Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 152 of 213
Found at i:45523135 original size:44 final size:44
Alignment explanation
Indices: 45523078--45523165 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
45523068 AGATCAATTG
* **
45523078 AAGGGTGGTTACATCAAAGACATTTCCAACCACAGTGTTTGAAA
1 AAGGGTGGTTACATCAAAGACATTGCCAACCACAACGTTTGAAA
*
45523122 AAGGGTGGTTACATCAAAGGCATTGCCAACCACAACGTTTGAAA
1 AAGGGTGGTTACATCAAAGACATTGCCAACCACAACGTTTGAAA
45523166 GACTAGTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (44 bp):
AAGGGTGGTTACATCAAAGACATTGCCAACCACAACGTTTGAAA
Found at i:45523736 original size:22 final size:21
Alignment explanation
Indices: 45523706--45523768 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
45523696 TTATTGTGAA
**
45523706 TATAA-AAAATTATTTTTACAT
1 TATAATAAAATTAAATTTA-AT
45523727 TATAATAAAATTAAATTTAAT
1 TATAATAAAATTAAATTTAAT
* *
45523748 TATAAATTAAATTAAAATTAA
1 TAT-AATAAAATTAAATTTAA
45523769 AATTTGATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 10 0.28
22 26 0.72
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAATAAAATTAAATTTAAT
Found at i:45531387 original size:23 final size:23
Alignment explanation
Indices: 45531332--45531410 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 23
45531322 GTCCTTTGTT
*
45531332 TTATTATTTTTATTAGTTTACTA
1 TTATTATTATTATTAGTTTACTA
*
45531355 TTGGTT-TTATT-TTAGTGTTACTA
1 TT-ATTATTATTATTAGT-TTACTA
*
45531378 TTATTATTATTA-T--TTAAC-A
1 TTATTATTATTATTAGTTTACTA
45531397 TTATTATTATTATT
1 TTATTATTATTATT
45531411 TTTTTTAATC
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
19 13 0.28
20 4 0.09
21 1 0.02
22 7 0.15
23 20 0.43
24 2 0.04
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (23 bp):
TTATTATTATTATTAGTTTACTA
Found at i:45534486 original size:31 final size:31
Alignment explanation
Indices: 45534442--45534514 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
45534432 AAAAAAACTT
*
45534442 AATAGTTCGATGACTTAAAT-AAAAGCTTTTA-
1 AATAGTTCAATGACTTAAATGAAAA-C-TTTAG
*
45534473 AATAATTCAATGACTTAAATGAAAACTTTAG
1 AATAGTTCAATGACTTAAATGAAAACTTTAG
45534504 AATAGTTCAAT
1 AATAGTTCAAT
45534515 AATCGTTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 4 0.11
31 29 0.78
32 4 0.11
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (31 bp):
AATAGTTCAATGACTTAAATGAAAACTTTAG
Found at i:45537857 original size:14 final size:13
Alignment explanation
Indices: 45537829--45537870 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
45537819 ATTTAAGAAC
*
45537829 AAATAACAAATAA
1 AAATAATAAATAA
45537842 AAATAATAATATAA
1 AAATAATAA-ATAA
45537856 AAATAAATAAATAA
1 AAAT-AATAAATAA
45537870 A
1 A
45537871 CAATTTAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 8 0.31
14 13 0.50
15 5 0.19
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAATAAATAA
Found at i:45539578 original size:26 final size:26
Alignment explanation
Indices: 45539531--45539580 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
45539521 CCCACACACC
* * *
45539531 AATATTGCAGCATAGTTACCAGTAAT
1 AATATCGCAGCAGAGCTACCAGTAAT
*
45539557 AATATCGCAGCAGAGCTGCCAGTA
1 AATATCGCAGCAGAGCTACCAGTA
45539581 CTGTATATGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (26 bp):
AATATCGCAGCAGAGCTACCAGTAAT
Found at i:45539620 original size:27 final size:27
Alignment explanation
Indices: 45539588--45539639 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
45539578 GTACTGTATA
45539588 TGTGGCAAAGCCACCAGTAACAGTAAT
1 TGTGGCAAAGCCACCAGTAACAGTAAT
* *
45539615 TGTGGCAGAGCCACTAGTAACAGTA
1 TGTGGCAAAGCCACCAGTAACAGTA
45539640 CTTCCTCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (27 bp):
TGTGGCAAAGCCACCAGTAACAGTAAT
Found at i:45551298 original size:22 final size:22
Alignment explanation
Indices: 45551267--45551308 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
45551257 TGTCATTAAC
45551267 TTAAGTTAATTAAAGATTAAGGT
1 TTAAGTTAATTAAA-ATTAAGGT
*
45551290 TTAA-TTAATTATAATTAAG
1 TTAAGTTAATTAAAATTAAG
45551309 TAAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (22 bp):
TTAAGTTAATTAAAATTAAGGT
Found at i:45555485 original size:39 final size:40
Alignment explanation
Indices: 45555368--45555550 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 40
45555358 GCTACTCGTT
*
45555368 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* * *
45555408 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
45555448 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
45555487 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
45555528 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
45555551 AACATCATTC
Statistics
Matches: 121, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 74 0.61
41 13 0.11
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:45555512 original size:79 final size:81
Alignment explanation
Indices: 45555368--45555550 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 81
45555358 GCTACTCGTT
* * *
45555368 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* * *
45555433 ATTTAGTAAC-TCGCG
66 ATATAGTAACTTAGCA
* **
45555448 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* *
45555510 GGATATGGTCACTTAGCA
64 GGATATAGTAACTTAGCA
45555528 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
45555551 AACATCATTC
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 4 0.05
79 54 0.61
80 30 0.34
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCA
Found at i:45564646 original size:18 final size:17
Alignment explanation
Indices: 45564623--45564681 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
45564613 TTCTTCCTTA
45564623 TTTTATTTTATATTTA-
1 TTTTATTTTATATTTAT
45564639 -TTTATTATTAT-TTCTAT
1 TTTTATT-TTATATT-TAT
*
45564656 TTCTATTATTATATTTAT
1 TTTTATT-TTATATTTAT
*
45564674 TTTCATTT
1 TTTTATTT
45564682 GTTTTCTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
15 8 0.23
16 6 0.17
17 1 0.03
18 18 0.51
19 2 0.06
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTATTTTATATTTAT
Found at i:45564656 original size:20 final size:21
Alignment explanation
Indices: 45564620--45564673 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
45564610 CCCTTCTTCC
45564620 TTATT-TTATTTTATATTTAT-
1 TTATTATTA-TTTATATTTATA
* *
45564640 TTATTATTATTTCTATTTCTA
1 TTATTATTATTTATATTTATA
45564661 TTATTA-TATTTAT
1 TTATTATTATTTAT
45564674 TTTCATTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (21 bp):
TTATTATTATTTATATTTATA
Found at i:45564662 original size:26 final size:26
Alignment explanation
Indices: 45564620--45564670 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
45564610 CCCTTCTTCC
45564620 TTATTTTATTTTATATTTATT-TATTA
1 TTATTTTATTTTATA-TTATTATATTA
*
45564646 TTATTTCTA-TTTCTATTATTATATT
1 TTATTT-TATTTTATATTATTATATT
45564671 TATTTTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 5 0.23
26 15 0.68
27 2 0.09
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (26 bp):
TTATTTTATTTTATATTATTATATTA
Found at i:45564691 original size:24 final size:24
Alignment explanation
Indices: 45564670--45564721 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
45564660 ATTATTATAT
**
45564670 TTATTTTCATTTGTTTTCTTATTC
1 TTATTTTCATTTACTTTCTTATTC
* *
45564694 TTCTTTTCATTTACTTTCTTATTA
1 TTATTTTCATTTACTTTCTTATTC
45564718 TTAT
1 TTAT
45564722 GCTTATTACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.13, G:0.02, T:0.69
Consensus pattern (24 bp):
TTATTTTCATTTACTTTCTTATTC
Found at i:45566342 original size:16 final size:17
Alignment explanation
Indices: 45566312--45566346 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
45566302 ACTAATTTTA
45566312 TTTCTTTTATTTTTCTT
1 TTTCTTTTATTTTTCTT
45566329 TTTCTTTT-TTTTTCTT
1 TTTCTTTTATTTTTCTT
45566345 TT
1 TT
45566347 AGTTGTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTCTTTTATTTTTCTT
Found at i:45566344 original size:27 final size:29
Alignment explanation
Indices: 45566307--45566366 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
45566297 AGACCACTAA
*
45566307 TTTTATTTCTTTTA-T-TTTTCTTTTTCT
1 TTTTATTTCTTTTAGTGTTTTCTTTTTAT
*
45566334 TTTTTTTTCTTTTAGTTGTTTTCTTTTTAT
1 TTTTATTTCTTTTAG-TGTTTTCTTTTTAT
45566364 TTT
1 TTT
45566367 CTTAGACTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 13 0.46
29 1 0.04
30 14 0.50
ACGTcount: A:0.07, C:0.08, G:0.03, T:0.82
Consensus pattern (29 bp):
TTTTATTTCTTTTAGTGTTTTCTTTTTAT
Found at i:45566380 original size:25 final size:24
Alignment explanation
Indices: 45566328--45566385 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
45566318 TTATTTTTCT
** * *
45566328 TTTTCTTTTTTTTTCTTTTAGTTG
1 TTTTCTTTTTTTTTCTTAGACTTC
45566352 TTTTCTTTTTATTTTCTTAGACTTC
1 TTTTCTTTTT-TTTTCTTAGACTTC
45566377 TTTT-TTTTT
1 TTTTCTTTTT
45566386 GTTTATTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 15 0.52
25 14 0.48
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.78
Consensus pattern (24 bp):
TTTTCTTTTTTTTTCTTAGACTTC
Found at i:45592999 original size:50 final size:50
Alignment explanation
Indices: 45592924--45593165 Score: 240
Period size: 50 Copynumber: 4.9 Consensus size: 50
45592914 CATTTGGGTA
*
45592924 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* * *
45592974 AAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGTCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* * ** * * *
45593024 GAGAGTTCCCCCGCAAGACCATGTCTGGGACATAGCATGGGCACCGATG-T
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-GAT
* ** * * * *
45593074 GAGAACTCCCATGTAAGACCATATCTGGGATATGTCATTGGCA--G-TAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
** *
45593121 AAGAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AAG--AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
45593166 TGTTATTATC
Statistics
Matches: 158, Mismatches: 30, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
47 3 0.02
48 1 0.01
49 34 0.22
50 119 0.75
51 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.22
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
Found at i:45595863 original size:19 final size:19
Alignment explanation
Indices: 45595835--45595873 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
45595825 GGGGGTTAAT
* *
45595835 GATGACAGTTTTTAGGGAA
1 GATGAAAGTTTCTAGGGAA
45595854 GATGAAAGTTTCTAGGGAA
1 GATGAAAGTTTCTAGGGAA
45595873 G
1 G
45595874 TTGGTGATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.33, T:0.28
Consensus pattern (19 bp):
GATGAAAGTTTCTAGGGAA
Found at i:45603380 original size:40 final size:40
Alignment explanation
Indices: 45603325--45603405 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
45603315 CAACATTTAG
45603325 TTGAAATTCCTCTTTGTCTTAAGCTACAATAGGCTCATCT
1 TTGAAATTCCTCTTTGTCTTAAGCTACAATAGGCTCATCT
* *
45603365 TTGAAATTCCTCTTTGTCTTGAGCTACAATAGGTTCATCT
1 TTGAAATTCCTCTTTGTCTTAAGCTACAATAGGCTCATCT
45603405 T
1 T
45603406 GAACCTCAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (40 bp):
TTGAAATTCCTCTTTGTCTTAAGCTACAATAGGCTCATCT
Found at i:45605124 original size:5 final size:5
Alignment explanation
Indices: 45605114--45605138 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
45605104 TTTAACTAAG
45605114 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
45605139 GTTCCAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:45606568 original size:10 final size:10
Alignment explanation
Indices: 45606549--45606598 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
45606539 GAATCTGTTG
*
45606549 AAAATAAATC
1 AAAATTAATC
45606559 AAAATTAATC
1 AAAATTAATC
*
45606569 AAAATTAATTAT
1 AAAATTAA-T-C
*
45606581 AAAATTAATT
1 AAAATTAATC
45606591 AAAATTAA
1 AAAATTAA
45606599 AAATATTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
10 26 0.72
11 2 0.06
12 8 0.22
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAATTAATC
Found at i:45607312 original size:25 final size:25
Alignment explanation
Indices: 45607284--45607372 Score: 88
Period size: 25 Copynumber: 3.6 Consensus size: 25
45607274 GCCTTTAGGA
* * *
45607284 AAATTATCTGAAGATCGTTTGTGAC
1 AAATTATCTAAAGAGCCTTTGTGAC
*
45607309 AAATTATCTAAAGAGCCTTTGTGGC
1 AAATTATCTAAAGAGCCTTTGTGAC
* * * * *
45607334 GAATTATATAAAGAGTCTTTTTGGC
1 AAATTATCTAAAGAGCCTTTGTGAC
*
45607359 GAATTATCTAAAGA
1 AAATTATCTAAAGA
45607373 ATCTTTTTTG
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 55 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (25 bp):
AAATTATCTAAAGAGCCTTTGTGAC
Found at i:45607377 original size:25 final size:25
Alignment explanation
Indices: 45607310--45607419 Score: 121
Period size: 25 Copynumber: 4.4 Consensus size: 25
45607300 GTTTGTGACA
*
45607310 AATTATCTAAAGAGCCTTTGTGGCG
1 AATTATCTAAAGAGCCTTTTTGGCG
* *
45607335 AATTATATAAAGAGTCTTTTTGGCG
1 AATTATCTAAAGAGCCTTTTTGGCG
* * *
45607360 AATTATCTAAAGAATCTTTTTTGGTG
1 AATTATCTAAAG-AGCCTTTTTGGCG
* * *
45607386 AATTATCTGAAGACCCTTTATGGCG
1 AATTATCTAAAGAGCCTTTTTGGCG
*
45607411 TATTATCTA
1 AATTATCTA
45607420 GAATGTCTAG
Statistics
Matches: 69, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
25 49 0.71
26 20 0.29
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (25 bp):
AATTATCTAAAGAGCCTTTTTGGCG
Found at i:45610319 original size:29 final size:29
Alignment explanation
Indices: 45610256--45610323 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
45610246 TAATCAACCG
*
45610256 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
45610285 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
45610314 CGCACACTTA
1 CGCACACTTA
45610324 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:45610435 original size:174 final size:174
Alignment explanation
Indices: 45610145--45610472 Score: 629
Period size: 174 Copynumber: 1.9 Consensus size: 174
45610135 AACTCAAGGT
* *
45610145 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
45610210 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
45610275 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
45610319 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
45610384 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
45610449 ACTTTAAACTCACACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
45610473 TGTACAATTT
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 151 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:45610466 original size:29 final size:29
Alignment explanation
Indices: 45610432--45610503 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
45610422 ATCAACCGCG
* * *
45610432 CACACTTAGTGCCATGCACTTTAAACTCA
1 CACACTTAGTGCCATACAATTTAAACCCA
** *
45610461 CACACTTAGTGCTGTACAATTTAAACCCG
1 CACACTTAGTGCCATACAATTTAAACCCA
45610490 CACACTTAGTGCCA
1 CACACTTAGTGCCA
45610504 ATCTCATGAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.26
Consensus pattern (29 bp):
CACACTTAGTGCCATACAATTTAAACCCA
Found at i:45613519 original size:50 final size:50
Alignment explanation
Indices: 45613380--45613605 Score: 192
Period size: 50 Copynumber: 4.5 Consensus size: 50
45613370 TGCCAAAGCT
* * * * * *
45613380 ATGTCCCAGACATAGTCTTACATGGGACGTTTCCTGTAC--T-CCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGGTGCCCAA-GAC
* * * ** * *
45613429 ATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGAC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCAAGAC
* ** *
45613479 ATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCGGTG-CCAACAC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCAAGAC
* *
45613528 AATGTCCCAGGCATGGTCTTACATGGGACCTCTCATCTCGGTG-CCAACGTC
1 -ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCAA-GAC
* *
45613579 ATGTCCCAAACATGTTCTTACATGGGA
1 ATGTCCCAGACATGGTCTTACATGGGA
45613606 TCTCATTCCC
Statistics
Matches: 141, Mismatches: 31, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
48 1 0.01
49 33 0.23
50 102 0.72
51 5 0.04
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCAAGAC
Found at i:45620716 original size:16 final size:16
Alignment explanation
Indices: 45620674--45620716 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
45620664 ATTAGGATCT
* *
45620674 TTACTTTCTTCTTTAC
1 TTACTTACTTGTTTAC
*
45620690 TTACTCACTTGTTTAC
1 TTACTTACTTGTTTAC
*
45620706 TTACTTGCTTG
1 TTACTTACTTG
45620717 CTTAAATATC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.14, C:0.23, G:0.07, T:0.56
Consensus pattern (16 bp):
TTACTTACTTGTTTAC
Found at i:45621049 original size:50 final size:50
Alignment explanation
Indices: 45620986--45621109 Score: 158
Period size: 50 Copynumber: 2.5 Consensus size: 50
45620976 TAATGTCATA
* ** * * *
45620986 TCCCAAATATGGTCTTACATGGGAGTTCTTATATCGGTGCCCATGCCATG
1 TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
** *
45621036 TCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
*
45621086 TCCCAGACATGGTCTTACATGGGA
1 TCCCAAACATGGTCTTACATGGGA
45621110 TCTCATTCCC
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (50 bp):
TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
Found at i:45632049 original size:33 final size:33
Alignment explanation
Indices: 45632005--45632074 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
45631995 CCTTTCTAGG
*
45632005 AGAAAGGTTAGAATCATCAAAAACAACATGCAT
1 AGAAAGATTAGAATCATCAAAAACAACATGCAT
*
45632038 AGAAAGATTAGAATCATCGAAAACAACATGCAT
1 AGAAAGATTAGAATCATCAAAAACAACATGCAT
45632071 AGAA
1 AGAA
45632075 TCTTCAACCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.53, C:0.14, G:0.16, T:0.17
Consensus pattern (33 bp):
AGAAAGATTAGAATCATCAAAAACAACATGCAT
Found at i:45633676 original size:55 final size:50
Alignment explanation
Indices: 45633600--45633840 Score: 200
Period size: 50 Copynumber: 4.7 Consensus size: 50
45633590 GGTAATGAGA
* *
45633600 TCCCATGTGAGACCATGTCTGGGACATGGCATT-GCATCATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATGAGAGG
*
45633655 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * * **
45633705 TCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * * * * **
45633755 TCCCATGTAAGACCATATTTGGGATATGGTATT-G-ACAGTACAAGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGG
* *
45633804 TCCCATGTAAGACCATTTCTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
45633841 TGTTATTATT
Statistics
Matches: 154, Mismatches: 28, Indels: 12
0.79 0.14 0.06
Matches are distributed among these distances:
48 3 0.02
49 34 0.22
50 78 0.51
51 1 0.01
52 1 0.01
53 2 0.01
55 32 0.21
56 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:45639853 original size:23 final size:24
Alignment explanation
Indices: 45639812--45639856 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
45639802 TCATCTTTAA
45639812 TTATGCTTAGTTTTAGTTGTTTTC
1 TTATGCTTAGTTTTAGTTGTTTTC
45639836 TTATGCTTAG-TTTAGTTGTTT
1 TTATGCTTAGTTTTAGTTGTTT
45639857 CCTATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.13, C:0.07, G:0.18, T:0.62
Consensus pattern (24 bp):
TTATGCTTAGTTTTAGTTGTTTTC
Found at i:45645861 original size:6 final size:6
Alignment explanation
Indices: 45645850--45645900 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
45645840 GTCGAAACCA
* *
45645850 TTCCTT TTCCTT TTCATT TTCCTT TTCTTT TTCCTT TTCCTT TTCCTT
1 TTCCTT TTCCTT TTCCTT TTCCTT TTCCTT TTCCTT TTCCTT TTCCTT
45645898 TTC
1 TTC
45645901 ATCAATGCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (6 bp):
TTCCTT
Found at i:45653097 original size:21 final size:22
Alignment explanation
Indices: 45653073--45653130 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
45653063 TTTTTCCCTT
45653073 CTTTTTATTAATAAAATA-TTA
1 CTTTTTATTAATAAAATACTTA
**
45653094 CTTTTTAAAAACTAAAATACTTA
1 CTTTTTATTAA-TAAAATACTTA
45653117 --TTTTATATAATAAA
1 CTTTTTAT-TAATAAA
45653131 TTTAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 18 0.60
22 9 0.30
23 3 0.10
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (22 bp):
CTTTTTATTAATAAAATACTTA
Found at i:45653560 original size:28 final size:27
Alignment explanation
Indices: 45653503--45653586 Score: 64
Period size: 28 Copynumber: 3.0 Consensus size: 27
45653493 AATAAGTAAT
* * *
45653503 AATAAAATATTATTTAATATAAGTAT-A
1 AATACAATATTATTTTATTTAA-TATAA
**
45653530 AATTTAATATATATTTTATTTAATATAA
1 AATACAATAT-TATTTTATTTAATATAA
*
45653558 AATACAATTATTTATTTTACTT-ATATAA
1 AATACAA-TA-TTATTTTATTTAATATAA
45653586 A
1 A
45653587 TTAATTTAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
27 11 0.24
28 23 0.50
29 11 0.24
30 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (27 bp):
AATACAATATTATTTTATTTAATATAA
Found at i:45658566 original size:21 final size:21
Alignment explanation
Indices: 45658536--45658576 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
45658526 TTAAATTAAA
*
45658536 TAAAAAATATGAA-AATTTTG
1 TAAAAAATATCAATAATTTTG
45658556 TAAATAAATATCAATAATTTT
1 TAAA-AAATATCAATAATTTT
45658577 ATTTAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
TAAAAAATATCAATAATTTTG
Found at i:45659604 original size:24 final size:23
Alignment explanation
Indices: 45659550--45659604 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
45659540 ATACATACTA
*
45659550 AATATATTAATAAAATTTTAATTT
1 AATAT-TTAATAAAACTTTAATTT
** *
45659574 ACCATTTAATTAAAACTTTATTTT
1 AATATTTAA-TAAAACTTTAATTT
45659598 AATATTT
1 AATATTT
45659605 TTATGCATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATTTAATAAAACTTTAATTT
Found at i:45665359 original size:11 final size:11
Alignment explanation
Indices: 45665343--45665371 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
45665333 CCACCACATT
45665343 CTCCTCCTTAG
1 CTCCTCCTTAG
45665354 CTCCTCCTTAG
1 CTCCTCCTTAG
45665365 CTCCTCC
1 CTCCTCC
45665372 CTTATTAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.52, G:0.07, T:0.34
Consensus pattern (11 bp):
CTCCTCCTTAG
Found at i:45669090 original size:22 final size:22
Alignment explanation
Indices: 45669062--45669103 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
45669052 ATCACTAATT
*
45669062 AAACCAAAGCCTCAACAAACAA
1 AAACCAAAACCTCAACAAACAA
*
45669084 AAACCAAAATCTCAACAAAC
1 AAACCAAAACCTCAACAAAC
45669104 CCAATAACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.31, G:0.02, T:0.07
Consensus pattern (22 bp):
AAACCAAAACCTCAACAAACAA
Found at i:45671978 original size:12 final size:12
Alignment explanation
Indices: 45671961--45671985 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45671951 CAACCATAAT
45671961 CGCAAGCTAGTG
1 CGCAAGCTAGTG
45671973 CGCAAGCTAGTG
1 CGCAAGCTAGTG
45671985 C
1 C
45671986 ATTTAAGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (12 bp):
CGCAAGCTAGTG
Found at i:45673431 original size:45 final size:45
Alignment explanation
Indices: 45673360--45673511 Score: 180
Period size: 45 Copynumber: 3.4 Consensus size: 45
45673350 CACATAGCAT
* * ** * *
45673360 CACCCTTATAGTCAATGATACTTGGTGGAATCAACACATAGCAAC
1 CACCTTTATAATCAATGATAAATGGTGGAATCAGCACACAGCAAC
* *
45673405 CACCTTCATAATCAATAGA-AAATGGTGGAATCAGCACACATCAAC
1 CACCTTTATAATCAAT-GATAAATGGTGGAATCAGCACACAGCAAC
*** *
45673450 CACCTTTATAATCAATGATACCCGGCGGAATCAGCACACAGCAAC
1 CACCTTTATAATCAATGATAAATGGTGGAATCAGCACACAGCAAC
45673495 CACCTTTATAATCAATG
1 CACCTTTATAATCAATG
45673512 GTACCCGGTA
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
44 2 0.02
45 87 0.96
46 2 0.02
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (45 bp):
CACCTTTATAATCAATGATAAATGGTGGAATCAGCACACAGCAAC
Found at i:45678090 original size:16 final size:17
Alignment explanation
Indices: 45678063--45678111 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
45678053 TAGAATTGAG
*
45678063 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
45678080 TTGAG-AAATTAATTAA
1 TTGAGAAAATTAATTAA
* *
45678096 TTAATTAAAATTAATT
1 TTGA-GAAAATTAATT
45678112 TATGATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 13 0.48
17 5 0.19
18 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:45678902 original size:26 final size:27
Alignment explanation
Indices: 45678854--45678904 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
45678844 AGTGTTCATC
*
45678854 TCTTTTTTCACTTATTATGTATTGTGT
1 TCTTTTTTCACTTATCATGTATTGTGT
45678881 TCTTTTTTCTAC-TATCAT-TATTGT
1 TCTTTTTTC-ACTTATCATGTATTGT
45678905 TAAAACTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 6 0.27
27 14 0.64
28 2 0.09
ACGTcount: A:0.16, C:0.14, G:0.08, T:0.63
Consensus pattern (27 bp):
TCTTTTTTCACTTATCATGTATTGTGT
Found at i:45680590 original size:106 final size:108
Alignment explanation
Indices: 45680407--45680719 Score: 404
Period size: 110 Copynumber: 2.9 Consensus size: 108
45680397 AAGAGGATAT
* * * *
45680407 TTGGCTATTTGGTT--AC-ATGAGAAATCAAAACCCAGCACATTAAGGCACG-TTCCTCGAATTT
1 TTGGCTATTTGGTTGAACGA-GAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTT
* *
45680468 CCAAATGCTAAACATTGCCTTATTTTGAAAATTTTGAAAGG-A-
65 CCAAACGCTAAACATTGCCTTATTTTGAAAATTTTAAAAGGAAC
* *
45680510 TTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCATATTAGGGCACGTTTTCTCAAATTTC
1 TTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTC
* *
45680575 CAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAAAGGATAC
66 CAAACGCTAAACATTGCCTTATTTTGAAA-ATTTTAAAAGGA-AC
** * *
45680620 TTAACTATTTGGTTGAACGAGAAAAATCGAAACTCAACACATTAGGGCACGTTTTCTCGAATTTC
1 TTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTC
* *
45680685 CAAACGCTAAATATTGCCTTATTTAGAAAAATTTT
66 CAAACGCTAAACATTGCCTTATTTTG-AAAATTTT
45680720 CCTTTTGAAG
Statistics
Matches: 181, Mismatches: 20, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
103 14 0.08
105 29 0.16
106 39 0.22
107 9 0.05
109 1 0.01
110 86 0.48
111 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (108 bp):
TTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTC
CAAACGCTAAACATTGCCTTATTTTGAAAATTTTAAAAGGAAC
Found at i:45680842 original size:4 final size:4
Alignment explanation
Indices: 45680833--45680893 Score: 54
Period size: 4 Copynumber: 15.0 Consensus size: 4
45680823 ATACCATAAC
* *
45680833 AAAT AAAT AAAT AAAT AAAT AAACT AAA- ACAT AAA- AAAG ACATAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT A-A-AT AAAT
*
45680882 AAAT ACAT AAAT
1 AAAT AAAT AAAT
45680894 GAACATAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
3 5 0.11
4 34 0.72
5 6 0.13
6 2 0.04
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:45680892 original size:37 final size:33
Alignment explanation
Indices: 45680838--45680913 Score: 98
Period size: 37 Copynumber: 2.2 Consensus size: 33
45680828 ATAACAAATA
45680838 AATAAATAAATAAATAAACTAAAACATAAAAAAGAC
1 AATAAATAAATAAATAAA-T-AAACATAAAAAA-AC
* *
45680874 ATATAAATAAATACATAAATGAACATAAAAAAAC
1 A-ATAAATAAATAAATAAATAAACATAAAAAAAC
45680908 AATAAA
1 AATAAA
45680914 GGAAAATAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
33 5 0.14
34 3 0.08
35 11 0.30
36 2 0.05
37 16 0.43
ACGTcount: A:0.71, C:0.08, G:0.03, T:0.18
Consensus pattern (33 bp):
AATAAATAAATAAATAAATAAACATAAAAAAAC
Found at i:45681196 original size:3 final size:3
Alignment explanation
Indices: 45681188--45681255 Score: 59
Period size: 3 Copynumber: 22.3 Consensus size: 3
45681178 AAGCTATTAT
* * * *
45681188 ATA ATA AT- ATG ATA AGTA ACA ATA AT- ATAA ACA ATA ATA AAA ATA
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
45681233 ATA ATA ATAA ATA ATA ATA ATA A
1 ATA ATA AT-A ATA ATA ATA ATA A
45681256 AATTACTGAA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
2 4 0.08
3 42 0.79
4 7 0.13
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:45681222 original size:12 final size:13
Alignment explanation
Indices: 45681205--45681256 Score: 72
Period size: 12 Copynumber: 4.2 Consensus size: 13
45681195 TATGATAAGT
45681205 AACAATAAT-ATA
1 AACAATAATAATA
45681217 AACAATAATAA-A
1 AACAATAATAATA
*
45681229 AATAATAATAATA
1 AACAATAATAATA
*
45681242 AATAATAATAATA
1 AACAATAATAATA
45681255 AA
1 AA
45681257 ATTACTGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
12 20 0.54
13 17 0.46
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (13 bp):
AACAATAATAATA
Found at i:45681239 original size:22 final size:21
Alignment explanation
Indices: 45681199--45681255 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
45681189 TAATAATATG
*
45681199 ATAAGTAACAATAATATAA-ACA
1 ATAA-TAAAAATAATATAATA-A
45681221 ATAATAAAAATAATAATAATAA
1 ATAATAAAAATAAT-ATAATAA
*
45681243 ATAATAATAATAA
1 ATAATAAAAATAA
45681256 AATTACTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 9 0.29
22 21 0.68
23 1 0.03
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (21 bp):
ATAATAAAAATAATATAATAA
Found at i:45682633 original size:132 final size:132
Alignment explanation
Indices: 45682482--45683211 Score: 1029
Period size: 132 Copynumber: 5.6 Consensus size: 132
45682472 ACTACTGCTT
* *
45682482 AGGGAGACAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
* * * ***
45682547 TTCGATCTGCTCCACTACTTCTTAGGGAGATTAGATCTGTAATCTTCAATCTATTCCACTGCTGC
66 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAA
45682612 CC
131 CC
* * *
45682614 AGTGAGATAGAATTTCTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAAT-TCGCCAT
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCT-GCCAT
* ***
45682678 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTG
65 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCA
*
45682743 CCC
130 ACC
** *
45682746 AGGGAGATAGAATTTTTGGCTTCAATATACTCCACTGTAACCACAGGGAGGTAAAATCAT-CCAT
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATC-TGCCAT
45682810 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCA
65 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCA
45682875 ACC
130 ACC
* * * * *
45682878 AGGGAGATAGAATTATTGGCTTCAATGTAAATCCACTATAATCACTGGGAGGTAAAATCTGCCAT
1 AGGGAGATAGAATTACTGGCTTCAATGT-ACTCCACTGTAACCACAGGGAGGTAAAATCTGCCAT
45682943 CTTCGATCTGCT-C-C-A---CTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCA
65 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCA
*
45683002 ATC
130 ACC
* * *
45683005 AGGGAGATAGAATTACTGGCTTCAATGTACTCCATTGTAATCACAGGGAGGTAAAATCTGCCATA
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
* *
45683070 TTCTATCTGCT----T-C-ACTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAA
66 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAA
*
45683129 TC
131 CC
* **
45683131 AGGGAGATAGAATTACTGGCTTCAATGTACTCTACTGTAACCACAGGGAGGTAAAATCTGATATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
45683196 TTCGATCTGCTCCACT
66 TTCGATCTGCTCCACT
45683212 GTCGATGCAG
Statistics
Matches: 548, Mismatches: 38, Indels: 26
0.90 0.06 0.04
Matches are distributed among these distances:
126 158 0.29
127 73 0.13
130 2 0.00
131 1 0.00
132 271 0.49
133 42 0.08
134 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (132 bp):
AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAA
CC
Found at i:45682737 original size:44 final size:44
Alignment explanation
Indices: 45682544--45682870 Score: 132
Period size: 44 Copynumber: 7.4 Consensus size: 44
45682534 AAAATCCGCC
* * * * *
45682544 ATCTTCGATCTGCTCCACTACTTCTTAGGGAGATTAGATCTGTA
1 ATCTTCAATCTACTCCACTACTGCTCAGGGAGATAAGATCTGTA
* * * * * *
45682588 ATCTTCAATCTATTCCACTGCTGCCCAGTGAGAT-AGAATTTCT-
1 ATCTTCAATCTACTCCACTACTGCTCAGGGAGATAAG-ATCTGTA
** * * * * * **
45682631 GGCTTCAATGTACTCCACTA-TAACCACAGGGAGGTAAAAT-TCGCC
1 ATCTTCAATCTACTCCACTACT--GCTCAGGGAGATAAGATCT-GTA
* * *
45682676 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
1 ATCTTCAATCTACTCCACTACTGCTCAGGGAGATAAGATCTGTA
* ** * * *
45682720 ATCTTCAATCTATTCCACTGTTGCCCAGGGAGAT-AGAAT-TTTT
1 ATCTTCAATCTACTCCACTACTGCTCAGGGAGATAAG-ATCTGTA
** * * * * **
45682763 GGCTTCAATATACTCCACTGTAAC--CACAGGGAGGTAAAATCAT-CC
1 ATCTTCAATCTACTCCAC--T-ACTGCTCAGGGAGATAAGATC-TGTA
* * * *
45682808 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAA
1 ATCTTCAATCTACTCCACTACTGCTCAGGGAGATAAGATCTGTA
*
45682852 ATCTTCAATCTATTCCACT
1 ATCTTCAATCTACTCCACT
45682871 GCCAACCAGG
Statistics
Matches: 197, Mismatches: 68, Indels: 36
0.65 0.23 0.12
Matches are distributed among these distances:
42 3 0.02
43 38 0.19
44 122 0.62
45 32 0.16
46 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.31
Consensus pattern (44 bp):
ATCTTCAATCTACTCCACTACTGCTCAGGGAGATAAGATCTGTA
Found at i:45683010 original size:44 final size:43
Alignment explanation
Indices: 45682834--45683139 Score: 119
Period size: 38 Copynumber: 7.2 Consensus size: 43
45682824 ACTACTGCTT
*
45682834 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACC
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTG-CAATC
* * * **
45682878 AGGGAGAT-AGAAT-T--ATTGGCTTCAATGTAAATCCACTATAATC
1 AGGGAGATAAG-ATCTGAAAT--CTTCAATCT-ATTCCACTGCAATC
* * ** * **
45682921 ACTGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT----T-
1 A--GGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCAATC
45682961 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAATC
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTG-CAATC
* * * * *
45683005 AGGGAGAT-AGAATTACTG---GCTTCAATGTACTCCATTGTAATCAC
1 AGGGAGATAAG-A-T-CTGAAATCTTCAATCTATTCCACTGCAAT--C
* * ** * * *
45683049 AGGGAGGTAAAATCTGCCATATTCTATCTGCTT-CACT----T-
1 AGGGAGATAAGATCTGAAATCTTCAATCT-ATTCCACTGCAATC
45683087 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAATC
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTG-CAATC
45683131 AGGGAGATA
1 AGGGAGATA
45683140 GAATTACTGG
Statistics
Matches: 187, Mismatches: 42, Indels: 66
0.63 0.14 0.22
Matches are distributed among these distances:
37 2 0.01
38 56 0.30
40 1 0.01
41 4 0.02
42 6 0.03
43 35 0.19
44 44 0.24
45 25 0.13
46 13 0.07
48 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (43 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCAATC
Found at i:45684656 original size:13 final size:14
Alignment explanation
Indices: 45684638--45684676 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
45684628 CCTCTCCTTC
45684638 CTTTTTTTCTT-TT
1 CTTTTTTTCTTCTT
45684651 C-TTTTTTCTTCTT
1 CTTTTTTTCTTCTT
45684664 C-TTTTTTCTTCTT
1 CTTTTTTTCTTCTT
45684677 TTTCCTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTTTTCTTCTT
Found at i:45684657 original size:7 final size:7
Alignment explanation
Indices: 45684638--45684704 Score: 57
Period size: 7 Copynumber: 9.0 Consensus size: 7
45684628 CCTCTCCTTC
45684638 CTTTTTT
1 CTTTTTT
*
45684645 -TCTTTT
1 CTTTTTT
45684651 CTTTTTT
1 CTTTTTT
45684658 CTTCTTCTT
1 CTT-TT-TT
45684667 -TTTTCTT
1 CTTTT-TT
45684674 CTTTTTCCT
1 CTTTTT--T
45684683 CTTTTTTT
1 C-TTTTTT
45684691 CTTTTTT
1 CTTTTTT
45684698 CTTTTTT
1 CTTTTTT
45684705 GAATCTGAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
6 5 0.10
7 27 0.53
8 10 0.20
9 4 0.08
10 5 0.10
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
CTTTTTT
Found at i:45684662 original size:10 final size:10
Alignment explanation
Indices: 45684647--45684704 Score: 63
Period size: 9 Copynumber: 6.2 Consensus size: 10
45684637 CCTTTTTTTC
45684647 TTTTCTT-TT
1 TTTTCTTCTT
45684656 TTCTTCTTCTT
1 TT-TTCTTCTT
45684667 TTTTCTTC-T
1 TTTTCTTCTT
*
45684676 TTTTCCTC-T
1 TTTTCTTCTT
45684685 TTTT-TTCTT
1 TTTTCTTCTT
45684694 TTTTCTT-TT
1 TTTTCTTCTT
45684703 TT
1 TT
45684705 GAATCTGAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
8 2 0.05
9 24 0.56
10 13 0.30
11 4 0.09
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTCTTCTT
Found at i:45689118 original size:109 final size:110
Alignment explanation
Indices: 45688919--45689235 Score: 471
Period size: 110 Copynumber: 2.9 Consensus size: 110
45688909 AGAATTCAAG
* * * *
45688919 AGGATATTTGGCTATTTGGTTAAATGAG--AAATCAAAACCCAACACATTAGGGCACG-TTCCTC
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGTTTTCTC
* *
45688981 GAATTTCCAAACGCAAAACATTGGCTTATTTTGAAA-TTTTTGAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAA
* *
45689025 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCATATTAGGGCACGTTTTCTC
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGTTTTCTC
45689090 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAA
* ** *
45689135 AGGATACTTAACTATTTGGTTGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGTTTTCTT
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGTTTTCTC
* * *
45689200 GAATTTCCAAACGCTAAATATTGCCTTATTTAGAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAA
45689236 AATTTTCCTT
Statistics
Matches: 190, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
106 26 0.14
108 25 0.13
109 40 0.21
110 99 0.52
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (110 bp):
AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAA
Found at i:45689558 original size:24 final size:24
Alignment explanation
Indices: 45689530--45689575 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
45689520 ATAAAATATA
45689530 TAATATATATAA-ATATACATATTT
1 TAATATATA-AATATATACATATTT
*
45689554 TAATATATAAATATATATATAT
1 TAATATATAAATATATACATAT
45689576 GAATAAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
TAATATATAAATATATACATATTT
Found at i:45689580 original size:22 final size:22
Alignment explanation
Indices: 45689525--45689580 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
45689515 GTAAGATAAA
45689525 ATATATAATATATATAAATATAC
1 ATATATAA-ATATATAAATATAC
* * *
45689548 ATATTTTAATATATAAATATAT
1 ATATATAAATATATAAATATAC
*
45689570 ATATATGAATA
1 ATATATAAATA
45689581 AGTATACACA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATATAAATATATAAATATAC
Found at i:45691322 original size:3 final size:3
Alignment explanation
Indices: 45691316--45691376 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
45691306 CTCCTCCCCC
45691316 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
45691364 TCA TCA TCA TCA T
1 TCA TCA TCA TCA T
45691377 GAGTTTTAGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:45700599 original size:37 final size:37
Alignment explanation
Indices: 45700544--45700623 Score: 142
Period size: 37 Copynumber: 2.2 Consensus size: 37
45700534 ATAATAATTT
*
45700544 AATTAAATTATCCAATTCAATTACTTAAAAATACTTA
1 AATTCAATTATCCAATTCAATTACTTAAAAATACTTA
*
45700581 AATTCAATTATCCAATTCAATTACTTTAAAATACTTA
1 AATTCAATTATCCAATTCAATTACTTAAAAATACTTA
45700618 AATTCA
1 AATTCA
45700624 TGTAATTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (37 bp):
AATTCAATTATCCAATTCAATTACTTAAAAATACTTA
Found at i:45701460 original size:15 final size:15
Alignment explanation
Indices: 45701440--45701479 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
45701430 AAAAACAAGG
45701440 TCCCAAAACCTTATT
1 TCCCAAAACCTTATT
*
45701455 TCCCAAAACGTTATT
1 TCCCAAAACCTTATT
45701470 TCCCAAAACC
1 TCCCAAAACC
45701480 ACTTGACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.03, T:0.28
Consensus pattern (15 bp):
TCCCAAAACCTTATT
Found at i:45704577 original size:39 final size:39
Alignment explanation
Indices: 45704532--45704672 Score: 165
Period size: 39 Copynumber: 3.6 Consensus size: 39
45704522 AACATGTTTT
* * *
45704532 TGAGTATTGTGATATATGATTGAATGTTATGTGATTATT
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * * ** *
45704571 TAAGTATTGCGATATGTGCTTAAACATTATGTAATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
45704610 TGAGTATCGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
45704649 TGTGTAATGTGATATATGTTTAAA
1 TGAGTATTGTGATATATGCTTAAA
45704673 AGTGAATATG
Statistics
Matches: 82, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.32, C:0.04, G:0.20, T:0.45
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:45708541 original size:30 final size:31
Alignment explanation
Indices: 45708486--45708543 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
45708476 ACCCTTAAAA
** *
45708486 TATTTACACTATTGGTCCTTCAAATTTTTTT
1 TATTTACACTATTACTCCCTCAAATTTTTTT
45708517 TATTTACACT-TTACTCCCTCAAATTTT
1 TATTTACACTATTACTCCCTCAAATTTT
45708544 GAGTATTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.24, C:0.21, G:0.03, T:0.52
Consensus pattern (31 bp):
TATTTACACTATTACTCCCTCAAATTTTTTT
Found at i:45710342 original size:50 final size:50
Alignment explanation
Indices: 45710275--45710621 Score: 340
Period size: 50 Copynumber: 6.7 Consensus size: 50
45710265 TTTTCTGTAC
* * * *
45710275 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGCTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGA
* ** * * * *
45710325 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGGCCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGA
* * *
45710375 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGA
*
45710425 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCAT-A--TC---GA
* * *
45710481 TGCCAATGTCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCAT-A--TC---GA
* * *
45710537 TGCCAATGCCATGTCCCAGACATGGCCTGACACTG-G--CTCACATATCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA-TGAGACCTCTCATATCGA
* * *
45710585 TGTCGATGCCATGTCCCAGACATGGTCTTATATGAGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGA
45710622 TCGAACACTG
Statistics
Matches: 257, Mismatches: 31, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
47 2 0.01
48 30 0.12
50 130 0.51
51 2 0.01
53 3 0.01
54 6 0.02
56 82 0.32
57 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGA
Found at i:45710494 original size:56 final size:56
Alignment explanation
Indices: 45710425--45710561 Score: 238
Period size: 56 Copynumber: 2.4 Consensus size: 56
45710415 CTCATCTCGG
*
45710425 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCTCAATGA
* * *
45710481 TGCCAATGTCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCTCAATGA
45710537 TGCCAATGCCATGTCCCAGACATGG
1 TGCCAATGCCATGTCCCAGACATGG
45710562 CCTGACACTG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 75 1.00
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.26
Consensus pattern (56 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCTCAATGA
Found at i:45717742 original size:25 final size:25
Alignment explanation
Indices: 45717713--45717825 Score: 127
Period size: 25 Copynumber: 4.5 Consensus size: 25
45717703 TTAACTATCC
*
45717713 CCTCTACTACATCGCCGTCAACACT
1 CCTCTACTGCATCGCCGTCAACACT
* * * *
45717738 CCTCTGCCGCATCGCCATCAACAGT
1 CCTCTACTGCATCGCCGTCAACACT
* *
45717763 CCTCTACCGCATCGCCGTCGACACT
1 CCTCTACTGCATCGCCGTCAACACT
* * * *
45717788 CCTCTATTGCGTCACCGTCGACACT
1 CCTCTACTGCATCGCCGTCAACACT
45717813 CCTCTACTGCATC
1 CCTCTACTGCATC
45717826 ATCATGTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 73 1.00
ACGTcount: A:0.19, C:0.44, G:0.13, T:0.24
Consensus pattern (25 bp):
CCTCTACTGCATCGCCGTCAACACT
Found at i:45719299 original size:19 final size:19
Alignment explanation
Indices: 45719275--45719328 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
45719265 AATCTTCAAG
* *
45719275 GATATGCAATCATAGATGT
1 GATATGCAATCTTAGATAT
*
45719294 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
45719313 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
45719329 AGATATGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:45719335 original size:22 final size:23
Alignment explanation
Indices: 45719307--45719351 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
45719297 ATGTAATCTT
45719307 AGATATGA-TATGCAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
* *
45719329 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
45719352 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:45719354 original size:22 final size:21
Alignment explanation
Indices: 45719288--45719354 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 21
45719278 ATGCAATCAT
*
45719288 AGATGTGATATGTAATCTT--
1 AGATATGATATGTAATCTTAG
*
45719307 AGATATGATATGCAATCTTAG
1 AGATATGATATGTAATCTTAG
*
45719328 AAGATATGATTTTGTAATCTTAG
1 -AGATATGA-TATGTAATCTTAG
45719351 AGAT
1 AGAT
45719355 TTAATTTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 17 0.43
22 12 0.30
23 11 0.28
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (21 bp):
AGATATGATATGTAATCTTAG
Found at i:45719578 original size:23 final size:23
Alignment explanation
Indices: 45719534--45719578 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
45719524 TCTTATTTTG
* *
45719534 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
45719557 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
45719579 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:45730171 original size:6 final size:6
Alignment explanation
Indices: 45730162--45730188 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
45730152 AGGAAATGAT
45730162 ATATGG ATATGG ATATGG ATATGG ATA
1 ATATGG ATATGG ATATGG ATATGG ATA
45730189 AAGATGTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (6 bp):
ATATGG
Found at i:45734374 original size:6 final size:6
Alignment explanation
Indices: 45734363--45734405 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
45734353 CTCCGTCCCC
*
45734363 CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT CTTCAC CTTCAT C
1 CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT C
45734406 CTTCCTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.16, C:0.37, G:0.00, T:0.47
Consensus pattern (6 bp):
CTTCAT
Found at i:45737470 original size:50 final size:50
Alignment explanation
Indices: 45737412--45737555 Score: 189
Period size: 51 Copynumber: 2.9 Consensus size: 50
45737402 TTGAGGTTAA
* *
45737412 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAAAT
** * *
45737462 GAGAGGTCCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGAAAT
1 GAGAGGT-CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAAAT
** * *
45737513 GAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
45737556 GTACAGAAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
50 37 0.47
51 42 0.53
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAAAT
Found at i:45737809 original size:12 final size:12
Alignment explanation
Indices: 45737792--45737830 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
45737782 ATGAGTTATT
45737792 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
45737804 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
45737816 TAAGTGAGTAAG
1 TAAGTAAGCAAG
45737828 TAA
1 TAA
45737831 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:45741666 original size:23 final size:23
Alignment explanation
Indices: 45741623--45741667 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
45741613 CTTTCCTCCC
**
45741623 TTTTCTTCCTCTTTCTTTCCTTG
1 TTTTCTTCCTCTTTCACTCCTTG
45741646 TTTTC-TCCTCTTTTCACTCCTT
1 TTTTCTTCCTC-TTTCACTCCTT
45741668 TTGTTCACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.02, C:0.33, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTTCTTCCTCTTTCACTCCTTG
Found at i:45744099 original size:6 final size:6
Alignment explanation
Indices: 45744083--45744125 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
45744073 TATGTTTCTC
*
45744083 AAAATG GAAATG AAAATG AAAATG AAAATG AAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG A
45744126 GATACTTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:45747798 original size:14 final size:15
Alignment explanation
Indices: 45747772--45747804 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
45747762 TCCCAAGCTG
45747772 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
45747787 GGAAGG-CCTTATTT
1 GGAAGGACCTTATGT
45747801 GGAA
1 GGAA
45747805 AAGCATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Found at i:45749294 original size:88 final size:88
Alignment explanation
Indices: 45749140--45749899 Score: 846
Period size: 88 Copynumber: 8.6 Consensus size: 88
45749130 ATCATTCAAG
* * * ** ** *
45749140 ATAGTAGATCTTGCCTTCCTGTACCGGCA-ATAGAGCAGATCAAAGACACCAG-CTTTGTCTCCC
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGA-AGCAGATTGAAGACACCAGTC-TTGCCTCCC
* *
45749203 TAGGTTGCAGCGGAGCAGGTTGAAA
64 TAGGTTGCAGTGGAGCAGATTGAAA
* * * *
45749228 ATAACAGATCTTGCCTTCCTGTACTGATAGCGAAACAGATTGAAGGCACCAGTCTTGCCTCCCTA
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTA
* * *
45749293 GGTTGCAGTGGAGTAGACTGAAG
66 GGTTGCAGTGGAGCAGATTGAAA
* * * *
45749316 ATAGCAGATCTTGCCTTCCTATACTTACAGTGAAGCAGATCGAAGACACCAGTCTTGCCTCCCTA
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTA
* *
45749381 GGTTGCAGTGGAGCAGACTGAAG
66 GGTTGCAGTGGAGCAGATTGAAA
* * * *
45749404 ATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGA-TCAAGGACACCAGCCTTGCCTCCTT
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAA-GACACCAGTCTTGCCTCCCT
* * *
45749468 GGGTTGCAGCGGAGCAGGTTGAAA
65 AGGTTGCAGTGGAGCAGATTGAAA
*
45749492 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCTCCCTA
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTA
* * *
45749557 GGTTGCAGTGGAGTAAATTGAAG
66 GGTTGCAGTGGAGCAGATTGAAA
* * * * * *
45749580 ATGGCAGATCTTGCCTTCCTGTACTGGCATCGAAGCAGATTAAAGATACCAGCCTTGCCTCCCT-
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTA
* *
45749644 GGATTGCAGCGGAGCAGGTTGAAA
66 GG-TTGCAGTGGAGCAGATTGAAA
* * * * *
45749668 ATAGTAGATCTTGCCTTCCTATACTGACAGTGAAGCAGATTGAAGACGCTAGTCTTGCCTCCCTA
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTA
* * *
45749733 GGTTGCAGTGGAACAGACTGAAG
66 GGTTGCAGTGGAGCAGATTGAAA
* * * * * * * * *
45749756 ATAGCAGATCTTACCTTTCTGTACCGGCAGCGAAGCAGATCGAAAACTCCGGTCTTGTCTCCCT-
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTA
** * *
45749820 GAGCAGCAGTGGAGTAGGTTGAAA
66 G-GTTGCAGTGGAGCAGATTGAAA
* * *
45749844 ATAGCAGATCTTGCCTTCCTGTACTGGCAGTGAAGCAGATTGAAGACATCAGTCTT
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACACCAGTCTT
45749900 ATTGCCTTGA
Statistics
Matches: 558, Mismatches: 107, Indels: 14
0.82 0.16 0.02
Matches are distributed among these distances:
87 5 0.01
88 547 0.98
89 6 0.01
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (88 bp):
ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTA
GGTTGCAGTGGAGCAGATTGAAA
Found at i:45749617 original size:264 final size:263
Alignment explanation
Indices: 45749137--45749899 Score: 967
Period size: 264 Copynumber: 2.9 Consensus size: 263
45749127 CAGATCATTC
* * * *
45749137 AAGATAGTAGATCTTGCCTTCCTGTACCGGCA-ATAGAGCAGATCAAAGACACCAGCTTTGTCTC
1 AAGATAGTAGATCTTGCCTTCCTGTACCGACAGAGA-AGCAGATC-AAGACACCAGCCTTGCCTC
* * *
45749201 CCTAGGTTGCAGCGGAGCAGGTTGAAAATAACAGATCTTGCCTTCCTGTACTGATAGCGAAACAG
64 CCTAGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAG
* * *
45749266 ATTGAAGGCACCAGTCTTGCCTCCCTAGGTTGCAGTGGAGTAGACTGAAGATAGCAGATCTTGCC
129 ATCGAAGACACCAGTCTTGCCTCCCTAGGTTGCAGTGGAGTAGATTGAAGATAGCAGATCTTGCC
* ** * *
45749331 TTCCTATACTTACAGTGAAGCAGATCGAAGACACCAGTCTTGCCTCCCTAGG-TTGCAGTGGAGC
194 TTCCTGTACTGGCAGTGAAGCAGATTGAAGACACCAGTCTTGCCTCCCT-GGATTGCAGCGGAGC
45749395 AGACTG
258 AGACTG
* *
45749401 AAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCAAGGACACCAGCCTTGCCTCC
1 AAGATAGTAGATCTTGCCTTCCTGTACCGACAGAGAAGCAGATCAA-GACACCAGCCTTGCCTCC
* *
45749466 TTGGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
65 CTAGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
* *
45749531 TCGAAGACACCAGTCTTGCCTCCCTAGGTTGCAGTGGAGTAAATTGAAGATGGCAGATCTTGCCT
130 TCGAAGACACCAGTCTTGCCTCCCTAGGTTGCAGTGGAGTAGATTGAAGATAGCAGATCTTGCCT
* * *
45749596 TCCTGTACTGGCA-TCGAAGCAGATTAAAGATACCAGCCTTGCCTCCCTGGATTGCAGCGGAGCA
195 TCCTGTACTGGCAGT-GAAGCAGATTGAAGACACCAGTCTTGCCTCCCTGGATTGCAGCGGAGCA
**
45749660 GGTTG
259 GACTG
* * * * * * * *
45749665 AAAATAGTAGATCTTGCCTTCCTATACTGACAGTGAAGCAGATTGAAGACGCTAGTCTTGCCTCC
1 AAGATAGTAGATCTTGCCTTCCTGTACCGACAGAGAAGCAGA-TCAAGACACCAGCCTTGCCTCC
* * ** * * * * *
45749730 CTAGGTTGCAGTGGAACAGACTGAAGATAGCAGATCTTACCTTTCTGTACCGGCAGCGAAGCAGA
65 CTAGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
* * * * ** * *
45749795 TCGAAAACTCCGGTCTTGTCTCCCT-GAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCC
130 TCGAAGACACCAGTCTTGCCTCCCTAG-GTTGCAGTGGAGTAGATTGAAGATAGCAGATCTTGCC
*
45749859 TTCCTGTACTGGCAGTGAAGCAGATTGAAGACATCAGTCTT
194 TTCCTGTACTGGCAGTGAAGCAGATTGAAGACACCAGTCTT
45749900 ATTGCCTTGA
Statistics
Matches: 432, Mismatches: 60, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
263 6 0.01
264 421 0.97
265 5 0.01
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (263 bp):
AAGATAGTAGATCTTGCCTTCCTGTACCGACAGAGAAGCAGATCAAGACACCAGCCTTGCCTCCC
TAGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGAT
CGAAGACACCAGTCTTGCCTCCCTAGGTTGCAGTGGAGTAGATTGAAGATAGCAGATCTTGCCTT
CCTGTACTGGCAGTGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTGGATTGCAGCGGAGCAGA
CTG
Found at i:45750041 original size:17 final size:19
Alignment explanation
Indices: 45750021--45750058 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
45750011 GTTAAGGCTT
45750021 GGATT-AGCTGAAGG-AGC
1 GGATTAAGCTGAAGGCAGC
45750038 GGATTAAAGCTGAAGGCAGC
1 GGATT-AAGCTGAAGGCAGC
45750058 G
1 G
45750059 AATCCTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.32, C:0.13, G:0.39, T:0.16
Consensus pattern (19 bp):
GGATTAAGCTGAAGGCAGC
Found at i:45750144 original size:115 final size:116
Alignment explanation
Indices: 45749969--45750208 Score: 365
Period size: 115 Copynumber: 2.1 Consensus size: 116
45749959 GCGTTGTAGC
* * *
45749969 GGAGCATATTGAAGCCATGACGATGAATCTTATCTTCCTGGCGTTAAGGCTTGGATTAGCTGAA-
1 GGAGCAGATTGAAGCCACGACGACGAATCTTATCTTCCTGGCGTTAAGGCTTGGATTAGCTGAAG
*
45750033 GGAGCGGATTAAAGCTGAAGGCAGCGAATCCTATCTCTTTGGCATTCCAGT
66 GGAGCGGATTAAAGCTGAAGGCAACGAATCCTATCTCTTTGGCATTCCAGT
* * *
45750084 GGAGCAGATTGAAGCCACGATGACGAATCTTATCTTCTTGGCGTTAAGGTTTGGATTAGCTGAAG
1 GGAGCAGATTGAAGCCACGACGACGAATCTTATCTTCCTGGCGTTAAGGCTTGGATTAGCTGAAG
** * *
45750149 TGGAGTTGATTAAAGCTGAGGGCAACGAATCCTATCTCTTTGGCATTGCAGT
66 -GGAGCGGATTAAAGCTGAAGGCAACGAATCCTATCTCTTTGGCATTCCAGT
45750201 GGAGCAGA
1 GGAGCAGA
45750209 CTGAGTAAGA
Statistics
Matches: 112, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
115 58 0.52
117 54 0.48
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (116 bp):
GGAGCAGATTGAAGCCACGACGACGAATCTTATCTTCCTGGCGTTAAGGCTTGGATTAGCTGAAG
GGAGCGGATTAAAGCTGAAGGCAACGAATCCTATCTCTTTGGCATTCCAGT
Found at i:45750248 original size:44 final size:44
Alignment explanation
Indices: 45750193--45750292 Score: 130
Period size: 44 Copynumber: 2.3 Consensus size: 44
45750183 TCTCTTTGGC
* * * *
45750193 ATTGCAGTGGAGCAGACTGAGT-AAGAAAGTCTTATCCCCCTAAA
1 ATTGTAGTGGAGCAGACTGAATGAACAAA-TCCTATCCCCCTAAA
*
45750237 ATTGTAGTGGAGCAGACTGAATGAACAAATCCTATCTCCCTAAA
1 ATTGTAGTGGAGCAGACTGAATGAACAAATCCTATCCCCCTAAA
*
45750281 GTTGTAGTGGAG
1 ATTGTAGTGGAG
45750293 TGGATTAGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
44 44 0.90
45 5 0.10
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (44 bp):
ATTGTAGTGGAGCAGACTGAATGAACAAATCCTATCCCCCTAAA
Found at i:45750775 original size:19 final size:19
Alignment explanation
Indices: 45750729--45750784 Score: 94
Period size: 21 Copynumber: 2.8 Consensus size: 19
45750719 AATCTTCAAG
45750729 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
45750748 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
45750769 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
45750785 AGATGTGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.46
21 19 0.54
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:45751296 original size:17 final size:17
Alignment explanation
Indices: 45751274--45751308 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
45751264 TTTATATACA
* *
45751274 TATATATATTTACATTT
1 TATATACATATACATTT
45751291 TATATACATATACATTT
1 TATATACATATACATTT
45751308 T
1 T
45751309 TTATTTCCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATACATATACATTT
Found at i:45751905 original size:6 final size:6
Alignment explanation
Indices: 45751889--45751930 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
45751879 TATGTTTCTC
*
45751889 AAAATG GAAATG AAAATG AAAATG AAAATG AAAATG AGAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG A-AAAT
45751931 ACTTCATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
6 29 0.88
7 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:45753640 original size:56 final size:55
Alignment explanation
Indices: 45753580--45753698 Score: 129
Period size: 56 Copynumber: 2.1 Consensus size: 55
45753570 ACATATTATA
45753580 TATATTTTATTATA-A-TTCTATTTGCATAACTTTTATATGCATATATATTTACA-TTT
1 TATATTTTA-TATACATTTCTATTT-CATAACTTTTATATGCATATATA--TACACTTT
** * *
45753636 TATA-TACATATACATTTTTTATTTCCTAACTTTTATATGCATATATATACACTTT
1 TATATTTTATATACA-TTTCTATTTCATAACTTTTATATGCATATATATACACTTT
45753691 TATATTTT
1 TATATTTT
45753699 TGTACTTTAC
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
54 8 0.15
55 10 0.19
56 27 0.52
57 7 0.13
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (55 bp):
TATATTTTATATACATTTCTATTTCATAACTTTTATATGCATATATATACACTTT
Found at i:45753845 original size:29 final size:27
Alignment explanation
Indices: 45753788--45753879 Score: 91
Period size: 27 Copynumber: 3.3 Consensus size: 27
45753778 ATTAATTTTA
45753788 ATATATGTAATTATTATTTGTTT-T-TAT
1 ATATATGTAATTATT-TTT-TTTATATAT
45753815 ATATATGTAATTATCTTTTTTTATAATAT
1 ATATATGTAATTAT-TTTTTTTAT-ATAT
*
45753844 ATATATGTAGA-TAATTTTTTTATATAT
1 ATATATGTA-ATTATTTTTTTTATATAT
* *
45753871 GTACATGTA
1 ATATATGTA
45753880 TATATTTATA
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
26 3 0.05
27 29 0.51
28 10 0.18
29 14 0.25
30 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.57
Consensus pattern (27 bp):
ATATATGTAATTATTTTTTTTATATAT
Found at i:45757561 original size:54 final size:54
Alignment explanation
Indices: 45757450--45757564 Score: 124
Period size: 54 Copynumber: 2.1 Consensus size: 54
45757440 GTAACTTCGA
* * * * * *
45757450 GTTTACTGTCACGACAGACTACCCCGTGTTTATTGTCCTAGTAGACTACTCTAT
1 GTTTACTATCACGACAGACTACCCCATGTTTACTGTCCGAGTAGACTACCCCAT
* * * *
45757504 GTTTACTATCTCGACGGACTACCCCATGTTTACTGTCCCGA-TGGACTACCCCGT
1 GTTTACTATCACGACAGACTACCCCATGTTTACTGT-CCGAGTAGACTACCCCAT
45757558 GTTTACT
1 GTTTACT
45757565 GTCCTTACGA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
54 47 0.94
55 3 0.06
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (54 bp):
GTTTACTATCACGACAGACTACCCCATGTTTACTGTCCGAGTAGACTACCCCAT
Found at i:45757565 original size:27 final size:27
Alignment explanation
Indices: 45757450--45757568 Score: 105
Period size: 27 Copynumber: 4.4 Consensus size: 27
45757440 GTAACTTCGA
* *
45757450 GTTTACTGTCACGACAGACTACCCCGT
1 GTTTACTGTCCCGACAGACTACCCCAT
* * * * *
45757477 GTTTATTGT-CCTAGTAGACTACTCTAT
1 GTTTACTGTCCCGA-CAGACTACCCCAT
* * *
45757504 GTTTACTATCTCGACGGACTACCCCAT
1 GTTTACTGTCCCGACAGACTACCCCAT
** *
45757531 GTTTACTGTCCCGATGGACTACCCCGT
1 GTTTACTGTCCCGACAGACTACCCCAT
45757558 GTTTACTGTCC
1 GTTTACTGTCC
45757569 TTACGAACTA
Statistics
Matches: 71, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
26 2 0.03
27 67 0.94
28 2 0.03
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (27 bp):
GTTTACTGTCCCGACAGACTACCCCAT
Found at i:45767119 original size:14 final size:14
Alignment explanation
Indices: 45767100--45767146 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
45767090 GTAGAAAATT
45767100 TAGAGAAAAGAAAA
1 TAGAGAAAAGAAAA
45767114 TAGAGAAAAGGAAGAA
1 TAGAGAAAA-GAA-AA
**
45767130 -AGAGAGGAGAAAA
1 TAGAGAAAAGAAAA
45767143 TAGA
1 TAGA
45767147 TAACAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 2 0.07
14 15 0.54
15 9 0.32
16 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.06
Consensus pattern (14 bp):
TAGAGAAAAGAAAA
Found at i:45770335 original size:62 final size:59
Alignment explanation
Indices: 45770266--45770380 Score: 167
Period size: 62 Copynumber: 1.9 Consensus size: 59
45770256 AGTGATTATC
* * *
45770266 TTAATATTAAATTTAATTTAATTTTTATCTTATAGATAAATATTTTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATTTTTATC-T-T-GATAAATATTATATTAATTTAATAAGAT
*
45770328 TTAATATTAAATTTAATCTAATTTTTCTCTTGATAAATATTATATTAATTTAA
1 TTAATATTAAATTTAATCTAATTTTTATCTTGATAAATATTATATTAATTTAA
45770381 CTTTAAAATG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 20 0.41
60 1 0.02
61 1 0.02
62 27 0.55
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATTTTTATCTTGATAAATATTATATTAATTTAATAAGAT
Found at i:45784327 original size:6 final size:6
Alignment explanation
Indices: 45784316--45784362 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
45784306 TATCTTTGTC
* * *
45784316 TTTAAT TGTAAT CTTTAAT TTTAAT TTTAAT TTTAAT GTTAGT TTTA
1 TTTAAT TTTAAT -TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTA
45784363 TTTATTTTGC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
6 30 0.86
7 5 0.14
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (6 bp):
TTTAAT
Found at i:45784332 original size:13 final size:13
Alignment explanation
Indices: 45784314--45784352 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
45784304 TTTATCTTTG
*
45784314 TCTTTAATTGTAA
1 TCTTTAATTTTAA
45784327 TCTTTAATTTTAA
1 TCTTTAATTTTAA
45784340 T-TTTAATTTTAA
1 TCTTTAATTTTAA
45784352 T
1 T
45784353 GTTAGTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (13 bp):
TCTTTAATTTTAA
Found at i:45787655 original size:38 final size:38
Alignment explanation
Indices: 45787613--45787687 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
45787603 TACCTTCACC
45787613 TATTTTTAGTAAACTTAAACCTATTTCCATCATCCCTT
1 TATTTTTAGTAAACTTAAACCTATTTCCATCATCCCTT
45787651 TATTTTTAGTAAACTTAAACCTATTTCCATCATCCCT
1 TATTTTTAGTAAACTTAAACCTATTTCCATCATCCCT
45787688 CATCACTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.24, G:0.03, T:0.44
Consensus pattern (38 bp):
TATTTTTAGTAAACTTAAACCTATTTCCATCATCCCTT
Found at i:45792261 original size:19 final size:19
Alignment explanation
Indices: 45792237--45792275 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
45792227 ATGAAAAAAA
45792237 ATAGAAAAATTCATACTAC
1 ATAGAAAAATTCATACTAC
45792256 ATAGAAAAATTCATACTAC
1 ATAGAAAAATTCATACTAC
45792275 A
1 A
45792276 GGAGTCATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.26
Consensus pattern (19 bp):
ATAGAAAAATTCATACTAC
Found at i:45794499 original size:26 final size:26
Alignment explanation
Indices: 45794469--45794539 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
45794459 CCTGTACATA
*
45794469 TATGCTCACACGATCTGTGAAATGAG
1 TATGCTCACACGAGCTGTGAAATGAG
* *
45794495 TATGCTCACATGAGATGTGAAATGAG
1 TATGCTCACACGAGCTGTGAAATGAG
**
45794521 CCTGCTCACACGAGCTGTG
1 TATGCTCACACGAGCTGTG
45794540 GGTCAGAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (26 bp):
TATGCTCACACGAGCTGTGAAATGAG
Found at i:45797979 original size:50 final size:50
Alignment explanation
Indices: 45797868--45798114 Score: 219
Period size: 50 Copynumber: 4.8 Consensus size: 50
45797858 ATTTGGGTAA
* * *
45797868 AGAGATCCCATATAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATG
* *
45797924 AGAGGTTCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
45797974 AGAGGTCCCCCGTAAGACTATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * * *
45798024 AGAGCTCCCATGTAAGACCATATATGGGATATGACATTGGCA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * * *
45798073 AAACATCCCATGTAAGACCATGTTTGGGATATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
45798115 TGTTATTATC
Statistics
Matches: 161, Mismatches: 29, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
48 1 0.01
49 39 0.24
50 79 0.49
52 1 0.01
53 2 0.01
55 1 0.01
56 38 0.24
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:45811066 original size:599 final size:600
Alignment explanation
Indices: 45809928--45811112 Score: 2068
Period size: 599 Copynumber: 2.0 Consensus size: 600
45809918 TTATTTTATT
*
45809928 ATTATTTTAATGTTTATGGAATTTTAGTAAGTTCATATAAAAATTTTGTTAAGAAATTTTGACGT
1 ATTATTTTAATGTTTATGGAATTTTAGTAAGTTCATATAAAAATTTTGTTAAGAAATTTTGACAT
* * *
45809993 TTGCATGTTTAATTATGTAAAAATGACTAAATCATACAAGGTACAGAGTTCTATTAGTTAAAAGG
66 TTGCATGTTTAATTACGTAAAAATGACTAAATCATAAAAGGTACAGAGTTCTATTAGTTAAAAAG
*
45810058 GTTAAATGACTATGAAACTTTAAAGTGAAATGACTTAGATTGTAATTAGACCATTTGAGTGGTTA
131 GTTAAATGACTATGAAACTTTAAAGTGAAAGGACTTAGATTGTAATTAGACCATTTGAGTGGTTA
*
45810123 GTGGATATTCATGGCAAGGTTTATTTGAAATTTTGAATGTTTTTAAAGGTTAAAAAGGTAAATGA
196 GTGGATATTCATGGCAAGGTTTATTTGAAAATTTGAATGTTTTTAAAGGTTAAAAAGGTAAATGA
*
45810188 GTAAATCAGGGTAAATTAAATAAAACAAAATATTTTCCCATTTTCATTCATCTTCTTCCACCGAA
261 GTAAATAAGGGTAAATTAAATAAAACAAAATATTTTCCCATTTTCATTCATCTTCTTCCACCGAA
* *
45810253 ATTGAAGGTAGAAGAAACCATTTTTAGGGTTCTTGATTTCGACAAGCTTGGGTGGTGCATGTAAG
326 ATTGAAGGGAGAAGAAACCATTTTTAGGGTTCCTGATTTCGACAAGCTTGGGTGGTGCATGTAAG
** *
45810318 TGATTTTTGAGCTTGTTTTTAATGATTTTCATGTTTTTGGGATCGTTGTAGCTTAATCTAGCTAA
391 TGATTTTTGAGCTCATTTTTAATGATTTTCATGTTTTTGGGACCGTTGTAGCTTAATCTAGCTAA
* * *
45810383 CCAGGGGATCAATTTGCAAAAATTTTAAAGATTTAGGGTTTTCCTATGAATGTTCTTGCATGATT
456 CCAGGGGATCAATTTGCAAAAATTTTAAAAATTTAGGGTTTTCCCATGAATGTTCTTGCACGATT
45810448 CTTGATGTTTTATGAAAGATTATGAGTCCTTGCTGATAAATAAACAAGTTTTGAAAAGTAATTTT
521 CTTGATGTTTTATGAAAGATTATGAGTCCTTGCTGATAAATAAACAAGTTTTGAAAAGTAATTTT
45810513 TATGAAATTGTAAAG
586 TATGAAATTGTAAAG
*
45810528 ATTATTTTAATGTTTATGGAATTTTAGTAAGTTCGTATAAAAATTTTGTTAAGAAATTTTGACAT
1 ATTATTTTAATGTTTATGGAATTTTAGTAAGTTCATATAAAAATTTTGTTAAGAAATTTTGACAT
* * *
45810593 TTGTATGTTTAATTACGTAAAAATGACTAAATCGTAAAAGGTGCAGAGTTCTATTAGTTAAAAAG
66 TTGCATGTTTAATTACGTAAAAATGACTAAATCATAAAAGGTACAGAGTTCTATTAGTTAAAAAG
* * *
45810658 GTTAAATGACTATGACACTTTAAAGTGGAAGGACTTAGATTGTAATTAGACCGTTTGAGTGGTTA
131 GTTAAATGACTATGAAACTTTAAAGTGAAAGGACTTAGATTGTAATTAGACCATTTGAGTGGTTA
*
45810723 GTGGATATTCATGGCAAGGTTTATTTGAAAATTTGAATGTTTTTAAAGGTTAAAAAGGTAAGTG-
196 GTGGATATTCATGGCAAGGTTTATTTGAAAATTTGAATGTTTTTAAAGGTTAAAAAGGTAAATGA
45810787 GTAAATAAGGGTAAATTAAATAAAACAAAATATTTTCCCATTTTCATTCATCTTCTTCCACCGAA
261 GTAAATAAGGGTAAATTAAATAAAACAAAATATTTTCCCATTTTCATTCATCTTCTTCCACCGAA
45810852 ATTGAAGGGAGAAGAAACCATTTTTAGGGTTCCTGATTTCGACAAGCTTGGGTGGTGCATGTAAG
326 ATTGAAGGGAGAAGAAACCATTTTTAGGGTTCCTGATTTCGACAAGCTTGGGTGGTGCATGTAAG
*
45810917 TGATTTTTGAGCTCATTTTTAATGATTTTTAT-TTTTCTGGGACCGTTGTAGCTTAATCTAGCTA
391 TGATTTTTGAGCTCATTTTTAATGATTTTCATGTTTT-TGGGACCGTTGTAGCTTAATCTAGCTA
* * * * *
45810981 GCCTGGTGATCAATTTGCAAAACTTTTAAAAATTTAGGGTTTTCCCATGAATTTTCTTGCACGAT
455 ACCAGGGGATCAATTTGCAAAAATTTTAAAAATTTAGGGTTTTCCCATGAATGTTCTTGCACGAT
* *
45811046 TCTTGATGTTTTATGAAAGATTATGAGTCCTTGCTTATAAATAAACAAGTTTTGTAAAGTAATTT
520 TCTTGATGTTTTATGAAAGATTATGAGTCCTTGCTGATAAATAAACAAGTTTTGAAAAGTAATTT
45811111 TT
585 TT
45811113 TTTATGAAAT
Statistics
Matches: 553, Mismatches: 31, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
598 4 0.01
599 304 0.55
600 245 0.44
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.39
Consensus pattern (600 bp):
ATTATTTTAATGTTTATGGAATTTTAGTAAGTTCATATAAAAATTTTGTTAAGAAATTTTGACAT
TTGCATGTTTAATTACGTAAAAATGACTAAATCATAAAAGGTACAGAGTTCTATTAGTTAAAAAG
GTTAAATGACTATGAAACTTTAAAGTGAAAGGACTTAGATTGTAATTAGACCATTTGAGTGGTTA
GTGGATATTCATGGCAAGGTTTATTTGAAAATTTGAATGTTTTTAAAGGTTAAAAAGGTAAATGA
GTAAATAAGGGTAAATTAAATAAAACAAAATATTTTCCCATTTTCATTCATCTTCTTCCACCGAA
ATTGAAGGGAGAAGAAACCATTTTTAGGGTTCCTGATTTCGACAAGCTTGGGTGGTGCATGTAAG
TGATTTTTGAGCTCATTTTTAATGATTTTCATGTTTTTGGGACCGTTGTAGCTTAATCTAGCTAA
CCAGGGGATCAATTTGCAAAAATTTTAAAAATTTAGGGTTTTCCCATGAATGTTCTTGCACGATT
CTTGATGTTTTATGAAAGATTATGAGTCCTTGCTGATAAATAAACAAGTTTTGAAAAGTAATTTT
TATGAAATTGTAAAG
Found at i:45811157 original size:9 final size:9
Alignment explanation
Indices: 45811143--45811169 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
45811133 GGACTTATTT
45811143 GTAAAAGTA
1 GTAAAAGTA
45811152 GTAAAAGTA
1 GTAAAAGTA
45811161 GTAAAAGTA
1 GTAAAAGTA
45811170 AATGGTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (9 bp):
GTAAAAGTA
Found at i:45814550 original size:23 final size:22
Alignment explanation
Indices: 45814519--45814570 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
45814509 AAGTGATAAT
*
45814519 AATTAAATATTATAAAAAAGATA
1 AATTTAATATTATAAAAAA-ATA
* *
45814542 AATTTAATATTTTTAAAAAATA
1 AATTTAATATTATAAAAAAATA
*
45814564 ATTTTAA
1 AATTTAA
45814571 ACTTTTAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AATTTAATATTATAAAAAAATA
Found at i:45814576 original size:21 final size:23
Alignment explanation
Indices: 45814533--45814578 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
45814523 AAATATTATA
*
45814533 AAAAAGATAAATTTAATATTTTT
1 AAAAAGATAAATTTAATACTTTT
*
45814556 AAAAA-ATAATTTTAA-ACTTTT
1 AAAAAGATAAATTTAATACTTTT
45814577 AA
1 AA
45814579 TCCAGTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 9 0.43
23 5 0.24
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
AAAAAGATAAATTTAATACTTTT
Found at i:45816739 original size:12 final size:12
Alignment explanation
Indices: 45816724--45816766 Score: 70
Period size: 12 Copynumber: 3.6 Consensus size: 12
45816714 TAAATATTAG
45816724 ATTAAATTTAAT
1 ATTAAATTTAAT
45816736 ATTAAATATTAA-
1 ATTAAAT-TTAAT
45816748 ATTAAATTTAAT
1 ATTAAATTTAAT
45816760 ATTAAAT
1 ATTAAAT
45816767 CTATTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.14
12 21 0.72
13 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTAAATTTAAT
Found at i:45816742 original size:24 final size:24
Alignment explanation
Indices: 45816714--45816766 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
45816704 TTTATCAAGA
*
45816714 TAAATATTAGATTAAATTTAATAT
1 TAAATATTAAATTAAATTTAATAT
45816738 TAAATATTAAATTAAATTTAATAT
1 TAAATATTAAATTAAATTTAATAT
45816762 TAAAT
1 TAAAT
45816767 CTATTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TAAATATTAAATTAAATTTAATAT
Found at i:45818735 original size:144 final size:144
Alignment explanation
Indices: 45818475--45818759 Score: 525
Period size: 144 Copynumber: 2.0 Consensus size: 144
45818465 AATCCTCTCA
*
45818475 TTGGTATTACATTGTTGATGAAAAGTAAACGTGGCCACGAGTCATTCGTCTTTGAGATGAATGAC
1 TTGGTATTACATTGTTGATGAAAAGTAAACGTGGCCACGAGTCATTCGTCTTTAAGATGAATGAC
* * *
45818540 TTGAATTATTTTTTGATAGAAATTGACTTTTGAAGAATGAAGATGCAATGGTTGTCATGAGATAA
66 TTGAATTATTATTTGATAGAAATTGACTTTTCAAGAATGAAGATGCAATGGTTGTCATGAAATAA
*
45818605 AATATGATTATTAT
131 AATACGATTATTAT
45818619 TTGGTATTACATTGTTGATGAAAAGTAAACGTGGCCACGAGTCATTCGTCTTTAAGATGAATGAC
1 TTGGTATTACATTGTTGATGAAAAGTAAACGTGGCCACGAGTCATTCGTCTTTAAGATGAATGAC
45818684 TTGAATTATTATTTGATAGAAATTGACTTTTCAAGAATGAAGATGCAATGGTTGTCATGAAATAA
66 TTGAATTATTATTTGATAGAAATTGACTTTTCAAGAATGAAGATGCAATGGTTGTCATGAAATAA
45818749 AATACGATTAT
131 AATACGATTAT
45818760 ACTGGGAGAA
Statistics
Matches: 136, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
144 136 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (144 bp):
TTGGTATTACATTGTTGATGAAAAGTAAACGTGGCCACGAGTCATTCGTCTTTAAGATGAATGAC
TTGAATTATTATTTGATAGAAATTGACTTTTCAAGAATGAAGATGCAATGGTTGTCATGAAATAA
AATACGATTATTAT
Found at i:45824390 original size:50 final size:50
Alignment explanation
Indices: 45824149--45824390 Score: 251
Period size: 50 Copynumber: 4.9 Consensus size: 50
45824139 GATAATAACA
* * * * * *
45824149 TGCCAAAGCTATGTCGCAGACATAGTCTTACATGGGA--TGTT-TCTTGTAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCG--G
* * * ** * *
45824198 TGGCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
* * *
45824248 TGCCCATGCCATGTCCCAAACATGGTCTT--ATGGAGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-G-GGACCTCTTATCTCGG
*
45824298 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAACTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
*
45824348 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
45824391 TACCCAAATG
Statistics
Matches: 161, Mismatches: 25, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
48 2 0.01
49 31 0.19
50 120 0.75
51 3 0.02
52 5 0.03
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
Found at i:45832293 original size:23 final size:23
Alignment explanation
Indices: 45832256--45832299 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
45832246 AGAATCCTAC
45832256 CCATCAACCTCTACACACCATCT
1 CCATCAACCTCTACACACCATCT
45832279 CCATCCAACCT-TACACACCAT
1 CCAT-CAACCTCTACACACCAT
45832300 GTGGGGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.20
Consensus pattern (23 bp):
CCATCAACCTCTACACACCATCT
Found at i:45834278 original size:39 final size:39
Alignment explanation
Indices: 45834224--45834400 Score: 212
Period size: 39 Copynumber: 4.5 Consensus size: 39
45834214 AACATGTTGT
*
45834224 TGAGTATTGTGATATATGCTTGAATGTTAACTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTAAGTGATTATA
* * * *
45834263 TGAGTATTGTGATATATGCTTGAAAGTTATGTAATTATT
1 TGAGTATTGTGATATATGCTTGAATGTTAAGTGATTATA
** *
45834302 TGAGTATTAAGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTAAGTGATTATA
* * *
45834341 TGAGTATTGTGCTATATGTTTGATTGTTATA-TGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTA-AGTGATTATA
* * *
45834380 TGTGTAATGTGCTATATGCTT
1 TGAGTATTGTGATATATGCTT
45834401 AAAAGTGAAT
Statistics
Matches: 118, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
39 118 1.00
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTGAATGTTAAGTGATTATA
Found at i:45835207 original size:20 final size:20
Alignment explanation
Indices: 45835167--45835207 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
45835157 TTAAAGAAAA
*
45835167 TATCGATACACTAGTGTTAG
1 TATCGATACACTAGTGATAG
45835187 TATCGATAC-CTACGTGATAG
1 TATCGATACACTA-GTGATAG
45835207 T
1 T
45835208 TTTGAGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (20 bp):
TATCGATACACTAGTGATAG
Found at i:45837981 original size:55 final size:55
Alignment explanation
Indices: 45837899--45838010 Score: 145
Period size: 54 Copynumber: 2.0 Consensus size: 55
45837889 AAGAAATGAA
* *
45837899 AATCATTTAGGAAATGATTATGGTTTTCCCCAAAATGAAAATGAAAATGAAAATGG
1 AATCATTTAGGAAATAAATATGGTTTT-CCCAAAATGAAAATGAAAATGAAAATGG
* * * * *
45837955 AATCATTT-GGAAATAAATGTGGTTTTCTCAAAATGGAAATGGAAATGGAAATGG
1 AATCATTTAGGAAATAAATATGGTTTTCCCAAAATGAAAATGAAAATGAAAATGG
45838009 AA
1 AA
45838011 ATAAAAATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
54 26 0.53
55 15 0.31
56 8 0.16
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.29
Consensus pattern (55 bp):
AATCATTTAGGAAATAAATATGGTTTTCCCAAAATGAAAATGAAAATGAAAATGG
Found at i:45837996 original size:6 final size:6
Alignment explanation
Indices: 45837985--45838026 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
45837975 GGTTTTCTCA
**
45837985 AAATGG AAATGG AAATGG AAATGG AAATAA AAATGAG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATG-G AAATG
45838027 AATTCATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.26, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:45839201 original size:57 final size:58
Alignment explanation
Indices: 45839140--45839260 Score: 174
Period size: 57 Copynumber: 2.1 Consensus size: 58
45839130 AGAAATGGTA
*
45839140 AAAATGGAGAAATGAGAAACATTT-AAAATGAATGAGGTTTTCT-ACAAAATGAAAAAG
1 AAAATGGAGAAATGA-AAACATTTGAAAATGAATGAGGTTTTCTCAAAAAATGAAAAAG
* * * *
45839197 AAAATAGAGAAATGAAAACATTTGGAAATGAATGTGGTTTTCTCAAAAAATGAAAATG
1 AAAATGGAGAAATGAAAACATTTGAAAATGAATGAGGTTTTCTCAAAAAATGAAAAAG
45839255 AAAATG
1 AAAATG
45839261 AACTAGAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
56 8 0.14
57 31 0.55
58 17 0.30
ACGTcount: A:0.52, C:0.05, G:0.19, T:0.24
Consensus pattern (58 bp):
AAAATGGAGAAATGAAAACATTTGAAAATGAATGAGGTTTTCTCAAAAAATGAAAAAG
Found at i:45841610 original size:25 final size:24
Alignment explanation
Indices: 45841564--45841616 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
45841554 TTATTTAATC
* * *
45841564 TTAATTAATTAACTTAATTATTAT
1 TTAATTAAATAACTTAACTATTAA
*
45841588 TTAATTATAATAATTTAACTATTAA
1 TTAATTA-AATAACTTAACTATTAA
45841613 TTAA
1 TTAA
45841617 ACTAAATGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
TTAATTAAATAACTTAACTATTAA
Found at i:45844670 original size:30 final size:30
Alignment explanation
Indices: 45844620--45844684 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
45844610 TAAAAGAGTG
45844620 TGTGATATAATTGATATATGATA-TATGATA
1 TGTGATATAATTGATATATGA-AGTATGATA
*
45844650 TGTGATATGAA-T-ATAGTATGAAGTATGTTA
1 TGTGATAT-AATTGATA-TATGAAGTATGATA
45844680 TGTGA
1 TGTGA
45844685 AATTGTACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
29 4 0.13
30 25 0.81
31 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.42
Consensus pattern (30 bp):
TGTGATATAATTGATATATGAAGTATGATA
Found at i:45849504 original size:19 final size:20
Alignment explanation
Indices: 45849471--45849517 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
45849461 CAGTAAAATG
45849471 TTTTCTGGAAAATGATTTCC
1 TTTTCTGGAAAATGATTTCC
*
45849491 TTTTCTGG-AAATGATTTGC
1 TTTTCTGGAAAATGATTTCC
45849510 TTTTCTGG
1 TTTTCTGG
45849518 TGTTTGGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.49
Consensus pattern (20 bp):
TTTTCTGGAAAATGATTTCC
Found at i:45849634 original size:16 final size:17
Alignment explanation
Indices: 45849601--45849640 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
45849591 TTTTTACACG
45849601 TATTAATAAATTTTTATA
1 TATTAATAAA-TTTTATA
45849619 TATTAATAAA-TTTATA
1 TATTAATAAATTTTATA
*
45849635 TTTTAA
1 TATTAA
45849641 ATTGTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
18 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTAATAAATTTTATA
Found at i:45850881 original size:32 final size:32
Alignment explanation
Indices: 45850835--45850895 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
45850825 TGTCAATCAT
45850835 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
*
45850867 TTCAATATCTAACAAGCTTAAAACATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
45850896 CAATATCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:45850902 original size:27 final size:30
Alignment explanation
Indices: 45850835--45850908 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 30
45850825 TGTCAATCAT
*
45850835 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCTAACAAGCTTAAAAC--AATAAA
45850867 TTCAATATCTAACAAGCTTAAAAC-AT-AA
1 TTCAATATCTAACAAGCTTAAAACAATAAA
45850895 -TCAATATCTAACAA
1 TTCAATATCTAACAA
45850909 ATTCAAGACA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 14 0.34
28 2 0.05
29 2 0.05
32 23 0.56
ACGTcount: A:0.51, C:0.19, G:0.03, T:0.27
Consensus pattern (30 bp):
TTCAATATCTAACAAGCTTAAAACAATAAA
Found at i:45850919 original size:27 final size:27
Alignment explanation
Indices: 45850836--45850922 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 27
45850826 GTCAATCATT
* *
45850836 TCAATATCCAACAAGCTTAAAACATAATAAA
1 TCAATATCTAACAAGATTAAAAC---AT-AA
*
45850867 TTCAATATCTAACAAGCTTAAAACATAA
1 -TCAATATCTAACAAGATTAAAACATAA
*
45850895 TCAATATCTAACAA-ATTCAAGACATAA
1 TCAATATCTAACAAGATT-AAAACATAA
45850922 T
1 T
45850923 AATTTCAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
26 2 0.04
27 23 0.45
28 2 0.04
29 2 0.04
32 22 0.43
ACGTcount: A:0.52, C:0.18, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCTAACAAGATTAAAACATAA
Found at i:45851131 original size:9 final size:9
Alignment explanation
Indices: 45851119--45851144 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
45851109 ATTCTCTTGC
45851119 TTCTTCTCT
1 TTCTTCTCT
45851128 TTCTTCTCT
1 TTCTTCTCT
45851137 TTCTTCTC
1 TTCTTCTC
45851145 GCTCCGTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (9 bp):
TTCTTCTCT
Done.