Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 8 of 131
Found at i:2519293 original size:24 final size:23
Alignment explanation
Indices: 2519248--2519293 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
2519238 TATACATACC
* *
2519248 TTATTATATATCTTTATATCTTA
1 TTATTATATATATCTATATCTTA
*
2519271 TTATGTATATATATCTATCTCTT
1 TTAT-TATATATATCTATATCTT
2519294 TTTAAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.28, C:0.11, G:0.02, T:0.59
Consensus pattern (23 bp):
TTATTATATATATCTATATCTTA
Found at i:2519469 original size:16 final size:15
Alignment explanation
Indices: 2519448--2519481 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2519438 TATATATATC
*
2519448 TTTTATGTTTTTTTAG
1 TTTTATATTTTTTT-G
2519464 TTTTATATTTTTTTG
1 TTTTATATTTTTTTG
2519479 TTT
1 TTT
2519482 ATTTCTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (15 bp):
TTTTATATTTTTTTG
Found at i:2520090 original size:109 final size:109
Alignment explanation
Indices: 2519894--2520198 Score: 427
Period size: 109 Copynumber: 2.8 Consensus size: 109
2519884 TTAAATAATA
* * *
2519894 AAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTCTCGATTTTTC
1 AAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTC
*
2519959 TCGTTCAACCAAATAGCCAAATATCCTTTCAAAAATTCCAAAAT
66 TCGTTCAACCAAATAGCCAAATATCCTTCCAAAAATTCCAAAAT
* * *
2520003 AAGGCAATGTTTTGCATTTGGGAATTCGAGAAAACATGCCCTAATATGCTGGGTTTCGATTTTTC
1 AAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTC
* * * *
2520068 TTGTTCAACCAAATGGCTAAATATCCTTCCAAAAATTTCAAAAT
66 TCGTTCAACCAAATAGCCAAATATCCTTCCAAAAATTCCAAAAT
* * * * *
2520112 AAGACAGTGTTTTGCATTTGGAAATTCGAG-GAACGTGCCCTAATGTGTTGGGTTCCGA--TTTC
1 AAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTC
* *
2520174 TCGTTTAACCAAATTGCCAAATATC
66 TCGTTCAACCAAATAGCCAAATATC
2520199 TTTTTGAATT
Statistics
Matches: 173, Mismatches: 23, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
106 25 0.14
108 23 0.13
109 125 0.72
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (109 bp):
AAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTC
TCGTTCAACCAAATAGCCAAATATCCTTCCAAAAATTCCAAAAT
Found at i:2521607 original size:11 final size:11
Alignment explanation
Indices: 2521588--2521631 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
2521578 AACACCGAAC
*
2521588 TTTTTGGGTAA
1 TTTTCGGGTAA
2521599 TTTTCGGGTAA
1 TTTTCGGGTAA
2521610 --TTCGGGTAA
1 TTTTCGGGTAA
2521619 TTTTCGGGTAA
1 TTTTCGGGTAA
2521630 TT
1 TT
2521632 CGGTTAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 9 0.30
11 21 0.70
ACGTcount: A:0.18, C:0.07, G:0.27, T:0.48
Consensus pattern (11 bp):
TTTTCGGGTAA
Found at i:2521615 original size:9 final size:9
Alignment explanation
Indices: 2521601--2521675 Score: 98
Period size: 9 Copynumber: 8.2 Consensus size: 9
2521591 TTGGGTAATT
2521601 TTCGGGTAA
1 TTCGGGTAA
2521610 TTCGGGTAA
1 TTCGGGTAA
2521619 TTTTCGGGTAA
1 --TTCGGGTAA
*
2521630 TTCGGTTAA
1 TTCGGGTAA
*
2521639 TTCGGTTAA
1 TTCGGGTAA
*
2521648 TTCGGTTAA
1 TTCGGGTAA
2521657 -TCGGGTAA
1 TTCGGGTAA
2521665 TTCGGGTAA
1 TTCGGGTAA
2521674 TT
1 TT
2521676 TTTAACCAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
8 7 0.11
9 45 0.74
11 9 0.15
ACGTcount: A:0.21, C:0.11, G:0.28, T:0.40
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:2521618 original size:20 final size:20
Alignment explanation
Indices: 2521593--2521677 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
2521583 CGAACTTTTT
2521593 GGGTAATTTTCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
2521613 GGGTAATTTTCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
* *
2521633 GGTTAA--TTCGGTTAATTC
1 GGGTAATTTTCGGGTAATTC
*
2521651 GGTTAA---TCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
2521668 GGGTAATTTT
1 GGGTAATTTT
2521678 TAACCAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
17 15 0.26
18 17 0.29
20 26 0.45
ACGTcount: A:0.21, C:0.09, G:0.28, T:0.41
Consensus pattern (20 bp):
GGGTAATTTTCGGGTAATTC
Found at i:2521854 original size:12 final size:12
Alignment explanation
Indices: 2521837--2521861 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2521827 AGCAATTTCG
2521837 GGTCGGTTAACC
1 GGTCGGTTAACC
2521849 GGTCGGTTAACC
1 GGTCGGTTAACC
2521861 G
1 G
2521862 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:2536343 original size:3 final size:3
Alignment explanation
Indices: 2536337--2536408 Score: 90
Period size: 3 Copynumber: 24.0 Consensus size: 3
2536327 ACTAATTAGG
* *
2536337 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
2536385 TTA ATA TTA CTG TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
2536409 CATTTCCATT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2547701 original size:111 final size:111
Alignment explanation
Indices: 2547507--2547723 Score: 425
Period size: 111 Copynumber: 2.0 Consensus size: 111
2547497 TTTCGCTCCT
2547507 TTGGCTCCCAAATGCTCTCTTAAGTATAGAAACATGAATTTAAAGGATTAGAAGCATCAAATTCA
1 TTGGCTCCCAAATGCTCTCTTAAGTATAGAAACATGAATTTAAAGGATTAGAAGCATCAAATTCA
*
2547572 CTCATTTGCATAATTAATCATCTAAAAATGCATTAATAATATTAAA
66 CTCATTTGCATAATTAATCATCTAAAAATGCATTAAGAATATTAAA
2547618 TTGGCTCCCAAATGCTCTCTTAAGTATAGAAACATGAATTTAAAGGATTAGAAGCATCAAATTCA
1 TTGGCTCCCAAATGCTCTCTTAAGTATAGAAACATGAATTTAAAGGATTAGAAGCATCAAATTCA
2547683 CTCATTTGCATAATTAATCATCTAAAAATGCATTAAGAATA
66 CTCATTTGCATAATTAATCATCTAAAAATGCATTAAGAATA
2547724 ATATTAAAAT
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (111 bp):
TTGGCTCCCAAATGCTCTCTTAAGTATAGAAACATGAATTTAAAGGATTAGAAGCATCAAATTCA
CTCATTTGCATAATTAATCATCTAAAAATGCATTAAGAATATTAAA
Found at i:2549507 original size:3 final size:3
Alignment explanation
Indices: 2549501--2549572 Score: 90
Period size: 3 Copynumber: 24.0 Consensus size: 3
2549491 ACTAATTAGG
* *
2549501 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
2549549 TTA ATA TTA CTG TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
2549573 CATTTCCATT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2549904 original size:4 final size:4
Alignment explanation
Indices: 2549890--2549919 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
2549880 TTTTTATAAT
2549890 TTTA TTTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA T
2549920 GCTTTCATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2555381 original size:14 final size:14
Alignment explanation
Indices: 2555362--2555399 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2555352 AGTTTTAGTT
2555362 TATAAAGATAAT-AA
1 TATAAA-ATAATAAA
*
2555376 TATAAAAAAATAAA
1 TATAAAATAATAAA
2555390 TATAAAATAA
1 TATAAAATAA
2555400 AGTAAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
TATAAAATAATAAA
Found at i:2563724 original size:113 final size:113
Alignment explanation
Indices: 2563445--2563905 Score: 678
Period size: 113 Copynumber: 4.1 Consensus size: 113
2563435 CGCTTAACGC
* * *
2563445 AAAACGCCGCTGTAGAACGGA-TTATTAGCGGCGTTTGGGAAAATACCGCCACTAGTGTTCCAAA
1 AAAACGCCGCTGTAGAACGGAGTT-TTAGCGGCGCTTGGGAAAA-ACCGCCACTAATGTTCCCAA
* * ** * *
2563509 ATATACGAAAACGGCGTCGTTCTGTGTTACTGTATTTGCGACGCATTT-TGT
64 ATATATGAAAACGGCGTCGTTCTGTATTACTCCA-TTGCGGCGC-TTTGTAT
* * * *
2563560 AAAACGCCGCTGAAGAATGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAAT
1 AAAACGCCGCTGTAGAACGGAGTTTTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAAT
2563625 ATATGAAAACGGCGTCGTTCTGTATTACTCCATTGCGGCGCTTTGTAT
66 ATATGAAAACGGCGTCGTTCTGTATTACTCCATTGCGGCGCTTTGTAT
2563673 AAAACGCCGCTGTAGAACGGAGTTTTAGCGGCGCTT-GGAAATAACCGCCACTAATGTTCCCAAA
1 AAAACGCCGCTGTAGAACGGAGTTTTAGCGGCGCTTGGGAAA-AACCGCCACTAATGTTCCCAAA
2563737 TATATGAAAACGGCGTCGTTCTGTATTACTCCATTGCGGCGCTTTGTAT
65 TATATGAAAACGGCGTCGTTCTGTATTACTCCATTGCGGCGCTTTGTAT
2563786 AAAACGCCGCTGTAGAACGGAGTTTTAGCGGCGCTT-GGAAATAACCGCCACTAATGTTCCCAAA
1 AAAACGCCGCTGTAGAACGGAGTTTTAGCGGCGCTTGGGAAA-AACCGCCACTAATGTTCCCAAA
* * * * *
2563850 TATATGAAAACGGCGTCGTTCTGTGTGACTCTATTGCGGCGCTTTTTGT
65 TATATGAAAACGGCGTCGTTCTGTATTACTCCATTGCGGCGCTTTGTAT
2563899 AAAACGC
1 AAAACGC
2563906 TGTTAATGCT
Statistics
Matches: 321, Mismatches: 22, Indels: 8
0.91 0.06 0.02
Matches are distributed among these distances:
112 7 0.02
113 229 0.71
114 48 0.15
115 36 0.11
116 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (113 bp):
AAAACGCCGCTGTAGAACGGAGTTTTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAAT
ATATGAAAACGGCGTCGTTCTGTATTACTCCATTGCGGCGCTTTGTAT
Found at i:2566552 original size:27 final size:28
Alignment explanation
Indices: 2566521--2566574 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
2566511 AATTTTTGTA
*
2566521 ATTTTTATAATTAAAT-TTAAATAAAAT
1 ATTTTAATAATTAAATATTAAATAAAAT
* *
2566548 ATTTTAATCATTAAATATTAATTAAAA
1 ATTTTAATAATTAAATATTAAATAAAA
2566575 ATATAAGCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
ATTTTAATAATTAAATATTAAATAAAAT
Found at i:2577993 original size:9 final size:9
Alignment explanation
Indices: 2577976--2578005 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2577966 TTTTTTCTCC
2577976 AAAACCCTA
1 AAAACCCTA
*
2577985 AAAATCCTA
1 AAAACCCTA
2577994 AAAACCCTA
1 AAAACCCTA
2578003 AAA
1 AAA
2578006 TCCTAAACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAACCCTA
Found at i:2578015 original size:15 final size:16
Alignment explanation
Indices: 2577976--2578030 Score: 76
Period size: 15 Copynumber: 3.4 Consensus size: 16
2577966 TTTTTTCTCC
2577976 AAAACCCTAAAAATCCT
1 AAAACCCT-AAAATCCT
2577993 AAAAACCCTAAAATCCT
1 -AAAACCCTAAAATCCT
*
2578010 -AAACCCTAAAATCCA
1 AAAACCCTAAAATCCT
2578025 AAAACC
1 AAAACC
2578031 TACAAGTGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
15 14 0.40
16 5 0.14
17 8 0.23
18 8 0.23
ACGTcount: A:0.55, C:0.31, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAACCCTAAAATCCT
Found at i:2583557 original size:11 final size:11
Alignment explanation
Indices: 2583541--2583569 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2583531 TATAGAAGAA
2583541 TGTAAAATTTC
1 TGTAAAATTTC
2583552 TGTAAAATTTC
1 TGTAAAATTTC
2583563 TGTAAAA
1 TGTAAAA
2583570 ATCAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (11 bp):
TGTAAAATTTC
Found at i:2586562 original size:28 final size:28
Alignment explanation
Indices: 2586510--2586563 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
2586500 CCTAATCCTC
* *
2586510 AAGTTAAGTGTATTACTCGACCAAAAAA
1 AAGTTAAGTATATTACTCGAACAAAAAA
2586538 AAGTTAAGTATATTACAT-GAACAAAA
1 AAGTTAAGTATATTAC-TCGAACAAAA
2586564 GCCATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (28 bp):
AAGTTAAGTATATTACTCGAACAAAAAA
Found at i:2586939 original size:5 final size:5
Alignment explanation
Indices: 2586931--2586956 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2586921 GAGATGGAAT
2586931 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
2586957 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:2586956 original size:26 final size:26
Alignment explanation
Indices: 2586905--2586956 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
2586895 TGAAGTTTTC
* * *
2586905 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
2586931 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
2586957 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:2587576 original size:30 final size:30
Alignment explanation
Indices: 2587542--2587598 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
2587532 AGAAAGGAGG
2587542 GGAGTAAAAGTTTTGGGGGGAAAGTGGGAA
1 GGAGTAAAAGTTTTGGGGGGAAAGTGGGAA
*
2587572 GGAGTAAAAGTTTTGGGGGGGAAGTGG
1 GGAGTAAAAGTTTTGGGGGGAAAGTGG
2587599 ACAGGTTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.49, T:0.21
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGGGGGGAAAGTGGGAA
Found at i:2592123 original size:19 final size:18
Alignment explanation
Indices: 2592073--2592130 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 18
2592063 AAATTATATA
*
2592073 TTAAATATATATTTTTATT
1 TTAAATATATATATTT-TT
* *
2592092 TTTAATCAAATATACTTTTT
1 TTAAAT-ATATATA-TTTTT
2592112 TTAAATATATATATTTTT
1 TTAAATATATATATTTTT
2592130 T
1 T
2592131 GGACTTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
20 12 0.38
21 3 0.09
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAAATATATATATTTTT
Found at i:2593274 original size:19 final size:18
Alignment explanation
Indices: 2593224--2593281 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 18
2593214 AAATTATATA
*
2593224 TTAAATATATATTTTTATT
1 TTAAATATATATATTT-TT
* *
2593243 TTTAATCAAATATACTTTTT
1 TTAAAT-ATATATA-TTTTT
2593263 TTAAATATATATATTTTT
1 TTAAATATATATATTTTT
2593281 T
1 T
2593282 GGACTTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
20 12 0.38
21 3 0.09
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAAATATATATATTTTT
Found at i:2594023 original size:19 final size:18
Alignment explanation
Indices: 2593973--2594030 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 18
2593963 AAATTATATA
*
2593973 TTAAATATATATTTTTATT
1 TTAAATATATATATTT-TT
* *
2593992 TTTAATCAAATATACTTTTT
1 TTAAAT-ATATATA-TTTTT
2594012 TTAAATATATATATTTTT
1 TTAAATATATATATTTTT
2594030 T
1 T
2594031 GGACTTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
20 12 0.38
21 3 0.09
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAAATATATATATTTTT
Found at i:2594579 original size:749 final size:748
Alignment explanation
Indices: 2593131--2594627 Score: 2949
Period size: 749 Copynumber: 2.0 Consensus size: 748
2593121 ATATGGATTT
*
2593131 GGGTAAACAAACGAGGCCCGTTTAGAAAACTAGTCGAGCCTCAGGTAAGACTTTTTTAGCTCGGG
1 GGGTAAACAAACGAGGCCCGTTTAGAAAACTAGGCGAGCCTCAGGTAAGACTTTTTTAGCTCGGG
2593196 CCCGGCCTGGCCCGACCCAAATTATATATTAAATATATATTTTTATTTTTAATCAAATATACTTT
66 CCCGGCCTGGCCCGACCCAAATTATATATTAAATATATATTTTTATTTTTAATCAAATATACTTT
2593261 TTTTAAATATATATATTTTTTGGACTTTTAATCTGAATTATATATTAAATATATATATTTTATTT
131 TTTTAAATATATATATTTTTTGGACTTTTAATCTGAATTATATATTAAATATATATATTTTATTT
2593326 TTAATCAAATATGGTTCGGGCCGGACCCGGTACAAGCAATTTTCTTTCGGGTCAGGCTGGGCCAA
196 TTAATCAAATATGGTTCGGGCCGGACCCGGTACAAGCAATTTTCTTTCGGGTCAGGCTGGGCCAA
2593391 GCAATTTTCTTTCGGGCCGGGCTTGGACAAATTTTTAGGCCCATATTTCGAGCCGAGCCCTGGCC
261 GCAATTTTCTTTCGGGCCGGGCTTGGACAAATTTTTAGGCCCATATTTCGAGCCGAGCCCTGGCC
2593456 TAAAAAATGGGTCTAAAATTTTGTCTGGGCCCGACTGAACCCGGCCCGGCCCATGATCACCTCTA
326 TAAAAAATGGGTCTAAAATTTTGTCTGGGCCCGACTGAACCCGGCCCGGCCCATGATCACCTCTA
2593521 GTGCTACCTATTTATAGATAAAATATGACAATTTCTTGAGTAATTAAAACAATATTTAATTTAAG
391 GTGCTACCTATTTATAGATAAAATATGACAATTTCTTGAGTAATTAAAACAATATTTAATTTAAG
2593586 CATTATCTAAGATAAAAGCCTTCCATTTTGAATTTCTAATGAAAAACATTAAACCCTAAACCTTA
456 CATTATCTAAGATAAAAGCCTTCCATTTTGAATTTCTAATGAAAAACATTAAACCCTAAACCTTA
2593651 AATCCTAATTTGACTAAAATCTATCAGCAACCTTGAAAGATAAATAAAAACACAACTTGTATTGA
521 AATCCTAATTTGACTAAAATCTATCAGCAACCTTGAAAGATAAATAAAAACACAACTTGTATTGA
2593716 ATTGCTTGAAATGTATATATACATTTGGATATATCTCAAAACTATACATGAATTATGATTTAACG
586 ATTGCTTGAAATGTATATATACATTTGGATATATCTCAAAACTATACATGAATTATGATTTAACG
2593781 TGTAATTGTATACATAGCCTTTTATTTTGTACAATTTTATATATAAAATTTTGATTTGATCAAAT
651 TGTAATTGTATACATAGCCTTTTATTTTGTACAATTTTATATATAAAATTTTGATTTGATCAAAT
2593846 TCTTGTAAATTATTAACACAATTATTAATATAA
716 TCTTGTAAATTATTAACACAATTATTAATATAA
* * *
2593879 GGGTGAAACACACGAGGCCCGTTTAGAAAATTGGGCGAGCCTCAGGTAAGACTTTTTTAGCTCGG
1 GGGT-AAACAAACGAGGCCCGTTTAGAAAACTAGGCGAGCCTCAGGTAAGACTTTTTTAGCTCGG
2593944 GCCCGGCCTGGCCCGACCCAAATTATATATTAAATATATATTTTTATTTTTAATCAAATATACTT
65 GCCCGGCCTGGCCCGACCCAAATTATATATTAAATATATATTTTTATTTTTAATCAAATATACTT
2594009 TTTTTAAATATATATATTTTTTGGACTTTTAATCTGAATTATATATTAAATATATATATTTTATT
130 TTTTTAAATATATATATTTTTTGGACTTTTAATCTGAATTATATATTAAATATATATATTTTATT
2594074 TTTAATCAAATATGGTTCGGGCCGGACCCGGTACAAGCAATTTTCTTTCGGGTCAGGCTGGGCCA
195 TTTAATCAAATATGGTTCGGGCCGGACCCGGTACAAGCAATTTTCTTTCGGGTCAGGCTGGGCCA
2594139 AGCAATTTTCTTTCGGGCCGGGCTTGGACAAATTTTTAGGCCCATATTTCGAGCCGAGCCCTGGC
260 AGCAATTTTCTTTCGGGCCGGGCTTGGACAAATTTTTAGGCCCATATTTCGAGCCGAGCCCTGGC
2594204 CTAAAAAATGGGTCTAAAATTTTGTCTGGGCCCGACTGAACCCGGCCCGGCCCATGATCACCTCT
325 CTAAAAAATGGGTCTAAAATTTTGTCTGGGCCCGACTGAACCCGGCCCGGCCCATGATCACCTCT
2594269 AGTGCTACCTATTTATAGATAAAATATGACAATTTCTTGAGTAATTAAAACAATATTTAATTTAA
390 AGTGCTACCTATTTATAGATAAAATATGACAATTTCTTGAGTAATTAAAACAATATTTAATTTAA
2594334 GCATTATCTAAGATAAAAGCCTTCCATTTTGAATTTCTAATGAAAAACATTAAACCCTAAACCTT
455 GCATTATCTAAGATAAAAGCCTTCCATTTTGAATTTCTAATGAAAAACATTAAACCCTAAACCTT
2594399 AAATCCTAATTTGACTAAAATCTATCAGCAACCTTGAAAGATAAATAAAAACACAACTTGTATTG
520 AAATCCTAATTTGACTAAAATCTATCAGCAACCTTGAAAGATAAATAAAAACACAACTTGTATTG
2594464 AATTGCTTGAAATGTATATATACATTTGGATATATCTCAAAACTATACATGAATTATGATTTAAC
585 AATTGCTTGAAATGTATATATACATTTGGATATATCTCAAAACTATACATGAATTATGATTTAAC
2594529 GTGTAATTGTATACATAGCCTTTTATTTTGTACAATTTTATATATAAAATTTTGATTTGATCAAA
650 GTGTAATTGTATACATAGCCTTTTATTTTGTACAATTTTATATATAAAATTTTGATTTGATCAAA
2594594 TTCTTGTAAATTATTAACACAATTATTAATATAA
715 TTCTTGTAAATTATTAACACAATTATTAATATAA
2594628 CATCATTTTA
Statistics
Matches: 744, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
748 4 0.01
749 740 0.99
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (748 bp):
GGGTAAACAAACGAGGCCCGTTTAGAAAACTAGGCGAGCCTCAGGTAAGACTTTTTTAGCTCGGG
CCCGGCCTGGCCCGACCCAAATTATATATTAAATATATATTTTTATTTTTAATCAAATATACTTT
TTTTAAATATATATATTTTTTGGACTTTTAATCTGAATTATATATTAAATATATATATTTTATTT
TTAATCAAATATGGTTCGGGCCGGACCCGGTACAAGCAATTTTCTTTCGGGTCAGGCTGGGCCAA
GCAATTTTCTTTCGGGCCGGGCTTGGACAAATTTTTAGGCCCATATTTCGAGCCGAGCCCTGGCC
TAAAAAATGGGTCTAAAATTTTGTCTGGGCCCGACTGAACCCGGCCCGGCCCATGATCACCTCTA
GTGCTACCTATTTATAGATAAAATATGACAATTTCTTGAGTAATTAAAACAATATTTAATTTAAG
CATTATCTAAGATAAAAGCCTTCCATTTTGAATTTCTAATGAAAAACATTAAACCCTAAACCTTA
AATCCTAATTTGACTAAAATCTATCAGCAACCTTGAAAGATAAATAAAAACACAACTTGTATTGA
ATTGCTTGAAATGTATATATACATTTGGATATATCTCAAAACTATACATGAATTATGATTTAACG
TGTAATTGTATACATAGCCTTTTATTTTGTACAATTTTATATATAAAATTTTGATTTGATCAAAT
TCTTGTAAATTATTAACACAATTATTAATATAA
Found at i:2608995 original size:29 final size:30
Alignment explanation
Indices: 2608962--2609041 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
2608952 AACCTAAGAT
2608962 ATAAAAT-TTTAATATTTATATTTAATACA
1 ATAAAATATTTAATATTTATATTTAATACA
* * *
2608991 ATAAAATATTT-AT-TTGTGTTTTTAATATA
1 ATAAAATATTTAATATT-TATATTTAATACA
2609020 ATAAAATATTTATTATATTTAT
1 ATAAAATATTTA--ATATTTAT
2609042 GATAGTGCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
28 2 0.05
29 30 0.73
30 3 0.07
32 4 0.10
33 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (30 bp):
ATAAAATATTTAATATTTATATTTAATACA
Found at i:2610205 original size:62 final size:62
Alignment explanation
Indices: 2610108--2610229 Score: 217
Period size: 62 Copynumber: 2.0 Consensus size: 62
2610098 AAAAAGATAA
* *
2610108 CCACTAAGAATGAAACAATTGGTGAATTGAACTAAATCTATAACTTTAGGCATAATACATAG
1 CCACTAAGAATGAAACAATTGGTGAACTGAACTAAATCTACAACTTTAGGCATAATACATAG
*
2610170 CCACTAAGAATGAACCAATTGGTGAACTGAACTAAATCTACAACTTTAGGCATAATACAT
1 CCACTAAGAATGAAACAATTGGTGAACTGAACTAAATCTACAACTTTAGGCATAATACAT
2610230 GACTAATGAC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (62 bp):
CCACTAAGAATGAAACAATTGGTGAACTGAACTAAATCTACAACTTTAGGCATAATACATAG
Found at i:2610612 original size:20 final size:20
Alignment explanation
Indices: 2610589--2610631 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
2610579 TCATGGTTTT
*
2610589 AAAAATT-TTAAAAAATATTA
1 AAAAATTCTGAAAAAATA-TA
2610609 AAAAATTCTGAAAAAATATA
1 AAAAATTCTGAAAAAATATA
2610629 AAA
1 AAA
2610632 TATAGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAAATTCTGAAAAAATATA
Found at i:2614701 original size:2 final size:2
Alignment explanation
Indices: 2614694--2614734 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2614684 AGCTGTAAAA
2614694 AG 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 AG A
2614735 AAATCACATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2616330 original size:31 final size:31
Alignment explanation
Indices: 2616292--2616351 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
2616282 ATTTGGCCAG
* *
2616292 TGAACTATTCGAAAG-TTTTCGTTTAAGTCAC
1 TGAACTATTCAAAAGCTTTT-ATTTAAGTCAC
2616323 TGAACTATTCAAAAGCTTTTATTTAAGTC
1 TGAACTATTCAAAAGCTTTTATTTAAGTC
2616352 GTCGTGCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (31 bp):
TGAACTATTCAAAAGCTTTTATTTAAGTCAC
Found at i:2625580 original size:20 final size:20
Alignment explanation
Indices: 2625543--2625588 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2625533 AATGGGCATG
* *
2625543 AATTATTATTTAAATAATGA
1 AATTATTATCTAAATAATCA
**
2625563 AATTATTATCTACTTAATCA
1 AATTATTATCTAAATAATCA
2625583 AATTAT
1 AATTAT
2625589 AAAAATATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (20 bp):
AATTATTATCTAAATAATCA
Found at i:2627358 original size:29 final size:30
Alignment explanation
Indices: 2627312--2627368 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
2627302 GCAATGTTAT
2627312 ACATGAACTTTGATTTTG-TGCAATTTTGA
1 ACATGAACTTTGATTTTGATGCAATTTTGA
*
2627341 ACATGATACTTTGA-TTTGATTCAATTTT
1 ACATGA-ACTTTGATTTTGATGCAATTTT
2627369 TTTTAGCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (30 bp):
ACATGAACTTTGATTTTGATGCAATTTTGA
Found at i:2627720 original size:55 final size:55
Alignment explanation
Indices: 2627649--2627763 Score: 203
Period size: 55 Copynumber: 2.1 Consensus size: 55
2627639 CACAAAATCT
2627649 TTCAAATGAAAATAAAAGCAAAGCAAAAAAAACCACTTCATGAAAACATCAACAA
1 TTCAAATGAAAATAAAAGCAAAGCAAAAAAAACCACTTCATGAAAACATCAACAA
* * *
2627704 TTCAAATGAAAATAAAAGCAAAGCAAAAAAAACCACTTTATGGAATCATCAACAA
1 TTCAAATGAAAATAAAAGCAAAGCAAAAAAAACCACTTCATGAAAACATCAACAA
2627759 TTCAA
1 TTCAA
2627764 CTTGGAATAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.57, C:0.17, G:0.08, T:0.17
Consensus pattern (55 bp):
TTCAAATGAAAATAAAAGCAAAGCAAAAAAAACCACTTCATGAAAACATCAACAA
Found at i:2631855 original size:31 final size:33
Alignment explanation
Indices: 2631820--2631881 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
2631810 ATGTGTAGAA
*
2631820 TTGAATCAAAAT-TAAAGTTT-TATGTATATTT
1 TTGAATCAAAATCAAAAGTTTATATGTATATTT
*
2631851 TTGAATTAAAATCAAAAGTTTAATATGTATA
1 TTGAATCAAAATCAAAAGTTT-ATATGTATA
2631882 ATTGCACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 11 0.42
32 7 0.27
34 8 0.31
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (33 bp):
TTGAATCAAAATCAAAAGTTTATATGTATATTT
Found at i:2632033 original size:53 final size:54
Alignment explanation
Indices: 2631976--2632087 Score: 208
Period size: 54 Copynumber: 2.1 Consensus size: 54
2631966 CACAGAATCT
*
2631976 TTCAAATGAAAATAAAAGCAAAGC-AAAAAACTACTTTATGGAAACATCAACAA
1 TTCAAATGAAAATAAAAGCAAAGCAAAAAAACCACTTTATGGAAACATCAACAA
2632029 TTCAAATGAAAATAAAAGCAAAGCAAAAAAACCACTTTATGGAAACATCAACAA
1 TTCAAATGAAAATAAAAGCAAAGCAAAAAAACCACTTTATGGAAACATCAACAA
2632083 TTCAA
1 TTCAA
2632088 CTTGGAATAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
53 24 0.42
54 33 0.58
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.19
Consensus pattern (54 bp):
TTCAAATGAAAATAAAAGCAAAGCAAAAAAACCACTTTATGGAAACATCAACAA
Found at i:2632682 original size:2 final size:2
Alignment explanation
Indices: 2632671--2632700 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2632661 TTAATTCATT
2632671 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2632701 GATGAGATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2633243 original size:31 final size:30
Alignment explanation
Indices: 2633203--2633262 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
2633193 TTTAAATATG
2633203 TACATTGAATCA-AAATCAAAGCTTCATGTA
1 TACATTGAATCACAAATCAAA-CTTCATGTA
* *
2633233 TACATATGAATTACAATTCAAACTTCATGT
1 TACAT-TGAATCACAAATCAAACTTCATGT
2633263 GTATAATTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 5 0.19
31 14 0.54
32 7 0.27
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (30 bp):
TACATTGAATCACAAATCAAACTTCATGTA
Found at i:2638609 original size:15 final size:15
Alignment explanation
Indices: 2638585--2638616 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2638575 TATGCATGCA
*
2638585 AAATATAAAAGACAT
1 AAATACAAAAGACAT
2638600 AAATACAAAAGACAT
1 AAATACAAAAGACAT
2638615 AA
1 AA
2638617 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:2640386 original size:53 final size:53
Alignment explanation
Indices: 2640328--2640513 Score: 131
Period size: 59 Copynumber: 3.2 Consensus size: 53
2640318 TTTCAAACTC
2640328 ATTTAATAATTTAAAGTTAGTTTAAAGCTTATTTATTATTCAATCATTGTATA
1 ATTTAATAATTTAAAGTTAGTTTAAAGCTTATTTATTATTCAATCATTGTATA
* * ** * * *
2640381 ATTTAATAATATTATTATAGTTTGTGTACAAATTTTATTTATAATAT-AATTATTAAAAATTATA
1 ATTTAATAAT-TTA--A-AGTTAGT-T-TAAAGCTTATTTATTAT-TCAATCATT-----GTATA
*
2640445 TTTATTGTTTTATAATTTAAAGTTAGTTTAAAGCTTATTTATTATTCAATCATTGTATA
1 ---A---TTTAATAATTTAAAGTTAGTTTAAAGCTTATTTATTATTCAATCATTGTATA
2640504 ATTTAATAAT
1 ATTTAATAAT
2640514 ATTATTATAG
Statistics
Matches: 98, Mismatches: 16, Indels: 38
0.64 0.11 0.25
Matches are distributed among these distances:
53 18 0.18
54 3 0.03
56 2 0.02
57 6 0.06
58 1 0.01
59 23 0.23
60 1 0.01
63 1 0.01
64 23 0.23
65 1 0.01
66 6 0.06
67 2 0.02
69 3 0.03
70 8 0.08
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (53 bp):
ATTTAATAATTTAAAGTTAGTTTAAAGCTTATTTATTATTCAATCATTGTATA
Found at i:2640420 original size:59 final size:59
Alignment explanation
Indices: 2640356--2640545 Score: 179
Period size: 59 Copynumber: 3.1 Consensus size: 59
2640346 AGTTTAAAGC
2640356 TTATTTATTATTCAATCATTGTATAATTTAATAATATTATTATAGTTTGTGTACAAATT
1 TTATTTATTATTCAATCATTGTATAATTTAATAATATTATTATAGTTTGTGTACAAATT
* * * * * * * * **
2640415 TTATTTATAATAT-AATTATT-AAAAATTATATTTAT-TGTTTTATAATTTAAAGTTAGTTTAAA
1 TTATTTATTAT-TCAATCATTGTATAATT-TAATAATAT-TATTATAGTTT---G-T-GTACAAA
**
2640477 GC
58 TT
2640479 TTATTTATTATTCAATCATTGTATAATTTAATAATATTATTATAGTTTGTGTACAAATT
1 TTATTTATTATTCAATCATTGTATAATTTAATAATATTATTATAGTTTGTGTACAAATT
2640538 TTATTTAT
1 TTATTTAT
2640546 AATATAATTA
Statistics
Matches: 96, Mismatches: 24, Indels: 22
0.68 0.17 0.15
Matches are distributed among these distances:
58 6 0.06
59 43 0.45
60 2 0.02
61 1 0.01
62 1 0.01
63 2 0.02
64 35 0.36
65 6 0.06
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (59 bp):
TTATTTATTATTCAATCATTGTATAATTTAATAATATTATTATAGTTTGTGTACAAATT
Found at i:2640471 original size:123 final size:124
Alignment explanation
Indices: 2640333--2640582 Score: 493
Period size: 123 Copynumber: 2.0 Consensus size: 124
2640323 AACTCATTTA
2640333 ATAATTTAAAGTTAGTTTAAAGCTTATTTATTATTCAATCATTGTATAATTTAATAATATTATTA
1 ATAATTTAAAGTTAGTTTAAAGCTTATTTATTATTCAATCATTGTATAATTTAATAATATTATTA
2640398 TAGTTTGTGTACAAATTTTATTTATAATATAATTATTAAAAATTATA-TTTATTGTTTT
66 TAGTTTGTGTACAAATTTTATTTATAATATAATTATTAAAAATTATATTTTATTGTTTT
2640456 ATAATTTAAAGTTAGTTTAAAGCTTATTTATTATTCAATCATTGTATAATTTAATAATATTATTA
1 ATAATTTAAAGTTAGTTTAAAGCTTATTTATTATTCAATCATTGTATAATTTAATAATATTATTA
2640521 TAGTTTGTGTACAAATTTTATTTATAATATAATTATTAAAAATTATATTTTATTGTTTT
66 TAGTTTGTGTACAAATTTTATTTATAATATAATTATTAAAAATTATATTTTATTGTTTT
2640580 ATA
1 ATA
2640583 TCGAAAAAAT
Statistics
Matches: 126, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
123 112 0.89
124 14 0.11
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.52
Consensus pattern (124 bp):
ATAATTTAAAGTTAGTTTAAAGCTTATTTATTATTCAATCATTGTATAATTTAATAATATTATTA
TAGTTTGTGTACAAATTTTATTTATAATATAATTATTAAAAATTATATTTTATTGTTTT
Found at i:2640522 original size:64 final size:64
Alignment explanation
Indices: 2640333--2640522 Score: 189
Period size: 64 Copynumber: 3.0 Consensus size: 64
2640323 AACTCATTTA
2640333 ATAATTTAAAGTTAGTTTAAAGCTTATTTATTATTCAATCATTGTATAATTTAATAATATTATT
1 ATAATTTAAAGTTAGTTTAAAGCTTATTTATTATTCAATCATTGTATAATTTAATAATATTATT
* ** ** * * * * * * *
2640397 ATAGTTT---G-T-GTACAAATTTTATTTATAATAT-AATTATT-AAAAATTATATTTAT-TGTT
1 ATAATTTAAAGTTAGTTTAAAGCTTATTTATTAT-TCAATCATTGTATAATT-TAATAATAT-TA
2640454 TT
63 TT
2640456 ATAATTTAAAGTTAGTTTAAAGCTTATTTATTATTCAATCATTGTATAATTTAATAATATTATT
1 ATAATTTAAAGTTAGTTTAAAGCTTATTTATTATTCAATCATTGTATAATTTAATAATATTATT
2640520 ATA
1 ATA
2640523 GTTTGTGTAC
Statistics
Matches: 91, Mismatches: 24, Indels: 22
0.66 0.18 0.16
Matches are distributed among these distances:
58 6 0.07
59 35 0.38
60 2 0.02
61 1 0.01
62 1 0.01
63 2 0.02
64 38 0.42
65 6 0.07
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (64 bp):
ATAATTTAAAGTTAGTTTAAAGCTTATTTATTATTCAATCATTGTATAATTTAATAATATTATT
Found at i:2642066 original size:13 final size:13
Alignment explanation
Indices: 2642031--2642068 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
2642021 TTTTTATGTA
2642031 AAATCTAAAAAAT
1 AAATCTAAAAAAT
*
2642044 GAAT-TAAAAAATT
1 AAATCTAAAAAA-T
2642057 AAATCTAAAAAA
1 AAATCTAAAAAA
2642069 ATATAGATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 7 0.33
13 7 0.33
14 7 0.33
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (13 bp):
AAATCTAAAAAAT
Found at i:2647541 original size:18 final size:18
Alignment explanation
Indices: 2647518--2647561 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
2647508 CTATTCACCT
2647518 AACCCAATTATCC-AACCC
1 AACCCAATTA-CCTAACCC
2647536 AACCCAATTACCTAACCC
1 AACCCAATTACCTAACCC
2647554 AACCCAAT
1 AACCCAAT
2647562 CATAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.16
Consensus pattern (18 bp):
AACCCAATTACCTAACCC
Found at i:2647729 original size:18 final size:18
Alignment explanation
Indices: 2647678--2647731 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
2647668 ATTATATAGT
*
2647678 GATTCAATTCGGTTAATTC
1 GATT-AATTCGGGTAATTC
** **
2647697 GGGTAATTCATGTAATTC
1 GATTAATTCGGGTAATTC
2647715 GATTAATTCGGGTAATT
1 GATTAATTCGGGTAATT
2647732 TTTAACCAAA
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
18 24 0.92
19 2 0.08
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (18 bp):
GATTAATTCGGGTAATTC
Found at i:2654050 original size:53 final size:52
Alignment explanation
Indices: 2653961--2654078 Score: 141
Period size: 54 Copynumber: 2.2 Consensus size: 52
2653951 TTTTTTTTTG
* * *
2653961 TTTTTTAAAAAAACGAAATTTTCGAACACGAAAA-TTTT-AGAAATACGAATT
1 TTTTTTTAAAAAACGAAATTTTCGAACACGAAAATTTTTCA-AAACACAAATT
* * *
2654012 TTTTTTTAAAACACGACAATTTTTGAAACACGATAATTTTTCAAAACACAAATT
1 TTTTTTTAAAAAACGA-AATTTTCG-AACACGAAAATTTTTCAAAACACAAATT
2654066 TTTTTTTAAAAAA
1 TTTTTTTAAAAAA
2654079 AAACATGACA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
51 14 0.25
52 7 0.12
53 9 0.16
54 25 0.45
55 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (52 bp):
TTTTTTTAAAAAACGAAATTTTCGAACACGAAAATTTTTCAAAACACAAATT
Found at i:2654051 original size:16 final size:17
Alignment explanation
Indices: 2654014--2654068 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
2654004 TACGAATTTT
2654014 TTTTTAAAACACGACAA
1 TTTTTAAAACACGACAA
* *
2654031 TTTTTGAAACACGATAA
1 TTTTTAAAACACGACAA
2654048 TTTTTCAAAACAC-A-AA
1 TTTTT-AAAACACGACAA
2654064 TTTTT
1 TTTTT
2654069 TTTTAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 7 0.21
17 21 0.62
18 6 0.18
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (17 bp):
TTTTTAAAACACGACAA
Found at i:2654052 original size:36 final size:34
Alignment explanation
Indices: 2653985--2654068 Score: 82
Period size: 36 Copynumber: 2.4 Consensus size: 34
2653975 GAAATTTTCG
* * * *
2653985 AACACGAAAATTTTAGAAATACGAATTTTTTTTTAA
1 AACACG-AAATTTTTGAAACACGAA-TATTTTTCAA
2654021 AACACGACAATTTTTGAAACACG-ATAATTTTTCAA
1 AACACGA-AATTTTTGAAACACGAAT-ATTTTTCAA
2654056 AACAC-AAATTTTT
1 AACACGAAATTTTT
2654069 TTTTAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
33 7 0.17
34 2 0.05
35 14 0.33
36 19 0.45
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (34 bp):
AACACGAAATTTTTGAAACACGAATATTTTTCAA
Found at i:2654181 original size:18 final size:18
Alignment explanation
Indices: 2654110--2654332 Score: 178
Period size: 17 Copynumber: 12.7 Consensus size: 18
2654100 ACTAGAGTCA
* *
2654110 TTGAAAACATGGAAATTT
1 TTGAAAACACGAAAATTT
* *
2654128 GTGAAAA-ACGAAATTTT
1 TTGAAAACACGAAAATTT
* *
2654145 TTG-AAGCAC-AGAATTTT
1 TTGAAAACACGA-AAATTT
2654162 TTAGAAAACACGAAAA-TT
1 TT-GAAAACACGAAAATTT
***
2654180 TTGAAAACACGTGGATTT
1 TTGAAAACACGAAAATTT
**
2654198 TTG-AAACACGAATTTTTT
1 TTGAAAACACGAA-AATTT
*
2654216 TTGAAAATACGAAAATTT
1 TTGAAAACACGAAAATTT
2654234 TTGAAAACAC-ATAAATTT
1 TTGAAAACACGA-AAATTT
* **
2654252 TT-AAAACTCGGGAATTT
1 TTGAAAACACGAAAATTT
2654269 TTG-AAACACTG-AAATTT
1 TTGAAAACAC-GAAAATTT
*
2654286 TTGAAAACACGAGAATTT
1 TTGAAAACACGAAAATTT
*
2654304 TTTAAAACACGAAAATTT
1 TTGAAAACACGAAAATTT
2654322 TTG-AAACACGA
1 TTGAAAACACGA
2654333 GAAAAAATTT
Statistics
Matches: 163, Mismatches: 28, Indels: 29
0.74 0.13 0.13
Matches are distributed among these distances:
16 3 0.02
17 72 0.44
18 72 0.44
19 15 0.09
20 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32
Consensus pattern (18 bp):
TTGAAAACACGAAAATTT
Found at i:2654187 original size:17 final size:17
Alignment explanation
Indices: 2654110--2654332 Score: 170
Period size: 18 Copynumber: 12.7 Consensus size: 17
2654100 ACTAGAGTCA
*
2654110 TTGAAAACATGGAAATTT
1 TTGAAAACA-CGAAATTT
*
2654128 GTGAAAA-ACGAAATTTT
1 TTGAAAACACGAAA-TTT
* *
2654145 TTG-AAGCACAGAATTTT
1 TTGAAAACAC-GAAATTT
*
2654162 TTAGAAAACACGAAAATT
1 TT-GAAAACACGAAATTT
**
2654180 TTGAAAACACGTGGATTT
1 TTGAAAACACG-AAATTT
*
2654198 TTG-AAACACGAATTTTTT
1 TTGAAAACACGAA--ATTT
*
2654216 TTGAAAATACGAAAATTT
1 TTGAAAACACG-AAATTT
*
2654234 TTGAAAACACATAAATTT
1 TTGAAAACAC-GAAATTT
* *
2654252 TT-AAAACTCGGGAATTT
1 TTGAAAACAC-GAAATTT
2654269 TTG-AAACACTGAAATTT
1 TTGAAAACAC-GAAATTT
2654286 TTGAAAACACGAGAATTT
1 TTGAAAACACGA-AATTT
*
2654304 TTTAAAACACGAAAATTT
1 TTGAAAACACG-AAATTT
2654322 TTG-AAACACGA
1 TTGAAAACACGA
2654333 GAAAAAATTT
Statistics
Matches: 163, Mismatches: 27, Indels: 32
0.73 0.12 0.14
Matches are distributed among these distances:
16 7 0.04
17 65 0.40
18 77 0.47
19 12 0.07
20 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32
Consensus pattern (17 bp):
TTGAAAACACGAAATTT
Found at i:2654199 original size:53 final size:54
Alignment explanation
Indices: 2654142--2654332 Score: 157
Period size: 53 Copynumber: 3.6 Consensus size: 54
2654132 AAAACGAAAT
*
2654142 TTTTTGAAGCACAGAA-TTTTTTAGAAAACACGAAAA-TTTTGAAAACACGTGGA
1 TTTTTGAAACAC-GAATTTTTTTAGAAAACACGAAAATTTTTGAAAACACGTGGA
* * * **
2654195 TTTTTGAAACACGAATTTTTTTTGAAAATACGAAAATTTTTGAAAACACATAAA
1 TTTTTGAAACACGAATTTTTTTAGAAAACACGAAAATTTTTGAAAACACGTGGA
* * * *
2654249 TTTTTAAAACTCGGGAA--TTTTT-G-AAACACTG-AAATTTTTGAAAACACGAGAA
1 TTTTTGAAACAC--GAATTTTTTTAGAAAACAC-GAAAATTTTTGAAAACACGTGGA
* **
2654301 TTTTTTAAAACACGAAAATTTTT-G-AAACACGA
1 -TTTTTGAAACACGAATTTTTTTAGAAAACACGA
2654333 GAAAAAATTT
Statistics
Matches: 116, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
51 3 0.03
52 27 0.23
53 54 0.47
54 29 0.25
56 3 0.03
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (54 bp):
TTTTTGAAACACGAATTTTTTTAGAAAACACGAAAATTTTTGAAAACACGTGGA
Found at i:2654670 original size:6 final size:6
Alignment explanation
Indices: 2654650--2654699 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
2654640 AAAAGTATTC
* *
2654650 AAAA-T AAAA-T AAAATT AAAATT -GAATT AAATTT AAAATTT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAA-TT AAAATT
2654696 AAAA
1 AAAA
2654700 ATATAAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
5 13 0.34
6 19 0.50
7 6 0.16
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:2654748 original size:26 final size:25
Alignment explanation
Indices: 2654704--2654760 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
2654694 TTAAAAATAT
* *
2654704 AAATACAAAAATATAAAAATGCACA
1 AAATACAAAAATATAAAAATGAAAA
* *
2654729 AAATACTAATAATATTAAAATGAAAA
1 AAATAC-AAAAATATAAAAATGAAAA
2654755 AAATAC
1 AAATAC
2654761 GAGCATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.21
Consensus pattern (25 bp):
AAATACAAAAATATAAAAATGAAAA
Found at i:2654878 original size:17 final size:17
Alignment explanation
Indices: 2654858--2654899 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2654848 TTTTTTTCCC
*
2654858 TTTTTTCTTTTCTCTCT
1 TTTTTTCTTCTCTCTCT
* *
2654875 TTTTTTCTTCTCTTTTT
1 TTTTTTCTTCTCTCTCT
2654892 TTTTTTCT
1 TTTTTTCT
2654900 GGCCTGCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTCTTCTCTCTCT
Found at i:2654889 original size:29 final size:28
Alignment explanation
Indices: 2654845--2654899 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
2654835 CAAATTGAAC
2654845 CTTTTTTTTTCCCTTTTTTCTTTTCTCT
1 CTTTTTTTTTCCCTTTTTTCTTTTCTCT
* *
2654873 CTTTTTTTCTTCTCTTTTTTTTTTTCT
1 CTTTTTTT-TTCCCTTTTTTCTTTTCT
2654900 GGCCTGCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (28 bp):
CTTTTTTTTTCCCTTTTTTCTTTTCTCT
Found at i:2655124 original size:7 final size:7
Alignment explanation
Indices: 2655112--2655166 Score: 74
Period size: 7 Copynumber: 7.6 Consensus size: 7
2655102 TATTTATTTA
2655112 TTTTTCT
1 TTTTTCT
2655119 TTTTTCT
1 TTTTTCT
2655126 TTTTTCT
1 TTTTTCT
*
2655133 TTCTTCTT
1 TTTTTC-T
2655141 TTTCTTCT
1 TTT-TTCT
2655149 TTTTTCT
1 TTTTTCT
*
2655156 TTCTTCT
1 TTTTTCT
2655163 TTTT
1 TTTT
2655167 CTTCTTCCCC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
7 32 0.76
8 7 0.17
9 3 0.07
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:2655144 original size:9 final size:9
Alignment explanation
Indices: 2655132--2655172 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
2655122 TTCTTTTTTC
2655132 TTTCTTCTT
1 TTTCTTCTT
2655141 TTTCTTC-T
1 TTTCTTCTT
2655149 TTT-TTC--
1 TTTCTTCTT
2655155 TTTCTTCTT
1 TTTCTTCTT
2655164 TTTCTTCTT
1 TTTCTTCTT
2655173 CCCCGTTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 3 0.10
7 6 0.21
8 4 0.14
9 16 0.55
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTCTTCTT
Found at i:2655152 original size:23 final size:23
Alignment explanation
Indices: 2655118--2655172 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
2655108 TTTATTTTTC
2655118 TTTT-TTCTTTTTTCTTTCTTCT
1 TTTTCTTCTTTTTTCTTTCTTCT
2655140 TTTTCTTCTTTTTTCTTTCTTCT
1 TTTTCTTCTTTTTTCTTTCTTCT
2655163 TTTTCTTCTT
1 TTTTCTTCTT
2655173 CCCCGTTCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.12
23 28 0.88
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTCTTCTTTTTTCTTTCTTCT
Found at i:2655169 original size:20 final size:21
Alignment explanation
Indices: 2655098--2655166 Score: 86
Period size: 23 Copynumber: 3.2 Consensus size: 21
2655088 CCCGACTGAA
* *
2655098 TTTTTATTTATTTATTT-TTCT
1 TTTTTCTTT-TTTCTTTCTTCT
2655119 TTTTTCTTTTTTCTTTCTTCTT
1 TTTTTCTTTTTTCTTTCTTC-T
2655141 TTTCTTCTTTTTTCTTTCTTCT
1 TTT-TTCTTTTTTCTTTCTTCT
2655163 TTTT
1 TTTT
2655167 CTTCTTCCCC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.14
21 12 0.28
22 8 0.19
23 17 0.40
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTCTTTTTTCTTTCTTCT
Found at i:2655287 original size:17 final size:17
Alignment explanation
Indices: 2655255--2655331 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 17
2655245 ACGCTCCTCC
2655255 CTTTTCTTTCTCTTCTTTT
1 CTTTT-TTT-TCTTCTTTT
2655274 CTTTTTTTTCTTC--TT
1 CTTTTTTTTCTTCTTTT
*
2655289 -TGTTTTTTCTTGCTTGTT
1 CTTTTTTTTCTT-CTT-TT
*
2655307 GTTGTTTTTTCTT-TCTTT
1 CTT-TTTTTTCTTCT-TTT
2655325 CTTTTTT
1 CTTTTTT
2655332 ATTTTTGCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
14 10 0.21
15 3 0.06
17 9 0.19
18 10 0.21
19 7 0.15
20 9 0.19
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (17 bp):
CTTTTTTTTCTTCTTTT
Found at i:2655336 original size:20 final size:19
Alignment explanation
Indices: 2655256--2655328 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 19
2655246 CGCTCCTCCC
2655256 TTTTCTTTCTCTTCTTT-TCT
1 TTTTCTTTCT-TTCTTTGT-T
2655276 TTTT-TTTC-TTCTTTGTT
1 TTTTCTTTCTTTCTTTGTT
*
2655293 TTTTCTTGCTTGT-TGTTGTT
1 TTTTCTTTCTT-TCT-TTGTT
2655313 TTTTCTTTCTTTCTTT
1 TTTTCTTTCTTTCTTT
2655329 TTTATTTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
17 11 0.24
18 4 0.09
19 9 0.20
20 21 0.47
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (19 bp):
TTTTCTTTCTTTCTTTGTT
Found at i:2655688 original size:30 final size:30
Alignment explanation
Indices: 2655654--2655802 Score: 169
Period size: 30 Copynumber: 5.0 Consensus size: 30
2655644 GGGCCGAAAC
* * *
2655654 GTAATTTTGAGAAAGTTAAAGGGTTCAAAT
1 GTAATTTTAAGAAAGTTTAAGGGTTAAAAT
* *
2655684 GTAATTTCAAGAAAGTTTAAGGGTCAAAAT
1 GTAATTTTAAGAAAGTTTAAGGGTTAAAAT
* * *
2655714 GTAA-TTT-AGAAAAGTTTAGGGGTTGAACT
1 GTAATTTTAAG-AAAGTTTAAGGGTTAAAAT
*
2655743 GTAATTTTAAGAAAGTTTAGGGGTTAAAAT
1 GTAATTTTAAGAAAGTTTAAGGGTTAAAAT
*
2655773 GCAATTTT-AGAAAAGTTTAAGGGTTAAAAT
1 GTAATTTTAAG-AAAGTTTAAGGGTTAAAAT
2655803 ACAAAAAAAT
Statistics
Matches: 101, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.02
29 23 0.23
30 74 0.73
31 2 0.02
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (30 bp):
GTAATTTTAAGAAAGTTTAAGGGTTAAAAT
Found at i:2655737 original size:59 final size:59
Alignment explanation
Indices: 2655654--2655802 Score: 190
Period size: 59 Copynumber: 2.5 Consensus size: 59
2655644 GGGCCGAAAC
* * *
2655654 GTAATTTTGAGAAAGTTAAAGGGTTCAAATGTAATTTCAAGAAAGTTTAAGGGTCAAAAT
1 GTAATTTAGA-AAAGTTTAAGGGTTAAAATGTAATTTCAAGAAAGTTTAAGGGTCAAAAT
* * * * * *
2655714 GTAATTTAGAAAAGTTTAGGGGTTGAACTGTAATTTTAAGAAAGTTTAGGGGTTAAAAT
1 GTAATTTAGAAAAGTTTAAGGGTTAAAATGTAATTTCAAGAAAGTTTAAGGGTCAAAAT
*
2655773 GCAATTTTAGAAAAGTTTAAGGGTTAAAAT
1 GTAA-TTTAGAAAAGTTTAAGGGTTAAAAT
2655803 ACAAAAAAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
59 45 0.59
60 31 0.41
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (59 bp):
GTAATTTAGAAAAGTTTAAGGGTTAAAATGTAATTTCAAGAAAGTTTAAGGGTCAAAAT
Found at i:2657508 original size:27 final size:28
Alignment explanation
Indices: 2657467--2657536 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
2657457 TTTGTAATAT
*
2657467 ATATTGTCAAATGAGCATA-GTCTAGGCG
1 ATATTGGC-AATGAGCATAGGTCTAGGCG
* *
2657495 ATATTGGCAATGAGGATAGGTGTAGGCG
1 ATATTGGCAATGAGCATAGGTCTAGGCG
2657523 ATATTGGCAATGAG
1 ATATTGGCAATGAG
2657537 TGCATTGGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 9 0.24
28 29 0.76
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.27
Consensus pattern (28 bp):
ATATTGGCAATGAGCATAGGTCTAGGCG
Found at i:2664170 original size:14 final size:12
Alignment explanation
Indices: 2664142--2664174 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2664132 TGTGAAACCC
2664142 ATATATTTTGGT
1 ATATATTTTGGT
*
2664154 ATATATTTTGGG
1 ATATATTTTGGT
2664166 ATATATTTT
1 ATATATTTT
2664175 AAAGTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (12 bp):
ATATATTTTGGT
Found at i:2664203 original size:19 final size:19
Alignment explanation
Indices: 2664179--2664219 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2664169 TATTTTAAAG
2664179 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
2664198 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
2664217 TTA
1 TTA
2664220 GAATAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (19 bp):
TTATTTAGGTAGATAAATC
Found at i:2664310 original size:41 final size:41
Alignment explanation
Indices: 2664258--2664336 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
2664248 TATTTTATTT
2664258 TATCATTTAGTAGTTTATTAGAATAAGGAAATTATTTTCCG
1 TATCATTTAGTAGTTTATTAGAATAAGGAAATTATTTTCCG
* *
2664299 TATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTT
1 TATCATTTAGTAGTTTATTAGAATAAGGAAATTATTTT
2664337 TCTAATTAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (41 bp):
TATCATTTAGTAGTTTATTAGAATAAGGAAATTATTTTCCG
Found at i:2681028 original size:1 final size:1
Alignment explanation
Indices: 2681024--2681055 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
2681014 ATTTGGTTCC
*
2681024 TTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2681056 GAACCAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:2681074 original size:1 final size:1
Alignment explanation
Indices: 2681070--2681105 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
2681060 CAATAGTTCA
*
2681070 TTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2681106 GCCTTTGTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:2685534 original size:11 final size:11
Alignment explanation
Indices: 2685518--2685554 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2685508 AAGCCCATTT
2685518 TATTTTTTTAA
1 TATTTTTTTAA
2685529 TATTTTTTT-A
1 TATTTTTTTAA
2685539 T-TTTATTTTAA
1 TATTT-TTTTAA
2685550 TATTT
1 TATTT
2685555 AATAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 3 0.13
10 6 0.26
11 11 0.48
12 3 0.13
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TATTTTTTTAA
Found at i:2685539 original size:19 final size:21
Alignment explanation
Indices: 2685515--2685554 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2685505 CCAAAGCCCA
2685515 TTTTA-TTT-TTTTAATATTT
1 TTTTATTTTATTTTAATATTT
2685534 TTTTATTTTATTTTAATATTT
1 TTTTATTTTATTTTAATATTT
2685555 AATAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 3 0.16
21 11 0.58
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTATTTTATTTTAATATTT
Found at i:2685562 original size:21 final size:21
Alignment explanation
Indices: 2685523--2685565 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2685513 CATTTTATTT
** *
2685523 TTTTAATATTTTTTTATTTTA
1 TTTTAATATTTAATAATTTTA
2685544 TTTTAATATTTAATAATTTTA
1 TTTTAATATTTAATAATTTTA
2685565 T
1 T
2685566 ACAGTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTAATATTTAATAATTTTA
Found at i:2692384 original size:20 final size:18
Alignment explanation
Indices: 2692359--2692414 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 18
2692349 TAAAAAATAT
*
2692359 TTTTAAAAATTGTTATAAAA
1 TTTTAAAAATT-AT-TAAAA
2692379 TTTTAAAACATTATTAAAA
1 TTTTAAAA-ATTATTAAAA
2692398 TTTATAAAAA-TATTAAA
1 TTT-TAAAAATTATTAAA
2692415 TAAAGTTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 7 0.21
19 9 0.27
20 14 0.42
21 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
TTTTAAAAATTATTAAAA
Found at i:2692395 original size:11 final size:9
Alignment explanation
Indices: 2692359--2692414 Score: 51
Period size: 10 Copynumber: 5.8 Consensus size: 9
2692349 TAAAAAATAT
2692359 TTTTAAAAA
1 TTTTAAAAA
2692368 TTGTTATAAAA
1 TT-TTA-AAAA
2692379 TTTTAAAACA
1 TTTTAAAA-A
2692389 TTATT-AAAA
1 TT-TTAAAAA
2692398 TTTATAAAAA
1 TTT-TAAAAA
*
2692408 TATTAAA
1 TTTTAAA
2692415 TAAAGTTCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
8 1 0.03
9 13 0.32
10 18 0.45
11 8 0.20
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:2692401 original size:18 final size:19
Alignment explanation
Indices: 2692374--2692414 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
2692364 AAAATTGTTA
*
2692374 TAAAATTTTA-AAACATTAT
1 TAAAATTTTATAAA-AATAT
2692393 TAAAA-TTTATAAAAATAT
1 TAAAATTTTATAAAAATAT
2692411 TAAA
1 TAAA
2692415 TAAAGTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAATTTTATAAAAATAT
Found at i:2692412 original size:21 final size:19
Alignment explanation
Indices: 2692359--2692412 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
2692349 TAAAAAATAT
*
2692359 TTTTAAAAATTGTTATAAAA
1 TTTTAAAAA-TATTATAAAA
*
2692379 TTTT-AAAACATTATTAAAA
1 TTTTAAAAATATTA-TAAAA
2692398 TTTATAAAAATATTA
1 TTT-TAAAAATATTA
2692413 AATAAAGTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.11
19 12 0.43
20 5 0.18
21 8 0.29
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
TTTTAAAAATATTATAAAA
Found at i:2692878 original size:20 final size:21
Alignment explanation
Indices: 2692840--2692881 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2692830 CAATAAAAAA
*
2692840 TAAACATTTCTTTTAATTTTT
1 TAAAAATTTCTTTTAATTTTT
*
2692861 TAAAAATTT-TTTTGATTTTT
1 TAAAAATTTCTTTTAATTTTT
2692881 T
1 T
2692882 TTCTTGACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (21 bp):
TAAAAATTTCTTTTAATTTTT
Found at i:2695239 original size:4 final size:4
Alignment explanation
Indices: 2695224--2695262 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
2695214 TAAAAGCGGC
* *
2695224 TGTA TTTA TGTA TGTA TGTA TGTA TGTG TGTA TTGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -TGTA TG
2695263 CTGAGTTGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.54
Consensus pattern (4 bp):
TGTA
Found at i:2695394 original size:4 final size:4
Alignment explanation
Indices: 2695385--2695455 Score: 97
Period size: 4 Copynumber: 17.8 Consensus size: 4
2695375 TAAAAGCAGC
* *
2695385 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGCA TGTA TGTA TGCA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* **
2695433 TATA TGTA TGTA CATA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGT
2695456 GTATGCGTGT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.27, C:0.04, G:0.23, T:0.46
Consensus pattern (4 bp):
TGTA
Found at i:2700252 original size:14 final size:14
Alignment explanation
Indices: 2700233--2700262 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2700223 AGAAGAGACG
2700233 TGCTAAAAGTAGCA
1 TGCTAAAAGTAGCA
2700247 TGCTAAAAGTAGCA
1 TGCTAAAAGTAGCA
2700261 TG
1 TG
2700263 GAGGACTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (14 bp):
TGCTAAAAGTAGCA
Found at i:2702177 original size:43 final size:43
Alignment explanation
Indices: 2702059--2702192 Score: 121
Period size: 43 Copynumber: 3.2 Consensus size: 43
2702049 CTGGCATAGC
**
2702059 AGTGCATGATTAGAT-AACCGAAAG-AAAGATACTGGCACAAAT
1 AGTGCATGATTAGATAAACCG-AAGCAATCATACTGGCACAAAT
* * * * * * * * *
2702101 AGTGCATCATCAGACAATCTGAAACAGTTATACTGGCACACAT
1 AGTGCATGATTAGATAAACCGAAGCAATCATACTGGCACAAAT
* *
2702144 AGTGCATGATTGGATAAACCGAAGCAATCATACTGGCACATA-
1 AGTGCATGATTAGATAAACCGAAGCAATCATACTGGCACAAAT
2702186 AGTGCAT
1 AGTGCAT
2702193 CATCGAATTT
Statistics
Matches: 70, Mismatches: 20, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
42 21 0.30
43 49 0.70
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.22
Consensus pattern (43 bp):
AGTGCATGATTAGATAAACCGAAGCAATCATACTGGCACAAAT
Found at i:2702211 original size:42 final size:42
Alignment explanation
Indices: 2702138--2702366 Score: 144
Period size: 42 Copynumber: 5.4 Consensus size: 42
2702128 TTATACTGGC
* ** *
2702138 ACACAT-AGTGCATGATTGGATAAACCGAAGCAATCATACTG
1 ACACATAAGTGCATCATCAGATAAACCAAAGCAATCATACTG
* ** *
2702179 GCACATAAGTGCATCATC-GAATTTACCAAAGCAAAT-ATATTG
1 ACACATAAGTGCATCATCAG-ATAAACCAAAGC-AATCATACTG
* *
2702221 ACACATAAGCTACATCATCAGATAAACCGAAGCAATCATACTG
1 ACACATAAG-TGCATCATCAGATAAACCAAAGCAATCATACTG
* * ** * * * *
2702264 ACACATAAGTGTATAATTGGA-AGTACCAAAGTAAAT-ATATTA
1 ACACATAAGTGCATCATCAGATA-AACCAAAG-CAATCATACTG
* * * ** **
2702306 ACACACGAGGCGCATCATTGGATAAACTGAAGCAATCATACTG
1 ACACA-TAAGTGCATCATCAGATAAACCAAAGCAATCATACTG
2702349 ACACATAAGTGCATCATC
1 ACACATAAGTGCATCATC
2702367 TAATAGACCG
Statistics
Matches: 139, Mismatches: 38, Indels: 21
0.70 0.19 0.11
Matches are distributed among these distances:
41 7 0.05
42 68 0.49
43 62 0.45
44 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (42 bp):
ACACATAAGTGCATCATCAGATAAACCAAAGCAATCATACTG
Found at i:2702254 original size:43 final size:41
Alignment explanation
Indices: 2702156--2702273 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 41
2702146 TGCATGATTG
* *
2702156 GATAAACCGAAGCAATCATACTGGCACATAAGTGCATCATC
1 GATAAACCGAAGCAATCATACTGACACATAAGTACATCATC
** * *
2702197 GAATTTACCAAAGCAAAT-ATATTGACACATAAGCTACATCATC
1 G-ATAAACCGAAGC-AATCATACTGACACATAAG-TACATCATC
2702240 AGATAAACCGAAGCAATCATACTGACACATAAGT
1 -GATAAACCGAAGCAATCATACTGACACATAAGT
2702274 GTATAATTGG
Statistics
Matches: 62, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.02
42 26 0.42
43 34 0.55
44 1 0.02
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.21
Consensus pattern (41 bp):
GATAAACCGAAGCAATCATACTGACACATAAGTACATCATC
Found at i:2702381 original size:85 final size:85
Alignment explanation
Indices: 2702146--2702381 Score: 271
Period size: 85 Copynumber: 2.8 Consensus size: 85
2702136 GCACACATAG
* * * ** *
2702146 TGCATGATTGGATAAACCGAAGCAATCATACTGGCACATAAGTGCATCATCGAATTTACCAAAGC
1 TGCATCATTGGATAAACCGAAGCAATCATACTGACACATAAGTGCATCATCTAATAGACCAAAGT
* *
2702211 AAATATATTGACACATAAGC
66 AAATATATTAACACAGAAGC
* ** * * *
2702231 TACATCATCAGATAAACCGAAGCAATCATACTGACACATAAGTGTATAAT-TGGA-AGTACCAAA
1 TGCATCATTGGATAAACCGAAGCAATCATACTGACACATAAGTGCATCATCT-AATAG-ACCAAA
*
2702294 GTAAATATATTAACACACGAGGC
64 GTAAATATATTAACACA-GAAGC
* *
2702317 -GCATCATTGGATAAACTGAAGCAATCATACTGACACATAAGTGCATCATCTAATAGACCGAAGT
1 TGCATCATTGGATAAACCGAAGCAATCATACTGACACATAAGTGCATCATCTAATAGACCAAAGT
2702381 A
66 A
2702382 TAACCCGTAC
Statistics
Matches: 123, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
85 117 0.95
86 6 0.05
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (85 bp):
TGCATCATTGGATAAACCGAAGCAATCATACTGACACATAAGTGCATCATCTAATAGACCAAAGT
AAATATATTAACACAGAAGC
Found at i:2708286 original size:28 final size:25
Alignment explanation
Indices: 2708225--2708287 Score: 63
Period size: 30 Copynumber: 2.3 Consensus size: 25
2708215 ATAGTTGTGT
*
2708225 TTTTATTACTTTCATTTATATACTA
1 TTTTATTACTTTCACTTATATACTA
2708250 TAGTATTATTCCACTTTCACTTATATAGCTA
1 T--T-TTATT--ACTTTCACTTATATA-CTA
2708281 TTTTATT
1 TTTTATT
2708288 TCATTTTTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
25 1 0.03
27 1 0.03
28 10 0.32
29 1 0.03
30 14 0.45
31 4 0.13
ACGTcount: A:0.27, C:0.14, G:0.03, T:0.56
Consensus pattern (25 bp):
TTTTATTACTTTCACTTATATACTA
Found at i:2710541 original size:13 final size:13
Alignment explanation
Indices: 2710504--2710542 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
2710494 AATTTGTTAG
2710504 ATTTTTATATATAT
1 ATTTTTATAT-TAT
*
2710518 ATTTTCAATATTAT
1 ATTTT-TATATTAT
2710532 ATTTTTATATT
1 ATTTTTATATT
2710543 TTTTTTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 5 0.23
14 13 0.59
15 4 0.18
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTTATATTAT
Found at i:2711056 original size:11 final size:11
Alignment explanation
Indices: 2711042--2711070 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2711032 TTTAACTTTC
2711042 TTTCTTTTTTT
1 TTTCTTTTTTT
2711053 TTTCTTTTTTT
1 TTTCTTTTTTT
2711064 TTT-TTTT
1 TTTCTTTT
2711071 CTTTATTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:2711056 original size:15 final size:15
Alignment explanation
Indices: 2711038--2711079 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
2711028 TTCTTTTAAC
*
2711038 TTTCTTTCTTTTTTT
1 TTTCTTTATTTTTTT
*
2711053 TTTCTTTTTTTTTTT
1 TTTCTTTATTTTTTT
2711068 TTTCTTTATTTT
1 TTTCTTTATTTT
2711080 CCATTCTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTCTTTATTTTTTT
Found at i:2711355 original size:23 final size:23
Alignment explanation
Indices: 2711327--2711373 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2711317 AGAGGAAAGT
2711327 TTAAATAACATAAAAGGAAAAAA
1 TTAAATAACATAAAAGGAAAAAA
* *
2711350 TTAAATTACTTAAAAGGAAAAAA
1 TTAAATAACATAAAAGGAAAAAA
2711373 T
1 T
2711374 ATAGGGATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.23
Consensus pattern (23 bp):
TTAAATAACATAAAAGGAAAAAA
Found at i:2712697 original size:57 final size:57
Alignment explanation
Indices: 2712634--2712757 Score: 151
Period size: 59 Copynumber: 2.1 Consensus size: 57
2712624 GATAAAATTG
* * * *
2712634 AATAGTTGGATAACCATTTTGTAAC-TCATATTTAGGTGGCCAAAATAGAAATTTACT
1 AATAGTTGGATAA-CATTTTGTAACTTCATAGTTAGATGACCAAAAAAGAAATTTACT
* * *
2712691 AATAGTTGGATGATATTTTGTAACTTTTCATAGTTAGATGACTAAAAAAGAAATTTACT
1 AATAGTTGGATAACATTTTGTAAC--TTCATAGTTAGATGACCAAAAAAGAAATTTACT
2712750 AATAGTTG
1 AATAGTTG
2712758 ACTGACTACT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
56 10 0.18
57 12 0.21
59 35 0.61
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (57 bp):
AATAGTTGGATAACATTTTGTAACTTCATAGTTAGATGACCAAAAAAGAAATTTACT
Found at i:2713045 original size:2 final size:2
Alignment explanation
Indices: 2713032--2713096 Score: 114
Period size: 2 Copynumber: 33.0 Consensus size: 2
2713022 TGTTTAATCC
*
2713032 CT CT CT CC CT CT CT CT CT CT CT CT CT CT -T CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2713073 CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT
2713097 TTTCGGTTAG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2713950 original size:15 final size:15
Alignment explanation
Indices: 2713932--2713983 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
2713922 AGAGGAAGAG
*
2713932 GAGGAAGTGGAAGTT
1 GAGGAAGTGGAAGTA
* * *
2713947 GAGGAAGAGGTAGAA
1 GAGGAAGTGGAAGTA
2713962 GAGGAAGTGGAAGTA
1 GAGGAAGTGGAAGTA
*
2713977 GAAGAAG
1 GAGGAAG
2713984 AAGAAGAGGA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.46, T:0.12
Consensus pattern (15 bp):
GAGGAAGTGGAAGTA
Found at i:2713955 original size:24 final size:24
Alignment explanation
Indices: 2713923--2713969 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2713913 TGAAGAAATA
*
2713923 GAGGAAGAGG-AGGAAGTGGAAGTT
1 GAGGAAGAGGTA-GAAGAGGAAGTT
2713947 GAGGAAGAGGTAGAAGAGGAAGT
1 GAGGAAGAGGTAGAAGAGGAAGT
2713970 GGAAGTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.49, T:0.11
Consensus pattern (24 bp):
GAGGAAGAGGTAGAAGAGGAAGTT
Found at i:2713966 original size:30 final size:30
Alignment explanation
Indices: 2713922--2713990 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
2713912 ATGAAGAAAT
* * *
2713922 AGAGGAAGAGGAGGAAGTGGAAGTTGAGGA
1 AGAGGAAGAAGAGGAAGTGGAAGTAGAAGA
*
2713952 AGAGGTAGAAGAGGAAGTGGAAGTAGAAGA
1 AGAGGAAGAAGAGGAAGTGGAAGTAGAAGA
*
2713982 AGAAGAAGA
1 AGAGGAAGA
2713991 GGACGAGGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.45, T:0.09
Consensus pattern (30 bp):
AGAGGAAGAAGAGGAAGTGGAAGTAGAAGA
Found at i:2724748 original size:16 final size:17
Alignment explanation
Indices: 2724717--2724749 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2724707 TATGAAAACA
*
2724717 AATTTAAAATTTTATTT
1 AATTGAAAATTTTATTT
2724734 AATTGAAAA-TTTATTT
1 AATTGAAAATTTTATTT
2724750 TTTAAGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AATTGAAAATTTTATTT
Found at i:2752507 original size:18 final size:18
Alignment explanation
Indices: 2752484--2752518 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2752474 ATCGGTTAAA
*
2752484 ATAAAAATATTTAAATTC
1 ATAAAAATAATTAAATTC
*
2752502 ATAAAACTAATTAAATT
1 ATAAAAATAATTAAATT
2752519 ATATATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAAAATAATTAAATTC
Found at i:2752818 original size:33 final size:33
Alignment explanation
Indices: 2752781--2752846 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
2752771 AAATGAAATT
2752781 TTAATTTTAGCTCAATTATACATATACCAACAA
1 TTAATTTTAGCTCAATTATACATATACCAACAA
*
2752814 TTAATTTTAGCTCAATTATACATATACCTACAA
1 TTAATTTTAGCTCAATTATACATATACCAACAA
2752847 ATTTTAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAATTTTAGCTCAATTATACATATACCAACAA
Found at i:2754261 original size:37 final size:37
Alignment explanation
Indices: 2754208--2754282 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
2754198 AACATGCCTC
2754208 AGCACGTAATGATATTGAAAGATGCTTTGGGTTATTA
1 AGCACGTAATGATATTGAAAGATGCTTTGGGTTATTA
*
2754245 AGCACGTAATGTTATTGAAAGATGCTTTGGGTTATTA
1 AGCACGTAATGATATTGAAAGATGCTTTGGGTTATTA
2754282 A
1 A
2754283 AACTTAGATG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (37 bp):
AGCACGTAATGATATTGAAAGATGCTTTGGGTTATTA
Found at i:2754761 original size:49 final size:49
Alignment explanation
Indices: 2754706--2754809 Score: 163
Period size: 49 Copynumber: 2.1 Consensus size: 49
2754696 TCATGTGTTA
* * * *
2754706 TAATTTTATATAGTGTTGAGCTTTTAATTCATGATATTTAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTAATTCATGATATTAAACTTAATTT
*
2754755 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTAATTCATGATATTAAACTTAATTT
2754804 TAATTT
1 TAATTT
2754810 GTTTTTTTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.52
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTAATTCATGATATTAAACTTAATTT
Found at i:2756435 original size:15 final size:16
Alignment explanation
Indices: 2756407--2756436 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2756397 TAAATTCATA
2756407 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
2756423 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
2756437 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:2756854 original size:20 final size:20
Alignment explanation
Indices: 2756814--2756854 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2756804 GTTAAAGTAG
**
2756814 AATTAACTAGAAATATGCAA
1 AATTAACTAGAAATAAACAA
*
2756834 AATTAACTAGAATTAAACAA
1 AATTAACTAGAAATAAACAA
2756854 A
1 A
2756855 TAACAGTATT
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:0.59, C:0.10, G:0.07, T:0.24
Consensus pattern (20 bp):
AATTAACTAGAAATAAACAA
Found at i:2756994 original size:26 final size:26
Alignment explanation
Indices: 2756965--2757018 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2756955 TTTAAAAAAG
*
2756965 TTTGAATCGAGTTGAGT-AAATAGAAA
1 TTTGAATCGAGTTGAATCAAAT-GAAA
* *
2756991 TTTGAGTTGAGTTGAATCAAATGAAA
1 TTTGAATCGAGTTGAATCAAATGAAA
2757017 TT
1 TT
2757019 GTTTGAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (26 bp):
TTTGAATCGAGTTGAATCAAATGAAA
Found at i:2757248 original size:21 final size:18
Alignment explanation
Indices: 2757217--2757282 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 18
2757207 TATTTTAGAT
2757217 TTTTTAAAATTTTTTATATA
1 TTTTT-AAATTTTTTA-ATA
2757237 TTCTTTAGAA-TTTTTAATA
1 TT-TTTA-AATTTTTTAATA
* *
2757256 TTTTTAAATTTCTGTAATT
1 TTTTTAAATTT-TTTAATA
2757275 TTTTTAAA
1 TTTTTAAA
2757283 AAATATACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 2 0.05
18 6 0.15
19 18 0.45
20 9 0.22
21 5 0.12
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTTAAATTTTTTAATA
Found at i:2758100 original size:18 final size:17
Alignment explanation
Indices: 2758067--2758103 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
2758057 ATCCGATCCG
2758067 ATTTAAATATAATTTTA
1 ATTTAAATATAATTTTA
*
2758084 ATTTAAATTTGAATTTTA
1 ATTTAAATAT-AATTTTA
2758102 AT
1 AT
2758104 AAAGGACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTAAATATAATTTTA
Found at i:2761051 original size:22 final size:23
Alignment explanation
Indices: 2761001--2761051 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2760991 TATTCTGCTG
2761001 TTATT-TTACTATCATTTTATTA
1 TTATTATTACTATCATTTTATTA
* *
2761023 TTA-TATTGCTATTATTTTATT-
1 TTATTATTACTATCATTTTATTA
2761044 TTATTATT
1 TTATTATT
2761052 TAGATATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (23 bp):
TTATTATTACTATCATTTTATTA
Found at i:2765832 original size:31 final size:29
Alignment explanation
Indices: 2765794--2765867 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
2765784 ACTACCAAAA
* *
2765794 TAGTCACTTTTGTTTGACTCAGGTTACATTT
1 TAGTCACTTATGTTTGA--AAGGTTACATTT
* *
2765825 TAGTCACTTATGTTTGAAATGTTACGTTT
1 TAGTCACTTATGTTTGAAAGGTTACATTT
2765854 TAGTCACTTATGTT
1 TAGTCACTTATGTT
2765868 ATCACATTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 23 0.59
31 16 0.41
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.49
Consensus pattern (29 bp):
TAGTCACTTATGTTTGAAAGGTTACATTT
Found at i:2765889 original size:31 final size:29
Alignment explanation
Indices: 2765819--2765892 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
2765809 GACTCAGGTT
* *
2765819 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* *
2765848 ACGTTTTAGTCACTTATGTTATCACATTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
2765879 ACATTTTAGTCACT
1 ACATTTTAGTCACT
2765893 GAGCCGTTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 19 0.50
30 2 0.05
31 17 0.45
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:2766500 original size:29 final size:29
Alignment explanation
Indices: 2766453--2766522 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
2766443 CACGATAACG
2766453 TAAGTGACTAAAACATAACATT-TCAAACA
1 TAAGTGACTAAAACATAAC-TTGTCAAACA
**
2766482 TAAGTGACTAAAATGTAACTTGAGTCAAACA
1 TAAGTGACTAAAACATAACTT--GTCAAACA
*
2766513 AAAGTGACTA
1 TAAGTGACTA
2766523 TTTTGATACT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.06
29 17 0.49
31 16 0.46
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.24
Consensus pattern (29 bp):
TAAGTGACTAAAACATAACTTGTCAAACA
Found at i:2768268 original size:3 final size:3
Alignment explanation
Indices: 2768260--2768293 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2768250 ACCTATAACC
2768260 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2768294 GAAGTTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2768347 original size:18 final size:18
Alignment explanation
Indices: 2768312--2768347 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2768302 TAACATTTAA
* *
2768312 AGTGAGATTTTATTATAT
1 AGTGAGATTTCATGATAT
2768330 AGTGAGATTTCATGATAT
1 AGTGAGATTTCATGATAT
2768348 CGTTTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.44
Consensus pattern (18 bp):
AGTGAGATTTCATGATAT
Found at i:2779954 original size:29 final size:30
Alignment explanation
Indices: 2779903--2779959 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
2779893 AGAATTGGAG
* *
2779903 CAAATTAAGATTTCATGTTTAAAATTATTC
1 CAAATTAAGAATTCATGTATAAAATTATTC
2779933 CAAATTAA-AATTCATGTATAAAATTAT
1 CAAATTAAGAATTCATGTATAAAATTAT
2779960 ATATTAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (30 bp):
CAAATTAAGAATTCATGTATAAAATTATTC
Found at i:2789495 original size:122 final size:127
Alignment explanation
Indices: 2789359--2789606 Score: 344
Period size: 122 Copynumber: 2.0 Consensus size: 127
2789349 TACAATACCC
* * *
2789359 TTATAGGACATTTAGTAACCCATTGACTTTGCTTGTGAAGTTTAAAAGTTCCGCTAGTAGTGTAC
1 TTATAGGACATTTAGTAACCCATTGACTTTACTTGTGAAGTTTAAAAGCTCCACTAGTAGTGTAC
*
2789424 AAAATA-TATATTT-TTTA-T-T-TTATTAATAATATTTATTTATTGCTACCGTTATTTATT
66 AAAATATTATATTTCTTTATTATGTTATTAATAATATTTATTTACTGCTACCGTTATTTATT
* * *
2789481 TTATAGGACATTTAGTAACCCCTTGACTTTACTTGTGGAGTTTAAAAGCTCCACTGGTAGTGTAC
1 TTATAGGACATTTAGTAACCCATTGACTTTACTTGTGAAGTTTAAAAGCTCCACTAGTAGTGTAC
* * * *
2789546 TAAATATTTTTTTTCTTTATTTTATGTTATTAATAATATTTATTTACTGCTATCGTTATTT
66 AAAATATTATATTTCTTTA--TTATGTTATTAATAATATTTATTTACTGCTACCGTTATTT
2789607 TTAGATAAAT
Statistics
Matches: 108, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
122 64 0.59
123 5 0.05
124 4 0.04
127 1 0.01
128 1 0.01
129 33 0.31
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (127 bp):
TTATAGGACATTTAGTAACCCATTGACTTTACTTGTGAAGTTTAAAAGCTCCACTAGTAGTGTAC
AAAATATTATATTTCTTTATTATGTTATTAATAATATTTATTTACTGCTACCGTTATTTATT
Found at i:2789946 original size:17 final size:18
Alignment explanation
Indices: 2789918--2789957 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2789908 TTGATTTGAT
2789918 TAAATAAAATAAAATTTA
1 TAAATAAAATAAAATTTA
*
2789936 TAAAT-AAATAAATTTTA
1 TAAATAAAATAAAATTTA
*
2789953 AAAAT
1 TAAAT
2789958 TAGTACTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAATAAAATAAAATTTA
Found at i:2793108 original size:34 final size:35
Alignment explanation
Indices: 2793070--2793136 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
2793060 CAGTAAAATA
*
2793070 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
2793104 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
2793137 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:2793110 original size:20 final size:20
Alignment explanation
Indices: 2793085--2793124 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2793075 CGTAAAATGA
*
2793085 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
2793105 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
2793125 GGAAAATATT
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:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:2793140 original size:14 final size:15
Alignment explanation
Indices: 2793064--2793140 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
2793054 GATTGCCAGT
* *
2793064 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
2793078 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
2793092 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
2793112 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
2793127 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
2793141 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:2793370 original size:22 final size:24
Alignment explanation
Indices: 2793345--2793388 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
2793335 TGAAAAAAAC
2793345 TAATT-AAAAAACAAG-TATTGAA
1 TAATTAAAAAAACAAGTTATTGAA
2793367 TAATTAAAAAAACAAGTTATTG
1 TAATTAAAAAAACAAGTTATTG
2793389 GAAAATCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 10 0.50
24 5 0.25
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.30
Consensus pattern (24 bp):
TAATTAAAAAAACAAGTTATTGAA
Found at i:2795281 original size:16 final size:16
Alignment explanation
Indices: 2795246--2795278 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2795236 ATTTAGATTA
*
2795246 TTAAGTCAAACTAAAT
1 TTAAATCAAACTAAAT
2795262 TTAAATCAAA-TAAAT
1 TTAAATCAAACTAAAT
2795277 TT
1 TT
2795279 TAATATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (16 bp):
TTAAATCAAACTAAAT
Found at i:2809026 original size:262 final size:263
Alignment explanation
Indices: 2808561--2809086 Score: 1045
Period size: 262 Copynumber: 2.0 Consensus size: 263
2808551 CTTGTTTCAC
2808561 TCCACCACCCTCCATGAATTGAAATAAAATATTGTTTATCATGTCAGAAGATATAACAAGTGCTT
1 TCCACCACCCTCCATGAATTGAAATAAAATATTGTTTATCATGTCAGAAGATATAACAAGTGCTT
2808626 TATATTTTCGATATTTATTTAAAATTTTTATGTCAATTTTCTTTGGATACTATATCAATTGTGAT
66 TATATTTTCGATATTTATTTAAAATTTTTATGTCAATTTTCTTTGGATACTATATCAATTGTGAT
2808691 TAGTTTAATATTAACTCACATGTAGAAAAATTAATAATTATAAGTAAATATAATTTTAAAACTAG
131 TAGTTTAATATTAACTCACATGTAGAAAAATTAATAATTATAAGTAAATATAATTTTAAAACTAG
2808756 AACAATAATGGTACCTACCAATACAAATTATAATCTATGACCTATCTAGGCAACAGG-CAGGCTA
196 AACAATAATGGTACCTACCAATACAAATTATAATCTATGACCTATCTAGGCAACAGGTCAGGCTA
2808820 CAA
261 CAA
2808823 TCCACCACCCTCCATGAATTGAAATAAAATATTGTTTATCATGTCAGAAGATATAACAAGTGCTT
1 TCCACCACCCTCCATGAATTGAAATAAAATATTGTTTATCATGTCAGAAGATATAACAAGTGCTT
2808888 TATATTTTCGATATTTATTTAAAATTTTTATGTCAATTTTCTTTGGATACTATATCAATTGTGAT
66 TATATTTTCGATATTTATTTAAAATTTTTATGTCAATTTTCTTTGGATACTATATCAATTGTGAT
2808953 TAGTTTAATATTAACTCACATGTAGAAAAATTAATAATTATAAGTAAATATAATTTTAAAACTAG
131 TAGTTTAATATTAACTCACATGTAGAAAAATTAATAATTATAAGTAAATATAATTTTAAAACTAG
2809018 AACAATAATGGTACCTACCAATACAAATTATAATCTATGACCTATCTAGGCAACAGGTCAGGCTA
196 AACAATAATGGTACCTACCAATACAAATTATAATCTATGACCTATCTAGGCAACAGGTCAGGCTA
2809083 CAA
261 CAA
2809086 T
1 T
2809087 TAAAATATTT
Statistics
Matches: 263, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
262 252 0.96
263 11 0.04
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (263 bp):
TCCACCACCCTCCATGAATTGAAATAAAATATTGTTTATCATGTCAGAAGATATAACAAGTGCTT
TATATTTTCGATATTTATTTAAAATTTTTATGTCAATTTTCTTTGGATACTATATCAATTGTGAT
TAGTTTAATATTAACTCACATGTAGAAAAATTAATAATTATAAGTAAATATAATTTTAAAACTAG
AACAATAATGGTACCTACCAATACAAATTATAATCTATGACCTATCTAGGCAACAGGTCAGGCTA
CAA
Found at i:2810930 original size:18 final size:17
Alignment explanation
Indices: 2810907--2810952 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2810897 CTAATCAAAT
*
2810907 AAATTATAAAAATTTACA
1 AAATTATAAAAAATTA-A
*
2810925 AAATTAGAAAAAATTAA
1 AAATTATAAAAAATTAA
*
2810942 AAATTTTAAAA
1 AAATTATAAAA
2810953 TCGGATTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
AAATTATAAAAAATTAA
Done.