACTCCAAGAAATACACTCATGATTCCCT
66 CCGGACAAAATGAGGTGTCTACAGCTTCCTTCAAACTACTCCAAGAAATACACTCATGATTCCCT
388354 TTGACCTTAATATGTTCTTATATCCAAGCTTCAGTAGACG
131 TTGACCTTAATATGTTCTTATATCCAAGCTTCAGTAGACG
* **
388394 AATTCGTCCCCACATATGTCAAATCCTCCACCTACTAGTTAGGCCTCAAATTGTCGAAAATTGAC
1 AATTCGTCCCCACATATATCAAATCCTCCACCTACTAACTAGGCCTCAAATTGTCGAAAATTGAC
*
388459 CCGGACAAAATGAGGTGTCTACAGCTTCCTTCAAACTACTCTAAGAAATACACTCATGATTCCCT
66 CCGGACAAAATGAGGTGTCTACAGCTTCCTTCAAACTACTCCAAGAAATACACTCATGATTCCCT
* *
388524 TTGACCTTAATGTGTTTTTATATCCAAGCTTCAGTAG
131 TTGACCTTAATATGTTCTTATATCCAAGCTTCAGTAG
388561 CCCCGGTGAC
Statistics
Matches: 159, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
170 159 1.00
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (170 bp):
AATTCGTCCCCACATATATCAAATCCTCCACCTACTAACTAGGCCTCAAATTGTCGAAAATTGAC
CCGGACAAAATGAGGTGTCTACAGCTTCCTTCAAACTACTCCAAGAAATACACTCATGATTCCCT
TTGACCTTAATATGTTCTTATATCCAAGCTTCAGTAGACG
Found at i:394439 original size:17 final size:18
Alignment explanation
Indices: 394414--394448 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
394404 AAATATTTTC
*
394414 ATATTATATTTTA-ATTA
1 ATATCATATTTTATATTA
394431 ATATCATATTTTATATTA
1 ATATCATATTTTATATTA
394449 TTTATCGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATCATATTTTATATTA
Found at i:395036 original size:20 final size:20
Alignment explanation
Indices: 394999--395036 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
394989 TTAATGTCAT
*
394999 AAATTATAAAAATTAAATTC
1 AAATTATAAAAATAAAATTC
*
395019 AAATTATAATAATAAAAT
1 AAATTATAAAAATAAAAT
395037 AAATTAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATTATAAAAATAAAATTC
Found at i:395320 original size:37 final size:38
Alignment explanation
Indices: 395249--395321 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 38
395239 TTTATTTTGA
* *
395249 TTTAGTTTAAAATTATAATTTTAAATTAATAATATATT
1 TTTAGTTTAAAATTATAATTATAAAATAATAATATATT
395287 TTTA-TTT-AAATT-TAATTATAAAATATATAAATATA
1 TTTAGTTTAAAATTATAATTATAAAATA-AT-AATATA
395322 AAAATTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 11 0.35
36 7 0.23
37 9 0.29
38 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (38 bp):
TTTAGTTTAAAATTATAATTATAAAATAATAATATATT
Found at i:395390 original size:20 final size:20
Alignment explanation
Indices: 395351--395406 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
395341 AATAGTAAAT
*
395351 TTAAATTTATGAATTAAATTAA
1 TTAAATTT-T-AATTTAATTAA
**
395373 TTAAATTTTAATTTAATTTT
1 TTAAATTTTAATTTAATTAA
*
395393 TTTAATTTTAATTT
1 TTAAATTTTAATTT
395407 GATTTAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 21 0.70
21 1 0.03
22 8 0.27
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTAAATTTTAATTTAATTAA
Found at i:395397 original size:25 final size:25
Alignment explanation
Indices: 395369--395416 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
395359 ATGAATTAAA
395369 TTAA-TTAAATTTTAATTTAATTTTT
1 TTAATTTAAA-TTTAATTTAATTTTT
* *
395394 TTAATTTTAATTTGATTTAATTT
1 TTAATTTAAATTTAATTTAATTT
395417 ATAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
TTAATTTAAATTTAATTTAATTTTT
Found at i:395431 original size:12 final size:11
Alignment explanation
Indices: 395411--395443 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
395401 TAATTTGATT
395411 TAATTTATAAA
1 TAATTTATAAA
395422 TAATTT-TATAA
1 TAATTTATA-AA
395433 TAATTTATAAA
1 TAATTTATAAA
395444 ACAATAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.10
11 16 0.80
12 2 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TAATTTATAAA
Found at i:396576 original size:21 final size:21
Alignment explanation
Indices: 396519--396576 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 21
396509 AAGTTTTGTT
*
396519 ATTCAAACTTTATTTTTCTTTA
1 ATTCAAACTTTA-GTTTCTTTA
*
396541 A-T-AAA-TAT-G-TTCTTTA
1 ATTCAAACTTTAGTTTCTTTA
396557 ATTCAAACTTTAGTTTCTTT
1 ATTCAAACTTTAGTTTCTTT
396577 TTATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 11
0.67 0.07 0.26
Matches are distributed among these distances:
16 8 0.29
17 1 0.04
18 3 0.11
19 4 0.14
20 4 0.14
21 7 0.25
22 1 0.04
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTCAAACTTTAGTTTCTTTA
Found at i:396805 original size:2 final size:2
Alignment explanation
Indices: 396798--396834 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
396788 AAAGATTCTG
*
396798 AT AT AT AT AT AT AT AT GT AT AT AT AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
396835 ATAACCTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:405021 original size:15 final size:15
Alignment explanation
Indices: 405001--405035 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
404991 TGAGTATTTA
405001 TATATATAT-TAATAT
1 TATATATATGT-ATAT
405016 TATATATATGTATAT
1 TATATATATGTATAT
405031 TATAT
1 TATAT
405036 TGTACATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 18 0.95
16 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TATATATATGTATAT
Found at i:405085 original size:22 final size:22
Alignment explanation
Indices: 405051--405114 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
405041 ATATCGAAGA
*
405051 ATTATATACATTAAATTATGTTT
1 ATTA-ATAAATTAAATTATGTTT
*
405074 ATTAATAAATTATAATATATTTTT
1 ATTAATAAATTA-AAT-TATGTTT
*
405098 ATT-GTAATATTAAATTA
1 ATTAATAA-ATTAAATTA
405115 AAAATAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
22 9 0.26
23 13 0.37
24 13 0.37
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (22 bp):
ATTAATAAATTAAATTATGTTT
Found at i:405841 original size:16 final size:16
Alignment explanation
Indices: 405816--405851 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
405806 TTTTATTATG
405816 ATATTAATATATATTA
1 ATATTAATATATATTA
* *
405832 ATATTCATATATTTTA
1 ATATTAATATATATTA
405848 ATAT
1 ATAT
405852 ATCACTTTGA
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:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTAATATATATTA
Found at i:410085 original size:91 final size:90
Alignment explanation
Indices: 409944--410120 Score: 300
Period size: 91 Copynumber: 2.0 Consensus size: 90
409934 TTTATTTGTA
* *
409944 GGGTTAGGTTGCTTTTAAATTATCATCTTGAAAAGGTGACCTTTCAAGTGTTGGCATTTTAGTTT
1 GGGTTAGGTTGCTCTTAAATTATCATCTTGAAAAGGTGACCTTTCAAGTGTTGGCATTTTAGTCT
410009 GGAGAATAATGTTGCTAAATTTGGG
66 GGAGAATAATGTTGCTAAATTTGGG
*
410034 GGGTTAGGTTGCTCTTAAATTATCAATCTTGAAAAGGTGACCTTTCTAGTGTTGGCATTTTAGTC
1 GGGTTAGGTTGCTCTTAAATTATC-ATCTTGAAAAGGTGACCTTTCAAGTGTTGGCATTTTAGTC
* *
410099 TGTAGTATAATGTTGCTAAATT
65 TGGAGAATAATGTTGCTAAATT
410121 CCATTTGGAC
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 23 0.28
91 58 0.72
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (90 bp):
GGGTTAGGTTGCTCTTAAATTATCATCTTGAAAAGGTGACCTTTCAAGTGTTGGCATTTTAGTCT
GGAGAATAATGTTGCTAAATTTGGG
Found at i:412363 original size:4 final size:4
Alignment explanation
Indices: 412354--412392 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
412344 TAAGCTTGAA
*
412354 TTCT TTCT TTCT TTCT TTCT TTC- TTCT TCCT TT-T TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
412393 AATGAGTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 6 0.19
4 25 0.81
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:412371 original size:12 final size:12
Alignment explanation
Indices: 412354--412392 Score: 55
Period size: 11 Copynumber: 3.4 Consensus size: 12
412344 TAAGCTTGAA
412354 TTCTTTCTTTCT
1 TTCTTTCTTTCT
412366 TTCTTTCTTTC-
1 TTCTTTCTTTCT
*
412377 TTCTTCCTTT-T
1 TTCTTTCTTTCT
412388 TTCTT
1 TTCTT
412393 AATGAGTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTCTTTCTTTCT
Found at i:417772 original size:16 final size:16
Alignment explanation
Indices: 417751--417783 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
417741 TTTTGTAAAC
*
417751 AATTTAAAATAATTTA
1 AATTTAAAATAAATTA
417767 AATTTAAAATAAATTA
1 AATTTAAAATAAATTA
417783 A
1 A
417784 TTTGAACATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTTAAAATAAATTA
Found at i:417919 original size:15 final size:16
Alignment explanation
Indices: 417853--417923 Score: 53
Period size: 17 Copynumber: 4.6 Consensus size: 16
417843 AAAGTTTTGT
*
417853 TTAACAAAAATTTAAGA
1 TTAA-AAAAAATTAAGA
*
417870 TGAAAAAAAA-T-A-A
1 TTAAAAAAAATTAAGA
*
417883 TTAAAAAAAAGCTTGAGA
1 TTAAAAAAAA--TTAAGA
417901 -TAAAAAAAATT-AGA
1 TTAAAAAAAATTAAGA
417915 TTAAAAAAA
1 TTAAAAAAA
417924 TGTGTTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
13 10 0.22
14 4 0.09
15 11 0.24
16 6 0.13
17 13 0.29
18 1 0.02
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.23
Consensus pattern (16 bp):
TTAAAAAAAATTAAGA
Found at i:418915 original size:2 final size:2
Alignment explanation
Indices: 418908--418963 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
418898 CAAATTGCTT
418908 TA TA 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 TA TA
418950 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
418964 AAAGAATACA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:419804 original size:12 final size:12
Alignment explanation
Indices: 419784--419838 Score: 60
Period size: 11 Copynumber: 4.8 Consensus size: 12
419774 ATTTCATATC
419784 ATATAATATTTT
1 ATATAATATTTT
*
419796 ATATCATATTTT
1 ATATAATATTTT
* *
419808 A-ATTATTTTTT
1 ATATAATATTTT
*
419819 ATATAATA-TTC
1 ATATAATATTTT
419830 ATATAATAT
1 ATATAATAT
419839 AATCATAGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 19 0.54
12 16 0.46
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATAATATTTT
Found at i:421159 original size:11 final size:11
Alignment explanation
Indices: 421128--421181 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
421118 ATTTTTTTGG
421128 TTTTAAATATA
1 TTTTAAATATA
*
421139 TTTATTAAATGTA
1 -TT-TTAAATATA
421152 TTTTAAATATA
1 TTTTAAATATA
421163 TTTT-AA-ATA
1 TTTTAAATATA
421172 TTTTAAATAT
1 TTTTAAATAT
421182 TAATTAAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
9 7 0.19
10 4 0.11
11 14 0.38
12 4 0.11
13 8 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (11 bp):
TTTTAAATATA
Found at i:421173 original size:20 final size:23
Alignment explanation
Indices: 421128--421181 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 23
421118 ATTTTTTTGG
421128 TTTTAAATATATTTATTAAATGTA
1 TTTTAAATATATTTATTAAA-GTA
421152 TTTTAAATATA-TT-TTAAA-TA
1 TTTTAAATATATTTATTAAAGTA
421172 TTTTAAATAT
1 TTTTAAATAT
421182 TAATTAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 12 0.40
22 5 0.17
23 2 0.07
24 11 0.37
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTTAAATATATTTATTAAAGTA
Found at i:421188 original size:20 final size:21
Alignment explanation
Indices: 421136--421188 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
421126 GGTTTTAAAT
*
421136 ATATTTATTAAATGTATTTTAA
1 ATATTAATTAAA-GTATTTTAA
*
421158 ATA-TATTTTAAA-TATTTTAA
1 ATATTA-ATTAAAGTATTTTAA
421178 ATATTAATTAA
1 ATATTAATTAA
421189 GTTACTTCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 15 0.58
21 3 0.12
22 8 0.31
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATATTAATTAAAGTATTTTAA
Found at i:422065 original size:167 final size:166
Alignment explanation
Indices: 421834--422136 Score: 419
Period size: 167 Copynumber: 1.8 Consensus size: 166
421824 GTAAGATTAA
* * * *
421834 AGTTTATTTGTAAATATTGAAAAATTTTGTTTCAAGGTCAAAAGTAATTGGCCAAATCTTTCTTA
1 AGTTTATTTGTAAATATTGAAAAATTTTATTCCAAGGCCAAAAGTAATTGGCCAAATATTTCTTA
* * ** * *
421899 TGATTTTTGGATGTGATTTTTGTGTTGTTTTTTTATATATTTAATGCTTAATTTTGTCTTTTAAT
66 TAATTTTCGGATGTGATTTTTGTGTTG-ACTTTGATATACTTAATGCTTAATTTTGTCTTTTAAT
421964 TATGTAATAGCCAATTTACATATTTAGAACATTTAGG
130 TATGTAATAGCCAATTTACATATTTAGAACATTTAGG
* * **
422001 AGTTTATTTGTAAATATT-AAAATATTTTATTCCAAGGCCAAAGGTGATTGGCTGAATATTTCTT
1 AGTTTATTTGTAAATATTGAAAA-ATTTTATTCCAAGGCCAAAAGTAATTGGCCAAATATTTCTT
* * * *
422065 ATAATTTTCGGATGTGATTTTTTTGTTGACTTTGATATACTTGATGTTTAATTTTGTGTTTTAAT
65 ATAATTTTCGGATGTGATTTTTGTGTTGACTTTGATATACTTAATGCTTAATTTTGTCTTTTAAT
422130 TATGTAA
130 TATGTAA
422137 GGACTAATTT
Statistics
Matches: 117, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
166 41 0.35
167 76 0.65
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (166 bp):
AGTTTATTTGTAAATATTGAAAAATTTTATTCCAAGGCCAAAAGTAATTGGCCAAATATTTCTTA
TAATTTTCGGATGTGATTTTTGTGTTGACTTTGATATACTTAATGCTTAATTTTGTCTTTTAATT
ATGTAATAGCCAATTTACATATTTAGAACATTTAGG
Found at i:424332 original size:15 final size:15
Alignment explanation
Indices: 424309--424338 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
424299 ATTTTTAAAT
*
424309 AAAGTATAAATATAA
1 AAAGCATAAATATAA
424324 AAAGCATAAATATAA
1 AAAGCATAAATATAA
424339 TAAAAATACA
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:0.67, C:0.03, G:0.07, T:0.23
Consensus pattern (15 bp):
AAAGCATAAATATAA
Found at i:424558 original size:27 final size:29
Alignment explanation
Indices: 424495--424559 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 29
424485 TATAACATCA
424495 TTTAACATAATATTTTTCTACTGTTTAATT
1 TTTAA-ATAATATTTTTCTACTGTTTAATT
*
424525 ATT--ATAATATTTTT-T-CT-TTTAATT
1 TTTAAATAATATTTTTCTACTGTTTAATT
424549 TTTAAGATAAT
1 TTTAA-ATAAT
424560 TTACTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
24 9 0.30
25 2 0.07
26 1 0.03
27 16 0.53
30 2 0.07
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (29 bp):
TTTAAATAATATTTTTCTACTGTTTAATT
Found at i:425148 original size:17 final size:18
Alignment explanation
Indices: 425120--425153 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
425110 TATATATGTG
425120 TATCATTTAATTATATTA
1 TATCATTTAATTATATTA
*
425138 TATCA-TTAATTTTATT
1 TATCATTTAATTATATT
425154 TTTTATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (18 bp):
TATCATTTAATTATATTA
Found at i:425841 original size:7 final size:6
Alignment explanation
Indices: 425820--425877 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 6
425810 TGAATACTTT
* * *
425820 AAATAA AAATAA AAACATA AAATAAA AAATAA AAATGAA AAA-CA AACTAA
1 AAATAA AAATAA AAATA-A AAAT-AA AAATAA AAAT-AA AAATAA AAATAA
425870 AAATAA AA
1 AAATAA AA
425878 TAATTGAGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 3 0.07
6 24 0.57
7 14 0.33
8 1 0.02
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (6 bp):
AAATAA
Found at i:425843 original size:13 final size:14
Alignment explanation
Indices: 425822--425877 Score: 62
Period size: 13 Copynumber: 3.9 Consensus size: 14
425812 AATACTTTAA
425822 ATAAAAATAAAAAC
1 ATAAAAATAAAAAC
425836 AT-AAAATAAAAA-
1 ATAAAAATAAAAAC
425848 ATAAAAATGAAAAAC
1 ATAAAAAT-AAAAAC
425863 AAACTAAAAATAAAA
1 --A-TAAAAATAAAA
425878 TAATTGAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 2 0.06
13 15 0.42
14 7 0.19
17 5 0.14
18 7 0.19
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (14 bp):
ATAAAAATAAAAAC
Found at i:425860 original size:19 final size:18
Alignment explanation
Indices: 425820--425880 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
425810 TGAATACTTT
425820 AAAT-AAAAATAAAAACATA
1 AAATAAAAAAT-AAAA-ATA
425839 AAATAAAAAATAAAAATGA
1 AAATAAAAAATAAAAAT-A
* *
425858 AAA-ACAAACTAAAAATA
1 AAATAAAAAATAAAAATA
425875 AAATAA
1 AAATAA
425881 TTGAGATGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 4 0.11
18 14 0.39
19 12 0.33
20 6 0.17
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.15
Consensus pattern (18 bp):
AAATAAAAAATAAAAATA
Found at i:426842 original size:2 final size:2
Alignment explanation
Indices: 426835--426864 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
426825 GTGACTTTCA
426835 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
426865 GTTTATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:430143 original size:17 final size:17
Alignment explanation
Indices: 430110--430144 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
430100 TTTTGCTAGT
* *
430110 TATATCCATGTTGAACA
1 TATATCCATATTCAACA
430127 TATATCCATATTCAACA
1 TATATCCATATTCAACA
430144 T
1 T
430145 TCACCCCTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (17 bp):
TATATCCATATTCAACA
Found at i:434457 original size:10 final size:10
Alignment explanation
Indices: 434436--434470 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
434426 TTTTGAGATT
434436 AAGAGAGA-A
1 AAGAGAGAGA
434445 AAGAGAGAGA
1 AAGAGAGAGA
434455 AAGAGAGAGA
1 AAGAGAGAGA
*
434465 GAGAGA
1 AAGAGA
434471 CCGTTGCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (10 bp):
AAGAGAGAGA
Found at i:434727 original size:27 final size:25
Alignment explanation
Indices: 434652--434750 Score: 67
Period size: 27 Copynumber: 3.7 Consensus size: 25
434642 TCATATTTTT
*
434652 ATTATTTTTTATATATTTTATGTATTGTA
1 ATTA-TTTTT-TATA-TTTATTTATT-TA
* *
434681 ATTATTATTAATAATTTATTTATTTAA
1 ATTATTTTTTAT-ATTTATTTATTT-A
434708 ATTATTTTTTATATTATATTATATTT-
1 ATTATTTTTTATATT-TATT-TATTTA
* *
434734 TTTA-ATTTTATATTTAT
1 ATTATTTTTTATATTTAT
434751 ATCGTATAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
24 3 0.05
25 9 0.15
26 7 0.12
27 26 0.44
28 10 0.17
29 4 0.07
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (25 bp):
ATTATTTTTTATATTTATTTATTTA
Found at i:434735 original size:20 final size:21
Alignment explanation
Indices: 434710--434752 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
434700 TTATTTAAAT
434710 TATTTTTT-ATATTATA-TTA
1 TATTTTTTAATATTATATTTA
*
434729 TATTTTTTAATTTTATATTTA
1 TATTTTTTAATATTATATTTA
434750 TAT
1 TAT
434753 CGTATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 7 0.33
21 6 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TATTTTTTAATATTATATTTA
Found at i:435030 original size:10 final size:10
Alignment explanation
Indices: 435017--435045 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
435007 GTCAAAAAAA
435017 TTCAAATTTC
1 TTCAAATTTC
435027 TTCAAATTTC
1 TTCAAATTTC
435037 TTCAAATTT
1 TTCAAATTT
435046 GATTTAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (10 bp):
TTCAAATTTC
Found at i:435837 original size:29 final size:30
Alignment explanation
Indices: 435764--435839 Score: 74
Period size: 29 Copynumber: 2.6 Consensus size: 30
435754 TATATGGTCA
435764 TCAATTTCATGCATTTTA-AGACCATTTAG
1 TCAATTTCATGCATTTTAGAGACCATTTAG
*
435793 TC-ATTTACTATG--TTTTAGAGACTA-TTA-
1 TCAATTT-C-ATGCATTTTAGAGACCATTTAG
435820 TGCAATTTCATGCATTTTAG
1 T-CAATTTCATGCATTTTAG
435840 TCATTTACTA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
27 4 0.10
28 14 0.36
29 18 0.46
30 3 0.08
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (30 bp):
TCAATTTCATGCATTTTAGAGACCATTTAG
Found at i:436002 original size:59 final size:57
Alignment explanation
Indices: 435884--436021 Score: 145
Period size: 58 Copynumber: 2.4 Consensus size: 57
435874 TTCAGAATTT
* * *
435884 TTATGTAATTTCATGCATTTTAGGGACAATGAAGTCATTTTCCATGCATTTATGGACTA
1 TTATGTAATTTCATGCATTTTA--GACAATGAAATCATTTTCCATGCATTAAGGGACTA
* * *
435943 TTATGTAATTTCATGCATCTTTAGTCATTTAAATCATTTT-CATGCATTAAGGG-CTA
1 TTATGTAATTTCATGCAT-TTTAGACAATGAAATCATTTTCCATGCATTAAGGGACTA
**
435999 CTATATACAATTTCATGCATTTT
1 -T-TATGTAATTTCATGCATTTT
436022 TAGGCCATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
56 3 0.04
57 15 0.22
58 28 0.41
59 18 0.26
60 4 0.06
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.43
Consensus pattern (57 bp):
TTATGTAATTTCATGCATTTTAGACAATGAAATCATTTTCCATGCATTAAGGGACTA
Found at i:436069 original size:58 final size:56
Alignment explanation
Indices: 435918--436077 Score: 144
Period size: 58 Copynumber: 2.8 Consensus size: 56
435908 GACAATGAAG
* * * * *
435918 TCATTTTCCATGCATTTATGGACTATTATGTAATTTCATGCATCTTTAGTCATTTAAA
1 TCATTTT-CA-GCATTAAGGGACTATTATATAATTTCATGCATTTTTAGCCATTTAAA
* * *
435976 TCATTTTCATGCATTAAGGG-CTACTATATACAATTTCATGCATTTTTAGGCCATTTTAG
1 TCATTTTCA-GCATTAAGGGACTA-T-TATATAATTTCATGCATTTTTA-GCCATTTAAA
* *
436035 TCATTCTTC-GTATTTAAGGGACTATTATATAATTTCAAGCATT
1 TCATT-TTCAGCA-TTAAGGGACTATTATATAATTTCATGCATT
436078 GTAGCCCCAT
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
56 3 0.04
57 12 0.14
58 44 0.52
59 20 0.24
60 6 0.07
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (56 bp):
TCATTTTCAGCATTAAGGGACTATTATATAATTTCATGCATTTTTAGCCATTTAAA
Found at i:437328 original size:25 final size:27
Alignment explanation
Indices: 437284--437335 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
437274 CATACGAATC
437284 TTTATTTTTTAAAGTGAACT-TCAAAA
1 TTTATTTTTTAAAGTGAACTCTCAAAA
*
437310 TTTATTTTTTAAGGT-AACTCTCAAAA
1 TTTATTTTTTAAAGTGAACTCTCAAAA
437336 GATGATTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.46
Consensus pattern (27 bp):
TTTATTTTTTAAAGTGAACTCTCAAAA
Found at i:439169 original size:14 final size:15
Alignment explanation
Indices: 439143--439173 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
439133 AAAAGAATAG
439143 GAAAGATAAAAAAAA
1 GAAAGATAAAAAAAA
439158 GAAAGA-AAAAAAAA
1 GAAAGATAAAAAAAA
439172 GA
1 GA
439174 GGAGTAGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (15 bp):
GAAAGATAAAAAAAA
Found at i:441142 original size:57 final size:57
Alignment explanation
Indices: 441048--441160 Score: 190
Period size: 57 Copynumber: 2.0 Consensus size: 57
441038 ATTTAGAAAG
* *
441048 GAAGATTTTTTAGTTTTGAATTGATTTTAGAACGACATACATCAATTAATGCTATAA
1 GAAGATTTTTGAGTTTTGAATTGATTTTAGAACGACATACATCAATCAATGCTATAA
**
441105 GAAGATTTTTGAGTTTTGAATTGATTTTAGAGTGACATACATCAATCAATGCTATA
1 GAAGATTTTTGAGTTTTGAATTGATTTTAGAACGACATACATCAATCAATGCTATA
441161 CTTTGCAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (57 bp):
GAAGATTTTTGAGTTTTGAATTGATTTTAGAACGACATACATCAATCAATGCTATAA
Found at i:443484 original size:15 final size:14
Alignment explanation
Indices: 443465--443507 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
443455 GATTTTTTTT
443465 AAAAAAATTTTGAA
1 AAAAAAATTTTGAA
*
443479 ATAAAAAATTTAAGAA
1 A-AAAAAATTT-TGAA
443495 AAATAAAATTTTG
1 AAA-AAAATTTTG
443508 TTTCAGCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 1 0.04
15 12 0.50
16 11 0.46
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (14 bp):
AAAAAAATTTTGAA
Found at i:445994 original size:18 final size:17
Alignment explanation
Indices: 445971--446021 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
445961 CATTTTATTC
445971 AATAAAATATTTAATTAT
1 AATAAAATA-TTAATTAT
445989 AATAAAAATAATT-ATTAT
1 AAT-AAAAT-ATTAATTAT
* *
446007 ATTCAAATATTAATT
1 AATAAAATATTAATT
446022 CAAATTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 3 0.11
17 7 0.25
18 10 0.36
19 7 0.25
20 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AATAAAATATTAATTAT
Found at i:446032 original size:11 final size:12
Alignment explanation
Indices: 446001--446035 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
445991 TAAAAATAAT
446001 TATTATATTCAAA
1 TATTA-ATTCAAA
446014 TATTAATTCAAA
1 TATTAATTCAAA
446026 T-TTAATTCAA
1 TATTAATTCAA
446036 TAATAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 9 0.41
12 8 0.36
13 5 0.23
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (12 bp):
TATTAATTCAAA
Found at i:446335 original size:18 final size:17
Alignment explanation
Indices: 446280--446407 Score: 60
Period size: 17 Copynumber: 7.6 Consensus size: 17
446270 TTAAAAATTT
446280 TTAATATAATATAAT-TA
1 TTAATATAATA-AATATA
*
446297 TATAATA-AGTTAAGATA-A
1 T-TAATATA-ATAA-ATATA
446315 TTAAATATAATAAATATA
1 TT-AATATAATAAATATA
*
446333 TTAATATATTAAA-ATTA
1 TTAATATAATAAATA-TA
*
446350 TTTA-AT-ATAAAT-TA
1 TTAATATAATAAATATA
*
446364 TTAATAT-ATTAATATA
1 TTAATATAATAAATATA
*
446380 -TATATATAA-ATAATATT
1 TTA-ATATAATA-AATATA
446397 TTAAATATAAT
1 TT-AATATAAT
446408 TATTATAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 32
0.67 0.07 0.25
Matches are distributed among these distances:
14 5 0.06
15 13 0.15
16 9 0.11
17 28 0.33
18 28 0.33
19 2 0.02
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
TTAATATAATAAATATA
Found at i:446340 original size:8 final size:8
Alignment explanation
Indices: 446327--446380 Score: 60
Period size: 8 Copynumber: 6.9 Consensus size: 8
446317 AAATATAATA
446327 AATATATT
1 AATATATT
446335 AATATATT
1 AATATATT
*
446343 AAAATTATTT
1 AATA-TA-TT
446353 AATATA--
1 AATATATT
446359 AAT-TATT
1 AATATATT
446366 AATATATT
1 AATATATT
446374 AATATAT
1 AATATAT
446381 ATATATAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
5 2 0.05
6 3 0.08
7 3 0.08
8 22 0.56
9 4 0.10
10 5 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATATATT
Found at i:446760 original size:15 final size:14
Alignment explanation
Indices: 446740--446773 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
446730 AATAAGCATG
*
446740 ATATAATATATTTAA
1 ATATAATATA-ATAA
446755 ATATAATATAATAA
1 ATATAATATAATAA
446769 ATATA
1 ATATA
446774 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATAATATAATAA
Found at i:446925 original size:17 final size:17
Alignment explanation
Indices: 446903--446935 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
446893 AACTTATGCT
446903 GAAATAAAATAAAAGCC
1 GAAATAAAATAAAAGCC
446920 GAAATAAAATAAAAGC
1 GAAATAAAATAAAAGC
446936 TCATGGTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.09, G:0.12, T:0.12
Consensus pattern (17 bp):
GAAATAAAATAAAAGCC
Found at i:447903 original size:77 final size:78
Alignment explanation
Indices: 447814--447971 Score: 221
Period size: 77 Copynumber: 2.0 Consensus size: 78
447804 TTTACAAATT
* * * *
447814 AAATTAATTAACAATAAA-AGTAAATCAATCAGCGGCTGTGACATTAA-TTTTTTAATTACTTGA
1 AAATTAATTAACAATAAAGA-TAAATCAATCAACAGATGTGACATTAATTTTTTTAATTACTTAA
*
447877 TCAACTTGATTCTC
65 TCAACTTAATTCTC
* * *
447891 AAATTAATTAACAATAAAGATAAATCGATTAACAGATGTGATATTAATTTTTTTAATTACTTAAT
1 AAATTAATTAACAATAAAGATAAATCAATCAACAGATGTGACATTAATTTTTTTAATTACTTAAT
447956 CAACTTAATTCTC
66 CAACTTAATTCTC
447969 AAA
1 AAA
447972 AGATCCTCCA
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
77 39 0.55
78 32 0.45
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.37
Consensus pattern (78 bp):
AAATTAATTAACAATAAAGATAAATCAATCAACAGATGTGACATTAATTTTTTTAATTACTTAAT
CAACTTAATTCTC
Found at i:452752 original size:77 final size:77
Alignment explanation
Indices: 452670--452822 Score: 191
Period size: 77 Copynumber: 2.0 Consensus size: 77
452660 TACAGATTAC
* * * * *
452670 AATCAATTAAAAATAAAAACAAATTAATCAGTAGCTGTGACATTAA-TTCTTTAATTACTTGGTT
1 AATCAATTAAAAATAAAAACAAATCAATCAGCAACTGTGACATTAATTTC-TTAATTACTTGATC
452734 AACTTAATTCTCT
65 AACTTAATTCTCT
*** * * *
452747 AATCAATTGGCAATAAAAGCAAATCAATCAGCAATTGTGATATTAATTTCTTAATTACTTGATCA
1 AATCAATTAAAAATAAAAACAAATCAATCAGCAACTGTGACATTAATTTCTTAATTACTTGATCA
452812 ACTTAATTCTC
66 ACTTAATTCTC
452823 AAAAGATCCT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
77 61 0.95
78 3 0.05
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (77 bp):
AATCAATTAAAAATAAAAACAAATCAATCAGCAACTGTGACATTAATTTCTTAATTACTTGATCA
ACTTAATTCTCT
Found at i:453778 original size:3 final size:3
Alignment explanation
Indices: 453772--453804 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
453762 AAAATAATAT
*
453772 TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
453805 CCATCGTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:454176 original size:22 final size:22
Alignment explanation
Indices: 454148--454209 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
454138 ATTAAAATAT
*
454148 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTAAA
454170 TATTTTTATAATTAAATTTAAA
1 TATTTTTATAATTAAATTTAAA
*
454192 TAATTTTATTAATTAAAT
1 TATTTTTA-TAATTAAAT
454210 AATGATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 22 0.61
23 14 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTAAA
Found at i:454471 original size:24 final size:25
Alignment explanation
Indices: 454444--454498 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
454434 ATTAAATCAA
454444 ATTAAGTTATAATTAAAATTT-TTT-
1 ATTAAGTTA-AATTAAAATTTATTTG
* *
454468 ATTAGATTTAAATTAAATTTTATTTG
1 ATTA-AGTTAAATTAAAATTTATTTG
454494 ATTAA
1 ATTAA
454499 AAAATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 14 0.54
25 8 0.31
26 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (25 bp):
ATTAAGTTAAATTAAAATTTATTTG
Found at i:454490 original size:21 final size:18
Alignment explanation
Indices: 454464--454507 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 18
454454 AATTAAAATT
454464 TTTTATTAGATTTAAATTAAA
1 TTTTATTAGA-TTAAA--AAA
*
454485 TTTTATTTGATTAAAAAA
1 TTTTATTAGATTAAAAAA
454503 TTTTA
1 TTTTA
454508 AATTATTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
20 5 0.23
21 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTTATTAGATTAAAAAA
Found at i:454546 original size:19 final size:21
Alignment explanation
Indices: 454522--454592 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 21
454512 ATTATGTAAA
454522 ATATTAAAATT-T-TATTTTT
1 ATATTAAAATTATATATTTTT
*
454541 ATATTAATATTTATATATTTTT
1 ATATTAA-AATTATATATTTTT
*
454563 ATAATTAAATTTATATAATTTTT
1 AT-ATTAAAATTATAT-ATTTTT
*
454586 TTATTAA
1 ATATTAA
454593 TTATAAAGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
19 7 0.16
20 3 0.07
21 1 0.02
22 22 0.49
23 12 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTAAAATTATATATTTTT
Found at i:454562 original size:22 final size:22
Alignment explanation
Indices: 454534--454593 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
454524 ATTAAAATTT
454534 TATTTTTATATTAATATTTATA
1 TATTTTTATATTAATATTTATA
454556 TATTTTTATAATTAA-ATTTATA
1 TATTTTTAT-ATTAATATTTATA
*
454578 TAATTTTTTTATTAAT
1 T-ATTTTTATATTAAT
454594 TATAAAGCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
22 22 0.65
23 12 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTTTTATATTAATATTTATA
Found at i:454872 original size:30 final size:34
Alignment explanation
Indices: 454809--454876 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
454799 GTAGCCTTCA
* *
454809 AAATACTTATTTTTTATTTTTCTAAATATTTTAT
1 AAATATTTATATTTTATTTTTCTAAATATTTTAT
*
454843 AAATATTTATATTTTATTTTT-TAAAT-TTATAT
1 AAATATTTATATTTTATTTTTCTAAATATTTTAT
454875 AA
1 AA
454877 TTTTTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 7 0.23
33 5 0.16
34 19 0.61
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (34 bp):
AAATATTTATATTTTATTTTTCTAAATATTTTAT
Found at i:454875 original size:22 final size:23
Alignment explanation
Indices: 454835--454889 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
454825 TTTTTCTAAA
*
454835 TATTTTATAAATATTTAT-ATTT
1 TATTTTTTAAATATTTATAATTT
454857 TATTTTTTAAAT-TTATATAATTT
1 TATTTTTTAAATATT-TATAATTT
*
454880 T-TTATTTAAA
1 TATTTTTTAAA
454890 AAATATTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 2 0.07
22 22 0.76
23 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTTTTTAAATATTTATAATTT
Found at i:455503 original size:18 final size:17
Alignment explanation
Indices: 455467--455525 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
455457 TATTTTATTA
*
455467 TTTATTAAAATTATTAAT
1 TTTA-TAAAATAATTAAT
455485 TTTATAAAATAATTAAAT
1 TTTATAAAATAATT-AAT
* * *
455503 TTAATAAAAAATATTATT
1 TTTATAAAATA-ATTAAT
455521 TTTAT
1 TTTAT
455526 TATTAAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 9 0.26
18 22 0.65
19 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTATAAAATAATTAAT
Found at i:455547 original size:20 final size:19
Alignment explanation
Indices: 455525--455573 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 19
455515 ATTATTTTTA
455525 TTATTAAATAAGAATTTAAAT
1 TTATTAAAT-A-AATTTAAAT
455546 TATATTAAATAAATTTAAAT
1 T-TATTAAATAAATTTAAAT
455566 TTATTAAA
1 TTATTAAA
455574 ATTTTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.26
20 10 0.37
21 2 0.07
22 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
TTATTAAATAAATTTAAAT
Found at i:455575 original size:20 final size:20
Alignment explanation
Indices: 455466--455575 Score: 65
Period size: 17 Copynumber: 5.6 Consensus size: 20
455456 TTATTTTATT
*
455466 ATTTATTAAAAT-TA-TTAA
1 ATTTATTAAAATAAATTTAA
*
455484 TTTTA-TAAAAT-AA-TTAA
1 ATTTATTAAAATAAATTTAA
* *
455501 ATTTAAT-AAA-AAATATTAT
1 ATTTATTAAAATAAAT-TTAA
*
455520 TTTTATTATTAAATAAGAATTTAA
1 ATTTATTA--AAAT-A-AATTTAA
455544 ATTATATT-AAATAAATTTAA
1 ATT-TATTAAAATAAATTTAA
455564 ATTTATTAAAAT
1 ATTTATTAAAAT
455576 TTTATTTTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 22
0.71 0.08 0.22
Matches are distributed among these distances:
17 20 0.28
18 5 0.07
19 12 0.17
20 14 0.19
21 1 0.01
22 7 0.10
24 6 0.08
25 7 0.10
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (20 bp):
ATTTATTAAAATAAATTTAA
Found at i:455575 original size:61 final size:60
Alignment explanation
Indices: 455441--455583 Score: 157
Period size: 61 Copynumber: 2.4 Consensus size: 60
455431 TTTTAATTTG
* * * *
455441 ATTTAATTTAAAATTTTA-TTTTATTATTTATTAAAATTATTAATTTTATAAAATAATTAA
1 ATTTAA-TTAAAATTTTATTTTTATTATTAAATAAAATTATAAATTATATAAAATAATTAA
* * *
455501 ATTTAATAAAAAATATTATTTTTATTATTAAATAAGAATT-TAAATTATATTAAATAAATTTAA
1 ATTTAAT-TAAAATTTTATTTTTATTATTAAATAA-AATTATAAATTATATAAAAT-AA-TTAA
455564 ATTT-ATTAAAATTTTATTTT
1 ATTTAATTAAAATTTTATTTT
455584 AAAGTAAATT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
59 1 0.01
60 14 0.20
61 38 0.55
62 8 0.12
63 8 0.12
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (60 bp):
ATTTAATTAAAATTTTATTTTTATTATTAAATAAAATTATAAATTATATAAAATAATTAA
Found at i:463145 original size:24 final size:24
Alignment explanation
Indices: 463113--463160 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
463103 ACGATTTATT
*
463113 TAGTTTTTATATTATATAAGAATC
1 TAGTTTTTATATTATATAAAAATC
463137 TAGTTTTTATATTATATAAAAATC
1 TAGTTTTTATATTATATAAAAATC
463161 GCTTTACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (24 bp):
TAGTTTTTATATTATATAAAAATC
Found at i:464577 original size:16 final size:18
Alignment explanation
Indices: 464556--464588 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
464546 CTTAGGAAAT
464556 ATTAAA-AAA-AAAAAAA
1 ATTAAAGAAACAAAAAAA
464572 ATTAAAGAAACAAAAAA
1 ATTAAAGAAACAAAAAA
464589 GGCATTCCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (18 bp):
ATTAAAGAAACAAAAAAA
Found at i:469767 original size:9 final size:9
Alignment explanation
Indices: 469753--469789 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
469743 TTATAAATAA
469753 AATTTATTT
1 AATTTATTT
469762 AATTTATTT
1 AATTTATTT
*
469771 AAATTA-TT
1 AATTTATTT
469779 -ATTTATTT
1 AATTTATTT
469787 AAT
1 AAT
469790 AAAATAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
7 4 0.17
8 4 0.17
9 16 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
AATTTATTT
Found at i:470803 original size:47 final size:45
Alignment explanation
Indices: 470726--470822 Score: 104
Period size: 47 Copynumber: 2.1 Consensus size: 45
470716 AGGAAAGATG
* ** * * *
470726 AAAGAAAGAACTTTGATTTTCTTTTTTGATCATTGCAGGAAGAAGA
1 AAAGAAAGAACTTTGATTTTCCTTCCTGATCACTGAAGGAA-AAAA
* *
470772 AAAGACAAGAGCTTTGGTTTTCCTTCCTGATCACTGAAGGAAAAAA
1 AAAGA-AAGAACTTTGATTTTCCTTCCTGATCACTGAAGGAAAAAA
470818 AAAGA
1 AAAGA
470823 GAGTAAGGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
46 13 0.31
47 29 0.69
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (45 bp):
AAAGAAAGAACTTTGATTTTCCTTCCTGATCACTGAAGGAAAAAA
Found at i:476030 original size:14 final size:14
Alignment explanation
Indices: 476011--476039 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
476001 TCCTGGTTAG
476011 ATAAGAAAGAAAGA
1 ATAAGAAAGAAAGA
476025 ATAAGAAAGAAAGA
1 ATAAGAAAGAAAGA
476039 A
1 A
476040 GATGGAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (14 bp):
ATAAGAAAGAAAGA
Found at i:479123 original size:21 final size:21
Alignment explanation
Indices: 479099--479147 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
479089 AATCAATAGC
479099 TCAATAAATAATAAGAT-AAAT
1 TCAATAAA-AATAAGATAAAAT
*
479120 TCAATATAAAATAATATAAAAT
1 TCAATA-AAAATAAGATAAAAT
479142 T-AATAA
1 TCAATAA
479148 TTTATAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.04
21 17 0.68
22 7 0.28
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (21 bp):
TCAATAAAAATAAGATAAAAT
Done.