Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 11 of 295
Found at i:3342286 original size:17 final size:16
Alignment explanation
Indices: 3342256--3342302 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
3342246 TCTCTTTTTT
*
3342256 AAAAAAAATTAAAAGA
1 AAAAAAAATAAAAAGA
* *
3342272 AGAAGAAAATAAAAATA
1 A-AAAAAAATAAAAAGA
3342289 AAAAAAAATAAAAA
1 AAAAAAAATAAAAA
3342303 AATTCTTCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (16 bp):
AAAAAAAATAAAAAGA
Found at i:3342301 original size:9 final size:10
Alignment explanation
Indices: 3342255--3342304 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
3342245 ATCTCTTTTT
*
3342255 TAAAAAAAAT
1 TAAAAAAAAA
*
3342265 TAAAAGAAGAA
1 TAAAA-AAAAA
*
3342276 GAAAATAAAAA
1 TAAAA-AAAAA
3342287 TAAAAAAAAA
1 TAAAAAAAAA
3342297 TAAAAAAA
1 TAAAAAAA
3342305 TTCTTCTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
10 18 0.55
11 15 0.45
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:3345471 original size:10 final size:10
Alignment explanation
Indices: 3345456--3345483 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3345446 AGGATTTAAT
3345456 TTTAATTATC
1 TTTAATTATC
3345466 TTTAATTATC
1 TTTAATTATC
3345476 TTTAATTA
1 TTTAATTA
3345484 AATGTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTAATTATC
Found at i:3350725 original size:12 final size:13
Alignment explanation
Indices: 3350708--3350744 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
3350698 CTTCCTTCTA
3350708 GCCTCAT-CCTTT
1 GCCTCATACCTTT
3350720 GCCTCATACC-TT
1 GCCTCATACCTTT
3350732 GCCTCATACCTTT
1 GCCTCATACCTTT
3350745 CAATGACGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.14, C:0.41, G:0.08, T:0.38
Consensus pattern (13 bp):
GCCTCATACCTTT
Found at i:3357017 original size:31 final size:31
Alignment explanation
Indices: 3356982--3357042 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
3356972 CATAAGTGGA
*
3356982 GATAGATAGAGACGATGGTCTTGACATAGTT
1 GATAGATAGAGACAATGGTCTTGACATAGTT
3357013 GATAGATAGAGACAATGGTCTTGACATAGT
1 GATAGATAGAGACAATGGTCTTGACATAGT
3357043 GTTCGTTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (31 bp):
GATAGATAGAGACAATGGTCTTGACATAGTT
Found at i:3362136 original size:12 final size:12
Alignment explanation
Indices: 3362119--3362151 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3362109 CGGCCCACCC
3362119 ATATTAATTTTT
1 ATATTAATTTTT
3362131 ATATT-ATTTTT
1 ATATTAATTTTT
3362142 ATA-TAATTTT
1 ATATTAATTTT
3362152 AAAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:3362176 original size:18 final size:18
Alignment explanation
Indices: 3362153--3362192 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3362143 TATAATTTTA
*
3362153 AAAAATA-TATAATACATC
1 AAAAATACTA-AAAACATC
3362171 AAAAATACTAAAAACATC
1 AAAAATACTAAAAACATC
3362189 AAAA
1 AAAA
3362193 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATACTAAAAACATC
Found at i:3365170 original size:22 final size:22
Alignment explanation
Indices: 3365145--3365187 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3365135 TATCGAAATA
3365145 ATAACAACAAAATAATAGTAAT
1 ATAACAACAAAATAATAGTAAT
* * *
3365167 ATAATAGCAAAATGATAGTAA
1 ATAACAACAAAATAATAGTAA
3365188 AACAACAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.23
Consensus pattern (22 bp):
ATAACAACAAAATAATAGTAAT
Found at i:3371289 original size:23 final size:24
Alignment explanation
Indices: 3371258--3371310 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
3371248 TAATCAAGAA
* *
3371258 CTAATTGAAAGTTTA-TATAAAATG
1 CTAAATGAAACTTTAGT-TAAAATG
3371282 C-AAATGAAACTTTAGTTAAAATG
1 CTAAATGAAACTTTAGTTAAAATG
3371305 CTAAAT
1 CTAAAT
3371311 TTGAAGTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (24 bp):
CTAAATGAAACTTTAGTTAAAATG
Found at i:3378599 original size:21 final size:20
Alignment explanation
Indices: 3378544--3378600 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
3378534 GAAAATAATT
* *
3378544 AAAATTAATAAATAATTATAG
1 AAAATT-ATAAAAAAGTATAG
* *
3378565 AAATTTACATAAAAAGTATAG
1 AAAATTATA-AAAAAGTATAG
3378586 AAAATTATTAAAAAA
1 AAAATTA-TAAAAAA
3378601 CCAGAAAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
20 2 0.07
21 25 0.89
22 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (20 bp):
AAAATTATAAAAAAGTATAG
Found at i:3378627 original size:19 final size:20
Alignment explanation
Indices: 3378605--3378662 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
3378595 AAAAAACCAG
3378605 AAAAGTATAAA-AATTGTAA
1 AAAAGTATAAAGAATTGTAA
* *
3378624 AAAAATATAAAGAAAT-TAA
1 AAAAGTATAAAGAATTGTAA
* *
3378643 AAATG-ATAAATAATTGTAA
1 AAAAGTATAAAGAATTGTAA
3378662 A
1 A
3378663 TAATTAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
18 8 0.26
19 20 0.65
20 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (20 bp):
AAAAGTATAAAGAATTGTAA
Found at i:3379667 original size:3 final size:3
Alignment explanation
Indices: 3379659--3379694 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3379649 TTTCATACTT
3379659 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3379695 CTGCATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3380030 original size:18 final size:18
Alignment explanation
Indices: 3380007--3380050 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
3379997 CAATAATTTT
3380007 TTTTAATATTTAAAAATA
1 TTTTAATATTTAAAAATA
* *
3380025 TTTTAATATTTTATAATA
1 TTTTAATATTTAAAAATA
3380043 TTTTAATA
1 TTTTAATA
3380051 ATTTTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAATATTTAAAAATA
Found at i:3380041 original size:10 final size:10
Alignment explanation
Indices: 3379999--3380059 Score: 56
Period size: 10 Copynumber: 6.3 Consensus size: 10
3379989 CACGTTAGCA
*
3379999 ATAATTTTTT
1 ATAATATTTT
* *
3380009 TTAATATTTA
1 ATAATATTTT
*
3380019 AAAATA-TTT
1 ATAATATTTT
3380028 -TAATATTTT
1 ATAATATTTT
3380037 ATAATATTTT
1 ATAATATTTT
3380047 AATAAT-TTTT
1 -ATAATATTTT
3380057 ATA
1 ATA
3380060 TAGTTTTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
8 4 0.10
9 8 0.20
10 24 0.59
11 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATAATATTTT
Found at i:3380066 original size:11 final size:10
Alignment explanation
Indices: 3379998--3380083 Score: 54
Period size: 10 Copynumber: 8.7 Consensus size: 10
3379988 TCACGTTAGC
3379998 AATAATTTTT
1 AATAATTTTT
** *
3380008 TTTAATATTT
1 AATAATTTTT
*
3380018 AAAAATATTTT
1 AATAAT-TTTT
3380029 AAT-A-TTTT
1 AATAATTTTT
3380037 -ATAATATTTT
1 AATAAT-TTTT
3380047 AATAATTTTT
1 AATAATTTTT
*
3380057 ATATAGTTTTT
1 A-ATAATTTTT
*
3380068 TA-AATTTTT
1 AATAATTTTT
*
3380077 AAAAATT
1 AATAATT
3380084 AATTTATTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
7 2 0.04
8 5 0.09
9 7 0.12
10 25 0.44
11 18 0.32
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (10 bp):
AATAATTTTT
Found at i:3383847 original size:22 final size:22
Alignment explanation
Indices: 3383819--3383871 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
3383809 ATATGGTAGC
* *
3383819 AAAACAAAAATATAACAGCAGT
1 AAAACAAAAACATAACAGCAGG
*
3383841 AAAACAACAACATAACAGCAGG
1 AAAACAAAAACATAACAGCAGG
3383863 AAAA-AAAAA
1 AAAACAAAAA
3383872 GTCATGTGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.68, C:0.15, G:0.09, T:0.08
Consensus pattern (22 bp):
AAAACAAAAACATAACAGCAGG
Found at i:3387282 original size:179 final size:179
Alignment explanation
Indices: 3386982--3387341 Score: 639
Period size: 179 Copynumber: 2.0 Consensus size: 179
3386972 TCAAAGCATC
3386982 AATCATTAGCTTTGCATCTTCAAAACCTTTTTCCTAAAGGAAGAATTAAATGCACAAGGACATAA
1 AATCATTAGCTTTGCATCTTCAAAACCTTTTTCCTAAAGGAAGAATTAAATGCACAAGGACATAA
*
3387047 ACTTCAAAAGAGATTCATCATTAAACATTAAATGCTTCCCTAGATAATGGTGTAGAAATGCAGAA
66 ACTTCAAAAGAGATTCATCATTAAACATTAAATGCTTCCCTAGATAATGATGTAGAAATGCAGAA
* * *
3387112 TGAACGGAACAAATTCAAAATCAAACCTATATCTATTGTGCAGAGACTA
131 TGAACGGAACAAATTCAAAATCAAACCTATACCTATTATGAAGAGACTA
*
3387161 AATCATTAGCTTTGCATCTTCAAAACGTTTTTCCTAAAGGAAGAATTAAATGCACAAGGACATAA
1 AATCATTAGCTTTGCATCTTCAAAACCTTTTTCCTAAAGGAAGAATTAAATGCACAAGGACATAA
* *
3387226 ACTTCAAAAGAGATTCATCATTAAACATTAGATGCTTCCCTAGGTAATGATGTAGAAATGCAGAA
66 ACTTCAAAAGAGATTCATCATTAAACATTAAATGCTTCCCTAGATAATGATGTAGAAATGCAGAA
* *
3387291 TGAACGGCACAAATTCAAGATCAAACCTATACCTATTATGAAGAGACTA
131 TGAACGGAACAAATTCAAAATCAAACCTATACCTATTATGAAGAGACTA
3387340 AA
1 AA
3387342 GCCAGTCTAG
Statistics
Matches: 172, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
179 172 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.27
Consensus pattern (179 bp):
AATCATTAGCTTTGCATCTTCAAAACCTTTTTCCTAAAGGAAGAATTAAATGCACAAGGACATAA
ACTTCAAAAGAGATTCATCATTAAACATTAAATGCTTCCCTAGATAATGATGTAGAAATGCAGAA
TGAACGGAACAAATTCAAAATCAAACCTATACCTATTATGAAGAGACTA
Found at i:3388417 original size:18 final size:18
Alignment explanation
Indices: 3388394--3388437 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3388384 GATATTAGCA
3388394 GATGATCAAAA-CTATGGT
1 GATGATCAAAATC-ATGGT
**
3388412 GATGATCATCATCATGGT
1 GATGATCAAAATCATGGT
3388430 GATGATCA
1 GATGATCA
3388438 TCATGGAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (18 bp):
GATGATCAAAATCATGGT
Found at i:3388432 original size:15 final size:15
Alignment explanation
Indices: 3388414--3388443 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3388404 ACTATGGTGA
3388414 TGATCATCATCATGG
1 TGATCATCATCATGG
*
3388429 TGATGATCATCATGG
1 TGATCATCATCATGG
3388444 AACAGAGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (15 bp):
TGATCATCATCATGG
Found at i:3388438 original size:18 final size:18
Alignment explanation
Indices: 3388407--3388441 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3388397 GATCAAAACT
3388407 ATGGTGATGATCATCATC
1 ATGGTGATGATCATCATC
3388425 ATGGTGATGATCATCAT
1 ATGGTGATGATCATCAT
3388442 GGAACAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (18 bp):
ATGGTGATGATCATCATC
Found at i:3391294 original size:86 final size:86
Alignment explanation
Indices: 3391184--3391355 Score: 206
Period size: 86 Copynumber: 2.0 Consensus size: 86
3391174 ATGTACCGTA
* * * * *
3391184 TGAATCTTTCCCGTTAAAATGCCAG-AAATCATGGGTAGGGAGAGGAGGAGGT-TAAGAAGGTAA
1 TGAATCTTTCCCGTGAAAATGCCAGAAAAT-ATGGGTAGCGACAGGA-GAAGTATAAGAAGGGAA
* *
3391247 TGTATGTATGTGTATATATATAT
64 TGCACGTATGTGTATATATATAT
* *
3391270 TGAAT-TTCTCCCGTGAAAATGCCAGAAAATGTGGGTATCGACAGGAGAAGTATAAGAAGGGAAT
1 TGAATCTT-TCCCGTGAAAATGCCAGAAAATATGGGTAGCGACAGGAGAAGTATAAGAAGGGAAT
*
3391334 GCACGTGTGTGTATATATATAT
65 GCACGTATGTGTATATATATAT
3391356 AATTTGGCCG
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
85 6 0.08
86 63 0.86
87 4 0.05
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.28
Consensus pattern (86 bp):
TGAATCTTTCCCGTGAAAATGCCAGAAAATATGGGTAGCGACAGGAGAAGTATAAGAAGGGAATG
CACGTATGTGTATATATATAT
Found at i:3391938 original size:31 final size:32
Alignment explanation
Indices: 3391877--3391939 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
3391867 TCAATTAATC
* *
3391877 GACTCTTTTTCAAAAGGTTGAAGGTCAAATTT
1 GACTCTTTTTCAAAAAGTTAAAGGTCAAATTT
*
3391909 GACTCTTTTT-AAAAAGTTAAAGGTTAAATTT
1 GACTCTTTTTCAAAAAGTTAAAGGTCAAATTT
3391940 AATTTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.40
Consensus pattern (32 bp):
GACTCTTTTTCAAAAAGTTAAAGGTCAAATTT
Found at i:3396228 original size:294 final size:286
Alignment explanation
Indices: 3395706--3396283 Score: 847
Period size: 294 Copynumber: 2.0 Consensus size: 286
3395696 TGTTTTAAGC
**
3395706 CAAGAATAACTAGTATTTAATAGGAGAAAATATAAGAATCCATAAAGCTATTTAAAAAAATGAAG
1 CAAGAATAACTAGTATTTAATAGGAGAAAATATAAGAATCCATAAAGCTATCGAAAAAAATGAA-
** **
3395771 CAAGCCATCTGCTAGAATATTCCTTTGTGTTTGACCACATTGATGGACTGTCAAAAGCACTTTGT
65 CAAGCCATCTGCTAGAATATTCCTCGGTGCGTGACCACATTGATGGACTGTCAAAAGCACTTTGT
*
3395836 ATGTCAAGGACCACACTGGGTAATCAAATTCTTAGGTGGTAACTTCATAGTGTGTAAAACTCATT
130 ATGTCAAGGACCACACTGAGTAATCAAATTCTTAGGTGGTAACTTCATAGTGTGTAAAACTCATT
* *
3395901 ATTGACCTAGGTAGAATATAAAAAAAACTTTTAATGAGGCTAGTAACCAGGGTACATGATTTTCA
195 ATTGACCTAGGAAGAATATAAAAAAAACTTTTAATGAGGCTAGTAACCAGGGTACATGATTTCCA
* *
3395966 TATGGGCGAGGGCATTTTTTGATGAGG
260 TATAGGCGAGGGCATTTTTCGATGAGG
*
3395993 CAAGAATAACTAGTATTTAATAGGAGAAAACACCTCGGTATAAGAATTCATAAAGCTATCGAAAA
1 CAAGAATAACTAGTATTTAATAGGAG-AAA-A------TATAAGAATCCATAAAGCTATCGAAAA
* *
3396058 AAATG-A-AA-TCATCTGCTAGAATATTCCTCGGTGCGTGACCACATTGATGGACTGTCAGAAGC
58 AAATGAACAAGCCATCTGCTAGAATATTCCTCGGTGCGTGACCACATTGATGGACTGTCAAAAGC
* *
3396120 ACTTTGTATGTCAAGGACCACACTTGTTATTAATCAAATTCTTAGGTGGTAACTTCATGGTGTGT
123 ACTTTGTATGTCAAGGACCACAC-TG--AGTAATCAAATTCTTAGGTGGTAACTTCATAGTGTGT
* * * *
3396185 AATACTCATTATTGACCTAGGAAGAATATATAAAAAGCTTTTAATGAGGCTAGTAACCGGGGTAC
185 AAAACTCATTATTGACCTAGGAAGAATATAAAAAAAACTTTTAATGAGGCTAGTAACCAGGGTAC
3396250 ATGATTTCCATATAGGCGAGGGCATTTTTCGATG
250 ATGATTTCCATATAGGCGAGGGCATTTTTCGATG
3396284 GTAGTAACCT
Statistics
Matches: 260, Mismatches: 20, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
287 26 0.10
288 3 0.01
289 1 0.00
291 71 0.27
292 4 0.02
294 126 0.48
295 29 0.11
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (286 bp):
CAAGAATAACTAGTATTTAATAGGAGAAAATATAAGAATCCATAAAGCTATCGAAAAAAATGAAC
AAGCCATCTGCTAGAATATTCCTCGGTGCGTGACCACATTGATGGACTGTCAAAAGCACTTTGTA
TGTCAAGGACCACACTGAGTAATCAAATTCTTAGGTGGTAACTTCATAGTGTGTAAAACTCATTA
TTGACCTAGGAAGAATATAAAAAAAACTTTTAATGAGGCTAGTAACCAGGGTACATGATTTCCAT
ATAGGCGAGGGCATTTTTCGATGAGG
Found at i:3398385 original size:20 final size:18
Alignment explanation
Indices: 3398346--3398382 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3398336 TATAGTTTAC
*
3398346 TTTTTTATATAGTTAAAA
1 TTTTTTATATAATTAAAA
3398364 TTTTTTATATTAATTAAAA
1 TTTTTTATA-TAATTAAAA
3398383 ATTAAGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTTTTATATAATTAAAA
Found at i:3399545 original size:27 final size:25
Alignment explanation
Indices: 3399501--3399560 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
3399491 TAAAATTAGA
3399501 AAAAAAATAAAATATATAGAA-TTAT
1 AAAAAAATAAAATATATA-AAGTTAT
*
3399526 AAAAAAATAAAAATTTTATAAAGTTAT
1 AAAAAAAT-AAAA-TATATAAAGTTAT
*
3399553 AAGAAAAT
1 AAAAAAAT
3399561 TATACAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 8 0.27
26 6 0.20
27 16 0.53
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (25 bp):
AAAAAAATAAAATATATAAAGTTAT
Found at i:3399826 original size:29 final size:29
Alignment explanation
Indices: 3399794--3399882 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
3399784 TTGCAAAAAA
*
3399794 ATTAATTTTTAATACTTTTTTTAAATTTT
1 ATTAATTTTTAATAATTTTTTTAAATTTT
* * *
3399823 ATTAAATTTTAATAATTTTTCTAAAATTT
1 ATTAATTTTTAATAATTTTTTTAAATTTT
* * *
3399852 ATTATTTATTATAATTATTTTTTTTAATTTT
1 ATTAATT-TT-TAATAATTTTTTTAAATTTT
3399883 TAATACGAGC
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 30 0.62
30 2 0.04
31 16 0.33
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (29 bp):
ATTAATTTTTAATAATTTTTTTAAATTTT
Found at i:3405503 original size:62 final size:63
Alignment explanation
Indices: 3405435--3405561 Score: 229
Period size: 62 Copynumber: 2.0 Consensus size: 63
3405425 TAAACATGTA
3405435 AATTAAAATTTATGTTAAAAACTATTTTCAATGTTTATAGTATTTTCAACTTTTTT-TTATTT
1 AATTAAAATTTATGTTAAAAACTATTTTCAATGTTTATAGTATTTTCAACTTTTTTATTATTT
* *
3405497 AATTAAAATTTATGTTAAAAATTATTTTCAATGTTTATAGTATTTTCAATTTTTTTATTATTT
1 AATTAAAATTTATGTTAAAAACTATTTTCAATGTTTATAGTATTTTCAACTTTTTTATTATTT
3405560 AA
1 AA
3405562 ATTTGCACCA
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
62 54 0.87
63 8 0.13
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (63 bp):
AATTAAAATTTATGTTAAAAACTATTTTCAATGTTTATAGTATTTTCAACTTTTTTATTATTT
Found at i:3405558 original size:18 final size:18
Alignment explanation
Indices: 3405517--3405559 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3405507 TATGTTAAAA
3405517 ATTATTTTCAATGTTTAT
1 ATTATTTTCAATGTTTAT
* * *
3405535 AGTATTTTCAATTTTTTT
1 ATTATTTTCAATGTTTAT
3405553 ATTATTT
1 ATTATTT
3405560 AAATTTGCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (18 bp):
ATTATTTTCAATGTTTAT
Found at i:3406164 original size:11 final size:11
Alignment explanation
Indices: 3406086--3406153 Score: 73
Period size: 11 Copynumber: 6.1 Consensus size: 11
3406076 ATTTTGCTGC
3406086 TATTTTATTAT
1 TATTTTATTAT
* *
3406097 TATTTAAATAT
1 TATTTTATTAT
* * *
3406108 TATATAATTTT
1 TATTTTATTAT
*
3406119 TATTTTATTGT
1 TATTTTATTAT
3406130 TAATTTTATTAT
1 T-ATTTTATTAT
3406142 TATTTTATTAT
1 TATTTTATTAT
3406153 T
1 T
3406154 TTATTGTTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
11 37 0.79
12 10 0.21
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:3408542 original size:13 final size:13
Alignment explanation
Indices: 3408524--3408551 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3408514 GGCTGTTATT
3408524 TAAAAATAAAAAA
1 TAAAAATAAAAAA
3408537 TAAAAATAAAAAA
1 TAAAAATAAAAAA
3408550 TA
1 TA
3408552 TTAAATTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:3412528 original size:41 final size:41
Alignment explanation
Indices: 3412483--3412600 Score: 105
Period size: 41 Copynumber: 3.1 Consensus size: 41
3412473 GAAGGTAATC
3412483 TTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGT
1 TTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGT
* * * * *
3412524 TTC-TTATAC-TT---TTC-TAC--TAT-GA-AGTTTAAT-T
1 TTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTT-GTGT
3412555 TTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGT
1 TTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGT
3412596 TTCTT
1 TTCTT
3412601 ATACTTTTCT
Statistics
Matches: 55, Mismatches: 10, Indels: 24
0.62 0.11 0.27
Matches are distributed among these distances:
31 9 0.16
32 7 0.13
33 4 0.07
35 2 0.04
36 6 0.11
37 2 0.04
39 4 0.07
40 7 0.13
41 14 0.25
ACGTcount: A:0.15, C:0.14, G:0.14, T:0.57
Consensus pattern (41 bp):
TTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGT
Found at i:3412600 original size:72 final size:72
Alignment explanation
Indices: 3412478--3412627 Score: 282
Period size: 72 Copynumber: 2.1 Consensus size: 72
3412468 TTCTGGAAGG
*
3412478 TAATCTTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGTTTCTTATACTTTTCTACTA
1 TAATTTTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGTTTCTTATACTTTTCTACTA
3412543 TGAAGTT
66 TGAAGTT
3412550 TAATTTTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGTTTCTTATACTTTTCTACTA
1 TAATTTTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGTTTCTTATACTTTTCTACTA
3412615 TGAAGTT
66 TGAAGTT
*
3412622 TGATTT
1 TAATTT
3412628 AATTTTTTAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.18, C:0.14, G:0.13, T:0.55
Consensus pattern (72 bp):
TAATTTTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGTTTCTTATACTTTTCTACTA
TGAAGTT
Found at i:3416828 original size:14 final size:14
Alignment explanation
Indices: 3416811--3416840 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3416801 TTGAAATAAA
3416811 TTTTTTAAATTTAT
1 TTTTTTAAATTTAT
3416825 TTTTTTAAATTTAT
1 TTTTTTAAATTTAT
3416839 TT
1 TT
3416841 AATTGAACCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTTTAAATTTAT
Found at i:3418182 original size:16 final size:16
Alignment explanation
Indices: 3418161--3418196 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
3418151 ACCACTAGAG
3418161 TTTTATTTTATTTT-AT
1 TTTTATTTT-TTTTAAT
3418177 TTTTATTTTTTTTAAT
1 TTTTATTTTTTTTAAT
3418193 TTTT
1 TTTT
3418197 TAAAGTACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTATTTTTTTTAAT
Found at i:3419895 original size:15 final size:16
Alignment explanation
Indices: 3419860--3419897 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
3419850 ATTTATCCAA
3419860 AATTACAAATATTTATT
1 AATTA-AAATATTTATT
3419877 -ATTAAAAT-TTTATT
1 AATTAAAATATTTATT
3419891 AATTAAA
1 AATTAAA
3419898 TACATAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.30
15 10 0.50
16 4 0.20
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAAAATATTTATT
Found at i:3426902 original size:22 final size:23
Alignment explanation
Indices: 3426869--3426913 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
3426859 TATGTGTATG
3426869 GATATTTTTTTTGGGGATAGATC
1 GATATTTTTTTTGGGGATAGATC
3426892 GATA-TTTTTTTGGGGATAGATC
1 GATATTTTTTTTGGGGATAGATC
3426914 CCAAAATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.22, C:0.04, G:0.27, T:0.47
Consensus pattern (23 bp):
GATATTTTTTTTGGGGATAGATC
Found at i:3431998 original size:28 final size:28
Alignment explanation
Indices: 3431958--3432017 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
3431948 TCGATTTTTA
3431958 AATAAATTTTTATTTGTTACCCGTTATC
1 AATAAATTTTTATTTGTTACCCGTTATC
3431986 AATAAATTTTTATTTGTTACCCGTTATC
1 AATAAATTTTTATTTGTTACCCGTTATC
3432014 AATA
1 AATA
3432018 TTTATATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.48
Consensus pattern (28 bp):
AATAAATTTTTATTTGTTACCCGTTATC
Found at i:3432021 original size:24 final size:26
Alignment explanation
Indices: 3431965--3432026 Score: 90
Period size: 28 Copynumber: 2.3 Consensus size: 26
3431955 TTAAATAAAT
3431965 TTTTATTTGTTACCCGTTATCAATAAA
1 TTTTATTTGTTACCCGTTATCAAT-AA
3431992 TTTTTATTTGTTACCCGTTATCAAT-A
1 -TTTTATTTGTTACCCGTTATCAATAA
3432018 TTTATATTT
1 TTT-TATTT
3432027 AAGATTTACG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
25 3 0.09
26 6 0.18
28 24 0.73
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (26 bp):
TTTTATTTGTTACCCGTTATCAATAA
Found at i:3432701 original size:23 final size:23
Alignment explanation
Indices: 3432653--3432701 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
3432643 CTATTCGAAT
* * *
3432653 TTCGAGTTAATCGAATTGAGTTA
1 TTCGAGTCAATCGAATTAAGTAA
3432676 TTCGAGTCAACTCGAA-TAAGTAA
1 TTCGAGTCAA-TCGAATTAAGTAA
3432699 TTC
1 TTC
3432702 AAGTTTTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (23 bp):
TTCGAGTCAATCGAATTAAGTAA
Found at i:3444400 original size:13 final size:13
Alignment explanation
Indices: 3444379--3444436 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
3444369 AAATTTTTTC
3444379 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
3444392 AAAGTACTTCTCA
1 AAAGCACTTCTCA
*
3444405 AAAGCACTTTTCA
1 AAAGCACTTCTCA
* * *
3444418 AAAGTAGTTTTCA
1 AAAGCACTTCTCA
3444431 AAAGCA
1 AAAGCA
3444437 ACGAAGAACT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (13 bp):
AAAGCACTTCTCA
Found at i:3444409 original size:26 final size:26
Alignment explanation
Indices: 3444379--3444436 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
3444369 AAATTTTTTC
3444379 AAAGCACTTCTCAAAAGTACTTCTCA
1 AAAGCACTTCTCAAAAGTACTTCTCA
* * *
3444405 AAAGCACTTTTCAAAAGTAGTTTTCA
1 AAAGCACTTCTCAAAAGTACTTCTCA
3444431 AAAGCA
1 AAAGCA
3444437 ACGAAGAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (26 bp):
AAAGCACTTCTCAAAAGTACTTCTCA
Found at i:3453508 original size:21 final size:22
Alignment explanation
Indices: 3453482--3453528 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3453472 CTCTGCTCAA
*
3453482 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
3453503 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
3453525 ACTC
1 ACTC
3453529 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:3458965 original size:5 final size:5
Alignment explanation
Indices: 3458951--3458985 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
3458941 ATAAACAGCA
3458951 AAAAC AAAAAC AAAAC AAAAC AAAAC AAAA- AAAAC
1 AAAAC -AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
3458986 TCTTTTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:3467641 original size:21 final size:19
Alignment explanation
Indices: 3467597--3467643 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
3467587 AATGATATAA
* *
3467597 AAATTATTAAAATATCATT
1 AAATAATTAAAATATCAAT
3467616 AAATAATTAAAAATATGCAAT
1 AAATAATT-AAAATAT-CAAT
3467637 AAATAAT
1 AAATAAT
3467644 ATGATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 7 0.29
21 10 0.42
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (19 bp):
AAATAATTAAAATATCAAT
Found at i:3468158 original size:25 final size:25
Alignment explanation
Indices: 3468130--3468184 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
3468120 TAAAATTTTA
3468130 AAATTA-TTATAAAATTATAAAAAAT
1 AAATTAGTT-TAAAATTATAAAAAAT
* *
3468155 AAA-TAGTTTTAAATTTTAAAAAAT
1 AAATTAGTTTAAAATTATAAAAAAT
*
3468179 TAATTA
1 AAATTA
3468185 AATGCTAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
AAATTAGTTTAAAATTATAAAAAAT
Found at i:3470237 original size:17 final size:16
Alignment explanation
Indices: 3470210--3470243 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3470200 AATTTTAATT
*
3470210 TATAAATAAATGAATC
1 TATAAATAAATCAATC
3470226 TATAACATAAATCAATC
1 TATAA-ATAAATCAATC
3470243 T
1 T
3470244 TCCACTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (16 bp):
TATAAATAAATCAATC
Found at i:3473717 original size:18 final size:18
Alignment explanation
Indices: 3473694--3473728 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3473684 TTCAACCTAA
3473694 ATTATCTT-TAATATTATT
1 ATTATCTTATAA-ATTATT
3473712 ATTATCTTATAAATTAT
1 ATTATCTTATAAATTAT
3473729 GGATGGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTATCTTATAAATTATT
Found at i:3477610 original size:125 final size:125
Alignment explanation
Indices: 3477383--3477627 Score: 427
Period size: 125 Copynumber: 2.0 Consensus size: 125
3477373 TTTTTACTAT
* * *
3477383 TTAAATACCGGATTCAGTCCGTAGTCCTAGTTATAACTAACTTGTCCAAATTTGATCTATCGTCG
1 TTAAATACCGGATTCAGTCCATAGTCCTAGCTATAACTAACTTGTCCAAAATTGATCTATCGTCG
* *
3477448 CAGCTATAACTGGCAAATGCTTAACCAAAGATGGATGTTTTTTCCCTGATTTGTCAGTAG
66 CAGCTATAACCGGCAAATGCTTAACCAAAGATAGATGTTTTTTCCCTGATTTGTCAGTAG
* *
3477508 TTAAATACCGGATTCAGTCCATAGTCCTAGCTATAACTAACTTGTCCAAAATTGATCTATTGTTG
1 TTAAATACCGGATTCAGTCCATAGTCCTAGCTATAACTAACTTGTCCAAAATTGATCTATCGTCG
3477573 CAGCTATAACCGGCAAATGCTTAACCAAAGATAGATGTTTTTTCCCTGATTTGTC
66 CAGCTATAACCGGCAAATGCTTAACCAAAGATAGATGTTTTTTCCCTGATTTGTC
3477628 CCAAGTGTTT
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
125 113 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (125 bp):
TTAAATACCGGATTCAGTCCATAGTCCTAGCTATAACTAACTTGTCCAAAATTGATCTATCGTCG
CAGCTATAACCGGCAAATGCTTAACCAAAGATAGATGTTTTTTCCCTGATTTGTCAGTAG
Found at i:3489253 original size:19 final size:20
Alignment explanation
Indices: 3489229--3489275 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
3489219 CCCAGCTTGG
3489229 ATACCTTAAC-AAAGTATCA
1 ATACCTTAACAAAAGTATCA
* *
3489248 ATACCTTTCACAAAAGTATCG
1 ATACC-TTAACAAAAGTATCA
3489269 ATACCTT
1 ATACCTT
3489276 GCCTAGTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 6 0.25
21 13 0.54
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.30
Consensus pattern (20 bp):
ATACCTTAACAAAAGTATCA
Found at i:3491428 original size:24 final size:26
Alignment explanation
Indices: 3491383--3491438 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
3491373 TTTAACGCTA
3491383 AATTTT-TTTAAAACTTTCAA-TTTT
1 AATTTTATTTAAAACTTTCAATTTTT
3491407 AATTTTATTT-AAA-TTTCTAATTTTT
1 AATTTTATTTAAAACTTTC-AATTTTT
3491432 AATTTTA
1 AATTTTA
3491439 ACCTCACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.14
24 11 0.38
25 14 0.48
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (26 bp):
AATTTTATTTAAAACTTTCAATTTTT
Found at i:3491823 original size:2 final size:2
Alignment explanation
Indices: 3491816--3491859 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
3491806 ACCAACAATT
*
3491816 TC TC TC TC TC TC TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3491858 TC
1 TC
3491860 CCTTTTATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3495721 original size:16 final size:16
Alignment explanation
Indices: 3495694--3495733 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3495684 AAAAAAAATG
* *
3495694 TAATTATTTTTTCTTTT
1 TAATT-TTTTTTCGTAT
3495711 TAATTTTTTTTCGTAT
1 TAATTTTTTTTCGTAT
3495727 TAATTTT
1 TAATTTT
3495734 GTATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (16 bp):
TAATTTTTTTTCGTAT
Found at i:3495931 original size:38 final size:38
Alignment explanation
Indices: 3495889--3495966 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
3495879 TATATCAAAC
3495889 TGTAATTTTATATTATTTTTATTTTTTTAATAGGAAAG
1 TGTAATTTTATATTATTTTTATTTTTTTAATAGGAAAG
*
3495927 TGTAATTTTATATTTTTTTTATTTTTTTAATAGGAAAG
1 TGTAATTTTATATTATTTTTATTTTTTTAATAGGAAAG
3495965 TG
1 TG
3495967 GTAAAAGTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (38 bp):
TGTAATTTTATATTATTTTTATTTTTTTAATAGGAAAG
Found at i:3499041 original size:208 final size:208
Alignment explanation
Indices: 3498677--3499092 Score: 751
Period size: 208 Copynumber: 2.0 Consensus size: 208
3498667 CTCATAAAAG
*
3498677 ATAAGAGATTCAGAATCTGTTCGGGTCTAAAGAATTTTTAATTTAGAGATGTACCTCAGACTCTC
1 ATAAGAGATTCAGAATCTGTTCGGGTCTAAAGAATTTTTAATTTAGAGATGTACCTCAGACTCCC
3498742 AACAAATCATGAAAAGAAAAGTATCTTTAAAAATCTTATTAATAAAGTTAGAAATAGAGTTGAGG
66 AACAAATCATGAAAAGAAAAGTATCTTTAAAAATCTTATTAATAAAGTTAGAAATAGAGTTGAGG
3498807 TTGGTTCGACAAATTTCTTGCTTTCAATGGAAGAGAAATTTTTATAAAAGTTGTTTTACAAGCTA
131 TTGGTTCGACAAATTTCTTGCTTTCAATGGAAGAGAAATTTTTATAAAAGTTGTTTTACAAGCTA
*
3498872 TCCTTATGTATAC
196 TCCTCATGTATAC
* *
3498885 ATAAGAGATTCAGAATTTGTTCGGGTCTAAAGAATTTTTAATTTAGAGATGTACCTTAGACTCCC
1 ATAAGAGATTCAGAATCTGTTCGGGTCTAAAGAATTTTTAATTTAGAGATGTACCTCAGACTCCC
* * * *
3498950 AACAGATCATGAAAAGAAAAGTATTTTTAAGAATCTTATTAATAAAGTTAGAGATAGAGTTGAGG
66 AACAAATCATGAAAAGAAAAGTATCTTTAAAAATCTTATTAATAAAGTTAGAAATAGAGTTGAGG
*
3499015 TTGGTTCGACAAATTTCTTTCTTTCAATGGAAGAGAAATTTTTATAAAAGTTGTTTTACAAGCTA
131 TTGGTTCGACAAATTTCTTGCTTTCAATGGAAGAGAAATTTTTATAAAAGTTGTTTTACAAGCTA
3499080 TCCTCATGTATAC
196 TCCTCATGTATAC
3499093 TGTACAATGC
Statistics
Matches: 199, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
208 199 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (208 bp):
ATAAGAGATTCAGAATCTGTTCGGGTCTAAAGAATTTTTAATTTAGAGATGTACCTCAGACTCCC
AACAAATCATGAAAAGAAAAGTATCTTTAAAAATCTTATTAATAAAGTTAGAAATAGAGTTGAGG
TTGGTTCGACAAATTTCTTGCTTTCAATGGAAGAGAAATTTTTATAAAAGTTGTTTTACAAGCTA
TCCTCATGTATAC
Found at i:3503826 original size:89 final size:89
Alignment explanation
Indices: 3503646--3503814 Score: 259
Period size: 89 Copynumber: 1.9 Consensus size: 89
3503636 AAGCTCAAGC
* * *
3503646 TGAATAATTAATTCGTAAAACTAACTCGACTTACCATTAAACATGGTTTGCATAGATGGTACTCG
1 TGAATAATTAATTCGTAAAACTAACTCAACTCACCATTAAACATGGTTTACATAGATGGTACTCG
3503711 AACATAGGTATATAAGCTCTAAAT
66 AACATAGGTATATAAGCTCTAAAT
* * *
3503735 TGAATATTTAATTCGTACAAAC-AATTCAACTCACGATTAAACATGGTTTACATAGATGGTACTC
1 TGAATAATTAATTCGTA-AAACTAACTCAACTCACCATTAAACATGGTTTACATAGATGGTACTC
*
3503799 GAACGTAGGTATATAA
65 GAACATAGGTATATAA
3503815 CTTGACAATT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
89 68 0.94
90 4 0.06
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (89 bp):
TGAATAATTAATTCGTAAAACTAACTCAACTCACCATTAAACATGGTTTACATAGATGGTACTCG
AACATAGGTATATAAGCTCTAAAT
Found at i:3507911 original size:22 final size:22
Alignment explanation
Indices: 3507831--3507912 Score: 60
Period size: 22 Copynumber: 3.6 Consensus size: 22
3507821 ACAATTTGTG
*
3507831 ATATATTA-ATATAATTTAAAAT
1 ATATATTATATTTAATTT-AAAT
* * *
3507853 ATATTTTAAATAATTAATATAAAT
1 ATATATT--ATATTTAATTTAAAT
* *
3507877 -TATTTGTAAATTTAATTTAAAT
1 ATATAT-TATATTTAATTTAAAT
3507899 ATATATTATATTTA
1 ATATATTATATTTA
3507913 TAATTTGTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
22 25 0.54
23 9 0.20
24 6 0.13
25 6 0.13
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (22 bp):
ATATATTATATTTAATTTAAAT
Found at i:3519487 original size:31 final size:31
Alignment explanation
Indices: 3519451--3519516 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
3519441 CACGCACACG
3519451 GATGACTAAAACAAGTAGTTAAATACTGTAT
1 GATGACTAAAACAAGTAGTTAAATACTGTAT
*
3519482 GATGACTAAAACAAGTAGTTAACTACTGTAT
1 GATGACTAAAACAAGTAGTTAAATACTGTAT
3519513 GATG
1 GATG
3519517 TTCTTTGTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (31 bp):
GATGACTAAAACAAGTAGTTAAATACTGTAT
Found at i:3527985 original size:26 final size:26
Alignment explanation
Indices: 3527947--3528002 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
3527937 TGATACAAAT
3527947 TGATAATGAGTTAGGTAAATGTTCCA
1 TGATAATGAGTTAGGTAAATGTTCCA
*
3527973 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGAGTTAGGTAAATGTTCCA
3527999 TGAT
1 TGAT
3528003 GGGAATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGAGTTAGGTAAATGTTCCA
Found at i:3535979 original size:3 final size:3
Alignment explanation
Indices: 3535971--3536001 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3535961 ACAGCCACAC
*
3535971 TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3536002 TTCTCTCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3539482 original size:20 final size:19
Alignment explanation
Indices: 3539457--3539495 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3539447 AGGACATTTT
* *
3539457 CATTTGTTTTGAGATCATTA
1 CATTTGCTTTAAGAT-ATTA
3539477 CATTTGCTTTAAGATATTA
1 CATTTGCTTTAAGATATTA
3539496 TTAGTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (19 bp):
CATTTGCTTTAAGATATTA
Found at i:3541484 original size:556 final size:546
Alignment explanation
Indices: 3540421--3541521 Score: 1255
Period size: 556 Copynumber: 2.0 Consensus size: 546
3540411 CGGAGGTTGT
* * * **
3540421 TCTTCACAGCGTGCTCCGTACGAGGGAGTAGAATGGTTTTGCATACTTGAAATTTGGAGAAGGCC
1 TCTTCACAGCATGCTCCGAACGAGGGAGTAGAACGGTTTTGCATACTTGAAATTTGGAGAAAACC
* *
3540486 ATTCATACATTTTTAAGTCACAAGTCAATTGCTCAATGAGTGACATGAATTTGATGTGCCTATGT
66 ATTCATACAATTTTAAGCCACAAGTCAATTGCTCAATGAGTGACATGAATTTGATGTGCCTATGT
* * *
3540551 GGACCTTTATGTGGTTGTGATGTGGTTGGGGATTTGAGGAAGCATCCTTAGACATTGTGCTCATG
131 GGACCTCTATGTGGTTGTAATGTGGTTGGGGATTTGAGGAAGCATCCTTAGACATTGTGCCCATG
* * *
3540616 TCCGTTTGGAGCAAACTTTTTAGAATCGGATCGGTAGTTCAACTGTTAGTTTTGATTCAATTTGT
196 TCCATTTGGAGCAAACTTTTTAGAATCGGATCGGTAGTTAAACTGTCAGTTTTGATTCAATTTGT
* * * **
3540681 TTGGTTTGATTAAATAAATTGTTAAAAAATATTAAAATAAAAAAAATTAGTTCAATCAGTTTGTA
261 TTGGGTTAATTAAATAAATTATTAAAAAATATTAAAATAAAAAAAATTAGTTCAATCAGTCCGTA
* * * * * * * *
3540746 CTGGATCTTGAATCAATTGATTTAGTGTCTTTCTCTAGATCGATACATTGATCAATTTTCGATCC
326 CTAGATCTTGAATCAATCGATCTAATATCTTTCTCCAGATCAATACATCGATCAATTTTCGATCC
* * * * * * ** **
3540811 AACCAGTCTAATCAATAAATCCAATTCAGTTCAAATAATATTGGTTTGTAGGCTTTAAGAAACCT
391 AACCAATCCAACCAATAAATCCAATTCAATTCAAACAACATCAGTTTAAAGGCTTTAAGAAACCT
* * * *
3540876 CCACATGGGCTGTGATGTACTTGACAAAGCAATCTTCACCCAATAGATTGTGGGTGCGTCTAAGG
456 CCACATGAGCTGTGATGTACTTGACAAAGCAACCTTCACCCAATAAATTGTGGGTGCGTCTAAAG
3540941 GTGTTGCATATAGAGGTGATGGTGGC
521 GTGTTGCATATAGAGGTGATGGTGGC
* *
3540967 TCTTCACTGCATGCTCCGAACGAGGGAGTAGAACGGTTTTGCATACTTGAAGTTTGGAGGAAAAA
1 TCTTCACAGCATGCTCCGAACGAGGGAGTAGAACGGTTTTGCATACTTGAAATTTGGA-G--AAA
* * *** * * *
3541032 ACTATTTATACAATTTTAAGCCATGTGTCGATTGTTCAATGAGTGACATGAATTTTATGTGCCTA
63 ACCATTCATACAATTTTAAGCCACAAGTCAATTGCTCAATGAGTGACATGAATTTGATGTGCCTA
* ** **
3541097 TTTGGACCTCTATGTGGTTGTAATG-GGCTTAGGGG-TTTG-GAGAAGTGTGTTTAGACATTGTG
128 TGTGGACCTCTATGTGGTTGTAATGTGG-TT-GGGGATTTGAG-GAAGCATCCTTAGACATTGTG
* * * * *
3541159 CCCATG-CCTATTTGTAGCAAAGTTTTTAGAATTGGATTGGTAGTTAAACTAGTCAGGTTATTGG
190 CCCATGTCC-ATTTGGAGCAAACTTTTTAGAATCGGATCGGTAGTTAAACT-GTCA-GTT-TTGA
*
3541223 TTCAATTAGTCCGTTTGGGTTAATTAAATAAATTATTAAAAACTATTAAAA-ATAAAAAAATTAG
251 TTCAATT--T--GTTTGGGTTAATTAAATAAATTATTAAAAAATATTAAAATA-AAAAAAATTAG
** * * * *
3541287 TTCAATTGGTCCGTA-TCAGATCTTGAATTAGTCGGTCTAATATCTTTTTCCAGATCAATATC-T
311 TTCAATCAGTCCGTACT-AGATCTTGAATCAATCGATCTAATATCTTTCTCCAGATCAATA-CAT
* * * ** * *
3541350 CGATCGATTTTCGATCCAATCAATCCCACCAATTGATCTAATTTAATTCAAACAACATCAGTTTA
374 CGATCAATTTTCGATCCAACCAATCCAACCAATAAATCCAATTCAATTCAAACAACATCAGTTTA
* ** * * *
3541415 AAGGCTTT-AGAACACCTCCACATGAGTTGTGATGTACTTGATGAAGCGACCTTCGCTCAATAAA
439 AAGGCTTTAAGAA-ACCTCCACATGAGCTGTGATGTACTTGACAAAGCAACCTTCACCCAATAAA
*
3541479 TTGTGGGTGCGTCTAAAGGTGTTGCATATGGAGGTGATGGTGG
503 TTGTGGGTGCGTCTAAAGGTGTTGCATATAGAGGTGATGGTGG
3541522 TGAAAGTGCT
Statistics
Matches: 456, Mismatches: 81, Indels: 26
0.81 0.14 0.05
Matches are distributed among these distances:
546 53 0.12
547 1 0.00
548 5 0.01
549 141 0.31
550 7 0.02
551 3 0.01
552 10 0.02
554 1 0.00
555 6 0.01
556 228 0.50
557 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.35
Consensus pattern (546 bp):
TCTTCACAGCATGCTCCGAACGAGGGAGTAGAACGGTTTTGCATACTTGAAATTTGGAGAAAACC
ATTCATACAATTTTAAGCCACAAGTCAATTGCTCAATGAGTGACATGAATTTGATGTGCCTATGT
GGACCTCTATGTGGTTGTAATGTGGTTGGGGATTTGAGGAAGCATCCTTAGACATTGTGCCCATG
TCCATTTGGAGCAAACTTTTTAGAATCGGATCGGTAGTTAAACTGTCAGTTTTGATTCAATTTGT
TTGGGTTAATTAAATAAATTATTAAAAAATATTAAAATAAAAAAAATTAGTTCAATCAGTCCGTA
CTAGATCTTGAATCAATCGATCTAATATCTTTCTCCAGATCAATACATCGATCAATTTTCGATCC
AACCAATCCAACCAATAAATCCAATTCAATTCAAACAACATCAGTTTAAAGGCTTTAAGAAACCT
CCACATGAGCTGTGATGTACTTGACAAAGCAACCTTCACCCAATAAATTGTGGGTGCGTCTAAAG
GTGTTGCATATAGAGGTGATGGTGGC
Found at i:3544020 original size:31 final size:31
Alignment explanation
Indices: 3543955--3544019 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
3543945 TTTCTTACAA
*
3543955 TTTTGGATAGTTAATTGACTTAAATGAAAAT
1 TTTTGAATAGTTAATTGACTTAAATGAAAAT
* *
3543986 TTTTGAATAGTTTAA-TGA-TTAAATTATAAT
1 TTTTGAATAG-TTAATTGACTTAAATGAAAAT
3544016 TTTT
1 TTTT
3544020 TTTAGTTAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 14 0.47
31 12 0.40
32 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (31 bp):
TTTTGAATAGTTAATTGACTTAAATGAAAAT
Found at i:3544298 original size:7 final size:7
Alignment explanation
Indices: 3544288--3544361 Score: 53
Period size: 7 Copynumber: 10.7 Consensus size: 7
3544278 TTGAAAACAC
3544288 TAAACCT
1 TAAACCT
3544295 TAAACCT
1 TAAACCT
3544302 TAAACCT
1 TAAACCT
*
3544309 T-GACCT
1 TAAACCT
*
3544315 ATAATCC-
1 -TAAACCT
3544322 TAAACCT
1 TAAACCT
*
3544329 TAAACTT
1 TAAACCT
* *
3544336 TGAATCT
1 TAAACCT
* *
3544343 CAAATCT
1 TAAACCT
*
3544350 CAAACCT
1 TAAACCT
3544357 TAAAC
1 TAAAC
3544362 TTGAACCCCC
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
6 9 0.17
7 41 0.79
8 2 0.04
ACGTcount: A:0.41, C:0.27, G:0.03, T:0.30
Consensus pattern (7 bp):
TAAACCT
Found at i:3548269 original size:32 final size:32
Alignment explanation
Indices: 3548223--3548298 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
3548213 ACTGCTTTAA
* *
3548223 ATACTACACACGAACCTATCACAACTTCCTGG
1 ATACTAGACTCGAACCTATCACAACTTCCTGG
3548255 ATACTAGACTCGAACCTATCACAACTTCCTGG
1 ATACTAGACTCGAACCTATCACAACTTCCTGG
3548287 ATACTAGACTCG
1 ATACTAGACTCG
3548299 GGTGCATCCG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.33, C:0.32, G:0.12, T:0.24
Consensus pattern (32 bp):
ATACTAGACTCGAACCTATCACAACTTCCTGG
Found at i:3549741 original size:69 final size:69
Alignment explanation
Indices: 3549630--3549764 Score: 261
Period size: 69 Copynumber: 2.0 Consensus size: 69
3549620 ACTCTATCAA
*
3549630 CCCTACCACCACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAACCTG
1 CCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAACCTG
3549695 TCAG
66 TCAG
3549699 CCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAACCTG
1 CCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAACCTG
3549764 T
66 T
3549765 TTTTCCTATC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.28, C:0.33, G:0.13, T:0.27
Consensus pattern (69 bp):
CCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAACCTG
TCAG
Found at i:3554930 original size:16 final size:17
Alignment explanation
Indices: 3554897--3554932 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3554887 TAAATTCAGC
*
3554897 TAATTTAAACTCAAAAA
1 TAATTCAAACTCAAAAA
3554914 TAATTCAAACT-AAAAA
1 TAATTCAAACTCAAAAA
3554930 TAA
1 TAA
3554933 CATAAAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (17 bp):
TAATTCAAACTCAAAAA
Found at i:3556043 original size:16 final size:16
Alignment explanation
Indices: 3556024--3556057 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3556014 CATTTCAAGT
3556024 TTAGGGTAACTTTGGG
1 TTAGGGTAACTTTGGG
* *
3556040 TTAGGGTCATTTTGGG
1 TTAGGGTAACTTTGGG
3556056 TT
1 TT
3556058 GTACATTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.06, G:0.35, T:0.44
Consensus pattern (16 bp):
TTAGGGTAACTTTGGG
Found at i:3559382 original size:22 final size:21
Alignment explanation
Indices: 3559341--3559398 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
3559331 AAGACCTATT
**
3559341 AATATAATTACGATAATTTAGA
1 AATATAATTAAAATAATTTA-A
*
3559363 AATATAATTAAAATATTTTAA
1 AATATAATTAAAATAATTTAA
*
3559384 AATTAAAATTAAAAT
1 AA-TATAATTAAAAT
3559399 TTAAAGAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (21 bp):
AATATAATTAAAATAATTTAA
Found at i:3565449 original size:16 final size:17
Alignment explanation
Indices: 3565430--3565463 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3565420 AAAGGCTAAG
3565430 CAATCAAAT-CAAGATT
1 CAATCAAATGCAAGATT
*
3565446 CAATCCAATGCAAGATT
1 CAATCAAATGCAAGATT
3565463 C
1 C
3565464 GAGGAAAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.24
Consensus pattern (17 bp):
CAATCAAATGCAAGATT
Found at i:3573988 original size:21 final size:21
Alignment explanation
Indices: 3573959--3574005 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
3573949 TTTGATAAAG
*
3573959 TCCTGGTTAATACAATATTGA
1 TCCTTGTTAATACAATATTGA
3573980 TCCTTGTTAATACAATATTGA
1 TCCTTGTTAATACAATATTGA
3574001 TCCTT
1 TCCTT
3574006 TAAAATTTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.43
Consensus pattern (21 bp):
TCCTTGTTAATACAATATTGA
Found at i:3581163 original size:46 final size:46
Alignment explanation
Indices: 3581110--3581285 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
3581100 TATTTGGGCA
*
3581110 TCCGAACTCGTTGAGTTGAGTCCTAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
3581156 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * * *
3581201 CATCTGAGCTCGTTGAGTTGATTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
3581249 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3581286 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.58
47 26 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:3581265 original size:93 final size:93
Alignment explanation
Indices: 3581106--3581278 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
3581096 GGGATATTTG
* * *
3581106 GGCATCCGAACTCGTTGAGTTGAGTCCTAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
3581171 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * * *
3581199 GGCATCTGAGCTCGTTGAGTTGATTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
3581264 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
3581279 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:3584065 original size:98 final size:97
Alignment explanation
Indices: 3583888--3584065 Score: 227
Period size: 97 Copynumber: 1.8 Consensus size: 97
3583878 AATATTATAA
* * * * *
3583888 AAATTAAAGTAGAAAGATTAATTCCTAAATTTTAGCATAGTAGAGGGACTAAAATCAGAATTAGA
1 AAATTAAAGTAAAAAGATTAATTCCTAAATTTTAACATAGTAGAGGGACTAAAACCACAATTAAA
3583953 GAAAAATAAAATATTGAAGGATCACTTATAGT
66 GAAAAATAAAATATTGAAGGATCACTTATAGT
* * *
3583985 AAATTAAAGTAAAAAGATTAAATTTC-AAGTTTTAAATATAGTAGAGGGACT-AAACCACAATTA
1 AAATTAAAGTAAAAAGATT-AATTCCTAAATTTT-AACATAGTAGAGGGACTAAAACCACAATTA
3584048 AACCG-AAAATAAAATATT
64 AA--GAAAAATAAAATATT
3584066 CAAAAGCAGG
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
97 35 0.51
98 33 0.48
99 1 0.01
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.28
Consensus pattern (97 bp):
AAATTAAAGTAAAAAGATTAATTCCTAAATTTTAACATAGTAGAGGGACTAAAACCACAATTAAA
GAAAAATAAAATATTGAAGGATCACTTATAGT
Found at i:3604038 original size:15 final size:15
Alignment explanation
Indices: 3604019--3604057 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3604009 TGAAAAACCA
*
3604019 AAAAAAAAAAATTAAT
1 AAAATAAAAAA-TAAT
3604035 AAAATAAAAAATAAT
1 AAAATAAAAAATAAT
3604050 AATAATAA
1 AA-AATAA
3604058 TAATTGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATAAAAAATAAT
Found at i:3604052 original size:3 final size:3
Alignment explanation
Indices: 3604031--3604081 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
3604021 AAAAAAAAAT
** *
3604031 TAA TAA -AA TAA -AA -AA TAA TAA TAA TAA TAA TTG TAA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3604076 TAA TAA
1 TAA TAA
3604082 GTCCGTTGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 6 0.15
3 34 0.85
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:3609099 original size:15 final size:15
Alignment explanation
Indices: 3609079--3609110 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3609069 TATCTCTTCC
3609079 AACAATATTATTTTT
1 AACAATATTATTTTT
3609094 AACAATATTATTTTT
1 AACAATATTATTTTT
3609109 AA
1 AA
3609111 GGTTTGAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (15 bp):
AACAATATTATTTTT
Found at i:3610681 original size:14 final size:14
Alignment explanation
Indices: 3610662--3610688 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3610652 CCTAACAAAC
3610662 ATGTATATATATAT
1 ATGTATATATATAT
3610676 ATGTATATATATA
1 ATGTATATATATA
3610689 AACAAGTTCT
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:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATGTATATATATAT
Found at i:3611806 original size:3 final size:3
Alignment explanation
Indices: 3611798--3611830 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3611788 ATGTTTATTT
3611798 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
3611831 ATGGAACAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:3612344 original size:20 final size:20
Alignment explanation
Indices: 3612319--3612360 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3612309 CTGAATTGAG
3612319 TATAGTTTGAGCATCCCAAT
1 TATAGTTTGAGCATCCCAAT
3612339 TATAGTTTGAGCATCCCAAT
1 TATAGTTTGAGCATCCCAAT
3612359 TA
1 TA
3612361 CTTGTTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
TATAGTTTGAGCATCCCAAT
Found at i:3612759 original size:14 final size:13
Alignment explanation
Indices: 3612722--3612765 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
3612712 CCCAGAACCC
3612722 TAAACCCTAAAAC-
1 TAAACCCT-AAACT
*
3612735 TAAATCCTAAACT
1 TAAACCCTAAACT
3612748 TCAAACCCTAAACT
1 T-AAACCCTAAACT
3612762 TAAA
1 TAAA
3612766 TCTTAAACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 4 0.15
13 11 0.41
14 12 0.44
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAACCCTAAACT
Found at i:3612781 original size:27 final size:26
Alignment explanation
Indices: 3612720--3612781 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
3612710 TACCCAGAAC
3612720 CCTAAACCCTAAAACTAAATCCTAAA
1 CCTAAACCCTAAAACTAAATCCTAAA
* *
3612746 CTTCAAACCCT-AAACTTAAATCTTAAA
1 CCT-AAACCCTAAAAC-TAAATCCTAAA
3612773 CCTAGAACC
1 CCTA-AACC
3612782 TCAAACCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 7 0.23
27 23 0.77
ACGTcount: A:0.45, C:0.31, G:0.02, T:0.23
Consensus pattern (26 bp):
CCTAAACCCTAAAACTAAATCCTAAA
Found at i:3614236 original size:34 final size:34
Alignment explanation
Indices: 3614193--3614260 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
3614183 CAGCCCAATG
3614193 ACTTAAATAAATTTTTTTGAATAATTCAATAACT
1 ACTTAAATAAATTTTTTTGAATAATTCAATAACT
3614227 ACTTAAATAAATTTTTTTGAATAATTCAATAACT
1 ACTTAAATAAATTTTTTTGAATAATTCAATAACT
3614261 TAAAATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (34 bp):
ACTTAAATAAATTTTTTTGAATAATTCAATAACT
Found at i:3614274 original size:34 final size:33
Alignment explanation
Indices: 3614197--3614269 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 33
3614187 CCAATGACTT
*
3614197 AAATAAATTTTTTTGAATAATTCAATAACTACTT
1 AAATAAATTTTTTTGAATAATTCAATAACTA-TA
3614231 AAATAAATTTTTTTGAATAATTCAATAACT-TA
1 AAATAAATTTTTTTGAATAATTCAATAACTATA
3614263 AAATAAA
1 AAATAAA
3614270 AATTTCAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 8 0.21
34 30 0.79
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (33 bp):
AAATAAATTTTTTTGAATAATTCAATAACTATA
Found at i:3627701 original size:3 final size:3
Alignment explanation
Indices: 3627693--3627727 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3627683 AAGGTTAGAG
3627693 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3627728 TTGCTTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3629786 original size:9 final size:9
Alignment explanation
Indices: 3629772--3629816 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
3629762 CTTGGTTAGA
3629772 TATTTATTT
1 TATTTATTT
3629781 TATTTA-TT
1 TATTTATTT
*
3629789 TATTTTAATT
1 TA-TTTATTT
3629799 TATTTATTT
1 TATTTATTT
*
3629808 TGTTTATTT
1 TATTTATTT
3629817 ACTTAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 4 0.12
9 24 0.75
10 4 0.12
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (9 bp):
TATTTATTT
Found at i:3629790 original size:13 final size:13
Alignment explanation
Indices: 3629772--3629817 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
3629762 CTTGGTTAGA
3629772 TATTTATTTTATT
1 TATTTATTTTATT
3629785 TATTTATTTTAATT
1 TATTTATTTT-ATT
*
3629799 TATTTATTTTGTT
1 TATTTATTTTATT
3629812 TATTTA
1 TATTTA
3629818 CTTAAATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 18 0.58
14 13 0.42
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (13 bp):
TATTTATTTTATT
Found at i:3632842 original size:15 final size:14
Alignment explanation
Indices: 3632805--3632856 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 14
3632795 AATTATAAAA
3632805 AATACATATTAAATT
1 AATA-ATATTAAATT
3632820 --TAATATTAAGA-T
1 AATAATATTAA-ATT
3632832 AATATATATTAAATT
1 AATA-ATATTAAATT
3632847 AATAATATTA
1 AATAATATTA
3632857 TTTGAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
12 8 0.25
13 3 0.09
14 9 0.28
15 12 0.38
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (14 bp):
AATAATATTAAATT
Found at i:3633414 original size:27 final size:28
Alignment explanation
Indices: 3633356--3633415 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
3633346 AATAATAATG
*
3633356 TTATTTTAAAAATGAAAAATGAAAAATA
1 TTATTTTAAAAATGAAAAATGAAAAAGA
3633384 -TATTTTAAAAAT-AAAAA-GAATAAAGA
1 TTATTTTAAAAATGAAAAATGAA-AAAGA
3633410 TTATTT
1 TTATTT
3633416 AATAGAACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.10
26 9 0.31
27 17 0.59
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (28 bp):
TTATTTTAAAAATGAAAAATGAAAAAGA
Found at i:3634645 original size:21 final size:22
Alignment explanation
Indices: 3634612--3634652 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3634602 AAAAATATAT
* *
3634612 AAAATTATTAAATTTTAAAATA
1 AAAATTATAAAATTTCAAAATA
3634634 AAAATTA-AAAATTTCAAAA
1 AAAATTATAAAATTTCAAAA
3634653 ATAATATGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATTATAAAATTTCAAAATA
Found at i:3635385 original size:29 final size:31
Alignment explanation
Indices: 3635333--3635402 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
3635323 TAGTCTAATC
* *
3635333 TTTTTATAATTTTTAAAGAGTTAAATTA-AA
1 TTTTTATCATTTTTAAAGAGTTAAAGTACAA
*
3635363 TTTTTATCATTTTTAGAGA-TTAAAGTACAA
1 TTTTTATCATTTTTAAAGAGTTAAAGTACAA
3635393 -TTTTATCATT
1 TTTTTATCATT
3635403 ACTAATCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.51
Consensus pattern (31 bp):
TTTTTATCATTTTTAAAGAGTTAAAGTACAA
Found at i:3636291 original size:33 final size:33
Alignment explanation
Indices: 3636251--3636313 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
3636241 GATAGAAATA
*
3636251 AAAATAATATAAA-AATAAATAGTAATTATTGAT
1 AAAATAATA-AAATAAAAAATAGTAATTATTGAT
3636284 AAAATAATAAAATAAAAAATAGTAATTATT
1 AAAATAATAAAATAAAAAATAGTAATTATT
3636314 AAAGTACATG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (33 bp):
AAAATAATAAAATAAAAAATAGTAATTATTGAT
Found at i:3641411 original size:40 final size:40
Alignment explanation
Indices: 3641317--3641411 Score: 95
Period size: 40 Copynumber: 2.4 Consensus size: 40
3641307 ACTGACTTGG
* **
3641317 AAATCAGCAGTTTC-ACAATTTATATGTAAGTAATTAGCAA
1 AAATCAGCAG-TTCAACAATTTATATGTAAGCAAGAAGCAA
** * *
3641357 AAATCAATAATTCAACAATTTATATGTGA-CACAGAAGCAA
1 AAATCAGCAGTTCAACAATTTATATGTAAGCA-AGAAGCAA
3641397 AAATCAGCAGTTCAA
1 AAATCAGCAGTTCAA
3641412 GTTCATGTGA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
39 4 0.09
40 39 0.91
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (40 bp):
AAATCAGCAGTTCAACAATTTATATGTAAGCAAGAAGCAA
Found at i:3644136 original size:3 final size:3
Alignment explanation
Indices: 3644123--3644160 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
3644113 GAGAGAAAAG
3644123 AGA AGGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
3644161 AAAAGGGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3644449 original size:92 final size:90
Alignment explanation
Indices: 3644328--3644526 Score: 239
Period size: 100 Copynumber: 2.2 Consensus size: 90
3644318 TTTGTTTTGT
*
3644328 TAATAA-TTTATAGGATTAGGTTACAAA-T-TG-TTAGT-GTTTAGTGTATTAGTGTATTGTGAT
1 TAATAATTTTATAGGATTAGGTTACAAATTATGTTTAGTAGTTTAGTGTATTAGTGTATTGCGAT
3644388 TTTTTTAGTAATAATATATTTTAAAAAA
66 TTTTTTAG---TAATATATTTTAAAAAA
*
3644416 -AATAATTTTATAGTTGATTAGGTTATATAAATTGTTAATGTTTAGTAGTTTAGTGTATTAGTGT
1 TAATAATTTTATAG--GATTAGG-T-TACAAA---TT-ATGTTTAGTAGTTTAGTGTATTAGTGT
3644480 ATTGCGATTTTTTTAGTAATATATTTTAAAAAA
58 ATTGCGATTTTTTTAGTAATATATTTTAAAAAA
3644513 TAATAATTTTATAG
1 TAATAATTTTATAG
3644527 CTATTTTATT
Statistics
Matches: 95, Mismatches: 2, Indels: 18
0.83 0.02 0.16
Matches are distributed among these distances:
87 5 0.05
88 7 0.07
90 7 0.07
91 1 0.01
92 5 0.05
96 1 0.01
97 17 0.18
98 15 0.16
99 5 0.05
100 32 0.34
ACGTcount: A:0.35, C:0.01, G:0.15, T:0.49
Consensus pattern (90 bp):
TAATAATTTTATAGGATTAGGTTACAAATTATGTTTAGTAGTTTAGTGTATTAGTGTATTGCGAT
TTTTTTAGTAATATATTTTAAAAAA
Found at i:3644577 original size:100 final size:100
Alignment explanation
Indices: 3644365--3644692 Score: 291
Period size: 114 Copynumber: 3.1 Consensus size: 100
3644355 TTGTTAGTGT
*
3644365 TTAGTGTATTAGTGTATTGTGATTTTTTTAGTAATAATATATTTTAAAAAAAATAATTTTATAGT
1 TTAGTGTATTAGTGTATTGTGATTTTTTTAG---TAATATATTTTAAAAAAAATAATTTTATAGC
* *
3644430 TGATTAGGTTA-TA-TAAATT--G-TTAATGTT-TAGT--AGT-
63 T-ATT---TTATTAGTAATTTAAGATTAA-GTTATA-TAAATTG
*
3644465 TTAGTGTATTAGTGTATTGCGATTTTTTTAGTAATATATTTTAAAAAATAATAATTTTATAGCTA
1 TTAGTGTATTAGTGTATTGTGATTTTTTTAGTAATATATTTTAAAAAA-AATAATTTTATAGCTA
3644530 TTTTATTAGTAATTTAAGATTAAGTTATATAAATTG
65 TTTTATTAGTAATTTAAGATTAAGTTATATAAATTG
3644566 TTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTAATTTTTTTAGTAATATATTTT-AAAAAAA
1 TTAGTG--TA-----TTAGTGTATT-GTG-A-T-T----TTTTTAGTAATATATTTTAAAAAAAA
* * *
3644630 TATTTTTATAGCTATTTTATTAGTAATTTAATATTAGGTTATATAAATTG
51 TAATTTTATAGCTATTTTATTAGTAATTTAAGATTAAGTTATATAAATTG
3644680 TTAGTGT-TTAGTG
1 TTAGTGTATTAGTG
3644693 GTTTAGTGTA
Statistics
Matches: 195, Mismatches: 8, Indels: 44
0.79 0.03 0.18
Matches are distributed among these distances:
94 3 0.02
95 2 0.01
96 5 0.03
97 20 0.10
98 19 0.10
99 6 0.03
100 32 0.16
101 6 0.03
103 2 0.01
106 6 0.03
108 10 0.05
109 2 0.01
110 1 0.01
111 1 0.01
112 2 0.01
114 55 0.28
115 5 0.03
116 18 0.09
ACGTcount: A:0.34, C:0.01, G:0.14, T:0.51
Consensus pattern (100 bp):
TTAGTGTATTAGTGTATTGTGATTTTTTTAGTAATATATTTTAAAAAAAATAATTTTATAGCTAT
TTTATTAGTAATTTAAGATTAAGTTATATAAATTG
Found at i:3644786 original size:115 final size:115
Alignment explanation
Indices: 3644431--3644876 Score: 704
Period size: 114 Copynumber: 3.9 Consensus size: 115
3644421 TTTTATAGTT
* * *
3644431 GATTAGGTTATATAAATTGTTAATGTTTAGTAGTTTAGTGTATTAGTGTATTGCGA-TTTTTTTA
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTTA
3644495 GTAATATATTTTAAAAAATAATAATTTTATAGCTATTTTATTAGTAATTTAA
66 GTAATATATTTT-AAAAA-AATAATTTTATAGCTATTTTATTAGTAATTTAA
* *
3644547 GATTAAGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGT-AATTTTTTTA
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTTA
*
3644611 GTAATATATTTTAAAAAAATATTTTTATAGCTATTTTATTAGTAATTTAA
66 GTAATATATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
* *
3644661 TATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTATATTGTGATTTTTTTTA
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTTA
* *
3644726 GTAATATATTTTAAAAAAATATTTTTATAGTTATTTTATTAGTAATTTAA
66 GTAATATATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
*
3644776 GATTATGTTATAT--ATTGTTAGTGTTTAGTGGTTTAGTGTGTATTAGTGTATTGTGATTTTTTT
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTA--GTGTATTAGTGTATTGTGATTTTTTT
* *
3644839 TAGTAATGTA-TTTAAAAAAATAATTTTATAGTTATTTT
64 TAGTAATATATTTTAAAAAAATAATTTTATAGCTATTTT
3644877 GGGTTAGTAT
Statistics
Matches: 311, Mismatches: 15, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
113 22 0.07
114 110 0.35
115 109 0.35
116 70 0.23
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.52
Consensus pattern (115 bp):
GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTTA
GTAATATATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
Found at i:3644825 original size:229 final size:229
Alignment explanation
Indices: 3644432--3644876 Score: 718
Period size: 229 Copynumber: 1.9 Consensus size: 229
3644422 TTTATAGTTG
*
3644432 ATTAGGTTATATAAATTGTTAATGTTTAGTAGTTTAGTGTATTAGTGTATTGCGATTTTTTTAGT
1 ATTAGGTTATATAAATTGTTAATGTTTAGTAGTTTAGTGTATTAGTATATTGCGATTTTTTTAGT
3644497 AATATATTTTAAAAAATAATAATTTTATAGCTATTTTATTAGTAATTTAAGATTAAGTTATATAA
66 AATATATTTTAAAAAATAATAATTTTATAGCTATTTTATTAGTAATTTAAGATTAAGTTATAT-A
3644562 ATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGT-AATTTTTTTAGTAATATATTTTAAA
130 ATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGAATTTTTTTAGTAATATA-TTTAAA
*
3644626 AAAATATTTTTATAGCTATTTTATTAGTAATTTAAT
194 AAAATAATTTTATAGCTATTTTATTAGTAATTTAAT
* * *
3644662 ATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTATATTGTGATTTTTTTTAG
1 ATTAGGTTATATAAATTGTTAATGTTTAGTAGTTTAGTGTATTAGTATATTGCGA-TTTTTTTAG
* * *
3644727 TAATATATTTT-AAAAA-AATATTTTTATAGTTATTTTATTAGTAATTTAAGATTATGTTATAT-
65 TAATATATTTTAAAAAATAATAATTTTATAGCTATTTTATTAGTAATTTAAGATTAAGTTATATA
* *
3644789 ATTGTTAGTGTTTAGTGGTTTAGTGTGTATTAGTGTATTGTGATTTTTTTTAGTAATGTATTTAA
130 ATTGTTAGTGTTTAGTGGTTTA--GTGTATTAGTGTATTGTGAATTTTTTTAGTAATATATTTAA
*
3644854 AAAAATAATTTTATAGTTATTTT
193 AAAAATAATTTTATAGCTATTTT
3644877 GGGTTAGTAT
Statistics
Matches: 200, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
227 22 0.11
229 86 0.43
230 72 0.36
231 20 0.10
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.53
Consensus pattern (229 bp):
ATTAGGTTATATAAATTGTTAATGTTTAGTAGTTTAGTGTATTAGTATATTGCGATTTTTTTAGT
AATATATTTTAAAAAATAATAATTTTATAGCTATTTTATTAGTAATTTAAGATTAAGTTATATAA
TTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGAATTTTTTTAGTAATATATTTAAAAA
AATAATTTTATAGCTATTTTATTAGTAATTTAAT
Found at i:3644959 original size:15 final size:16
Alignment explanation
Indices: 3644931--3644961 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3644921 GTGATTTTTC
3644931 AATGTAATTTTTATAT
1 AATGTAATTTTTATAT
3644947 AATGTAA-TTTTATAT
1 AATGTAATTTTTATAT
3644962 TATTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
AATGTAATTTTTATAT
Found at i:3649904 original size:27 final size:27
Alignment explanation
Indices: 3649874--3649931 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
3649864 CAAGAAGACA
* * *
3649874 CAACTAGTCGTGCCTGTCAGATAGGCT
1 CAACTAATCGAGCCTGTCAGATAGGCG
* *
3649901 CAACTAATTGAGCCTTTCAGATAGGCG
1 CAACTAATCGAGCCTGTCAGATAGGCG
3649928 CAAC
1 CAAC
3649932 ATGTATGTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (27 bp):
CAACTAATCGAGCCTGTCAGATAGGCG
Found at i:3650744 original size:5 final size:5
Alignment explanation
Indices: 3650734--3650760 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3650724 TTTTCAAACC
3650734 TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TA
3650761 GGATAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:3651070 original size:29 final size:30
Alignment explanation
Indices: 3651009--3651071 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
3650999 AAAACTTTTC
*
3651009 TAAAAATACATAGAAAATTTAAAATTTAAA
1 TAAAAATACATAGAAAATTTAAAATGTAAA
* *
3651039 TAAAAATTCATA-AAAATTTCAAAA-GTAGA
1 TAAAAATACATAGAAAATTT-AAAATGTAAA
3651068 TAAA
1 TAAA
3651072 GTGAGAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (30 bp):
TAAAAATACATAGAAAATTTAAAATGTAAA
Found at i:3662427 original size:7 final size:7
Alignment explanation
Indices: 3662415--3662444 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
3662405 ACTTCTAATT
3662415 AAATATA
1 AAATATA
3662422 AAATATA
1 AAATATA
3662429 AAATATA
1 AAATATA
3662436 AAATATA
1 AAATATA
3662443 AA
1 AA
3662445 GTATTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATATA
Found at i:3671703 original size:26 final size:24
Alignment explanation
Indices: 3671670--3671728 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 24
3671660 ATATTTCTTA
3671670 TTTTATTT-CATATTAATATAATTATT
1 TTTTATTTAC-TATTAATAT-A-TATT
3671696 TTTTATTTACTATTAATATATATT
1 TTTTATTTACTATTAATATATATT
3671720 TTTTATTTA
1 TTTTATTTA
3671729 ATTAGATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
24 13 0.41
25 1 0.03
26 17 0.53
27 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTATTTACTATTAATATATATT
Found at i:3672461 original size:12 final size:12
Alignment explanation
Indices: 3672446--3672476 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3672436 AAAGAAAACG
*
3672446 TAAAATATAAAA
1 TAAAAAATAAAA
3672458 TAAAAAATAAAA
1 TAAAAAATAAAA
3672470 TAAAAAA
1 TAAAAAA
3672477 AAGGCAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
TAAAAAATAAAA
Found at i:3680138 original size:17 final size:19
Alignment explanation
Indices: 3680116--3680153 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
3680106 TGAATCGGTT
3680116 TTTTAAAT-ATTT-TTAAA
1 TTTTAAATAATTTATTAAA
3680133 TTTTAAATAATTTATTAAA
1 TTTTAAATAATTTATTAAA
3680152 TT
1 TT
3680154 GAATCAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTAAATAATTTATTAAA
Found at i:3689607 original size:15 final size:15
Alignment explanation
Indices: 3689587--3689641 Score: 110
Period size: 15 Copynumber: 3.7 Consensus size: 15
3689577 TTCTGTCCGG
3689587 CCCAATACCCACAAA
1 CCCAATACCCACAAA
3689602 CCCAATACCCACAAA
1 CCCAATACCCACAAA
3689617 CCCAATACCCACAAA
1 CCCAATACCCACAAA
3689632 CCCAATACCC
1 CCCAATACCC
3689642 TCAGCCCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.44, C:0.49, G:0.00, T:0.07
Consensus pattern (15 bp):
CCCAATACCCACAAA
Found at i:3689611 original size:7 final size:7
Alignment explanation
Indices: 3689587--3689641 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
3689577 TTCTGTCCGG
3689587 CCCAATA
1 CCCAATA
*
3689594 CCCACAAA
1 CCCA-ATA
3689602 CCCAATA
1 CCCAATA
*
3689609 CCCACAAA
1 CCCA-ATA
3689617 CCCAATA
1 CCCAATA
*
3689624 CCCACAAA
1 CCCA-ATA
3689632 CCCAATA
1 CCCAATA
3689639 CCC
1 CCC
3689642 TCAGCCCAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 21 0.54
8 18 0.46
ACGTcount: A:0.44, C:0.49, G:0.00, T:0.07
Consensus pattern (7 bp):
CCCAATA
Found at i:3689619 original size:8 final size:8
Alignment explanation
Indices: 3689593--3689635 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
3689583 CCGGCCCAAT
3689593 ACCCACAA
1 ACCCACAA
*
3689601 ACCCA-AT
1 ACCCACAA
3689608 ACCCACAA
1 ACCCACAA
*
3689616 ACCCA-AT
1 ACCCACAA
3689623 ACCCACAA
1 ACCCACAA
3689631 ACCCA
1 ACCCA
3689636 ATACCCTCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 12 0.41
8 17 0.59
ACGTcount: A:0.47, C:0.49, G:0.00, T:0.05
Consensus pattern (8 bp):
ACCCACAA
Found at i:3689661 original size:30 final size:30
Alignment explanation
Indices: 3689587--3689664 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
3689577 TTCTGTCCGG
**
3689587 CCCAATACCCACAAACCCAATACCCACAAA
1 CCCAATACAAACAAACCCAATACCCACAAA
** * *
3689617 CCCAATACCCACAAACCCAATACCCTC-AG
1 CCCAATACAAACAAACCCAATACCCACAAA
3689646 CCCAATTACAAACAAACCC
1 CCCAA-TACAAACAAACCC
3689665 TAACCCAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 6 0.14
30 37 0.86
ACGTcount: A:0.44, C:0.46, G:0.01, T:0.09
Consensus pattern (30 bp):
CCCAATACAAACAAACCCAATACCCACAAA
Found at i:3701914 original size:1 final size:1
Alignment explanation
Indices: 3701908--3701933 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
3701898 TTTGCTTCCT
3701908 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
3701934 GGACTTTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3703225 original size:44 final size:46
Alignment explanation
Indices: 3703111--3703225 Score: 137
Period size: 46 Copynumber: 2.5 Consensus size: 46
3703101 ATGCAGGTCT
* * *
3703111 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATGTCAGATCC
* *
3703157 TATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-ATAGT-A-ATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAAT-GTCAGATCC
* *
3703201 TATCTCCTTGAGATTACAATGGAGC
1 TATCTCCCTGAGATTACAGTGGAGC
3703226 GGATTAAAAG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 25 0.42
45 3 0.05
46 32 0.53
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (46 bp):
TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATGTCAGATCC
Found at i:3703401 original size:128 final size:126
Alignment explanation
Indices: 3703154--3703548 Score: 485
Period size: 129 Copynumber: 3.1 Consensus size: 126
3703144 GAATTTCAGA
* * * *
3703154 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTG-AGATTAC
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGAAACT-ATCCTATCTCCCTGAAG-TTAC
* * **
3703218 AATGGAGCGGATT--AA-AAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGACCGCATCTGG
64 AGTGGAGCGGATTAAAATAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAAG
*
3703278 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGAAACTATCCTATCTCCCTGAAGTTACAG
*
3703343 TGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATCAAG
66 TGGAGCGGATTAAAAT-AA-GATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAAG
* * * * * *
3703406 TCTTATCTCCCTGA-AGTTGCAGTGGAGCAGATAGAAGAAACCAATCCTATCTCTCTGAAGTTGC
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCGAAGAAA-CTATCCTATCTCCCTGAAGTTAC
* * * * *
3703470 AGTAGAGCGGATTAAAATCACAGATCTTATCTCTTTGAAGTTGCAGTAGAGCAGATCGCATCAAG
64 AGTGGAGCGGATTAAAAT-A-AGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAAG
*
3703535 TCTTATTTCCCTGA
1 TCTTATCTCCCTGA
3703549 AGTACAATGG
Statistics
Matches: 238, Mismatches: 24, Indels: 13
0.87 0.09 0.05
Matches are distributed among these distances:
123 29 0.12
124 41 0.17
125 2 0.01
127 3 0.01
128 73 0.31
129 89 0.37
130 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (126 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGAAACTATCCTATCTCCCTGAAGTTACAG
TGGAGCGGATTAAAATAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAAG
Found at i:3703551 original size:41 final size:41
Alignment explanation
Indices: 3703324--3703551 Score: 152
Period size: 44 Copynumber: 5.3 Consensus size: 41
3703314 GACACTATCC
* * * * * *
3703324 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATGAAGGATCT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGA-TAGAATCAA-G-TCT
* * * * * *
3703368 TATCTCTCTGAGGTTACAGCAGAGTAGATCGCATCAAGTCT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATAGAATCAAGTCT
* * * *
3703409 TATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAGAAACCAA-TCC
1 TATCTCTCTGAAGTTGCAGTAGAGCAGAT---AG-AATCAAGTCT
* *
3703453 TATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGATCT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGA-TAGAATCA-AG-TCT
* * *
3703497 TATCTCTTTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATAGAATCAAGTCT
* *
3703538 TATTTCCCTGAAGT
1 TATCTCTCTGAAGT
3703552 ACAATGGATT
Statistics
Matches: 142, Mismatches: 34, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
41 44 0.31
42 5 0.04
43 10 0.07
44 78 0.55
45 5 0.04
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (41 bp):
TATCTCTCTGAAGTTGCAGTAGAGCAGATAGAATCAAGTCT
Found at i:3703751 original size:15 final size:15
Alignment explanation
Indices: 3703731--3703800 Score: 140
Period size: 15 Copynumber: 4.7 Consensus size: 15
3703721 TTCTGTCCGG
3703731 CCCAATACCCACAAA
1 CCCAATACCCACAAA
3703746 CCCAATACCCACAAA
1 CCCAATACCCACAAA
3703761 CCCAATACCCACAAA
1 CCCAATACCCACAAA
3703776 CCCAATACCCACAAA
1 CCCAATACCCACAAA
3703791 CCCAATACCC
1 CCCAATACCC
3703801 TCAGCCCAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 55 1.00
ACGTcount: A:0.44, C:0.49, G:0.00, T:0.07
Consensus pattern (15 bp):
CCCAATACCCACAAA
Found at i:3703763 original size:8 final size:8
Alignment explanation
Indices: 3703737--3703794 Score: 68
Period size: 8 Copynumber: 7.6 Consensus size: 8
3703727 CCGGCCCAAT
3703737 ACCCACAA
1 ACCCACAA
*
3703745 ACCCA-AT
1 ACCCACAA
3703752 ACCCACAA
1 ACCCACAA
*
3703760 ACCCA-AT
1 ACCCACAA
3703767 ACCCACAA
1 ACCCACAA
*
3703775 ACCCA-AT
1 ACCCACAA
3703782 ACCCACAA
1 ACCCACAA
3703790 ACCCA
1 ACCCA
3703795 ATACCCTCAG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
7 18 0.44
8 23 0.56
ACGTcount: A:0.47, C:0.48, G:0.00, T:0.05
Consensus pattern (8 bp):
ACCCACAA
Found at i:3703820 original size:30 final size:30
Alignment explanation
Indices: 3703731--3703823 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 30
3703721 TTCTGTCCGG
**
3703731 CCCAATACCCACAAACCCAATACCCACAAA
1 CCCAATACCCACAAACCCAATACAAACAAA
**
3703761 CCCAATACCCACAAACCCAATACCCACAAA
1 CCCAATACCCACAAACCCAATACAAACAAA
* *
3703791 CCCAATACCCTC-AGCCCAATTACAAACAAA
1 CCCAATACCCACAAACCCAA-TACAAACAAA
3703821 CCC
1 CCC
3703824 TAACCCAAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 6 0.10
30 52 0.90
ACGTcount: A:0.44, C:0.46, G:0.01, T:0.09
Consensus pattern (30 bp):
CCCAATACCCACAAACCCAATACAAACAAA
Found at i:3703820 original size:45 final size:45
Alignment explanation
Indices: 3703731--3703823 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
3703721 TTCTGTCCGG
**
3703731 CCCAATACCCACAAACCCAATACCCACAAACCCAATACCCACAAA
1 CCCAATACCCACAAACCCAATACCCACAAACCCAATACAAACAAA
* *
3703776 CCCAATACCCACAAACCCAATACCCTC-AGCCCAATTACAAACAAA
1 CCCAATACCCACAAACCCAATACCCACAAACCCAA-TACAAACAAA
3703821 CCC
1 CCC
3703824 TAACCCAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 6 0.14
45 37 0.86
ACGTcount: A:0.44, C:0.46, G:0.01, T:0.09
Consensus pattern (45 bp):
CCCAATACCCACAAACCCAATACCCACAAACCCAATACAAACAAA
Found at i:3717892 original size:18 final size:18
Alignment explanation
Indices: 3717869--3717957 Score: 151
Period size: 18 Copynumber: 4.9 Consensus size: 18
3717859 CCAACTACTG
3717869 TATACGTGAATAGTACCA
1 TATACGTGAATAGTACCA
*
3717887 TATACGTGAATAGTGCCA
1 TATACGTGAATAGTACCA
*
3717905 TATACGTGAATAGTACCG
1 TATACGTGAATAGTACCA
*
3717923 TATACGTGAATAGTGCCA
1 TATACGTGAATAGTACCA
3717941 TATACGTGAATAGTACC
1 TATACGTGAATAGTACC
3717958 GTAAACGGTC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (18 bp):
TATACGTGAATAGTACCA
Found at i:3717958 original size:36 final size:36
Alignment explanation
Indices: 3717869--3717960 Score: 175
Period size: 36 Copynumber: 2.6 Consensus size: 36
3717859 CCAACTACTG
*
3717869 TATACGTGAATAGTACCATATACGTGAATAGTGCCA
1 TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
3717905 TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
1 TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
3717941 TATACGTGAATAGTACCGTA
1 TATACGTGAATAGTACCGTA
3717961 AACGGTCGTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (36 bp):
TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
Found at i:3722482 original size:20 final size:20
Alignment explanation
Indices: 3722454--3722509 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
3722444 AAATTTAAAT
* **
3722454 ATTTTTTTTATTTGGACTAA
1 ATTTATTTTATTACGACTAA
*
3722474 ATTTATTTTAATTACTACTAA
1 ATTTATTTT-ATTACGACTAA
3722495 ATTTATTTTAATTAC
1 ATTTATTTT-ATTAC
3722510 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 8 0.26
21 23 0.74
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (20 bp):
ATTTATTTTATTACGACTAA
Done.