Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold20
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: 3599867
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 51021 characters in sequence are not A, C, G, or T
File 19 of 25
Found at i:2686468 original size:72 final size:71
Alignment explanation
Indices: 2686328--2686461 Score: 171
Period size: 72 Copynumber: 1.9 Consensus size: 71
2686318 AAAGCCTTTC
* * * *
2686328 AATAGAATGAAAATTTTTATTTACAAATGTGATAAATTTTATTATCCAATAAATACATTTAACCA
1 AATAGAATGAAAACTTTTATTTACAAATGTAATAAATTTTATTAT-CAATAAAAACATTTAAACA
2686393 AAAATTT
65 AAAATTT
* * * *
2686400 AATATAATTAAAACTTTTATTTATAAATGTAATAAATTTTATTAAT-AATAAAAATATTTAAA
1 AATAGAATGAAAACTTTTATTTACAAATGTAATAAATTTTATT-ATCAATAAAAACATTTAAA
2686462 ATAAAAAACT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
71 13 0.25
72 38 0.72
73 2 0.04
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (71 bp):
AATAGAATGAAAACTTTTATTTACAAATGTAATAAATTTTATTATCAATAAAAACATTTAAACAA
AAATTT
Found at i:2687869 original size:21 final size:20
Alignment explanation
Indices: 2687845--2687894 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
2687835 CTTTTCATTT
*
2687845 TTTTTATTTTTATTTTATTAA
1 TTTTTATTTTAATTTTATT-A
* *
2687866 TTTTTAATATAATTTTATTA
1 TTTTTATTTTAATTTTATTA
*
2687886 TTATTATTT
1 TTTTTATTT
2687895 AGTAAATATA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTATTTTAATTTTATTA
Found at i:2689804 original size:30 final size:30
Alignment explanation
Indices: 2689768--2689838 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
2689758 AATATAGATT
*
2689768 AATTTATTTAGATTTAAATTAAAAATTAAA
1 AATTTATTTAGATTCAAATTAAAAATTAAA
* *
2689798 AATTTATTTAGATTCGAATTAAAAGTTAAA
1 AATTTATTTAGATTCAAATTAAAAATTAAA
*
2689828 AGATATATTTA
1 A-ATTTATTTA
2689839 TACGTAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 28 0.78
31 8 0.22
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.42
Consensus pattern (30 bp):
AATTTATTTAGATTCAAATTAAAAATTAAA
Found at i:2700948 original size:190 final size:190
Alignment explanation
Indices: 2700625--2701007 Score: 757
Period size: 190 Copynumber: 2.0 Consensus size: 190
2700615 TTCTGGCATA
2700625 TTCGAGTGTATTTGTATCCGTAAACACTGGTATGAAAGTGGTTGCCATTTGTATATGCTTCATAG
1 TTCGAGTGTATTTGTATCCGTAAACACTGGTATGAAAGTGGTTGCCATTTGTATATGCTTCATAG
2700690 GTCATGAGATAGATCTCGTTCTCGCTGTCACAAATGTGCAGTTCATTCAAACGCGCTTGCAATCG
66 GTCATGAGATAGATCTCGTTCTCGCTGTCACAAATGTGCAGTTCATTCAAACGCGCTTGCAATCG
2700755 CACAAATTCATGCTTTTGGAGTTAGGGGCACTGAAATTGAAATGACTTGTATAAATAATT
131 CACAAATTCATGCTTTTGGAGTTAGGGGCACTGAAATTGAAATGACTTGTATAAATAATT
2700815 TTCGAGTGTATTTGTATCCGTAAACACTGGTATGAAAGTGGTTGCCATTTGTATATGCTTCATAG
1 TTCGAGTGTATTTGTATCCGTAAACACTGGTATGAAAGTGGTTGCCATTTGTATATGCTTCATAG
2700880 GTCATGAGATAGATCTCGTTCTCGCTGTCACAAATGTGCAGTTCATTCAAACGCGCTTGCAATCG
66 GTCATGAGATAGATCTCGTTCTCGCTGTCACAAATGTGCAGTTCATTCAAACGCGCTTGCAATCG
*
2700945 CACAAATTCGTGCTTTTGGAGTTAGGGGCACTGAAATTGAAATGACTTGTATAAATAATT
131 CACAAATTCATGCTTTTGGAGTTAGGGGCACTGAAATTGAAATGACTTGTATAAATAATT
2701005 TTC
1 TTC
2701008 ATGGAGAAAA
Statistics
Matches: 192, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
190 192 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (190 bp):
TTCGAGTGTATTTGTATCCGTAAACACTGGTATGAAAGTGGTTGCCATTTGTATATGCTTCATAG
GTCATGAGATAGATCTCGTTCTCGCTGTCACAAATGTGCAGTTCATTCAAACGCGCTTGCAATCG
CACAAATTCATGCTTTTGGAGTTAGGGGCACTGAAATTGAAATGACTTGTATAAATAATT
Found at i:2702490 original size:13 final size:15
Alignment explanation
Indices: 2702471--2702506 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
2702461 AGTCAAATAC
2702471 ATATTTTTA-TTAAT
1 ATATTTTTATTTAAT
2702485 -TA-TTTTATTTAAT
1 ATATTTTTATTTAAT
2702498 ATATTTTTA
1 ATATTTTTA
2702507 ATATTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.26
13 7 0.37
14 2 0.11
15 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATATTTTTATTTAAT
Found at i:2704768 original size:2 final size:2
Alignment explanation
Indices: 2704763--2704801 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2704753 TAACAAATGA
2704763 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2704802 AACAAATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2710389 original size:41 final size:40
Alignment explanation
Indices: 2710343--2710426 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 40
2710333 AATAATTTAT
*
2710343 ATATTTTAAATATATTT-TCAAA-AATTTAAAATTATAATAAA
1 ATATTTTAAATATATTTATCAAATAA--AAAAATTAT-ATAAA
**
2710384 ATATTTTTTATATATTTATCAAATAAAAAAATTATATAAA
1 ATATTTTAAATATATTTATCAAATAAAAAAATTATATAAA
2710424 ATA
1 ATA
2710427 ATTATCCAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
40 8 0.21
41 23 0.61
42 5 0.13
43 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (40 bp):
ATATTTTAAATATATTTATCAAATAAAAAAATTATATAAA
Found at i:2710875 original size:22 final size:22
Alignment explanation
Indices: 2710834--2710875 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2710824 GGTCAGTATC
** *
2710834 AAATTAATCTTATTTTATCATA
1 AAATTAATCTTAAGTAATCATA
2710856 AAATTAATCTTAAGTAATCA
1 AAATTAATCTTAAGTAATCA
2710876 AGTAATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATTAATCTTAAGTAATCATA
Found at i:2713737 original size:22 final size:22
Alignment explanation
Indices: 2713691--2713735 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2713681 TTCAATCTAA
2713691 ATAATTAAATTATAATTATGTT
1 ATAATTAAATTATAATTATGTT
* *
2713713 ATAATTATATT-TAA-TATATT
1 ATAATTAAATTATAATTATGTT
2713733 ATA
1 ATA
2713736 TATTCTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 3 0.14
22 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATAATTAAATTATAATTATGTT
Found at i:2716860 original size:47 final size:48
Alignment explanation
Indices: 2716771--2716862 Score: 118
Period size: 47 Copynumber: 1.9 Consensus size: 48
2716761 TTAATGTAAA
*
2716771 ATTAAATTAAATTAATATAATTTTTTATAAAATTAATATTTTAAAATC
1 ATTAAATTAAATTAATATAATTTTTTATAAAATTAAAATTTTAAAATC
* *
2716819 ATTAAATTTAA-T-ATATAATATTTTTATATACA-TAAAATTTTAAA
1 ATTAAATTAAATTAATATAAT-TTTTTATA-AAATTAAAATTTTAAA
2716863 TCAATTTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
46 7 0.18
47 20 0.51
48 12 0.31
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (48 bp):
ATTAAATTAAATTAATATAATTTTTTATAAAATTAAAATTTTAAAATC
Found at i:2717153 original size:41 final size:40
Alignment explanation
Indices: 2717099--2717182 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 40
2717089 AATAATTTAT
*
2717099 ATATTTTAAATATATTT-TCAAA-AATTTAAAATTATAATAAA
1 ATATTTTAAATATATTTATCAAATAA--AAAAATTAT-ATAAA
**
2717140 ATATTTTTTATATATTTATCAAATAAAAAAATTATATAAA
1 ATATTTTAAATATATTTATCAAATAAAAAAATTATATAAA
2717180 ATA
1 ATA
2717183 ATTATCCAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
40 8 0.21
41 23 0.61
42 5 0.13
43 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (40 bp):
ATATTTTAAATATATTTATCAAATAAAAAAATTATATAAA
Found at i:2717630 original size:22 final size:22
Alignment explanation
Indices: 2717589--2717630 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2717579 GGTCAGTATC
** *
2717589 AAATTAATCTTATTTTATCATA
1 AAATTAATCTTAAGTAATCATA
2717611 AAATTAATCTTAAGTAATCA
1 AAATTAATCTTAAGTAATCA
2717631 AGTAATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATTAATCTTAAGTAATCATA
Found at i:2719427 original size:23 final size:24
Alignment explanation
Indices: 2719383--2719432 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
2719373 TTTTATAATT
* *
2719383 AAATTTAAATAAAATAATTTAA-A
1 AAATTAAAATAAAATAAATTAACA
**
2719406 AAATTAAAATAACTTAAATTAACA
1 AAATTAAAATAAAATAAATTAACA
2719430 AAA
1 AAA
2719433 AAAAACTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATTAAAATAAAATAAATTAACA
Found at i:2724247 original size:27 final size:27
Alignment explanation
Indices: 2724209--2724261 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2724199 AACCACCAAT
* *
2724209 TGTTTGTTAAAAATTGTGGTTACTTTG
1 TGTTTGTAAAAAATGGTGGTTACTTTG
*
2724236 TGTTTGTAAAAAATGGTGGTTTCTTT
1 TGTTTGTAAAAAATGGTGGTTACTTT
2724262 TCATTTGTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.04, G:0.23, T:0.51
Consensus pattern (27 bp):
TGTTTGTAAAAAATGGTGGTTACTTTG
Found at i:2724268 original size:27 final size:27
Alignment explanation
Indices: 2724211--2724277 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
2724201 CCACCAATTG
* * *
2724211 TTTGTTAAAAATTGTGGTTACTTTGTG
1 TTTGTAAAAAATGGTGGTTACTTTGTA
*
2724238 TTTGTAAAAAATGGTGGTTTCTTT-TCA
1 TTTGTAAAAAATGGTGGTTACTTTGT-A
*
2724265 TTTGTCAAAAATG
1 TTTGTAAAAAATG
2724278 ATGGCATGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 1 0.03
27 33 0.97
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.48
Consensus pattern (27 bp):
TTTGTAAAAAATGGTGGTTACTTTGTA
Found at i:2726535 original size:2 final size:2
Alignment explanation
Indices: 2726528--2726555 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2726518 TCAAAACTTA
2726528 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
2726556 GAAAAATATT
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:2729832 original size:32 final size:31
Alignment explanation
Indices: 2729788--2729849 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
2729778 AAATTTATCA
* * *
2729788 TAATTATTTTTAATATTTATTAAATTTACGAG
1 TAATTATATTTAATATGTATCAAA-TTACGAG
2729820 TAATTATATTTAATATGTATCAAATTACGA
1 TAATTATATTTAATATGTATCAAATTACGA
2729850 TCAATATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.48
Consensus pattern (31 bp):
TAATTATATTTAATATGTATCAAATTACGAG
Found at i:2730562 original size:79 final size:79
Alignment explanation
Indices: 2730435--2730586 Score: 234
Period size: 79 Copynumber: 1.9 Consensus size: 79
2730425 GGCCAAGTCA
*
2730435 AGTTGAGCACAACCCTTAAAAGTTAAAGCCAAAACTAAACTTATTTTTAATTAAATTTAATATTT
1 AGTTGAGCACAACCCTTAAAAGTTAAAGCCAAAACTAAACTTATTTTTAATCAAATTTAATATTT
2730500 TTACTCAAATGTGG
66 TTACTCAAATGTGG
* * * **
2730514 AGTTGGGCACAACCCTTGAAAG-TAAAGCCAAAGCTATTCTTATCTTTTAATCAAATTTAATATT
1 AGTTGAGCACAACCCTTAAAAGTTAAAGCCAAAACTAAACTTAT-TTTTAATCAAATTTAATATT
2730578 TTTACTCAA
65 TTTACTCAA
2730587 GTCTATTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
78 18 0.27
79 48 0.73
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (79 bp):
AGTTGAGCACAACCCTTAAAAGTTAAAGCCAAAACTAAACTTATTTTTAATCAAATTTAATATTT
TTACTCAAATGTGG
Found at i:2730609 original size:16 final size:16
Alignment explanation
Indices: 2730590--2730634 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
2730580 TACTCAAGTC
2730590 TATTTTTTAAATTTAA
1 TATTTTTTAAATTTAA
2730606 TA-TTTTT--ATTTAA
1 TATTTTTTAAATTTAA
2730619 -ATTATTTTAAATTTAA
1 TATT-TTTTAAATTTAA
2730635 AACATAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 1 0.04
13 7 0.28
14 4 0.16
15 5 0.20
16 8 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTTTTAAATTTAA
Found at i:2730611 original size:15 final size:15
Alignment explanation
Indices: 2730591--2730635 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
2730581 ACTCAAGTCT
2730591 ATTTTTTAAATTT-A
1 ATTTTTTAAATTTAA
2730605 ATATTTTT--ATTTAA
1 AT-TTTTTAAATTTAA
2730619 ATTATTTTAAATTTAA
1 ATT-TTTTAAATTTAA
2730635 A
1 A
2730636 ACATAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 5 0.19
14 9 0.35
15 5 0.19
16 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTTTAAATTTAA
Found at i:2732388 original size:160 final size:161
Alignment explanation
Indices: 2732217--2732542 Score: 521
Period size: 160 Copynumber: 2.0 Consensus size: 161
2732207 AAACTCATTC
2732217 TTTTTAGAATATATTGGTTGATATTTGAGATTACTTTAAAAAAAATAAATTTACGTAGATTAATC
1 TTTTTAGAATATATTGGTTGATATTTGAGATTACTTTAAAAAAAATAAATTTACGTAGATTAATC
* *
2732282 ACACTTAATAAAAAAATTAGAGATGATTCTTTATTTATGTTTAATAGTAAAATATAATAT-AGAT
66 ACACTTAATAAAAAAATTAAAAATGATTCTTTATTTATGTTTAATAGTAAAATATAATATGA-AT
*
2732346 ACGTAGTTAAT-AAAAAAATAAATGACTTTTT
130 ACGTAATTAATAAAAAAAATAAATGACTTTTT
* * * *
2732377 TTTTTAGAATATATTGGTTGATTTTTGAGATTACTTTAAAAAGAATAGATTTATGTAGATTAATC
1 TTTTTAGAATATATTGGTTGATATTTGAGATTACTTTAAAAAAAATAAATTTACGTAGATTAATC
* * *
2732442 ATACTTAATAAAAAAATTAAAAATGATTCTTTATTTGTGTTTAATAGTAGAATATAATATGAATA
66 ACACTTAATAAAAAAATTAAAAATGATTCTTTATTTATGTTTAATAGTAAAATATAATATGAATA
**
2732507 CGTAATTAATAAAAAAAATAAATGTTTTTTT
131 CGTAATTAATAAAAAAAATAAATGACTTTTT
2732538 TTTTT
1 TTTTT
2732543 TTTTTTTTTT
Statistics
Matches: 152, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
160 128 0.84
161 24 0.16
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42
Consensus pattern (161 bp):
TTTTTAGAATATATTGGTTGATATTTGAGATTACTTTAAAAAAAATAAATTTACGTAGATTAATC
ACACTTAATAAAAAAATTAAAAATGATTCTTTATTTATGTTTAATAGTAAAATATAATATGAATA
CGTAATTAATAAAAAAAATAAATGACTTTTT
Found at i:2739103 original size:10 final size:11
Alignment explanation
Indices: 2739088--2739114 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2739078 TTTCTCTCAC
2739088 TTTTTTTTCTT
1 TTTTTTTTCTT
2739099 TTTTTTTTCTT
1 TTTTTTTTCTT
2739110 TTTTT
1 TTTTT
2739115 CTGTATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:2740110 original size:19 final size:19
Alignment explanation
Indices: 2740059--2740113 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
2740049 ATGGATATGG
2740059 AATATAAT-ATAAAAT-TA
1 AATATAATAATAAAATATA
*
2740076 AAAATTACATAA-AAAATATA
1 AATA-TA-ATAATAAAATATA
2740096 AATATAATAATAAAATAT
1 AATATAATAATAAAATAT
2740114 GCAGAGATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 3 0.10
18 6 0.19
19 16 0.52
20 6 0.19
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AATATAATAATAAAATATA
Found at i:2740273 original size:17 final size:17
Alignment explanation
Indices: 2740222--2740282 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
2740212 TTTTTTCGCC
* *
2740222 CTCTTTTCTTTCTTTCT
1 CTCTTTTCTCTCTCTCT
*
2740239 -TCTATTT-TCT-TCTTT
1 CTCT-TTTCTCTCTCTCT
2740254 CTCTTTTCTCTCTCTCT
1 CTCTTTTCTCTCTCTCT
2740271 CTCTTTTCTCTC
1 CTCTTTTCTCTC
2740283 CTTTCCCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
15 6 0.17
16 11 0.31
17 19 0.53
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.66
Consensus pattern (17 bp):
CTCTTTTCTCTCTCTCT
Found at i:2740467 original size:19 final size:18
Alignment explanation
Indices: 2740445--2740488 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
2740435 ATATATATAT
* *
2740445 ATATATAAATACATATAAC
1 ATATAAAAAAACATA-AAC
2740464 ATATAAAAAAACATAAAC
1 ATATAAAAAAACATAAAC
2740482 ATA-AAAA
1 ATATAAAA
2740489 TAAAAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 6 0.26
19 13 0.57
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (18 bp):
ATATAAAAAAACATAAAC
Found at i:2740780 original size:34 final size:34
Alignment explanation
Indices: 2740715--2740946 Score: 211
Period size: 34 Copynumber: 6.9 Consensus size: 34
2740705 GTTTTTGTTT
* * * * *
2740715 TTGTTGATTAAATG-GTGATTTGATGGCTTGCCA
1 TTGTTGACTAAATGAGAGATTTGGTAGTTTGCCA
*
2740748 TTGTTGACTAAATGAGAAATTTGGTAGTTTGCCA
1 TTGTTGACTAAATGAGAGATTTGGTAGTTTGCCA
* * * *
2740782 TTGTTGATTAAATG-GTGATTTGGTGGTTTGCTA
1 TTGTTGACTAAATGAGAGATTTGGTAGTTTGCCA
* * **
2740815 TTGTTAACTAAAT-AGAAGATTTGATAGTTTAACA
1 TTGTTGACTAAATGAG-AGATTTGGTAGTTTGCCA
* * * * *
2740849 TTGTTGATTAAATGGGTGATTTGGTGGTTTACCA
1 TTGTTGACTAAATGAGAGATTTGGTAGTTTGCCA
2740883 TTGTTGACTAAAT-ATGAGATTTGGTAGTTTGCCA
1 TTGTTGACTAAATGA-GAGATTTGGTAGTTTGCCA
* * * *
2740917 TTGTTGATTAAATGGGTGATTTGGTGGTTT
1 TTGTTGACTAAATGAGAGATTTGGTAGTTT
2740947 TTACCAAACC
Statistics
Matches: 158, Mismatches: 35, Indels: 11
0.77 0.17 0.05
Matches are distributed among these distances:
33 40 0.25
34 117 0.74
35 1 0.01
ACGTcount: A:0.25, C:0.06, G:0.26, T:0.43
Consensus pattern (34 bp):
TTGTTGACTAAATGAGAGATTTGGTAGTTTGCCA
Found at i:2740894 original size:68 final size:67
Alignment explanation
Indices: 2740715--2740946 Score: 342
Period size: 68 Copynumber: 3.4 Consensus size: 67
2740705 GTTTTTGTTT
* *
2740715 TTGTTGATTAAATGGTGATTTGATGGCTTGCCATTGTTGACTAAATGAGAA-ATTTGGTAGTTTG
1 TTGTTGATTAAATGGTGATTTGGTGGTTTGCCATTGTTGACTAAAT-AGAAGATTTGGTAGTTTG
2740779 CCA
65 CCA
* * * **
2740782 TTGTTGATTAAATGGTGATTTGGTGGTTTGCTATTGTTAACTAAATAGAAGATTTGATAGTTTAA
1 TTGTTGATTAAATGGTGATTTGGTGGTTTGCCATTGTTGACTAAATAGAAGATTTGGTAGTTTGC
2740847 CA
66 CA
*
2740849 TTGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATATG-AGATTTGGTAGTTT
1 TTGTTGATTAAAT-GGTGATTTGGTGGTTTGCCATTGTTGACTAAATA-GAAGATTTGGTAGTTT
2740913 GCCA
64 GCCA
2740917 TTGTTGATTAAATGGGTGATTTGGTGGTTT
1 TTGTTGATTAAAT-GGTGATTTGGTGGTTT
2740947 TTACCAAACC
Statistics
Matches: 149, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
66 4 0.03
67 68 0.46
68 76 0.51
69 1 0.01
ACGTcount: A:0.25, C:0.06, G:0.26, T:0.43
Consensus pattern (67 bp):
TTGTTGATTAAATGGTGATTTGGTGGTTTGCCATTGTTGACTAAATAGAAGATTTGGTAGTTTGC
CA
Found at i:2741274 original size:19 final size:19
Alignment explanation
Indices: 2741250--2741301 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
2741240 GTCGAGGTAT
* *
2741250 TATTCACGTATATAGGCAC
1 TATTCACGTATACAAGCAC
* *
2741269 TATTCACATATACAAGTAC
1 TATTCACGTATACAAGCAC
2741288 TATTCACGTATACA
1 TATTCACGTATACA
2741302 GTACTGTGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.33
Consensus pattern (19 bp):
TATTCACGTATACAAGCAC
Found at i:2741313 original size:18 final size:19
Alignment explanation
Indices: 2741267--2741315 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
2741257 GTATATAGGC
* *
2741267 ACTATTCACATATACAAGT
1 ACTATGCACGTATACAAGT
*
2741286 ACTATTCACGTATAC-AGT
1 ACTATGCACGTATACAAGT
*
2741304 ACTGTGCACGTA
1 ACTATGCACGTA
2741316 AAATAGTGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (19 bp):
ACTATGCACGTATACAAGT
Found at i:2745426 original size:34 final size:34
Alignment explanation
Indices: 2745366--2745592 Score: 246
Period size: 34 Copynumber: 6.7 Consensus size: 34
2745356 AAGTGGGAGA
* *
2745366 ATTGTTGATTAAATG-GTGATTTGGTAGTTTGGC
1 ATTGTTGATTAAATGAGAGATTTGGTAGTTTGCC
* *
2745399 ATTGTTGACTAAATGAGAGATTTGGTAGTTTGTC
1 ATTGTTGATTAAATGAGAGATTTGGTAGTTTGCC
* *
2745433 ATTGTTGATTAAAT-AG-GTAATTTGGTGGTTTGTC
1 ATTGTTGATTAAATGAGAG--ATTTGGTAGTTTGCC
* * *
2745467 ATTATTGACTAAATGGGAGATTTGGTAGTTTGCC
1 ATTGTTGATTAAATGAGAGATTTGGTAGTTTGCC
* * * *
2745501 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGAGAGATTTGGTAGTTTGCC
* * *
2745535 ATTATTGACTAAAT-AGGAGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGA-GAGATTTGGTAGTTTGCC
*
2745569 ATTGTTGATTAAATGAGTGATTTG
1 ATTGTTGATTAAATGAGAGATTTG
2745593 ATGATTTTTA
Statistics
Matches: 164, Mismatches: 23, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
32 1 0.01
33 16 0.10
34 144 0.88
35 2 0.01
36 1 0.01
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.43
Consensus pattern (34 bp):
ATTGTTGATTAAATGAGAGATTTGGTAGTTTGCC
Found at i:2745475 original size:68 final size:67
Alignment explanation
Indices: 2745366--2745592 Score: 330
Period size: 68 Copynumber: 3.3 Consensus size: 67
2745356 AAGTGGGAGA
* * *
2745366 ATTGTTGATTAAATGGTGATTTGGTAGTTTGGCATTGTTGACTAAATGAGAGATTTGGTAGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTGGTTTGCCATTATTGACTAAATGAGAGATTTGGTAGTTTG
*
2745431 TC
66 CC
* * *
2745433 ATTGTTGATTAAATAGGTAATTTGGTGGTTTGTCATTATTGACTAAATGGGAGATTTGGTAGTTT
1 ATTGTTGATTAAAT-GGTGATTTGGTGGTTTGCCATTATTGACTAAATGAGAGATTTGGTAGTTT
2745498 GCC
65 GCC
*
2745501 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACCATTATTGACTAAAT-AGGAGATTTGGTAGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTGGTTTGCCATTATTGACTAAATGA-GAGATTTGGTAGTT
*
2745565 TACC
64 TGCC
2745569 ATTGTTGATTAAATGAGTGATTTG
1 ATTGTTGATTAAATG-GTGATTTG
2745593 ATGATTTTTA
Statistics
Matches: 145, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
67 15 0.10
68 130 0.90
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.43
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTGGTTTGCCATTATTGACTAAATGAGAGATTTGGTAGTTTG
CC
Found at i:2745559 original size:102 final size:102
Alignment explanation
Indices: 2745370--2745592 Score: 279
Period size: 102 Copynumber: 2.2 Consensus size: 102
2745360 GGGAGAATTG
* **
2745370 TTGATTAAAT-GGTGATTTGGTAGTTTGGCATTGTTGACTAAATGAGAGATTTGGTAGTTTGTCA
1 TTGATTAAATGGGTGATTTGGTAGTTTGCCATTGTTGACTAAATGAGAGATTTGGTAGTTTACCA
* * * **
2745434 TTGTTGATTAAATAGGTAATTTGGTGGTTTGTCATTA
66 TTATTGACTAAATAGGTAATTTGGTAGTTTACCATTA
* * * * * *
2745471 TTGACTAAATGGGAGATTTGGTAGTTTGCCATTGTTGATTAAATGGGTGATTTGGTGGTTTACCA
1 TTGATTAAATGGGTGATTTGGTAGTTTGCCATTGTTGACTAAATGAGAGATTTGGTAGTTTACCA
*
2745536 TTATTGACTAAATAGG-AGATTTGGTAGTTTACCATTG
66 TTATTGACTAAATAGGTA-ATTTGGTAGTTTACCATTA
*
2745573 TTGATTAAATGAGTGATTTG
1 TTGATTAAATGGGTGATTTG
2745593 ATGATTTTTA
Statistics
Matches: 102, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
101 10 0.10
102 92 0.90
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.43
Consensus pattern (102 bp):
TTGATTAAATGGGTGATTTGGTAGTTTGCCATTGTTGACTAAATGAGAGATTTGGTAGTTTACCA
TTATTGACTAAATAGGTAATTTGGTAGTTTACCATTA
Found at i:2745935 original size:15 final size:15
Alignment explanation
Indices: 2745915--2745947 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2745905 AAAGTCAATA
2745915 GAGCTGA-TCTGAGCT
1 GAGCTGAGT-TGAGCT
2745930 GAGCTGAGTTGAGCT
1 GAGCTGAGTTGAGCT
2745945 GAG
1 GAG
2745948 TGCAAGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (15 bp):
GAGCTGAGTTGAGCT
Found at i:2746002 original size:15 final size:15
Alignment explanation
Indices: 2745982--2746012 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2745972 TGATCTGGCC
2745982 TTATCTGCTTTTCTA
1 TTATCTGCTTTTCTA
2745997 TTATCTGCTTTTCTA
1 TTATCTGCTTTTCTA
2746012 T
1 T
2746013 AATTAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.19, G:0.06, T:0.61
Consensus pattern (15 bp):
TTATCTGCTTTTCTA
Found at i:2746693 original size:15 final size:15
Alignment explanation
Indices: 2746656--2746694 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
2746646 ATTCAACACA
*
2746656 GAAAATTTAAGCTTT
1 GAAAATTTTAGCTTT
*
2746671 -AAATTTTTAGCTTT
1 GAAAATTTTAGCTTT
2746685 GAAAATTTTA
1 GAAAATTTTA
2746695 AGTACCAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (15 bp):
GAAAATTTTAGCTTT
Found at i:2748420 original size:13 final size:13
Alignment explanation
Indices: 2748404--2748450 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 13
2748394 TTTAAAATTT
2748404 TAATTTTTATTAA
1 TAATTTTTATTAA
2748417 TAATTTATTAATATAA
1 TAATTT-TT-AT-TAA
2748433 TAATTTTTATTAAA
1 TAATTTTTATT-AA
2748447 TAAT
1 TAAT
2748451 ATAGAAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 7 0.23
14 10 0.33
15 4 0.13
16 9 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TAATTTTTATTAA
Found at i:2748435 original size:16 final size:15
Alignment explanation
Indices: 2748404--2748450 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 15
2748394 TTTAAAATTT
2748404 TAATTTTT-AT-TAA
1 TAATTTTTAATATAA
2748417 TAATTTATTAATATAA
1 TAATTT-TTAATATAA
*
2748433 TAATTTTTATTA-AA
1 TAATTTTTAATATAA
2748447 TAAT
1 TAAT
2748451 ATAGAAATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 6 0.20
14 8 0.27
15 7 0.23
16 9 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTTTTAATATAA
Found at i:2750315 original size:16 final size:16
Alignment explanation
Indices: 2750294--2750326 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2750284 CCAATTTAAC
2750294 CATAACTTTGTAATAA
1 CATAACTTTGTAATAA
2750310 CATAACTTTGTAATAA
1 CATAACTTTGTAATAA
2750326 C
1 C
2750327 TTAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (16 bp):
CATAACTTTGTAATAA
Found at i:2751544 original size:24 final size:24
Alignment explanation
Indices: 2751487--2751545 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
2751477 TTTCGTGTAG
* *
2751487 TATTTATGTTA-TTTTTCGTATTA
1 TATTTATATTATTTTTTCATATTA
*
2751510 TATTT-TAATTATTTTTTTATATTA
1 TATTTAT-ATTATTTTTTCATATTA
2751534 TATTTATATTAT
1 TATTTATATTAT
2751546 GTCATAATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 1 0.03
23 8 0.27
24 20 0.67
25 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (24 bp):
TATTTATATTATTTTTTCATATTA
Found at i:2751574 original size:21 final size:22
Alignment explanation
Indices: 2751538--2751582 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2751528 ATATTATATT
2751538 TATATTATGTCATAATTCATTA
1 TATATTATGTCATAATTCATTA
* *
2751560 TATATTTTG-CATAATTTATTA
1 TATATTATGTCATAATTCATTA
2751581 TA
1 TA
2751583 GTGATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (22 bp):
TATATTATGTCATAATTCATTA
Found at i:2754943 original size:3 final size:3
Alignment explanation
Indices: 2754935--2754972 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
2754925 TAATTACCAA
*
2754935 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2754973 CAATTTTGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2756023 original size:23 final size:23
Alignment explanation
Indices: 2755997--2756040 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2755987 TGAGTAAATT
*
2755997 ACCCTTTTTATCATGTTATTTCA
1 ACCCTTTTTATCATATTATTTCA
*
2756020 ACCCTTTTTGTCATATTATTT
1 ACCCTTTTTATCATATTATTT
2756041 TTGAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.55
Consensus pattern (23 bp):
ACCCTTTTTATCATATTATTTCA
Found at i:2759117 original size:332 final size:333
Alignment explanation
Indices: 2758510--2759149 Score: 1124
Period size: 332 Copynumber: 1.9 Consensus size: 333
2758500 GAAAAAAAGC
2758510 AGTCAAAATAAACTCCATATGAAAAAGCGATTATTTCGCTTCATCTATGTTGCAGGTACCACTAT
1 AGTCAAAATAAACTCCATATGAAAAAGCGATTATTTCGCTTCATCTATGTTGCAGGTACCACTAT
* *
2758575 GAATGATTACATTACCAGTTTCAATCAACTGGTTACTGATCTGATGAACGTTGATGAATCTTTCA
66 GAATGATCACATTACCAGTTTCAATCAACTGGTTACTGATCTGATGAACATTGATGAATCTTTCA
* * *
2758640 AAGATGAGGATCTGGTATTGATGCTGTTGGGGTCACTTCTACAGGAGTTTGAGTTTCTCGAAACA
131 AAGATGAGGATCTGGCATTGATGCTGTTAGGGTCACTTCCACAGGAGTTTGAGTTTCTCGAAACA
*
2758705 ACTCTATTCCATGGAAAAGTTGCGGTATCCCTTCGTGAAGTATGTGCACCTTTGTATAGTTATGA
196 ACTCTATTCCATGGAAAAGTTGCGGTATCCCTTAGTGAAGTATGTGCACCTTTGTATAGTTATGA
2758770 ACTAAGGAAGAAAGACAAACAAGGAAGCTTTGATAGAGATGCAAAAGCGATTATTTCCATGGGAA
261 ACTAAGGAAGAAAGACAAACAAGGAAGCTTTGATAGAGATGCAAAAGCGATTATTTCCATGGGAA
2758835 AGACAAAT
326 AGACAAAT
2758843 AGTCAAAATAAACTCCATATGAAGAAA-CGATTATTTCGCTTCATCTATGTTGCA-GTACCACTA
1 AGTCAAAATAAACTCCATATGAA-AAAGCGATTATTTCGCTTCATCTATGTTGCAGGTACCACTA
* *
2758906 TGAATGATCACATTACCGGTTTCAATCAATTGGTTACTGATCTGATGAACATTGATGAATCTTTC
65 TGAATGATCACATTACCAGTTTCAATCAACTGGTTACTGATCTGATGAACATTGATGAATCTTTC
* *
2758971 AAAGATGAGGATCTGGCATTGATGCTGTTAGGGTCACTTCCAGAGGAGTTTGAGTTTCTCGAAAT
130 AAAGATGAGGATCTGGCATTGATGCTGTTAGGGTCACTTCCACAGGAGTTTGAGTTTCTCGAAAC
* *
2759036 AACTCTATTCCAT-GAGAAAGTTGCGGTATCCCTTAGTGAAGTATGTTCAGCTTTGTATAGTTAT
195 AACTCTATTCCATGGA-AAAGTTGCGGTATCCCTTAGTGAAGTATGTGCACCTTTGTATAGTTAT
*
2759100 GAACTAAGGAAGAAAGACAAACAAGGAAGCTTTGATAGAGATGCAGAAGC
259 GAACTAAGGAAGAAAGACAAACAAGGAAGCTTTGATAGAGATGCAAAAGC
2759150 TTTGGTGGTC
Statistics
Matches: 292, Mismatches: 13, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
331 2 0.01
332 237 0.81
333 50 0.17
334 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (333 bp):
AGTCAAAATAAACTCCATATGAAAAAGCGATTATTTCGCTTCATCTATGTTGCAGGTACCACTAT
GAATGATCACATTACCAGTTTCAATCAACTGGTTACTGATCTGATGAACATTGATGAATCTTTCA
AAGATGAGGATCTGGCATTGATGCTGTTAGGGTCACTTCCACAGGAGTTTGAGTTTCTCGAAACA
ACTCTATTCCATGGAAAAGTTGCGGTATCCCTTAGTGAAGTATGTGCACCTTTGTATAGTTATGA
ACTAAGGAAGAAAGACAAACAAGGAAGCTTTGATAGAGATGCAAAAGCGATTATTTCCATGGGAA
AGACAAAT
Found at i:2760703 original size:21 final size:22
Alignment explanation
Indices: 2760674--2760719 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2760664 TGTTCAGACA
** *
2760674 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2760696 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2760717 AGT
1 AGT
2760720 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2762665 original size:28 final size:27
Alignment explanation
Indices: 2762599--2762672 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
2762589 AAAAACCACC
*
2762599 CTTTGTGTTTGTCAAAAATGGTGGTTA
1 CTTTGTGTTTGTCAAAAATGGTGATTA
* *
2762626 CTTTGTATTTGTCAAAAATGGTGATTC
1 CTTTGTGTTTGTCAAAAATGGTGATTA
* *
2762653 CTTTTTTGTTTGTAAAAAAT
1 C-TTTGTGTTTGTCAAAAAT
2762673 TATGGCTTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 25 0.62
28 15 0.38
ACGTcount: A:0.26, C:0.08, G:0.19, T:0.47
Consensus pattern (27 bp):
CTTTGTGTTTGTCAAAAATGGTGATTA
Found at i:2763450 original size:28 final size:28
Alignment explanation
Indices: 2763395--2763451 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
2763385 TTAATTTGTA
* *
2763395 TTTGTAAAAAATAGTGATTTCTTTTTTG
1 TTTGTAAAAAATAGTGACTTCTTGTTTG
*
2763423 TTTGTAAAAAATTA-TGACTTGTTGTTTG
1 TTTGTAAAAAA-TAGTGACTTCTTGTTTG
2763451 T
1 T
2763452 CAAAATTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.28, C:0.04, G:0.16, T:0.53
Consensus pattern (28 bp):
TTTGTAAAAAATAGTGACTTCTTGTTTG
Found at i:2763620 original size:762 final size:765
Alignment explanation
Indices: 2762096--2763627 Score: 2656
Period size: 762 Copynumber: 2.0 Consensus size: 765
2762086 TGGTTATATT
* * *
2762096 TTTATTCTTGCAAAAGCTCTAATTAGTTGAAAATCCACCTTACAGTCAACAATAGCTCTGTCTAC
1 TTTACTCTTGCAAAAGCTCCAATTAGTTGAAAATCCACCTTACAGTC-ACAATAGCTCTATCTAC
2762161 TACAGAAGCAGAGTATATGGCATTAACAGAGGCTGTAAAAGAAGCAGTATGGCTTCAAGGGTTGC
65 TACAGAAGCAGAGTATATGGCATTAACAGAGGCTGTAAAAGAAGCAGTATGGCTTCAAGGGTTGC
*
2762226 TTGGTGAACTTGGAGTTGAACAGAAGCAAGTTATTCTACATTGTGATAGCCAGAGTGTTATTCAA
130 TTGGTGAACTTGGAGTTGAACAGAAGCAAGTTATTCTACATTGTGATAGCCAGAGTGCTATTCAA
*
2762291 TTGGCCAAAAACCTAGTTTACCATGTAAGAACGAAGCACATCGATGTTTATTATCATTTTGTACG
195 TTGGCCAAAAACCTAGTTTACCATGCAAGAACGAAGCACATCGATGTTTATTATCATTTTGTACG
*
2762356 AGAAATTCTGAATGAAGGTGGAGTAGAAATTCAGAAGATTCGAACATCTGAGAATCCTGTTAATA
260 AGAAATTCTGAATGAAGGTGGAGTAGAAATTCAGAAGATTCGAACATCTAAGAATCCTGTTAATA
* *
2762421 TGATAACAAAAGTTGTGACTATGATCAAGTTCCAACTATGTTTGGATTTGGTCAATATTGTCAGA
325 TGATAACAAAAGTTATGACTACGATCAAGTTCCAACTATGTTTGGATTTGGTCAATATTGTCAGA
* *
2762486 AGTTGAGATCGATATTGAAGACACTACCAGGATCCTTTATTGATAAGAATGAAGACTTGAAAAAT
390 AGTTGAGATCGATATTGAAGACACTACCAGGATCATTTATTAATAAGAATGAAGACTTGAAAAAT
* *
2762551 TCACCAAGGTGGAGACTTGTAGTGGGTGGATAGTCAACAAAAACCACCCTTTGTGTTTGTCAAAA
455 TCACCAAGGTGAAGACTTGTAGCGGGTGGATAGTCAACAAAAACCACCCTTTGTGTTTGTCAAAA
* * * * *
2762616 ATGGTGGTTACTTTGTATTTGTCAAAAATGGTGATTCCTTTTTTGTTTGTAAAAAATTATGGCTT
520 ATGATGGTTAATTTGTATTTGTAAAAAATAGTGATTCCTTTTTTGTTTGTAAAAAATTATGACTT
*
2762681 GTTGTTTGTCAAAATTGGTGGCTAATTTTTATTGTAAAATGGGGGAGGATGGCGCTTATAAAAGG
585 GTTGTTTGTCAAAATTGGTGGCTAATTTTTATTGTAAAATGGGGGAGGATGGCGCCTATAAAAGG
** *
2762746 AGGCTCCTTTATCCCTCTTGAGCATCCCTCTTTTGTATCCCTCTTTAATTCTTTCTCATAATAGA
650 AGGCTCCTTTATCCCTCTCAAGCATCCCTCTCTTGTATCCCTCTTTAATTCTTTCTCATAATAGA
*
2762811 ATTGGTGGTGTCCGAGGACGTAGGCATAAGTTGGTCGAACCTCGTTAAATC
715 ATTGGTGGTGTCCGAGGACGTAGGCATAAGTTGGCCGAACCTCGTTAAATC
* * *
2762862 TTTACTCTTGCAAAAGCTCCAATTAGTTGGAAATCCA-CTTACAGTC-CAGTGGCTCTATCTACT
1 TTTACTCTTGCAAAAGCTCCAATTAGTTGAAAATCCACCTTACAGTCACAATAGCTCTATCTACT
2762925 ACAGAAGCAGAGTATATGGCATTAACAGAGGCTGTAAAAGAAGCAGTATGGCTTCAAGGGTTGCT
66 ACAGAAGCAGAGTATATGGCATTAACAGAGGCTGTAAAAGAAGCAGTATGGCTTCAAGGGTTGCT
*
2762990 TGGTGAACTTGGAGTTGAACAGAAGCAAGTTATTGTACATTGTGATAGCCAGAGTGCTATTCAAT
131 TGGTGAACTTGGAGTTGAACAGAAGCAAGTTATTCTACATTGTGATAGCCAGAGTGCTATTCAAT
* * * *
2763055 TGGCGAAGAACCTAGTTTACCATGCAAGAACGAAGCACATCGATGTTTGTTATCA-TTTGTATGA
196 TGGCCAAAAACCTAGTTTACCATGCAAGAACGAAGCACATCGATGTTTATTATCATTTTGTACGA
* *
2763119 GAAATTCTGAATGAAGGTGGAGTAGAAATTCAGAAGATTCGAATATCTAAGAATCCTGTTGATAT
261 GAAATTCTGAATGAAGGTGGAGTAGAAATTCAGAAGATTCGAACATCTAAGAATCCTGTTAATAT
* * *
2763184 GATGATAAAAGTTATGACTGCGATCAAGTTCCAACTATGTTTGGATTTGGTCAATATTGTCAGAA
326 GATAACAAAAGTTATGACTACGATCAAGTTCCAACTATGTTTGGATTTGGTCAATATTGTCAGAA
* *
2763249 GTTGAGATCGATATTGAAGACACTACTAGGATCATTTATTAATAAGAATGAAGACTTGAAAATTT
391 GTTGAGATCGATATTGAAGACACTACCAGGATCATTTATTAATAAGAATGAAGACTTGAAAAATT
* *
2763314 CACCAAGGTGAAGATTTGTAGCGGGTGGATAGTCAACAAAAGCCACCCTTTGTGTTTGTCAAAAA
456 CACCAAGGTGAAGACTTGTAGCGGGTGGATAGTCAACAAAAACCACCCTTTGTGTTTGTCAAAAA
*
2763379 TGATGGTTAATTTGTATTTGTAAAAAATAGTGATTTCTTTTTTGTTTGTAAAAAATTATGACTTG
521 TGATGGTTAATTTGTATTTGTAAAAAATAGTGATTCCTTTTTTGTTTGTAAAAAATTATGACTTG
*
2763444 TTGTTTGTCAAAATTGGTGGCTAATTTTTATTGTAAAATGGGGGAGGATGGCGCCTGTAAAAGGA
586 TTGTTTGTCAAAATTGGTGGCTAATTTTTATTGTAAAATGGGGGAGGATGGCGCCTATAAAAGGA
*
2763509 GGCTCCTTTATCCCTCTCAAGCATCCCTCTCTTGTATCCCTCTTTAATTTTTTCTCATAATAGAA
651 GGCTCCTTTATCCCTCTCAAGCATCCCTCTCTTGTATCCCTCTTTAATTCTTTCTCATAATAGAA
2763574 TTGGTGGTGTCCGAGGACGTAGGCATAAGTTGGCCGAACCTCGTTAAATC
716 TTGGTGGTGTCCGAGGACGTAGGCATAAGTTGGCCGAACCTCGTTAAATC
2763624 TTTA
1 TTTA
2763628 GTGTTCTGTT
Statistics
Matches: 724, Mismatches: 42, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
762 488 0.67
763 193 0.27
765 9 0.01
766 34 0.05
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.33
Consensus pattern (765 bp):
TTTACTCTTGCAAAAGCTCCAATTAGTTGAAAATCCACCTTACAGTCACAATAGCTCTATCTACT
ACAGAAGCAGAGTATATGGCATTAACAGAGGCTGTAAAAGAAGCAGTATGGCTTCAAGGGTTGCT
TGGTGAACTTGGAGTTGAACAGAAGCAAGTTATTCTACATTGTGATAGCCAGAGTGCTATTCAAT
TGGCCAAAAACCTAGTTTACCATGCAAGAACGAAGCACATCGATGTTTATTATCATTTTGTACGA
GAAATTCTGAATGAAGGTGGAGTAGAAATTCAGAAGATTCGAACATCTAAGAATCCTGTTAATAT
GATAACAAAAGTTATGACTACGATCAAGTTCCAACTATGTTTGGATTTGGTCAATATTGTCAGAA
GTTGAGATCGATATTGAAGACACTACCAGGATCATTTATTAATAAGAATGAAGACTTGAAAAATT
CACCAAGGTGAAGACTTGTAGCGGGTGGATAGTCAACAAAAACCACCCTTTGTGTTTGTCAAAAA
TGATGGTTAATTTGTATTTGTAAAAAATAGTGATTCCTTTTTTGTTTGTAAAAAATTATGACTTG
TTGTTTGTCAAAATTGGTGGCTAATTTTTATTGTAAAATGGGGGAGGATGGCGCCTATAAAAGGA
GGCTCCTTTATCCCTCTCAAGCATCCCTCTCTTGTATCCCTCTTTAATTCTTTCTCATAATAGAA
TTGGTGGTGTCCGAGGACGTAGGCATAAGTTGGCCGAACCTCGTTAAATC
Found at i:2764310 original size:22 final size:22
Alignment explanation
Indices: 2764270--2764326 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
2764260 ATTAAAATAT
* *
2764270 TATTTTTATTTTAATATTTATA
1 TATTTTTATATTAATATTTAAA
2764292 TATTTTTATAATTAA-ATTTAAA
1 TATTTTTAT-ATTAATATTTAAA
2764314 TAATTTTT-TATTA
1 T-ATTTTTATATTA
2764327 TATAAACAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 4 0.13
22 17 0.55
23 10 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTTTTATATTAATATTTAAA
Found at i:2764708 original size:14 final size:13
Alignment explanation
Indices: 2764681--2764706 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2764671 TAAAAAAATT
2764681 TAAAATTTTTAAA
1 TAAAATTTTTAAA
2764694 TAAAATTTTTAAA
1 TAAAATTTTTAAA
2764707 ATGTTTTTTA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAAAATTTTTAAA
Found at i:2765118 original size:16 final size:18
Alignment explanation
Indices: 2765087--2765119 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2765077 AAGTTAAATG
2765087 ATATTAATATAATTAAAA
1 ATATTAATATAATTAAAA
2765105 ATATTAA-A-AATTAAA
1 ATATTAATATAATTAAA
2765120 TTATTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATATTAATATAATTAAAA
Found at i:2765181 original size:14 final size:14
Alignment explanation
Indices: 2765162--2765196 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2765152 TTTTTTTAAA
* *
2765162 ATATTTTATATAAT
1 ATATTTTAAAAAAT
2765176 ATATTTTAAAAAAT
1 ATATTTTAAAAAAT
2765190 ATATTTT
1 ATATTTT
2765197 CACTCATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATATTTTAAAAAAT
Found at i:2766600 original size:6 final size:6
Alignment explanation
Indices: 2766591--2766627 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
2766581 AAATTTAAAA
* *
2766591 TTAATT TTAATT TTAATT TTCATT TTAATT TTCATT T
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT T
2766628 ATATTTTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (6 bp):
TTAATT
Found at i:2766605 original size:18 final size:18
Alignment explanation
Indices: 2766584--2766622 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2766574 AATGAAAAAA
2766584 TTTAAAATTAATTTTAAT
1 TTTAAAATTAATTTTAAT
** *
2766602 TTTAATTTTCATTTTAAT
1 TTTAAAATTAATTTTAAT
2766620 TTT
1 TTT
2766623 CATTTATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTAAAATTAATTTTAAT
Found at i:2766615 original size:12 final size:12
Alignment explanation
Indices: 2766591--2766627 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
2766581 AAATTTAAAA
*
2766591 TTAATTTTAATT
1 TTAATTTTCATT
2766603 TTAATTTTCATT
1 TTAATTTTCATT
2766615 TTAATTTTCATT
1 TTAATTTTCATT
2766627 T
1 T
2766628 ATATTTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (12 bp):
TTAATTTTCATT
Found at i:2767586 original size:41 final size:42
Alignment explanation
Indices: 2767527--2767623 Score: 117
Period size: 41 Copynumber: 2.3 Consensus size: 42
2767517 TTCATTATCT
* *
2767527 CCTCTATC-ATAGTCCTTTTATGCCGATGATATGATGTTAGTA
1 CCTC-ATCGATAGGCCTTTTATACCGATGATATGATGTTAGTA
* * *
2767569 TCTCA-CGATAGGCCTTTTATACCTATGATATTATGTTAGTA
1 CCTCATCGATAGGCCTTTTATACCGATGATATGATGTTAGTA
*
2767610 CCTCATTGATAGGC
1 CCTCATCGATAGGC
2767624 GTTATATCTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
40 1 0.02
41 35 0.76
42 10 0.22
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (42 bp):
CCTCATCGATAGGCCTTTTATACCGATGATATGATGTTAGTA
Found at i:2767718 original size:26 final size:26
Alignment explanation
Indices: 2767662--2767719 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
2767652 TAAAATGGTG
* ** *
2767662 ATAAAGTAAAAATCACATTTTTTATA
1 ATAAAATAAAAATCACATTAATTAAA
* *
2767688 GTAAAATAAAATTCACATTAATTAAA
1 ATAAAATAAAAATCACATTAATTAAA
2767714 ATAAAA
1 ATAAAA
2767720 GCATACCAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (26 bp):
ATAAAATAAAAATCACATTAATTAAA
Found at i:2769218 original size:20 final size:20
Alignment explanation
Indices: 2769195--2769239 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2769185 TAATATAATA
*
2769195 AATATATCAT-ATTTATATAT
1 AATATAT-ATAATTTATAAAT
*
2769215 AATATATGTAATTTATAAAT
1 AATATATATAATTTATAAAT
2769235 AATAT
1 AATAT
2769240 TTATGTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
AATATATATAATTTATAAAT
Found at i:2769625 original size:21 final size:20
Alignment explanation
Indices: 2769601--2769648 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
2769591 ACTAAAATCA
*
2769601 TATATATATATATAT-TAA-
1 TATATATATATACATGTAAT
2769619 TATTATATAATATACATGTAAT
1 TA-TATAT-ATATACATGTAAT
2769641 TATATATA
1 TATATATA
2769649 CTAAGTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
19 5 0.20
20 8 0.32
21 8 0.32
22 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
TATATATATATACATGTAAT
Found at i:2769626 original size:23 final size:22
Alignment explanation
Indices: 2769585--2769632 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
2769575 TATATTACAA
2769585 ATATATACTAAAATCATATATAT
1 ATATATACTAAAATCATATA-AT
* * *
2769608 ATATATATTAATATTATATAAT
1 ATATATACTAAAATCATATAAT
2769630 ATA
1 ATA
2769633 CATGTAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATATACTAAAATCATATAAT
Found at i:2769656 original size:17 final size:17
Alignment explanation
Indices: 2769607--2769669 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
2769597 ATCATATATA
*
2769607 TATATATATTAA-T-AT
1 TATATATACTAAGTAAT
2769622 TATATAATA-TACATGTAAT
1 TATAT-ATACTA-A-GTAAT
2769641 TATATATACTAAGTAAT
1 TATATATACTAAGTAAT
*
2769658 TTTATATACTAA
1 TATATATACTAA
2769670 AATTATGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
15 7 0.17
16 4 0.10
17 16 0.39
18 5 0.12
19 9 0.22
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (17 bp):
TATATATACTAAGTAAT
Found at i:2769958 original size:24 final size:23
Alignment explanation
Indices: 2769921--2769970 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
2769911 GATCTGACAT
2769921 TTTTTTAATAATATAATATATAA
1 TTTTTTAATAATATAATATATAA
* * *
2769944 TTTTTTATATTATATATTATGTAA
1 TTTTTTA-ATAATATAATATATAA
2769968 TTT
1 TTT
2769971 ATAAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTTTAATAATATAATATATAA
Found at i:2771915 original size:233 final size:233
Alignment explanation
Indices: 2771519--2771943 Score: 638
Period size: 233 Copynumber: 1.8 Consensus size: 233
2771509 TAGAGAACGC
* * * * *
2771519 ATTGATGAAGAATTATATGATGATTATGAGACAGCTAAGGCTCGTGAGGTATCTTCACCTTCTAG
1 ATTGATGAAGAATTATATGATGATTATGAGACAGCTAAGGCCCATAAGGTATCTGCACCTTCTAA
* * * * ***
2771584 TGTGCATTCTCTATTGTTTTTAACTCTTGATTGAACTATGTAGAGGCTATGGGACTTTGGATTTC
66 TGTGCATTCTCTATTGTTTTTAACTCCTCATTGAACTATGTAGAGGCTACGCGACTCCAGATTTC
* * *
2771649 ACTTATATTTTGGAGTCCTATATGTGCTAAGTTCACTTGATGTGTTAAAATGGTTAGATTTGCAT
131 ACTTATATTTTGGAGTACTATATGTGATAAGTTCACTTGATGTATTAAAATGGTTAGATTTGCAT
2771714 TCTTGGTCCTGTTTTAATTTGTAGTTGATAGGGTATGT
196 TCTTGGTCCTGTTTTAATTTGTAGTTGATAGGGTATGT
*
2771752 ATTGATGAAGTATTATATGATGATTATGAGACAGCTAAGGCCCATAAGGTATCTGCACCTTCTAA
1 ATTGATGAAGAATTATATGATGATTATGAGACAGCTAAGGCCCATAAGGTATCTGCACCTTCTAA
* *
2771817 TGTGCATTCTCTATTGTTTTTAACTTCCTCATTGAACTATGTAGAATG-TACGCTACTCCAGATT
66 TGTGCATTCTCTATTGTTTTTAAC-TCCTCATTGAACTATGTAG-AGGCTACGCGACTCCAGATT
* *
2771881 T-ACTTATGTTTTGGAGTATTATATGTGATAAGTTCACTTGATGTATTAAAATGGTTAGATTTG
129 TCACTTATATTTTGGAGTACTATATGTGATAAGTTCACTTGATGTATTAAAATGGTTAGATTTG
2771944 TAATCTTGTG
Statistics
Matches: 170, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
233 140 0.82
234 28 0.16
235 2 0.01
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (233 bp):
ATTGATGAAGAATTATATGATGATTATGAGACAGCTAAGGCCCATAAGGTATCTGCACCTTCTAA
TGTGCATTCTCTATTGTTTTTAACTCCTCATTGAACTATGTAGAGGCTACGCGACTCCAGATTTC
ACTTATATTTTGGAGTACTATATGTGATAAGTTCACTTGATGTATTAAAATGGTTAGATTTGCAT
TCTTGGTCCTGTTTTAATTTGTAGTTGATAGGGTATGT
Found at i:2772140 original size:70 final size:70
Alignment explanation
Indices: 2772056--2772196 Score: 264
Period size: 70 Copynumber: 2.0 Consensus size: 70
2772046 TTTGTCAGTC
*
2772056 ATCTCAAATTCTCCTGCTCCAATTTGTTTTCGCTCATTCAGAAAAGATTAGCAAAGGAAGCTCGA
1 ATCTCAAATTCTCCTGCTCCAATTTGTTTTCGCTCATTCAAAAAAGATTAGCAAAGGAAGCTCGA
2772121 GCTCA
66 GCTCA
*
2772126 ATCTCAAATTCTCCTGCTCCAATTTGTTTTCGCTCATTCAAAAAAGGTTAGCAAAGGAAGCTCGA
1 ATCTCAAATTCTCCTGCTCCAATTTGTTTTCGCTCATTCAAAAAAGATTAGCAAAGGAAGCTCGA
2772191 GCTCA
66 GCTCA
2772196 A
1 A
2772197 GAAATACAAG
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (70 bp):
ATCTCAAATTCTCCTGCTCCAATTTGTTTTCGCTCATTCAAAAAAGATTAGCAAAGGAAGCTCGA
GCTCA
Found at i:2776830 original size:27 final size:27
Alignment explanation
Indices: 2776767--2776831 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
2776757 ATTATCGGAT
* *
2776767 AATTA-TAAATATAATTATGATTAAAA
1 AATTATTAAATATAATTATAAATAAAA
*
2776793 AAATATATAAATATAA-TATAAATAAATA
1 AATTAT-TAAATATAATTATAAATAAA-A
2776821 AATTATTAAAT
1 AATTATTAAAT
2776832 CTATTTAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
26 4 0.12
27 13 0.41
28 15 0.47
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
AATTATTAAATATAATTATAAATAAAA
Found at i:2777107 original size:13 final size:14
Alignment explanation
Indices: 2777084--2777133 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 14
2777074 CGTAATATAA
2777084 AATATAATATATTT
1 AATATAATATATTT
**
2777098 AATA-AATATA-AA
1 AATATAATATATTT
2777110 AATATAATATATTT
1 AATATAATATATTT
2777124 AATA-AATATA
1 AATATAATATA
2777134 AAATTAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
12 4 0.13
13 18 0.60
14 8 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATATATTT
Found at i:2777141 original size:24 final size:25
Alignment explanation
Indices: 2777077--2777144 Score: 120
Period size: 26 Copynumber: 2.7 Consensus size: 25
2777067 TTTTGAACGT
2777077 AATATAAAATATAATATATTTAATA
1 AATATAAAATATAATATATTTAATA
2777102 AATATAAAAATATAATATATTTAATA
1 AATAT-AAAATATAATATATTTAATA
2777128 AATATAAAAT-TAATATA
1 AATATAAAATATAATATA
2777145 AATTATATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
24 7 0.17
25 10 0.24
26 25 0.60
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
AATATAAAATATAATATATTTAATA
Found at i:2777175 original size:21 final size:21
Alignment explanation
Indices: 2777151--2777193 Score: 52
Period size: 24 Copynumber: 2.0 Consensus size: 21
2777141 TATAAATTAT
2777151 ATTT-TAATATGTTAGAATATG
1 ATTTATAATATGTT-GAATATG
2777172 ATTTGAATAATATGTTGAATAT
1 ATTT--ATAATATGTTGAATAT
2777194 TAATATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.21
23 6 0.32
24 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
ATTTATAATATGTTGAATATG
Found at i:2780175 original size:20 final size:20
Alignment explanation
Indices: 2780126--2780175 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2780116 GTTTTTTGTT
*
2780126 ATAATAATGATA-TTTTATA
1 ATAATAATTATATTTTTATA
*
2780145 ATAATAGTTATATTTTTATA
1 ATAATAATTATATTTTTATA
* *
2780165 TTACTAATTAT
1 ATAATAATTAT
2780176 TAAATTTGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (20 bp):
ATAATAATTATATTTTTATA
Found at i:2781098 original size:15 final size:15
Alignment explanation
Indices: 2781080--2781122 Score: 68
Period size: 16 Copynumber: 2.8 Consensus size: 15
2781070 ATATATTATT
2781080 AATTTATATTATAAA
1 AATTTATATTATAAA
*
2781095 AATTTAAATATATAAA
1 AATTTATAT-TATAAA
2781111 AATTTATATTAT
1 AATTTATATTAT
2781123 TTTTTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTATATTATAAA
Found at i:2781110 original size:16 final size:16
Alignment explanation
Indices: 2781054--2781116 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
2781044 ATTATATTTT
*
2781054 TATATAAAATATTTTAA
1 TATATAAAA-ATTTAAA
** *
2781071 TATATTATTAATTTATA
1 TATA-TAAAAATTTAAA
2781088 T-TATAAAAATTTAAA
1 TATATAAAAATTTAAA
2781103 TATATAAAAATTTA
1 TATATAAAAATTTA
2781117 TATTATTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 10 0.27
16 14 0.38
17 10 0.27
18 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATAAAAATTTAAA
Found at i:2781115 original size:31 final size:33
Alignment explanation
Indices: 2781032--2781122 Score: 95
Period size: 32 Copynumber: 2.9 Consensus size: 33
2781022 TATGTGTAAT
* *
2781032 AATATTTAAA-ATATT--ATATTTTTA-TATAA
1 AATATTTAAATATATTAAAAATTTATATTATAA
* **
2781061 AATATTTTAATATATTATTAATTTATATTATAA
1 AATATTTAAATATATTAAAAATTTATATTATAA
2781094 AA-ATTTAAATATA-TAAAAATTTATATTAT
1 AATATTTAAATATATTAAAAATTTATATTAT
2781123 TTTTTTATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
29 9 0.18
30 5 0.10
31 14 0.27
32 16 0.31
33 7 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
AATATTTAAATATATTAAAAATTTATATTATAA
Found at i:2793412 original size:109 final size:110
Alignment explanation
Indices: 2793221--2793419 Score: 307
Period size: 109 Copynumber: 1.8 Consensus size: 110
2793211 ACTATAAATA
*
2793221 GCATACCTGTAAAAGTGCAGCAATAGTACCAAAAGAATTCCACAACAATGGAGCCAAATCTTGAA
1 GCATACCTGTAAAAGTGCAGCAATAGTACCAAAAGAATTCCACAACAAAGGAGCCAAATCTTGAA
*
2793286 ATATTTCTCTTTTCT-AAAAATAAAAACAAAAACAAGTTTATTAG
66 ATAATTCTCTTTTCTAAAAAATAAAAACAAAAACAAGTTTATTAG
* *
2793330 GCATACCTG-AATGAGTGCAGCTATAGTACCAAAAGAATTCCAC-ACGAAAGGAGCCAAATCTTG
1 GCATACCTGTAA-AAGTGCAGCAATAGTACCAAAAGAATTCCACAAC-AAAGGAGCCAAATCTTG
2793393 AAATAATTC-CTTGTTCTAAAAAATAAA
64 AAATAATTCTCTT-TTCTAAAAAATAAA
2793420 CCAAAAGGTA
Statistics
Matches: 82, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
108 7 0.09
109 66 0.80
110 9 0.11
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.25
Consensus pattern (110 bp):
GCATACCTGTAAAAGTGCAGCAATAGTACCAAAAGAATTCCACAACAAAGGAGCCAAATCTTGAA
ATAATTCTCTTTTCTAAAAAATAAAAACAAAAACAAGTTTATTAG
Found at i:2795750 original size:28 final size:28
Alignment explanation
Indices: 2795718--2795802 Score: 81
Period size: 26 Copynumber: 3.2 Consensus size: 28
2795708 TATACATAAT
2795718 TTAAATATAATATATATATATAAATATA
1 TTAAATATAATATATATATATAAATATA
* * *
2795746 ATAAA-AT-TTATATATAT-TTAATAT-
1 TTAAATATAATATATATATATAAATATA
* *
2795770 TTTAATATAAT-TATAATATATAAAAATA
1 TTAAATATAATATAT-ATATATAAATATA
2795798 TTAAA
1 TTAAA
2795803 AAAATACTGA
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
24 3 0.07
25 11 0.26
26 14 0.33
27 7 0.16
28 8 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
TTAAATATAATATATATATATAAATATA
Found at i:2795751 original size:44 final size:47
Alignment explanation
Indices: 2795685--2795792 Score: 118
Period size: 44 Copynumber: 2.4 Consensus size: 47
2795675 ATATAGCCTA
* * *
2795685 ATATATATAAAAATTTATTAAAATATACATA-ATTTAA-A-TATAAT
1 ATATATATATAAATATAATAAAATATACATATATTTAATATTATAAT
* * *
2795729 ATATATATATAAATATAATAAAATTTATATATATTTAATATTTTAAT
1 ATATATATATAAATATAATAAAATATACATATATTTAATATTATAAT
2795776 ATA-AT-TATAATATATAA
1 ATATATATATAA-ATATAA
2795793 AAATATTAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
44 26 0.48
45 11 0.20
46 9 0.17
47 8 0.15
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (47 bp):
ATATATATATAAATATAATAAAATATACATATATTTAATATTATAAT
Found at i:2795777 original size:17 final size:20
Alignment explanation
Indices: 2795723--2795788 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 20
2795713 ATAATTTAAA
* *
2795723 TATAATA-TATATATATAAA
1 TATAATATTTTATATATAAT
*
2795742 TATAATAAAATTTATATAT-AT
1 TATAAT--ATTTTATATATAAT
2795763 T-TAATATTTTA-ATATAAT
1 TATAATATTTTATATATAAT
2795781 TATAATAT
1 TATAATAT
2795789 ATAAAAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 4 0.10
18 8 0.21
19 12 0.31
20 4 0.10
21 3 0.08
22 8 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATAATATTTTATATATAAT
Found at i:2795786 original size:6 final size:7
Alignment explanation
Indices: 2795722--2795792 Score: 55
Period size: 6 Copynumber: 10.9 Consensus size: 7
2795712 CATAATTTAA
2795722 ATATAAT
1 ATATAAT
2795729 ATAT-AT
1 ATATAAT
2795735 ATATAA-
1 ATATAAT
2795741 ATATAAT
1 ATATAAT
2795748 A-A-AAT
1 ATATAAT
*
2795753 TTATATAT
1 ATATA-AT
*
2795761 ATTTAAT
1 ATATAAT
* *
2795768 ATTTTA-
1 ATATAAT
2795774 ATATAAT
1 ATATAAT
2795781 -TATAAT
1 ATATAAT
2795787 ATATAA
1 ATATAA
2795793 AAATATTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
5 3 0.06
6 24 0.47
7 19 0.37
8 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
ATATAAT
Found at i:2798019 original size:27 final size:27
Alignment explanation
Indices: 2797981--2798144 Score: 195
Period size: 27 Copynumber: 6.1 Consensus size: 27
2797971 CGTTTAAGAT
* * *
2797981 CAAGCCGTGGTGATCAGCAACATGTAC
1 CAAGCCATGGTGATCAACAACCTGTAC
*
2798008 CAAGCCATGGTGATCAACAAGCTGTAC
1 CAAGCCATGGTGATCAACAACCTGTAC
* *
2798035 CAAGCCGTGGTGATCAACTACCTGTAC
1 CAAGCCATGGTGATCAACAACCTGTAC
* *
2798062 CAAG-CAGTGTTGATCAACCACCTGTAC
1 CAAGCCA-TGGTGATCAACAACCTGTAC
* * * *
2798089 CAAGTCGTGTTGATCAACCACCTGTAC
1 CAAGCCATGGTGATCAACAACCTGTAC
*
2798116 CAAGCCATGGTGATCAACAACCTGGAC
1 CAAGCCATGGTGATCAACAACCTGTAC
2798143 CA
1 CA
2798145 TCTCATGATG
Statistics
Matches: 119, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
26 1 0.01
27 117 0.98
28 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (27 bp):
CAAGCCATGGTGATCAACAACCTGTAC
Found at i:2798063 original size:54 final size:54
Alignment explanation
Indices: 2797981--2798144 Score: 222
Period size: 54 Copynumber: 3.0 Consensus size: 54
2797971 CGTTTAAGAT
* * *
2797981 CAAGCCGTGGTGATCAGCAACATGTACCAAGCCATGGTGATCAACAAGCTGTAC
1 CAAGCCGTGGTGATCAACAACCTGTACCAAGCCATGGTGATCAACAACCTGTAC
* * *
2798035 CAAGCCGTGGTGATCAACTACCTGTACCAAG-CAGTGTTGATCAACCACCTGTAC
1 CAAGCCGTGGTGATCAACAACCTGTACCAAGCCA-TGGTGATCAACAACCTGTAC
* * * *
2798089 CAAGTCGTGTTGATCAACCACCTGTACCAAGCCATGGTGATCAACAACCTGGAC
1 CAAGCCGTGGTGATCAACAACCTGTACCAAGCCATGGTGATCAACAACCTGTAC
2798143 CA
1 CA
2798145 TCTCATGATG
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
53 2 0.02
54 92 0.96
55 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (54 bp):
CAAGCCGTGGTGATCAACAACCTGTACCAAGCCATGGTGATCAACAACCTGTAC
Found at i:2802018 original size:16 final size:16
Alignment explanation
Indices: 2801999--2802036 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2801989 ATCAAAATTT
2801999 AAAAAGCCCAAACTCG
1 AAAAAGCCCAAACTCG
**
2802015 AAAAAGTTCAAACTCG
1 AAAAAGCCCAAACTCG
2802031 AAAAAG
1 AAAAAG
2802037 TTTGAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.55, C:0.21, G:0.13, T:0.11
Consensus pattern (16 bp):
AAAAAGCCCAAACTCG
Found at i:2802037 original size:16 final size:16
Alignment explanation
Indices: 2802007--2802038 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2801997 TTAAAAAGCC
2802007 CAAACTCGAAAAAGTT
1 CAAACTCGAAAAAGTT
2802023 CAAACTCGAAAAAGTT
1 CAAACTCGAAAAAGTT
2802039 TGAATACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (16 bp):
CAAACTCGAAAAAGTT
Found at i:2803233 original size:10 final size:10
Alignment explanation
Indices: 2803198--2803226 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2803188 ATTATATTTA
2803198 ATAAAA-AAT
1 ATAAAATAAT
2803207 ATAAAATAAT
1 ATAAAATAAT
2803217 ATAAAATAAT
1 ATAAAATAAT
2803227 TTTAAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAAAATAAT
Found at i:2803270 original size:16 final size:16
Alignment explanation
Indices: 2803245--2803315 Score: 81
Period size: 16 Copynumber: 4.4 Consensus size: 16
2803235 CAAAATTGAC
*
2803245 TCAAATTTAAAAAAAT
1 TCAAATCTAAAAAAAT
*
2803261 TCAAA-CTTAAAAAATT
1 TCAAATC-TAAAAAAAT
* *
2803277 TTAAATCTAAATAAAT
1 TCAAATCTAAAAAAAT
*
2803293 TTAAATCTAAAAAAAT
1 TCAAATCTAAAAAAAT
2803309 TCAAATC
1 TCAAATC
2803316 AAGAAACCTA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
16 45 0.98
17 1 0.02
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (16 bp):
TCAAATCTAAAAAAAT
Found at i:2803364 original size:19 final size:19
Alignment explanation
Indices: 2803340--2803382 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
2803330 AAACCTGCCC
2803340 AATTGCCAAAAAAGAATAT
1 AATTGCCAAAAAAGAATAT
**
2803359 AATTG-CAAAAGGGAATAT
1 AATTGCCAAAAAAGAATAT
2803377 AATTGC
1 AATTGC
2803383 AACTTTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.23
Consensus pattern (19 bp):
AATTGCCAAAAAAGAATAT
Found at i:2803727 original size:2 final size:2
Alignment explanation
Indices: 2803720--2803754 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2803710 GTAAGCTTCT
* *
2803720 TC TC TC TC TC TC TC TC TC TC TC TC TA TC TC CC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2803755 GCTGTTGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:2804539 original size:2 final size:2
Alignment explanation
Indices: 2804522--2804570 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
2804512 TATGTGCATG
* *
2804522 TA TA TG TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2804564 TA TA TA T
1 TA TA TA T
2804571 TCATTATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2804832 original size:16 final size:15
Alignment explanation
Indices: 2804786--2804832 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
2804776 TTATAAATGA
2804786 TTTAATAATTATTTT
1 TTTAATAATTATTTT
* **
2804801 TATAA-AATTACATT
1 TTTAATAATTATTTT
2804815 TTTAATATATTATTTT
1 TTTAATA-ATTATTTT
2804831 TT
1 TT
2804833 ATTAAATTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
14 11 0.46
15 5 0.21
16 8 0.33
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAATAATTATTTT
Found at i:2805478 original size:35 final size:35
Alignment explanation
Indices: 2805439--2805510 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
2805429 ATAGATTACC
2805439 AAAAGATATAATCAAAGAGATATATTTTAATTAGA
1 AAAAGATATAATCAAAGAGATATATTTTAATTAGA
2805474 AAAAGATATAATCAAAGAGATATATTTTAATTAGA
1 AAAAGATATAATCAAAGAGATATATTTTAATTAGA
2805509 AA
1 AA
2805511 GTTTTTTCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.31
Consensus pattern (35 bp):
AAAAGATATAATCAAAGAGATATATTTTAATTAGA
Found at i:2812061 original size:2 final size:2
Alignment explanation
Indices: 2812054--2812089 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2812044 TTAAGCTTAT
2812054 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2812090 CACAAACACA
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):
TA
Found at i:2816576 original size:24 final size:23
Alignment explanation
Indices: 2816517--2816584 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
2816507 ATTAAAAATA
* *
2816517 AATGATATAT-TTGATAAAATTT
1 AATGATATATATTTATTAAATTT
*
2816539 AATGATATAAATTTATTAAATTT
1 AATGATATATATTTATTAAATTT
* * *
2816562 AATTATTTTATATTTATTGAATT
1 AATGA-TATATATTTATTAAATT
2816585 CATATTAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
22 9 0.24
23 14 0.38
24 14 0.38
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (23 bp):
AATGATATATATTTATTAAATTT
Found at i:2819573 original size:24 final size:23
Alignment explanation
Indices: 2819534--2819607 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 23
2819524 GTCATATACA
2819534 TTTTTT-ATTCTT-TTTTTTCATT
1 TTTTTTAATT-TTATTTTTTCATT
2819556 TTTTTTAATTTTACTTTTTTC-TT
1 TTTTTTAATTTTA-TTTTTTCATT
*
2819579 ATTTTTTCATTTTATTTATTT-ATT
1 -TTTTTTAATTTTATTT-TTTCATT
2819603 TTTTT
1 TTTTT
2819608 CAAAGCAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
22 8 0.18
23 13 0.29
24 24 0.53
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTAATTTTATTTTTTCATT
Found at i:2819584 original size:33 final size:32
Alignment explanation
Indices: 2819536--2819608 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 32
2819526 CATATACATT
*
2819536 TTTTATTCTT-TTTTTTCATTTTTTTTAATTTTAC
1 TTTT-TTCTTATTTTTTCATTTTATTT-A-TTTAC
*
2819570 TTTTTTCTTATTTTTTCATTTTATTTATTTAT
1 TTTTTTCTTATTTTTTCATTTTATTTATTTAC
2819602 TTTTTTC
1 TTTTTTC
2819609 AAAGCAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
32 11 0.31
33 6 0.17
34 19 0.53
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (32 bp):
TTTTTTCTTATTTTTTCATTTTATTTATTTAC
Found at i:2825795 original size:15 final size:15
Alignment explanation
Indices: 2825752--2825800 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
2825742 AAAAGTTAAA
*
2825752 TATTTTTAT-TTATA
1 TATTTTTATATTATT
2825766 TATTTTT-TATTATT
1 TATTTTTATATTATT
*
2825780 TATTTTTATATAATTT
1 TATTTTTATATTA-TT
2825796 TATTT
1 TATTT
2825801 ATTAAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 1 0.03
14 18 0.60
15 4 0.13
16 7 0.23
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTTTTATATTATT
Found at i:2825803 original size:24 final size:22
Alignment explanation
Indices: 2825752--2825799 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2825742 AAAAGTTAAA
*
2825752 TATT-TTTATTTATATATTTTT
1 TATTATTTATTTATATATATTT
*
2825773 TATTATTTATTTTTATATAATTT
1 TATTATTTATTTATATAT-ATTT
2825796 TATT
1 TATT
2825800 TATTAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 12 0.52
23 7 0.30
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (22 bp):
TATTATTTATTTATATATATTT
Found at i:2829991 original size:22 final size:23
Alignment explanation
Indices: 2829945--2830000 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
2829935 TGGACATGTT
2829945 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
2829968 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
2829990 AAAAATGCATG
1 AAAAATGCATG
2830001 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:2830958 original size:20 final size:19
Alignment explanation
Indices: 2830911--2830985 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
2830901 AAAAAGATAT
*
2830911 AATGTATCGATACATTGAA
1 AATGTATCGATACATTCAA
*
2830930 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCA-A
* *
2830951 CATGTATCGATATA-TCGAAA
1 AATGTATCGATACATTC--AA
2830971 AATGTATCGATACAT
1 AATGTATCGATACAT
2830986 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 40 0.91
21 2 0.05
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (19 bp):
AATGTATCGATACATTCAA
Found at i:2831604 original size:34 final size:34
Alignment explanation
Indices: 2831539--2831610 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
2831529 CTTTTTTTTT
**
2831539 AAAAAAAATGTGCCACTAACTTGTGTAGGCTTCG
1 AAAAAAAATGTGCCACTAACACGTGTAGGCTTCG
* * *
2831573 AAAAAAAA-GTTGCCACTGACACGTGTGGGCTTTG
1 AAAAAAAATG-TGCCACTAACACGTGTAGGCTTCG
2831607 AAAA
1 AAAA
2831611 GAGTTTTACT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 1 0.03
34 31 0.97
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.24
Consensus pattern (34 bp):
AAAAAAAATGTGCCACTAACACGTGTAGGCTTCG
Found at i:2831698 original size:28 final size:28
Alignment explanation
Indices: 2831618--2832869 Score: 1302
Period size: 28 Copynumber: 43.8 Consensus size: 28
2831608 AAAGAGTTTT
*
2831618 ACTGACTTGCGTGGGCTTTAAAATGG-TGCC
1 ACTGACTT--GTGGGCTTTGAAA-GGATGCC
2831648 ACTGACTTGCGTGGGCTTTGAAAGGATGCC
1 ACTGACTT--GTGGGCTTTGAAAGGATGCC
2831678 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* *
2831706 ACTGACTCGTGGGTTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* *
2831734 ACTGACTCGTGGACTTTGAAAAAGG-TGCC
1 ACTGACTTGTGGGCTTTG--AAAGGATGCC
*
2831763 ACTGACTCGTGGGCTTTGAAAAGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* *
2831791 ACTGACTTGCGTGGGCTTTAAAAGGGTGCC
1 ACTGACTT--GTGGGCTTTGAAAGGATGCC
* * *
2831821 ACTAACTTGCGTGGGCTTTAAAAAGATGCC
1 ACTGACTT--GTGGGCTTTGAAAGGATGCC
2831851 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
*
2831879 ACTGACTCGTGGGCTTTGAAAAGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* *
2831907 ACTGACTCGTGGGC-TTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* *
2831934 ACTGACTCGTGGGCTTTAAAAGGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
*
2831963 ACTGACTTGTGTGGGCTTTGAAAGGGTGCC
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
*
2831993 ACTGACTTGTGGGCTTT-AAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * * * *
2832021 ACTAAATTGTGGGCTTCGCAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* *
2832049 ACTGACTTGTGTGCTTCGAAAAGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* *
2832077 ACTGACTTGTGGGCTCTAAAAGGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
*
2832106 ACTGACTTGTGTGGGCTTTGAAAGGGTGCC
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
*
2832136 ACTAACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * * *
2832164 ACTGAATTGTGGGCTTCGCAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* *
2832192 ACTGACTTGTGGGCTTCGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
*
2832220 ACTAACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * * * *
2832248 ACTGAATTATGGGCTTCGCAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
2832276 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
*
2832304 ACTGACTCGTGGGCTTTGAAAAGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
*
2832332 ACTGACTCGTGGGCTTTGAAAAGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
*
2832360 ACTGACTTGCGTGGGCTTTAAAAGGAGTGCC
1 ACTGACTT--GTGGGCTTTGAAAGGA-TGCC
*
2832391 ACTGACTTGTGTGGGCTTTGAAAGGGTGCC
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
* *
2832421 ACTGACTTGTGGGCTTCGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * *
2832449 ACTAACTTGTGGGCTCTAAAAGGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
*
2832478 ACTGACTTGTGTGGGCTTTGAAAGGGTGCC
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
* *
2832508 ACTGACTTGTGGGTTTTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
2832536 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * *
2832564 ACTGAATTGTGGGCTTCGCAATGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
*
2832592 ACTGACTTGTGGGCTTCGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* *
2832620 ACTAACTTGTGGGCTTTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
2832648 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * * *
2832676 ACTGAATTGTGGGCTTCGCAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * *
2832704 ACTGACTTGTGGGCTTCGATAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
2832732 ACTGACTTGTGGGCTTTGAAATGG-TGCC
1 ACTGACTTGTGGGCTTTGAAA-GGATGCC
* * *
2832760 ACTGACTTATGGGCTTTAAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* *
2832789 ACTGATTTGTGGGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* *
2832818 ACTGTCTTGTGGGCTTGGAAAGGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
2832847 ACTGACTTGTGGGCTTTGAAAGG
1 ACTGACTTGTGGGCTTTGAAAGG
2832870 GATGAACATT
Statistics
Matches: 1062, Mismatches: 110, Indels: 101
0.83 0.09 0.08
Matches are distributed among these distances:
26 6 0.01
27 42 0.04
28 644 0.61
29 163 0.15
30 138 0.13
31 67 0.06
32 1 0.00
33 1 0.00
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.27
Consensus pattern (28 bp):
ACTGACTTGTGGGCTTTGAAAGGATGCC
Found at i:2831736 original size:56 final size:56
Alignment explanation
Indices: 2831596--2832868 Score: 1470
Period size: 56 Copynumber: 22.3 Consensus size: 56
2831586 CACTGACACG
*** *
2831596 TGTGGGCTTTGAAAAGAGTTTTACTGACTTGCGTGGGCTTTAAAATG-GTGCCACTGACT
1 TGTGGGCTTTG-AAAGAGTGCCACTGACTT--GTGGGCTTTGAAA-GAGTGCCACTGACT
2831655 TGCGTGGGCTTTGAAAG-GATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
1 T--GTGGGCTTTGAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * * * *
2831713 CGTGGGTTTTGAAAGAGTGCCACTGACTCGTGGACTTTGAAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGACT
* * * *
2831770 CGTGGGCTTTGAAA-AGGTGCCACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGA-GTGCCACTGACTT--GTGGGCTTTGAAAGAGTGCCACTGACT
*
2831828 TGCGTGGGCTTT-AAAAAGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
1 T--GTGGGCTTTGAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
2831886 CGTGGGCTTTGAAA-AGGTGCCACTGACTCGTGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGA-GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
2831941 CGTGGGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAA-GAGTGCCACTGAC-T-TGTGGGCTTTGAAAGAGTGCCACTGACT
* * * * * *
2832000 TGTGGGCTTTAAAAGAGTGCCACTAAATTGTGGGCTTCGCAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * * *
2832056 TGTGTGCTTCGAAA-AGGTGCCACTGACTTGTGGGCTCTAAAAGGAGTGCCACTGACTT
1 TGTGGGCTTTGAAAGA-GTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGAC-T
* * *
2832114 GTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGAAT
1 -TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * * * * *
2832171 TGTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * * * *
2832227 TGTGGGCTTTGAAAGAGTGCCACTGAATTATGGGCTTCGCAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
*
2832283 TGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAA-AGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGACT
* *
2832339 CGTGGGCTTTGAAA-AGGTGCCACTGACTTGCGTGGGCTTTAAAAGGAGTGCCACTGACTT
1 TGTGGGCTTTGAAAGA-GTGCCACTGACTT--GTGGGCTTTGAAA-GAGTGCCACTGAC-T
* * * *
2832399 GTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTAACT
1 -TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
2832456 TGTGGGCTCTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAA-GAGTGCCACTGAC-T-TGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
2832515 TGTGGGTTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * * *
2832571 TGTGGGCTTCGCAATG-GTGCCACTGACTTGTGGGCTTCGAAAGAGTGCCACTAACT
1 TGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* *
2832627 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * * * * *
2832683 TGTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGCTTCGATAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
2832739 TGTGGGCTTTGAAATG-GTGCCACTGACTTATGGGCTTTAAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTT-GAAAGAGTGCCACTGACT
* *
2832796 TGTGGGCTTTGAAAAGAGTGCCACTGTCTTGTGGGCTTGGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGACT
2832854 TGTGGGCTTTGAAAG
1 TGTGGGCTTTGAAAG
2832869 GGATGAACAT
Statistics
Matches: 1053, Mismatches: 117, Indels: 90
0.84 0.09 0.07
Matches are distributed among these distances:
55 37 0.04
56 518 0.49
57 110 0.10
58 171 0.16
59 144 0.14
60 37 0.04
61 36 0.03
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (56 bp):
TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
Found at i:2831966 original size:84 final size:84
Alignment explanation
Indices: 2831596--2832870 Score: 1457
Period size: 84 Copynumber: 14.9 Consensus size: 84
2831586 CACTGACACG
* ***
2831596 TGTGGGCTTTGAAAAGAGTTTTACTGACTTGCGTGGGCTTT-AAAATGGTGCCACTGACTTGCGT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTT--GTGGGCTTTGAAAA-GGTGCCACTGACTT--GT
*
2831660 GGGCTTTGAAAGGATGCCACTGACT
61 GGGC-TTGAAAGGGTGCCACTGACT
* * * *
2831685 TGTGGGCTTTGAAA-GAGTGCCACTGACTCGTGGGTTTTG-AAAGAGTGCCACTGACTCGTGGAC
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGC
*
2831748 TTTGAAAAAGGTGCCACTGACT
65 -TTG-AAAGGGTGCCACTGACT
* * *
2831770 CGTGGGCTTTGAAAAG-GTGCCACTGACTTGCGTGGGCTTT-AAAAGGGTGCCACTAACTTGCGT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTT--GTGGGCTTTGAAAA-GGTGCCACTGACTT--GT
* * *
2831833 GGGCTTTAAAAAGATGCCACTGACT
61 GGGC-TTGAAAGGGTGCCACTGACT
* *
2831858 TGTGGGCTTTGAAA-GAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTCGTGGGCT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCT
2831922 TGAAAGGGTGCCACTGACT
66 TGAAAGGGTGCCACTGACT
* * *
2831941 CGTGGGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGG
1 TGTGGGCTTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGG
* * * *
2832006 CTTTAAAAGAGTGCCACTAAAT
64 C-TTGAAAGGGTGCCACTGACT
* * * *
2832028 TGTGGGCTTCGCAAGG-GTGCCACTGACTTGTGTGCTTCGAAAAGGTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCT
*
2832092 CTAAAAGGAGTGCCACTGACTT
66 -TGAAAGG-GTGCCACTGAC-T
* *
2832114 GTGTGGGCTTTGAAAGG-GTGCCACTAACTTGTGGGCTTTG-AAAGAGTGCCACTGAATTGTGGG
1 -TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGG
*
2832177 CTTCGCAAGGGTGCCACTGACT
64 CTT-GAAAGGGTGCCACTGACT
* * * *
2832199 TGTGGGCTTCGAAAGG-GTGCCACTAACTTGTGGGCTTTG-AAAGAGTGCCACTGAATTATGGGC
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGC
*
2832262 TTCGCAAGGGTGCCACTGACT
65 TT-GAAAGGGTGCCACTGACT
* *
2832283 TGTGGGCTTTGAAA-GAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTCGTGGGCT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGC-
*
2832347 TTGAAAAGGTGCCACTGACT
65 TTGAAAGGGTGCCACTGACT
* *
2832367 TGCGTGGGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTG
1 T--GTGGGCTTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAAGGTGCCACTGACTTGTG
*
2832432 GGCTTCGAAAGGGTGCCACTAACT
62 GGCTT-GAAAGGGTGCCACTGACT
* * *
2832456 TGTGGGCTCTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGG
1 TGTGGGCTTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGG
*
2832521 TTTTGAAAGGGTGCCACTGACT
64 -CTTGAAAGGGTGCCACTGACT
* * * *
2832543 TGTGGGCTTTGAAA-GAGTGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCT
* *
2832607 TCGAAAGAGTGCCACTAACT
66 T-GAAAGGGTGCCACTGACT
*
2832627 TGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGAATTGTGGGC
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGC
*
2832690 TTCGCAAGGGTGCCACTGACT
65 TT-GAAAGGGTGCCACTGACT
* * * *
2832711 TGTGGGCTTCGATAGG-GTGCCACTGACTTGTGGGCTTTGAAATGGTGCCACTGACTTATGGGCT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGC-
* * *
2832775 TTAAAAAGAGTGCCACTGATT
65 TT-GAAAGGGTGCCACTGACT
* * * *
2832796 TGTGGGCTTTGAAAAGAGTGCCACTGTCTTGTGGGCTTGGAAAGGAGTGCCACTGACTTGTGGGC
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGC
2832861 TTTGAAAGGG
65 -TTGAAAGGG
2832871 ATGAACATTC
Statistics
Matches: 1042, Mismatches: 105, Indels: 81
0.85 0.09 0.07
Matches are distributed among these distances:
83 36 0.03
84 387 0.37
85 93 0.09
86 159 0.15
87 238 0.23
88 58 0.06
89 71 0.07
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (84 bp):
TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCT
TGAAAGGGTGCCACTGACT
Found at i:2834121 original size:10 final size:11
Alignment explanation
Indices: 2834092--2834151 Score: 54
Period size: 10 Copynumber: 5.5 Consensus size: 11
2834082 CCCTTCTATT
*
2834092 TTTTTGCTATTT
1 TTTTTGCT-TTC
2834104 TTTCTTG-TTTC
1 TTT-TTGCTTTC
*
2834115 TTTTTG-TTTT
1 TTTTTGCTTTC
2834125 TTTTTGCTTT-
1 TTTTTGCTTTC
*
2834135 TTTTTGTTTTC
1 TTTTTGCTTTC
2834146 TTTTTG
1 TTTTTG
2834152 GGTGTAAAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
10 21 0.50
11 14 0.33
12 4 0.10
13 3 0.07
ACGTcount: A:0.02, C:0.08, G:0.10, T:0.80
Consensus pattern (11 bp):
TTTTTGCTTTC
Found at i:2834124 original size:20 final size:20
Alignment explanation
Indices: 2834101--2834144 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2834091 TTTTTTGCTA
2834101 TTTTTTCTTG-TTTCTTTTTG
1 TTTTTTCTTGCTTT-TTTTTG
*
2834121 TTTTTTTTTGCTTTTTTTTG
1 TTTTTTCTTGCTTTTTTTTG
2834141 TTTT
1 TTTT
2834145 CTTTTTGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (20 bp):
TTTTTTCTTGCTTTTTTTTG
Found at i:2834125 original size:31 final size:30
Alignment explanation
Indices: 2834090--2834151 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
2834080 GACCCTTCTA
2834090 TTTTTTTGCTATTTTTTCT-TGTTTCTTTTTGTT
1 TTTTTTTGCT-TTTTTT-TGT-TTTCTTTTTG-T
2834123 TTTTTTTGCTTTTTTTTGTTTTCTTTTTG
1 TTTTTTTGCTTTTTTTTGTTTTCTTTTTG
2834152 GGTGTAAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 11 0.39
32 7 0.25
33 10 0.36
ACGTcount: A:0.02, C:0.08, G:0.10, T:0.81
Consensus pattern (30 bp):
TTTTTTTGCTTTTTTTTGTTTTCTTTTTGT
Found at i:2836411 original size:15 final size:16
Alignment explanation
Indices: 2836385--2836414 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2836375 TTAAAGGACG
2836385 ACCAAGCACTGGCGGT
1 ACCAAGCACTGGCGGT
2836401 ACCAA-CACTGGCGG
1 ACCAAGCACTGGCGG
2836415 GTTTGACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.33, G:0.30, T:0.10
Consensus pattern (16 bp):
ACCAAGCACTGGCGGT
Found at i:2846997 original size:24 final size:24
Alignment explanation
Indices: 2846969--2847019 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
2846959 TGGACATGTT
2846969 AAAAATACATGAAACATAATAAAA
1 AAAAATACATGAAACATAATAAAA
*
2846993 AAAAATGCATGAAACATAATAAAA
1 AAAAATACATGAAACATAATAAAA
2847017 AAA
1 AAA
2847020 TGCATGGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.71, C:0.08, G:0.06, T:0.16
Consensus pattern (24 bp):
AAAAATACATGAAACATAATAAAA
Found at i:2847016 original size:22 final size:23
Alignment explanation
Indices: 2846969--2847025 Score: 89
Period size: 24 Copynumber: 2.5 Consensus size: 23
2846959 TGGACATGTT
*
2846969 AAAAATACATGAAACATAATAAAA
1 AAAAATGCATGAAACATAAT-AAA
2846993 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
2847015 AAAAATGCATG
1 AAAAATGCATG
2847026 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 13 0.41
24 19 0.59
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:2847982 original size:20 final size:19
Alignment explanation
Indices: 2847935--2848009 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
2847925 AAAAAGATAT
*
2847935 AATGTATCGATACATTGAA
1 AATGTATCGATACATTCAA
*
2847954 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCA-A
* *
2847975 CATGTATCGATATA-TCGAAA
1 AATGTATCGATACATTC--AA
2847995 AATGTATCGATACAT
1 AATGTATCGATACAT
2848010 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 40 0.91
21 2 0.05
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (19 bp):
AATGTATCGATACATTCAA
Found at i:2849893 original size:50 final size:50
Alignment explanation
Indices: 2849816--2849927 Score: 197
Period size: 50 Copynumber: 2.2 Consensus size: 50
2849806 TCATTTTATG
2849816 CAATTCACACAAGTACTAGAATCAATAAAGTTAAAAACCTTAAAGATTCCAT
1 CAATT-AC-CAAGTACTAGAATCAATAAAGTTAAAAACCTTAAAGATTCCAT
2849868 CAATTACCAAGTACTAGAATCAATAAAGTTAAAAACCTTAAAGATTCCAT
1 CAATTACCAAGTACTAGAATCAATAAAGTTAAAAACCTTAAAGATTCCAT
*
2849918 CATTTACCAA
1 CAATTACCAA
2849928 TCTCTTAATT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
50 52 0.88
51 2 0.03
52 5 0.08
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.26
Consensus pattern (50 bp):
CAATTACCAAGTACTAGAATCAATAAAGTTAAAAACCTTAAAGATTCCAT
Found at i:2851740 original size:39 final size:39
Alignment explanation
Indices: 2851692--2851770 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
2851682 GAAGCCAAAT
2851692 ATAGAAAATTTATCCGTGTAAATTAATCTAAACAATATC
1 ATAGAAAATTTATCCGTGTAAATTAATCTAAACAATATC
2851731 ATAGAAAATTTATCCGTGTAAATTAATCTAAACAATATC
1 ATAGAAAATTTATCCGTGTAAATTAATCTAAACAATATC
2851770 A
1 A
2851771 ATTAATATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.33
Consensus pattern (39 bp):
ATAGAAAATTTATCCGTGTAAATTAATCTAAACAATATC
Found at i:2857005 original size:28 final size:30
Alignment explanation
Indices: 2856965--2857023 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 30
2856955 TTCCACCATC
2856965 GAGGATACTCTAA-CCTCG-TTATTTCCAA
1 GAGGATACTCTAATCCTCGTTTATTTCCAA
*
2856993 GAGGATACTCTAATCCTGGTTTTATTTCCAA
1 GAGGATACTCTAATCCTCG-TTTATTTCCAA
2857024 AACATCAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 13 0.48
29 4 0.15
31 10 0.37
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (30 bp):
GAGGATACTCTAATCCTCGTTTATTTCCAA
Found at i:2857066 original size:79 final size:78
Alignment explanation
Indices: 2856933--2857373 Score: 374
Period size: 79 Copynumber: 5.6 Consensus size: 78
2856923 TCATTCATGT
* * * * * * * **
2856933 TTTTATTTTTAAAATATCGATTTTCCACCATCGAGGATAC-TCTAACCTCGTTATTTCCAAGAGG
1 TTTTATTTTCAAAACATCAATTTTTCACAATCGGGGATACTTC-AACC-CATTATTTTTAAGAGG
* **
2856997 ATACTCTAATCCTGG
64 ATACTCCAATCCTAA
* *
2857012 TTTTATTTCCAAAACATCAATTTTCCACAATCGGGGATACTTCAATCCCATTATTTTTAAG-GGA
1 TTTTATTTTCAAAACATCAATTTTTCACAATCGGGGATACTTCAA-CCCATTATTTTTAAGAGG-
* *
2857076 ATACTCCAACCCCAA
64 ATACTCCAATCCTAA
* * * * * * *
2857091 TTTTAGTTTTTAAAACACCGATTTTTCATAATTC-GGGATACTCCAACCCCATTATTTTTGAGGG
1 TTTTA-TTTTCAAAACATCAATTTTTCACAA-TCGGGGATACTTCAA-CCCATTATTTTTAAGAG
2857155 GATACTCCAAT-CTCAA
63 GATACTCCAATCCT-AA
* * * * ** *
2857171 TTTTATTTTCAAAACACCAATTTTTCACCATCGAGGATACTCCAACCCTATT-TTTTCGAGAGAA
1 TTTTATTTTCAAAACATCAATTTTTCACAATCGGGGATACTTCAACCC-ATTATTTTTAAGAGGA
* *
2857235 TATTCTAATCCTAA
65 TACTCCAATCCTAA
* * *
2857249 TTTTATTTTCAAAACATCGATTTTTCACCATCGGGGATACTTTAACCCCATTATTTTTAA-AGGT
1 TTTTATTTTCAAAACATCAATTTTTCACAATCGGGGATACTTCAA-CCCATTATTTTTAAGAGG-
* **
2857313 ATACTCCAACCCCGA
64 ATACTCCAATCCTAA
*
2857328 TTTTATTTTCAAAACA-CTAATTTTTCACAATCGGGGATACTCCAAC
1 TTTTATTTTCAAAACATC-AATTTTTCACAATCGGGGATACTTCAAC
2857374 TCTAGTTTTA
Statistics
Matches: 296, Mismatches: 52, Indels: 29
0.79 0.14 0.08
Matches are distributed among these distances:
78 72 0.24
79 156 0.53
80 64 0.22
81 4 0.01
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (78 bp):
TTTTATTTTCAAAACATCAATTTTTCACAATCGGGGATACTTCAACCCATTATTTTTAAGAGGAT
ACTCCAATCCTAA
Found at i:2857305 original size:157 final size:156
Alignment explanation
Indices: 2856933--2857382 Score: 490
Period size: 157 Copynumber: 2.9 Consensus size: 156
2856923 TCATTCATGT
* * * * * ** *
2856933 TTTTATTTTTAAAATATCGATTTTCCACCATCGAGGATACTCTAACCTCGTTATTTCCAAGAGGA
1 TTTTATTTTTAAAACATCGATTTTTCACCATCGGGGATACTCTAACCCCATTATTTTTAAGGGGA
* * * * * *
2856998 TACTCTAATCCTGGTTTTATTTCCAAAACATCAATTTTCCACAATCGGGGATACTTCAATCCC-A
66 TACTCCAATCC-GATTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAA-CCCTA
* *
2857062 TTATTTTTAAGGGAATACTCCAACCCCAA
129 TT-TTTTCAAGAGAATACTCCAACCCCAA
* ** * *
2857091 TTTTAGTTTTTAAAACACCGATTTTTCATAATTC-GGGATACTCCAACCCCATTATTTTTGAGGG
1 TTTTA-TTTTTAAAACATCGATTTTTCACCA-TCGGGGATACTCTAACCCCATTATTTTTAAGGG
* * *
2857155 GATACTCCAATCTCAATTTTATTTTCAAAACACCAATTTTTCACCATCGAGGATACTCCAACCCT
64 GATACTCCAATC-CGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCT
* * * * *
2857220 ATTTTTTCGAGAGAATATTCTAATCCTAA
128 ATTTTTTCAAGAGAATACTCCAACCCCAA
* * * *
2857249 TTTTATTTTCAAAACATCGATTTTTCACCATCGGGGATACTTTAACCCCATTATTTTTAAAGGTA
1 TTTTATTTTTAAAACATCGATTTTTCACCATCGGGGATACTCTAACCCCATTATTTTTAAGGGGA
* * * *
2857314 TACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTTCACAATCGGGGATACTCCAACTCTAG
66 TACTCCAA-TCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCTAT
2857379 TTTT
130 TTTT
2857383 ATTCCCAAAA
Statistics
Matches: 241, Mismatches: 45, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
156 2 0.01
157 108 0.45
158 33 0.14
159 95 0.39
160 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (156 bp):
TTTTATTTTTAAAACATCGATTTTTCACCATCGGGGATACTCTAACCCCATTATTTTTAAGGGGA
TACTCCAATCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCTATT
TTTTCAAGAGAATACTCCAACCCCAA
Found at i:2857372 original size:51 final size:52
Alignment explanation
Indices: 2857313--2857428 Score: 148
Period size: 51 Copynumber: 2.3 Consensus size: 52
2857303 TTTTAAAGGT
** *
2857313 ATACTCCAACCCCGA-TTTTATTTTCAAAACA-CTAATTTTTCACAATCGGGG
1 ATACTCCAACCCCGAGTTTTATTCCCAAAACATC-AATTTTTCACAATCAGGG
* *
2857364 ATACTCCAA-CTCTAGTTTTATTCCCAAAACATCAATTTTTCACAATCAGGG
1 ATACTCCAACCCCGAGTTTTATTCCCAAAACATCAATTTTTCACAATCAGGG
*
2857415 ATACTTCAACCCCG
1 ATACTCCAACCCCG
2857429 TTATTTTCAA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
50 3 0.06
51 48 0.89
52 3 0.06
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.32
Consensus pattern (52 bp):
ATACTCCAACCCCGAGTTTTATTCCCAAAACATCAATTTTTCACAATCAGGG
Found at i:2857495 original size:77 final size:79
Alignment explanation
Indices: 2857381--2857558 Score: 218
Period size: 77 Copynumber: 2.3 Consensus size: 79
2857371 AACTCTAGTT
* * * * *
2857381 TTATTCCCAAAACATCAATTTTTCACAATCAG-GGATACTTCAACCCCGTTA-TTTTCAA-GGAG
1 TTATTTCCAAAACATCAATTTTTCATAAT-TGTAGATACTCCAACCCCGTTATTTTTCAAGGGAG
2857443 ACTCCAACCCCGGCC
65 ACTCCAACCCCGGCC
* * * * *
2857458 TTATTTCTAAAATATCGATTTTTCATAATTGTAGATACTCCAACCCCGTTATTTTTGAAGGGATA
1 TTATTTCCAAAACATCAATTTTTCATAATTGTAGATACTCCAACCCCGTTATTTTTCAAGGGAGA
**
2857523 CTCCAACCCCGGTT
66 CTCCAACCCCGGCC
2857537 TTATTTCCAAAACATCAATTTT
1 TTATTTCCAAAACATCAATTTT
2857559 CACCATTGGG
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
76 1 0.01
77 41 0.49
78 6 0.07
79 35 0.42
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (79 bp):
TTATTTCCAAAACATCAATTTTTCATAATTGTAGATACTCCAACCCCGTTATTTTTCAAGGGAGA
CTCCAACCCCGGCC
Found at i:2870020 original size:12 final size:12
Alignment explanation
Indices: 2870003--2870046 Score: 72
Period size: 12 Copynumber: 3.7 Consensus size: 12
2869993 TCTTTTTTTA
2870003 AAAAAAAACAAC
1 AAAAAAAACAAC
2870015 AAAAAAAA-AAC
1 AAAAAAAACAAC
2870026 AAAAAAAACAAC
1 AAAAAAAACAAC
2870038 ATAAAAAAA
1 A-AAAAAAA
2870047 GAAAGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.37
12 12 0.40
13 7 0.23
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.02
Consensus pattern (12 bp):
AAAAAAAACAAC
Found at i:2870021 original size:14 final size:13
Alignment explanation
Indices: 2870002--2870064 Score: 65
Period size: 14 Copynumber: 4.7 Consensus size: 13
2869992 TTCTTTTTTT
2870002 AAAAAAAAACAACA
1 AAAAAAAAACAA-A
2870016 AAAAAAAAAC-AA
1 AAAAAAAAACAAA
*
2870028 AAAAAACAACATAA
1 AAAAAAAAACA-AA
* *
2870042 AAAAAGAAAGAAA
1 AAAAAAAAACAAA
2870055 AAAAGAAAAA
1 AAAA-AAAAA
2870065 AAGAACCTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
12 10 0.24
13 7 0.17
14 24 0.59
ACGTcount: A:0.86, C:0.08, G:0.05, T:0.02
Consensus pattern (13 bp):
AAAAAAAAACAAA
Found at i:2870055 original size:12 final size:11
Alignment explanation
Indices: 2870002--2870066 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 11
2869992 TTCTTTTTTT
*
2870002 AAAAAAAAACA
1 AAAAAAAAAGA
2870013 ACAAAAAAAA-A
1 A-AAAAAAAAGA
*
2870024 ACAAAAAAAACA
1 A-AAAAAAAAGA
2870036 ACATAAAAAAAGA
1 A-A-AAAAAAAGA
2870049 AAGAAAAAAAGA
1 AA-AAAAAAAGA
2870061 AAAAAA
1 AAAAAA
2870067 GAACCTACCT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
11 16 0.33
12 24 0.49
13 9 0.18
ACGTcount: A:0.86, C:0.08, G:0.05, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:2870066 original size:23 final size:23
Alignment explanation
Indices: 2870003--2870046 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2869993 TCTTTTTTTA
2870003 AAAAAAAACAACAAAAAAAAAAC
1 AAAAAAAACAACAAAAAAAAAAC
*
2870026 AAAAAAAACAACATAAAAAAA
1 AAAAAAAACAACAAAAAAAAA
2870047 GAAAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.02
Consensus pattern (23 bp):
AAAAAAAACAACAAAAAAAAAAC
Found at i:2871309 original size:122 final size:119
Alignment explanation
Indices: 2871127--2871478 Score: 395
Period size: 122 Copynumber: 2.9 Consensus size: 119
2871117 AAGTAGGATG
* * **
2871127 CCTTTTAAAGCCCACACAAGTTGATGACA-CTTTTCAGTGCTCAAAGAGCATGACAACTTTTCTT
1 CCTTTTAAAGCCCACACAAGTTGATGGCACCTTTT-AGTCCTCAAAGAGCATGA-TGCTTTTCTT
2871191 TTTAAAGCCCACACAAGTTGGTGGCATCTTTCAGTCCTCAAA-AAGCAAGACACCTTTT
64 TTTAAAGCCCACACAAGTTGGTGGCATCTTTCAGTCCTCAAAGAA-CAAGACA-C-TTT
* * * *
2871249 TCTTTTAAAGCCCACGCAAGTTGGTGGCACCTTTTAGTTCTCAAAGAGCATGATGTCTTTTCTTT
1 CCTTTTAAAGCCCACACAAGTTGATGGCACCTTTTAGTCCTCAAAGAGCATGATG-CTTTTCTTT
* * * ** * *
2871314 TTAAAGCCCACACAAGTTGGTGGTACCTTCCAGTTTTCAAAGAATAGGACACTTT
65 TTAAAGCCCACACAAGTTGGTGGCATCTTTCAGTCCTCAAAGAACAAGACACTTT
* * * * *
2871369 CCTTTTAAAGCCCATACAAGTT-ATGGCACCTTCTAATCCTCAAAGAGCAGGATGCTTTCTCCTT
1 CCTTTTAAAGCCCACACAAGTTGATGGCACCTTTTAGTCCTCAAAGAGCATGATGCTTT-TCTTT
** * * *
2871433 GCAAAGCCCACACAAGTTGGTGGCATCTTTTAGTCTTTAAAGAACA
65 TTAAAGCCCACACAAGTTGGTGGCATCTTTCAGTCCTCAAAGAACA
2871479 GGACGCACTT
Statistics
Matches: 194, Mismatches: 32, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
118 4 0.02
119 68 0.35
120 22 0.11
121 1 0.01
122 92 0.47
123 7 0.04
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (119 bp):
CCTTTTAAAGCCCACACAAGTTGATGGCACCTTTTAGTCCTCAAAGAGCATGATGCTTTTCTTTT
TAAAGCCCACACAAGTTGGTGGCATCTTTCAGTCCTCAAAGAACAAGACACTTT
Found at i:2871448 original size:60 final size:60
Alignment explanation
Indices: 2871053--2871466 Score: 317
Period size: 61 Copynumber: 7.0 Consensus size: 60
2871043 CTTTCAGTCA
** * * * * *
2871053 TCAAAGAGCAGGACAC-TTTCCTTTCAAAGCTCACACAGGTTGGTGGTACCTTCTAGTCC
1 TCAAAGAGCAGGATGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTTC
* * * * * *
2871112 TCAAAAAGTAGGATG-----CCTTTTAAAGCCCACACAAGTTGATGACA-CTTTTCAGTGC
1 TCAAAGAGCAGGATGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT-AGTTC
* ** * * *
2871167 TCAAAGAGCATGACAACTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCATCTT-TCAGTCC
1 TCAAAGAGCAGGA-TGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT-AGTTC
* * ** * * *
2871228 TCAAAAAGCAAGACACCTTTTTCTTTTAAAGCCCACGCAAGTTGGTGGCACCTTTTAGTTC
1 TCAAAGAGCAGGA-TGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTTC
* * * * *
2871289 TCAAAGAGCATGATGTCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGTACCTTCCAGTTT
1 TCAAAGAGCAGGATG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTTC
** ** * * * *
2871350 TCAAAGAATAGGACAC-TTTCCTTTTAAAGCCCATACAAGTT-ATGGCACCTTCTAATCC
1 TCAAAGAGCAGGATGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTTC
** * *
2871408 TCAAAGAGCAGGATGCTTTCTCCTTGCAAAGCCCACACAAGTTGGTGGCATCTTTTAGT
1 TCAAAGAGCAGGATGCTTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGT
2871467 CTTTAAAGAA
Statistics
Matches: 278, Mismatches: 64, Indels: 24
0.76 0.17 0.07
Matches are distributed among these distances:
54 4 0.01
55 37 0.13
58 23 0.08
59 36 0.13
60 21 0.08
61 153 0.55
62 4 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (60 bp):
TCAAAGAGCAGGATGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTTC
Found at i:2871690 original size:76 final size:75
Alignment explanation
Indices: 2871582--2871746 Score: 163
Period size: 76 Copynumber: 2.2 Consensus size: 75
2871572 AGTTTTTTTC
** ** ** *
2871582 TTTTCCTTTGTCCTCAAAGAACAAGATGCATTTTGTT-TCCTTTTTTTTTCATCCTCGAAGAGTA
1 TTTTCCTTTGTCCTCAAAGAACAAGACCCATTTCATTCT-CTTTTCCTTT-ATCCTCGAAGAGCA
2871646 AGATGTACTCTT
64 AGATGTACTCTT
* ** * * *
2871658 TTTTCCTTTGTCCTCAAGGAGTAGGACCCATTTCATTCTCTTTTCCTTTATGCTCGAAGAGCAGG
1 TTTTCCTTTGTCCTCAAAGAACAAGACCCATTTCATTCTCTTTTCCTTTATCCTCGAAGAGCAAG
* *
2871723 GTGTGCTCTT
66 ATGTACTCTT
2871733 TTTT-CTTTGTCCTC
1 TTTTCCTTTGTCCTC
2871747 TTGTAAAGTT
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
74 10 0.14
75 25 0.34
76 37 0.51
77 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.44
Consensus pattern (75 bp):
TTTTCCTTTGTCCTCAAAGAACAAGACCCATTTCATTCTCTTTTCCTTTATCCTCGAAGAGCAAG
ATGTACTCTT
Done.