Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold109
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: 1855911
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.34
Warning! 69956 characters in sequence are not A, C, G, or T
File 5 of 13
Found at i:588629 original size:263 final size:262
Alignment explanation
Indices: 588321--588916 Score: 1012
Period size: 263 Copynumber: 2.3 Consensus size: 262
588311 AAATAACGGG
* * * *
588321 GTTGGAGTATCCCCAATGAAAAGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCC
1 GTTGGAGTAT-CCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGAGGTTGGAGTATCCC
*
588386 TGATTGTGAAAAATTAGTGTTTTAGAGATAAAACCGGGGTTGAAGTATCCCCGATTATGGAAAAT
65 CGATTGTGAAAAATTAGTGTTTTAGAGATAAAACCGGGGTTGAAGTATCCCCGATTATGGAAAAT
* *
588451 TGATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTTGGAGGTAATGGGGTTGGAGTATCCC
130 TGATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGCAATGGGGTTGGAGTATCCC
* *
588516 CGATGAAATAACGAGATTGGAGTATCCTCGCTTGTGAAAAATTGGTGTTTTTTGGAAATAAAATC
195 CGATGAAATAACGAGATTGGAGTATCCTCGCTTGTGAAAAATTAGTATTTTTTGGAAATAAAATC
588581 GGA
260 GGA
588584 GTTGGAGTATCCCTGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGAGGTTGGAGTATCCC
1 GTTGGAGTATCCC-GATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGAGGTTGGAGTATCCC
* *
588649 CGATTGTGGAAAATTAGTGTTTTAGAGATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAT
65 CGATTGTGAAAAATTAGTGTTTTAGAGATAAAACCGGGGTTGAAGTATCCCCGATTATGGAAAAT
* **
588714 TGATATTTTGGAAATAACGCCGGGGTTGGAGTATCCCCTCGGAGGCAATGGGGTTGGAGTATCTG
130 TGATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGCAATGGGGTTGGAGTATCCC
*
588779 CGATGAAATAACGAGGTTGGAGTATCCTCGCTTGTGAAAAATTAGTATTTTTTGGAAATAAAATC
195 CGATGAAATAACGAGATTGGAGTATCCTCGCTTGTGAAAAATTAGTATTTTTTGGAAATAAAATC
588844 GGA
260 GGA
* *
588847 GTTGGAGTATCTCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGAGATTGGAGTATCCC
1 GTTGGAGTATC-CCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGAGGTTGGAGTATCCC
588912 CGATT
65 CGATT
588917 ATAAATAATT
Statistics
Matches: 314, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
262 3 0.01
263 309 0.98
264 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (262 bp):
GTTGGAGTATCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGAGGTTGGAGTATCCCC
GATTGTGAAAAATTAGTGTTTTAGAGATAAAACCGGGGTTGAAGTATCCCCGATTATGGAAAATT
GATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGCAATGGGGTTGGAGTATCCCC
GATGAAATAACGAGATTGGAGTATCCTCGCTTGTGAAAAATTAGTATTTTTTGGAAATAAAATCG
GA
Found at i:591357 original size:13 final size:13
Alignment explanation
Indices: 591339--591390 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
591329 AGCTTCGTAG
591339 CGATACATTGTAT
1 CGATACATTGTAT
591352 CGATACAACACTTATGTAT
1 CGAT---ACA-TT--GTAT
591371 CGATACATTGTAT
1 CGATACATTGTAT
591384 CGATACA
1 CGATACA
591391 ACATTTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 15 0.45
15 2 0.06
16 6 0.18
17 2 0.06
19 8 0.24
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:591371 original size:19 final size:17
Alignment explanation
Indices: 591346--591410 Score: 66
Period size: 19 Copynumber: 3.8 Consensus size: 17
591336 TAGCGATACA
591346 TTGTATCGATACAACACT
1 TTGTATCGATACAACA-T
591364 TATGTATCGAT---ACA-
1 T-TGTATCGATACAACAT
591378 TTGTATCGATACAACATTT
1 TTGTATCGATACAACA--T
591397 TTGTATCGATACAA
1 TTGTATCGATACAA
591411 ATCATTGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 9 0.22
14 1 0.03
16 6 0.15
18 1 0.03
19 23 0.57
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (17 bp):
TTGTATCGATACAACAT
Found at i:591380 original size:32 final size:32
Alignment explanation
Indices: 591339--591409 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
591329 AGCTTCGTAG
591339 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
* *
591371 CGATACATTGTATCGATACAACATTTTTGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
591403 CGATACA
1 CGATACA
591410 AATCATTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:591523 original size:10 final size:11
Alignment explanation
Indices: 591495--591523 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
591485 ACAAAAATGT
591495 TTTTTTTTAAA
1 TTTTTTTTAAA
591506 TTTTTTTT-AA
1 TTTTTTTTAAA
591516 TTTTTTTT
1 TTTTTTTT
591524 CTTTATCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTTTAAA
Found at i:591744 original size:2 final size:2
Alignment explanation
Indices: 591737--591764 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
591727 AAGTGTCTAC
591737 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
591765 GAGTGGATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:593993 original size:2 final size:2
Alignment explanation
Indices: 593988--594019 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
593978 TGTGTGTGTG
593988 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
594020 TAGATGGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:594008 original size:15 final size:15
Alignment explanation
Indices: 593988--594017 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
593978 TGTGTGTGTG
593988 TATATATATATATAT
1 TATATATATATATAT
594003 TATATATATATATAT
1 TATATATATATATAT
594018 ATTAGATGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:594010 original size:17 final size:17
Alignment explanation
Indices: 593988--594021 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
593978 TGTGTGTGTG
593988 TATATATATATATATTA
1 TATATATATATATATTA
594005 TATATATATATATATTA
1 TATATATATATATATTA
594022 GATGGTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATTA
Found at i:594209 original size:13 final size:12
Alignment explanation
Indices: 594175--594211 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
594165 TATCGAATAC
594175 ATATTATATTCG
1 ATATTATATTCG
594187 -TATTATATTCG
1 ATATTATATTCG
594198 ATATTCATATTCG
1 ATATT-ATATTCG
594211 A
1 A
594212 ATTCGAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.48
12 4 0.17
13 8 0.35
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (12 bp):
ATATTATATTCG
Found at i:594457 original size:40 final size:39
Alignment explanation
Indices: 594406--594485 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 39
594396 TCGAGTAATT
* *
594406 TGTTTCGTTCGGTTTGATTTGGGTTCGGTCTGGTTCGAG
1 TGTTTCGTTCGGTTTAATTTGGGTTCGGTCTAGTTCGAG
594445 TGTTTCAGTTCGGTTTAATTTGGGTTCGGTCTAGTTCGAG
1 TGTTTC-GTTCGGTTTAATTTGGGTTCGGTCTAGTTCGAG
594485 T
1 T
594486 TTAATTCAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 6 0.16
40 32 0.84
ACGTcount: A:0.09, C:0.12, G:0.33, T:0.46
Consensus pattern (39 bp):
TGTTTCGTTCGGTTTAATTTGGGTTCGGTCTAGTTCGAG
Found at i:594548 original size:20 final size:19
Alignment explanation
Indices: 594524--594573 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
594514 ATCAGTTCAA
*
594524 TTTAATTTAAATTATTATT
1 TTTAATTTAAATTAATATT
*
594543 TATTAA-TTAAAATAATATT
1 T-TTAATTTAAATTAATATT
594562 TTT-ATTTAAATT
1 TTTAATTTAAATT
594574 TAATTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 1 0.04
18 8 0.31
19 13 0.50
20 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAATTTAAATTAATATT
Found at i:594603 original size:20 final size:20
Alignment explanation
Indices: 594568--594614 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
594558 TATTTTTATT
594568 TAAAT-TTAATTAAAAATATA
1 TAAATATTAATTAAAAATA-A
594588 TAAATATTAATT-AAAATAA
1 TAAATATTAATTAAAAATAA
*
594607 TTAATATT
1 TAAATATT
594615 TATATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 8 0.32
20 11 0.44
21 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATATTAATTAAAAATAA
Found at i:594662 original size:7 final size:7
Alignment explanation
Indices: 594650--594678 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
594640 TTAATCAATA
594650 TAAATTT
1 TAAATTT
594657 TAAATTT
1 TAAATTT
594664 TAAATTT
1 TAAATTT
594671 TAAATTT
1 TAAATTT
594678 T
1 T
594679 TTTGAATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TAAATTT
Found at i:595038 original size:33 final size:36
Alignment explanation
Indices: 594992--595060 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 36
594982 ATTTTTAATT
594992 ATATTATATTAATT-A-TAATAATAAATA-TAATAA
1 ATATTATATTAATTAATTAATAATAAATATTAATAA
*
595025 ATATTAT-TGTAATTAATTTATAATAAATATTAATAA
1 ATATTATAT-TAATTAATTAATAATAAATATTAATAA
595061 TAAAAACATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 1 0.03
33 12 0.39
34 1 0.03
35 11 0.35
36 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (36 bp):
ATATTATATTAATTAATTAATAATAAATATTAATAA
Found at i:595382 original size:7 final size:7
Alignment explanation
Indices: 595335--595439 Score: 56
Period size: 7 Copynumber: 15.0 Consensus size: 7
595325 ATTAATTTTT
595335 ATTT-AA
1 ATTTAAA
595341 ATTT-AA
1 ATTTAAA
595347 ATTTAAA
1 ATTTAAA
* *
595354 TTTTAATT
1 ATTTAA-A
595362 ATTT-AA
1 ATTTAAA
**
595368 ATAAAAA
1 ATTTAAA
595375 ATTTAAA
1 ATTTAAA
**
595382 ATTTATG
1 ATTTAAA
595389 ATTATAAA
1 ATT-TAAA
* *
595397 AATCATAA
1 ATTTA-AA
*
595405 ATTTTAA
1 ATTTAAA
*
595412 ATATAAA
1 ATTTAAA
595419 ATTTTAAA
1 A-TTTAAA
595427 ATTT-AA
1 ATTTAAA
595433 ATTTAAA
1 ATTTAAA
595440 TCTAAATTTT
Statistics
Matches: 72, Mismatches: 20, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
6 18 0.25
7 37 0.51
8 17 0.24
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (7 bp):
ATTTAAA
Found at i:595426 original size:21 final size:21
Alignment explanation
Indices: 595336--595439 Score: 77
Period size: 21 Copynumber: 4.9 Consensus size: 21
595326 TTAATTTTTA
*
595336 TTTAAA-TTTAAAT-TTAAAT
1 TTTAAATTTTAAATATAAAAT
* *
595355 TTTAATTATTTAAATAAAAAAT
1 TTTAAAT-TTTAAATATAAAAT
* * *
595377 TTAAAATTTATGATTATAAAAAT
1 TTTAAATTT-TAAATAT-AAAAT
**
595400 CATAAATTTTAAATATAAAAT
1 TTTAAATTTTAAATATAAAAT
* *
595421 TTTAAAATTTAAATTTAAA
1 TTTAAATTTTAAATATAAA
595440 TCTAAATTTT
Statistics
Matches: 63, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
19 5 0.08
21 29 0.46
22 18 0.29
23 11 0.17
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (21 bp):
TTTAAATTTTAAATATAAAAT
Found at i:595645 original size:21 final size:21
Alignment explanation
Indices: 595621--595660 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
595611 TATTTTTATT
*
595621 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TAAAAAATATA
595642 TAAATATTAATAAAAAATA
1 TAAATATTAATAAAAAATA
595661 ATTTGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATATTAATAAAAAATATA
Found at i:595719 original size:24 final size:24
Alignment explanation
Indices: 595660--595719 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 24
595650 AATAAAAAAT
* *
595660 AATTTGAAATATTTTATTATATTTTA
1 AATTT-AAAT-TTATATTATATATTA
*
595686 AA-TAATAATTTATATTATATATTA
1 AATTTA-AATTTATATTATATATTA
595710 AATTTAAATT
1 AATTTAAATT
595720 AAAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
24 20 0.71
25 6 0.21
26 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
AATTTAAATTTATATTATATATTA
Found at i:600788 original size:12 final size:12
Alignment explanation
Indices: 600773--600812 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
600763 AATTTTTATT
600773 TAAATATAATTA
1 TAAATATAATTA
600785 TAAATTATAA-TA
1 TAAA-TATAATTA
600797 TAAATATAAATTA
1 TAAATAT-AATTA
600810 TAA
1 TAA
600813 TTTTTTTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.12
12 12 0.48
13 10 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TAAATATAATTA
Found at i:600788 original size:24 final size:25
Alignment explanation
Indices: 600754--600818 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
600744 AATTATTATT
* *
600754 TAAATAATAAATTTTTATTTAAATA
1 TAAATTATAAATTTTTATATAAATA
* *
600779 T-AATTATAAATTATAATATAAATA
1 TAAATTATAAATTTTTATATAAATA
*
600803 TAAATTATAATTTTTT
1 TAAATTATAAATTTTT
600819 TATCGATTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
24 20 0.62
25 12 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TAAATTATAAATTTTTATATAAATA
Found at i:600796 original size:18 final size:18
Alignment explanation
Indices: 600775--600813 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
600765 TTTTTATTTA
*
600775 AATATAATTATAAATTAT
1 AATATAAATATAAATTAT
600793 AATATAAATATAAATTAT
1 AATATAAATATAAATTAT
600811 AAT
1 AAT
600814 TTTTTTATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATAAATATAAATTAT
Found at i:601744 original size:17 final size:17
Alignment explanation
Indices: 601715--601765 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
601705 TTATAATTTT
*
601715 ATTTAAAAAATTTTAT-
1 ATTTAATAAATTTTATA
601731 ATTTATATAAATTTTAATA
1 ATTTA-ATAAATTTT-ATA
*
601750 ATTTAATAATTTTTAT
1 ATTTAATAAATTTTAT
601766 TATATTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 5 0.17
17 10 0.33
18 10 0.33
19 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTAATAAATTTTATA
Found at i:602065 original size:24 final size:24
Alignment explanation
Indices: 602035--602081 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
602025 AAAAAAAATT
602035 AAATCCAAACTCAATCTTAATTAA
1 AAATCCAAACTCAATCTTAATTAA
*
602059 AAATCCAAACTCAATTTTAATTA
1 AAATCCAAACTCAATCTTAATTA
602082 GAAGTTAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATCCAAACTCAATCTTAATTAA
Found at i:607145 original size:3 final size:3
Alignment explanation
Indices: 607137--607164 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
607127 GGAATTAGTT
607137 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
607165 GTGAATGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:607508 original size:26 final size:28
Alignment explanation
Indices: 607474--607530 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
607464 TTATGAATTT
607474 AAATAATTTTAATTATTATTAAATTA-A
1 AAATAATTTTAATTATTATTAAATTATA
* * *
607501 AAAT-ATTTTTATTTTTATTTAATTATA
1 AAATAATTTTAATTATTATTAAATTATA
607528 AAA
1 AAA
607531 ATATATCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AAATAATTTTAATTATTATTAAATTATA
Found at i:607619 original size:23 final size:20
Alignment explanation
Indices: 607572--607618 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 20
607562 AAAATTTTTC
607572 TAAAATAGCAAAACAAGCTA
1 TAAAATAGCAAAACAAGCTA
607592 TAAAATTAGCATAAACTAAGCT-
1 TAAAA-TAGCA-AAAC-AAGCTA
607614 TAAAA
1 TAAAA
607619 AAATTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.21
21 5 0.21
22 9 0.38
23 5 0.21
ACGTcount: A:0.57, C:0.13, G:0.09, T:0.21
Consensus pattern (20 bp):
TAAAATAGCAAAACAAGCTA
Found at i:608167 original size:18 final size:18
Alignment explanation
Indices: 608108--608155 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
608098 TTATCAATTT
608108 AAATAAAAATT--A-ATA
1 AAATAAAAATTAAAGATA
608123 AAATAAATAAATTAAAGATA
1 AAAT-AA-AAATTAAAGATA
608143 AAATAAAAATTAA
1 AAATAAAAATTAA
608156 TGATGAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 4 0.14
16 2 0.07
17 5 0.18
18 7 0.25
19 3 0.11
20 7 0.25
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (18 bp):
AAATAAAAATTAAAGATA
Found at i:609757 original size:22 final size:21
Alignment explanation
Indices: 609719--609760 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
609709 AAATTAAAAT
* *
609719 ATTTAATTATTTTTAATTTTA
1 ATTTAATTATATATAATTTTA
609740 ATTTAATTTATATATAATTTT
1 ATTTAA-TTATATATAATTTT
609761 TTAATTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTAATTATATATAATTTTA
Found at i:610687 original size:24 final size:24
Alignment explanation
Indices: 610631--610687 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
610621 TAATATATTT
610631 TATTTAAAT-TTAATTATAAAATA
1 TATTTAAATATTAATTATAAAATA
* *
610654 TATATCAATATTAA-TATAAAATAA
1 TATTTAAATATTAATTATAAAAT-A
*
610678 TTTTTAAATA
1 TATTTAAATA
610688 ATTTTTAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
TATTTAAATATTAATTATAAAATA
Found at i:611013 original size:18 final size:19
Alignment explanation
Indices: 610976--611013 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
610966 AAAAATAAGT
610976 AAATAATTTATATTTGTAA
1 AAATAATTTATATTTGTAA
610995 AAAT-ATTTAATATTT-TAA
1 AAATAATTT-ATATTTGTAA
611013 A
1 A
611014 TAAGTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
AAATAATTTATATTTGTAA
Found at i:611534 original size:18 final size:20
Alignment explanation
Indices: 611508--611549 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
611498 CAATGATGAT
*
611508 TATTGAATAGTTTT-A-AAA
1 TATTGAATAATTTTCATAAA
*
611526 TATTTAATAATTTTCATAAA
1 TATTGAATAATTTTCATAAA
611546 TATT
1 TATT
611550 ACGTCACACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
19 1 0.05
20 7 0.35
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (20 bp):
TATTGAATAATTTTCATAAA
Found at i:611626 original size:16 final size:16
Alignment explanation
Indices: 611605--611642 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
611595 ATAGATTGAT
611605 TTAATTTAAAATTAAA
1 TTAATTTAAAATTAAA
*
611621 TTAA-TTAAAATTTAA
1 TTAATTTAAAATTAAA
*
611636 TAAATTT
1 TTAATTT
611643 TTAAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAATTTAAAATTAAA
Found at i:612376 original size:2 final size:2
Alignment explanation
Indices: 612369--612399 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
612359 TTCTTAGAAT
612369 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 A
612400 AAGAATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:613475 original size:25 final size:25
Alignment explanation
Indices: 613447--613498 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
613437 AACAAAAATG
613447 AAAAATAATTTGAGTTTACGAATTA
1 AAAAATAATTTGAGTTTACGAATTA
613472 AAAAATAATTTGAGTTTACGAATTA
1 AAAAATAATTTGAGTTTACGAATTA
613497 AA
1 AA
613499 TCAAACCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.35
Consensus pattern (25 bp):
AAAAATAATTTGAGTTTACGAATTA
Found at i:618236 original size:18 final size:18
Alignment explanation
Indices: 618213--618249 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
618203 CAGAGAAGGG
618213 TTATTTAATTGAACATCC
1 TTATTTAATTGAACATCC
618231 TTATTTAATTGAACATCC
1 TTATTTAATTGAACATCC
618249 T
1 T
618250 ATCCAATCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.46
Consensus pattern (18 bp):
TTATTTAATTGAACATCC
Found at i:620240 original size:24 final size:24
Alignment explanation
Indices: 620211--620258 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
620201 AAAACACTCC
620211 TCACTTTCATGTAAAATTAAAGTA
1 TCACTTTCATGTAAAATTAAAGTA
620235 TCACTTTCATGTAAAATTAAAGTA
1 TCACTTTCATGTAAAATTAAAGTA
620259 GAAATGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (24 bp):
TCACTTTCATGTAAAATTAAAGTA
Found at i:623961 original size:14 final size:15
Alignment explanation
Indices: 623939--623972 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
623929 ATATTTTTAA
623939 TAAAAT-AAAAAATT
1 TAAAATAAAAAAATT
*
623953 TAAATTAAAAAAATT
1 TAAAATAAAAAAATT
623968 TAAAA
1 TAAAA
623973 GTAAGGGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAATAAAAAAATT
Found at i:624435 original size:15 final size:14
Alignment explanation
Indices: 624410--624440 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
624400 GATCTTTATT
624410 TTTAAAATTTTTAA
1 TTTAAAATTTTTAA
*
624424 TTTAAAATTTTTTA
1 TTTAAAATTTTTAA
624438 TTT
1 TTT
624441 TATTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTAAAATTTTTAA
Found at i:624442 original size:15 final size:14
Alignment explanation
Indices: 624404--624442 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
624394 ACTCGTGATC
624404 TTTATTTTTAAAATT
1 TTTA-TTTTAAAATT
*
624419 TTTAATTTAAAATTT
1 TTTATTTTAAAA-TT
624434 TTTATTTTA
1 TTTATTTTA
624443 TTTAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTTAAAATT
Found at i:625094 original size:29 final size:30
Alignment explanation
Indices: 625033--625113 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
625023 TATTTAAACT
* * * *
625033 TAAATTAAAGATTAAAATTTTTATTGAGTA
1 TAAATTAAAAATTAAAATTTATATTCAATA
*
625063 TAATTTAAAAATTAAAATTTAT-TTCAATA
1 TAAATTAAAAATTAAAATTTATATTCAATA
* * *
625092 TAAATTAATAATAAAAAATTAT
1 TAAATTAAAAATTAAAATTTAT
625114 CTTGATGGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 23 0.55
30 19 0.45
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (30 bp):
TAAATTAAAAATTAAAATTTATATTCAATA
Found at i:625295 original size:20 final size:24
Alignment explanation
Indices: 625251--625293 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
625241 TAGTTAATAT
625251 ATTAAATATATTTATTAATTTTTA
1 ATTAAATATATTTATTAATTTTTA
625275 ATTAAAT-T-TTTATT-ATTTT
1 ATTAAATATATTTATTAATTTT
625294 AAAAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 6 0.32
23 1 0.05
24 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTAAATATATTTATTAATTTTTA
Found at i:625304 original size:18 final size:18
Alignment explanation
Indices: 625252--625310 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
625242 AGTTAATATA
*
625252 TTAAATATATTTATTAATTT
1 TTAAAAATATTTATT-A-TT
*
625272 TTAATTAAATTTTTATTATT
1 TTAA--AAATATTTATTATT
*
625292 TTAAAAATATTTAATATT
1 TTAAAAATATTTATTATT
625310 T
1 T
625311 AATGTCGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 13 0.39
20 10 0.30
21 1 0.03
22 9 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAAAAATATTTATTATT
Found at i:625498 original size:36 final size:35
Alignment explanation
Indices: 625458--625536 Score: 83
Period size: 35 Copynumber: 2.2 Consensus size: 35
625448 AATTATTTGT
625458 TAAATAATAA-A-AATTATTTT-TATTTAAATTTAATTA
1 TAAATAATAATATAATT-TTTTAT-TTTAAA-TT-ATTA
* *
625494 TAAATATTAATATAATTTTTTATTTTTAATTATTA
1 TAAATAATAATATAATTTTTTATTTTAAATTATTA
625529 TAAATAAT
1 TAAATAAT
625537 GAAACAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
35 11 0.30
36 11 0.30
37 10 0.27
38 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (35 bp):
TAAATAATAATATAATTTTTTATTTTAAATTATTA
Found at i:631766 original size:25 final size:25
Alignment explanation
Indices: 631729--631803 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 25
631719 ATAATATTAA
*
631729 AATATTAAAATATTATTTTTATATT
1 AATATTTAAATATTATTTTTATATT
631754 AATATTT--ATA-TATTTTTATAATT
1 AATATTTAAATATTATTTTTAT-ATT
**
631777 AA-ATTTAAATAAAATTTTTATCATT
1 AATATTTAAATATTATTTTTAT-ATT
631802 AA
1 AA
631804 ATAAATTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
22 13 0.30
23 8 0.19
24 3 0.07
25 19 0.44
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (25 bp):
AATATTTAAATATTATTTTTATATT
Found at i:631770 original size:22 final size:22
Alignment explanation
Indices: 631742--631783 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
631732 ATTAAAATAT
631742 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
631764 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
631784 AATAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:632770 original size:22 final size:22
Alignment explanation
Indices: 632745--632787 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
632735 AATTTAAATT
632745 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
632767 TAAATATTAATATAAAAATAT
1 TAAATATTAATATAAAAATAT
632788 TATTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:637453 original size:31 final size:31
Alignment explanation
Indices: 637415--637479 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
637405 GATTTACCTC
637415 ACCCAAATTTTACCGAAATCAACTAAATCGA
1 ACCCAAATTTTACCGAAATCAACTAAATCGA
637446 ACCCAAATTTTACCGAAATCAACTAAATCGA
1 ACCCAAATTTTACCGAAATCAACTAAATCGA
637477 ACC
1 ACC
637480 GAATGAACCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.45, C:0.28, G:0.06, T:0.22
Consensus pattern (31 bp):
ACCCAAATTTTACCGAAATCAACTAAATCGA
Found at i:641103 original size:25 final size:25
Alignment explanation
Indices: 641043--641103 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
641033 AGAAAGATTT
**
641043 TTTTATTTGAATTAATTTAATTTAAA
1 TTTTATTT-AATTAATTTAAAATAAA
641069 TTATTA-TTAATTAA-TTAAAATAATA
1 TT-TTATTTAATTAATTTAAAATAA-A
641094 TTTTATTTAA
1 TTTTATTTAA
641104 ATTTAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
24 10 0.33
25 13 0.43
26 4 0.13
27 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTTATTTAATTAATTTAAAATAAA
Found at i:641108 original size:42 final size:40
Alignment explanation
Indices: 641057--641139 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 40
641047 ATTTGAATTA
* **
641057 ATTTAATTTAAATTATTATTAATTAATT-AAAATAATATTTT
1 ATTTAATTTAAA-TATAAAAAATTAATTAAAAATAAT-TTTT
641098 ATTTAAATTTAAATATAAAAAATTAATTAAAAATAATTTTT
1 ATTT-AATTTAAATATAAAAAATTAATTAAAAATAATTTTT
641139 A
1 A
641140 ATATTTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 21 0.57
42 16 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (40 bp):
ATTTAATTTAAATATAAAAAATTAATTAAAAATAATTTTT
Found at i:641806 original size:11 final size:12
Alignment explanation
Indices: 641770--641804 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
641760 AATTTTGATA
*
641770 TATTTATATATT
1 TATTTTTATATT
641782 TATTTTT-TATT
1 TATTTTTATATT
641793 TATTTTTATATT
1 TATTTTTATATT
641805 ATAATATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TATTTTTATATT
Found at i:642336 original size:22 final size:23
Alignment explanation
Indices: 642311--642361 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
642301 AATAATATTT
* *
642311 TTATTTAAATTTTATTATAA-AA
1 TTATTTAAATATTAATATAATAA
*
642333 TTATATAAATATTAATATAATAA
1 TTATTTAAATATTAATATAATAA
*
642356 TAATTT
1 TTATTT
642362 TTTTAATATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTATTTAAATATTAATATAATAA
Found at i:643123 original size:2 final size:2
Alignment explanation
Indices: 643116--643169 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
643106 AAGCTGCGGA
* * *
643116 AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
643158 TT AT AT AT AT AT
1 AT AT AT AT AT AT
643170 TGTTACTAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:644494 original size:19 final size:20
Alignment explanation
Indices: 644448--644510 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
644438 ATTAATATTT
644448 TTATTTAAATATTATTATATTAA
1 TTATTTAAATA-TATT-T-TTAA
*
644471 -CATTTAAATAT-TTTTTAA
1 TTATTTAAATATATTTTTAA
*
644489 TTATTTAAATTTATTTTTAA
1 TTATTTAAATATATTTTTAA
644509 TT
1 TT
644511 TAAAAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
18 4 0.11
19 10 0.29
20 11 0.31
21 1 0.03
22 9 0.26
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATTTAAATATATTTTTAA
Found at i:644506 original size:22 final size:22
Alignment explanation
Indices: 644448--644506 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
644438 ATTAATATTT
* *
644448 TTATTTAAATATTATTATATTAA
1 TTATTTAAAT-TTATTTTTTTAA
*
644471 -CATTTAAA--TA-TTTTTTAA
1 TTATTTAAATTTATTTTTTTAA
644489 TTATTTAAATTTATTTTT
1 TTATTTAAATTTATTTTT
644507 AATTTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 9
0.68 0.10 0.22
Matches are distributed among these distances:
18 6 0.21
19 9 0.32
21 2 0.07
22 11 0.39
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATTTAAATTTATTTTTTTAA
Found at i:644690 original size:21 final size:20
Alignment explanation
Indices: 644649--644706 Score: 55
Period size: 23 Copynumber: 2.8 Consensus size: 20
644639 ATGTTTAAAT
**
644649 TTTTTATAT-TTTTGAATTA
1 TTTTTATATATTTAAAATTA
644668 TTTTTATATATTTAAAATATA
1 TTTTTATATATTTAAAAT-TA
*
644689 TTTTAAATTATATTTAAA
1 TTTT-TA-TATATTTAAA
644707 TTTAATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 9 0.28
20 6 0.19
21 6 0.19
22 1 0.03
23 10 0.31
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTTATATATTTAAAATTA
Found at i:644716 original size:13 final size:11
Alignment explanation
Indices: 644674--644719 Score: 56
Period size: 12 Copynumber: 3.9 Consensus size: 11
644664 ATTATTTTTA
*
644674 TATATTTAAAA
1 TATATTTAAAT
644685 TATATTTTAAAT
1 TATA-TTTAAAT
644697 TATATTTAAATT
1 TATATTTAAA-T
644709 TAATATTTAAA
1 T-ATATTTAAA
644720 AATTTTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 10 0.32
12 12 0.39
13 9 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TATATTTAAAT
Found at i:645469 original size:21 final size:23
Alignment explanation
Indices: 645445--645487 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
645435 TATTTTTATT
*
645445 TAAAT-TTAAT-TATAAATAATA
1 TAAATATTAATATAAAAATAATA
645466 TAAATATTAATATAAAAATAAT
1 TAAATATTAATATAAAAATAAT
645488 TTTTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 5 0.26
23 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAATATTAATATAAAAATAATA
Found at i:648960 original size:25 final size:25
Alignment explanation
Indices: 648926--648973 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
648916 AGTTTTAGAG
648926 ATCTTGGTTGTAGACATTCAGTAAA
1 ATCTTGGTTGTAGACATTCAGTAAA
648951 ATCTTGGTTGTAGACATTCAGTA
1 ATCTTGGTTGTAGACATTCAGTA
648974 CTCTTTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (25 bp):
ATCTTGGTTGTAGACATTCAGTAAA
Found at i:652544 original size:19 final size:18
Alignment explanation
Indices: 652522--652572 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
652512 ATTAATAAAA
652522 ATAATAAATTTATTTTTAT
1 ATAATAAATTTATTTTT-T
**
652541 ATAAATATTTTTATTTTTT
1 AT-AATAAATTTATTTTTT
652560 ATAATTAAATTTA
1 ATAA-TAAATTTA
652573 AATAAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 2 0.08
19 11 0.42
20 13 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATAATAAATTTATTTTTT
Found at i:652608 original size:19 final size:19
Alignment explanation
Indices: 652520--652609 Score: 51
Period size: 19 Copynumber: 4.7 Consensus size: 19
652510 AAATTAATAA
* *
652520 AAATAATAAATTTATTTTT
1 AAATAATAATTTTATTATT
* *
652539 ATATAAATATTTTTATT-TT
1 AAAT-AATAATTTTATTATT
** * * *
652558 TTATAATTAAATTTA-AATA
1 AAATAA-TAATTTTATTATT
652577 AAAT-ATAATTTTTATTATT
1 AAATAATAA-TTTTATTATT
652596 AAATAATAATTTTA
1 AAATAATAATTTTA
652610 AATAGATTAG
Statistics
Matches: 52, Mismatches: 13, Indels: 12
0.68 0.17 0.16
Matches are distributed among these distances:
17 3 0.06
18 7 0.13
19 28 0.54
20 14 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATAATAATTTTATTATT
Found at i:653138 original size:21 final size:20
Alignment explanation
Indices: 653114--653171 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
653104 TAATTAAAAA
653114 AATTTTAAATATAGAATAAAT
1 AATTTTAAATATA-AATAAAT
* *
653135 AATTTTAATTTTAAATAAAT
1 AATTTTAAATATAAATAAAT
653155 -A--TTAAATAT-AATAAAT
1 AATTTTAAATATAAATAAAT
653171 A
1 A
653172 TTTAATTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
16 7 0.22
17 6 0.19
19 1 0.03
20 7 0.22
21 11 0.34
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AATTTTAAATATAAATAAAT
Found at i:653160 original size:38 final size:34
Alignment explanation
Indices: 653100--653178 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 34
653090 TAAACCAAAT
*
653100 TATTTAA--TTAAAAAAATTTTAAATATAGAATAAA
1 TATTTAATTTTAAAAAAATATTAAATAT--AATAAA
*
653134 TAATTTTAATTTTAAATAAATATTAAATATAATAAA
1 T-A-TTTAATTTTAAAAAAATATTAAATATAATAAA
653170 TATTTAATT
1 TATTTAATT
653179 AAAATATACT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
34 8 0.21
35 2 0.05
36 12 0.31
38 17 0.44
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (34 bp):
TATTTAATTTTAAAAAAATATTAAATATAATAAA
Found at i:654368 original size:3 final size:3
Alignment explanation
Indices: 654360--654397 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
654350 TAGGCAAATG
654360 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
654398 GAAAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:654576 original size:31 final size:31
Alignment explanation
Indices: 654541--654603 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
654531 TTAATAAGTT
* *
654541 TAATAAATT-TGATTTAATTTATATATAAATA
1 TAATAAATTATAATTTAAATTA-ATATAAATA
* *
654572 TAATAATTTATAATTTAAATTAATTTAAATA
1 TAATAAATTATAATTTAAATTAATATAAATA
654603 T
1 T
654604 TTTTATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (31 bp):
TAATAAATTATAATTTAAATTAATATAAATA
Found at i:655536 original size:21 final size:21
Alignment explanation
Indices: 655512--655551 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
655502 TATTTTTATT
*
655512 TAAATT-TGATTATAAAATACA
1 TAAATTGTAATTA-AAAATACA
655533 TAAATTGTAATTAAAAATA
1 TAAATTGTAATTAAAAATA
655552 TTAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (21 bp):
TAAATTGTAATTAAAAATACA
Found at i:660658 original size:3 final size:3
Alignment explanation
Indices: 660650--660680 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
660640 TGAGTAATCA
660650 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
660681 GCATCTGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:662176 original size:2 final size:2
Alignment explanation
Indices: 662169--662201 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
662159 GTGAGTGAGT
662169 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
662202 TTAAGGAGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:662558 original size:8 final size:8
Alignment explanation
Indices: 662542--662574 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
662532 TAAATTCAGA
662542 TAAAAATT
1 TAAAAATT
*
662550 TAAAGATT
1 TAAAAATT
662558 TAAAAATT
1 TAAAAATT
662566 TAAAAATT
1 TAAAAATT
662574 T
1 T
662575 TAATTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (8 bp):
TAAAAATT
Found at i:662634 original size:16 final size:15
Alignment explanation
Indices: 662593--662640 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
662583 TTAATTCAAG
*
662593 TTAAATTAATTTATTA
1 TTAAATTAATTT-TTT
* *
662609 TAAAAATAATTTTTT
1 TTAAATTAATTTTTT
662624 TTAATATTAATTTTTT
1 TTAA-ATTAATTTTTT
662640 T
1 T
662641 ATTCATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAAATTAATTTTTT
Found at i:663159 original size:20 final size:20
Alignment explanation
Indices: 663134--663192 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
663124 AAGAATCGAT
663134 TTTTTTTTAAGAAAGATTAA
1 TTTTTTTTAAGAAAGATTAA
*
663154 TTTTTTATAA-AAA-A-TAA
1 TTTTTTTTAAGAAAGATTAA
* *
663171 TATTTTTTTAGGACAGATTAA
1 T-TTTTTTTAAGAAAGATTAA
663192 T
1 T
663193 CTATTTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
17 4 0.13
18 8 0.26
19 5 0.16
20 10 0.32
21 4 0.13
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (20 bp):
TTTTTTTTAAGAAAGATTAA
Found at i:664820 original size:18 final size:20
Alignment explanation
Indices: 664786--664827 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
664776 TTAATTTATT
*
664786 AAATTATTAATAATATA-AA
1 AAATTATTAAGAATATATAA
664805 AAATTA-TAAGAATATATAA
1 AAATTATTAAGAATATATAA
664824 AAAT
1 AAAT
664828 AAATTCAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAATTATTAAGAATATATAA
Found at i:666169 original size:21 final size:21
Alignment explanation
Indices: 666143--666215 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 21
666133 TTAATAAAAA
666143 AAAATATTTAAAT-TTAATTAT
1 AAAATATTTAAATATTAATT-T
666164 AAAATA--TAAATATTAATTT
1 AAAATATTTAAATATTAATTT
* *
666183 AAAAAATTTTAATATT-ATTT
1 AAAATATTTAAATATTAATTT
*
666203 -AAATATTAAAATA
1 AAAATATTTAAATA
666216 AATTATTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
19 21 0.48
20 10 0.23
21 13 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAATATTTAAATATTAATTT
Found at i:666179 original size:26 final size:25
Alignment explanation
Indices: 666136--666184 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
666126 TTATTGTTTA
666136 ATAAAAAAAAATATTTAAATTTAATT
1 ATAAAAAAAAATATTT-AATTTAATT
*
666162 ATAAAATATAAATA-TTAATTTAA
1 ATAAAA-AAAAATATTTAATTTAA
666185 AAAATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 8 0.38
27 6 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAAAAAAAAATATTTAATTTAATT
Found at i:666187 original size:20 final size:20
Alignment explanation
Indices: 666151--666205 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
666141 AAAAAATATT
666151 TAAAT-TTAA-TTATAAAATA
1 TAAATATTAATTTA-AAAATA
*
666170 TAAATATTAATTTAAAAAATT
1 TAAATATTAATTT-AAAAATA
*
666191 TTAATATT-ATTTAAA
1 TAAATATTAATTTAAA
666206 TATTAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 8 0.26
20 8 0.26
21 14 0.45
22 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATATTAATTTAAAAATA
Found at i:666233 original size:20 final size:21
Alignment explanation
Indices: 666196--666234 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
666186 AAATTTTAAT
**
666196 ATTATTTAAATATTAAAATAA
1 ATTATTTAAATAAAAAAATAA
666217 ATTA-TTAAATAAAAAAAT
1 ATTATTTAAATAAAAAAAT
666235 TTTGGATGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTATTTAAATAAAAAAATAA
Found at i:666518 original size:25 final size:23
Alignment explanation
Indices: 666490--666536 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
666480 ATATAATTAT
*
666490 ATTTAAATATTATAATATTTAATAA
1 ATTTAAA-ATT-TAAAATTTAATAA
666515 ATTTAAAATTTAAAATTTAATA
1 ATTTAAAATTTAAAATTTAATA
666537 TTTATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.52
24 3 0.14
25 7 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTAAAATTTAAAATTTAATAA
Found at i:666532 original size:14 final size:14
Alignment explanation
Indices: 666488--666545 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
666478 TCATATAATT
666488 ATATTTAAATATTATA
1 ATATTTAAA-ATT-TA
666504 ATATTTAATAAATTTA
1 ATATTT-A-AAATTTA
*
666520 AAATTTAAAATTTA
1 ATATTTAAAATTTA
*
666534 ATATTTATAATT
1 ATATTTAAAATT
666546 ATTTATCTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 17 0.46
15 1 0.03
16 13 0.35
17 4 0.11
18 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATTTAAAATTTA
Found at i:666751 original size:28 final size:28
Alignment explanation
Indices: 666678--666753 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 28
666668 AAGTTTTATC
* *
666678 ATATATTTTAAAA-AATAATTTATATTTAA
1 ATATA-TTTAAAATAA-AATTTAAATATAA
* *
666707 ATATATATCAAATATAAATTTTAAATATAA
1 ATATAT-TTAAA-ATAAAATTTAAATATAA
666737 ATATATTTAAAATAAAA
1 ATATATTTAAAATAAAA
666754 AGATTTCAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
28 6 0.16
29 13 0.34
30 17 0.45
31 2 0.05
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
ATATATTTAAAATAAAATTTAAATATAA
Found at i:666934 original size:49 final size:46
Alignment explanation
Indices: 666853--666947 Score: 111
Period size: 49 Copynumber: 2.0 Consensus size: 46
666843 GATCGACCCG
* *
666853 AAAATATATTAAATAATTAAAAGATAATTTTTAAAAATTTAATTAA
1 AAAATATATAAAATAATTAAAAGATAAATTTTAAAAATTTAATTAA
* *
666899 AAAATATATAAATATTAATATAAAA-ATAAAATTTTAAAATTTTTATTAA
1 AAAATATATAAA-A-TAAT-TAAAAGAT-AAATTTTAAAAATTTAATTAA
666948 TAATAAAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
46 11 0.27
47 1 0.02
48 6 0.15
49 23 0.56
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (46 bp):
AAAATATATAAAATAATTAAAAGATAAATTTTAAAAATTTAATTAA
Found at i:671382 original size:21 final size:22
Alignment explanation
Indices: 671358--671408 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
671348 CATCAAAATA
* *
671358 TATAATATTATATTTT-TATTT
1 TATATTATTATATTTTAAATTT
*
671379 TATATTA-CATATTTTAAATTT
1 TATATTATTATATTTTAAATTT
671400 TATATTATT
1 TATATTATT
671409 GAAGTTATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TATATTATTATATTTTAAATTT
Found at i:671884 original size:17 final size:17
Alignment explanation
Indices: 671833--671887 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
671823 TTTAAATTAT
671833 TTTATATT-TA-TATAAA
1 TTTATATTATATTA-AAA
* *
671849 TTT-TAATAAATTAATAA
1 TTTATATTATATTAA-AA
671866 TTTATATTATATTAAAA
1 TTTATATTATATTAAAA
671883 TTTAT
1 TTTAT
671888 CGTATTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 3 0.10
16 5 0.16
17 14 0.45
18 9 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTATATTATATTAAAA
Found at i:672360 original size:2 final size:2
Alignment explanation
Indices: 672353--672388 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
672343 ATTAGAATCA
672353 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
672389 GTATGTATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:677102 original size:3 final size:3
Alignment explanation
Indices: 677094--677134 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
677084 GAGAAAGCAG
677094 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
677135 ACCAAATCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:679402 original size:27 final size:27
Alignment explanation
Indices: 679339--679408 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
679329 TAGATATGAC
* * *
679339 ATAAAATAAATAATAAAAATGTTATAAAA
1 ATAAAAT--ATAAAAAAAATATTACAAAA
* *
679368 ATACAATATAAAAAAAATATTACAAAT
1 ATAAAATATAAAAAAAATATTACAAAA
679395 ATAAAATA-AAAAAA
1 ATAAAATATAAAAAA
679409 TAATTATTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
26 6 0.17
27 23 0.66
29 6 0.17
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.24
Consensus pattern (27 bp):
ATAAAATATAAAAAAAATATTACAAAA
Found at i:679477 original size:11 final size:11
Alignment explanation
Indices: 679455--679495 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
679445 TTTATATAAA
679455 TATAAAATATT
1 TATAAAATATT
679466 T-TAAACATATT
1 TATAAA-ATATT
*
679477 TATAAAATATA
1 TATAAAATATT
679488 TA-AAAATA
1 TATAAAATA
679496 ATAAAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 10 0.37
11 13 0.48
12 4 0.15
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (11 bp):
TATAAAATATT
Found at i:679493 original size:10 final size:10
Alignment explanation
Indices: 679424--679509 Score: 54
Period size: 10 Copynumber: 8.9 Consensus size: 10
679414 ATTTTGAAAT
*
679424 ATATATAATA
1 ATATATAAAA
* *
679434 ATTTATCAAA
1 ATATATAAAA
* *
679444 ATTTATATAA
1 ATATATAAAA
*
679454 ATATA-AAAT
1 ATATATAAAA
* *
679463 AT-TTTAAAC
1 ATATATAAAA
*
679472 ATATTTATAAA
1 ATATATA-AAA
679483 ATATATAAAA
1 ATATATAAAA
679493 ATA-AT-AAA
1 ATATATAAAA
679501 ATATATAAA
1 ATATATAAA
679510 TTATCAAACT
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
8 7 0.12
9 13 0.22
10 31 0.53
11 8 0.14
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.38
Consensus pattern (10 bp):
ATATATAAAA
Found at i:679503 original size:8 final size:9
Alignment explanation
Indices: 679424--679509 Score: 59
Period size: 9 Copynumber: 9.0 Consensus size: 9
679414 ATTTTGAAAT
679424 ATATATAATA
1 ATATATAA-A
*
679434 ATTTATCAAA
1 ATATAT-AAA
* *
679444 ATTTATATA
1 ATATATAAA
679453 A-ATATAAA
1 ATATATAAA
*
679461 ATATTTTAAA
1 ATA-TATAAA
679471 CATATTTATAAA
1 -ATA--TATAAA
679483 ATATATAAA
1 ATATATAAA
679492 A-ATAATAAA
1 ATAT-ATAAA
679501 ATATATAAA
1 ATATATAAA
679510 TTATCAAACT
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
8 8 0.13
9 22 0.35
10 19 0.30
11 8 0.13
12 6 0.10
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.38
Consensus pattern (9 bp):
ATATATAAA
Found at i:679744 original size:3 final size:3
Alignment explanation
Indices: 679738--679777 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
679728 TTTTTTAATG
679738 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
679778 GTGCTTGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:680088 original size:34 final size:33
Alignment explanation
Indices: 680026--680107 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 33
680016 TAACAAAAAA
680026 ATAATATAAATATATGAATATATAAAAATTTAT
1 ATAATATAAATATATGAATATATAAAAATTTAT
* * * *
680059 ATAATATAAATTATATTATTTTATTAAAATTTAT
1 ATAATATAAA-TATATGAATATATAAAAATTTAT
680093 ATAAATATATAATAT
1 AT-AATATA-AATAT
680108 TTTAATACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 10 0.24
34 21 0.50
35 9 0.21
36 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (33 bp):
ATAATATAAATATATGAATATATAAAAATTTAT
Found at i:680333 original size:17 final size:18
Alignment explanation
Indices: 680282--680337 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
680272 AACTATCTTT
*
680282 TTAACTTTTTGAAT-AAA
1 TTAATTTTTTGAATAAAA
*
680299 TTAATTTTTT-AACCAAAA
1 TTAATTTTTTGAA-TAAAA
*
680317 TT-TTTTTTTGAATAAAA
1 TTAATTTTTTGAATAAAA
680334 TTAA
1 TTAA
680338 AATCATCATA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
16 2 0.07
17 21 0.70
18 7 0.23
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (18 bp):
TTAATTTTTTGAATAAAA
Found at i:680358 original size:2 final size:2
Alignment explanation
Indices: 680345--680387 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
680335 TAAAATCATC
*
680345 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
680387 A
1 A
680388 CTTATTAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:683012 original size:18 final size:18
Alignment explanation
Indices: 682989--683043 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
682979 TTCTCTTTTT
682989 TTTAATATTATATAATAA
1 TTTAATATTATATAATAA
*
683007 TTTAATAAATATATAA-AA
1 TTTAAT-ATTATATAATAA
*
683025 TTTATTTATTATATAATAA
1 TTTA-ATATTATATAATAA
683044 ATATATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 20 0.65
19 11 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAATATTATATAATAA
Found at i:684097 original size:16 final size:17
Alignment explanation
Indices: 684054--684099 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
684044 TGACTTGACA
*
684054 TAAATAAAAATTAAATT
1 TAAATAAAATTTAAATT
*
684071 TAAAGT-CAATTTAAA-T
1 TAAA-TAAAATTTAAATT
684087 TAAATAAAATTTA
1 TAAATAAAATTTA
684100 TCCAAAACGA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 1 0.04
16 11 0.46
17 11 0.46
18 1 0.04
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
TAAATAAAATTTAAATT
Found at i:684349 original size:9 final size:9
Alignment explanation
Indices: 684324--684384 Score: 50
Period size: 9 Copynumber: 6.1 Consensus size: 9
684314 TAAATTAAAT
684324 TTTAAATAAA
1 TTTAAAT-AA
684334 GTTTAAATAA
1 -TTTAAATAA
684344 TTTAAATTAA
1 TTTAAA-TAA
* *
684354 TTTAATTTA
1 TTTAAATAA
684363 TTTAAATTATAA
1 TTT-AA--ATAA
684375 TTTAAATAA
1 TTTAAATAA
684384 T
1 T
684385 AAAAATTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 16 0.38
10 12 0.29
11 9 0.21
12 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (9 bp):
TTTAAATAA
Found at i:684365 original size:19 final size:20
Alignment explanation
Indices: 684324--684384 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
684314 TAAATTAAAT
*
684324 TTTAAATAAAGTTTAAATAA
1 TTTAAATTAAGTTTAAATAA
* *
684344 TTTAAATTAA-TTTAATTTA
1 TTTAAATTAAGTTTAAATAA
*
684363 TTTAAATTATAATTTAAATAA
1 TTTAAATTA-AGTTTAAATAA
684384 T
1 T
684385 AAAAATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 16 0.47
20 10 0.29
21 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTAAATTAAGTTTAAATAA
Found at i:684556 original size:2 final size:2
Alignment explanation
Indices: 684549--684584 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
684539 ATCCGAAGTA
684549 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
684585 TCTAGTGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:684912 original size:2 final size:2
Alignment explanation
Indices: 684907--684945 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
684897 CGTGTGTGTG
684907 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
684946 GTATTGGTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:687233 original size:238 final size:238
Alignment explanation
Indices: 686815--687292 Score: 850
Period size: 238 Copynumber: 2.0 Consensus size: 238
686805 TCTCATTATC
686815 ATGTTAGAAAAGAATTAAGGAACTAAACTTAAAACCAAAGCATAATTACATCATATGGGACACAA
1 ATGTTAGAAAAGAATTAAGGAACTAAACTTAAAACCAAAGCATAATTACATCATATGGGACACAA
*
686880 ATTAAATCACCCACAGCTTTTTTCTATAGTGTAAAACATAATTAATTATAACTATGAGAATCTAA
66 ATTAAATCACCCACAGCTTTTTTCTATAGTGTAAAACATAATTAATTATAAATATGAGAATCTAA
* * *
686945 TTCCCAAATTAATGAAAATTTTTACATTTAATGCATTATTTTTATTAAATTTAATAAAAATAATA
131 TTCCCAAATTAATGAAAATTTTTACATTTAATGCATTATATTTATTAAATTCAATAAAAAGAATA
*
687010 TATTAATTATAAATTTGTTTTCTTAAATATCAACTTAATTAGT
196 TATTAATTATAAATTTATTTTCTTAAATATCAACTTAATTAGT
* *
687053 ATGTTAGAAAAGAATTAAGGAACTAAACTTAAAACCAAAGCATAATTATATCATATGTGACACAA
1 ATGTTAGAAAAGAATTAAGGAACTAAACTTAAAACCAAAGCATAATTACATCATATGGGACACAA
687118 ATTAAATCACCCACAGCTTTTTTCTA-AGGTGTAAAACATAATTAATTATAAATATGAGAATCTA
66 ATTAAATCACCCACAGCTTTTTTCTATA-GTGTAAAACATAATTAATTATAAATATGAGAATCTA
* * *
687182 ATTCCCAAATTAATGAAAATTTTTACATTTAATGTATTATATTTATTAAATTCGATAAAAGGAAT
130 ATTCCCAAATTAATGAAAATTTTTACATTTAATGCATTATATTTATTAAATTCAATAAAAAGAAT
687247 ATATTAATTATAAATTTATTTTCTTAAATATCAACTTAATTAGT
195 ATATTAATTATAAATTTATTTTCTTAAATATCAACTTAATTAGT
687291 AT
1 AT
687293 CATTAGGCAT
Statistics
Matches: 229, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
237 1 0.00
238 228 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (238 bp):
ATGTTAGAAAAGAATTAAGGAACTAAACTTAAAACCAAAGCATAATTACATCATATGGGACACAA
ATTAAATCACCCACAGCTTTTTTCTATAGTGTAAAACATAATTAATTATAAATATGAGAATCTAA
TTCCCAAATTAATGAAAATTTTTACATTTAATGCATTATATTTATTAAATTCAATAAAAAGAATA
TATTAATTATAAATTTATTTTCTTAAATATCAACTTAATTAGT
Found at i:688134 original size:2 final size:2
Alignment explanation
Indices: 688127--688153 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
688117 AAAATAAACT
688127 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
688154 GATTTCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:692003 original size:23 final size:24
Alignment explanation
Indices: 691977--692026 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
691967 ATACGGCACC
691977 TTAAAATAAAAAAATTA-TAAATA
1 TTAAAATAAAAAAATTATTAAATA
* ** *
692000 TTAATATTTAAAATTTATTAAATA
1 TTAAAATAAAAAAATTATTAAATA
692024 TTA
1 TTA
692027 TGAATAATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TTAAAATAAAAAAATTATTAAATA
Found at i:695344 original size:2 final size:2
Alignment explanation
Indices: 695337--695372 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
695327 AATCAGAAAT
*
695337 TC TC TC TC TC TC TC TC TC TC TC GC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
695373 GGATATGTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
TC
Found at i:695608 original size:18 final size:17
Alignment explanation
Indices: 695587--695630 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
695577 TGTTTAATCT
695587 TAAATTATTATTTAATAA
1 TAAATTATTATTTAA-AA
*
695605 TAAATTTTTTATTTAAAA
1 TAAA-TTATTATTTAAAA
*
695623 TTAATTAT
1 TAAATTAT
695631 AAAATATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.14
18 9 0.41
19 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TAAATTATTATTTAAAA
Found at i:696099 original size:20 final size:20
Alignment explanation
Indices: 696074--696130 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
696064 TAAGCTCACT
696074 TATATTTTTTAATTTTTAAA
1 TATATTTTTTAATTTTTAAA
***
696094 TATA-TTTTTAACAATTAAA
1 TATATTTTTTAATTTTTAAA
696113 TATATTTTTTAATATTTT
1 TATATTTTTTAAT-TTTT
696131 TTTGTTAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 16 0.55
20 11 0.38
21 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TATATTTTTTAATTTTTAAA
Found at i:696239 original size:23 final size:21
Alignment explanation
Indices: 696202--696258 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
696192 TAACATCTAG
696202 TTAAATAAAAT-TATAACTATTA
1 TTAAA-AAAATATATAACTA-TA
* *
696224 TTATAAAATATATATAATTATA
1 TTA-AAAAAATATATAACTATA
696246 TTAAAAAAATATA
1 TTAAAAAAATATA
696259 AATTTTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 9 0.30
22 12 0.40
23 9 0.30
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAAAAAATATATAACTATA
Found at i:698573 original size:20 final size:18
Alignment explanation
Indices: 698539--698578 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
698529 CGGTTTAAAT
698539 TTTTTAAATTCAAAAATAA
1 TTTTTAAATTCAAAAA-AA
*
698558 TTTTTAAATTTGAAAAAAA
1 TTTTTAAA-TTCAAAAAAA
698577 TT
1 TT
698579 ATATACATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
TTTTTAAATTCAAAAAAA
Found at i:699616 original size:18 final size:18
Alignment explanation
Indices: 699593--699636 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
699583 CTGGAGCACG
699593 ACTTGGAGCACAATGAAA
1 ACTTGGAGCACAATGAAA
**
699611 ACTTGGAGCACAATGTGA
1 ACTTGGAGCACAATGAAA
699629 ACTTGGAG
1 ACTTGGAG
699637 GGAAGTCCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.20
Consensus pattern (18 bp):
ACTTGGAGCACAATGAAA
Found at i:701059 original size:179 final size:178
Alignment explanation
Indices: 700760--701117 Score: 617
Period size: 179 Copynumber: 2.0 Consensus size: 178
700750 GACATTCATT
* *
700760 TGCATTTATTTTCTTTATTGTGTCTATATGAAGCTATTTTGTTGGTACTATGATGTGGAAATTAT
1 TGCATTTATTTTCTTTATTGTGCCTATATGAAGCTATTTTGTTGGTACAATGATGTGGAAATTAT
700825 TTTCACTAAAGTAAAGATAAAGCTTGCTCTGCAATTTTAGCTTGATTCCTTGTTTTAGGACTGCA
66 TTTCACTAAAGTAAAGATAAAGCTTGCTCTGCAATTTTAGCTTGATTCCTTGTTTTAGGACTGCA
*
700890 TACATACATGATATATTGGTTTATCTAATCTACAACAAACCACGAAAA
131 TACATACATGATACATTGGTTTATCTAATCTACAACAAACCACGAAAA
700938 TGCATTTATTTTCTTTATTGTGCCTATAATGAAGCTATTTTGTTGGTACAATGATGTGGAAATTA
1 TGCATTTATTTTCTTTATTGTGCCTAT-ATGAAGCTATTTTGTTGGTACAATGATGTGGAAATTA
* * *
701003 TTTTCACTAAAGTGAAGATAAAGCTTGCTCTTCGATTTTAGCTTGATTCCTTGTTTTAGGACTGC
65 TTTTCACTAAAGTAAAGATAAAGCTTGCTCTGCAATTTTAGCTTGATTCCTTGTTTTAGGACTGC
* * * *
701068 ATGCATACATGATACATTGGTTTATCTAATCTACCACGAACCATGAAAA
130 ATACATACATGATACATTGGTTTATCTAATCTACAACAAACCACGAAAA
701117 T
1 T
701118 AATAAAAAGG
Statistics
Matches: 169, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
178 26 0.15
179 143 0.85
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (178 bp):
TGCATTTATTTTCTTTATTGTGCCTATATGAAGCTATTTTGTTGGTACAATGATGTGGAAATTAT
TTTCACTAAAGTAAAGATAAAGCTTGCTCTGCAATTTTAGCTTGATTCCTTGTTTTAGGACTGCA
TACATACATGATACATTGGTTTATCTAATCTACAACAAACCACGAAAA
Found at i:706358 original size:25 final size:27
Alignment explanation
Indices: 706298--706364 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 27
706288 TATTTTATTA
*
706298 ATTAATAATAATATTTAAATTATTTTAT
1 ATTAAT-ATAATATTTAAATTATGTTAT
* * *
706326 GTTTATATAA-ATTTTAA-TATGTTAT
1 ATTAATATAATATTTAAATTATGTTAT
706351 ATTAATATAATATT
1 ATTAATATAATATT
706365 ATATTTTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
25 15 0.47
26 9 0.28
27 4 0.12
28 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (27 bp):
ATTAATATAATATTTAAATTATGTTAT
Found at i:706383 original size:12 final size:13
Alignment explanation
Indices: 706360--706394 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
706350 TATTAATATA
706360 ATATTATATTTTT
1 ATATTATATTTTT
*
706373 A-ATTATTTTTTT
1 ATATTATATTTTT
706385 ATATTATATT
1 ATATTATATT
706395 CGTTGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATATTATATTTTT
Found at i:706902 original size:7 final size:7
Alignment explanation
Indices: 706890--706914 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
706880 TAAGAAAATT
706890 AATTTGA
1 AATTTGA
706897 AATTTGA
1 AATTTGA
706904 AATTTGA
1 AATTTGA
706911 AATT
1 AATT
706915 GTTTTTGTTT
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:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (7 bp):
AATTTGA
Found at i:707764 original size:19 final size:17
Alignment explanation
Indices: 707726--707764 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
707716 TTGTGTTGAA
*
707726 TTATAATTTTATTTATT
1 TTATAATTTTATTTAGT
707743 TTATATATTTTATTTAAGT
1 TTATA-ATTTTATTT-AGT
707762 TTA
1 TTA
707765 ATTTGAGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 9 0.47
19 5 0.26
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTATAATTTTATTTAGT
Found at i:724557 original size:2 final size:2
Alignment explanation
Indices: 724550--724579 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
724540 TAAAATTTGC
724550 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
724580 TTCCAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:726907 original size:16 final size:17
Alignment explanation
Indices: 726886--726923 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
726876 AATATTAATA
726886 TAATTTTT-T-AATATTT
1 TAATTTTTATAAAT-TTT
726902 TAATTTTTATAAATTTT
1 TAATTTTTATAAATTTT
726919 TAATT
1 TAATT
726924 AAACTAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.40
17 9 0.45
18 3 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TAATTTTTATAAATTTT
Found at i:727168 original size:3 final size:3
Alignment explanation
Indices: 727160--727188 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
727150 AAAATACCCA
727160 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
727189 AATCAAAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:733942 original size:20 final size:20
Alignment explanation
Indices: 733904--733942 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
733894 GAAGGTAAAG
*
733904 TTTATACTAATTTCTTATGA
1 TTTATACTAATTTATTATGA
733924 TTTATAC-AATTTATATATG
1 TTTATACTAATTTAT-TATG
733943 GAACAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTATACTAATTTATTATGA
Found at i:734515 original size:193 final size:195
Alignment explanation
Indices: 734139--734526 Score: 472
Period size: 197 Copynumber: 2.0 Consensus size: 195
734129 TTATTCATTT
* *
734139 AATTTCTAAATTACTATTATAAATATTTTTTGTATTAATAAGATTTATCTAATTTATAAGTGATA
1 AATTTCTAAATTACTATTATAAATATTTTTTGTATTAATAAGATTTATCTAATTTATAAGTAAGA
**
734204 ATTTTAATTTTATTAAAAAACTATTAAATAAATTTATTTTATAATAATGAAAAATTAAGATTTAC
66 ATTTTAATTTTATTAAAAAACTATTAAATAAATTTATTCGATAATAAT-AAAAA-TAAGA-TTAC
* *
734269 ATTAAATTACTTTATTTTCAAAGTTCTAATTTTTCATTAACCTAAAAAAGTAAATAAA-TTATTT
128 ATGAAATTACTTTATTTTCAAAATTCTAATTTTTCATTAA-CTAAAAAAGTAAATAAATTTATTT
734333 ACTA
192 ACTA
* *
734337 AATTTCTAAATTGCTATTGT-AA-ATTTTTTGTTATTAATAAGATTTATCCT-ATTTATAAGTAA
1 AATTTCTAAATTACTATTATAAATATTTTTTG-TATTAATAAGATTTAT-CTAATTTATAAGTAA
* ** *
734399 GAATTTTAATTTTTTTAAAAGATTTGTGTTAAATAAATTTATTCGATAATAA-ATAAAA-AAG-T
64 GAATTTTAATTTTATTAAAA-A--ACTATTAAATAAATTTATTCGATAATAATA-AAAATAAGAT
**
734461 TA-A-GAAATTGTTTTATTTTCAAAATTCTAATTTTTCATTAA-TAATAAAAAGTAAATAAATTT
125 TACATGAAATTACTTTATTTTCAAAATTCTAATTTTTCATTAACT-A-AAAAAGTAAATAAATTT
734523 ATTT
188 ATTT
734527 GATTAATAAA
Statistics
Matches: 167, Mismatches: 14, Indels: 22
0.82 0.07 0.11
Matches are distributed among these distances:
191 1 0.01
192 1 0.01
193 48 0.29
194 7 0.04
195 3 0.02
196 8 0.05
197 50 0.30
198 22 0.13
199 4 0.02
200 23 0.14
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (195 bp):
AATTTCTAAATTACTATTATAAATATTTTTTGTATTAATAAGATTTATCTAATTTATAAGTAAGA
ATTTTAATTTTATTAAAAAACTATTAAATAAATTTATTCGATAATAATAAAAATAAGATTACATG
AAATTACTTTATTTTCAAAATTCTAATTTTTCATTAACTAAAAAAGTAAATAAATTTATTTACTA
Found at i:735591 original size:26 final size:26
Alignment explanation
Indices: 735562--735613 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
735552 ATTTGTAAAA
735562 TATACAATTATACG-TTAAAAAGAATT
1 TATACAATTATACGTTTAAAAA-AATT
*
735588 TATACAATTATATGTTTAAAAAAATT
1 TATACAATTATACGTTTAAAAAAATT
735614 ATAAAATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (26 bp):
TATACAATTATACGTTTAAAAAAATT
Found at i:736764 original size:10 final size:10
Alignment explanation
Indices: 736732--736757 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
736722 ATTTATCCCT
736732 TTTTTAAATA
1 TTTTTAAATA
736742 TTTTTAAATA
1 TTTTTAAATA
736752 TTTTTA
1 TTTTTA
736758 TCTATTTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:742213 original size:13 final size:13
Alignment explanation
Indices: 742177--742214 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
742167 ATAAAAAATA
*
742177 TTATTTTAATTAT
1 TTATTTTAATTTT
*
742190 TGATTTT-ATTTT
1 TTATTTTAATTTT
742202 TTATTTTAATTTT
1 TTATTTTAATTTT
742215 AAAAATATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TTATTTTAATTTT
Done.