Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 6 of 135
Found at i:2469985 original size:24 final size:24
Alignment explanation
Indices: 2469958--2470023 Score: 123
Period size: 24 Copynumber: 2.8 Consensus size: 24
2469948 AAGTAAACCA
2469958 TGAGACAAGTAAACTATGGAAGAG
1 TGAGACAAGTAAACTATGGAAGAG
*
2469982 TGAGACAAGTAAACTATGGAAGAT
1 TGAGACAAGTAAACTATGGAAGAG
2470006 TGAGACAAGTAAACTATG
1 TGAGACAAGTAAACTATG
2470024 TTACCTTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.45, C:0.09, G:0.26, T:0.20
Consensus pattern (24 bp):
TGAGACAAGTAAACTATGGAAGAG
Found at i:2470848 original size:16 final size:16
Alignment explanation
Indices: 2470827--2470860 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2470817 GATGGAAGAG
*
2470827 TGAGACAAGTAATCTA
1 TGAGACAAGTAAACTA
2470843 TGAGACAAGTAAACTA
1 TGAGACAAGTAAACTA
2470859 TG
1 TG
2470861 GAAGAGTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.24
Consensus pattern (16 bp):
TGAGACAAGTAAACTA
Found at i:2508061 original size:17 final size:17
Alignment explanation
Indices: 2508029--2508060 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2508019 TCATCCACCA
2508029 AATCTCTTATTTTTTTC
1 AATCTCTTATTTTTTTC
2508046 AATCT-TTATTTTTTT
1 AATCTCTTATTTTTTT
2508061 TAAAATCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (17 bp):
AATCTCTTATTTTTTTC
Found at i:2508444 original size:100 final size:100
Alignment explanation
Indices: 2508279--2508556 Score: 529
Period size: 100 Copynumber: 2.8 Consensus size: 100
2508269 GTATGAGAAA
* *
2508279 GAGAAACTAATACATAAGCTTAACCAAGTTCTATCAAGGGACAGCAAAATTTTGTGTTGGACTTT
1 GAGAAACTAACACATAATCTTAACCAAGTTCTATCAAGGGACAGCAAAATTTTGTGTTGGACTTT
2508344 CCCATACAATATTAGTTTCTCATACAATATCGTAT
66 CCCATACAATATTAGTTTCTCATACAATATCGTAT
2508379 GAGAAACTAACACATAATCTTAACCAAGTTCTATCAAGGGACAGCAAAATTTTGTGTTGGACTTT
1 GAGAAACTAACACATAATCTTAACCAAGTTCTATCAAGGGACAGCAAAATTTTGTGTTGGACTTT
2508444 CCCATACAATATTAGTTTCTCATACAATATCGTAT
66 CCCATACAATATTAGTTTCTCATACAATATCGTAT
2508479 GAGAAACTAACACATAATCTTAACCAAGTTCTATCAAGGGACAGCAAAATTTTGTGTTGGGACTT
1 GAGAAACTAACACATAATCTTAACCAAGTTCTATCAAGGGACAGCAAAATTTTGTGTT-GGACTT
2508544 TCCCATACAATAT
65 TCCCATACAATAT
2508557 CTGGAAATGC
Statistics
Matches: 175, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
100 156 0.89
101 19 0.11
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (100 bp):
GAGAAACTAACACATAATCTTAACCAAGTTCTATCAAGGGACAGCAAAATTTTGTGTTGGACTTT
CCCATACAATATTAGTTTCTCATACAATATCGTAT
Found at i:2517045 original size:2 final size:2
Alignment explanation
Indices: 2517038--2517076 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2517028 TACCAGAACT
2517038 AG AG AG AG AG 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 AG AG AG AG AG A
2517077 TTTCTAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2526598 original size:116 final size:116
Alignment explanation
Indices: 2526394--2526627 Score: 450
Period size: 116 Copynumber: 2.0 Consensus size: 116
2526384 AGAGTAAGAA
2526394 CAACTAATATCGAGCCTTTTTGTTCTCAGATGACATCAAGCCTTGGTATAGATGTTCCTCGAAGG
1 CAACTAATATCGAGCCTTTTTGTTCTCAGATGACATCAAGCCTTGGTATAGATGTTCCTCGAAGG
2526459 GTTTCATATGAGGGGTCTGTAGGCATGCTACCAATGACAAGCTCCCATCAT
66 GTTTCATATGAGGGGTCTGTAGGCATGCTACCAATGACAAGCTCCCATCAT
* *
2526510 CAACTAATATCGAGCCTTTTTGTTCTCAGATGACGTCAAGCCTTGGTATAGTTGTTCCTCGAAGG
1 CAACTAATATCGAGCCTTTTTGTTCTCAGATGACATCAAGCCTTGGTATAGATGTTCCTCGAAGG
2526575 GTTTCATATGAGGGGTCTGTAGGCATGCTACCAATGACAAGCTCCCATCAT
66 GTTTCATATGAGGGGTCTGTAGGCATGCTACCAATGACAAGCTCCCATCAT
2526626 CA
1 CA
2526628 GTTGGACTTG
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 116 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (116 bp):
CAACTAATATCGAGCCTTTTTGTTCTCAGATGACATCAAGCCTTGGTATAGATGTTCCTCGAAGG
GTTTCATATGAGGGGTCTGTAGGCATGCTACCAATGACAAGCTCCCATCAT
Found at i:2528225 original size:19 final size:19
Alignment explanation
Indices: 2528174--2528226 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 19
2528164 ACTTGTTTTG
2528174 AATTTGTAATCCATGGTT-
1 AATTTGTAATCCATGGTTA
* *
2528192 -AGTT-T-A-CCATAGTTA
1 AATTTGTAATCCATGGTTA
2528207 AATTTGTAATCCATGGTTA
1 AATTTGTAATCCATGGTTA
2528226 A
1 A
2528227 TTTTTTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 9
0.67 0.10 0.23
Matches are distributed among these distances:
14 7 0.27
15 1 0.04
16 4 0.15
17 4 0.15
18 1 0.04
19 9 0.35
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (19 bp):
AATTTGTAATCCATGGTTA
Found at i:2528824 original size:22 final size:22
Alignment explanation
Indices: 2528798--2528839 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2528788 ACTGAAATAT
2528798 TGAATTTATTCATTAAATCTCG
1 TGAATTTATTCATTAAATCTCG
*
2528820 TGAATTTATTTATTAAATCT
1 TGAATTTATTCATTAAATCT
2528840 GTTAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (22 bp):
TGAATTTATTCATTAAATCTCG
Found at i:2539868 original size:22 final size:22
Alignment explanation
Indices: 2539840--2539884 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2539830 AAAGTGAAGC
2539840 AGTTTGGTCTCAGTTATTACAA
1 AGTTTGGTCTCAGTTATTACAA
2539862 AGTTTGGTCTCAGTTATTACAA
1 AGTTTGGTCTCAGTTATTACAA
2539884 A
1 A
2539885 CTTCCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (22 bp):
AGTTTGGTCTCAGTTATTACAA
Found at i:2548154 original size:23 final size:22
Alignment explanation
Indices: 2548111--2548154 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2548101 TATATGTTGA
*
2548111 ATATGGTAAAAACATTTTAATT
1 ATATGGTAAAAACATTATAATT
* *
2548133 ATATGTTAAAAATTATTATAAT
1 ATATGGTAAAAA-CATTATAAT
2548155 ATTTAAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (22 bp):
ATATGGTAAAAACATTATAATT
Found at i:2556797 original size:2 final size:2
Alignment explanation
Indices: 2556792--2556822 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2556782 TAGTATCACT
2556792 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2556823 TACATGAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2561056 original size:50 final size:50
Alignment explanation
Indices: 2560948--2561130 Score: 235
Period size: 50 Copynumber: 3.6 Consensus size: 50
2560938 ACATGTCAAA
* ** * *
2560948 GCCATGTCCCAGACATGGTCTTACATGGAATGTTCTCA-CGTCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATC-TCGGTGCCAAC
**
2560999 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
* *
2561049 GCCATGTCTCAGACATGGTCTTGCATGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
*
2561099 GCCATG-CCCTAGGCATGGTCTTACATGGGACC
1 GCCATGTCCC-AGACATGGTCTTACATGGGACC
2561131 ATATGGAGCT
Statistics
Matches: 116, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
49 2 0.02
50 86 0.74
51 28 0.24
ACGTcount: A:0.19, C:0.32, G:0.25, T:0.25
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
Found at i:2569025 original size:20 final size:20
Alignment explanation
Indices: 2569000--2569039 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2568990 AATATTTTCC
*
2569000 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
2569020 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
2569040 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:2569628 original size:24 final size:25
Alignment explanation
Indices: 2569577--2569637 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
2569567 TTACTCTTAG
2569577 TTTTTAAATA-TAATTTTTAATATA
1 TTTTTAAATATTAATTTTTAATATA
* *
2569601 TTTTTAAGTATTACTTTTTAA-AT-
1 TTTTTAAATATTAATTTTTAATATA
*
2569624 TTTTTGAATTATTA
1 TTTTT-AAATATTA
2569638 TTAGTTTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 5 0.16
24 18 0.56
25 9 0.28
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (25 bp):
TTTTTAAATATTAATTTTTAATATA
Found at i:2571151 original size:23 final size:23
Alignment explanation
Indices: 2571104--2571152 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2571094 TATTTTTTAA
**
2571104 TTTTTTTAATTTTAAAATACTTT
1 TTTTTTTAATTTTAAAATAAATT
*
2571127 TTTTTTTATTTTTAAAATAAATT
1 TTTTTTTAATTTTAAAATAAATT
2571150 TTT
1 TTT
2571153 GGTGTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTTTTAATTTTAAAATAAATT
Found at i:2573793 original size:16 final size:16
Alignment explanation
Indices: 2573751--2573798 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
2573741 AACTATAATC
*
2573751 TATTAAATAAAA-ATGA
1 TATT-AATAAAATATTA
*
2573767 TATTAGTTAAAATATTA
1 TATTA-ATAAAATATTA
2573784 TATTAATAAAATATT
1 TATTAATAAAATATT
2573799 TAATTTTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 1 0.04
16 18 0.67
17 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
TATTAATAAAATATTA
Found at i:2580613 original size:11 final size:11
Alignment explanation
Indices: 2580597--2580622 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2580587 AAATTGAAAC
2580597 GAAACAGGGGA
1 GAAACAGGGGA
2580608 GAAACAGGGGA
1 GAAACAGGGGA
2580619 GAAA
1 GAAA
2580623 GAAAGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:2580825 original size:12 final size:13
Alignment explanation
Indices: 2580796--2580827 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2580786 TGTAGCTTAT
2580796 ATTGAATTAGTGG
1 ATTGAATTAGTGG
2580809 A-TGAATTAGT-G
1 ATTGAATTAGTGG
2580820 ATTGAATT
1 ATTGAATT
2580828 GATGGAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 15 0.83
13 1 0.06
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (13 bp):
ATTGAATTAGTGG
Found at i:2581333 original size:24 final size:22
Alignment explanation
Indices: 2581301--2581391 Score: 94
Period size: 22 Copynumber: 4.0 Consensus size: 22
2581291 TCTCTGATTA
*
2581301 TTAGCACGTTGGTGCTCTCTGATT
1 TTAGCACGTTAGTGCTCTCTG--T
* *
2581325 TTAGCACGTCAGTGTTCTCTGT
1 TTAGCACGTTAGTGCTCTCTGT
*
2581347 TTAGCACATCT-GTGCTCTCTGT
1 TTAGCACGT-TAGTGCTCTCTGT
* *
2581369 ATAGCACTTTAGTGCTCTCTGT
1 TTAGCACGTTAGTGCTCTCTGT
2581391 T
1 T
2581392 CATTAGTGCA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
21 1 0.02
22 37 0.66
24 18 0.32
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.42
Consensus pattern (22 bp):
TTAGCACGTTAGTGCTCTCTGT
Found at i:2582519 original size:32 final size:32
Alignment explanation
Indices: 2582478--2582542 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
2582468 ATCAGCATGG
2582478 GCCATGTATTTGACTGAATTCACAAATGAAAA
1 GCCATGTATTTGACTGAATTCACAAATGAAAA
2582510 GCCATGTATTTGACTGAATTCACAAATGAAAA
1 GCCATGTATTTGACTGAATTCACAAATGAAAA
2582542 G
1 G
2582543 ATTTTCGAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (32 bp):
GCCATGTATTTGACTGAATTCACAAATGAAAA
Found at i:2600076 original size:2 final size:2
Alignment explanation
Indices: 2600069--2600094 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2600059 GCATCCTTTA
2600069 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
2600095 TTATTCAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2600121 original size:37 final size:37
Alignment explanation
Indices: 2600080--2600159 Score: 142
Period size: 37 Copynumber: 2.2 Consensus size: 37
2600070 TATATATATA
*
2600080 TATATATATATATATTTATTCAAGTTTGTATATTTTT
1 TATATATATATATATATATTCAAGTTTGTATATTTTT
2600117 TATATATATATATATATATTCAAGTTTGTATATTTTT
1 TATATATATATATATATATTCAAGTTTGTATATTTTT
*
2600154 TTTATA
1 TATATA
2600160 ATTGTGATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.59
Consensus pattern (37 bp):
TATATATATATATATATATTCAAGTTTGTATATTTTT
Found at i:2600391 original size:26 final size:26
Alignment explanation
Indices: 2600356--2600405 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
2600346 AAACAAAATA
2600356 ATTATATATACATTTTCAATACTAAT
1 ATTATATATACATTTTCAATACTAAT
2600382 ATTATATATACATTTTCAATACTA
1 ATTATATATACATTTTCAATACTA
2600406 TTCTAAGAAA
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:0.12, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTATATATACATTTTCAATACTAAT
Found at i:2603967 original size:19 final size:19
Alignment explanation
Indices: 2603943--2603981 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2603933 GAGTTGGTCC
2603943 AAATTGGATTGCTGAAAAG
1 AAATTGGATTGCTGAAAAG
2603962 AAATTGGATTGCTGAAAAG
1 AAATTGGATTGCTGAAAAG
2603981 A
1 A
2603982 TTTCCTTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.26
Consensus pattern (19 bp):
AAATTGGATTGCTGAAAAG
Found at i:2619704 original size:26 final size:27
Alignment explanation
Indices: 2619621--2619705 Score: 79
Period size: 26 Copynumber: 3.3 Consensus size: 27
2619611 AGCGAGCCAT
*
2619621 ATCGGGAAGCTC-CGATGAGCCAT-TA
1 ATCGGGAAGCTCACGAAGAGCCATATA
* * * * *
2619646 ATCACGAAAGCTCACAAAGTGCC-TTTA
1 ATC-GGGAAGCTCACGAAGAGCCATATA
2619673 ATCGGGAAGCTCACGAAGAGCCATATA
1 ATCGGGAAGCTCACGAAGAGCCATATA
2619700 A-CGGGA
1 ATCGGGA
2619706 CACTCATAAG
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
25 3 0.07
26 28 0.61
27 15 0.33
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.18
Consensus pattern (27 bp):
ATCGGGAAGCTCACGAAGAGCCATATA
Found at i:2619796 original size:24 final size:25
Alignment explanation
Indices: 2619769--2619816 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2619759 GGATGCTCCG
*
2619769 AAGAGCTAT-TAACAGGAAGCTCGC
1 AAGAACTATATAACAGGAAGCTCGC
* *
2619793 AAGAACTGTATAACGGGAAGCTCG
1 AAGAACTATATAACAGGAAGCTCG
2619817 AGAGGGCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.17
Consensus pattern (25 bp):
AAGAACTATATAACAGGAAGCTCGC
Found at i:2624583 original size:14 final size:13
Alignment explanation
Indices: 2624559--2624589 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
2624549 ACTATTAGTG
2624559 ACAAAAAACAAAT
1 ACAAAAAACAAAT
2624572 ACAAATAAACAAAT
1 ACAAA-AAACAAAT
2624586 ACAA
1 ACAA
2624590 TTTTCTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.74, C:0.16, G:0.00, T:0.10
Consensus pattern (13 bp):
ACAAAAAACAAAT
Found at i:2624736 original size:30 final size:30
Alignment explanation
Indices: 2624700--2624759 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2624690 TAAAAAAAAA
*
2624700 AATCACACAATACTCAAATATGCATGTATT
1 AATCACACAATACTCAAATAAGCATGTATT
*
2624730 AATCACACAATACTCAAGTAAGCATGTATT
1 AATCACACAATACTCAAATAAGCATGTATT
2624760 GAGCATACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.28
Consensus pattern (30 bp):
AATCACACAATACTCAAATAAGCATGTATT
Found at i:2624770 original size:30 final size:30
Alignment explanation
Indices: 2624703--2624770 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
2624693 AAAAAAAAAT
* *
2624703 CACACAATACTCAAATATGCATGTATTAAT
1 CACACAATACTCAAATAAGCATGTATTAAG
* *
2624733 CACACAATACTCAAGTAAGCATGTATTGAG
1 CACACAATACTCAAATAAGCATGTATTAAG
*
2624763 CATACAAT
1 CACACAAT
2624771 TTTTTAAACA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (30 bp):
CACACAATACTCAAATAAGCATGTATTAAG
Found at i:2627794 original size:26 final size:26
Alignment explanation
Indices: 2627758--2627810 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2627748 TTTCATTCTT
2627758 CTAGTATCATGTGCAGACTGTTTTAA
1 CTAGTATCATGTGCAGACTGTTTTAA
2627784 CTAGTATCATGTGCAGACTGTTTTAA
1 CTAGTATCATGTGCAGACTGTTTTAA
2627810 C
1 C
2627811 ATAATTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (26 bp):
CTAGTATCATGTGCAGACTGTTTTAA
Found at i:2637508 original size:32 final size:31
Alignment explanation
Indices: 2637470--2637535 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
2637460 ATGTATAAGA
*
2637470 AAACAAAATAAAAGAAAAAGAAATAGAAAAAG
1 AAACAAAATAAAAGAAAAAGAAAGA-AAAAAG
* * * *
2637502 AAACAAAGTGAACGAAACAGAAAGAAAAAAG
1 AAACAAAATAAAAGAAAAAGAAAGAAAAAAG
2637533 AAA
1 AAA
2637536 GAAAGAAGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.74, C:0.06, G:0.15, T:0.05
Consensus pattern (31 bp):
AAACAAAATAAAAGAAAAAGAAAGAAAAAAG
Found at i:2638227 original size:24 final size:24
Alignment explanation
Indices: 2638200--2638246 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2638190 ATTGAAATGG
2638200 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
2638224 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
2638247 GATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:2644387 original size:7 final size:8
Alignment explanation
Indices: 2644370--2644394 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2644360 ATAATATTTC
2644370 AAAAATAA
1 AAAAATAA
2644378 AAAAATAA
1 AAAAATAA
2644386 AAAAATAA
1 AAAAATAA
2644394 A
1 A
2644395 TAAACTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:2645275 original size:27 final size:27
Alignment explanation
Indices: 2645245--2645340 Score: 192
Period size: 27 Copynumber: 3.6 Consensus size: 27
2645235 AACAAAATGC
2645245 AATCCCTTCTGCATTTTCAAATATATA
1 AATCCCTTCTGCATTTTCAAATATATA
2645272 AATCCCTTCTGCATTTTCAAATATATA
1 AATCCCTTCTGCATTTTCAAATATATA
2645299 AATCCCTTCTGCATTTTCAAATATATA
1 AATCCCTTCTGCATTTTCAAATATATA
2645326 AATCCCTTCTGCATT
1 AATCCCTTCTGCATT
2645341 GCTCACTGTA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (27 bp):
AATCCCTTCTGCATTTTCAAATATATA
Found at i:2645846 original size:18 final size:18
Alignment explanation
Indices: 2645805--2645846 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2645795 GTTTAACAAT
*
2645805 TTTTTTATCTAAATAGTG
1 TTTTTTACCTAAATAGTG
*
2645823 CTTTTTACCTCAAA-AGTG
1 TTTTTTACCT-AAATAGTG
2645841 TTTTTT
1 TTTTTT
2645847 TTATCAACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.55
Consensus pattern (18 bp):
TTTTTTACCTAAATAGTG
Found at i:2650190 original size:17 final size:18
Alignment explanation
Indices: 2650168--2650201 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2650158 TTTTTTGTCG
2650168 GGGAAA-GACTGGAAAAA
1 GGGAAATGACTGGAAAAA
2650185 GGGAAATGACTGGAAAA
1 GGGAAATGACTGGAAAA
2650202 GTGCCTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.50, C:0.06, G:0.35, T:0.09
Consensus pattern (18 bp):
GGGAAATGACTGGAAAAA
Found at i:2656825 original size:24 final size:24
Alignment explanation
Indices: 2656798--2656874 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
2656788 TGCAAGAACG
2656798 TCCCGTTATTAGCTCTCTTGAGCA
1 TCCCGTTATTAGCTCTCTTGAGCA
* * ** *
2656822 TCCCGATATTGGCTCTCCGGAGCT
1 TCCCGTTATTAGCTCTCTTGAGCA
2656846 TCCCGTTATTTAGCTCT-TATGAGCA
1 TCCCGTTA-TTAGCTCTCT-TGAGCA
2656871 TCCC
1 TCCC
2656875 AACATATGGC
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
24 26 0.63
25 15 0.37
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.35
Consensus pattern (24 bp):
TCCCGTTATTAGCTCTCTTGAGCA
Found at i:2656910 original size:25 final size:27
Alignment explanation
Indices: 2656884--2656956 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 27
2656874 CAACATATGG
* *
2656884 CTCTTACGAGCTTCTCAATTAAAGGCT
1 CTCTCACGAGCTTCCCAATTAAAGGCT
* *
2656911 CTCTCATGAGCTTCCCAATTAATGGCT
1 CTCTCACGAGCTTCCCAATTAAAGGCT
* *
2656938 CTC-C-GGAGCTTCCCGATTA
1 CTCTCACGAGCTTCCCAATTA
2656957 CGACTCTCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.32
26 1 0.03
27 26 0.65
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (27 bp):
CTCTCACGAGCTTCCCAATTAAAGGCT
Found at i:2656970 original size:24 final size:25
Alignment explanation
Indices: 2656911--2656974 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
2656901 ATTAAAGGCT
* *
2656911 CTCTCATGAGCTTCCCAATTAATGG
1 CTCTCATGAGCTTCCCAATTAACGA
** *
2656936 CTCTCCGGAGCTTCCCGATT-ACGA
1 CTCTCATGAGCTTCCCAATTAACGA
2656960 CTCTCATGAGCTTCC
1 CTCTCATGAGCTTCC
2656975 TGTTACATGG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 15 0.47
25 17 0.53
ACGTcount: A:0.19, C:0.34, G:0.17, T:0.30
Consensus pattern (25 bp):
CTCTCATGAGCTTCCCAATTAACGA
Found at i:2685920 original size:21 final size:21
Alignment explanation
Indices: 2685878--2685920 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2685868 AGACTGTTAT
*
2685878 ACACCTATATCAACATTCGAG
1 ACACCTATAACAACATTCGAG
* * *
2685899 ACACTTATAACAATATTTGAG
1 ACACCTATAACAACATTCGAG
2685920 A
1 A
2685921 TTTAAATCAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (21 bp):
ACACCTATAACAACATTCGAG
Found at i:2696194 original size:27 final size:26
Alignment explanation
Indices: 2696161--2696213 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
2696151 TAATCTTTTT
* *
2696161 TTTATTTACTAAAATATTATAAAAAAA
1 TTTATTTACCAAAATA-TACAAAAAAA
2696188 TTTATTTACCAAAATATACAAAAAAA
1 TTTATTTACCAAAATATACAAAAAAA
2696214 ACAGAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.36
Consensus pattern (26 bp):
TTTATTTACCAAAATATACAAAAAAA
Found at i:2696746 original size:19 final size:19
Alignment explanation
Indices: 2696689--2696748 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
2696679 TATAATTATA
*
2696689 AATAACTCTATTTTAATTT
1 AATAACTATATTTTAATTT
* *
2696708 AATAA--ACTATTCTCATTT
1 AATAACTA-TATTTTAATTT
*
2696726 AATAACTATATTTTAAATT
1 AATAACTATATTTTAATTT
2696745 AATA
1 AATA
2696749 GAAATACCAG
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
18 14 0.44
19 17 0.53
20 1 0.03
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (19 bp):
AATAACTATATTTTAATTT
Found at i:2697312 original size:26 final size:27
Alignment explanation
Indices: 2697255--2697322 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
2697245 GTTTTTTTGG
*
2697255 TATATTTTGATAAATAAAAAAAATTAT
1 TATATTTTGATAAATAAAAAAAATGAT
*
2697282 AATATTTT-AGTAAATAAAAAAAA-GAT
1 TATATTTTGA-TAAATAAAAAAAATGAT
2697308 TATATTTTGATAAAT
1 TATATTTTGATAAAT
2697323 TTTTATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 15 0.42
27 21 0.58
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (27 bp):
TATATTTTGATAAATAAAAAAAATGAT
Found at i:2697333 original size:18 final size:19
Alignment explanation
Indices: 2697307--2697345 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2697297 AAAAAAAAGA
2697307 TTATATTTTGATAA-ATTT
1 TTATATTTTGATAATATTT
* *
2697325 TTATTTTTTTATAATATTT
1 TTATATTTTGATAATATTT
2697344 TT
1 TT
2697346 GTAAAAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
TTATATTTTGATAATATTT
Found at i:2701649 original size:15 final size:15
Alignment explanation
Indices: 2701629--2701663 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2701619 GGTTAAAAAC
*
2701629 ATAATTTTATCATTT
1 ATAATTTCATCATTT
2701644 ATAATTTCATCATTT
1 ATAATTTCATCATTT
*
2701659 TTAAT
1 ATAAT
2701664 ACGTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (15 bp):
ATAATTTCATCATTT
Found at i:2702323 original size:84 final size:85
Alignment explanation
Indices: 2702182--2702350 Score: 331
Period size: 84 Copynumber: 2.0 Consensus size: 85
2702172 TATTTTTTAT
2702182 ATTTAGTGTTGTTTGAACAGTTAACTGTGTATCCATATATATATATATATACGTGTGTGTTTTTA
1 ATTTAGTGTTGTTTGAACAGTTAACTGTGTATCCATATATATATATATATACGTGTGTGTTTTTA
2702247 TGCCGTATA-TGTGAAAAGC
66 TGCCGTATATTGTGAAAAGC
2702266 ATTTAGTGTTGTTTGAACAGTTAACTGTGTATCCATATATATATATATATACGTGTGTGTTTTTA
1 ATTTAGTGTTGTTTGAACAGTTAACTGTGTATCCATATATATATATATATACGTGTGTGTTTTTA
2702331 TGCCGTATATTGTGAAAAGC
66 TGCCGTATATTGTGAAAAGC
2702351 CTCTGTAATA
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 74 0.88
85 10 0.12
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.43
Consensus pattern (85 bp):
ATTTAGTGTTGTTTGAACAGTTAACTGTGTATCCATATATATATATATATACGTGTGTGTTTTTA
TGCCGTATATTGTGAAAAGC
Found at i:2711162 original size:31 final size:31
Alignment explanation
Indices: 2711122--2711181 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2711112 ATTTAACCGC
*
2711122 TTAGTGACTTAAATAAAAACTTTTGAATAGT
1 TTAGGGACTTAAATAAAAACTTTTGAATAGT
* **
2711153 TTAGGGACTTGAATAAAATTTTTTGAATA
1 TTAGGGACTTAAATAAAAACTTTTGAATA
2711182 ATTCAATCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (31 bp):
TTAGGGACTTAAATAAAAACTTTTGAATAGT
Found at i:2717426 original size:13 final size:14
Alignment explanation
Indices: 2717403--2717431 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2717393 AGAGGCAGAT
2717403 AATCGGAAGGAGAG
1 AATCGGAAGGAGAG
2717417 AATC-GAAGGAGAG
1 AATCGGAAGGAGAG
2717430 AA
1 AA
2717432 GGTCTTCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.07, G:0.38, T:0.07
Consensus pattern (14 bp):
AATCGGAAGGAGAG
Found at i:2730536 original size:28 final size:28
Alignment explanation
Indices: 2730504--2730559 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2730494 GTTAAGCTTT
**
2730504 CAACATAGGATGTCGAATGACACGTGGA
1 CAACATAGGATGTCGAACAACACGTGGA
*
2730532 CAACATAGGATGTTGAACAACACGTGGA
1 CAACATAGGATGTCGAACAACACGTGGA
2730560 TAAATTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.18
Consensus pattern (28 bp):
CAACATAGGATGTCGAACAACACGTGGA
Found at i:2732537 original size:21 final size:20
Alignment explanation
Indices: 2732496--2732533 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2732486 TAATTATATG
2732496 ATACTTTAAAAAATAAAACT
1 ATACTTTAAAAAATAAAACT
2732516 ATACTTTAAAAAATAAAA
1 ATACTTTAAAAAATAAAA
2732534 ACTAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (20 bp):
ATACTTTAAAAAATAAAACT
Found at i:2736748 original size:11 final size:11
Alignment explanation
Indices: 2736732--2736761 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
2736722 GTTTAACCAG
2736732 TTCAAAACACA
1 TTCAAAACACA
2736743 TTC-AAACACA
1 TTCAAAACACA
2736753 TTCAAAACA
1 TTCAAAACA
2736762 TATTAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (11 bp):
TTCAAAACACA
Found at i:2737006 original size:11 final size:11
Alignment explanation
Indices: 2736990--2737014 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2736980 ATTTTTTAAC
2736990 TTTAAAATACT
1 TTTAAAATACT
2737001 TTTAAAATACT
1 TTTAAAATACT
2737012 TTT
1 TTT
2737015 TTTTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAAAATACT
Found at i:2737018 original size:40 final size:40
Alignment explanation
Indices: 2736974--2737112 Score: 189
Period size: 40 Copynumber: 3.5 Consensus size: 40
2736964 AATATTTTTA
* **
2736974 TTTTTT-ATTTTTTAACTTTAAAATACTTTTAAAATACTT
1 TTTTTTAATTTTTTAATTTTAAAATTTTTTTAAAATACTT
*
2737013 TTTTTTAATTTTTTTAATTTTAAATTTTTTTTAAAATAC-T
1 TTTTTTAA-TTTTTTAATTTTAAAATTTTTTTAAAATACTT
2737053 TTTTTTAATTTTTTAAATTTTAAAATTTTTTTAAAATAC-T
1 TTTTTTAATTTTTT-AATTTTAAAATTTTTTTAAAATACTT
2737093 TTTTTTAA-TTTTT-ATTTTAA
1 TTTTTTAATTTTTTAATTTTAA
2737113 TTTTTAAAAT
Statistics
Matches: 92, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
37 7 0.08
39 17 0.18
40 42 0.46
41 26 0.28
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (40 bp):
TTTTTTAATTTTTTAATTTTAAAATTTTTTTAAAATACTT
Found at i:2739550 original size:16 final size:16
Alignment explanation
Indices: 2739529--2739560 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2739519 TAATTTGGTT
2739529 TTACTTTTGTCTTTTA
1 TTACTTTTGTCTTTTA
*
2739545 TTACTTTTTTCTTTTA
1 TTACTTTTGTCTTTTA
2739561 CTTATTTGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.72
Consensus pattern (16 bp):
TTACTTTTGTCTTTTA
Found at i:2739604 original size:12 final size:12
Alignment explanation
Indices: 2739589--2739647 Score: 57
Period size: 12 Copynumber: 4.7 Consensus size: 12
2739579 TAAGATAACC
2739589 TATTATAATATA
1 TATTATAATATA
* *
2739601 TATTTTAACTTTAA
1 TATTATAA-TAT-A
2739615 TATTATAATATA
1 TATTATAATATA
2739627 TA-TATATATATA
1 TATTATA-ATATA
2739639 TATATATAA
1 TAT-TATAA
2739648 CAAATTTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
11 4 0.11
12 17 0.45
13 5 0.13
14 12 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
TATTATAATATA
Found at i:2739629 original size:2 final size:2
Alignment explanation
Indices: 2739614--2739646 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2739604 TTTAACTTTA
2739614 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2739647 ACAAATTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2760396 original size:19 final size:20
Alignment explanation
Indices: 2760360--2760397 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2760350 TCTTTTATAG
*
2760360 TTTTATAGTTTTTTTCTTTC
1 TTTTATAGTTTATTTCTTTC
2760380 TTTTATAG-TTATTTCTTT
1 TTTTATAGTTTATTTCTTT
2760398 TTTAAAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.13, C:0.08, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTTATAGTTTATTTCTTTC
Found at i:2760495 original size:30 final size:29
Alignment explanation
Indices: 2760442--2760515 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
2760432 TATAATTTAA
* *
2760442 TATGTAATTGTATATATAAATTTTAATTT
1 TATGTAATTTTATACATAAATTTTAATTT
*
2760471 TATGTAATTTTATACATAAAATTTTGATTT
1 TATGTAATTTTATACAT-AAATTTTAATTT
* *
2760501 AATCTAATTCTTATA
1 TATGTAATT-TTATA
2760516 AATTATTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 15 0.39
30 18 0.47
31 5 0.13
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (29 bp):
TATGTAATTTTATACATAAATTTTAATTT
Found at i:2769933 original size:3 final size:3
Alignment explanation
Indices: 2769927--2770022 Score: 81
Period size: 3 Copynumber: 32.0 Consensus size: 3
2769917 TTTAGCACTT
* * *
2769927 TTA TTA TTA TTA TTA TT- TT- TTC TTCA TTA TT- TTA ATG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
* * * *
2769970 TCTT TTA TTA TTA TGA TTA TTA ATA TTA TTA TTA TTAA TTA TTA TCA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
2770017 TTA TTA
1 TTA TTA
2770023 GTTTTATTTG
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
2 6 0.08
3 62 0.83
4 7 0.09
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2769968 original size:31 final size:31
Alignment explanation
Indices: 2769931--2770022 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
2769921 GCACTTTTAT
* * *
2769931 TATTATTATTATTTTTTCTTCATTATT-TTAA
1 TATTATTATTATTTATTATT-ATGATTATTAA
*
2769962 TGTTATTATCT-TTTATTATTATGATTATTAA
1 TATTATTAT-TATTTATTATTATGATTATTAA
* *
2769993 TATTATTATTATTAATTATTATCATTATTA
1 TATTATTATTATTTATTATTATGATTATTA
2770023 GTTTTATTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
30 6 0.12
31 44 0.86
32 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (31 bp):
TATTATTATTATTTATTATTATGATTATTAA
Found at i:2770817 original size:108 final size:108
Alignment explanation
Indices: 2770627--2770935 Score: 550
Period size: 108 Copynumber: 2.9 Consensus size: 108
2770617 TCTAAAAAAT
* * * *
2770627 AATAAGGTAATATTTAGCGTTTGGAAATTCGAGGAAACGTGCCCTAATGTGCTGGGTTTCGATTT
1 AATAAGGCAATGTTTCGCGTTTGGTAATTCGAGG-AACGTGCCCTAATGTGCTGGGTTTCGATTT
2770692 TTCTCGTTCAACCAAATAGCCAAATATCCTTTCAAAAATTTCAA
65 TTCTCGTTCAACCAAATAGCCAAATATCCTTTCAAAAATTTCAA
2770736 AATAAGGCAATGTTTCGCGTTTGGTAATTCGAGGAACGTGCCCTAATGTGCTGGGTTTCGATTTT
1 AATAAGGCAATGTTTCGCGTTTGGTAATTCGAGGAACGTGCCCTAATGTGCTGGGTTTCGATTTT
2770801 TCTCGTTCAACCAAATAGCCAAATATCCTTTCAAAAATTTCAA
66 TCTCGTTCAACCAAATAGCCAAATATCCTTTCAAAAATTTCAA
2770844 AATAAGGCAATGTTTCGCGTTTGGTAATTCGAGGAACGTGCCCTAATGTGCTGGGTTTCGA--TT
1 AATAAGGCAATGTTTCGCGTTTGGTAATTCGAGGAACGTGCCCTAATGTGCTGGGTTTCGATTTT
*
2770907 TCTCGTTTAACCAAATAGCCAAATATCCT
66 TCTCGTTCAACCAAATAGCCAAATATCCT
2770936 ATTGAATTTT
Statistics
Matches: 195, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
106 30 0.15
108 135 0.69
109 30 0.15
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (108 bp):
AATAAGGCAATGTTTCGCGTTTGGTAATTCGAGGAACGTGCCCTAATGTGCTGGGTTTCGATTTT
TCTCGTTCAACCAAATAGCCAAATATCCTTTCAAAAATTTCAA
Found at i:2771348 original size:46 final size:46
Alignment explanation
Indices: 2771277--2771406 Score: 208
Period size: 46 Copynumber: 2.8 Consensus size: 46
2771267 TGGTGTCAAC
* * *
2771277 ACTCAGTATGGTTTTCGTTATTGAAATATCATACCTACTTCTT-ACA
1 ACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTT-TTCACA
2771323 ACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCACA
1 ACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCACA
*
2771369 ACTCAGTATGATTTTCTTTACTGAAATACCATACCTAC
1 ACTCAGTATGGTTTTCTTTACTGAAATACCATACCTAC
2771407 GTTCCACACT
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 2 0.03
46 77 0.97
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.39
Consensus pattern (46 bp):
ACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCACA
Found at i:2773076 original size:31 final size:29
Alignment explanation
Indices: 2773038--2773105 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
2773028 AATCTGAAAA
* *
2773038 TTATACATAAACTTTAGTCTAATATGTAATT
1 TTATACATAAACTTTAAT-T-ATATATAATT
* *
2773069 TTATACATGAACTTTAATTTTATATAATT
1 TTATACATAAACTTTAATTATATATAATT
2773098 TTATACAT
1 TTATACAT
2773106 GAAAATTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 1 0.03
31 16 0.48
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATACATAAACTTTAATTATATATAATT
Found at i:2774385 original size:20 final size:20
Alignment explanation
Indices: 2774344--2774385 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2774334 TCTTAAGCTT
* *
2774344 TTAAATATGTTTTTAAACTA
1 TTAAATATGATTTTAAAATA
2774364 TTAAATAT-ATTTTAACAATA
1 TTAAATATGATTTTAA-AATA
2774384 TT
1 TT
2774386 TTTATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (20 bp):
TTAAATATGATTTTAAAATA
Found at i:2801258 original size:122 final size:123
Alignment explanation
Indices: 2801034--2801273 Score: 383
Period size: 122 Copynumber: 2.0 Consensus size: 123
2801024 AGTTGAATCT
* *
2801034 TAGTTTTGATCTGCTCAGCTTTTGCTCGTAGTCTAGTAAAACTGTAGCATTTGTTTTTTTATTAA
1 TAGTATTGATCTACTCAGCTTTTGCTCGTAGTCTAGTAAAACTGTAGCATTTGTTTTTTTATTAA
*
2801099 ATGCACATTGATCGACTTATGATGAGTTTACAATCATGCGGATGAATATGATCATCAA
66 ATGCACATTGATCGACTTATGATGAGTTTACAATCATGCAGATGAATATGATCATCAA
* * * *
2801157 TAGTATTGATCTACTCGGCTTTTGCTCTTAGTCTAGTTAAACTTTAGCATTTG-TTTTTTATTAA
1 TAGTATTGATCTACTCAGCTTTTGCTCGTAGTCTAGTAAAACTGTAGCATTTGTTTTTTTATTAA
* * *
2801221 ATGCACATTGATTGACTTATGATGGGTTTATAATCATGCAGATGAATATGATC
66 ATGCACATTGATCGACTTATGATGAGTTTACAATCATGCAGATGAATATGATC
2801274 GTGCTATTGA
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
122 60 0.56
123 47 0.44
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (123 bp):
TAGTATTGATCTACTCAGCTTTTGCTCGTAGTCTAGTAAAACTGTAGCATTTGTTTTTTTATTAA
ATGCACATTGATCGACTTATGATGAGTTTACAATCATGCAGATGAATATGATCATCAA
Found at i:2807169 original size:19 final size:20
Alignment explanation
Indices: 2807131--2807170 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2807121 AATTTGTAAG
* *
2807131 TTAATACATTTTAATTATAT
1 TTAATACATTTAAATAATAT
2807151 TTAATA-ATTTAAATAATAT
1 TTAATACATTTAAATAATAT
2807170 T
1 T
2807171 ATTTTACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAATACATTTAAATAATAT
Found at i:2808459 original size:77 final size:78
Alignment explanation
Indices: 2808368--2808533 Score: 307
Period size: 77 Copynumber: 2.1 Consensus size: 78
2808358 TGGTGTAATT
2808368 ATATATATAGAATTTGAATTGTGATTTATATGTATACATAAAATTTTAATTTTGATTCAATTGTA
1 ATATATATAGAATTTGAATTGTGATTTATATGTATACATAAAATTTTAATTTTGATTCAATTGTA
2808433 CA-ATTTAAAAAA
66 CATATTTAAAAAA
2808445 ATATATATAGAATTTGAATTGTGATTTATATGTATACATAAAATTTTAATTTTGATTCAATTGTA
1 ATATATATAGAATTTGAATTGTGATTTATATGTATACATAAAATTTTAATTTTGATTCAATTGTA
2808510 CATATTTAAAAAA
66 CATATTTAAAAAA
2808523 ATTAATATATA
1 A-T-ATATATA
2808534 TTTATTTTTA
Statistics
Matches: 86, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
77 67 0.78
78 11 0.13
79 1 0.01
80 7 0.08
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (78 bp):
ATATATATAGAATTTGAATTGTGATTTATATGTATACATAAAATTTTAATTTTGATTCAATTGTA
CATATTTAAAAAA
Found at i:2811219 original size:5 final size:5
Alignment explanation
Indices: 2811209--2811235 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2811199 GACCACAACT
2811209 GATGG GATGG GATGG GATGG GATGG GA
1 GATGG GATGG GATGG GATGG GATGG GA
2811236 CGGGCCTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.59, T:0.19
Consensus pattern (5 bp):
GATGG
Found at i:2816594 original size:3 final size:3
Alignment explanation
Indices: 2816586--2816630 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
2816576 CCTCGTGATG
* * *
2816586 TTC TTC TTC TTC TTC TTC TTC TTC TTC CTC CTC CTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2816631 AATAGCGAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (3 bp):
TTC
Found at i:2825804 original size:19 final size:19
Alignment explanation
Indices: 2825780--2825816 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2825770 CATGTCAATA
2825780 TTAATATTATATTAAAATG
1 TTAATATTATATTAAAATG
2825799 TTAATATTATATTAAAAT
1 TTAATATTATATTAAAAT
2825817 AATTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TTAATATTATATTAAAATG
Found at i:2827015 original size:17 final size:18
Alignment explanation
Indices: 2826988--2827023 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2826978 AATTATAAAC
2826988 AAAAGATATAAAAATTTT
1 AAAAGATATAAAAATTTT
*
2827006 AAAA-ATATAAACATTTT
1 AAAAGATATAAAAATTTT
2827023 A
1 A
2827024 TTAAAATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAAGATATAAAAATTTT
Found at i:2827173 original size:20 final size:19
Alignment explanation
Indices: 2827132--2827178 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2827122 AAAACAAACT
*
2827132 TAAAATTTTAAAGTTTTCA
1 TAAAATTTTAAAGTTTTAA
* *
2827151 TAAAATTTTATGATTTTTAA
1 TAAAATTTTA-AAGTTTTAA
2827171 TAAAATTT
1 TAAAATTT
2827179 AAACTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (19 bp):
TAAAATTTTAAAGTTTTAA
Found at i:2828872 original size:20 final size:20
Alignment explanation
Indices: 2828847--2828886 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2828837 CATTTCATTT
2828847 ATGCAATTGCTTTATCCATA
1 ATGCAATTGCTTTATCCATA
*
2828867 ATGCAATTGTTTTATCCATA
1 ATGCAATTGCTTTATCCATA
2828887 CCATATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (20 bp):
ATGCAATTGCTTTATCCATA
Found at i:2830116 original size:6 final size:6
Alignment explanation
Indices: 2830048--2830131 Score: 55
Period size: 6 Copynumber: 14.0 Consensus size: 6
2830038 TTCTCCTTCC
* * * * *
2830048 TTCTTT CTT-TTT TTCTTT TTTTTCT TTCCTT CTCTAT TTC-GT TTCTTT
1 TTCTTT -TTCTTT TTCTTT TTCTT-T TTCTTT TTCTTT TTCTTT TTCTTT
* ** *
2830096 CTCTCC TTCTTT TTCTAT TTCTTT TTCTTT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
2830132 ATCATTATAA
Statistics
Matches: 57, Mismatches: 17, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
5 6 0.11
6 45 0.79
7 6 0.11
ACGTcount: A:0.02, C:0.23, G:0.01, T:0.74
Consensus pattern (6 bp):
TTCTTT
Found at i:2830185 original size:35 final size:36
Alignment explanation
Indices: 2830139--2830229 Score: 98
Period size: 35 Copynumber: 2.6 Consensus size: 36
2830129 TTTATCATTA
* *
2830139 TAATATAATAATATATATACT-TA-ACTTTTAAGTTT
1 TAATATTATAATATATATACTATATA-TTTTAAATTT
*
2830174 TAATATTATAATAT-TATAATATATATTTTAAATTT
1 TAATATTATAATATATATACTATATATTTTAAATTT
* *
2830209 AAATATTTTTAATATATATAC
1 TAATA-TTATAATATATATAC
2830230 ACTTATTCCG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
34 5 0.11
35 28 0.61
36 9 0.20
37 4 0.09
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (36 bp):
TAATATTATAATATATATACTATATATTTTAAATTT
Found at i:2831399 original size:53 final size:53
Alignment explanation
Indices: 2831319--2831426 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
2831309 TCCCTGTTCT
*
2831319 GTCTTTGCTATCATTTTTGTTACAGTCGCAACTTTGACTCGTTTTCGTTTTCC
1 GTCTTTGCTATCATTTTTGTTACAGTCGCAACTTTGACTCGCTTTCGTTTTCC
2831372 GTCTTTGCTATCATTTTTGTTACAGTCGCAACTTTGACTCGCTTTCGTTTTCC
1 GTCTTTGCTATCATTTTTGTTACAGTCGCAACTTTGACTCGCTTTCGTTTTCC
2831425 GT
1 GT
2831427 TGTTGTACTA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (53 bp):
GTCTTTGCTATCATTTTTGTTACAGTCGCAACTTTGACTCGCTTTCGTTTTCC
Found at i:2831407 original size:29 final size:29
Alignment explanation
Indices: 2831321--2831407 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 29
2831311 CCTGTTCTGT
2831321 CTTTGCTATCATTTTTGTTACAGTCGCAA
1 CTTTGCTATCATTTTTGTTACAGTCGCAA
* * * **
2831350 CTTTG--ACTCGTTTTCGTT---TTC-CGT
1 CTTTGCTA-TCATTTTTGTTACAGTCGCAA
2831374 CTTTGCTATCATTTTTGTTACAGTCGCAA
1 CTTTGCTATCATTTTTGTTACAGTCGCAA
2831403 CTTTG
1 CTTTG
2831408 ACTCGCTTTC
Statistics
Matches: 41, Mismatches: 10, Indels: 14
0.63 0.15 0.22
Matches are distributed among these distances:
24 6 0.15
25 11 0.27
26 1 0.02
27 1 0.02
28 11 0.27
29 11 0.27
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (29 bp):
CTTTGCTATCATTTTTGTTACAGTCGCAA
Found at i:2841804 original size:42 final size:42
Alignment explanation
Indices: 2841748--2841841 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
2841738 CGCTTCTGGA
* * *
2841748 TTTCAGTTCAGCTCTTTTGAGCTTCAGTTTAACCCTAATGGG
1 TTTCAGTTTAGCTCTTTTGAGCTTCAGATGAACCCTAATGGG
* * *
2841790 TTTCCGTTTAGCTCTTTTGAGCTTTAGATGAACCCTTATGGG
1 TTTCAGTTTAGCTCTTTTGAGCTTCAGATGAACCCTAATGGG
*
2841832 TTTCTGTTTA
1 TTTCAGTTTA
2841842 CGATGTACTC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (42 bp):
TTTCAGTTTAGCTCTTTTGAGCTTCAGATGAACCCTAATGGG
Found at i:2848222 original size:60 final size:60
Alignment explanation
Indices: 2848125--2848405 Score: 485
Period size: 60 Copynumber: 4.7 Consensus size: 60
2848115 TACTCCTCCA
* * * *
2848125 CCTTTGC-CTCCAACGTTCACATGGGTGCCACCTCCTGGCTTTCCAGTGTTCACCCCAACT
1 CCTTTGCGC-CCAACGTTCACATGAGTGCCACCCCCTGGCTTTCCTGTGTTCACTCCAACT
*
2848185 CCTTTGC-CTCCAACATTCACATGAGTGCCACCCCCTGGCTTTCCTGTGTTCACTCCAACT
1 CCTTTGCGC-CCAACGTTCACATGAGTGCCACCCCCTGGCTTTCCTGTGTTCACTCCAACT
2848245 CCTTTGCGCCCAACGTTCACATGAGTGCCACCCCCTGGCTTTCCTGTGTTCACTCCAACT
1 CCTTTGCGCCCAACGTTCACATGAGTGCCACCCCCTGGCTTTCCTGTGTTCACTCCAACT
2848305 CCTTTGCGCCCAACGTTCACATGAGTGCCACCCCCTGGCTTTCCTGTGTTCACTCCAACT
1 CCTTTGCGCCCAACGTTCACATGAGTGCCACCCCCTGGCTTTCCTGTGTTCACTCCAACT
2848365 CCTTTGCGCCCAACGTTCACATGAGTGCCACCCCCTGGCTT
1 CCTTTGCGCCCAACGTTCACATGAGTGCCACCCCCTGGCTT
2848406 CCCTTTTCCT
Statistics
Matches: 214, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
60 213 1.00
61 1 0.00
ACGTcount: A:0.15, C:0.40, G:0.16, T:0.28
Consensus pattern (60 bp):
CCTTTGCGCCCAACGTTCACATGAGTGCCACCCCCTGGCTTTCCTGTGTTCACTCCAACT
Found at i:2859760 original size:15 final size:15
Alignment explanation
Indices: 2859725--2859769 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
2859715 AGAATACATA
2859725 AATTTTTTATTAAAAT
1 AATTTTTTA-TAAAAT
2859741 AATTTTTTATAACAAT
1 AATTTTTTATAA-AAT
2859757 -ATTTTTTCATAAA
1 AATTTTTT-ATAAA
2859770 TTTTTAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTTTTTATAAAAT
Found at i:2878367 original size:108 final size:105
Alignment explanation
Indices: 2878207--2878542 Score: 448
Period size: 107 Copynumber: 3.2 Consensus size: 105
2878197 TAATACTGAT
* * *
2878207 ATACGAAAAAGA-AAAAAAAAT-TTTGGGTGCTGGCCTGTGAATGGCCGGCACCCAATGA-ACAG
1 ATACGAAAAAAATAAAAAAAATATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGT-ACACAG
*** *
2878269 TAAAATTTTTTTTCTTTTTTTTCATGTCAGAATAAGATATAAAA
65 TAAAA---AAATTCTTTTTTTTCATGTCAGAATCAGATATAAAA
*
2878313 ATACGAAAAAAATAAAAAAAATATTTGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTACACAGT
1 ATACGAAAAAAATAAAAAAAATATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGT
*
2878378 AAAAAAAAATTCTTTTTTTTCATATCAGAATCAGATATAAAA
66 --AAAAAAATTCTTTTTTTTCATGTCAGAATCAGATATAAAA
* *
2878420 ATAAGAAAAAAAT-AAAAAAA-ATTTGGGTGCTGGCCTGTCAATGACCGGCACCCAGTACACAGT
1 ATACGAAAAAAATAAAAAAAATATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGT
* * *
2878483 AAAAAAATTATTTTTTTTCGTGTTAGAATCAGATATAAAA
66 AAAAAAATTCTTTTTTTTCATGTCAGAATCAGATATAAAA
*
2878523 ATACGAAAAAAATATAAAAA
1 ATACGAAAAAAATAAAAAAA
2878543 TTTCTATTTC
Statistics
Matches: 206, Mismatches: 18, Indels: 14
0.87 0.08 0.06
Matches are distributed among these distances:
103 48 0.23
104 5 0.02
105 41 0.20
106 18 0.09
107 53 0.26
108 37 0.18
110 4 0.02
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (105 bp):
ATACGAAAAAAATAAAAAAAATATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGT
AAAAAAATTCTTTTTTTTCATGTCAGAATCAGATATAAAA
Found at i:2878468 original size:105 final size:105
Alignment explanation
Indices: 2878207--2878542 Score: 446
Period size: 103 Copynumber: 3.2 Consensus size: 105
2878197 TAATACTGAT
* * *
2878207 ATACGAAAAAGAA-AAAAAAATTTTGGGTGCTGGCCTGTGAATGGCCGGCACCCAATGA-ACAGT
1 ATACGAAAAA-AATAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGT-ACACAGT
***** *
2878270 AAAATTTTTTTTCTTTTTTTTCATGTCAGAATAAGATATAAAA
64 AAAA-AAAAATTCTTTTTTTTCATGTCAGAATCAGATATAAAA
*
2878313 ATACGAAAAAAATAAAAAAAATATTTGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTACACAGT
1 ATACGAAAAAAAT-AAAAAAA-ATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGT
*
2878378 AAAAAAAAATTCTTTTTTTTCATATCAGAATCAGATATAAAA
64 AAAAAAAAATTCTTTTTTTTCATGTCAGAATCAGATATAAAA
* *
2878420 ATAAGAAAAAAATAAAAAAAATTTGGGTGCTGGCCTGTCAATGACCGGCACCCAGTACACAGT--
1 ATACGAAAAAAATAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAA
* * *
2878483 AAAAAAATTATTTTTTTTCGTGTTAGAATCAGATATAAAA
66 AAAAAAATTCTTTTTTTTCATGTCAGAATCAGATATAAAA
*
2878523 ATACGAAAAAAATATAAAAA
1 ATACGAAAAAAATAAAAAAA
2878543 TTTCTATTTC
Statistics
Matches: 206, Mismatches: 20, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
103 54 0.26
105 43 0.21
106 17 0.08
107 51 0.25
108 41 0.20
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (105 bp):
ATACGAAAAAAATAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAA
AAAAAAATTCTTTTTTTTCATGTCAGAATCAGATATAAAA
Found at i:2878747 original size:59 final size:60
Alignment explanation
Indices: 2878657--2878774 Score: 195
Period size: 59 Copynumber: 2.0 Consensus size: 60
2878647 TATAAATTTT
*
2878657 TTTATTTCTTTTCATATTTTTATATCTGATTCTGATACGAAAAAAAA-AAGAAAAAAATTA
1 TTTATTTCTTTTCATATTTTTATATCTGATTCTGACACGAAAAAAAAGAA-AAAAAAATTA
*
2878717 TTTATTT-TTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAAATT
1 TTTATTTCTTTTCATATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAAATT
2878775 TACTGTTCAC
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
59 46 0.84
60 9 0.16
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (60 bp):
TTTATTTCTTTTCATATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAAATTA
Found at i:2885494 original size:16 final size:16
Alignment explanation
Indices: 2885473--2885540 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
2885463 GATTTGCTAT
2885473 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2885489 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
2885505 TACACCTCCAATCCAA
1 TACACCTCTAATCCAA
2885521 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2885537 TACA
1 TACA
2885541 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.24
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:2899375 original size:16 final size:15
Alignment explanation
Indices: 2899352--2899395 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 15
2899342 ATAATAAATT
2899352 TAAAATTATATAATA
1 TAAAATTATATAATA
2899367 T-AAA-TAT-TAA-A
1 TAAAATTATATAATA
2899378 TAAAAATTATATAATA
1 T-AAAATTATATAATA
2899394 TA
1 TA
2899396 CTTTTTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
11 2 0.08
12 3 0.12
13 6 0.25
14 6 0.25
15 5 0.21
16 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAAATTATATAATA
Found at i:2899549 original size:21 final size:21
Alignment explanation
Indices: 2899525--2899578 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
2899515 ATTCAATTAT
*
2899525 AAAATATATTGGGAAAATG-GA
1 AAAATA-ATTGGGAAAATGAAA
**
2899546 AAAATAACAGGGAAAATGAAA
1 AAAATAATTGGGAAAATGAAA
2899567 AAAATAGATTGG
1 AAAATA-ATTGG
2899579 AATTTGGATG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 10 0.38
21 13 0.50
22 3 0.12
ACGTcount: A:0.57, C:0.02, G:0.22, T:0.19
Consensus pattern (21 bp):
AAAATAATTGGGAAAATGAAA
Found at i:2907395 original size:17 final size:18
Alignment explanation
Indices: 2907370--2907407 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
2907360 ATTTTATTAG
2907370 TTTTCCTTTTCTTTT-TT
1 TTTTCCTTTTCTTTTCTT
*
2907387 TTTTTCTTTTCTTTTCTT
1 TTTTCCTTTTCTTTTCTT
2907405 TTT
1 TTT
2907408 GGGCCATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTCCTTTTCTTTTCTT
Found at i:2909065 original size:111 final size:111
Alignment explanation
Indices: 2908775--2909236 Score: 620
Period size: 111 Copynumber: 4.1 Consensus size: 111
2908765 GTAAGTGGGC
* * *
2908775 CTGCTGCTGCCGAACCAGCTGGCCATTCCAGGCAGGACCTGTGCCTTGAGCACATGACTGCTCAT
1 CTGCTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATATGACTGCTCAT
* * * *
2908840 ATCGAGGCGAGCCCATGTTTGATACATTTCCATTTC-CATAAAAGTTATT
66 ATCGAGGTGATCCCATGTTTGATACAGTTCCA-TTCGCATGAAA---ATT
* * * *
2908889 CTGATGATGCTGCTGAACCAGCTGACCATTCCAGGCAGGACCTGTGCCTTGAGCATATGTCTGCT
1 C---TGCTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATATGACTGCT
* * *
2908954 CATATCGAGGTGATCCCATGTTCGATACAGTTCCGTTCACATGAAAATT
63 CATATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
* * *
2909003 CTGCTGCTGCTGAACCATCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATACGAGTGCTCAT
1 CTGCTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATATGACTGCTCAT
* *
2909068 ATCGAGGTGATCCCATGTTTGGTACAATTCCATTCGCATGAAAATT
66 ATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
* * * ** *
2909114 CTGCTGCTGCTGAGCCATCTGGCCATTCCAGGCATGACCCATCCCTTGAACATATGACTGCTCAT
1 CTGCTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATATGACTGCTCAT
*
2909179 ATCGAGGTGATCCCATGTTAGATACAGTTCCATTCGCATGAAAATT
66 ATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
2909225 CTGCTGCTGCTG
1 CTGCTGCTGCTG
2909237 CTGAATTTGA
Statistics
Matches: 311, Mismatches: 33, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
111 211 0.68
114 5 0.02
116 3 0.01
117 92 0.30
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (111 bp):
CTGCTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATATGACTGCTCAT
ATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
Found at i:2912636 original size:28 final size:28
Alignment explanation
Indices: 2912596--2912651 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
2912586 TGATAAATAA
2912596 CCATCATATTTAAACACTCAACGTGATT
1 CCATCATATTTAAACACTCAACGTGATT
2912624 CCATCATATTTAAACACTCAACGTGATT
1 CCATCATATTTAAACACTCAACGTGATT
2912652 AGGCACAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (28 bp):
CCATCATATTTAAACACTCAACGTGATT
Found at i:2928966 original size:11 final size:11
Alignment explanation
Indices: 2928950--2928974 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2928940 TTTTTATATA
2928950 TTTTTTAAAAT
1 TTTTTTAAAAT
2928961 TTTTTTAAAAT
1 TTTTTTAAAAT
2928972 TTT
1 TTT
2928975 ATACATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTTAAAAT
Found at i:2953657 original size:23 final size:22
Alignment explanation
Indices: 2953614--2953657 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
2953604 TATTAAATTG
* **
2953614 AAAAAATATTAAGATTTTTTTA
1 AAAAAATATTAAAATCCTTTTA
2953636 AAAATAATATTAAAATCCTTTT
1 AAAA-AATATTAAAATCCTTTT
2953658 TAACATGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAAAATATTAAAATCCTTTTA
Found at i:2954213 original size:20 final size:21
Alignment explanation
Indices: 2954184--2954225 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
2954174 TGAATATAAT
2954184 AAATA-TTTTTTATTTTTTTA
1 AAATACTTTTTTATTTTTTTA
2954204 AAATACTTTTTTTATTTTTTTA
1 AAATAC-TTTTTTATTTTTTTA
2954226 TTTTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
22 15 0.75
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
AAATACTTTTTTATTTTTTTA
Found at i:2954242 original size:29 final size:29
Alignment explanation
Indices: 2954187--2954243 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
2954177 ATATAATAAA
* *
2954187 TATTTTTTATTTTTTTAAAATACTTTTTT
1 TATTTTTTATATTTTTAAAATAATTTTTT
*
2954216 TATTTTTT-TATTTTTAAAATAAATTTTT
1 TATTTTTTATATTTTTAAAATAATTTTTT
2954244 GGTGTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (29 bp):
TATTTTTTATATTTTTAAAATAATTTTTT
Found at i:2955274 original size:20 final size:20
Alignment explanation
Indices: 2955234--2955274 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2955224 CATTCAATGA
* *
2955234 TTTTTATGATTTTTTCATAG
1 TTTTTATAATTTTTACATAG
*
2955254 TTTTTATAATTTTTACTTAG
1 TTTTTATAATTTTTACATAG
2955274 T
1 T
2955275 GTTGAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.22, C:0.05, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTTTATAATTTTTACATAG
Found at i:2961711 original size:17 final size:17
Alignment explanation
Indices: 2961689--2961722 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2961679 ACAAACGGTT
*
2961689 GTTTAATCCACTTTTTA
1 GTTTAAACCACTTTTTA
*
2961706 GTTTAAACCAGTTTTTA
1 GTTTAAACCACTTTTTA
2961723 ATTAAAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (17 bp):
GTTTAAACCACTTTTTA
Found at i:2963437 original size:6 final size:7
Alignment explanation
Indices: 2963421--2963458 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
2963411 TATATAATAG
2963421 TTTTTCT
1 TTTTTCT
2963428 TTTTTCT
1 TTTTTCT
2963435 TTTTTCT
1 TTTTTCT
2963442 TTTCATT-T
1 TTT--TTCT
2963450 TTTTTCT
1 TTTTTCT
2963457 TT
1 TT
2963459 CTATAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 2 0.07
7 20 0.71
8 4 0.14
9 2 0.07
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:2963450 original size:19 final size:19
Alignment explanation
Indices: 2963422--2963460 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2963412 ATATAATAGT
*
2963422 TTTTC-TTTTTTCTTTTTTC
1 TTTTCATTTTTT-TTCTTTC
2963441 TTTTCATTTTTTTTCTTTC
1 TTTTCATTTTTTTTCTTTC
2963460 T
1 T
2963461 ATAAAAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTCATTTTTTTTCTTTC
Found at i:2967300 original size:15 final size:16
Alignment explanation
Indices: 2967280--2967309 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2967270 TTTGTACGTT
2967280 AAAAGAAAA-GAAAAA
1 AAAAGAAAAGGAAAAA
2967295 AAAAGAAAAGGAAAA
1 AAAAGAAAAGGAAAA
2967310 TCTGTTGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGGAAAAA
Found at i:2969479 original size:22 final size:22
Alignment explanation
Indices: 2969448--2969493 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2969438 ATTGAAAATA
* *
2969448 AATTTTAAAAAAATGTATACTT
1 AATTTAAAAAAAATGTAAACTT
*
2969470 AATTTAAAAAATATGTAAACTT
1 AATTTAAAAAAAATGTAAACTT
2969492 AA
1 AA
2969494 ATAACACTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (22 bp):
AATTTAAAAAAAATGTAAACTT
Found at i:2969606 original size:14 final size:14
Alignment explanation
Indices: 2969587--2969616 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2969577 ATCCAAACAA
2969587 TAGCAACAAAATAG
1 TAGCAACAAAATAG
*
2969601 TAGCAACATAATAG
1 TAGCAACAAAATAG
2969615 TA
1 TA
2969617 AAATGGTAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (14 bp):
TAGCAACAAAATAG
Found at i:2970701 original size:30 final size:31
Alignment explanation
Indices: 2970644--2970704 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2970634 CGTTGTGAAC
* * *
2970644 TAATTTAAATATTTGTTAGTAATTAAATATT
1 TAATTCAAATATTTATTAATAATTAAATATT
2970675 TAATTCAAATATTTATTAAT-ATTAAATATT
1 TAATTCAAATATTTATTAATAATTAAATATT
2970705 ACTGAAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (31 bp):
TAATTCAAATATTTATTAATAATTAAATATT
Found at i:2971820 original size:6 final size:6
Alignment explanation
Indices: 2971811--2971842 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
2971801 TTTCTTTTTC
2971811 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TT
2971843 AATGATACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:2978648 original size:17 final size:18
Alignment explanation
Indices: 2978628--2978661 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2978618 ATTATAAATA
*
2978628 TTAACTAATAT-TTATTT
1 TTAAATAATATCTTATTT
2978645 TTAAATAATATCTTATT
1 TTAAATAATATCTTATT
2978662 ATTAGCCGAT
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:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAAATAATATCTTATTT
Found at i:2997810 original size:25 final size:25
Alignment explanation
Indices: 2997774--2997842 Score: 111
Period size: 25 Copynumber: 2.8 Consensus size: 25
2997764 ACTTTAGCGC
*
2997774 GCTCTCTAATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
2997799 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
* *
2997824 GCTATCTGATTACTAGCAC
1 GCTCTCTGATTATTAGCAC
2997843 ATCAGTGCTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTGGT
Found at i:2997850 original size:25 final size:25
Alignment explanation
Indices: 2997797--2997851 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
2997787 TAGCACGTTG
* * * **
2997797 GTGCTCTCTGATTATTAGCACGTTG
1 GTGCTATCTGATTACTAGCACATCA
2997822 GTGCTATCTGATTACTAGCACATCA
1 GTGCTATCTGATTACTAGCACATCA
2997847 GTGCT
1 GTGCT
2997852 CTATGTTTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (25 bp):
GTGCTATCTGATTACTAGCACATCA
Found at i:2997865 original size:22 final size:22
Alignment explanation
Indices: 2997837--2997897 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
2997827 ATCTGATTAC
*
2997837 TAGCACATCAGTGCTCTATGTT
1 TAGCACATCAGTGCTCTATGTA
* *
2997859 TAGCACA-CATGTACTCTCTGTA
1 TAGCACATCA-GTGCTCTATGTA
* *
2997881 TAGCACTTTAGTGCTCT
1 TAGCACATCAGTGCTCT
2997898 CTATTCATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.90
23 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (22 bp):
TAGCACATCAGTGCTCTATGTA
Found at i:3006389 original size:15 final size:15
Alignment explanation
Indices: 3006365--3006414 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
3006355 CATCAGCAAA
3006365 AAAATATTTTTTTTC
1 AAAATATTTTTTTTC
**
3006380 AAAAT-TTTTTTTAAG
1 AAAATATTTTTTT-TC
3006395 AAAATAATTTTTTTTC
1 AAAAT-ATTTTTTTTC
3006411 AAAA
1 AAAA
3006415 ATAATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
14 7 0.25
15 10 0.36
16 4 0.14
17 7 0.25
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (15 bp):
AAAATATTTTTTTTC
Found at i:3006405 original size:18 final size:17
Alignment explanation
Indices: 3006382--3006420 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
3006372 TTTTTTTCAA
3006382 AATTTTTTTTAAGAAAAT
1 AATTTTTTTTAA-AAAAT
*
3006400 AATTTTTTTTCAAAAAT
1 AATTTTTTTTAAAAAAT
3006417 AATT
1 AATT
3006421 AAAATGTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
AATTTTTTTTAAAAAAT
Found at i:3006415 original size:17 final size:17
Alignment explanation
Indices: 3006364--3006420 Score: 61
Period size: 13 Copynumber: 3.6 Consensus size: 17
3006354 ACATCAGCAA
3006364 AAAAAT-ATTTTTTTTC
1 AAAAATAATTTTTTTTC
*
3006380 ---AA-AATTTTTTTTA
1 AAAAATAATTTTTTTTC
3006393 AGAAAATAATTTTTTTTC
1 A-AAAATAATTTTTTTTC
3006411 AAAAATAATT
1 AAAAATAATT
3006421 AAAATGTCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
13 11 0.33
17 11 0.33
18 11 0.33
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (17 bp):
AAAAATAATTTTTTTTC
Found at i:3032766 original size:18 final size:18
Alignment explanation
Indices: 3032725--3032767 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
3032715 CAAGATAAAC
3032725 ATTCATTGATATAACAAG
1 ATTCATTGATATAACAAG
* *
3032743 --TCATTGGTATAATAAG
1 ATTCATTGATATAACAAG
3032759 ATTCATTGA
1 ATTCATTGA
3032768 AGATCTAGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 4
0.74 0.11 0.15
Matches are distributed among these distances:
16 14 0.70
18 6 0.30
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (18 bp):
ATTCATTGATATAACAAG
Found at i:3043363 original size:18 final size:18
Alignment explanation
Indices: 3043326--3043359 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3043316 TAAATTAAAT
*
3043326 TTTTTTTTATTAGTATTA
1 TTTTTTATATTAGTATTA
3043344 TTTTTTATATTA-TATT
1 TTTTTTATATTAGTATT
3043360 TATTAAATAC
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:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTTTATATTAGTATTA
Found at i:3047423 original size:29 final size:29
Alignment explanation
Indices: 3047391--3047472 Score: 76
Period size: 31 Copynumber: 2.7 Consensus size: 29
3047381 AATATGTAAT
3047391 TATATACATTAACTTTAATTTGGTGCAAA
1 TATATACATTAACTTTAATTTGGTGCAAA
* * * * *
3047420 TATACACATGAAACTCTAGTTGTGGTTCAAA
1 TATATACAT-TAACTTTAATT-TGGTGCAAA
3047451 TATATAC-TTACAACTTTAATTT
1 TATATACATT--AACTTTAATTT
3047473 TGATTTAATC
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
29 8 0.20
30 10 0.25
31 22 0.55
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (29 bp):
TATATACATTAACTTTAATTTGGTGCAAA
Found at i:3048596 original size:13 final size:12
Alignment explanation
Indices: 3048560--3048592 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3048550 TTGTAAATGT
3048560 TAATTTTTTAATA
1 TAATTTTTTAA-A
3048573 TAA-TTTTTAAA
1 TAATTTTTTAAA
3048584 TAATTTTTT
1 TAATTTTTT
3048593 TAAAGTGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.21
12 12 0.63
13 3 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TAATTTTTTAAA
Found at i:3056255 original size:23 final size:23
Alignment explanation
Indices: 3056226--3056271 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3056216 TAAGGAATAT
3056226 TTTTAATATCACTTTCATTTATG
1 TTTTAATATCACTTTCATTTATG
3056249 TTTTAATATCACTTTCATTTATG
1 TTTTAATATCACTTTCATTTATG
3056272 CGGGCTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTTAATATCACTTTCATTTATG
Found at i:3058583 original size:2 final size:2
Alignment explanation
Indices: 3058541--3058571 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3058531 CAAATCTTTA
3058541 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3058572 ATTTTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3066502 original size:56 final size:56
Alignment explanation
Indices: 3066441--3066607 Score: 140
Period size: 56 Copynumber: 3.1 Consensus size: 56
3066431 AATATTTGGA
3066441 TTTAAATACAGCTATAGCAGGGTATTGACAATAAAATTGATTATTATAAATATTAC
1 TTTAAATACAGCTATAGCAGGGTATTGACAATAAAATTGATTATTATAAATATTAC
* ** *** * * *
3066497 TTTAAA-A-TGTTCTTATAATATAATAAAT-A-AATAAAATTCA--GTT-T--ATATTA-
1 TTTAAATACAG--C-TATAGCAGGGT-ATTGACAATAAAATTGATTATTATAAATATTAC
3066547 -TTAAATACAGCTATAGCAGGGTATTGACAATAAAATTGATTATTATAAATATTAC
1 TTTAAATACAGCTATAGCAGGGTATTGACAATAAAATTGATTATTATAAATATTAC
3066602 TTTAAA
1 TTTAAA
3066608 ATGTTCTTAT
Statistics
Matches: 78, Mismatches: 18, Indels: 30
0.62 0.14 0.24
Matches are distributed among these distances:
47 2 0.03
48 7 0.09
49 16 0.21
50 1 0.01
51 9 0.12
52 1 0.01
53 1 0.01
54 9 0.12
55 1 0.01
56 22 0.28
57 7 0.09
58 2 0.03
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (56 bp):
TTTAAATACAGCTATAGCAGGGTATTGACAATAAAATTGATTATTATAAATATTAC
Found at i:3066564 original size:105 final size:106
Alignment explanation
Indices: 3066442--3066652 Score: 415
Period size: 105 Copynumber: 2.0 Consensus size: 106
3066432 ATATTTGGAT
3066442 TTAAATACAGCTATAGCAGGGTATTGACAATAAAATTGATTATTATAAATATTACTTTAAAATGT
1 TTAAATACAGCTATAGCAGGGTATTGACAATAAAATTGATTATTATAAATATTACTTTAAAATGT
3066507 TCTTATAATATAATAAATAAATAAAATTCA-GTTTATATTA
66 TCTTATAATATAATAAATAAATAAAATTCATGTTTATATTA
3066547 TTAAATACAGCTATAGCAGGGTATTGACAATAAAATTGATTATTATAAATATTACTTTAAAATGT
1 TTAAATACAGCTATAGCAGGGTATTGACAATAAAATTGATTATTATAAATATTACTTTAAAATGT
3066612 TCTTATAATATAATAAATAAATAAAATTCATGTTTATATTA
66 TCTTATAATATAATAAATAAATAAAATTCATGTTTATATTA
3066653 AATAATAAAA
Statistics
Matches: 105, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
105 95 0.90
106 10 0.10
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (106 bp):
TTAAATACAGCTATAGCAGGGTATTGACAATAAAATTGATTATTATAAATATTACTTTAAAATGT
TCTTATAATATAATAAATAAATAAAATTCATGTTTATATTA
Found at i:3089120 original size:37 final size:37
Alignment explanation
Indices: 3089011--3089120 Score: 86
Period size: 37 Copynumber: 3.1 Consensus size: 37
3089001 AAAGGAATGG
3089011 GTCTTGTGGACTATCTTACAGTGTCTTTTTCTTATAA
1 GTCTTGTGGACTATCTTACAGTGTCTTTTTCTTATAA
* * ** * * ** *
3089048 GT-TTATATGA-TAAATT-TAGT-ACTACCTT-TTGTAA
1 GTCTTGT-GGACTATCTTACAGTGTCT-TTTTCTTATAA
3089082 GTCTTGTGGACTATCTTACAGTGTCTTTTTCTTATAA
1 GTCTTGTGGACTATCTTACAGTGTCTTTTTCTTATAA
3089119 GT
1 GT
3089121 TTATCTGATA
Statistics
Matches: 48, Mismatches: 18, Indels: 14
0.60 0.22 0.17
Matches are distributed among these distances:
34 11 0.23
35 12 0.25
36 12 0.25
37 13 0.27
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.48
Consensus pattern (37 bp):
GTCTTGTGGACTATCTTACAGTGTCTTTTTCTTATAA
Found at i:3089130 original size:71 final size:71
Alignment explanation
Indices: 3089011--3089294 Score: 541
Period size: 71 Copynumber: 4.0 Consensus size: 71
3089001 AAAGGAATGG
* *
3089011 GTCTTGTGGACTATCTTACAGTGTCTTTTTCTTATAAGTTTATATGATAAATTTAGTACTACCTT
1 GTCTTGTGGACTATCTTACAGTGTCTTTTTCTTAAAAGTTTATCTGATAAATTTAGTACTACCTT
3089076 TTGTAA
66 TTGTAA
*
3089082 GTCTTGTGGACTATCTTACAGTGTCTTTTTCTTATAAGTTTATCTGATAAATTTAGTACTACCTT
1 GTCTTGTGGACTATCTTACAGTGTCTTTTTCTTAAAAGTTTATCTGATAAATTTAGTACTACCTT
3089147 TTGTAA
66 TTGTAA
3089153 GTCTTGTGGACTATCTTACAGTGTCTTTTTCTTAAAAGTTTATCTGATAAATTTAGTACTACCTT
1 GTCTTGTGGACTATCTTACAGTGTCTTTTTCTTAAAAGTTTATCTGATAAATTTAGTACTACCTT
3089218 TTGTAA
66 TTGTAA
3089224 GTCTTGTGGACTATCTTACAGTGTCTTTTTCTTAAAAGTTTATCTGATAAATTTAGTACTACCTT
1 GTCTTGTGGACTATCTTACAGTGTCTTTTTCTTAAAAGTTTATCTGATAAATTTAGTACTACCTT
3089289 TTGTAA
66 TTGTAA
3089295 TTAATGAATA
Statistics
Matches: 211, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 211 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (71 bp):
GTCTTGTGGACTATCTTACAGTGTCTTTTTCTTAAAAGTTTATCTGATAAATTTAGTACTACCTT
TTGTAA
Found at i:3092877 original size:22 final size:22
Alignment explanation
Indices: 3092828--3092868 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
3092818 TTATGGTTCG
3092828 AAGTTTTTTAAGTTTAGTGCAC
1 AAGTTTTTTAAGTTTAGTGCAC
3092850 AAGTTTTTT-AGTTTAGTGC
1 AAGTTTTTTAAGTTTAGTGC
3092869 TTAAGGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.49
Consensus pattern (22 bp):
AAGTTTTTTAAGTTTAGTGCAC
Done.