Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 32 of 325
Found at i:9482008 original size:5 final size:5
Alignment explanation
Indices: 9482000--9482026 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
9481990 TTTGTTTTGT
9482000 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
9482027 ATTAAATTAT
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:9482550 original size:44 final size:42
Alignment explanation
Indices: 9482502--9482631 Score: 122
Period size: 43 Copynumber: 3.0 Consensus size: 42
9482492 ATTTAATATA
*
9482502 TTATTGCTATTATTATTATTATGTTTCTATTTATATTTATTTTT
1 TTATT-CTAATATTATTATTAT-TTTCTATTTATATTTATTTTT
* *
9482546 TTATTCTAATACTATTATTATTTATCTAATTTTTATTTATCTATTT
1 TTATTCTAATATTATTATTATTT-TCT-ATTTATATTTAT-T-TTT
* * *
9482592 ATATTTCTACTATTATTA-TA-TTTCTATTTAT-TATATTTTT
1 TTA-TTCTAATATTATTATTATTTTCTATTTATATTTATTTTT
9482632 ATTTCTATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
40 3 0.04
41 1 0.01
42 6 0.08
43 22 0.30
44 19 0.26
45 3 0.04
46 7 0.10
47 12 0.16
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (42 bp):
TTATTCTAATATTATTATTATTTTCTATTTATATTTATTTTT
Found at i:9482560 original size:29 final size:28
Alignment explanation
Indices: 9482511--9482622 Score: 83
Period size: 29 Copynumber: 3.9 Consensus size: 28
9482501 ATTATTGCTA
*
9482511 TTAT-TATTATTATGTT-TCTATTTATAT
1 TTATCTATTTTTAT-TTATCTATTTATAT
9482538 TTAT-T-TTTTTATTCTAATACTA-TTATTAT
1 TTATCTATTTTTATT-T-AT-CTATTTA-TAT
9482567 TTATCTAATTTTTATTTATCTATTTATAT
1 TTATCT-ATTTTTATTTATCTATTTATAT
* *
9482596 TTCTACTATTATTATATT-TCTATTTAT
1 TTAT-CTATTTTTAT-TTATCTATTTAT
9482623 TATATTTTTA
Statistics
Matches: 71, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
25 1 0.01
26 7 0.10
27 5 0.07
28 4 0.06
29 35 0.49
30 10 0.14
31 1 0.01
32 8 0.11
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (28 bp):
TTATCTATTTTTATTTATCTATTTATAT
Found at i:9482612 original size:17 final size:15
Alignment explanation
Indices: 9482517--9482635 Score: 67
Period size: 15 Copynumber: 8.1 Consensus size: 15
9482507 GCTATTATTA
*
9482517 TTATTATGTTTCTAT
1 TTATTATATTTCTAT
*
9482532 TTATATTTATTT-T-T
1 TTAT-TATATTTCTAT
* * *
9482546 TTATTCTAATACTA-
1 TTATTATATTTCTAT
9482560 TTATTAT-TTATCTAAT
1 TTATTATATT-TCT-AT
9482576 TT-TTAT-TTATCTA-
1 TTATTATATT-TCTAT
9482589 -T-TTATATTTCTACT
1 TTATTATATTTCTA-T
9482603 ATTATTATATTTCTAT
1 -TTATTATATTTCTAT
*
9482619 TTATTATATTTTTAT
1 TTATTATATTTCTAT
9482634 TT
1 TT
9482636 CTATTTATAT
Statistics
Matches: 83, Mismatches: 9, Indels: 24
0.72 0.08 0.21
Matches are distributed among these distances:
12 9 0.11
13 7 0.08
14 15 0.18
15 32 0.39
16 9 0.11
17 11 0.13
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (15 bp):
TTATTATATTTCTAT
Found at i:9482634 original size:29 final size:29
Alignment explanation
Indices: 9482509--9482634 Score: 75
Period size: 29 Copynumber: 4.3 Consensus size: 29
9482499 ATATTATTGC
* * *
9482509 TATTATTATTATTATGTTTCTATTTATATT
1 TATTTTTATTATTATATTTCTATTTAT-TA
* * *
9482539 TATTTTT-TTATTCTAATACTA-TTATTA
1 TATTTTTATTATTATATTTCTATTTATTA
* *
9482566 T-TTATCTAATTTTTAT-TTATCTATTTA-TA
1 TATT-T-TTATTATTATATT-TCTATTTATTA
*
9482595 T-TTCTACTATTATTATATTTCTATTTATTA
1 TATT-T-TTATTATTATATTTCTATTTATTA
9482625 TATTTTTATT
1 TATTTTTATT
9482635 TCTATTTATA
Statistics
Matches: 71, Mismatches: 17, Indels: 17
0.68 0.16 0.16
Matches are distributed among these distances:
26 2 0.03
27 3 0.04
28 6 0.08
29 43 0.61
30 15 0.21
31 2 0.03
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (29 bp):
TATTTTTATTATTATATTTCTATTTATTA
Found at i:9482635 original size:44 final size:43
Alignment explanation
Indices: 9482515--9482670 Score: 155
Period size: 44 Copynumber: 3.6 Consensus size: 43
9482505 TTGCTATTAT
9482515 TATTATTATGTTTCTATTTA-TATTTATTT-TTTTATTCTAATAC
1 TATTATTAT-TTTCTATTTATTATTTATTTATTTTATT-TAATAC
* *
9482558 TATTATTATTTATCTAATTT-TTATTTATCTATTTATATTT-CTAC
1 TATTATTATTT-TCT-ATTTATTATTTATTTATTT-TATTTAATAC
9482602 TATTATTATATTTCTATTTATTATATT-TTTATTTCTATTTATATAC
1 TATTATTAT-TTTCTATTTATTAT-TTATTTATTT-TATTTA-ATAC
*
9482648 TAATATTATTTTC-A-TTATTATTT
1 TATTATTATTTTCTATTTATTATTT
9482671 TTCTTATATA
Statistics
Matches: 97, Mismatches: 6, Indels: 21
0.78 0.05 0.17
Matches are distributed among these distances:
42 4 0.04
43 23 0.24
44 43 0.44
45 12 0.12
46 15 0.15
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.65
Consensus pattern (43 bp):
TATTATTATTTTCTATTTATTATTTATTTATTTTATTTAATAC
Found at i:9482679 original size:52 final size:54
Alignment explanation
Indices: 9482558--9482679 Score: 125
Period size: 52 Copynumber: 2.4 Consensus size: 54
9482548 ATTCTAATAC
* * *
9482558 TATTATTATTTATC-TA-ATTTTTATTTATCTATTTATATTTCTACTATTATTA
1 TATTATTATTTTTCTTATATTTTTATTTATCTATTTATATTACTAATATTATTA
* *
9482610 TATT-TCTA--TTTATTATATTTTTA-TT-TCTATTTATA-TACTAATATTATTT
1 TATTAT-TATTTTTCTTATATTTTTATTTATCTATTTATATTACTAATATTATTA
9482659 TCATTATTATTTTTCTTATAT
1 T-ATTATTATTTTTCTTATAT
9482680 ATGTTTTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
49 12 0.21
50 17 0.30
51 6 0.11
52 22 0.39
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (54 bp):
TATTATTATTTTTCTTATATTTTTATTTATCTATTTATATTACTAATATTATTA
Found at i:9482835 original size:25 final size:23
Alignment explanation
Indices: 9482742--9482836 Score: 61
Period size: 25 Copynumber: 3.9 Consensus size: 23
9482732 CATTTTTTGT
*
9482742 TATTATGTATTTTAACTTTTTATA
1 TATTATGTA-TTTAAATTTTTATA
*
9482766 TA--ACGCTCATTTCAAATTTTTATA
1 TATTATG-T-ATTT-AAATTTTTATA
*
9482790 CATTACT-TACTTTAATATTTTTATA
1 TATTA-TGTA-TTTAA-ATTTTTATA
9482815 TATTATGTATTTCAAACTTTTT
1 TATTATGTATTT-AAA-TTTTT
9482837 TTTACACATT
Statistics
Matches: 55, Mismatches: 5, Indels: 21
0.68 0.06 0.26
Matches are distributed among these distances:
22 2 0.04
23 4 0.07
24 22 0.40
25 26 0.47
26 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.56
Consensus pattern (23 bp):
TATTATGTATTTAAATTTTTATA
Found at i:9485477 original size:14 final size:15
Alignment explanation
Indices: 9485458--9485488 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
9485448 TAATATACAT
9485458 AATTGTTCA-ATAAA
1 AATTGTTCATATAAA
9485472 AATTGTTCATATAAA
1 AATTGTTCATATAAA
9485487 AA
1 AA
9485489 AAAGGATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (15 bp):
AATTGTTCATATAAA
Found at i:9487532 original size:15 final size:15
Alignment explanation
Indices: 9487508--9487537 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9487498 GGTATGGAGC
9487508 GATTACGGTAATTGT
1 GATTACGGTAATTGT
*
9487523 GATTATGGTAATTGT
1 GATTACGGTAATTGT
9487538 TTGCCCTATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.27, T:0.43
Consensus pattern (15 bp):
GATTACGGTAATTGT
Found at i:9487703 original size:9 final size:9
Alignment explanation
Indices: 9487685--9487715 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
9487675 ATATTTACTT
9487685 AAAT-TTAA
1 AAATATTAA
9487693 AAATATTAA
1 AAATATTAA
9487702 AAATATTAA
1 AAATATTAA
9487711 AAATA
1 AAATA
9487716 AATAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.18
9 18 0.82
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAATATTAA
Found at i:9488793 original size:13 final size:13
Alignment explanation
Indices: 9488775--9488800 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9488765 TTTTCTTCAT
9488775 TGATTCCTATGTC
1 TGATTCCTATGTC
9488788 TGATTCCTATGTC
1 TGATTCCTATGTC
9488801 ATTAACTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
TGATTCCTATGTC
Found at i:9490609 original size:22 final size:22
Alignment explanation
Indices: 9490584--9490628 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
9490574 ATCTTCTCTC
9490584 TAAAACACCTTTTGACATCTAT
1 TAAAACACCTTTTGACATCTAT
9490606 TAAAACACCTTTTGACATCTAT
1 TAAAACACCTTTTGACATCTAT
9490628 T
1 T
9490629 TTGTTTTACT
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:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (22 bp):
TAAAACACCTTTTGACATCTAT
Found at i:9494652 original size:16 final size:16
Alignment explanation
Indices: 9494611--9494643 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
9494601 AAACCCTGAA
9494611 AACCCG-AAAACAAAG
1 AACCCGAAAAACAAAG
9494626 AACCCGAAAAACAAAG
1 AACCCGAAAAACAAAG
9494642 AA
1 AA
9494644 TCCTCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.64, C:0.24, G:0.12, T:0.00
Consensus pattern (16 bp):
AACCCGAAAAACAAAG
Found at i:9496562 original size:24 final size:24
Alignment explanation
Indices: 9496517--9496563 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
9496507 ATAAAAACTA
*
9496517 AACCCTAAAAACTTGAAAACAAAG
1 AACCCTAAAAACGTGAAAACAAAG
*
9496541 AACCCTCAAAACGT-AAACACAAA
1 AACCCTAAAAACGTGAAA-ACAAA
9496564 ATTCTCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.57, C:0.26, G:0.06, T:0.11
Consensus pattern (24 bp):
AACCCTAAAAACGTGAAAACAAAG
Found at i:9499928 original size:38 final size:38
Alignment explanation
Indices: 9499865--9500053 Score: 220
Period size: 38 Copynumber: 4.9 Consensus size: 38
9499855 ATTTGATGTG
* *
9499865 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGGAATTA
1 TATCCGGG-TTAAA-TCCCGCAGGCT-TCGTGCTGGAATTA
*
9499905 TATCCGGGTTAAATCTCGCAGGCTTCGTGCTGGTAA-TA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGG-AATTA
*
9499943 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGAATTA
* * *
9499981 TATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGAATTA
* * *
9500019 TATCTGAGTTTAAAGTCCCGTAGGCTTCGTGCTGG
1 TATCCG-GGTTAAA-TCCCGCAGGCTTCGTGCTGG
9500054 TGTTATGTTT
Statistics
Matches: 132, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
37 2 0.02
38 92 0.70
39 13 0.10
40 25 0.19
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.30
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGAATTA
Found at i:9502158 original size:3 final size:3
Alignment explanation
Indices: 9502142--9502331 Score: 75
Period size: 3 Copynumber: 63.0 Consensus size: 3
9502132 TATTTATTTC
* * * * *
9502142 TAT TAT TTT CTAT TAT TAT CAT TAT TAA TAT ATAC CAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
* * * *
9502189 TAT TA- TAT TAT TAT TAT TAA TAT TAT CAT TATT TACA TGT TAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TA-T
* * * * * * *** *
9502236 TCT TTT TCT TTT TCT TTT TAT TAT GGC T-T TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
9502283 TAC TAT TTT TAT CT-T TAT TAT TAT TAT CA- TCT TAT T-T TAT TAC
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9502326 TAT TAT
1 TAT TAT
9502332 CAATTTTGTA
Statistics
Matches: 134, Mismatches: 43, Indels: 20
0.68 0.22 0.10
Matches are distributed among these distances:
2 6 0.04
3 117 0.87
4 11 0.08
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:9502324 original size:22 final size:23
Alignment explanation
Indices: 9502291--9502333 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
9502281 ATTACTATTT
*
9502291 TTATCTTTATTATTATTATCATC
1 TTATCTTTATTACTATTATCATC
9502314 TTAT-TTTATTACTATTATCA
1 TTATCTTTATTACTATTATCA
9502334 ATTTTGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (23 bp):
TTATCTTTATTACTATTATCATC
Found at i:9502396 original size:16 final size:18
Alignment explanation
Indices: 9502365--9502397 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
9502355 TTGTATTATT
9502365 TCTATTATTATATTTTCA
1 TCTATTATTATATTTTCA
9502383 TCTA-TATT-TATTTTC
1 TCTATTATTATATTTTC
9502398 TTATTACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (18 bp):
TCTATTATTATATTTTCA
Found at i:9502424 original size:17 final size:17
Alignment explanation
Indices: 9502399--9502437 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
9502389 TTTATTTTCT
*
9502399 TATTACTTATCTATTTA
1 TATTTCTTATCTATTTA
*
9502416 TATTTCTTATTTATTTA
1 TATTTCTTATCTATTTA
9502433 TATTT
1 TATTT
9502438 TTGTTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTCTTATCTATTTA
Found at i:9502462 original size:17 final size:17
Alignment explanation
Indices: 9502430--9502464 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9502420 TCTTATTTAT
* *
9502430 TTATATTTTTGTTATTA
1 TTATATTTTAGGTATTA
9502447 TTATATTTTAGGTATTA
1 TTATATTTTAGGTATTA
9502464 T
1 T
9502465 ATCTCTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (17 bp):
TTATATTTTAGGTATTA
Found at i:9502499 original size:26 final size:26
Alignment explanation
Indices: 9502443--9502500 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
9502433 TATTTTTGTT
9502443 ATTA-TTATATTTTAGGTATTATATC
1 ATTATTTATATTTTAGGTATTATATC
*
9502468 -TCTATTTATA-TTTATGTATTAATATC
1 AT-TATTTATATTTTAGGTATT-ATATC
9502494 ATTATTT
1 ATTATTT
9502501 TACTATTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
24 1 0.04
25 11 0.39
26 15 0.54
27 1 0.04
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (26 bp):
ATTATTTATATTTTAGGTATTATATC
Found at i:9502540 original size:15 final size:15
Alignment explanation
Indices: 9502522--9502551 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9502512 TATTTTTCAC
*
9502522 ACTATTATTATCATT
1 ACTATTACTATCATT
9502537 ACTATTACTATCATT
1 ACTATTACTATCATT
9502552 TTTAATAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (15 bp):
ACTATTACTATCATT
Found at i:9504529 original size:26 final size:26
Alignment explanation
Indices: 9504500--9504581 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
9504490 TGATACAAAT
9504500 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
9504526 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
9504552 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
9504578 TGAT
1 TGAT
9504582 GGAAATTTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:9509525 original size:19 final size:18
Alignment explanation
Indices: 9509501--9509545 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
9509491 TGCCTTTTTT
*
9509501 TTTGCATCCATTTCATTCA
1 TTTGCATACATTTCA-TCA
9509520 TTTGCATTACATTTCATCA
1 TTTGCA-TACATTTCATCA
*
9509539 TATGCAT
1 TTTGCAT
9509546 TAAATTTCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 14 0.61
20 8 0.35
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.47
Consensus pattern (18 bp):
TTTGCATACATTTCATCA
Found at i:9509546 original size:19 final size:20
Alignment explanation
Indices: 9509509--9509554 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
9509499 TTTTTGCATC
*
9509509 CATTTCATTCATTTGCATTA
1 CATTTCATTCATATGCATTA
9509529 CATTTCA-TCATATGCATTA
1 CATTTCATTCATATGCATTA
*
9509548 AATTTCA
1 CATTTCA
9509555 CGAAAAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.46
Consensus pattern (20 bp):
CATTTCATTCATATGCATTA
Found at i:9517792 original size:130 final size:130
Alignment explanation
Indices: 9517515--9517769 Score: 343
Period size: 130 Copynumber: 2.0 Consensus size: 130
9517505 TCCATGAGGT
* *
9517515 AGTAATGGAGCAGATCGAAGATGACGAATCTTGTCTCCCTAAGCAGTAGTGGAACAGATTTAAGC
1 AGTAACGGAGCAGATCGAAGATGACGAATCTTGTCTCCCTAAGCAGTAGTGGAACAAATTTAAGC
* * ** *
9517580 CACCATCCTATCTGCCTAAGCAGTAGTGGAGTAGGCTGAAAATTACAGATCTTATCTTCTTAAGC
66 CACCATCCTATCTCCCTAAGCAGTAGTGGAGCAGGCTGAAAACCACAGATCGTATCTTCTTAAGC
** * * * *
9517645 AGTAGTGAAGCAGATCGAAGATGGCGAATCTTGTCTCTCTAAGCAGTAGTGGAGCAAATTTAAGC
1 AGTAACGGAGCAGATCGAAGATGACGAATCTTGTCTCCCTAAGCAGTAGTGGAACAAATTTAAGC
* * *
9517710 CACCATCTTATCTCCCTAAGCAGTAGTGGAGCAGGTTG-AAACCACA-ATTCGTATTTTCTT
66 CACCATCCTATCTCCCTAAGCAGTAGTGGAGCAGGCTGAAAACCACAGA-TCGTATCTTCTT
9517770 GAAGTTTCAA
Statistics
Matches: 110, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
128 1 0.01
129 16 0.15
130 93 0.85
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (130 bp):
AGTAACGGAGCAGATCGAAGATGACGAATCTTGTCTCCCTAAGCAGTAGTGGAACAAATTTAAGC
CACCATCCTATCTCCCTAAGCAGTAGTGGAGCAGGCTGAAAACCACAGATCGTATCTTCTTAAGC
Found at i:9517847 original size:88 final size:88
Alignment explanation
Indices: 9517751--9518284 Score: 791
Period size: 88 Copynumber: 6.1 Consensus size: 88
9517741 CAGGTTGAAA
* * * *
9517751 CCACAATTCGTATTTTCTTGAAGTTTCAACGGAGTAGATCGAGGCTACAAATCTCTTCTCCCTAA
1 CCACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAGGCTACAAATCTCTTCTCCCTGA
*
9517816 AATGGCATTGGAGTGGCTCGAAG
66 AATGGCATTGGAGCGGCTCGAAG
* * ** * *
9517839 CCACAATTCGTATCTCCTTAAAGTTTCAGCAGAGTTTATCGATGCTACAAATCTCTTCTCCCTAA
1 CCACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAGGCTACAAATCTCTTCTCCCTGA
9517904 AATGGCATTGGAGCGGCTCGAAG
66 AATGGCATTGGAGCGGCTCGAAG
*
9517927 CCACAATTCGTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAGGCTACAAATCTCTTCTCCCTGA
1 CCACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAGGCTACAAATCTCTTCTCCCTGA
* * *
9517992 AATGGTATTGGAGCGGCTCAAAA
66 AATGGCATTGGAGCGGCTCGAAG
* * *
9518015 CCACAATTCGTATCTCATTGAAGTTTCAGCAGAGTAGATCGACGCTACAAATCTCTTCTCCCTGA
1 CCACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAGGCTACAAATCTCTTCTCCCTGA
*
9518080 AATGGCATTGGAGCAGCTCGAAG
66 AATGGCATTGGAGCGGCTCGAAG
* * * **
9518103 CCACAATTCGTATCTCCTTGAAGTTCCAGCGGGGTAGATCGATGCTACAAATCTCTTCTCATTGA
1 CCACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAGGCTACAAATCTCTTCTCCCTGA
*
9518168 AATGGCATTGGAGCGACTCGAAG
66 AATGGCATTGGAGCGGCTCGAAG
* *
9518191 CCACAATTCGTATCTCCTTGAAG-TTCTAGCGGAGTAGATCAAGGCTACAAATCTCTTCTTCCTG
1 CCACAATTCGTATCTCCTTGAAGTTTC-AGCGGAGTAGATCGAGGCTACAAATCTCTTCTCCCTG
**
9518255 AAATGGCATTGGAGCGGCTTAAAG
65 AAATGGCATTGGAGCGGCTCGAAG
9518279 CCACAA
1 CCACAA
9518285 ATCACAAACC
Statistics
Matches: 399, Mismatches: 46, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
87 2 0.01
88 397 0.99
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (88 bp):
CCACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAGGCTACAAATCTCTTCTCCCTGA
AATGGCATTGGAGCGGCTCGAAG
Found at i:9518392 original size:45 final size:45
Alignment explanation
Indices: 9518289--9518912 Score: 319
Period size: 44 Copynumber: 13.8 Consensus size: 45
9518279 CCACAAATCA
* * * * ** *
9518289 CAAACCTTATCTCCCTGAAGTAGCAGTGAAGCAGGTCAAAGTTA-
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * * *
9518333 CAAGTCTTATCTCCCTAAAGTTACAGTGGAGCAGACTGAAGATAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * * *
9518378 CGAATCTTATCTCCCTTAAGTTGCAGTGGAGTAGATTGAAGCTAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * *
9518423 AAATCACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA-
1 ------CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * * * *
9518473 CAAGTCTTATCTCCTTGAATTTGCAGTGGAGCAGACTGGAGATAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * * *
9518518 CAAATCTCATTTCCCTGAAGATGCAGTGGAACAGATTGAAGTTATA-
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--ATAG
* * * * **
9518564 AATAGATCTTATC-CCCTGAAGTTACAGT--AGAACA-T-ATCATAG
1 CA-A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * * * * **
9518606 AAAATCTTATCTCCCTTAAGTTGTAGTCGAGTAGATTGAAGCCA-
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * * * * * *
9518650 CTAACCTTATCCCCCTAAAATTGCAGTGGAACAGATTGAAGTTATAAATAAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG------AT-AG
* * * * *
9518702 CAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGA-T---CATAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * * * * **
9518743 AAAATATTATCTCCCTTAAGTTGTAGTGGAGTAGATTGAAGCCA-
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * * * * * *
9518787 CTAACCTTATCCCCCTGAAATTACAGTGGGGCA-AGTT-ATAGTTA-
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTGA-AGATAG
* *
9518831 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
* * *
9518876 CAGATCTTATCTCCTTGAAGTTGCAATGGAGCAGATT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
9518913 AAGCTACAAT
Statistics
Matches: 422, Mismatches: 123, Indels: 69
0.69 0.20 0.11
Matches are distributed among these distances:
40 8 0.02
41 43 0.10
42 5 0.01
43 7 0.02
44 160 0.38
45 110 0.26
46 1 0.00
47 17 0.04
48 6 0.01
51 40 0.09
52 25 0.06
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (45 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
Found at i:9518500 original size:140 final size:140
Alignment explanation
Indices: 9518283--9518558 Score: 408
Period size: 140 Copynumber: 2.0 Consensus size: 140
9518273 TTAAAGCCAC
9518283 AAATCACAAACCTTATCTCCCTGAAGTAGCAGTGAAGCAGGTCAAAGTTACAAGTCTTATCTCCC
1 AAATCACAAACCTTATCTCCCTGAAGTAGCAGTGAAGCAGGTCAAAGTTACAAGTCTTATCTCCC
* * * * **
9518348 TAAAGTTACAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTTAAGTTGCAGTGGAGTAGA
66 TAAAGTTACAGTGGAGCAGACTGAAGATAGCAAATCTCATCTCCCTGAAGATGCAGTGGAACAGA
9518413 TTGAAGCTAG
131 TTGAAGCTAG
* * ** *
9518423 AAATCACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGTCTTATCTCCT
1 AAATCACAAACCTTATCTCCCTGAAGTAGCAGTGAAGCAGGTCAAAGTTACAAGTCTTATCTCCC
* * * * *
9518488 TGAATTTGCAGTGGAGCAGACTGGAGATAGCAAATCTCATTTCCCTGAAGATGCAGTGGAACAGA
66 TAAAGTTACAGTGGAGCAGACTGAAGATAGCAAATCTCATCTCCCTGAAGATGCAGTGGAACAGA
9518553 TTGAAG
131 TTGAAG
9518559 TTATAAATAG
Statistics
Matches: 120, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
140 120 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (140 bp):
AAATCACAAACCTTATCTCCCTGAAGTAGCAGTGAAGCAGGTCAAAGTTACAAGTCTTATCTCCC
TAAAGTTACAGTGGAGCAGACTGAAGATAGCAAATCTCATCTCCCTGAAGATGCAGTGGAACAGA
TTGAAGCTAG
Found at i:9518523 original size:96 final size:96
Alignment explanation
Indices: 9518338--9518523 Score: 234
Period size: 96 Copynumber: 1.9 Consensus size: 96
9518328 AGTTACAAGT
9518338 CTTATCTCCCTAAAGTTACAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTTAAGTTGCA
1 CTTATCTCCCTAAAGTTACAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTTAAGTTGCA
* * *
9518403 GTGGAGTAGATTGAAGCTAGAAATCACAAAC
66 GTGGAGCAGACTGAAGATAGAAATCACAAAC
* * ** * *
9518434 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA-C-AAGTCTTATCT-CCTTGAATTTG
1 CTTATCTCCCTAAAGTTACAGTGGAGCAGACTGAAGATAGCGAA-TCTTATCTCCCTT-AAGTTG
*
9518496 CAGTGGAGCAGACTGGAGATAGCAAATC
64 CAGTGGAGCAGACTGAAGATAG-AAATC
9518524 TCATTTCCCT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
94 6 0.08
95 32 0.42
96 39 0.51
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (96 bp):
CTTATCTCCCTAAAGTTACAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTTAAGTTGCA
GTGGAGCAGACTGAAGATAGAAATCACAAAC
Found at i:9518830 original size:137 final size:136
Alignment explanation
Indices: 9518541--9518815 Score: 450
Period size: 137 Copynumber: 2.0 Consensus size: 136
9518531 CCTGAAGATG
*
9518541 CAGTGGAACAGATTGAAGTTATAAAT----AGATCTTATCCCCTGAAGTTACAGTAGAACATATC
1 CAGTGGAACAGATTGAAGTTATAAATAAACAGATCTTATCCCCTGAAGTTACAGTAGAACAGATC
*
9518602 ATAGAAAATCTTATCTCCCTTAAGTTGTAGTCGAGTAGATTGAAGCCACTAACCTTATCCCCCTA
66 ATAGAAAATATTATCTCCCTTAAGTTGTAGTCGAGTAGATTGAAGCCACTAACCTTATCCCCCTA
*
9518667 AAATTG
131 AAATTA
* *
9518673 CAGTGGAACAGATTGAAGTTATAAATAAACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGAT
1 CAGTGGAACAGATTGAAGTTATAAATAAACAGATCTTATC-CCCTGAAGTTACAGTAGAACAGAT
*
9518738 CATAGAAAATATTATCTCCCTTAAGTTGTAGTGGAGTAGATTGAAGCCACTAACCTTATCCCCCT
65 CATAGAAAATATTATCTCCCTTAAGTTGTAGTCGAGTAGATTGAAGCCACTAACCTTATCCCCCT
*
9518803 GAAATTA
130 AAAATTA
9518810 CAGTGG
1 CAGTGG
9518816 GGCAAGTTAT
Statistics
Matches: 131, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
132 26 0.20
136 10 0.08
137 95 0.73
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (136 bp):
CAGTGGAACAGATTGAAGTTATAAATAAACAGATCTTATCCCCTGAAGTTACAGTAGAACAGATC
ATAGAAAATATTATCTCCCTTAAGTTGTAGTCGAGTAGATTGAAGCCACTAACCTTATCCCCCTA
AAATTA
Found at i:9520373 original size:3 final size:3
Alignment explanation
Indices: 9520358--9520534 Score: 74
Period size: 3 Copynumber: 58.0 Consensus size: 3
9520348 TTCAAAATTA
* *
9520358 ATT ATT TTT ATT ATT ATT TTCT ATT ATT A-T ATTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT A-TT ATT ATT ATT ATT
* * * * * * * * * *
9520404 GTT -TT ACT ACT ATT ACT ACT ATT ATC CTT GTT GACAT AGT A-T ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -A-TT ATT ATT A-TT
* * * * * **
9520450 ATT ACT ATT ATT TTCT ATT ATT GTC ATT ATT AAT ATAT ACC ATT ATT
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
* *
9520497 ATT ATT AAT A-T ATT ATT ATT ATT ATT ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9520535 TACATGTTAT
Statistics
Matches: 130, Mismatches: 33, Indels: 22
0.70 0.18 0.12
Matches are distributed among these distances:
2 8 0.06
3 110 0.85
4 11 0.08
5 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:9520400 original size:31 final size:32
Alignment explanation
Indices: 9520359--9520418 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
9520349 TCAAAATTAA
* *
9520359 TTATTTTTATTATTATTTT-CTATTATTATAT
1 TTATTATTATTATTATTTTACTACTATTATAT
*
9520390 TTATTATTATTATTGTTTTACTACTATTA
1 TTATTATTATTATTATTTTACTACTATTA
9520419 CTACTATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (32 bp):
TTATTATTATTATTATTTTACTACTATTATAT
Found at i:9520582 original size:3 final size:3
Alignment explanation
Indices: 9520576--9520649 Score: 55
Period size: 3 Copynumber: 25.3 Consensus size: 3
9520566 TATTATGGCT
* * * *
9520576 TTA TTA TTA TTA CTA TTA TTA CTA TTT TTA TCT- TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
* * *
9520621 TTA TTA TCA -TC TTA TT- TTA TTA CTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
9520650 CAATTTTGTA
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
2 3 0.06
3 49 0.92
4 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:9520742 original size:17 final size:17
Alignment explanation
Indices: 9520717--9520755 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
9520707 TTTATTTTCT
*
9520717 TATTACTTATCTATTTA
1 TATTTCTTATCTATTTA
*
9520734 TATTTCTTATTTATTTA
1 TATTTCTTATCTATTTA
9520751 TATTT
1 TATTT
9520756 TTGTTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTCTTATCTATTTA
Found at i:9520780 original size:17 final size:17
Alignment explanation
Indices: 9520748--9520782 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9520738 TCTTATTTAT
* *
9520748 TTATATTTTTGTTATTA
1 TTATATTTTAGGTATTA
9520765 TTATATTTTAGGTATTA
1 TTATATTTTAGGTATTA
9520782 T
1 T
9520783 ATCTCTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (17 bp):
TTATATTTTAGGTATTA
Found at i:9520817 original size:26 final size:26
Alignment explanation
Indices: 9520761--9520818 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
9520751 TATTTTTGTT
9520761 ATTA-TTATATTTTAGGTATTATATC
1 ATTATTTATATTTTAGGTATTATATC
*
9520786 -TCTATTTATA-TTTATGTATTAATATC
1 AT-TATTTATATTTTAGGTATT-ATATC
9520812 ATTATTT
1 ATTATTT
9520819 TACTATTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
24 1 0.04
25 11 0.39
26 15 0.54
27 1 0.04
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (26 bp):
ATTATTTATATTTTAGGTATTATATC
Found at i:9522723 original size:42 final size:43
Alignment explanation
Indices: 9522541--9522725 Score: 173
Period size: 43 Copynumber: 4.3 Consensus size: 43
9522531 TTAAAATTTC
* * *
9522541 AGACCATGACTTTTAGCGGCGCTTTCTT-CGCAAACGCCGCTAA
1 AGACCACGACCTTTAGCGGCGCTTT-TTCCACAAACGCCGCTAA
* *** * * *
9522584 AGATCACGGTTTTTAGCGGCACTTTTCCCAAAAACGCCGCTAA
1 AGACCACGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAA
*
9522627 AGACCACGACCTTTAACGGCGC-TTTTCCTACAAACGCCGCTATA
1 AGACCACGACCTTTAGCGGCGCTTTTTCC-ACAAACGCCGCTA-A
* * *
9522671 A-AACA-AACCTTTAGCGGCGCTTTTTTCACAAACGCC-CTAA
1 AGACCACGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAA
*
9522711 AGACCATGACCTTTA
1 AGACCACGACCTTTA
9522726 AAAAAATATT
Statistics
Matches: 114, Mismatches: 22, Indels: 13
0.77 0.15 0.09
Matches are distributed among these distances:
40 2 0.02
41 6 0.05
42 35 0.31
43 69 0.61
44 2 0.02
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (43 bp):
AGACCACGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAA
Found at i:9525982 original size:16 final size:16
Alignment explanation
Indices: 9525961--9525996 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
9525951 TTATGCAACT
9525961 TTAATTAATCCCATCG
1 TTAATTAATCCCATCG
9525977 TTAATTAATCCCATCG
1 TTAATTAATCCCATCG
9525993 TTAA
1 TTAA
9525997 CTGGAGCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (16 bp):
TTAATTAATCCCATCG
Found at i:9526980 original size:40 final size:40
Alignment explanation
Indices: 9526925--9527008 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
9526915 AAAATTGAAT
* * *
9526925 AGATCGAGTATTAGCGGTGTTTCT-AGAAAAGCGCCGCTAA
1 AGATCGAGAATTAGCGGCGTTTCTAAG-AAAGCGCCGCAAA
* *
9526965 AGATCGAGAATTAGCGGCGTTTTTAAGGAAGCGCCGCAAA
1 AGATCGAGAATTAGCGGCGTTTCTAAGAAAGCGCCGCAAA
9527005 AGAT
1 AGAT
9527009 TGACCTATAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
40 36 0.95
41 2 0.05
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.23
Consensus pattern (40 bp):
AGATCGAGAATTAGCGGCGTTTCTAAGAAAGCGCCGCAAA
Found at i:9532590 original size:23 final size:23
Alignment explanation
Indices: 9532560--9532609 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
9532550 AACATTAATC
9532560 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
9532583 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
9532606 AAAT
1 AAAT
9532610 AAACTTGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (23 bp):
AAATGTATGAATTGCAGCCCTTT
Found at i:9533165 original size:241 final size:241
Alignment explanation
Indices: 9532742--9533228 Score: 893
Period size: 241 Copynumber: 2.0 Consensus size: 241
9532732 ATGAATTAAT
*
9532742 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTACTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
*
9532807 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACTTGACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
* * **
9532872 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAATGCCACGTATGATGAATTTTAAAATTTTC
131 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATATTAAAAAATTC
9532937 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
196 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
9532983 TTTATTACCATGTAGCTTACTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTACTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
9533048 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
*
9533113 CTGTAAGATATAATGGATCCTCTCTAGGTGTAACAACGCCACGTATGATGAATATTAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATATTAAAAAATTC
* *
9533178 AAAAAGACTTGGAAAAAGTTCTATCGATCTCATTTACTATTGAATA
196 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
9533224 TTTAT
1 TTTAT
9533229 ATAACCTTAA
Statistics
Matches: 237, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
241 237 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (241 bp):
TTTATTACCATGTAGCTTACTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATATTAAAAAATTC
AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
Found at i:9533477 original size:9 final size:9
Alignment explanation
Indices: 9533409--9533575 Score: 136
Period size: 9 Copynumber: 17.6 Consensus size: 9
9533399 ATTGATCATT
*
9533409 ACTTAAATA
1 ACTTACATA
*
9533418 AATTACATA
1 ACTTACATA
*
9533427 ACTTATATA
1 ACTTACATA
* *
9533436 ACTCATATA
1 ACTTACATA
*
9533445 ACTTACACA
1 ACTTACATA
*
9533454 ATTTACATAACA
1 ACTTACAT---A
9533466 ACTTACATA
1 ACTTACATA
*
9533475 ACTCACATA
1 ACTTACATA
9533484 ACTTACATA
1 ACTTACATA
*
9533493 ATTTACATAACA
1 ACTTACAT---A
9533505 ACTTACATA
1 ACTTACATA
*
9533514 ACTCACATA
1 ACTTACATA
9533523 ACTTACATA
1 ACTTACATA
*
9533532 ATTTACATA
1 ACTTACATA
*
9533541 ACTCACATA
1 ACTTACATA
*
9533550 ACGTACATAACA
1 ACTTACAT---A
9533562 ACTTACATA
1 ACTTACATA
9533571 ACTTA
1 ACTTA
9533576 ACTAATACAT
Statistics
Matches: 126, Mismatches: 23, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
9 102 0.81
12 24 0.19
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:9533479 original size:39 final size:39
Alignment explanation
Indices: 9533426--9533542 Score: 207
Period size: 39 Copynumber: 3.0 Consensus size: 39
9533416 TAAATTACAT
* * *
9533426 AACTTATATAACTCATATAACTTACACAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
9533465 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
9533504 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
9533543 TCACATAACG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTTACATAATTTACATAAC
Found at i:9533526 original size:57 final size:57
Alignment explanation
Indices: 9533465--9533573 Score: 173
Period size: 57 Copynumber: 1.9 Consensus size: 57
9533455 TTTACATAAC
* **
9533465 AACTTACATAACTCACATAACTTACATAATTTACATAACAACTTACATAACTCACAT
1 AACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTCACAT
* *
9533522 AACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAACT
1 AACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACT
9533574 TAACTAATAC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.29
Consensus pattern (57 bp):
AACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTCACAT
Found at i:9533571 original size:39 final size:37
Alignment explanation
Indices: 9533409--9533560 Score: 184
Period size: 39 Copynumber: 4.1 Consensus size: 37
9533399 ATTGATCATT
* * * *
9533409 ACTTAAATAAATTACAT-AACTTATATAACTCATATA
1 ACTTACATAATTTACATAAACTTACATAACTCACATA
*
9533445 ACTTACACAATTTACATAACAACTTACATAACTCACATA
1 ACTTACATAATTTACAT-A-AACTTACATAACTCACATA
9533484 ACTTACATAATTTACATAACAACTTACATAACTCACATA
1 ACTTACATAATTTACAT-A-AACTTACATAACTCACATA
*
9533523 ACTTACATAATTTACAT-AACTCACATAACGT-ACATA
1 ACTTACATAATTTACATAAACTTACATAAC-TCACATA
9533559 AC
1 AC
9533561 AACTTACATA
Statistics
Matches: 105, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
36 32 0.30
37 1 0.01
39 72 0.69
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.31
Consensus pattern (37 bp):
ACTTACATAATTTACATAAACTTACATAACTCACATA
Found at i:9533574 original size:48 final size:47
Alignment explanation
Indices: 9533420--9533575 Score: 168
Period size: 48 Copynumber: 3.3 Consensus size: 47
9533410 CTTAAATAAA
* * * * *
9533420 TTACATAACTTATATAACTCATATAACTTACACAATTTACATAACAAC
1 TTACATAACTTACATAACTTACATAACTTACATAA-CTACATAACAAC
* * * * *
9533468 TTACATAACTCACATAACTTACATAATTTACATAACAACTTACATAAC
1 TTACATAACTTACATAACTTACATAACTTACATAACTACATA-ACAAC
* * *
9533516 TCACATAACTTACATAATTTACATAACTCACATAACGTACATAACAAC
1 TTACATAACTTACATAACTTACATAACTTACATAAC-TACATAACAAC
9533564 TTACATAACTTA
1 TTACATAACTTA
9533576 ACTAATACAT
Statistics
Matches: 87, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
47 4 0.05
48 79 0.91
49 4 0.05
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.31
Consensus pattern (47 bp):
TTACATAACTTACATAACTTACATAACTTACATAACTACATAACAAC
Found at i:9540006 original size:25 final size:25
Alignment explanation
Indices: 9539961--9540008 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
9539951 AACACCTAAA
*
9539961 ACTTAAACCCCAACCCTTAAACCAC
1 ACTTAAACCACAACCCTTAAACCAC
*
9539986 ACTTAAACCATAATCCC-TAAACC
1 ACTTAAACCACAA-CCCTTAAACC
9540009 TTAAAATAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.19
Consensus pattern (25 bp):
ACTTAAACCACAACCCTTAAACCAC
Found at i:9540653 original size:41 final size:40
Alignment explanation
Indices: 9540523--9540653 Score: 136
Period size: 41 Copynumber: 3.2 Consensus size: 40
9540513 GTTATATAAC
* * * * **
9540523 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACAAAAAACGCCGATATTGCTC-CAT
* * * * *
9540564 TTTTAGCAGCGATTTACAAAAAAATGCCGATATTTCTCTAT
1 TTTTAGCGGCGTTTTAC-AAAAAACGCCGATATTGCTCCAT
9540605 TTTTAGCGGCGTTTTAACAAAAAACGCCGATATTGCTCCAT
1 TTTTAGCGGCGTTTT-ACAAAAAACGCCGATATTGCTCCAT
9540646 TTTTAGCG
1 TTTTAGCG
9540654 TGCTCTGTGT
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
41 57 0.78
42 16 0.22
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACAAAAAACGCCGATATTGCTCCAT
Found at i:9542524 original size:20 final size:20
Alignment explanation
Indices: 9542494--9542573 Score: 63
Period size: 20 Copynumber: 3.8 Consensus size: 20
9542484 TTATTATTAA
9542494 ATTAAATTTAATATTAAATAT
1 ATTAAA-TTAATATTAAATAT
*
9542515 ATTAAATTAATA-GAATATTTAT
1 ATTAAATTAATATTAA-A--TAT
* *
9542537 GTATAAGATAAATATTAAATAT
1 AT-TAA-ATTAATATTAAATAT
*
9542559 ATTAAAATAATATTA
1 ATTAAATTAATATTA
9542574 TTTTTGGAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
19 2 0.04
20 15 0.33
21 9 0.20
22 8 0.17
23 3 0.07
24 7 0.15
25 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (20 bp):
ATTAAATTAATATTAAATAT
Found at i:9542541 original size:26 final size:23
Alignment explanation
Indices: 9542464--9542533 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 23
9542454 AATCATTTTA
9542464 ATATTAAATTAATATAATACTTAT
1 ATATTAAATTAATATAATA-TTAT
*
9542488 -TATTAAATTAAATTTAATATTAAAT
1 ATATTAAATT-AATATAATATT--AT
*
9542513 ATATTAAATTAATAGAATATT
1 ATATTAAATTAATATAATATT
9542534 TATGTATAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 11 0.28
24 8 0.21
25 11 0.28
26 9 0.23
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (23 bp):
ATATTAAATTAATATAATATTAT
Found at i:9549652 original size:5 final size:5
Alignment explanation
Indices: 9549644--9549671 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
9549634 TTCAAAACAA
9549644 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
9549672 GGAAAGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:9554425 original size:7 final size:7
Alignment explanation
Indices: 9554413--9554437 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9554403 GTGTGGAAAC
9554413 ATAATGA
1 ATAATGA
9554420 ATAATGA
1 ATAATGA
9554427 ATAATGA
1 ATAATGA
9554434 ATAA
1 ATAA
9554438 AGAAAAGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (7 bp):
ATAATGA
Found at i:9566409 original size:18 final size:18
Alignment explanation
Indices: 9566381--9566424 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
9566371 GAGAGCAGGG
9566381 AAAGG-AAAGAAAGAA-A
1 AAAGGAAAAGAAAGAAGA
9566397 AAAGAGAAAAGAAAGAAGA
1 AAAG-GAAAAGAAAGAAGA
9566416 AAAGGAAAA
1 AAAGGAAAA
9566425 ATTGAAGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.16
17 1 0.04
18 15 0.60
19 5 0.20
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (18 bp):
AAAGGAAAAGAAAGAAGA
Found at i:9568413 original size:46 final size:46
Alignment explanation
Indices: 9568361--9568635 Score: 354
Period size: 46 Copynumber: 6.0 Consensus size: 46
9568351 GCTCTCTGAA
* * * *
9568361 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCTACCTGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
9568407 ATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
9568453 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
9568499 ATGAAATGAATAAGACCATGGTTGAAACATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
9568545 GGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
9568592 A-GAAAACGAGTAAAACCATAGTTGAAAGATACTATGGCATCATG
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
9568636 TCGAAGATAA
Statistics
Matches: 208, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
46 166 0.80
47 42 0.20
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:9569933 original size:15 final size:16
Alignment explanation
Indices: 9569906--9569935 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9569896 TATAACAATT
9569906 AATATATATTATATAA
1 AATATATATTATATAA
9569922 AATATA-ATTATATA
1 AATATATATTATATA
9569936 TTAGTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATATTATATAA
Found at i:9569936 original size:22 final size:21
Alignment explanation
Indices: 9569896--9569938 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
9569886 ATGTAATGTT
9569896 TATAACAATTAATATATATTA
1 TATAACAATTAATATATATTA
9569917 TATAA-AATATAATTATATATTA
1 TATAACAAT-TAA-TATATATTA
9569939 GTTATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 3 0.15
21 8 0.40
22 9 0.45
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TATAACAATTAATATATATTA
Found at i:9573660 original size:44 final size:42
Alignment explanation
Indices: 9573610--9573762 Score: 127
Period size: 44 Copynumber: 3.7 Consensus size: 42
9573600 TGTGTTTTGG
*
9573610 TGTAAGACCACATCTGGGACATTGGTATC-CACTTATGATTTACA
1 TGTAAGACCACATCTGGGACATTGGCATCGCA-TT-TGATTT-CA
* * * *
9573654 TGTAAGACCACGTTTGGGACGTTGGCATCGTATTTGATTTCA
1 TGTAAGACCACATCTGGGACATTGGCATCGCATTTGATTTCA
* * * * *
9573696 TGTAAGA-C-C-T-TGAGATAGTGGCATCGATATTTGATTACA
1 TGTAAGACCACATCTGGGACATTGGCATCG-CATTTGATTTCA
* *
9573735 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACATCTGGGACATTGGCAT
9573763 TGTACGAGCT
Statistics
Matches: 89, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
38 12 0.13
39 19 0.21
40 2 0.02
41 2 0.02
42 10 0.11
43 16 0.18
44 27 0.30
45 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (42 bp):
TGTAAGACCACATCTGGGACATTGGCATCGCATTTGATTTCA
Found at i:9577641 original size:18 final size:18
Alignment explanation
Indices: 9577618--9577652 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9577608 GAGTTTTTAT
9577618 TTATGCCTTTCAGATTAG
1 TTATGCCTTTCAGATTAG
*
9577636 TTATGCCTTTCGGATTA
1 TTATGCCTTTCAGATTA
9577653 ACGAATGCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (18 bp):
TTATGCCTTTCAGATTAG
Found at i:9587131 original size:9 final size:9
Alignment explanation
Indices: 9587117--9587144 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
9587107 ATTGATAGCC
9587117 TATTTTATT
1 TATTTTATT
9587126 TATTTTATT
1 TATTTTATT
9587135 TATTTTATT
1 TATTTTATT
9587144 T
1 T
9587145 TTGTTGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TATTTTATT
Found at i:9592609 original size:36 final size:36
Alignment explanation
Indices: 9592540--9592610 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 36
9592530 GTAAAGTACC
** *
9592540 TCAGTCAAAATAGATTTGAAAGGCTGCTAAACTGAG
1 TCAGTCAAAATAGATCCGAAAGGCTACTAAACTGAG
* * *
9592576 TCAGTCAGAATAGATCCGAAAGGTTACTGAACTGA
1 TCAGTCAAAATAGATCCGAAAGGCTACTAAACTGA
9592611 ATAGAGTCTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (36 bp):
TCAGTCAAAATAGATCCGAAAGGCTACTAAACTGAG
Found at i:9595098 original size:49 final size:49
Alignment explanation
Indices: 9595041--9595135 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
9595031 TGTCCTAACA
9595041 GACTTCATATGTTACCATAGCCCAACTATGGTCTTACACAACATAAGCG
1 GACTTCATATGTTACCATAGCCCAACTATGGTCTTACACAACATAAGCG
*** * *
9595090 GACTTCATATGTTGTTATAGCCCAGCTATGGTCTTATACAACATAA
1 GACTTCATATGTTACCATAGCCCAACTATGGTCTTACACAACATAA
9595136 TCTCGTGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (49 bp):
GACTTCATATGTTACCATAGCCCAACTATGGTCTTACACAACATAAGCG
Found at i:9596016 original size:2 final size:2
Alignment explanation
Indices: 9596009--9596038 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9595999 ATTTCTCCCT
9596009 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
9596039 TACATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:9598614 original size:28 final size:28
Alignment explanation
Indices: 9598574--9598666 Score: 109
Period size: 28 Copynumber: 3.3 Consensus size: 28
9598564 ATTTTTTTAA
* *
9598574 CTTGAACCCTAAACCATAGATCTTGGAC
1 CTTGGACCCTAAACCATAGACCTTGGAC
9598602 CTTGGACCCTAAACCATAGACCTTGGAC
1 CTTGGACCCTAAACCATAGACCTTGGAC
* * *
9598630 CTAGGATTCC-AAACCCT-GAACCTTGGAC
1 CTTGGA-CCCTAAACCATAG-ACCTTGGAC
9598658 CTTGGACCC
1 CTTGGACCC
9598667 AAGGTTTAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
27 3 0.05
28 51 0.91
29 2 0.04
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (28 bp):
CTTGGACCCTAAACCATAGACCTTGGAC
Found at i:9609295 original size:3 final size:3
Alignment explanation
Indices: 9609289--9609323 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
9609279 AAAAGCGTCT
*
9609289 TCC TCC TCC TCC TCC TCC TCT TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
9609324 AAGGTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (3 bp):
TCC
Found at i:9614586 original size:23 final size:23
Alignment explanation
Indices: 9614552--9614614 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
9614542 TGCACTGAAA
* *
9614552 TGCCA-TTACACTTGCATCGTAG
1 TGCCACTTTCACTTGCATCATAG
*
9614574 TGCCACTTTCACTTGCACCATAG
1 TGCCACTTTCACTTGCATCATAG
* *
9614597 TGCCACTATCATTTGCAT
1 TGCCACTTTCACTTGCAT
9614615 TCTTACTCAC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 5 0.15
23 29 0.85
ACGTcount: A:0.22, C:0.30, G:0.14, T:0.33
Consensus pattern (23 bp):
TGCCACTTTCACTTGCATCATAG
Found at i:9616968 original size:26 final size:26
Alignment explanation
Indices: 9616939--9616990 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
9616929 GACAACTAAG
*
9616939 AATAGCCTCTATGGCGAACTCTGAAA
1 AATAGCATCTATGGCGAACTCTGAAA
* *
9616965 AATAGCATTTGTGGCGAACTCTGAAA
1 AATAGCATCTATGGCGAACTCTGAAA
9616991 GGAAAGCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (26 bp):
AATAGCATCTATGGCGAACTCTGAAA
Found at i:9617016 original size:27 final size:27
Alignment explanation
Indices: 9616950--9617027 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
9616940 ATAGCCTCTA
* *
9616950 TGGCGAACTCTGAAA--AATAGCATTTG
1 TGGCAAACTCTGAAAGGAA-AGCCTTTG
*
9616976 TGGCGAACTCTGAAAGGAAAGCCTTTG
1 TGGCAAACTCTGAAAGGAAAGCCTTTG
* * * *
9617003 TGGCAAATTTTGAATGGAATGCCTT
1 TGGCAAACTCTGAAAGGAAAGCCTT
9617028 GGAGGCATAC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 15 0.34
27 27 0.61
28 2 0.05
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (27 bp):
TGGCAAACTCTGAAAGGAAAGCCTTTG
Found at i:9624150 original size:19 final size:19
Alignment explanation
Indices: 9624126--9624165 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
9624116 TACCAATGCC
9624126 TAAGTCGAAATTTGAGGAA
1 TAAGTCGAAATTTGAGGAA
9624145 TAAGTCGAAATTTGAGGAA
1 TAAGTCGAAATTTGAGGAA
9624164 TA
1 TA
9624166 TTGAAGGCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (19 bp):
TAAGTCGAAATTTGAGGAA
Found at i:9628116 original size:38 final size:38
Alignment explanation
Indices: 9628073--9628167 Score: 163
Period size: 38 Copynumber: 2.5 Consensus size: 38
9628063 TGAACTAACA
9628073 GTATGTTGCAGATTGATTGCAAAAAGAAGACATGAAAT
1 GTATGTTGCAGATTGATTGCAAAAAGAAGACATGAAAT
*
9628111 GTATGTTGCAGATTGATTGTAAAAAGAAGACATGAAAT
1 GTATGTTGCAGATTGATTGCAAAAAGAAGACATGAAAT
* *
9628149 GTATGCTGCAGATCGATTG
1 GTATGTTGCAGATTGATTG
9628168 GAACCAGATT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (38 bp):
GTATGTTGCAGATTGATTGCAAAAAGAAGACATGAAAT
Found at i:9629510 original size:8 final size:8
Alignment explanation
Indices: 9629499--9629527 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
9629489 TGAAAAAACC
9629499 AAAAAAGA
1 AAAAAAGA
9629507 AAAAAAG-
1 AAAAAAGA
9629514 AAAAAAGA
1 AAAAAAGA
9629522 AAAAAA
1 AAAAAA
9629528 AAGGGGAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:9629510 original size:15 final size:15
Alignment explanation
Indices: 9629490--9629527 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
9629480 GAAAAGCAGT
*
9629490 GAAAAAACCAAAAAA
1 GAAAAAAACAAAAAA
*
9629505 GAAAAAAAGAAAAAA
1 GAAAAAAACAAAAAA
9629520 GAAAAAAA
1 GAAAAAAA
9629528 AAGGGGAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (15 bp):
GAAAAAAACAAAAAA
Found at i:9630304 original size:22 final size:22
Alignment explanation
Indices: 9630279--9630322 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
9630269 AATTATTAAC
*
9630279 ATAATGAATTTTAATTAATTTT
1 ATAATAAATTTTAATTAATTTT
*
9630301 ATAATAAATTTTGATTAATTTT
1 ATAATAAATTTTAATTAATTTT
9630323 GGTCATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATAATAAATTTTAATTAATTTT
Found at i:9632095 original size:20 final size:20
Alignment explanation
Indices: 9632051--9632095 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
9632041 TAGGCTTCGA
* *
9632051 CTCACAGGAGTTGAAGGGAG
1 CTCACAGGAGTTAAAGAGAG
9632071 CTCACAGGAGTTAAAGAGAG
1 CTCACAGGAGTTAAAGAGAG
*
9632091 TTCAC
1 CTCAC
9632096 GGTCCCAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.18, G:0.31, T:0.18
Consensus pattern (20 bp):
CTCACAGGAGTTAAAGAGAG
Found at i:9635594 original size:27 final size:26
Alignment explanation
Indices: 9635493--9635604 Score: 127
Period size: 27 Copynumber: 4.2 Consensus size: 26
9635483 AGGAAGCGTC
* * * *
9635493 CTGGTGGCTATGCCATAAATATCTGAT
1 CTGGTGGCTCTGCCA-CATTATCTGTT
9635520 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
9635547 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGT-T
*
9635575 CTGGTGACTCT-CTCACATTATCTGTT
1 CTGGTGGCTCTGC-CACATTATCTGTT
9635601 CTGG
1 CTGG
9635605 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.08
27 54 0.71
28 16 0.21
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:9635597 original size:54 final size:54
Alignment explanation
Indices: 9635493--9635604 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 54
9635483 AGGAAGCGTC
* *
9635493 CTGGTGGCTATGCCATAAATATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
9635547 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCT-CTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGC-CACATATATCTGTT
9635601 CTGG
1 CTGG
9635605 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
54 34 0.67
55 17 0.33
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:9641169 original size:71 final size:71
Alignment explanation
Indices: 9641094--9641358 Score: 189
Period size: 71 Copynumber: 3.8 Consensus size: 71
9641084 TGATCTTAGG
* *
9641094 GCTTGCAGTTTTAATACCGTAGCCCCCAAAAATAGTTAACGAAAGCTAAAGCTCCCAGCTATAGT
1 GCTTGCAGGTTCAATACCGTAGCCCCCAAAAATAGTTAACGAAAGCTAAAGCTCCCAGCTATAGT
9641159 ATTAAT
66 ATTAAT
* * * * * * * * * * *
9641165 GCTTGTAAGTTCAACACCATAG-CCTCTAAAATAGTTAGCTAGAGCT-AAGCTCCCAGCTGTAAT
1 GCTTGCAGGTTCAATACCGTAGCCCCCAAAAATAGTTAACGAAAGCTAAAGCTCCCAGCTATAGT
* **
9641228 CTTAGG
66 ATTAAT
* * * ** * * * *
9641234 GCCTGCAGGTTCAATATCC-TAGCCTCCAAAAATAGTTAATGACGGTTAAGGCTCTCAGCTA-CG
1 GCTTGCAGGTTCAATA-CCGTAGCCCCCAAAAATAGTTAACGAAAGCTAAAGCTCCCAGCTATAG
9641297 ATATTAAT
65 -TATTAAT
* * * * * *
9641305 GCTAGCAGGTTCAATATCGCAACCCCGAAAAATAGTTAAC-AAGAGCTAAGGCTC
1 GCTTGCAGGTTCAATACCGTAGCCCCCAAAAATAGTTAACGAA-AGCTAAAGCTC
9641359 TTAGTTTTGA
Statistics
Matches: 140, Mismatches: 48, Indels: 12
0.70 0.24 0.06
Matches are distributed among these distances:
69 33 0.24
70 38 0.27
71 69 0.49
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (71 bp):
GCTTGCAGGTTCAATACCGTAGCCCCCAAAAATAGTTAACGAAAGCTAAAGCTCCCAGCTATAGT
ATTAAT
Found at i:9641269 original size:70 final size:70
Alignment explanation
Indices: 9640840--9641623 Score: 464
Period size: 70 Copynumber: 11.2 Consensus size: 70
9640830 GATCCTCTAA
* * *
9640840 AAAAATAGTTAGCGAA-AGCTAAGGCTCCCAGCTGTAATCTTAAGGCTCACATGTTTAATACCAT
1 AAAAATAGTTAGC-AAGAGCTAAGGCTCCCAGCTGTAATCTTAAGGCTCGCAGGTTCAATACCAT
*
9640904 AGCCCCC
65 AG-CCTC
* * * * * * *
9640911 AAAAACATTTAACTAGAGCTAAGGCTCCCA-TTGTTATCTTAAGGCTCGCAGGTTCAATACCACA
1 AAAAATAGTTAGCAAGAGCTAAGGCTCCCAGCTGTAATCTTAAGGCTCGCAGGTTCAATACCATA
*
9640975 TCCTC
66 GCCTC
* * * * ** * * *
9640980 TAAAATAGATAGGAAGAACTAAGGCTCCCAATTATGATCTTAAGGCTCGCAGGTTTAATACCATA
1 AAAAATAGTTAGCAAGAGCTAAGGCTCCCAGCTGTAATCTTAAGGCTCGCAGGTTCAATACCATA
9641045 GCCTC
66 GCCTC
* * ** * * * * * *
9641050 TAAAATAGTTAGCAAGAGTTCAA-GCTCTAAGCTGTGATCTTAGGGCTTGCAGTTTTAATACCGT
1 AAAAATAGTTAGCAAGAGCT-AAGGCTCCCAGCTGTAATCTTAAGGCTCGCAGGTTCAATACCAT
*
9641114 AGCCCCC
65 AG-CCTC
* * * * * * * * * *
9641121 AAAAATAGTTAACGAA-AGCTAAAGCTCCCAGCTATAGTATTAATGCTTGTAAGTTCAACACCAT
1 AAAAATAGTTAGC-AAGAGCTAAGGCTCCCAGCTGTAATCTTAAGGCTCGCAGGTTCAATACCAT
9641185 AGCCTC
65 AGCCTC
* * *
9641191 TAAAATAGTTAGCTAGAGCTAA-GCTCCCAGCTGTAATCTTAGGGC-CTGCAGGTTCAATATCC-
1 AAAAATAGTTAGCAAGAGCTAAGGCTCCCAGCTGTAATCTTAAGGCTC-GCAGGTTCAATA-CCA
9641253 TAGCCTCC
64 TAGCCT-C
* * * *** * * *
9641261 AAAAATAGTTA--ATGACGGTTAAGGCTCTCAGCTACGATATTAATGCTAGCAGGTTCAATATCG
1 AAAAATAGTTAGCAAGA--GCTAAGGCTCCCAGCTGTAATCTTAAGGCTCGCAGGTTCAATA-C-
*
9641324 CA-A-CCCC
62 CATAGCCTC
* ** * * * * **
9641331 GAAAAATAGTTAACAAGAGCTAAGGCTCTTAGTTTTGATCTTAAGGCTCGCAGGCTCAATACTGT
1 -AAAAATAGTTAGCAAGAGCTAAGGCTCCCAGCTGTAATCTTAAGGCTCGCAGGTTCAATACCAT
*
9641396 ATCCTC
65 AGCCTC
* * * * * * * * *
9641402 TAAAACAGTTAGCGAGAGTTAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGTTCAATACCGTA
1 AAAAATAGTTAGCAAGAGCTAAGGCTCCCAGCTGTAATCTTAAGGCTCGCAGGTTCAATACCATA
9641467 GCCTC
66 GCCTC
* * * * * * * ** *
9641472 TAAAATAGTTAGCGAGAGCTCAA-GCTCTCAGCTGTGATCTTAAGGTTTGCAGGATCAATGTCAC
1 AAAAATAGTTAGCAAGAGCT-AAGGCTCCCAGCTGTAATCTTAAGGCTCGCAGGTTCAATACCAT
9641536 AGCCTC
65 AGCCTC
* * * * ** *
9641542 TAAAACT-GTTAGCGAGAGCTCAA-GCTCCTA-CTTGTGATCTTAAGGCTCATAGGTTCAACACC
1 -AAAAATAGTTAGCAAGAGCT-AAGGCTCCCAGC-TGTAATCTTAAGGCTCGCAGGTTCAATACC
*
9641604 ACAGCCTC
63 ATAGCCTC
* *
9641612 CAAAACAGTTAG
1 AAAAATAGTTAG
9641624 TACAACCTGA
Statistics
Matches: 551, Mismatches: 137, Indels: 51
0.75 0.19 0.07
Matches are distributed among these distances:
68 2 0.00
69 63 0.11
70 321 0.58
71 158 0.29
72 4 0.01
73 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (70 bp):
AAAAATAGTTAGCAAGAGCTAAGGCTCCCAGCTGTAATCTTAAGGCTCGCAGGTTCAATACCATA
GCCTC
Found at i:9641501 original size:211 final size:208
Alignment explanation
Indices: 9640906--9641504 Score: 589
Period size: 211 Copynumber: 2.8 Consensus size: 208
9640896 AATACCATAG
* * *
9640906 CCCCCAAAAACATTTAACTAGAGCTAAGGCTCCCA-TTGTTATCTTAAGGCTCGCAGGTTCAATA
1 CCCCCAAAAATAGTTAACAAGAGCTAAGGCTCCCAGTT-TTATCTTAAGGCTCGCAGGTTCAATA
* * * *
9640970 CCACATCCTCTAAAATAGATAG-GAAGAACTAAGGCTCCCAATTATGATCTTAAGGCTCGCAGGT
65 CCATATCCTCTAAAATAGTTAGCG-AGAGCTAAGGCTCCCAACTATGATCTTAAGGCTCGCAGGT
* * * ** * * *
9641034 TTAATACCATAGCCTCTAAAATAGTTAGCAAGAGTTCAAGCTCTAAGCTGTGATCTTAGGGCTTG
129 TCAATACC-TAGCCTCTAAAATAGTTAGCGAGAG-TCAAGCTCTCAGCTACGATATTAAGGCTAG
* * * *
9641099 CAGTTTTAATACCGTAG
192 CAGGTTCAATACCGCAA
* * * * * * * * *
9641116 CCCCCAAAAATAGTTAACGAA-AGCTAAAGCTCCCAGCTATAGTATTAATGCTTGTAAGTTCAAC
1 CCCCCAAAAATAGTTAAC-AAGAGCTAAGGCTCCCAGTTTTA-TCTTAAGGCTCGCAGGTTCAAT
* * * * * *
9641180 ACCATAGCCTCTAAAATAGTTAGCTAGAGCTAA-GCTCCCAGCTGTAATCTTAGGGC-CTGCAGG
64 ACCATATCCTCTAAAATAGTTAGCGAGAGCTAAGGCTCCCAACTATGATCTTAAGGCTC-GCAGG
* ** * *
9641243 TTCAATATCCTAGCCTCCAAAAATAGTTAATGACG-GTTAAGGCTCTCAGCTACGATATTAATGC
128 TTCAATA-CCTAGCCT-CTAAAATAGTTAGCGA-GAGTCAA-GCTCTCAGCTACGATATTAAGGC
*
9641307 TAGCAGGTTCAATATCGCAA
189 TAGCAGGTTCAATACCGCAA
* ** *
9641327 CCCCGAAAAATAGTTAACAAGAGCTAAGGCTCTTAGTTTTGATCTTAAGGCTCGCAGGCTCAATA
1 CCCCCAAAAATAGTTAACAAGAGCTAAGGCTCCCAGTTTT-ATCTTAAGGCTCGCAGGTTCAATA
** * * *
9641392 CTGTATCCTCTAAAACAGTTAGCGAGAGTTAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGTT
65 CCATATCCTCTAAAATAGTTAGCGAGAGCTAAGGCTCCCAACTATGATCTTAAGGCTCGCAGGTT
9641457 CAATACCGTAGCCTCTAAAATAGTTAGCGAGAGCTCAAGCTCTCAGCT
130 CAATACC-TAGCCTCTAAAATAGTTAGCGAGAG-TCAAGCTCTCAGCT
9641505 GTGATCTTAA
Statistics
Matches: 305, Mismatches: 68, Indels: 31
0.75 0.17 0.08
Matches are distributed among these distances:
209 1 0.00
210 72 0.24
211 190 0.62
212 41 0.13
213 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (208 bp):
CCCCCAAAAATAGTTAACAAGAGCTAAGGCTCCCAGTTTTATCTTAAGGCTCGCAGGTTCAATAC
CATATCCTCTAAAATAGTTAGCGAGAGCTAAGGCTCCCAACTATGATCTTAAGGCTCGCAGGTTC
AATACCTAGCCTCTAAAATAGTTAGCGAGAGTCAAGCTCTCAGCTACGATATTAAGGCTAGCAGG
TTCAATACCGCAA
Found at i:9641524 original size:140 final size:139
Alignment explanation
Indices: 9640841--9641623 Score: 535
Period size: 140 Copynumber: 5.6 Consensus size: 139
9640831 ATCCTCTAAA
* * * * * ** * *
9640841 AAAATAGTTAGCGAAAGCTAAGGCTCCCAGCTGTAATCTTAAGGCTCACATGTTTAATACCATAG
1 AAAATAGTTAGCGAGAGTTAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGTTCAATACCATAG
* * * * * * * * * *
9640906 CCCCCAAAAACATTTAACTAGAGCTAAGGCTCCCA-TTGTTATCTTAAGGCTCGCAGGTTCAATA
66 -CCTCTAAAATAGTTAGCAAGAGCTAA-GCTCTCAGCTGTGATCTTAAGGCTTGCAGGTTCAATA
* * *
9640970 CCACATCCTCT
129 CTATAGCCTCT
* ** * * *
9640981 AAAATAGATAG-GAAGAACTAAGGCTCCCAATTATGATCTTAAGGCTCGCAGGTTTAATACCATA
1 AAAATAGTTAGCG-AGAGTTAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGTTCAATACCATA
* * * * *
9641045 GCCTCTAAAATAGTTAGCAAGAGTTCAAGCTCTAAGCTGTGATCTTAGGGCTTGCAGTTTTAATA
65 GCCTCTAAAATAGTTAGCAAGAGCT-AAGCTCTCAGCTGTGATCTTAAGGCTTGCAGGTTCAATA
** * *
9641110 CCGTAGCCCCCA
129 CTATAG-CCTCT
* * * * * * * * * *
9641122 AAAATAGTTAACGAAAGCTAAAGCTCCCAGCTAT-AGTATTAATGCTTGTAAGTTCAACACCATA
1 AAAATAGTTAGCGAGAGTTAAGGCTCCCAACTATGA-TCTTAAGGCTCGTAGGTTCAATACCATA
* * * * *
9641186 GCCTCTAAAATAGTTAGCTAGAGCTAAGCTCCCAGCTGTAATCTTAGGGCCTGCAGGTTCAATA-
65 GCCTCTAAAATAGTTAGCAAGAGCTAAGCTCTCAGCTGTGATCTTAAGGCTTGCAGGTTCAATAC
* *
9641250 TCCTAGCCTCCA
130 T-ATAGCCT-CT
** * * * * * * *
9641262 AAAATAGTTAATGACG-GTTAAGGCTCTCAGCTACGATATTAATGCTAGCAGGTTCAATATCGCA
1 AAAATAGTTAGCGA-GAGTTAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGTTCAATA-C-CA
* * * * * * * *
9641326 -A-CCCCGAAAAATAGTTAACAAGAGCTAAGGCTCTTAGTTTTGATCTTAAGGCTCGCAGGCTCA
63 TAGCCTC-TAAAATAGTTAGCAAGAGCTAA-GCTCTCAGCTGTGATCTTAAGGCTTGCAGGTTCA
* *
9641389 ATACTGTATCCTCT
126 ATACTATAGCCTCT
* *
9641403 AAAACAGTTAGCGAGAGTTAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGTTCAATACCGTAG
1 AAAATAGTTAGCGAGAGTTAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGTTCAATACCATAG
* * * *
9641468 CCTCTAAAATAGTTAGCGAGAGCTCAAGCTCTCAGCTGTGATCTTAAGGTTTGCAGGATCAAT-G
66 CCTCTAAAATAGTTAGCAAGAGCT-AAGCTCTCAGCTGTGATCTTAAGGCTTGCAGGTTCAATAC
*
9641532 TCACAGCCTCT
130 T-ATAGCCTCT
* * * * *
9641543 AAAACT-GTTAGCGAGAGCTCAA-GCT-CCTACTTGTGATCTTAAGGCTCATAGGTTCAACACCA
1 AAAA-TAGTTAGCGAGAG-TTAAGGCTCCCAAC-TATGATCTTAAGGCTCGTAGGTTCAATACCA
* * *
9641605 CAGCCTCCAAAACAGTTAG
63 TAGCCTCTAAAATAGTTAG
9641624 TACAACCTGA
Statistics
Matches: 505, Mismatches: 115, Indels: 46
0.76 0.17 0.07
Matches are distributed among these distances:
139 31 0.06
140 287 0.57
141 150 0.30
142 36 0.07
143 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (139 bp):
AAAATAGTTAGCGAGAGTTAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGTTCAATACCATAG
CCTCTAAAATAGTTAGCAAGAGCTAAGCTCTCAGCTGTGATCTTAAGGCTTGCAGGTTCAATACT
ATAGCCTCT
Found at i:9641684 original size:422 final size:419
Alignment explanation
Indices: 9640919--9641691 Score: 891
Period size: 422 Copynumber: 1.8 Consensus size: 419
9640909 CCAAAAACAT
* *
9640919 TTAACTAGAGCTAAGGCTCCCATTGTTATCTTAAGGCTCGCAGGTTCAATACCACATCCTCTAAA
1 TTAACAAGAGCTAAGGCTCCCATTGTTATCTTAAGGCTCGCAGGCTCAATACCACATCCTCTAAA
* * *
9640984 ATAGATAGGAAGAACTAAGGCTCCCAATTATGATCTTAAGGCTCGCAGGTTTAATACCATAGCCT
66 ACAGATAGGAAGAACTAAGGCTCCCAACTATGATCTTAAGGCTCGCAGGTTCAATACCATAGCCT
* * ** * **
9641049 CTAAAATAGTTAGCAAGAGTTCAAGCTCTAAGCTGTGATCTTAGGGCTTGCAGTTTTAATACCGT
131 CTAAAATAGTTAGCAAGAGCTCAAGCTCTAAGCTGTGATCTTAAGGCTTGCAGGATCAATACCAC
* **
9641114 AGCCCCCAAAAATAGTTAACGAAAGCTAAAGCTCCCAGCTATAGTATTAATGCTTGTAAGTTCAA
196 AGCCCCCAAAAATAGTTAACGAAAGCTAAAGCTCCCAGCTATAGTATTAAGGCTCATAAGTTCAA
* * * * * * * *
9641179 CACCATAGCCTCTAAAATAGTTAGCTAGAGCTAAGCTCCCAGCTGTAATCTTAGGGCCTGCAGGT
261 CACCACAGCCTCCAAAACAGTTAGCTAAACCTAAGCTCCCAACTGTAATCTTAAGGCCT-CAGAT
* *
9641244 TCAATATCCTAGCCTCCAAAAATAGTTAATGACGGTTAAGGCTCTCAGCTACGATATTAATGCTA
325 TCAACATCCTAACCTCC-AAAATAGTTAATGACGGTTAAGGCTCTCAGCTACGATATTAATGCTA
9641309 GCAGGTTCAATATCGCAACCCCGAAAAATAG
389 GCAGGTTCAATATCGCAACCCCGAAAAATAG
** ***
9641340 TTAACAAGAGCTAAGGCTCTTAGTT-TTGATCTTAAGGCTCGCAGGCTCAATACTGTATCCTCTA
1 TTAACAAGAGCTAAGGCTCCCA-TTGTT-ATCTTAAGGCTCGCAGGCTCAATACCACATCCTCTA
* ** * *
9641404 AAACAGTTAGCG-AGAGTTAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGTTCAATACCGTAG
64 AAACAGATAG-GAAGAACTAAGGCTCCCAACTATGATCTTAAGGCTCGCAGGTTCAATACCATAG
* * * **
9641468 CCTCTAAAATAGTTAGCGAGAGCTCAAGCTCTCAGCTGTGATCTTAAGGTTTGCAGGATCAATGT
128 CCTCTAAAATAGTTAGCAAGAGCTCAAGCTCTAAGCTGTGATCTTAAGGCTTGCAGGATCAATAC
* * * * * * * *
9641533 CACAGCCTCTAAAACT-GTTAGCGAGAGCTCAAGCTCCTA-CT-T-GTGATCTTAAGGCTCATAG
193 CACAGCCCCCAAAAATAGTTAACGAAAGCTAAAGCTCCCAGCTATAGT-A--TTAAGGCTCATAA
* * *
9641594 GTTCAACACCACAGCCTCCAAAACAGTTAG-TACAACCTGAATCTCCCAATTGT-AGCTTTAAGG
255 GTTCAACACCACAGCCTCCAAAACAGTTAGCTA-AACCT-AAGCTCCCAACTGTAATC-TTAAGG
9641657 -CTCATAGATTCAACATCGC-AACCTCCAAAATAGTT
317 CCTC--AGATTCAACATC-CTAACCTCCAAAATAGTT
9641692 CAAGCTCATG
Statistics
Matches: 289, Mismatches: 51, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
418 2 0.01
419 2 0.01
420 5 0.02
421 92 0.32
422 186 0.64
423 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.27
Consensus pattern (419 bp):
TTAACAAGAGCTAAGGCTCCCATTGTTATCTTAAGGCTCGCAGGCTCAATACCACATCCTCTAAA
ACAGATAGGAAGAACTAAGGCTCCCAACTATGATCTTAAGGCTCGCAGGTTCAATACCATAGCCT
CTAAAATAGTTAGCAAGAGCTCAAGCTCTAAGCTGTGATCTTAAGGCTTGCAGGATCAATACCAC
AGCCCCCAAAAATAGTTAACGAAAGCTAAAGCTCCCAGCTATAGTATTAAGGCTCATAAGTTCAA
CACCACAGCCTCCAAAACAGTTAGCTAAACCTAAGCTCCCAACTGTAATCTTAAGGCCTCAGATT
CAACATCCTAACCTCCAAAATAGTTAATGACGGTTAAGGCTCTCAGCTACGATATTAATGCTAGC
AGGTTCAATATCGCAACCCCGAAAAATAG
Found at i:9642721 original size:24 final size:24
Alignment explanation
Indices: 9642668--9642721 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
9642658 GGTGACACAG
* *
9642668 AGCTAGCTTACCATTGTTTTCAGC
1 AGCTAGCTCACCACTGTTTTCAGC
* *
9642692 AACTAGCTCACCACTGTTTTCAGT
1 AGCTAGCTCACCACTGTTTTCAGC
9642716 AGCTAG
1 AGCTAG
9642722 TTCCCTAGCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (24 bp):
AGCTAGCTCACCACTGTTTTCAGC
Found at i:9644611 original size:33 final size:33
Alignment explanation
Indices: 9644574--9644636 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
9644564 AGGGAAGCTT
* **
9644574 GCGATATCGGCTCACGGGAGTTGAAGGGAGTTC
1 GCGATATCAGCTCACAAGAGTTGAAGGGAGTTC
*
9644607 GCGATATCAGCTCGCAAGAGTTGAAGGGAG
1 GCGATATCAGCTCACAAGAGTTGAAGGGAG
9644637 CTCATAGCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.25, C:0.17, G:0.38, T:0.19
Consensus pattern (33 bp):
GCGATATCAGCTCACAAGAGTTGAAGGGAGTTC
Found at i:9647021 original size:13 final size:14
Alignment explanation
Indices: 9646979--9647023 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
9646969 TAATAATGAT
9646979 TAAAGTATATTATAA
1 TAAAGTA-ATTATAA
9646994 TAATA-TAA-TATAA
1 TAA-AGTAATTATAA
9647007 TAAAGTAATTA-AA
1 TAAAGTAATTATAA
9647020 TAAA
1 TAAA
9647024 ACAAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.04
13 17 0.63
14 3 0.11
15 5 0.19
16 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (14 bp):
TAAAGTAATTATAA
Found at i:9647900 original size:20 final size:20
Alignment explanation
Indices: 9647877--9647915 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
9647867 TGTGTCCATA
9647877 AGACACTATATCTGTCGACG
1 AGACACTATATCTGTCGACG
*
9647897 AGACACTATATGTGTCGAC
1 AGACACTATATCTGTCGAC
9647916 TACTATGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (20 bp):
AGACACTATATCTGTCGACG
Found at i:9650316 original size:17 final size:17
Alignment explanation
Indices: 9650291--9650327 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
9650281 TTGTTAAAGA
*
9650291 ATCTATTTGGATTTTGC
1 ATCTATTTGGATTTTAC
*
9650308 ATCTGTTTGGATTTTAC
1 ATCTATTTGGATTTTAC
9650325 ATC
1 ATC
9650328 AATCTGTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (17 bp):
ATCTATTTGGATTTTAC
Found at i:9650355 original size:3 final size:3
Alignment explanation
Indices: 9650342--9650378 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
9650332 TGTTGAAGAA
*
9650342 TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
9650379 TTATGCTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:9652297 original size:15 final size:15
Alignment explanation
Indices: 9652277--9652308 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
9652267 AATGCATTTC
9652277 TTGTATTGTTCTAAG
1 TTGTATTGTTCTAAG
*
9652292 TTGTATTGTTCTGAG
1 TTGTATTGTTCTAAG
9652307 TT
1 TT
9652309 TTAAGTATAT
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:0.16, C:0.06, G:0.22, T:0.56
Consensus pattern (15 bp):
TTGTATTGTTCTAAG
Found at i:9652759 original size:21 final size:22
Alignment explanation
Indices: 9652735--9652789 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
9652725 TTTAATATAA
* *
9652735 TAAAATATTT-TTTTTACAATT
1 TAAAATATTTAATTTTAAAATT
*
9652756 TAAAGTATTTAATTTTAAAATT
1 TAAAATATTTAATTTTAAAATT
*
9652778 TAAAATAATTAA
1 TAAAATATTTAA
9652790 GTCCAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TAAAATATTTAATTTTAAAATT
Found at i:9655950 original size:8 final size:8
Alignment explanation
Indices: 9655934--9655966 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
9655924 TAATCATTCT
*
9655934 TTATTTTA
1 TTATATTA
9655942 TTATATTA
1 TTATATTA
9655950 TTATATTA
1 TTATATTA
9655958 TTATATTA
1 TTATATTA
9655966 T
1 T
9655967 ATTTAGTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTATATTA
Found at i:9657483 original size:96 final size:96
Alignment explanation
Indices: 9657319--9657508 Score: 380
Period size: 96 Copynumber: 2.0 Consensus size: 96
9657309 CTAAAATGAG
9657319 CTGATTTCGTAAGTCGATCAACGATTACCCAGATAGCATTCTTTTTACTTGTAGACAGTGGCAAC
1 CTGATTTCGTAAGTCGATCAACGATTACCCAGATAGCATTCTTTTTACTTGTAGACAGTGGCAAC
9657384 CCAGTTACAAAATCCATTGTTATTCGGTCTC
66 CCAGTTACAAAATCCATTGTTATTCGGTCTC
9657415 CTGATTTCGTAAGTCGATCAACGATTACCCAGATAGCATTCTTTTTACTTGTAGACAGTGGCAAC
1 CTGATTTCGTAAGTCGATCAACGATTACCCAGATAGCATTCTTTTTACTTGTAGACAGTGGCAAC
9657480 CCAGTTACAAAATCCATTGTTATTCGGTC
66 CCAGTTACAAAATCCATTGTTATTCGGTC
9657509 CCATTTCAAT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (96 bp):
CTGATTTCGTAAGTCGATCAACGATTACCCAGATAGCATTCTTTTTACTTGTAGACAGTGGCAAC
CCAGTTACAAAATCCATTGTTATTCGGTCTC
Found at i:9663266 original size:13 final size:13
Alignment explanation
Indices: 9663250--9663286 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
9663240 ATAATCATTC
*
9663250 TTTATTTTATTAT
1 TTTATTATATTAT
9663263 TTTATTATATTAT
1 TTTATTATATTAT
*
9663276 TATATTATATT
1 TTTATTATATT
9663287 TAGTAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTATTATATTAT
Found at i:9664424 original size:27 final size:27
Alignment explanation
Indices: 9664380--9664466 Score: 84
Period size: 27 Copynumber: 3.0 Consensus size: 27
9664370 TTTTGAAATT
* * *
9664380 ATTATGTCTTGAATTTGTTAGATATTG
1 ATTATGTTTTAAACTTGTTAGATATTG
9664407 ATTATGTTTTAAACTTGTTAGATATTG
1 ATTATGTTTTAAACTTGTTAGATATTG
* *
9664434 AATTTATTATGTTTTAAGCTTGTTGGATATTG
1 -----ATTATGTTTTAAACTTGTTAGATATTG
9664466 A
1 A
9664467 ATTTATTATG
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
27 25 0.50
32 25 0.50
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.52
Consensus pattern (27 bp):
ATTATGTTTTAAACTTGTTAGATATTG
Found at i:9664446 original size:32 final size:32
Alignment explanation
Indices: 9664407--9664499 Score: 150
Period size: 32 Copynumber: 2.9 Consensus size: 32
9664397 TTAGATATTG
*
9664407 ATTATGTTTTAAACTTGTTAGATATTGAATTT
1 ATTATGTTTTAAACTTGTTGGATATTGAATTT
*
9664439 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
1 ATTATGTTTTAAACTTGTTGGATATTGAATTT
* *
9664471 ATTATGTTTCAAACTTGTTGGATTTTGAA
1 ATTATGTTTTAAACTTGTTGGATATTGAA
9664500 ATTGACAATG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.28, C:0.04, G:0.16, T:0.52
Consensus pattern (32 bp):
ATTATGTTTTAAACTTGTTGGATATTGAATTT
Found at i:9665484 original size:29 final size:29
Alignment explanation
Indices: 9665445--9665504 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
9665435 TTTTAATGTG
9665445 GTGTAATATTAGTTATGCACTTGGACAAT
1 GTGTAATATTAGTTATGCACTTGGACAAT
9665474 GTGTAATATTAGTTATGCACTTGGACAAT
1 GTGTAATATTAGTTATGCACTTGGACAAT
9665503 GT
1 GT
9665505 TGTTGTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (29 bp):
GTGTAATATTAGTTATGCACTTGGACAAT
Found at i:9665821 original size:24 final size:24
Alignment explanation
Indices: 9665764--9665821 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
9665754 AAAAATAATT
9665764 TAAAATATAAATTTATTAATATATA
1 TAAAA-ATAAATTTATTAATATATA
* * * *
9665789 TATATATAAATTTATTTATATATG
1 TAAAAATAAATTTATTAATATATA
9665813 TAAAAATAA
1 TAAAAATAA
9665822 CTTTTTCGGA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 24 0.89
25 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TAAAAATAAATTTATTAATATATA
Found at i:9665920 original size:19 final size:20
Alignment explanation
Indices: 9665896--9665936 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
9665886 CAAACACCAC
*
9665896 AAAGTAAATTA-TTTCCAGA
1 AAAGTAAATCATTTTCCAGA
9665915 AAAGTAAATCATTTTCCAGA
1 AAAGTAAATCATTTTCCAGA
9665935 AA
1 AA
9665937 TCATTTTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (20 bp):
AAAGTAAATCATTTTCCAGA
Found at i:9665950 original size:14 final size:14
Alignment explanation
Indices: 9665920--9665965 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
9665910 CCAGAAAAGT
**
9665920 AAATCATTTTCCAG
1 AAATCATTTTCTGG
9665934 AAATCATTTTCTGG
1 AAATCATTTTCTGG
*
9665948 AAAACATTTTACTGG
1 AAATCATTTT-CTGG
9665963 AAA
1 AAA
9665966 ATAAACGGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 21 0.75
15 7 0.25
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (14 bp):
AAATCATTTTCTGG
Found at i:9668269 original size:14 final size:15
Alignment explanation
Indices: 9668245--9668293 Score: 75
Period size: 14 Copynumber: 3.4 Consensus size: 15
9668235 TTTATTGGAT
9668245 TTATATTGATTGAAA
1 TTATATTGATTGAAA
*
9668260 TTAT-TTGATTGAAT
1 TTATATTGATTGAAA
9668274 TTATATTGATTG-AA
1 TTATATTGATTGAAA
9668288 TTATAT
1 TTATAT
9668294 AATATATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:9668275 original size:29 final size:27
Alignment explanation
Indices: 9668234--9668291 Score: 89
Period size: 29 Copynumber: 2.1 Consensus size: 27
9668224 TATGCGATGA
*
9668234 ATTTATTGGATTTATATTGATTGAAATT
1 ATTTATTGAATTTATATTGATTG-AATT
9668262 ATTTGATTGAATTTATATTGATTGAATT
1 ATTT-ATTGAATTTATATTGATTGAATT
9668290 AT
1 AT
9668292 ATAATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (27 bp):
ATTTATTGAATTTATATTGATTGAATT
Found at i:9668695 original size:23 final size:23
Alignment explanation
Indices: 9668665--9668751 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
9668655 GCTTTATCGA
* *
9668665 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
9668688 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
9668709 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
9668731 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
9668752 ACTGATTAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:9676973 original size:19 final size:19
Alignment explanation
Indices: 9676945--9676983 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
9676935 TTTAAAACAA
*
9676945 AGAGAGAGTCGAATTCAAC
1 AGAGAAAGTCGAATTCAAC
*
9676964 AGAGAAAGTCGAATTTAAC
1 AGAGAAAGTCGAATTCAAC
9676983 A
1 A
9676984 TCCCTCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.13, G:0.23, T:0.18
Consensus pattern (19 bp):
AGAGAAAGTCGAATTCAAC
Found at i:9684251 original size:104 final size:105
Alignment explanation
Indices: 9684042--9684253 Score: 363
Period size: 104 Copynumber: 2.0 Consensus size: 105
9684032 TGTTGCTCTA
*
9684042 ATACAAATGTTATTATAGTACTACTCTAATTTGTTTCCTCAAGTGTGTTTTTTTTTGTTGTTGTA
1 ATACAAATGTTATTATAGTACTACTCTAATTTGTTTCCTCAAGTGTG-TCTTTTTTGTTGTTGTA
*
9684107 ATAAAGCATGTTATGAAGAGTTAGTATGCTTTTAATTGTGC
65 ATAAAGCATGTTATGAAGAGTTAGTATGCTTTGAATTGTGC
* *
9684148 ATACAGATGTTATTATAGTACTACTCTAATTTGTTTCCTCAAGTGTG-CTTTTTTGTTGTTGTAC
1 ATACAAATGTTATTATAGTACTACTCTAATTTGTTTCCTCAAGTGTGTCTTTTTTGTTGTTGTAA
*
9684212 TGAAGCATGTTATGAAGAGTTAGTATGCTTTGAATTGTGC
66 TAAAGCATGTTATGAAGAGTTAGTATGCTTTGAATTGTGC
9684252 AT
1 AT
9684254 TTGTATATAG
Statistics
Matches: 101, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
104 55 0.54
106 46 0.46
ACGTcount: A:0.25, C:0.10, G:0.18, T:0.46
Consensus pattern (105 bp):
ATACAAATGTTATTATAGTACTACTCTAATTTGTTTCCTCAAGTGTGTCTTTTTTGTTGTTGTAA
TAAAGCATGTTATGAAGAGTTAGTATGCTTTGAATTGTGC
Found at i:9701539 original size:6 final size:6
Alignment explanation
Indices: 9701528--9701557 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
9701518 TATACACAAT
9701528 TGCATG TGCATG TGCATG TGCATG TGCATG
1 TGCATG TGCATG TGCATG TGCATG TGCATG
9701558 GCCTTAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (6 bp):
TGCATG
Found at i:9708225 original size:127 final size:127
Alignment explanation
Indices: 9708073--9708329 Score: 340
Period size: 127 Copynumber: 2.0 Consensus size: 127
9708063 AAAATGGAAA
* * *
9708073 AACTCCTCAATAGAAGATAAGAAACTACAGACAAAAGGAGATTTCACTATAATCAATGAGAGTAC
1 AACTCCTCAAAAGAAGATAAAAAACTACAGACAAAAGGAGATTTCACTATAATAAATGAGAGTAC
*
9708138 AAAACAT-AGAGAGAATTAAAAGAAAAACTCGAAA-CCCACAAGAAAAACCCCTT-GAAACAAAG
66 AAAACATGA-AGAGAATTAAAA-AAAAACTCAAAACCCCACAAGAAAAA-CCCTTCGAAACAAAG
* * * ** *
9708200 AACTCCTTAAAAGAGGATAAAAAACTACGGACAAAAGGAGATTTTGCTATAATAAATTAGAGTAC
1 AACTCCTCAAAAGAAGATAAAAAACTACAGACAAAAGGAGATTTCACTATAATAAATGAGAGTAC
* * * *
9708265 AAAAGATGAAGAGGATTAAAAAAAAACTCAAAACCCCATAAGAAAAATCCTTCGAAACAAAG
66 AAAACATGAAGAGAATTAAAAAAAAACTCAAAACCCCACAAGAAAAACCCTTCGAAACAAAG
9708327 AAC
1 AAC
9708330 GAAATTCTCT
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
126 15 0.13
127 97 0.86
128 1 0.01
ACGTcount: A:0.53, C:0.16, G:0.14, T:0.16
Consensus pattern (127 bp):
AACTCCTCAAAAGAAGATAAAAAACTACAGACAAAAGGAGATTTCACTATAATAAATGAGAGTAC
AAAACATGAAGAGAATTAAAAAAAAACTCAAAACCCCACAAGAAAAACCCTTCGAAACAAAG
Found at i:9710764 original size:5 final size:5
Alignment explanation
Indices: 9710754--9710787 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
9710744 AAATGCATCG
*
9710754 AATTA AATTA AATTA AATT- AATTA GATTA AATTA
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA
9710788 TCTTTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (5 bp):
AATTA
Found at i:9710776 original size:14 final size:14
Alignment explanation
Indices: 9710754--9710787 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
9710744 AAATGCATCG
9710754 AATTAAATTAAATTA
1 AATT-AATTAAATTA
*
9710769 AATTAATTAGATTA
1 AATTAATTAAATTA
9710783 AATTA
1 AATTA
9710788 TCTTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
AATTAATTAAATTA
Found at i:9714482 original size:31 final size:31
Alignment explanation
Indices: 9714422--9714482 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
9714412 GAGAAATTAT
* * **
9714422 TTTTACTCTCTTAATTAATTAATGTAAAATA
1 TTTTAATCTCTTAATAAATTAATAAAAAATA
*
9714453 TTTTAATCTCTTACTAAATTAATAAAAAAT
1 TTTTAATCTCTTAATAAATTAATAAAAAAT
9714483 GTCTTTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.46
Consensus pattern (31 bp):
TTTTAATCTCTTAATAAATTAATAAAAAATA
Found at i:9715922 original size:44 final size:44
Alignment explanation
Indices: 9715871--9715962 Score: 166
Period size: 44 Copynumber: 2.1 Consensus size: 44
9715861 AATTCATAAT
* *
9715871 TTAATTTATTTATTTTAATATTATACATATTTCATGTGTTTTTA
1 TTAATTTATTTATTTTAATACTATACATATTTCATGTGTTATTA
9715915 TTAATTTATTTATTTTAATACTATACATATTTCATGTGTTATTA
1 TTAATTTATTTATTTTAATACTATACATATTTCATGTGTTATTA
9715959 TTAA
1 TTAA
9715963 GTCATATAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (44 bp):
TTAATTTATTTATTTTAATACTATACATATTTCATGTGTTATTA
Found at i:9716032 original size:19 final size:20
Alignment explanation
Indices: 9716005--9716042 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
9715995 TATATGTTAC
*
9716005 TTTTAAATATGT-ATTTTTA
1 TTTTAAATACGTAATTTTTA
*
9716024 TTTTGAATACGTAATTTTT
1 TTTTAAATACGTAATTTTT
9716043 TTACATCTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (20 bp):
TTTTAAATACGTAATTTTTA
Found at i:9719279 original size:14 final size:14
Alignment explanation
Indices: 9719260--9719302 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
9719250 TTGAATAAAA
9719260 AAATATAATAATTT
1 AAATATAATAATTT
*
9719274 AAATAT-CTAATGTT
1 AAATATAATAAT-TT
*
9719288 AAAAATAATAATTT
1 AAATATAATAATTT
9719302 A
1 A
9719303 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 4 0.17
14 16 0.67
15 4 0.17
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (14 bp):
AAATATAATAATTT
Found at i:9724707 original size:37 final size:36
Alignment explanation
Indices: 9724637--9724709 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
9724627 GTTGCTACCA
* *
9724637 TTTTGTTGTTAATGTTTGAATATTGTATAACATTTG
1 TTTTATTGTTAATGTTTGAATATTGTAGAACATTTG
9724673 TTTTATTGTTAAT-TTTGCTAATATT-TAGAGACATTTG
1 TTTTATTGTTAATGTTTG--AATATTGTAGA-ACATTTG
9724710 CTTGTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 4 0.12
36 15 0.47
37 13 0.41
ACGTcount: A:0.26, C:0.04, G:0.15, T:0.55
Consensus pattern (36 bp):
TTTTATTGTTAATGTTTGAATATTGTAGAACATTTG
Found at i:9733574 original size:12 final size:12
Alignment explanation
Indices: 9733557--9733581 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9733547 AATTTAGATT
9733557 AAATAATTTTAA
1 AAATAATTTTAA
9733569 AAATAATTTTAA
1 AAATAATTTTAA
9733581 A
1 A
9733582 TATATTAATG
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATAATTTTAA
Found at i:9738649 original size:18 final size:20
Alignment explanation
Indices: 9738628--9738677 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
9738618 AATCAATATA
9738628 ATTTTTAAAATT-TAAAA-T
1 ATTTTTAAAATTCTAAAATT
*
9738646 ATTTATAAGAATTCTAAAATTT
1 ATTTTTAA-AATTCTAAAA-TT
9738668 ATTTTTAAAA
1 ATTTTTAAAA
9738678 AAAATTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 7 0.27
19 4 0.15
20 5 0.19
21 2 0.08
22 8 0.31
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTTTTAAAATTCTAAAATT
Found at i:9739821 original size:8 final size:8
Alignment explanation
Indices: 9739808--9739832 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9739798 AAAAAAAGAT
9739808 ATTCAAAA
1 ATTCAAAA
9739816 ATTCAAAA
1 ATTCAAAA
9739824 ATTCAAAA
1 ATTCAAAA
9739832 A
1 A
9739833 AGTAAAACCT
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:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (8 bp):
ATTCAAAA
Found at i:9742105 original size:20 final size:20
Alignment explanation
Indices: 9742076--9742121 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
9742066 GAGAGTGATT
*
9742076 AATTAAAGTTTAATGAAGCA
1 AATTAGAGTTTAATGAAGCA
9742096 AATTAGAGTTTAATGAAGCA
1 AATTAGAGTTTAATGAAGCA
9742116 AATTAG
1 AATTAG
9742122 CTTAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.30
Consensus pattern (20 bp):
AATTAGAGTTTAATGAAGCA
Found at i:9742672 original size:85 final size:85
Alignment explanation
Indices: 9742529--9742695 Score: 325
Period size: 85 Copynumber: 2.0 Consensus size: 85
9742519 AACCCTGTTC
*
9742529 TGGCGACAGTATAGGGTTAGGAGACGTTACAAAGTAAGTTTTTTTGGAACTGCCATTCAAAAAAA
1 TGGCGACAGTATAGGGTTAGGAGACATTACAAAGTAAGTTTTTTTGGAACTGCCATTCAAAAAAA
9742594 AGTTATTCAGTGCTATATTA
66 AGTTATTCAGTGCTATATTA
9742614 TGGCGACAGTATAGGGTTAGGAGACATTACAAAGTAAGTTTTTTTGGAACTGCCATTCAAAAAAA
1 TGGCGACAGTATAGGGTTAGGAGACATTACAAAGTAAGTTTTTTTGGAACTGCCATTCAAAAAAA
9742679 AGTTATTCAGTGCTATA
66 AGTTATTCAGTGCTATA
9742696 GTCGGATGTC
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (85 bp):
TGGCGACAGTATAGGGTTAGGAGACATTACAAAGTAAGTTTTTTTGGAACTGCCATTCAAAAAAA
AGTTATTCAGTGCTATATTA
Found at i:9756318 original size:20 final size:20
Alignment explanation
Indices: 9756293--9756330 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9756283 AAGTATTATT
*
9756293 AGATATTTATTATTTAAAAA
1 AGATATTTATTAATTAAAAA
9756313 AGATATTTATTAATTAAA
1 AGATATTTATTAATTAAA
9756331 TAATTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
AGATATTTATTAATTAAAAA
Found at i:9757743 original size:18 final size:18
Alignment explanation
Indices: 9757722--9757781 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
9757712 GACTGACTGC
*
9757722 TACTGAATAATTGACTAT
1 TACTGAATAAATGACTAT
*
9757740 TACTGAATAAACGACTGA-
1 TACTGAATAAATGACT-AT
* *
9757758 TACTGAATAAATGATTGT
1 TACTGAATAAATGACTAT
9757776 TACTGA
1 TACTGA
9757782 TTAACCGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 34 0.97
19 1 0.03
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (18 bp):
TACTGAATAAATGACTAT
Done.