Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold15
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: 4011073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 11440 characters in sequence are not A, C, G, or T
File 16 of 25
Found at i:2447295 original size:16 final size:17
Alignment explanation
Indices: 2447266--2447301 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2447256 TTTATTTTTA
*
2447266 TTATTTTGTATAATTCT
1 TTATTTTGTATAATTAT
2447283 TTATTTT-TATAATTAT
1 TTATTTTGTATAATTAT
2447299 TTA
1 TTA
2447302 ATTAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (17 bp):
TTATTTTGTATAATTAT
Found at i:2447534 original size:20 final size:20
Alignment explanation
Indices: 2447509--2447548 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2447499 TTTTAAAAAT
*
2447509 TATTTTTCT-ATTAATATTTA
1 TATTTTTATAATTAA-ATTTA
2447529 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
2447549 AAATAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTATAATTAAATTTA
Found at i:2452028 original size:52 final size:52
Alignment explanation
Indices: 2451950--2452078 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
2451940 CGAAATATGA
*
2451950 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
2452002 AAATTTACCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
2452054 AAATTTGCCTGCATGTATCGATACA
1 AAATTTACCTGCATGTATCGATACA
2452079 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (52 bp):
AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:2452091 original size:52 final size:51
Alignment explanation
Indices: 2451950--2452098 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
2451940 CGAAATATGA
2451950 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
2452002 AAATTTACCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
2452054 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTACCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
2452099 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTACCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:2452189 original size:33 final size:33
Alignment explanation
Indices: 2452152--2452218 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2452142 AGTAGCTTAA
2452152 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2452185 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2452218 A
1 A
2452219 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2452192 original size:13 final size:13
Alignment explanation
Indices: 2452174--2452198 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2452164 CAAAAAAATA
2452174 TGTATCGATACAT
1 TGTATCGATACAT
2452187 TGTATCGATACA
1 TGTATCGATACA
2452199 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2454090 original size:14 final size:14
Alignment explanation
Indices: 2454071--2454097 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2454061 TGCAAATGTC
2454071 TCAAACATGTTAGA
1 TCAAACATGTTAGA
2454085 TCAAACATGTTAG
1 TCAAACATGTTAG
2454098 GCACGTCGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (14 bp):
TCAAACATGTTAGA
Found at i:2458038 original size:18 final size:17
Alignment explanation
Indices: 2458004--2458045 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
2457994 GAGTACATTA
**
2458004 TTAAAAAAAAAGGAGTT
1 TTAAAAAAAAAACAGTT
2458021 TTAAAAGAAAAAACAGTT
1 TTAAAA-AAAAAACAGTT
2458039 TTAAAAA
1 TTAAAAA
2458046 CAGGAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.62, C:0.02, G:0.12, T:0.24
Consensus pattern (17 bp):
TTAAAAAAAAAACAGTT
Found at i:2459544 original size:141 final size:140
Alignment explanation
Indices: 2459280--2459553 Score: 424
Period size: 141 Copynumber: 1.9 Consensus size: 140
2459270 TTACTTCTTC
* * *
2459280 TTAAATAATCTTATTATTAATAATAAGGTTATTTTGGTGTTATATATTAAACAATTTTTTTTTTG
1 TTAAATAATCTTATTATTAACAATAAGGTTATTTTGGTGTTATACATTAAACAATTTTTTTTTGG
*
2459345 AAATATTAAACACAATGATTTAACATTACTAATAATCTAATATATTATACCAAATACTAGAATTT
66 AAATATTAAACACAATGATTTAACATCACTAATAATCTAATATATTATACCAAATACTAGAATTT
2459410 AAGCTTCTCA
131 AAGCTTCTCA
* *
2459420 TTAAATGATCTTATTATTAACAATGAA-GTTATTTTGGTGTTATACATTAAATAATCTTTTTTTT
1 TTAAATAATCTTATTATTAACAAT-AAGGTTATTTTGGTGTTATACATTAAACAAT-TTTTTTTT
* * * * *
2459484 GGAAATATTTAACATAATGATTTAATATCACTAATAATCTATTATATTATATCAAATACTAGAAT
64 GGAAATATTAAACACAATGATTTAACATCACTAATAATCTAATATATTATACCAAATACTAGAAT
2459549 TTAAG
129 TTAAG
2459554 ATCACTAGTG
Statistics
Matches: 121, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
140 48 0.40
141 73 0.60
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.44
Consensus pattern (140 bp):
TTAAATAATCTTATTATTAACAATAAGGTTATTTTGGTGTTATACATTAAACAATTTTTTTTTGG
AAATATTAAACACAATGATTTAACATCACTAATAATCTAATATATTATACCAAATACTAGAATTT
AAGCTTCTCA
Found at i:2459676 original size:19 final size:20
Alignment explanation
Indices: 2459635--2459676 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2459625 AGTAAAAGTA
* *
2459635 TAATAATTTTTTTTAGAAGT
1 TAATAATTTTTTATAGAAAT
*
2459655 TAATAGTTTTTTATA-AAAT
1 TAATAATTTTTTATAGAAAT
2459674 TAA
1 TAA
2459677 ATAAATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (20 bp):
TAATAATTTTTTATAGAAAT
Found at i:2461089 original size:20 final size:20
Alignment explanation
Indices: 2461064--2461109 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
2461054 TTTTAAAATT
2461064 TTAAAATA-TATGAAATAA-AA
1 TTAAAATATTAT-AAA-AATAA
2461084 TTAAAATATTATAAAAATAA
1 TTAAAATATTATAAAAATAA
2461104 TTAAAA
1 TTAAAA
2461110 AATAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
TTAAAATATTATAAAAATAA
Found at i:2465691 original size:52 final size:52
Alignment explanation
Indices: 2465634--2465751 Score: 175
Period size: 52 Copynumber: 2.3 Consensus size: 52
2465624 AATTAACTAG
* * *
2465634 ATGTATCGATACATT-AATAAATGTATCGATACATCTGGGTAAAAAAAATAGA
1 ATGTATCGATACATTGAA-AAATATATCGATACATCTAGGTAAAAAAAACAGA
* *
2465686 ATGTATCGATACATTGAAAAATATATCGATATATCTAGGTAGAAAAAACAGA
1 ATGTATCGATACATTGAAAAATATATCGATACATCTAGGTAAAAAAAACAGA
2465738 ATGTATCGATACAT
1 ATGTATCGATACAT
2465752 GTACTGTTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 58 0.97
53 2 0.03
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (52 bp):
ATGTATCGATACATTGAAAAATATATCGATACATCTAGGTAAAAAAAACAGA
Found at i:2476601 original size:16 final size:16
Alignment explanation
Indices: 2476580--2476611 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2476570 GCTATTTGCA
2476580 AAAGCAAAGGGCAGAG
1 AAAGCAAAGGGCAGAG
2476596 AAAGCAAAGGGCAGAG
1 AAAGCAAAGGGCAGAG
2476612 TCTCTTAGAA
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:0.12, G:0.38, T:0.00
Consensus pattern (16 bp):
AAAGCAAAGGGCAGAG
Found at i:2479032 original size:1 final size:1
Alignment explanation
Indices: 2479026--2479052 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
2479016 ATTTCATGTT
2479026 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
2479053 AAAGCTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:2486112 original size:19 final size:18
Alignment explanation
Indices: 2486083--2486125 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2486073 AATTACATCT
2486083 TTTAT-AAATATATAAATA
1 TTTATAAAATATA-AAATA
2486101 TTTATAAAATATAAAATA
1 TTTATAAAATATAAAATA
*
2486119 GTTATAA
1 TTTATAA
2486126 TTGTATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
TTTATAAAATATAAAATA
Found at i:2486338 original size:16 final size:16
Alignment explanation
Indices: 2486313--2486346 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
2486303 TATTACTTTA
2486313 ATTTTTAAAAAT-ATT
1 ATTTTTAAAAATAATT
2486328 ATTTTTGAAAAATAATT
1 ATTTTT-AAAAATAATT
2486345 AT
1 AT
2486347 CTAATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTTTAAAAATAATT
Found at i:2488159 original size:12 final size:12
Alignment explanation
Indices: 2488128--2488153 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2488118 CTACATTTAC
2488128 AAGAAATTTTCA
1 AAGAAATTTTCA
2488140 AAGAAATTTTCA
1 AAGAAATTTTCA
2488152 AA
1 AA
2488154 ATAATTATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (12 bp):
AAGAAATTTTCA
Found at i:2488465 original size:9 final size:9
Alignment explanation
Indices: 2488451--2488482 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
2488441 CAATTATCAA
2488451 TTTTTATAT
1 TTTTTATAT
2488460 TTTTTATAT
1 TTTTTATAT
2488469 TTTTT-TAT
1 TTTTTATAT
2488477 TTTTTA
1 TTTTTA
2488483 CTCAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTATAT
Found at i:2488470 original size:17 final size:17
Alignment explanation
Indices: 2488450--2488482 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2488440 TCAATTATCA
2488450 ATTTTTATATTTTTTAT
1 ATTTTTATATTTTTTAT
*
2488467 ATTTTTTTATTTTTTA
1 ATTTTTATATTTTTTA
2488483 CTCAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
ATTTTTATATTTTTTAT
Found at i:2488506 original size:18 final size:18
Alignment explanation
Indices: 2488474--2488521 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
2488464 TATATTTTTT
2488474 TATTTTTT-ACT-CAAAA
1 TATTTTTTAACTACAAAA
2488490 TATTTTTTAACTACAAAA
1 TATTTTTTAACTACAAAA
*
2488508 T-TATCTTTAACTAC
1 TAT-TTTTTAACTAC
2488522 TATTAAGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 8 0.29
17 4 0.14
18 16 0.57
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.48
Consensus pattern (18 bp):
TATTTTTTAACTACAAAA
Found at i:2490262 original size:19 final size:19
Alignment explanation
Indices: 2490240--2490279 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2490230 ATATTCTTTC
2490240 ATTACATATATATATATAT
1 ATTACATATATATATATAT
* * *
2490259 ATTACGTATATGTTTATAT
1 ATTACATATATATATATAT
2490278 AT
1 AT
2490280 AAATATAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (19 bp):
ATTACATATATATATATAT
Found at i:2490492 original size:16 final size:17
Alignment explanation
Indices: 2490473--2490508 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2490463 GAAAAATCAA
2490473 ATAAATA-AAAAATTTT
1 ATAAATATAAAAATTTT
2490489 ATAAATATAAAAATTTT
1 ATAAATATAAAAATTTT
2490506 ATA
1 ATA
2490509 CCTAACCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAATATAAAAATTTT
Found at i:2494531 original size:28 final size:27
Alignment explanation
Indices: 2494470--2494541 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
2494460 TAGTATATAA
* **
2494470 ATTTATATATTAACTATAAATTATATC
1 ATTTATTTATTAAAAATAAATTATATC
2494497 ATATTATTTATTAAAAATATAATTATTAT-
1 AT-TTATTTATTAAAAATA-AATTA-TATC
2494526 ATTTATTT-TTAAAAAT
1 ATTTATTTATTAAAAAT
2494542 TTTTATTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 10 0.26
28 19 0.49
29 7 0.18
30 3 0.08
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTATTTATTAAAAATAAATTATATC
Found at i:2494724 original size:5 final size:5
Alignment explanation
Indices: 2494714--2494746 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
2494704 AAAAATTAAA
*
2494714 ATAAG ATAAG ATAAG ATAAG ATAA- ATAAA ATAA
1 ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATAA
2494747 TGAGAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (5 bp):
ATAAG
Found at i:2494734 original size:15 final size:14
Alignment explanation
Indices: 2494710--2494746 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
2494700 AATAAAAAAT
2494710 TAAAATAAGATAAGA
1 TAAAATAAGATAA-A
*
2494725 TAAGATAAGATAAA
1 TAAAATAAGATAAA
2494739 TAAAATAA
1 TAAAATAA
2494747 TGAGAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.22
Consensus pattern (14 bp):
TAAAATAAGATAAA
Found at i:2495643 original size:18 final size:19
Alignment explanation
Indices: 2495620--2495664 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
2495610 ATTTAAAAAA
*
2495620 TTAAAATAAAATTTTA-TT
1 TTAAAATAAAATTTAATTT
**
2495638 TTAAAATTTAATTTAATTT
1 TTAAAATAAAATTTAATTT
2495657 TTAAAATA
1 TTAAAATA
2495665 TTTAATATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAATAAAATTTAATTT
Found at i:2495879 original size:22 final size:22
Alignment explanation
Indices: 2495851--2495901 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
2495841 TTATTTGTAT
**
2495851 ATTAATTCTTTAAATTATTAAA
1 ATTAATTCTTTAAAAAATTAAA
*
2495873 ATTAATTTTTTTAAAAAATTAAA
1 ATTAA-TTCTTTAAAAAATTAAA
2495896 A-TAATT
1 ATTAATT
2495902 AACAGCAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 8 0.32
23 15 0.60
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTAATTCTTTAAAAAATTAAA
Found at i:2497504 original size:29 final size:30
Alignment explanation
Indices: 2497447--2497504 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
2497437 TAATAGTATT
* *
2497447 AAGTATAATTATATAAATATGATATGAATG
1 AAGTATAATTATATAAATATGAAACGAATG
2497477 AAGTA-AATTA-ATAAAATATGAAACGAAT
1 AAGTATAATTATAT-AAATATGAAACGAAT
2497505 ATATATCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 18 0.72
30 5 0.20
ACGTcount: A:0.55, C:0.02, G:0.12, T:0.31
Consensus pattern (30 bp):
AAGTATAATTATATAAATATGAAACGAATG
Found at i:2497581 original size:33 final size:33
Alignment explanation
Indices: 2497514--2497576 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
2497504 TATATATCTC
* *
2497514 AAAATTTATAT-AATATAAATTATTAAAGTATT
1 AAAAATTATATAAATATAAATTATTAAAATATT
2497546 AAAAATTATATAAATATAAA-TA-TAAAATATT
1 AAAAATTATATAAATATAAATTATTAAAATATT
2497577 TTAAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 8 0.29
32 12 0.43
33 8 0.29
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (33 bp):
AAAAATTATATAAATATAAATTATTAAAATATT
Found at i:2497611 original size:28 final size:28
Alignment explanation
Indices: 2497553--2497622 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
2497543 ATTAAAAATT
* *
2497553 ATATAAATATAAATATAAAATATTTTAA
1 ATATAAATATAAATAAAAAATATTATAA
* *
2497581 ATATAATTATAATATAAAAAATA-TATGA
1 ATATAAATATAA-ATAAAAAATATTATAA
*
2497609 ATA-AAATATGAATA
1 ATATAAATATAAATA
2497623 CACATATTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 3 0.09
27 6 0.17
28 17 0.49
29 9 0.26
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (28 bp):
ATATAAATATAAATAAAAAATATTATAA
Found at i:2497809 original size:14 final size:16
Alignment explanation
Indices: 2497778--2497811 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2497768 ATAATTATAA
2497778 AATTATAAATATTTTT
1 AATTATAAATATTTTT
2497794 AATTATAAA-A-TTTT
1 AATTATAAATATTTTT
2497808 AATT
1 AATT
2497812 TCTTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 1 0.06
16 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTATAAATATTTTT
Found at i:2497817 original size:24 final size:23
Alignment explanation
Indices: 2497756--2497817 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
2497746 TATTTTAATC
*
2497756 TTTTAATATTTTATAATTATAAAA
1 TTTTAAT-TTTTTTAATTATAAAA
* *
2497780 TTATAAATATTTTTAATTATAAAA
1 TT-TTAATTTTTTTAATTATAAAA
2497804 TTTTAATTTCTTTT
1 TTTTAATTT-TTTT
2497818 TATTTATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 5 0.16
24 22 0.71
25 4 0.13
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTAATTTTTTTAATTATAAAA
Found at i:2498380 original size:11 final size:11
Alignment explanation
Indices: 2498366--2498503 Score: 51
Period size: 11 Copynumber: 12.7 Consensus size: 11
2498356 ATGTATTCAG
2498366 ATTATATTTTT
1 ATTATATTTTT
*
2498377 ATTATATATTT
1 ATTATATTTTT
*
2498388 A-TATAAATTTT
1 ATTAT-ATTTTT
** * *
2498399 AAAATATTAATA
1 ATTATATT-TTT
2498411 ATT-TA-TTTT
1 ATTATATTTTT
*
2498420 ATGTA-AATTTT
1 AT-TATATTTTT
*
2498431 AATAT-T-TTT
1 ATTATATTTTT
*
2498440 A-TATATTTAT
1 ATTATATTTTT
2498450 ATTAT-TTTTT
1 ATTATATTTTT
2498460 ATTATATATTTT
1 ATTATAT-TTTT
2498472 AATTAT-TTTTCAT
1 -ATTATATTTT--T
* *
2498485 ATTATGTTTGT
1 ATTATATTTTT
2498496 ATTATATT
1 ATTATATT
2498504 ATGTTTTCTT
Statistics
Matches: 94, Mismatches: 17, Indels: 32
0.66 0.12 0.22
Matches are distributed among these distances:
8 3 0.03
9 8 0.09
10 20 0.21
11 40 0.43
12 14 0.15
13 9 0.10
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (11 bp):
ATTATATTTTT
Found at i:2498489 original size:25 final size:23
Alignment explanation
Indices: 2498438--2498481 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
2498428 TTTAATATTT
2498438 TTATATATTTATATTATTTTTTA
1 TTATATATTTATATTATTTTTTA
2498461 TTATATATTT-TAATTATTTTT
1 TTATATATTTAT-ATTATTTTT
2498482 CATATTATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATATATTTATATTATTTTTTA
Found at i:2502670 original size:21 final size:21
Alignment explanation
Indices: 2502644--2502712 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
2502634 ATTTGCATCA
2502644 ATACAAACAGTAAATGTATCG
1 ATACAAACAGTAAATGTATCG
* *
2502665 ATACAAA-AGTGAATATATCG
1 ATACAAACAGTAAATGTATCG
** *
2502685 ATACATGC-CTAAAATGTATCG
1 ATACAAACAGT-AAATGTATCG
2502706 ATACAAA
1 ATACAAA
2502713 ACTATCATGC
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.25
Consensus pattern (21 bp):
ATACAAACAGTAAATGTATCG
Found at i:2502685 original size:20 final size:21
Alignment explanation
Indices: 2502644--2502689 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
2502634 ATTTGCATCA
*
2502644 ATACAAACAGTAAATGTATCG
1 ATACAAACAGTAAATATATCG
*
2502665 ATACAAA-AGTGAATATATCG
1 ATACAAACAGTAAATATATCG
2502685 ATACA
1 ATACA
2502690 TGCCTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (21 bp):
ATACAAACAGTAAATATATCG
Found at i:2506506 original size:20 final size:20
Alignment explanation
Indices: 2506480--2506534 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
2506470 ATAAAAAGAC
* *
2506480 AATGTATCGATATATTCATA
1 AATGTATCGATACATTCAAA
* * *
2506500 CATGTATCGTTACATTGAAA
1 AATGTATCGATACATTCAAA
2506520 AATGTATCGATACAT
1 AATGTATCGATACAT
2506535 CTTGGTAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:2507522 original size:28 final size:28
Alignment explanation
Indices: 2507463--2507902 Score: 520
Period size: 28 Copynumber: 15.5 Consensus size: 28
2507453 CACTAACTTG
*
2507463 TGTGGGCTTTGAAAGGTTATGCCACTGACT
1 TGTGGGCTTTGAAAGG--GTGCCACTGACT
*
2507493 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
2507521 TGTGGGTTTTGAAGGGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2507549 TGTGGGCTTTGAAAAGGTGTCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
2507577 TATGGGCTTTGAGAGGCTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
2507605 TGTGAGCTTTGGAAGGGTGCCACTGATTT
1 TGTGGGCTTTGAAAGGGTGCCACTGA-CT
2507634 GTGTGGGCTTTGAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2507663 TGTGGACTTTGAAAGGGTGCCACTGATTT
1 TGTGGGCTTTGAAAGGGTGCCACTGA-CT
2507692 GTGTGGGCTTTGAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
*
2507721 TGTGGGCTTTGAAAGGGTGCCACTGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
2507749 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
2507777 TGTGGTCTTTTGAAAAGATACCACTGACT
1 TGTGGGC-TTTGAAAGGGTGCCACTGACT
* * *
2507806 TGTGGGCTTTCAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
2507834 TGTGGGCTTTGAAAAGATGTCATTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*** *
2507862 TGTGGGCTTTGAAAAAATGTCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
2507890 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
2507903 GAGATGAACG
Statistics
Matches: 358, Mismatches: 47, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
28 264 0.74
29 29 0.08
30 65 0.18
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.32
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:2507673 original size:86 final size:83
Alignment explanation
Indices: 2507448--2507902 Score: 487
Period size: 86 Copynumber: 5.3 Consensus size: 83
2507438 TAGAAAAAAA
* *
2507448 GGTACCACTAACTTGTGTGGGCTTTGAAAGGTTATGCCACTGACTTGTGGGCTTTGAAAGGGTGC
1 GGTACCACTGAC-T-TGTGGGCTTTGAAAGG--GTGCCACTGACTTGTGGGCTTTGAAAGGGTGC
* * *
2507513 CACTAACTTGTGGGTTTTGAAGG
62 CACTGACTTGT-GGCTTTGAAAG
* * * * *
2507536 GGTACCACTGACTTGTGGGCTTTGAAAAGGTGTCACTGACTTATGGGCTTTGAGAGGCTGCCACT
1 GGTACCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
*
2507601 GACTTGTGAGCTTTGGAAG
66 GACTTGTG-GCTTTGAAAG
* * *
2507620 GGTGCCACTGATTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGACTTTGAAAGGGTGCCA
1 GGTACCACTGA-CT-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
*
2507685 CTGATTTGTGTGGGCTTTGAAAG
64 CTGA-CT-TGT-GGCTTTGAAAG
* * *
2507708 GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGATTTGTGGGCTTTGAAAGGATGCCACT
1 GGTACCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
*
2507773 GACTTGTGGTCTTTTGAAAA
66 GACTTGTGG-C-TTTGAAAG
* * * * * * * *
2507793 GATACCACTGACTTGTGGGCTTTCAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGATGTCATT
1 GGTACCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
* *
2507858 AACTTGTGGGCTTTGAAAA
66 GACTTGT-GGCTTTGAAAG
** **
2507877 AATGTCACTGACTTGTGGGCTTTGAA
1 GGTACCACTGACTTGTGGGCTTTGAA
2507903 GAGATGAACG
Statistics
Matches: 317, Mismatches: 41, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
83 3 0.01
84 88 0.28
85 72 0.23
86 116 0.37
87 3 0.01
88 34 0.11
89 1 0.00
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.31
Consensus pattern (83 bp):
GGTACCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
GACTTGTGGCTTTGAAAG
Found at i:2509146 original size:1 final size:1
Alignment explanation
Indices: 2509140--2509263 Score: 77
Period size: 1 Copynumber: 124.0 Consensus size: 1
2509130 TCTAGACCCC
* * * ** ** * **
2509140 TTTTTTTGTTTTTTTGTTTTTTTTTGTTTTTTTTTGCTTTTGGTTTTTTGTTTTTTTTTTTTGCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * ** * ** * *
2509205 TTTTTTGTTTTTTTTCTTGGTTTTTTTTCTTGGTTTTTTTTTGTTTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2509264 GGTACGAAAG
Statistics
Matches: 93, Mismatches: 30, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 93 1.00
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.85
Consensus pattern (1 bp):
T
Found at i:2509164 original size:13 final size:13
Alignment explanation
Indices: 2509140--2509260 Score: 98
Period size: 14 Copynumber: 8.5 Consensus size: 13
2509130 TCTAGACCCC
2509140 TTTTTTTGTTTTT
1 TTTTTTTGTTTTT
*
2509153 TTGTTTTTTTTTGTT
1 TT-TTTTTGTTT-TT
*
2509168 TTTTTTTGCTTTTG
1 TTTTTTTG-TTTTT
*
2509182 GTTTTTTGTTTTT
1 TTTTTTTGTTTTT
2509195 TTTTTTTGCTTTTT
1 TTTTTTTG-TTTTT
*
2509209 TTGTTTTTTTTCTTGGT
1 TT-TTTTTGTT-TT--T
* *
2509226 TTTTTTTCTTGGTT
1 TTTTTTTGTT-TTT
2509240 TTTTTTTGTTTTT
1 TTTTTTTGTTTTT
2509253 TTTATTTT
1 TTT-TTTT
2509261 TTTGGTACGA
Statistics
Matches: 87, Mismatches: 12, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
13 18 0.21
14 44 0.51
15 14 0.16
16 8 0.09
17 3 0.03
ACGTcount: A:0.01, C:0.03, G:0.12, T:0.84
Consensus pattern (13 bp):
TTTTTTTGTTTTT
Found at i:2509181 original size:34 final size:33
Alignment explanation
Indices: 2509143--2509264 Score: 124
Period size: 34 Copynumber: 3.7 Consensus size: 33
2509133 AGACCCCTTT
2509143 TTTTGTTTTTTTGTTTTTTTTTGTTTTTTTTTG
1 TTTTGTTTTTTTGTTTTTTTTTGTTTTTTTTTG
* *
2509176 CTTTTGGTTTTTTGTTTTTTTTTTTTGCTTTTTTTG
1 -TTTTGTTTTTTTGTTTTTTTTTGTT--TTTTTTTG
* * * **
2509212 TTTT-TTTTCTTGGTTTTTTTTCTTGGTTTTT-
1 TTTTGTTTTTTTGTTTTTTTTTGTTTTTTTTTG
*
2509243 TTTTGTTTTTTT-TATTTTTTTG
1 TTTTGTTTTTTTGTTTTTTTTTG
2509265 GTACGAAAGA
Statistics
Matches: 73, Mismatches: 12, Indels: 9
0.78 0.13 0.10
Matches are distributed among these distances:
31 11 0.15
32 11 0.15
34 39 0.53
35 4 0.05
36 8 0.11
ACGTcount: A:0.01, C:0.03, G:0.12, T:0.84
Consensus pattern (33 bp):
TTTTGTTTTTTTGTTTTTTTTTGTTTTTTTTTG
Found at i:2509208 original size:55 final size:53
Alignment explanation
Indices: 2509140--2509264 Score: 164
Period size: 55 Copynumber: 2.3 Consensus size: 53
2509130 TCTAGACCCC
* *
2509140 TTTTTTTGTTTTTTTG-TTTTTTT-TTGTTTTTTTTTGCTTTTGGTTTTTTGTTTTT
1 TTTTTTTGTTTTTTTGTTTTTTTTCTTGGTTTTTTTT-C--TTGGTTTTTT-TTTGT
2509195 TTTTTTTGCTTTTTTTGTTTTTTTTCTTGGTTTTTTTTCTTGGTTTTTTTTTGT
1 TTTTTTTG-TTTTTTTGTTTTTTTTCTTGGTTTTTTTTCTTGGTTTTTTTTTGT
*
2509249 TTTTTTTATTTTTTTG
1 TTTTTTTGTTTTTTTG
2509265 GTACGAAAGA
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
53 8 0.12
54 11 0.17
55 18 0.28
56 8 0.12
57 8 0.12
58 11 0.17
ACGTcount: A:0.01, C:0.03, G:0.12, T:0.84
Consensus pattern (53 bp):
TTTTTTTGTTTTTTTGTTTTTTTTCTTGGTTTTTTTTCTTGGTTTTTTTTTGT
Found at i:2509253 original size:36 final size:33
Alignment explanation
Indices: 2509148--2509263 Score: 87
Period size: 32 Copynumber: 3.5 Consensus size: 33
2509138 CCTTTTTTTG
**
2509148 TTTTTTTGTTTTTTTTTGTTTTTTTTTGCTTTTGGTT
1 TTTTTTTGTTTTTTTTT-TGGTTTTTT--TTTT-GTT
* *
2509185 TTTTGTT-TTTTTTTTTTGCTTTTTTTGTTT-TT
1 TTTTTTTGTTTTTTTTTTGGTTTTTTT-TTTGTT
* *
2509217 TTTCTTGGTTTTTTTTCTTGG-TTTTTTTTTG-T
1 TTTTTTTGTTTTTTTT-TTGGTTTTTTTTTTGTT
*
2509249 TTTTTTTATTTTTTT
1 TTTTTTTGTTTTTTT
2509264 GGTACGAAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
32 22 0.34
33 15 0.23
34 6 0.09
35 7 0.11
36 9 0.14
37 6 0.09
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.84
Consensus pattern (33 bp):
TTTTTTTGTTTTTTTTTTGGTTTTTTTTTTGTT
Found at i:2513672 original size:13 final size:13
Alignment explanation
Indices: 2513654--2513678 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2513644 CATTTTGTGG
2513654 TGTATCGATACAA
1 TGTATCGATACAA
2513667 TGTATCGATACA
1 TGTATCGATACA
2513679 TATTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2513694 original size:32 final size:33
Alignment explanation
Indices: 2513631--2513698 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
2513621 CGTTACAAGC
*
2513631 CAATGTATCGATACATTTTGTGGTGTATCGATA
1 CAATGTATCGATACATATTGTGGTGTATCGATA
2513664 CAATGTATCGATACATATTGT-GTGTATCGATA
1 CAATGTATCGATACATATTGTGGTGTATCGATA
2513696 CAA
1 CAA
2513699 ATTTAGCTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 14 0.41
33 20 0.59
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATATTGTGGTGTATCGATA
Found at i:2513790 original size:13 final size:13
Alignment explanation
Indices: 2513772--2513796 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2513762 ATTTGGTCAT
2513772 GTATCGATACAAG
1 GTATCGATACAAG
2513785 GTATCGATACAA
1 GTATCGATACAA
2513797 TGCAATCTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (13 bp):
GTATCGATACAAG
Found at i:2513810 original size:20 final size:20
Alignment explanation
Indices: 2513785--2513834 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2513775 TCGATACAAG
*
2513785 GTATCGATACAATGCAATCT
1 GTATCGATACAATGAAATCT
* * *
2513805 GTATCGATACATTTAAATGT
1 GTATCGATACAATGAAATCT
2513825 GTATCGATAC
1 GTATCGATAC
2513835 TTTTCAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
GTATCGATACAATGAAATCT
Found at i:2515815 original size:21 final size:21
Alignment explanation
Indices: 2515784--2515835 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
2515774 GCTGTTAGTG
* *
2515784 TGGGGGCTGCCCGGTTGCGACT
1 TGGGGG-TGCCCGGTCGCGACC
2515806 TGGGGGTG-CCGGTCGCGACC
1 TGGGGGTGCCCGGTCGCGACC
2515826 TGGTGGGTGC
1 TGG-GGGTGC
2515836 TGCTTAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 13 0.50
21 7 0.27
22 6 0.23
ACGTcount: A:0.04, C:0.25, G:0.50, T:0.21
Consensus pattern (21 bp):
TGGGGGTGCCCGGTCGCGACC
Found at i:2516288 original size:13 final size:13
Alignment explanation
Indices: 2516270--2516308 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2516260 ATAATCCCCT
2516270 TGTATCGATACAG
1 TGTATCGATACAG
*
2516283 TGTATCGATACAA
1 TGTATCGATACAG
2516296 TGTATCGATACAG
1 TGTATCGATACAG
2516309 AGAATGCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2521842 original size:13 final size:13
Alignment explanation
Indices: 2521824--2521848 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2521814 CATTTTGTGG
2521824 TGTATCGATACAA
1 TGTATCGATACAA
2521837 TGTATCGATACA
1 TGTATCGATACA
2521849 TATTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2521864 original size:32 final size:33
Alignment explanation
Indices: 2521801--2521868 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
2521791 CGTTACAAGC
* *
2521801 CAATGTATCTATACATTTTGTGGTGTATCGATA
1 CAATGTATCGATACATATTGTGGTGTATCGATA
2521834 CAATGTATCGATACATATTGT-GTGTATCGATA
1 CAATGTATCGATACATATTGTGGTGTATCGATA
2521866 CAA
1 CAA
2521869 ATTTAGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (33 bp):
CAATGTATCGATACATATTGTGGTGTATCGATA
Found at i:2521984 original size:20 final size:20
Alignment explanation
Indices: 2521941--2521991 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2521931 CATTTGGTCA
*
2521941 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
2521961 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
*
2521981 TGTATTGATAC
1 TGTATCGATAC
2521992 TTTTCAGGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:2529959 original size:21 final size:21
Alignment explanation
Indices: 2529935--2529979 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
2529925 CACTTTGAAA
2529935 ACTGGGTATTTCGTGTCAAGC
1 ACTGGGTATTTCGTGTCAAGC
*
2529956 ACT--GTATTTTGTGTCAAGC
1 ACTGGGTATTTCGTGTCAAGC
2529975 ACTGG
1 ACTGG
2529980 AGAGATACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 18 0.86
21 3 0.14
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.36
Consensus pattern (21 bp):
ACTGGGTATTTCGTGTCAAGC
Found at i:2529964 original size:19 final size:19
Alignment explanation
Indices: 2529940--2529978 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2529930 TGAAAACTGG
2529940 GTATTTCGTGTCAAGCACT
1 GTATTTCGTGTCAAGCACT
*
2529959 GTATTTTGTGTCAAGCACT
1 GTATTTCGTGTCAAGCACT
2529978 G
1 G
2529979 GAGAGATACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (19 bp):
GTATTTCGTGTCAAGCACT
Found at i:2532674 original size:20 final size:20
Alignment explanation
Indices: 2532648--2532703 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
2532638 AAAAAGATAG
*
2532648 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
2532668 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
2532688 AATGTATCGATACATT
1 AATGTATCGATACATT
2532704 TGGGTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:2533885 original size:111 final size:111
Alignment explanation
Indices: 2533756--2533955 Score: 328
Period size: 111 Copynumber: 1.8 Consensus size: 111
2533746 ACTCATCCTT
* *
2533756 GGTGAAATGATGCAACACCTCTCGAAATGTGACTGATTACTTAAGTAATGAAACTTGTTTATTAT
1 GGTGAAATGATGCAACACCTCTCGAAATATGACTGATTACTTAAGTAATGAAACTCGTTTATTAT
*
2533821 CACTTATTCATTGGCGTATATTAACGATCTAACCGAGTTAAACCCA
66 CACTTATTCATTGACGTATATTAACGATCTAACCGAGTTAAACCCA
* * * * *
2533867 GGTGAAATGATGCGACACCTCTCGGAATATGATTTATTACTTAAGTAATGAAACTCGTTTATTGT
1 GGTGAAATGATGCAACACCTCTCGAAATATGACTGATTACTTAAGTAATGAAACTCGTTTATTAT
2533932 CACTTATTCATTGACGTATATTAA
66 CACTTATTCATTGACGTATATTAA
2533956 GATATCAATC
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 81 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (111 bp):
GGTGAAATGATGCAACACCTCTCGAAATATGACTGATTACTTAAGTAATGAAACTCGTTTATTAT
CACTTATTCATTGACGTATATTAACGATCTAACCGAGTTAAACCCA
Found at i:2538250 original size:20 final size:20
Alignment explanation
Indices: 2538240--2538278 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2538230 CGATATATTG
2538240 ACCTATGTATCAATACATTC
1 ACCTATGTATCAATACATTC
*
2538260 ACTTATGTATCAATACATT
1 ACCTATGTATCAATACATT
2538279 TTGGCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (20 bp):
ACCTATGTATCAATACATTC
Found at i:2539271 original size:16 final size:17
Alignment explanation
Indices: 2539250--2539281 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2539240 AAATTTTAAC
2539250 TCTAAAA-TATTATTTA
1 TCTAAAATTATTATTTA
2539266 TCTAAAATTATTATTT
1 TCTAAAATTATTATTT
2539282 CATAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TCTAAAATTATTATTTA
Found at i:2541161 original size:24 final size:21
Alignment explanation
Indices: 2541119--2541172 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 21
2541109 ATTTTCAATT
2541119 TTTTTAATTTCAAAAATTTTGAA
1 TTTTTAATTTCAAAAA-TTTG-A
***
2541142 TATTTTAATTTCACTTATTTGA
1 T-TTTTAATTTCAAAAATTTGA
2541164 TTTTTAATT
1 TTTTTAATT
2541173 AAATTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 8 0.30
22 2 0.07
23 5 0.19
24 12 0.44
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (21 bp):
TTTTTAATTTCAAAAATTTGA
Found at i:2543366 original size:13 final size:14
Alignment explanation
Indices: 2543348--2543384 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
2543338 CTTATTCCAC
*
2543348 ATTTAAATTTAA-A
1 ATTTAAATATAATA
2543361 ATTT-AATATAATA
1 ATTTAAATATAATA
2543374 ATTTAAATATA
1 ATTTAAATATA
2543385 TAAAAATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 6 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTTAAATATAATA
Found at i:2547475 original size:22 final size:22
Alignment explanation
Indices: 2547448--2547506 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
2547438 TATTTAATGC
*
2547448 TATTTACAACATATT-TTTAAAA
1 TATTTACAA-ATATTCTATAAAA
*
2547470 TATTTACCAATATTCTATAAAA
1 TATTTACAAATATTCTATAAAA
2547492 T-TTTACTTAAATATT
1 TATTTAC--AAATATT
2547507 TATTGAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 10 0.32
22 15 0.48
23 6 0.19
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.47
Consensus pattern (22 bp):
TATTTACAAATATTCTATAAAA
Found at i:2547482 original size:21 final size:23
Alignment explanation
Indices: 2547448--2547497 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
2547438 TATTTAATGC
*
2547448 TATTTACAACATATT-TTTAAAA
1 TATTTACAACATATTCTATAAAA
*
2547470 TATTTACCA-ATATTCTATAAAA
1 TATTTACAACATATTCTATAAAA
2547492 T-TTTAC
1 TATTTAC
2547498 TTAAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (23 bp):
TATTTACAACATATTCTATAAAA
Found at i:2547712 original size:11 final size:11
Alignment explanation
Indices: 2547675--2547719 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
2547665 AGACTGTGAA
2547675 AGAAGGAAAAAG
1 AGAA-GAAAAAG
*
2547687 AGAGGAAAAAG
1 AGAAGAAAAAG
2547698 AGAAGAAAAAG
1 AGAAGAAAAAG
2547709 AGAA-AAAAAG
1 AGAAGAAAAAG
2547719 A
1 A
2547720 AAAAGAATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 7 0.23
11 21 0.68
12 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
AGAAGAAAAAG
Found at i:2551230 original size:16 final size:15
Alignment explanation
Indices: 2551205--2551253 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
2551195 CGAGATAATC
2551205 TAAACTAAAAATTATT
1 TAAA-TAAAAATTATT
2551221 TAAATAAAAA--ATT
1 TAAATAAAAATTATT
*
2551234 TAAATTTAAAATTATT
1 TAAA-TAAAAATTATT
2551250 TAAA
1 TAAA
2551254 CTGAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 7 0.24
14 5 0.17
15 6 0.21
16 11 0.38
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAATAAAAATTATT
Found at i:2551260 original size:16 final size:15
Alignment explanation
Indices: 2551205--2551260 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
2551195 CGAGATAATC
2551205 TAAACTAAAAATTATT
1 TAAACT-AAAATTATT
*
2551221 TAAA-TAAAA-AATT
1 TAAACTAAAATTATT
*
2551234 TAAATTTAAAATTATT
1 TAAA-CTAAAATTATT
2551250 TAAACTGAAAA
1 TAAACT-AAAA
2551261 AATATTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
13 7 0.21
14 4 0.12
15 7 0.21
16 15 0.45
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.36
Consensus pattern (15 bp):
TAAACTAAAATTATT
Found at i:2551266 original size:17 final size:16
Alignment explanation
Indices: 2551205--2551272 Score: 61
Period size: 17 Copynumber: 4.4 Consensus size: 16
2551195 CGAGATAATC
*
2551205 TAAACTAAAAATTATT
1 TAAACTAAAAAATATT
2551221 TAAA-T-AAAAA-ATT
1 TAAACTAAAAAATATT
* * *
2551234 TAAATTTAAAATTATT
1 TAAACTAAAAAATATT
2551250 TAAACTGAAAAAATATT
1 TAAACT-AAAAAATATT
*
2551267 AAAACT
1 TAAACT
2551273 CGAAATGATC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
13 7 0.17
14 5 0.12
15 5 0.12
16 12 0.29
17 13 0.31
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (16 bp):
TAAACTAAAAAATATT
Found at i:2553614 original size:29 final size:30
Alignment explanation
Indices: 2553554--2553614 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 30
2553544 CTTCAATTTT
* ** * *
2553554 AAAATTAAAGAAATAAAAAAATGTTATGAA
1 AAAAATAAAGAAATAAAAAAAAATAATAAA
2553584 AAAAATAAA-AAATAAAAAAAAATAATAAA
1 AAAAATAAAGAAATAAAAAAAAATAATAAA
2553613 AA
1 AA
2553615 CAAAGCAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (30 bp):
AAAAATAAAGAAATAAAAAAAAATAATAAA
Found at i:2554398 original size:113 final size:113
Alignment explanation
Indices: 2554195--2554417 Score: 383
Period size: 113 Copynumber: 2.0 Consensus size: 113
2554185 GATTTGAACT
* *
2554195 TAGGTCACCCATGAAGAAAAAAAGCTCCAACCATTGGACCTCAATTATTGTTTTAATATAAAATA
1 TAGGCCACCCATGAAGAAAAAAAGCTCCAACCATTGGACCTCAATTACTGTTTTAATATAAAATA
*
2554260 TCAAAACAATTCTTTTAAGCTATTATTTCCGTAAAAGATTACAAATCC
66 TCAAAACAATTCTTTTAAGCCATTATTTCCGTAAAAGATTACAAATCC
* *
2554308 TAGGCCACCCATGAAGAAAAAAAGCTTCAACCATTGGACCTCAATTACTGTTTTGATATAAAATA
1 TAGGCCACCCATGAAGAAAAAAAGCTCCAACCATTGGACCTCAATTACTGTTTTAATATAAAATA
* *
2554373 TCAAAACAATTCTTTTAAGCCATTATTTCCGTAAATGATTGCAAA
66 TCAAAACAATTCTTTTAAGCCATTATTTCCGTAAAAGATTACAAA
2554418 ATTGAATGGC
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
113 103 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (113 bp):
TAGGCCACCCATGAAGAAAAAAAGCTCCAACCATTGGACCTCAATTACTGTTTTAATATAAAATA
TCAAAACAATTCTTTTAAGCCATTATTTCCGTAAAAGATTACAAATCC
Found at i:2559334 original size:14 final size:15
Alignment explanation
Indices: 2559317--2559361 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
2559307 ACACACAAAC
2559317 AAAAGTAAAAAAAAA
1 AAAAGTAAAAAAAAA
2559332 AAAGAGT-AAAAAAAA
1 AAA-AGTAAAAAAAAA
*
2559347 AACAGTCAAAAAAAA
1 AAAAGT-AAAAAAAA
2559362 GTGCAAAGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.12
15 13 0.50
16 10 0.38
ACGTcount: A:0.80, C:0.04, G:0.09, T:0.07
Consensus pattern (15 bp):
AAAAGTAAAAAAAAA
Found at i:2559342 original size:13 final size:14
Alignment explanation
Indices: 2559325--2559361 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2559315 ACAAAAGTAA
2559325 AAAAAAAAAAGAGT
1 AAAAAAAAAAGAGT
*
2559339 AAAAAAAAAACAGT
1 AAAAAAAAAAGAGT
2559353 CAAAAAAAA
1 -AAAAAAAA
2559362 GTGCAAAGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.81, C:0.05, G:0.08, T:0.05
Consensus pattern (14 bp):
AAAAAAAAAAGAGT
Found at i:2559640 original size:29 final size:26
Alignment explanation
Indices: 2559599--2559663 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 26
2559589 GTTCTTTTTC
2559599 AAAA-AAGAAACAAAACAAAAAAGGAAAA
1 AAAAGAAGAAAC-AAACAAAAAA--AAAA
*
2559627 AAAAGAAGAAACAAACAAACAAAAAA
1 AAAAGAAGAAACAAACAAAAAAAAAA
2559653 AAAAGAAGAAA
1 AAAAGAAGAAA
2559664 GGAAAAACCC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
26 15 0.43
28 13 0.37
29 7 0.20
ACGTcount: A:0.82, C:0.08, G:0.11, T:0.00
Consensus pattern (26 bp):
AAAAGAAGAAACAAACAAAAAAAAAA
Found at i:2560663 original size:33 final size:33
Alignment explanation
Indices: 2560626--2560731 Score: 128
Period size: 33 Copynumber: 3.3 Consensus size: 33
2560616 CCCACGGCTC
2560626 AGTGGCATCTTTCCTTCTTAAAGTCCACAATTT
1 AGTGGCATCTTTCCTTCTTAAAGTCCACAATTT
* * * *** *
2560659 AGTGGCATC--TCTTTC-CAAAGCCCACGGCTC
1 AGTGGCATCTTTCCTTCTTAAAGTCCACAATTT
2560689 AGTGGCATCTTTCCTTCTTAAAGTCCACAATTT
1 AGTGGCATCTTTCCTTCTTAAAGTCCACAATTT
2560722 AGTGGCATCT
1 AGTGGCATCT
2560732 CTTTCCAAAG
Statistics
Matches: 56, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
30 18 0.32
31 5 0.09
32 5 0.09
33 28 0.50
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (33 bp):
AGTGGCATCTTTCCTTCTTAAAGTCCACAATTT
Found at i:2560695 original size:30 final size:31
Alignment explanation
Indices: 2560602--2560758 Score: 122
Period size: 33 Copynumber: 5.0 Consensus size: 31
2560592 AATTCTTCAA
* *
2560602 ATCT-CTTCTCAAAGCCCACGGCTCAGTGGC
1 ATCTCCTTCTCAAAGTCCACGACTCAGTGGC
* * * *
2560632 ATCTTTCCTTCTTAAAGTCCACAATTTAGTGGC
1 ATC--TCCTTCTCAAAGTCCACGACTCAGTGGC
* * *
2560665 ATCTCTTTC-CAAAGCCCACGGCTCAGTGGC
1 ATCTCCTTCTCAAAGTCCACGACTCAGTGGC
* * * *
2560695 ATCTTTCCTTCTTAAAGTCCACAATTTAGTGGC
1 ATC--TCCTTCTCAAAGTCCACGACTCAGTGGC
* *
2560728 ATCTCTTTC-CAAAGTCCACGACTCCGTGGC
1 ATCTCCTTCTCAAAGTCCACGACTCAGTGGC
2560758 A
1 A
2560759 CCTTTTTCTT
Statistics
Matches: 95, Mismatches: 26, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
30 38 0.40
31 10 0.11
32 6 0.06
33 41 0.43
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (31 bp):
ATCTCCTTCTCAAAGTCCACGACTCAGTGGC
Found at i:2560701 original size:63 final size:63
Alignment explanation
Indices: 2560602--2560782 Score: 276
Period size: 63 Copynumber: 2.9 Consensus size: 63
2560592 AATTCTTCAA
2560602 ATCTC-TTCTCAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAATTTAGTGGC
1 ATCTCTTTC-CAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAATTTAGTGGC
2560665 ATCTCTTTCCAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAATTTAGTGGC
1 ATCTCTTTCCAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAATTTAGTGGC
* * * * *
2560728 ATCTCTTTCCAAAGTCCACGACTCCGTGGCACCTTTTTCTT-TTCAAAGTCCACAA
1 ATCTCTTTCCAAAGCCCACGGCTCAGTGGCATC-TTTCCTTCTT-AAAGTCCACAA
2560783 CTCCGTAGCA
Statistics
Matches: 110, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
63 90 0.82
64 20 0.18
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.32
Consensus pattern (63 bp):
ATCTCTTTCCAAAGCCCACGGCTCAGTGGCATCTTTCCTTCTTAAAGTCCACAATTTAGTGGC
Found at i:2560775 original size:34 final size:33
Alignment explanation
Indices: 2560738--2561119 Score: 336
Period size: 34 Copynumber: 11.8 Consensus size: 33
2560728 ATCTCTTTCC
*
2560738 AAAGTCCACGACTCCGTGGCACCTTTTTCTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* *
2560771 CAAAGTCCACAACTCCGTAGCA-C--TCT-TTTT
1 -AAAGTCCACAACTCCGTGGCACCTTTTTCTTTT
*
2560801 AAAGCCCACAACTCCGTGGCACC-----CTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * *
2560829 -AAGCCCACAACTCTGTGGCACTCTTCTTCCTTTT
1 AAAGTCCACAACTCCGTGGCAC-CTT-TTTCTTTT
*
2560863 -AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAAGTCCACAACTCCGTGGCAC-CTTTTT-CTTTT
*
2560897 -AAGTCCACAACTCCATGGCACC-----CTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* *
2560924 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAAGTCCACAACTCCGTGGCAC-CTTTTT-CTTTT
*
2560958 -AAGTCCACAACTCCATGGCACCTTTTTCTTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTC-TTTT
* *
2560991 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAAGTCCACAACTCCGTGGCAC-CTTTTT-CTTTT
2561026 -AAGTCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGTCCACAACTCCGTGGCAC-CTTTTT--CTTTT
* *
2561061 AAAGCCCACAACTCCGTGGCACCTTGTTCTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * *
2561094 TAAGTCCACAACTTCGTGGCATCTTT
1 AAAGTCCACAACTCCGTGGCACCTTT
2561120 CACCCTTTCT
Statistics
Matches: 295, Mismatches: 30, Indels: 47
0.79 0.08 0.13
Matches are distributed among these distances:
27 43 0.15
28 6 0.02
29 19 0.06
30 5 0.02
31 2 0.01
32 1 0.00
33 39 0.13
34 140 0.47
35 19 0.06
36 21 0.07
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (33 bp):
AAAGTCCACAACTCCGTGGCACCTTTTTCTTTT
Found at i:2560922 original size:61 final size:61
Alignment explanation
Indices: 2560857--2561106 Score: 304
Period size: 61 Copynumber: 3.9 Consensus size: 61
2560847 CACTCTTCTT
*
2560857 CCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCATGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCATGGCAC
2560918 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCATGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCATGGCAC
*
2560979 CTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGG
1 C-----C-TTTT-AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCATGG
2561044 CACTCTTTTTC
59 CA--------C
* * *
2561055 CCTTTTAAAGCCCACAACTCCGTGGCAC-CTTGTTCTTTTTAAGTCCACAACT
1 CCTTTT-AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACT
2561107 TCGTGGCATC
Statistics
Matches: 169, Mismatches: 5, Indels: 22
0.86 0.03 0.11
Matches are distributed among these distances:
61 61 0.36
66 1 0.01
67 4 0.02
68 53 0.31
69 21 0.12
70 26 0.15
71 1 0.01
76 2 0.01
ACGTcount: A:0.20, C:0.35, G:0.11, T:0.34
Consensus pattern (61 bp):
CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCATGGCAC
Found at i:2560935 original size:95 final size:95
Alignment explanation
Indices: 2560743--2561114 Score: 429
Period size: 95 Copynumber: 3.9 Consensus size: 95
2560733 TTTCCAAAGT
* *
2560743 CCACGACTCCGTGGCAC-CTTTTT-CTTTTCAAAGTCCACAACTCCGTAGCA-C----TCTTTTT
1 CCACAACTCCGTGGCACTCTTTTTCCTTTT-AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
2560801 AAAGCCCACAACTCCGTGGCACCCTTTTAAGC
65 -AAGCCCACAACTCCGTGGCACCCTTTTAAGC
* * * *
2560833 CCACAACTCTGTGGCACTCTTCTTCCTTTT-AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAAGTCCACAACTCCGTGGCAC-CTTTTTCTTTTT
* *
2560897 AAGTCCACAACTCCATGGCACCCTTTTAAGC
65 AAGCCCACAACTCCGTGGCACCCTTTTAAGC
* *
2560928 CCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGTCCACAACTCCATGGCACCTTTTTCTTTTTA
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT-
* *
2560992 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGT
65 AAGCCCACAACTCCGTGGCA--C-----CCTTTTAAGC
* *
2561030 CCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCTTTTT
1 CCACAACTCCGTGGCACTCTTTTT-CCTTTTAAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
* *
2561095 AAGTCCACAACTTCGTGGCA
65 AAGCCCACAACTCCGTGGCA
2561115 TCTTTCACCC
Statistics
Matches: 240, Mismatches: 24, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
90 34 0.14
91 5 0.02
92 6 0.03
94 10 0.04
95 94 0.39
96 5 0.02
97 1 0.00
102 32 0.13
103 23 0.10
104 30 0.12
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.32
Consensus pattern (95 bp):
CCACAACTCCGTGGCACTCTTTTTCCTTTTAAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTA
AGCCCACAACTCCGTGGCACCCTTTTAAGC
Found at i:2561164 original size:33 final size:33
Alignment explanation
Indices: 2561123--2561283 Score: 229
Period size: 33 Copynumber: 4.9 Consensus size: 33
2561113 CATCTTTCAC
2561123 CCTT-TCTAAAGCCCACACAAGTCGGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
*
2561155 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
* *
2561188 CCTTCTCTAAAGCCCACACTAGTTGGTGGC-AA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
**
2561220 CCCCCTCTAAAGCCCACACAAGTCGGTGGC-AA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
* *
2561252 CCTTCTTCAAAAGCCCACACAAGTTGGTGGCA
1 CCTTC-TCTAAAGCCCACACAAGTCGGTGGCA
2561284 TCTTCTTTTA
Statistics
Matches: 114, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
32 36 0.32
33 78 0.68
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (33 bp):
CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
Found at i:2561239 original size:65 final size:65
Alignment explanation
Indices: 2561121--2561283 Score: 249
Period size: 65 Copynumber: 2.5 Consensus size: 65
2561111 GGCATCTTTC
* **
2561121 ACCCTT-TCTAAAGCCCACACAAGTCGGTGGCAAACCTTCTCTAAAGCCCACACAAGTCGGTGGC
1 ACCCTTCTCTAAAGCCCACACAAGTTGGTGGC-AACCCCCTCTAAAGCCCACACAAGTCGGTGGC
2561185 A
65 A
*
2561186 ACCCTTCTCTAAAGCCCACACTAGTTGGTGGCAACCCCCTCTAAAGCCCACACAAGTCGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTTGGTGGCAACCCCCTCTAAAGCCCACACAAGTCGGTGGCA
*
2561251 A-CCTTCTTCAAAAGCCCACACAAGTTGGTGGCA
1 ACCCTTC-TCTAAAGCCCACACAAGTTGGTGGCA
2561284 TCTTCTTTTA
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
64 5 0.06
65 62 0.69
66 23 0.26
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.19
Consensus pattern (65 bp):
ACCCTTCTCTAAAGCCCACACAAGTTGGTGGCAACCCCCTCTAAAGCCCACACAAGTCGGTGGCA
Found at i:2561401 original size:43 final size:43
Alignment explanation
Indices: 2561338--2561611 Score: 341
Period size: 43 Copynumber: 6.1 Consensus size: 43
2561328 GCACCTTCAT
* *
2561338 CTTTAAGTCCAATGTAGCTGGCTTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
2561381 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
* *
2561428 ATCTTTAAGTCCAATGTAGCAGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
2561473 CTTTAAGTCCAATATTGCTAGCCTTGAATCAGCATATTGGCACC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C
*
2561517 TTCTTCATTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --C-T--TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
2561565 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
2561608 CTTT
1 CTTT
2561612 TCCATCTTTA
Statistics
Matches: 200, Mismatches: 19, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
43 118 0.59
44 1 0.00
45 2 0.01
46 2 0.01
47 2 0.01
48 1 0.00
49 74 0.37
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:2561447 original size:92 final size:92
Alignment explanation
Indices: 2561290--2561664 Score: 615
Period size: 92 Copynumber: 4.0 Consensus size: 92
2561280 GGCATCTTCT
* *
2561290 TTTAAGTCCAATATAGCTGGCCTTGAATCAACATAATGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
*
2561355 CTGGCTTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
*
2561382 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
*
2561447 CAGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* * * *
2561474 TTTAAGTCCAATATTGCTAGCCTTGAATCAGCATATTGGCACCTTCTTCATTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
2561539 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
*
2561566 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAATG
*
2561631 TAGCTGGCCTTGAATCAGCACATTGACATCC
63 TAGCTGGCCTTGAATCAGCACATTGGCA-CC
2561662 TTT
1 TTT
2561665 TTCTCATCTT
Statistics
Matches: 263, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
92 215 0.82
94 2 0.01
95 41 0.16
96 5 0.02
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (92 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCACC
Found at i:2561643 original size:52 final size:53
Alignment explanation
Indices: 2561565--2561718 Score: 186
Period size: 52 Copynumber: 2.9 Consensus size: 53
2561555 ACATTGGCAC
2561565 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * *
2561617 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * * * *
2561672 CTTTAAGCCCAATATCGTTGG-CTGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCT-TGAATCAGCATATTGGCACCTTT
2561719 ATCACTTTTC
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
52 38 0.45
53 5 0.06
54 8 0.09
55 34 0.40
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:2562604 original size:13 final size:13
Alignment explanation
Indices: 2562586--2562642 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
2562576 CATAAAGTGT
2562586 TGTATCGATACAA
1 TGTATCGATACAA
2562599 TGTATCGATACATAA
1 TGTATCGATAC--AA
2562614 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
2562631 TGTATCGATACA
1 TGTATCGATACA
2562643 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2562621 original size:32 final size:32
Alignment explanation
Indices: 2562566--2562663 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
2562556 TTCAACGATT
2562566 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
2562599 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
2562631 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
2562663 T
1 T
2562664 TTAAGCTACT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 51 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:2562623 original size:19 final size:18
Alignment explanation
Indices: 2562564--2562661 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
2562554 ATTTCAACGA
2562564 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
2562583 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
2562599 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
2562615 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
2562631 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
2562647 TTTTGTATCGATACA
1 -TTTGTATCGATACA
2562662 ATTTAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 24 0.36
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:2562722 original size:13 final size:13
Alignment explanation
Indices: 2562704--2562728 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2562694 ATTACTCAAA
2562704 TGTATCGATACAT
1 TGTATCGATACAT
2562717 TGTATCGATACA
1 TGTATCGATACA
2562729 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2562793 original size:52 final size:52
Alignment explanation
Indices: 2562737--2562861 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
2562727 CACTGATCTT
*
2562737 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2562789 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2562841 TGAATCGATACATGCAGGCAA
1 TGTATCGATACATGCAGGCAA
2562862 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2576450 original size:28 final size:28
Alignment explanation
Indices: 2576410--2576597 Score: 220
Period size: 28 Copynumber: 6.6 Consensus size: 28
2576400 CCCTAATGGT
2576410 ACCCTTTTAAAGCCCATAAGTCAGTGGC
1 ACCCTTTTAAAGCCCATAAGTCAGTGGC
2576438 ACCCTTTTAAAGCCCATGAA-TCAGTGGC
1 ACCCTTTTAAAGCCCAT-AAGTCAGTGGC
* *
2576466 ACCC-TTCAAAGCTCATAAGTCAGTGGC
1 ACCCTTTTAAAGCCCATAAGTCAGTGGC
*
2576493 ACCCTTTTAAAACCCATAAGTCAGTGGC
1 ACCCTTTTAAAGCCCATAAGTCAGTGGC
** * *
2576521 A-ATTTTTCAAAGCCCACAAGTTAGTGGC
1 ACCCTTTT-AAAGCCCATAAGTCAGTGGC
* *
2576549 ACCCTTTTCAAAGCCCACAAGTTAGTGGC
1 ACCCTTTT-AAAGCCCATAAGTCAGTGGC
*
2576578 AGCTCTTTTCAAAGCCCATA
1 A-CCCTTTT-AAAGCCCATA
2576598 CAAGTCGGTG
Statistics
Matches: 140, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.01
27 26 0.19
28 68 0.49
29 28 0.20
30 16 0.11
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (28 bp):
ACCCTTTTAAAGCCCATAAGTCAGTGGC
Found at i:2576483 original size:55 final size:56
Alignment explanation
Indices: 2576418--2576597 Score: 211
Period size: 55 Copynumber: 3.2 Consensus size: 56
2576408 GTACCCTTTT
2576418 AAAGCCCATAAGTCAGTGGCACCCTTTTAAAGCCCATGAA-TCAGTGGC-ACCCTTC
1 AAAGCCCATAAGTCAGTGGCACCCTTTTAAAGCCCAT-AAGTCAGTGGCAACCCTTC
* * ***
2576473 AAAGCTCATAAGTCAGTGGCACCCTTTTAAAACCCATAAGTCAGTGGCAATTTTTC
1 AAAGCCCATAAGTCAGTGGCACCCTTTTAAAGCCCATAAGTCAGTGGCAACCCTTC
* * * * * *
2576529 AAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGTTAGTGGCAGCTCTTTTC
1 AAAGCCCATAAGTCAGTGGCACCCTTTT-AAAGCCCATAAGTCAGTGGCAAC-C-CTTC
2576588 AAAGCCCATA
1 AAAGCCCATA
2576598 CAAGTCGGTG
Statistics
Matches: 105, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
54 2 0.02
55 43 0.41
56 29 0.28
57 18 0.17
59 13 0.12
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (56 bp):
AAAGCCCATAAGTCAGTGGCACCCTTTTAAAGCCCATAAGTCAGTGGCAACCCTTC
Found at i:2576549 original size:83 final size:84
Alignment explanation
Indices: 2576410--2576642 Score: 238
Period size: 83 Copynumber: 2.7 Consensus size: 84
2576400 CCCTAATGGT
** * *
2576410 ACCCTTTTAAAGCCCATAAGTCAGTGGCACCCTTTT-AAAGCCCATGAA-TCAGTGGCACCC-TT
1 ACCCTTTTAAAGCCCATAAGTCAGTGGCA-ATTTTTCAAAGCCCA-CAAGTTAGTGGCACCCTTT
* *
2576472 CAAAGCTCATAAGTCAGTGGC
64 CAAAGCCCACAAGTCAGTGGC
*
2576493 ACCCTTTTAAAACCCATAAGTCAGTGGCAATTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTTC
1 ACCCTTTTAAAGCCCATAAGTCAGTGGCAATTTTTCAAAGCCCACAAGTTAGTGGCACCC-TTTC
*
2576558 AAAGCCCACAAGTTAGTGGC
65 AAAGCCCACAAGTCAGTGGC
* * * *
2576578 AGCTCTTTTCAAAGCCCATACAAGTCGGTGGTAACTCTTTTCAAAGTCCACACAAGTTGGTGGCA
1 A-CCCTTTT-AAAGCCCAT--AAGTCAGTGGCAA-T-TTTTCAAAG-CC-CACAAGTTAGTGGCA
2576643 ACTTTTTTCA
Statistics
Matches: 125, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
82 6 0.05
83 47 0.38
85 21 0.17
86 6 0.05
87 8 0.06
89 11 0.09
90 1 0.01
91 9 0.07
92 2 0.02
93 14 0.11
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (84 bp):
ACCCTTTTAAAGCCCATAAGTCAGTGGCAATTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCA
AAGCCCACAAGTCAGTGGC
Found at i:2576652 original size:64 final size:59
Alignment explanation
Indices: 2576414--2576657 Score: 200
Period size: 55 Copynumber: 4.2 Consensus size: 59
2576404 AATGGTACCC
* * * *
2576414 TTTT-AAAGCCCATAAGTCAGTGGCACCCTTTT-AAAGCCCATGAA-TCAGTGGC-AC--
1 TTTTCAAAGCCCACAAGTCAGTGGAACCCTTTTCAAAGCCCA-CAAGTTAGTGGCAACTT
** * * * * * *
2576468 CCTTCAAAGCTCATAAGTCAGTGGCACCCTTTT-AAAACCCATAAGTCAGTGGCAA--T
1 TTTTCAAAGCCCACAAGTCAGTGGAACCCTTTTCAAAGCCCACAAGTTAGTGGCAACTT
* * * *
2576524 TTTTCAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGTTAGTGGCAGCTC
1 TTTTCAAAGCCCACAAGTCAGTGGAACCCTTTTCAAAGCCCACAAGTTAGTGGCAACTT
* * *
2576583 TTTTCAAAGCCCATACAAGTCGGTGGTAACTCTTTTCAAAGTCCACACAAGTTGGTGGCAACTT
1 TTTTCAAAGCCC--ACAAGTCAGTGG-AACCCTTTTCAAAG-CC-CACAAGTTAGTGGCAACTT
2576647 TTTTCAAAGCC
1 TTTTCAAAGCC
2576658 TACACAAATA
Statistics
Matches: 156, Mismatches: 22, Indels: 14
0.81 0.11 0.07
Matches are distributed among these distances:
54 4 0.03
55 42 0.27
56 29 0.19
57 18 0.12
59 12 0.08
61 10 0.06
62 12 0.08
63 2 0.01
64 27 0.17
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (59 bp):
TTTTCAAAGCCCACAAGTCAGTGGAACCCTTTTCAAAGCCCACAAGTTAGTGGCAACTT
Found at i:2576663 original size:32 final size:31
Alignment explanation
Indices: 2576510--2576664 Score: 167
Period size: 32 Copynumber: 5.1 Consensus size: 31
2576500 TAAAACCCAT
*
2576510 AAGTCAGTGGCAA-T-TTTTCAAAGCC-CAC
1 AAGTTAGTGGCAACTCTTTTCAAAGCCACAC
*
2576538 AAGTTAGTGGC-ACCCTTTTCAAAGCC-CAC
1 AAGTTAGTGGCAACTCTTTTCAAAGCCACAC
* *
2576567 AAGTTAGTGGCAGCTCTTTTCAAAGCCCATAC
1 AAGTTAGTGGCAACTCTTTTCAAAG-CCACAC
** *
2576599 AAGTCGGTGGTAACTCTTTTCAAAGTCCACAC
1 AAGTTAGTGGCAACTCTTTTCAAAG-CCACAC
* *
2576631 AAGTTGGTGGCAACTTTTTTCAAAGCCTACAC
1 AAGTTAGTGGCAACTCTTTTCAAAGCC-ACAC
2576663 AA
1 AA
2576665 ATAGGTGCAC
Statistics
Matches: 107, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
27 1 0.01
28 10 0.09
29 25 0.23
30 11 0.10
31 4 0.04
32 56 0.52
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (31 bp):
AAGTTAGTGGCAACTCTTTTCAAAGCCACAC
Found at i:2576774 original size:28 final size:28
Alignment explanation
Indices: 2576718--2577028 Score: 252
Period size: 28 Copynumber: 10.6 Consensus size: 28
2576708 GGTGGCAACT
*
2576718 CTTTTCAAAGCCCACACAAATCGATGGCAC
1 CTTTTCAAAG-CC-CACAAGTCGATGGCAC
* * *
2576748 CCTTTCAAAGCCCACAAGTTGACGGCAC
1 CTTTTCAAAGCCCACAAGTCGATGGCAC
* * *
2576776 CTTCTCAAAGCCCACAAGAC-AGTGGCAT
1 CTTTTCAAAGCCCACAAGTCGA-TGGCAC
* *
2576804 CTTTTCAAAGCCCATAAAT-GAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCGA-TGGCA-C
* *
2576833 ATTTTCAAAGCCCACAAGTCAATGGCAC
1 CTTTTCAAAGCCCACAAGTCGATGGCAC
*
2576861 CTTTTCAAAGCCCACAAGAC-AGTGGCATC
1 CTTTTCAAAGCCCACAAGTCGA-TGGCA-C
* *
2576890 CTTTTAAAAGCCCACAAGTCGGTGGCAC
1 CTTTTCAAAGCCCACAAGTCGATGGCAC
* *
2576918 CCTTTCAAAGCCCACACAAGTCGGTGGCAAC
1 CTTTTCAAAG-CC-CACAAGTCGATGGC-AC
*
2576949 TCTTTTTTCAAAGCCTACAAGTC-AGTGGCAC
1 -C--TTTTCAAAGCCCACAAGTCGA-TGGCAC
* *
2576980 CCTTTCAAAGCCCACACAAGTCGGTGGCAAC
1 CTTTTCAAAG-CC-CACAAGTCGATGGC-AC
*
2577011 TTTTTACAAAGCCCACAA
1 CTTTT-CAAAGCCCACAA
2577029 AAGTTAGTGG
Statistics
Matches: 228, Mismatches: 34, Indels: 38
0.76 0.11 0.13
Matches are distributed among these distances:
27 2 0.01
28 96 0.42
29 51 0.22
30 41 0.18
31 11 0.05
32 17 0.07
33 2 0.01
34 8 0.04
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.22
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCGATGGCAC
Found at i:2576859 original size:57 final size:57
Alignment explanation
Indices: 2576709--2577042 Score: 284
Period size: 57 Copynumber: 5.6 Consensus size: 57
2576699 ACCTTTCATG
* * *
2576709 GTGGCAACTCTTTTCAAAGCCCACACAAATC-GATGGCACCCTTTCAAAGCCCACAAGTTGA
1 GTGGCATC-CTTTTCAAAG-CC-CACAAGTCAG-TGGCACCCTTTCAAAGCCCACAA-ATGA
* * * * * *
2576770 -CGGCA-CCTTCTCAAAGCCCACAAGACAGTGGCATCTTTTCAAAGCCCATAAATGA
1 GTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATGA
* * * *
2576825 GTGGCATCATTTTCAAAGCCCACAAGTCAATGGCACCTTTTCAAAGCCCACAAGA-CA
1 GTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAA-ATGA
* *
2576882 GTGGCATCCTTTTAAAAGCCCACAAGTCGGTGGCACCCTTTCAAAGCCCACACAAGTCG-
1 GTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACA-AA-T-GA
* *
2576941 GTGGCAACTCTTTTTTCAAAGCCTACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCG-
1 GTGGC-A-TC-CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACA-AA-T-GA
* * *
2577003 GTGGCAACTTTTTACAAAGCCCACAAAAGTTAGTGGCACC
1 GTGGCATCCTTTT-CAAAGCCCAC--AAGTCAGTGGCACC
2577043 TTTTTTTAAA
Statistics
Matches: 230, Mismatches: 29, Indels: 27
0.80 0.10 0.09
Matches are distributed among these distances:
55 3 0.01
56 30 0.13
57 92 0.40
58 11 0.05
59 11 0.05
60 15 0.07
61 3 0.01
62 65 0.28
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.22
Consensus pattern (57 bp):
GTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATGA
Found at i:2576861 original size:85 final size:84
Alignment explanation
Indices: 2576717--2577028 Score: 320
Period size: 85 Copynumber: 3.5 Consensus size: 84
2576707 TGGTGGCAAC
* ** * * *
2576717 TCTTTTCAAAGCCCACACAAATCGATGGCACCCTTTCAAAGCCCACAAGTTGACGGCACCTTCTC
1 TCTTTTCAAAG-CC-CACAAATCGGTGGCACATTTTCAAAGCCCACAAGTCGATGGCACCTTTTC
2576782 AAAGCCCACAAGACAGTGGCA
64 AAAGCCCACAAGACAGTGGCA
* *
2576803 TCTTTTCAAAGCCCATAAAT-GAGTGGCATCATTTTCAAAGCCCACAAGTCAATGGCACCTTTTC
1 TCTTTTCAAAGCCCACAAATCG-GTGGCA-CATTTTCAAAGCCCACAAGTCGATGGCACCTTTTC
2576867 AAAGCCCACAAGACAGTGGCA
64 AAAGCCCACAAGACAGTGGCA
* * ** *
2576888 TCCTTTTAAAAGCCCACAAGTCGGTGGCACCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTT
1 T-CTTTTCAAAGCCCACAAATCGGTGGCACATTTTCAAAG-CC-CACAAGTCGATGGC-AC-C--
* *
2576953 TTTTCAAAGCCTACAAGTCAGTGGCA
59 TTTTCAAAGCCCACAAGACAGTGGCA
* * *
2576979 CCCTTTCAAAGCCCACACAAGTCGGTGGCAACTTTTTACAAAGCCCACAA
1 TCTTTTCAAAGCCCACA-AA-TCGGTGGC-ACATTTT-CAAAGCCCACAA
2577029 AAGTTAGTGG
Statistics
Matches: 189, Mismatches: 23, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
83 1 0.01
84 11 0.06
85 62 0.33
86 35 0.19
87 13 0.07
88 2 0.01
89 1 0.01
90 14 0.07
91 25 0.13
92 13 0.07
93 7 0.04
94 5 0.03
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.22
Consensus pattern (84 bp):
TCTTTTCAAAGCCCACAAATCGGTGGCACATTTTCAAAGCCCACAAGTCGATGGCACCTTTTCAA
AGCCCACAAGACAGTGGCA
Found at i:2577182 original size:45 final size:48
Alignment explanation
Indices: 2577109--2577219 Score: 120
Period size: 45 Copynumber: 2.4 Consensus size: 48
2577099 ATCTTAAAGT
* * * *
2577109 CCAATATCGTTGGCATTGAATCAACATATTAG-CAC-CTTT-ATTAGC
1 CCAATGTCGCTGGCCTTAAATCAACATATTAGCCACTCTTTCATTAGC
* * * *
2577154 CCAATGTCGCTGGCCTTAAATCAGCATATTGGTCCACTTTTTCCTTAGC
1 CCAATGTCGCTGGCCTTAAATCAACATATTAG-CCACTCTTTCATTAGC
2577203 CCAATGTCGCTGGCCTT
1 CCAATGTCGCTGGCCTT
2577220 GAATTGGCAC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
45 26 0.48
47 3 0.06
48 3 0.06
49 22 0.41
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.33
Consensus pattern (48 bp):
CCAATGTCGCTGGCCTTAAATCAACATATTAGCCACTCTTTCATTAGC
Found at i:2580944 original size:21 final size:23
Alignment explanation
Indices: 2580920--2580973 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
2580910 AAAAGGCTGT
*
2580920 TGTCGACCAGGGA-T-AGTTTTA
1 TGTCGACCAGGAATTGAGTTTTA
**
2580941 TGTCGATTAGGAATTGAGTTTTA
1 TGTCGACCAGGAATTGAGTTTTA
*
2580964 TGCCGACCAG
1 TGTCGACCAG
2580974 AAACCGATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 10 0.40
22 1 0.04
23 14 0.56
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (23 bp):
TGTCGACCAGGAATTGAGTTTTA
Found at i:2585252 original size:19 final size:18
Alignment explanation
Indices: 2585228--2585290 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
2585218 AAACAGTAAA
2585228 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
2585247 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
*
2585260 TGTATCAATACATAAGTTT
1 TGTATCGATACATAAG-TT
2585279 TGTATCGATACA
1 TGTATCGATACA
2585291 ATGTATCGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
15 2 0.06
17 2 0.06
19 22 0.61
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:2585271 original size:32 final size:32
Alignment explanation
Indices: 2585226--2585297 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
2585216 ACAAACAGTA
*
2585226 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCAATACATAAGTGTTGTATCGATAC
*
2585258 AATGTATCAATACATAAGTTTTGTATCGATAC
1 AATGTATCAATACATAAGTGTTGTATCGATAC
2585290 AATGTATC
1 AATGTATC
2585298 GCTATGAAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (32 bp):
AATGTATCAATACATAAGTGTTGTATCGATAC
Found at i:2585341 original size:21 final size:21
Alignment explanation
Indices: 2585315--2585356 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2585305 AGCTACTGCC
2585315 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
*
2585336 AAGGAAATGTATTGATACATT
1 AAGGAAATGTATCGATACATT
2585357 GTATCGATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:2585365 original size:13 final size:13
Alignment explanation
Indices: 2585343--2585404 Score: 62
Period size: 13 Copynumber: 5.2 Consensus size: 13
2585333 ATTAAGGAAA
*
2585343 TGTATTGATACAT
1 TGTATCGATACAT
2585356 TGTATCGATACA-
1 TGTATCGATACAT
**
2585368 T-TAAGGA-A-A-
1 TGTATCGATACAT
2585377 TGTATCGATACAT
1 TGTATCGATACAT
2585390 TGTATCGATACAT
1 TGTATCGATACAT
2585403 TG
1 TG
2585405 ATCTTTCGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
9 2 0.05
10 5 0.12
11 5 0.12
12 2 0.05
13 26 0.65
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2585365 original size:34 final size:34
Alignment explanation
Indices: 2585322--2585403 Score: 155
Period size: 34 Copynumber: 2.4 Consensus size: 34
2585312 GCCAAGGAAA
*
2585322 TGTATCGATACATTAAGGAAATGTATTGATACAT
1 TGTATCGATACATTAAGGAAATGTATCGATACAT
2585356 TGTATCGATACATTAAGGAAATGTATCGATACAT
1 TGTATCGATACATTAAGGAAATGTATCGATACAT
2585390 TGTATCGATACATT
1 TGTATCGATACATT
2585404 GATCTTTCGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (34 bp):
TGTATCGATACATTAAGGAAATGTATCGATACAT
Found at i:2587827 original size:51 final size:51
Alignment explanation
Indices: 2587759--2587940 Score: 233
Period size: 51 Copynumber: 3.6 Consensus size: 51
2587749 TTAATTTTCT
* * * *
2587759 CAATTTTTCATAATCGGGGATACTCCAAAC-CCGGTTTTATTTTTAAAACAC
1 CAATTTTCCACAATCGGGGATACTCC-AACTCCGATTTTATTTCTAAAACAC
*
2587810 TAATTTTCCACAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACAC
1 CAATTTTCCACAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACAC
* * *
2587861 CCATTTTCCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
1 CAATTTTCCACAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACAC
* * *
2587912 CGACTTTT-CACAATCAGGGATTCTCCAAC
1 C-AATTTTCCACAATCGGGGATACTCCAAC
2587941 CCCGTTATTT
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
50 3 0.03
51 108 0.94
52 4 0.03
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.32
Consensus pattern (51 bp):
CAATTTTCCACAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACAC
Found at i:2588011 original size:79 final size:79
Alignment explanation
Indices: 2587876--2588087 Score: 302
Period size: 79 Copynumber: 2.7 Consensus size: 79
2587866 TTCCATAATC
* * * * *
2587876 GGGGATACTCCAA-CTCCGATTTTATTTCCAAAACACCGACTTTTCACAATCAGGGATTCTCCAA
1 GGGGATACTCCAACCT-CGGTTTTATTTCTAAAACACCAATTTTTCACAATCAGGGATACTCCAA
2587940 CCCCGTTATTTTCGA
65 CCCCGTTATTTTCGA
* * *
2587955 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTTTTCACAATCAGGGATACTCCAAC
2588020 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
* * *
2588034 GGGGATACTCGAACCTCGGTTTTATTTCTAAAACACCAATTCTCCACAAT-AGGG
1 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTTTTCACAATCAGGG
2588088 GATATTTCAA
Statistics
Matches: 118, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
78 3 0.03
79 113 0.96
80 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (79 bp):
GGGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTTTTCACAATCAGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:2588195 original size:28 final size:28
Alignment explanation
Indices: 2588138--2588208 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
2588128 TCACAATCGA
* * **
2588138 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
2588166 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
2588194 GGATACTCAAACCCC
1 GGATACTCCAACCCC
2588209 TGCTTTATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:2588365 original size:237 final size:236
Alignment explanation
Indices: 2587928--2588417 Score: 551
Period size: 237 Copynumber: 2.1 Consensus size: 236
2587918 TTCACAATCA
* * * * * * *
2587928 GGGATTCTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTCGGTTTTATTTCTAAAACATCA
1 GGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCAAACCCCGGCTTTATTTCCAAAACATCA
* * * * *
2587993 ATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCGAACCTCGGTTTTA
66 ATTTCTCATAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCTCGCTTTAA
* * * **
2588058 TTTCTAAAACACCAATTCTCCACAATAGGGGATATTTCAACTTTGATTTTATTTTCAAAACACTA
131 TTTCTAAAACACCAATTCTCCACAATAGGGGACACTTCAACCTTGACCTTATTTTCAAAACACTA
* *
2588123 ATTTTTCACAATCGAGGATACTCCAACCTCGTTA-TTTCATCG
196 ATTTTTCACAATCGAGGATACTACAACCCCGTTATTTTCA--G
* * **
2588165 GGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCAAACCCCTGCTTTATTTCCAAAATATTG
1 GGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCAAACCCCGGCTTTATTTCCAAAACATCA
* *
2588230 ATTTCTCATAATTGGGGATACTCCAACCCCATTATTTTC-ACGGGGATACTCCAATCTCGACTTT
66 ATTTCTCATAATCGGGGATACTCCAACCCCATTATTTTCGA-GGGGATACTCCAACCTCG-CTTT
* * * * * * * *
2588294 AATTT-TGAAACATCTATTTTCTATAATCGGGGACACTTCAACCCTTG-CCTTA-TTTCTAAATC
129 AATTTCTAAAACACCAATTCTCCACAATAGGGGACACTTCAA-CCTTGACCTTATTTTC-AAAAC
* *
2588356 A-TCAATTTTTCACAATCGGGGATTCTACAACCCCGTTATTTTCGAG
192 ACT-AATTTTTCACAATCGAGGATACTACAACCCCGTTATTTTC-AG
2588402 GGGATACTCCAACCCC
1 GGGATACTCCAACCCC
2588418 ATTATTATCT
Statistics
Matches: 211, Mismatches: 35, Indels: 14
0.81 0.13 0.05
Matches are distributed among these distances:
236 6 0.03
237 189 0.90
238 15 0.07
239 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (236 bp):
GGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCAAACCCCGGCTTTATTTCCAAAACATCA
ATTTCTCATAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCTCGCTTTAA
TTTCTAAAACACCAATTCTCCACAATAGGGGACACTTCAACCTTGACCTTATTTTCAAAACACTA
ATTTTTCACAATCGAGGATACTACAACCCCGTTATTTTCAG
Found at i:2598479 original size:2 final size:2
Alignment explanation
Indices: 2598472--2598519 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
2598462 AGGCATCTAC
* * * *
2598472 AT AT AT AT AT AT AT AT AT TT AT AT AG AT AT AT AC AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2598514 -T AT AT A
1 AT AT AT A
2598520 CATGTACATG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2600420 original size:16 final size:16
Alignment explanation
Indices: 2600399--2600433 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2600389 GTACATGTCG
2600399 ATATAAAATTAAAACA
1 ATATAAAATTAAAACA
2600415 ATATAAAATTAAAACA
1 ATATAAAATTAAAACA
2600431 ATA
1 ATA
2600434 CAGTATTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
ATATAAAATTAAAACA
Found at i:2602227 original size:19 final size:19
Alignment explanation
Indices: 2602203--2602246 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2602193 TTTTATTTTT
2602203 ATAATTAAATTAAATAAA-A
1 ATAATTAAATT-AATAAATA
**
2602222 ATAATTTTATTAATAAATA
1 ATAATTAAATTAATAAATA
2602241 ATAATT
1 ATAATT
2602247 TAAGATAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAATTAAATTAATAAATA
Found at i:2603256 original size:20 final size:20
Alignment explanation
Indices: 2603231--2603268 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2603221 TAGATAATAA
*
2603231 TAAATAAAATTATAATTTTT
1 TAAATAAAATTAAAATTTTT
2603251 TAAATAAAATTAAAATTT
1 TAAATAAAATTAAAATTT
2603269 AATAAGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATAAAATTAAAATTTTT
Found at i:2603316 original size:53 final size:52
Alignment explanation
Indices: 2603203--2603304 Score: 129
Period size: 53 Copynumber: 1.9 Consensus size: 52
2603193 AGATTCTTTG
*
2603203 AAAATTAAAATTAAGTAGTAGATAATAATAAATAAAATTATAATTTTTTAAAT
1 AAAATTAAAATTAAGTAGTAGATAATAATAAAT-AAATTATAATTATTTAAAT
*
2603256 AAAATTAAAATTTAA-TAAGTA-ATAATAATAAAT-AATTCATTATTATTTA
1 AAAATTAAAA-TTAAGT-AGTAGATAATAATAAATAAATT-ATAATTATTTA
2603305 TATTTAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
51 4 0.09
52 9 0.20
53 23 0.52
54 8 0.18
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (52 bp):
AAAATTAAAATTAAGTAGTAGATAATAATAAATAAATTATAATTATTTAAAT
Found at i:2603915 original size:13 final size:13
Alignment explanation
Indices: 2603897--2603922 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2603887 AAAATTAATG
2603897 TAAAATAAAAAAA
1 TAAAATAAAAAAA
2603910 TAAAATAAAAAAA
1 TAAAATAAAAAAA
2603923 GAAAGAGAAG
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
TAAAATAAAAAAA
Found at i:2604272 original size:21 final size:20
Alignment explanation
Indices: 2604248--2604286 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2604238 ATTAAAAATT
2604248 TAATTAATTTAATTTTTGATA
1 TAATT-ATTTAATTTTTGATA
* *
2604269 TAATTTTTTATTTTTTGA
1 TAATTATTTAATTTTTGA
2604287 ATTAAATCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (20 bp):
TAATTATTTAATTTTTGATA
Found at i:2615913 original size:1 final size:1
Alignment explanation
Indices: 2615903--2615996 Score: 80
Period size: 1 Copynumber: 94.0 Consensus size: 1
2615893 TGGCAATTGG
* * * ** * * * **
2615903 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAAAACAAAACAAAAAAAAGGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
2615968 AAAGAAAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2615997 GTGAAGATTT
Statistics
Matches: 73, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.87, C:0.05, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:2615952 original size:34 final size:34
Alignment explanation
Indices: 2615902--2615997 Score: 160
Period size: 34 Copynumber: 2.8 Consensus size: 34
2615892 ATGGCAATTG
2615902 GAAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAA
1 GAAAAA-AAAAAAACAAAACAAAAAAAAGGAAAAA
2615937 GAAAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
1 GAAAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
2615971 GAAAAAAAAAAAA-AACAA-AAAAAAAAG
1 GAAAAAAAAAAAACAA-AACAAAAAAAAG
2615998 TGAAGATTTG
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
33 11 0.18
34 43 0.72
35 6 0.10
ACGTcount: A:0.85, C:0.05, G:0.09, T:0.00
Consensus pattern (34 bp):
GAAAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
Found at i:2619654 original size:24 final size:21
Alignment explanation
Indices: 2619598--2619656 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 21
2619588 ATGATAAATA
**
2619598 TATTTTATTATCTATAAGATT
1 TATTTTATTATAAATAAGATT
2619619 TATTTTATTTATAAATAAGAAATT
1 TATTTTA-TTATAAATAAG--ATT
2619643 TAATTTTATTATAA
1 T-ATTTTATTATAA
2619657 TTTATTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 7 0.22
22 9 0.28
24 10 0.31
25 6 0.19
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTTATTATAAATAAGATT
Found at i:2619661 original size:31 final size:30
Alignment explanation
Indices: 2619617--2619686 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
2619607 ATCTATAAGA
* *
2619617 TTTATTTTATTTATAAATAAGAAATTTAAT
1 TTTATTTAATTTATAAATAAAAAATTTAAT
*
2619647 TTTATTATAATTTATTAATAAAAAATTTAAT
1 TTTATT-TAATTTATAAATAAAAAATTTAAT
*
2619678 TTAATTTAA
1 TTTATTTAA
2619687 GTAAAAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 9 0.26
31 26 0.74
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (30 bp):
TTTATTTAATTTATAAATAAAAAATTTAAT
Found at i:2619675 original size:25 final size:23
Alignment explanation
Indices: 2619647--2619701 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
2619637 GAAATTTAAT
2619647 TTTATTATAATTTATTAATAAAAAA
1 TTTATTATAATTTA--AATAAAAAA
* *
2619672 TTTAATT-TAATTTAAGTAAAAAT
1 TTT-ATTATAATTTAAATAAAAAA
2619695 TTTATTA
1 TTTATTA
2619702 AATAGATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 3 0.12
23 10 0.38
25 10 0.38
26 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTATTATAATTTAAATAAAAAA
Found at i:2620308 original size:2 final size:2
Alignment explanation
Indices: 2620301--2620335 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2620291 CTCCGTACGT
*
2620301 TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2620336 GAAATAATCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Done.