Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 133 of 221
Found at i:40980231 original size:19 final size:19
Alignment explanation
Indices: 40980202--40980293 Score: 130
Period size: 19 Copynumber: 4.8 Consensus size: 19
40980192 AATCTTCAAG
40980202 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
40980221 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* * *
40980240 GATATGCGACCTTAGAAAT
1 GATATGCAATCTTAGATAT
*
40980259 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40980278 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
40980294 ATATATGATT
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 61 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40980254 original size:38 final size:38
Alignment explanation
Indices: 40980202--40980294 Score: 150
Period size: 38 Copynumber: 2.4 Consensus size: 38
40980192 AATCTTCAAG
*
40980202 GATATGCAATCTTAGATATGATATATAATCTTAGATAT
1 GATATGCAATCTTAGAAATGATATATAATCTTAGATAT
* * *
40980240 GATATGCGACCTTAGAAATGATATGTAATCTTAGATAT
1 GATATGCAATCTTAGAAATGATATATAATCTTAGATAT
40980278 GATATGCAATCTTAGAA
1 GATATGCAATCTTAGAA
40980295 TATATGATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (38 bp):
GATATGCAATCTTAGAAATGATATATAATCTTAGATAT
Found at i:40980548 original size:23 final size:23
Alignment explanation
Indices: 40980504--40980548 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
40980494 TCTTATTTTG
* *
40980504 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
40980527 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
40980549 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:40980782 original size:3 final size:3
Alignment explanation
Indices: 40980774--40980814 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
40980764 ATCTTGTATC
40980774 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
40980815 ATTCATGCGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:40987533 original size:26 final size:28
Alignment explanation
Indices: 40987504--40987555 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
40987494 TTGTTCAAAC
*
40987504 TCTTCTAAA-AAAAACTCA-AGAGAAAT
1 TCTTCAAAAGAAAAACTCAGAGAGAAAT
*
40987530 TCTTGAAAAGAAAAACTCAGAGAGAA
1 TCTTCAAAAGAAAAACTCAGAGAGAA
40987556 TTTATTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 9 0.41
28 6 0.27
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.19
Consensus pattern (28 bp):
TCTTCAAAAGAAAAACTCAGAGAGAAAT
Found at i:40994336 original size:29 final size:29
Alignment explanation
Indices: 40994294--40994355 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
40994284 ACAAGACACA
40994294 AGTT-CAAGCAAGAACCAGACAAGCATAG
1 AGTTCCAAGCAAGAACCAGACAAGCATAG
40994322 AGTTCCAAGCAAGAACCAGACAAGCATAG
1 AGTTCCAAGCAAGAACCAGACAAGCATAG
40994351 AGTTC
1 AGTTC
40994356 AAATTCATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.13
Consensus pattern (29 bp):
AGTTCCAAGCAAGAACCAGACAAGCATAG
Found at i:40995405 original size:25 final size:25
Alignment explanation
Indices: 40995308--40995431 Score: 76
Period size: 25 Copynumber: 5.0 Consensus size: 25
40995298 AATGGGTAGG
*
40995308 TCCGAAGAGCCATTAA-CGGGAAGC
1 TCCGGAGAGCCATTAATCGGGAAGC
* * *
40995332 TTCGGATAGCCA-TATATCGGGAAGT
1 TCCGGAGAGCCATTA-ATCGGGAAGC
** * * * *
40995357 TCAAGTGACCCA-T-ATCAGGTAGC
1 TCCGGAGAGCCATTAATCGGGAAGC
40995380 TCCGGAGAGCCATTAATCGGGAAGC
1 TCCGGAGAGCCATTAATCGGGAAGC
** * *
40995405 TCACAAAAAGCCTTTAATCGGGAAGC
1 TC-CGGAGAGCCATTAATCGGGAAGC
40995431 T
1 T
40995432 TACGAAGAGC
Statistics
Matches: 72, Mismatches: 23, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
23 17 0.24
24 11 0.15
25 24 0.33
26 20 0.28
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (25 bp):
TCCGGAGAGCCATTAATCGGGAAGC
Found at i:40995442 original size:26 final size:26
Alignment explanation
Indices: 40995385--40995444 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
40995375 GTAGCTCCGG
40995385 AGAGCCATTAATCGGGAAGCTCACAA
1 AGAGCCATTAATCGGGAAGCTCACAA
* * * *
40995411 AAAGCCTTTAATCGGGAAGCTTACGA
1 AGAGCCATTAATCGGGAAGCTCACAA
40995437 AGAGCCAT
1 AGAGCCAT
40995445 ATAACATGAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATCGGGAAGCTCACAA
Found at i:41002465 original size:26 final size:26
Alignment explanation
Indices: 41002436--41002492 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 26
41002426 CTATTTTTTT
* *
41002436 AATAAACACAAAAAAATTATTTTAAA
1 AATAAAAACAAAAAAAGTATTTTAAA
*
41002462 AATAAAAAATAAAAAAAGTATTTTAAA
1 AAT-AAAAACAAAAAAAGTATTTTAAA
41002489 AATA
1 AATA
41002493 TTTTAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (26 bp):
AATAAAAACAAAAAAAGTATTTTAAA
Found at i:41005358 original size:31 final size:31
Alignment explanation
Indices: 41005320--41005383 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
41005310 CATACTTACA
*
41005320 AAATTTAATAACTCCACTACCACAGAATGAG
1 AAATTTAATAACTCCACTACCACAAAATGAG
41005351 AAATTTAATAACTCCACTACCACAAAATGAG
1 AAATTTAATAACTCCACTACCACAAAATGAG
41005382 AA
1 AA
41005384 TATAGATCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.22, G:0.08, T:0.22
Consensus pattern (31 bp):
AAATTTAATAACTCCACTACCACAAAATGAG
Found at i:41009781 original size:21 final size:19
Alignment explanation
Indices: 41009755--41009827 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 19
41009745 ATCTAATTAC
41009755 AAATATTTAATTATTATATTT
1 AAATATTTAATTA-TAT-TTT
*
41009776 AAATATTTAAATATATTTT
1 AAATATTTAATTATATTTT
* *
41009795 ATATATTCTAATTAAATTTAAT
1 AAATATT-TAATTATATTT--T
*
41009817 AAATAATTAAT
1 AAATATTTAAT
41009828 ATTAATTACT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 9 0.21
20 12 0.28
21 16 0.37
22 6 0.14
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATTTAATTATATTTT
Found at i:41013382 original size:16 final size:16
Alignment explanation
Indices: 41013361--41013393 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41013351 GGACATGATA
41013361 GACTCTTTGACACATT
1 GACTCTTTGACACATT
41013377 GACTCTTTGACACATT
1 GACTCTTTGACACATT
41013393 G
1 G
41013394 GTGTCTTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (16 bp):
GACTCTTTGACACATT
Found at i:41018727 original size:24 final size:24
Alignment explanation
Indices: 41018685--41018738 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
41018675 AATCAAAGTC
** **
41018685 AAATATATTATGTTAATAAATGTT
1 AAATATATTATACTAATAAATACT
*
41018709 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
41018733 AAATAT
1 AAATAT
41018739 TCTAGAAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:41019020 original size:20 final size:20
Alignment explanation
Indices: 41018979--41019020 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
41018969 TCATAACACA
* *
41018979 TCTCTCATTCTATATTCTTT
1 TCTCTCATTCCATATTCGTT
41018999 TCTCTCATTCCAT-TTCCGTT
1 TCTCTCATTCCATATT-CGTT
41019019 TC
1 TC
41019021 CTTTTTCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.12, C:0.31, G:0.02, T:0.55
Consensus pattern (20 bp):
TCTCTCATTCCATATTCGTT
Found at i:41021855 original size:25 final size:25
Alignment explanation
Indices: 41021784--41021855 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 25
41021774 AATTTTCTTG
** *
41021784 AAATTTTACCGGGAGTAAAATCGTCA
1 AAATTTTACTAGG-GTAAAATCATCA
*
41021810 AATTTTTACTAAGGGTAAAATCATCA
1 AAATTTTACT-AGGGTAAAATCATCA
41021836 AAATTTTACTAGGGTAAAAT
1 AAATTTTACTAGGGTAAAAT
41021856 TAGGATGAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
25 10 0.25
26 28 0.70
27 2 0.05
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (25 bp):
AAATTTTACTAGGGTAAAATCATCA
Found at i:41035967 original size:15 final size:15
Alignment explanation
Indices: 41035947--41035977 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41035937 TATAATACAC
41035947 TTATTACTGGAGTGA
1 TTATTACTGGAGTGA
*
41035962 TTATTAGTGGAGTGA
1 TTATTACTGGAGTGA
41035977 T
1 T
41035978 AATAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.42
Consensus pattern (15 bp):
TTATTACTGGAGTGA
Found at i:41036600 original size:93 final size:93
Alignment explanation
Indices: 41036480--41036654 Score: 350
Period size: 93 Copynumber: 1.9 Consensus size: 93
41036470 ATAGATCTTG
41036480 AACTGTTTATGGATTTATTCACTTATGACGTTCAAAGTGTGGCATACCTAAATTCTGAGTGGATG
1 AACTGTTTATGGATTTATTCACTTATGACGTTCAAAGTGTGGCATACCTAAATTCTGAGTGGATG
41036545 ACAGACTATGTATGCATACCTAAATTCA
66 ACAGACTATGTATGCATACCTAAATTCA
41036573 AACTGTTTATGGATTTATTCACTTATGACGTTCAAAGTGTGGCATACCTAAATTCTGAGTGGATG
1 AACTGTTTATGGATTTATTCACTTATGACGTTCAAAGTGTGGCATACCTAAATTCTGAGTGGATG
41036638 ACAGACTATGTATGCAT
66 ACAGACTATGTATGCAT
41036655 GACCCGTATA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 82 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.35
Consensus pattern (93 bp):
AACTGTTTATGGATTTATTCACTTATGACGTTCAAAGTGTGGCATACCTAAATTCTGAGTGGATG
ACAGACTATGTATGCATACCTAAATTCA
Found at i:41042110 original size:21 final size:21
Alignment explanation
Indices: 41042084--41042124 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
41042074 TCAACAATTG
41042084 ATGAGACTTTGGGTACTCATA
1 ATGAGACTTTGGGTACTCATA
41042105 ATGAGACTTTGGGTACTCAT
1 ATGAGACTTTGGGTACTCAT
41042125 GATGGGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (21 bp):
ATGAGACTTTGGGTACTCATA
Found at i:41047641 original size:21 final size:20
Alignment explanation
Indices: 41047615--41047706 Score: 60
Period size: 21 Copynumber: 4.4 Consensus size: 20
41047605 GAGGTTGAGA
41047615 TTTAGGGTTTGAGGTTATGGG
1 TTTAGGGTTT-AGGTTATGGG
* *
41047636 TTTAGGGATCTAGGTTTTGGG
1 TTTAGGG-TTTAGGTTATGGG
* * * * *
41047657 TTTATGGTTAAGGATTCTTGA
1 TTTAGGGTTTAGG-TTATGGG
*
41047678 TTTAGGGTTCAGGGTT-TGGG
1 TTTAGGGTTTA-GGTTATGGG
41047698 TTTTAGGGT
1 -TTTAGGGT
41047707 AAAAAATAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
20 6 0.11
21 45 0.82
22 4 0.07
ACGTcount: A:0.15, C:0.03, G:0.37, T:0.45
Consensus pattern (20 bp):
TTTAGGGTTTAGGTTATGGG
Found at i:41048754 original size:27 final size:27
Alignment explanation
Indices: 41048713--41048781 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
41048703 TGGGGTTTGT
* * *
41048713 GTTTAGGATTTAAGGTTGAAGGTTCAA
1 GTTTAGGGTTCAAGGTTCAAGGTTCAA
*
41048740 GTTTGGGGTTCAAGGTTCAAGGTTCAA
1 GTTTAGGGTTCAAGGTTCAAGGTTCAA
*
41048767 GTTTAGTGTTCAAGG
1 GTTTAGGGTTCAAGG
41048782 GTTTGGGGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.25, C:0.07, G:0.32, T:0.36
Consensus pattern (27 bp):
GTTTAGGGTTCAAGGTTCAAGGTTCAA
Found at i:41064655 original size:44 final size:44
Alignment explanation
Indices: 41064592--41065094 Score: 287
Period size: 44 Copynumber: 11.6 Consensus size: 44
41064582 CCACTAATCC
* *
41064592 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAGTAACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAACAGATCT
* * * ** * * *
41064636 TATCTCACTGAAGTGGCAGTAGAGTGGA-T--CGTATCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAACAGATCT
* * * *
41064677 TATCTCCCTGAAGGTGCAGCGGAGCAGACT-AAGTAAGCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAA-CAGATCT
* * * ** *
41064721 TATCCCCCTGAAGTTGCAGTGGGGCAGATCAAAGATGGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TAACAGATCT
* * ** * *
41064766 TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TAACAGATCT
* ** *
41064810 TATCTCCCTGAAGTTGCAG-CGAGC-GAATTAAAACATCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAGTAACAGATCT
* * * * * ** *
41064853 TATC-CCTTGAAGTTGCAGTGGGGTAGATCGAAGGTGGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT-TAAAGTAACAGATCT
* * * * *
41064897 TATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGTCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGT-AACAGATCT
* * * ** *
41064941 TATCTCCCTGAAGTTGTAGCGGAGCGGATTAAAACATCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAACAGATCT
* * * * * *
41064985 TATCTCTCTGAAGTTGTACTAGAGCAGA-T--CGCAACCAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAA-CAGATCT
* * * * *
41065026 CATCTCCCTGAAGTTGCAGTGGAGCAGA-CACAAGAAACAAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTA-AAGTAACAGATCT
*
41065070 TATCTCCCTGAAGTTGCAGCGGAGC
1 TATCTCCCTGAAGTTGCAGTGGAGC
41065095 GGATCAAAAT
Statistics
Matches: 344, Mismatches: 97, Indels: 36
0.72 0.20 0.08
Matches are distributed among these distances:
41 58 0.17
42 20 0.06
43 28 0.08
44 176 0.51
45 61 0.18
46 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAACAGATCT
Found at i:41064881 original size:131 final size:132
Alignment explanation
Indices: 41064677--41065095 Score: 469
Period size: 131 Copynumber: 3.2 Consensus size: 132
41064667 TATCAGGTCT
* * * * * *
41064677 TATCTCCCTGAAGGTGCAGCGGAGC-AGACTAAGTA-AGCAGGTCTTATCCCCCTGAAGTTGCAG
1 TATCTCCCTGAAGTTGCAGCGGAGCGA-ATTAA-AACATCAGATCTTAT-CCCTTGAAGTTGCAG
*
41064740 TGGGGCAGATCAAAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGAT
63 TGGGGCAGATCAAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCGAT
41064805 AATCC
128 AATCC
41064810 TATCTCCCTGAAGTTGCAGC-GAGCGAATTAAAACATCAGATCTTATCCCTTGAAGTTGCAGTGG
1 TATCTCCCTGAAGTTGCAGCGGAGCGAATTAAAACATCAGATCTTATCCCTTGAAGTTGCAGTGG
* * * * *
41064874 GGTAGATCGAAGGTGGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGTCGATAAT
66 GGCAGATCAAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCGATAAT
41064939 CC
131 CC
* * * * * *
41064941 TATCTCCCTGAAGTTGTAGCGGAGCGGATTAAAACATCAGATCTTATCTCTCTGAAGTTGTACTA
1 TATCTCCCTGAAGTTGCAGCGGAGCGAATTAAAACATCAGATCTTATCCCT-TGAAGTTGCAGTG
* ** * * * *** *
41065006 GAGCAGATCGCA-A---CCAGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACACAAGAAAC-A-
65 GGGCAGATCAAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--CCGAT
41065065 AATCC
128 AATCC
41065070 TATCTCCCTGAAGTTGCAGCGGAGCG
1 TATCTCCCTGAAGTTGCAGCGGAGCG
41065096 GATCAAAATG
Statistics
Matches: 249, Mismatches: 31, Indels: 16
0.84 0.10 0.05
Matches are distributed among these distances:
129 64 0.26
130 1 0.00
131 99 0.40
132 46 0.18
133 39 0.16
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (132 bp):
TATCTCCCTGAAGTTGCAGCGGAGCGAATTAAAACATCAGATCTTATCCCTTGAAGTTGCAGTGG
GGCAGATCAAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCGATAAT
CC
Found at i:41065069 original size:129 final size:129
Alignment explanation
Indices: 41064758--41065143 Score: 406
Period size: 129 Copynumber: 3.0 Consensus size: 129
41064748 ATCAAAGATG
* * *** *
41064758 GCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAG
1 GCAAATCTCATCTCCCTGAAGTTGCAGTGGAGCAGACACAAGACGATAATCCTATCTCCCTGAAG
* * * * *
41064823 TTGCAGC-GAGCGAATTAAAACATCAGATCTTATCCCT-TGAAGTTGCAGTGGGGTAGATCGAA
66 TTGCAGCGGAGCGGATTAAAACATCAGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATCGAA
* * *** *
41064885 GGTGGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGTCGATAATCCTATCTCCCT
1 ----GCAAATCTCATCTCCCTGAAGTTGCAGTGGAGCAGACACAAGACGATAATCCTATCTCCCT
* * *
41064950 GAAGTTGTAGCGGAGCGGATTAAAACATCAGATCTTATCTCTCTGAAGTTGTACTAGAGCAGATC
62 GAAGTTGCAGCGGAGCGGATTAAAACATCAGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATC
41065015 GCAA
127 G-AA
* *
41065019 -CCAGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACACAAGAAAC-A-AATCCTATCTCCCTGA
1 GCAAATCTCATCTCCCTGAAGTTGCAGTGGAGCAGACACAAG--ACGATAATCCTATCTCCCTGA
* * * * * *
41065081 AGTTGCAGCGGAGCGGATCAAAATGAT-GGGTCTCATCTATCTGAAGTTGTAGTAGAGTAGATC
64 AGTTGCAGCGGAGCGGATTAAAA-CATCAGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATC
41065144 ATATCAGTCT
Statistics
Matches: 221, Mismatches: 28, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
129 101 0.46
130 3 0.01
131 69 0.31
132 28 0.13
133 18 0.08
134 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (129 bp):
GCAAATCTCATCTCCCTGAAGTTGCAGTGGAGCAGACACAAGACGATAATCCTATCTCCCTGAAG
TTGCAGCGGAGCGGATTAAAACATCAGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATCGAA
Found at i:41068343 original size:28 final size:29
Alignment explanation
Indices: 41068285--41068344 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
41068275 TGCATATATT
* *
41068285 TATTATATATAATAAAACCCACACATATA
1 TATTATATATAACAAAACCCACACAAATA
* *
41068314 TATTATATATAGCAAAA-CCACGCAAATA
1 TATTATATATAACAAAACCCACACAAATA
41068342 TAT
1 TAT
41068345 GCTGTATGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.30
Consensus pattern (29 bp):
TATTATATATAACAAAACCCACACAAATA
Found at i:41070028 original size:12 final size:12
Alignment explanation
Indices: 41070011--41070058 Score: 87
Period size: 12 Copynumber: 3.9 Consensus size: 12
41070001 CTCGAGCCCA
41070011 CAATCTAATACC
1 CAATCTAATACC
41070023 CAATCTAATACC
1 CAATCTAATACC
41070035 CAATCTAATACC
1 CAATCTAATACC
41070047 ACAATCTAATAC
1 -CAATCTAATAC
41070059 ACATAATCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 24 0.69
13 11 0.31
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (12 bp):
CAATCTAATACC
Found at i:41071638 original size:7 final size:6
Alignment explanation
Indices: 41071593--41071637 Score: 63
Period size: 6 Copynumber: 7.0 Consensus size: 6
41071583 TGACTAGATT
41071593 AAAATA AAAATA AAAATA AAAATA AAATATA AAATATA TAAAATA
1 AAAATA AAAATA AAAATA AAAATA AAA-ATA AAA-ATA -AAAATA
41071638 TTATTTGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
6 21 0.57
7 13 0.35
8 3 0.08
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:41076679 original size:19 final size:19
Alignment explanation
Indices: 41076655--41076696 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
41076645 GAGTTGTCTT
41076655 AAAAGAGTAAAAAAATCCA
1 AAAAGAGTAAAAAAATCCA
41076674 AAAAGAGTAAAAAAATCCA
1 AAAAGAGTAAAAAAATCCA
41076693 AAAA
1 AAAA
41076697 TCTTGGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (19 bp):
AAAAGAGTAAAAAAATCCA
Found at i:41091271 original size:5 final size:5
Alignment explanation
Indices: 41091261--41091285 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
41091251 TTCTATATTG
41091261 ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA
41091286 TGTCTGTTTT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:41092392 original size:33 final size:33
Alignment explanation
Indices: 41092348--41092513 Score: 224
Period size: 33 Copynumber: 5.0 Consensus size: 33
41092338 TCAACATAAG
* *
41092348 TGATTGGAACATCTATTAGGGCAGCTTCATCAA
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* *
41092381 TGATTGAAACATCTATCAGGGTAGCTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* *
41092414 TGATTGGGACATCTATCAAGGCAGCTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* **
41092447 TGAGTGGAACATCTATTGGGGCAGCTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* * *
41092480 TGATTGCAGCATCTATCAGGGCAACTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
41092513 T
1 T
41092514 CTATTCGACT
Statistics
Matches: 114, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 114 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (33 bp):
TGATTGGAACATCTATCAGGGCAGCTTCATCAT
Found at i:41097590 original size:21 final size:23
Alignment explanation
Indices: 41097564--41097608 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
41097554 GAAAGGTATC
* *
41097564 TACAAATTAA-ATC-TCTATGAT
1 TACAAAATAATATCTTCTAAGAT
41097585 TACAAAATAATATCTTCTAAGAT
1 TACAAAATAATATCTTCTAAGAT
41097608 T
1 T
41097609 GCATATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 3 0.15
23 8 0.40
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.38
Consensus pattern (23 bp):
TACAAAATAATATCTTCTAAGAT
Found at i:41098271 original size:131 final size:132
Alignment explanation
Indices: 41098057--41098444 Score: 609
Period size: 131 Copynumber: 2.9 Consensus size: 132
41098047 CAGTGAAACT
* ** * *
41098057 TCAGGGAGATAAGG-CTAGTGGCTTAAATCTGCTTCCCTACTACCTCGAAAAGGTAAGACTCGCC
1 TCAGGGAGAT-AGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGACTCACC
* *
41098121 ATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATATACAATCTTCAACCTACTCCACTAC
65 GTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTAC
41098186 TGC
130 TGC
* * *
41098189 TCAGGGAGATAGGACTGGTGGCTTAAATCTGGTT-CCTATTATCTCGGGAAGATAAGACTCACCG
1 TCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGACTCACCG
41098253 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTACT
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTACT
41098318 GC
131 GC
* * * * * *
41098320 TCAAGGAGATAGGACTGGTGGCTTAAATCTGTTTCCCTACTACCTTGGGAGGATAAGATTCACTG
1 TCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGACTCACCG
41098385 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCA
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCA
41098445 TTGCAAACTC
Statistics
Matches: 236, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
131 124 0.53
132 112 0.47
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (132 bp):
TCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGACTCACCG
TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTACT
GC
Found at i:41098571 original size:89 final size:89
Alignment explanation
Indices: 41098448--41098796 Score: 439
Period size: 89 Copynumber: 3.9 Consensus size: 89
41098438 TACTCCATTG
* * * * * *
41098448 CAAACTCAGAGAGGCAAGGCTGGTGTTTTTGATCTGCTTCACTGCCAGTAAAGGAAGACAAGATC
1 CAAACTCAGGGAAGCAAGGCTGGTGTCTTCGATCTGCTTCACTGCCAATACAGGAAGACAAGATC
* * *
41098513 CGCTATTTTCACTCTGCTCCGCTA
66 TGCTATCTTCAGTCTGCTCCGCTA
* * * *
41098537 CAAAGTCAGGGAAGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGCCAATACAGAAAGACAAGATC
1 CAAACTCAGGGAAGCAAGGCTGGTGTCTTCGATCTGCTTCACTGCCAATACAGGAAGACAAGATC
41098602 TGCTATCTTCAGTCTGCTCCGCTA
66 TGCTATCTTCAGTCTGCTCCGCTA
* * *
41098626 CAAACTCA-GGAAGACAAGGCTGGTGTCTTCGATCTGTTTCACTGCCAATATAGGATGACAAGAT
1 CAAACTCAGGGAAG-CAAGGCTGGTGTCTTCGATCTGCTTCACTGCCAATACAGGAAGACAAGAT
* ** *
41098690 CTGCTATCTTCAGTCTACTCTACTG
65 CTGCTATCTTCAGTCTGCTCCGCTA
* * * * *
41098715 TAAACTCAGGGACGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGCCAATACAGGAAGACAAGATC
1 CAAACTCAGGGAAGCAAGGCTGGTGTCTTCGATCTGCTTCACTGCCAATACAGGAAGACAAGATC
* *
41098780 TGTTATCTTTAGTCTGC
66 TGCTATCTTCAGTCTGC
41098797 CCTGTTGCAA
Statistics
Matches: 223, Mismatches: 35, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
88 5 0.02
89 214 0.96
90 4 0.02
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (89 bp):
CAAACTCAGGGAAGCAAGGCTGGTGTCTTCGATCTGCTTCACTGCCAATACAGGAAGACAAGATC
TGCTATCTTCAGTCTGCTCCGCTA
Found at i:41098640 original size:45 final size:44
Alignment explanation
Indices: 41098499--41098705 Score: 131
Period size: 45 Copynumber: 4.7 Consensus size: 44
41098489 CTGCCAGTAA
* * *
41098499 AGGAAGACAAGATCCGCTATTTTCACTCTGCTCCGCTACAAAGTC
1 AGGAAGACAAGATCTGCTATCTTCAGTCTGCTCCGCTACAAA-TC
* * * * *
41098544 AGGGAAG-CAAG-GCTAG-TGTCTTC-GATCTGCTTCGCTGCCAATAC
1 A-GGAAGACAAGATCT-GCTATCTTCAG-TCTGCTCCGCTACAAAT-C
*
41098588 AGAAAGACAAGATCTGCTATCTTCAGTCTGCTCCGCTACAAACTC
1 AGGAAGACAAGATCTGCTATCTTCAGTCTGCTCCGCTACAAA-TC
* * * * * * *
41098633 AGGAAGACAAG-GCTGGTGTCTTC-GATCTGTTTCACTGCCAATAT-
1 AGGAAGACAAGATCTGCTATCTTCAG-TCTGCTCCGCT-ACAA-ATC
*
41098677 AGGATGACAAGATCTGCTATCTTCAGTCT
1 AGGAAGACAAGATCTGCTATCTTCAGTCT
41098706 ACTCTACTGT
Statistics
Matches: 122, Mismatches: 26, Indels: 28
0.69 0.15 0.16
Matches are distributed among these distances:
43 6 0.05
44 53 0.43
45 54 0.44
46 9 0.07
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (44 bp):
AGGAAGACAAGATCTGCTATCTTCAGTCTGCTCCGCTACAAATC
Found at i:41098810 original size:178 final size:177
Alignment explanation
Indices: 41098440--41098821 Score: 487
Period size: 178 Copynumber: 2.1 Consensus size: 177
41098430 CTTCAACCTA
* * * *
41098440 CTCCATTGCAAACTCAGAGAGGCAAGGCTGGTGTTTTTGATCTGCTTCACTGCCAGTAAAGGAAG
1 CTCCGTTGCAAACTCAGA-AGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGCCAATAAAGGAAG
* * * *
41098505 ACAAGATCCGCTATTTTCACTCTGCTCCGCTACAAAGTCAGGGAAGCAAGGCTAGTGTCTTCGAT
65 ACAAGATCCGCTATCTTCACTCTACTCCACTACAAACTCAGGGAAGCAAGGCTAGTGTCTTCGAT
41098570 CTGCTTCGCTGCCAATACAGAAAGACAAGATCTGCTATCTTCAGTCTG
130 CTGCTTCGCTGCCAATACAGAAAGACAAGATCTGCTATCTTCAGTCTG
* * * * * *
41098618 CTCCGCTACAAACTCAGGAAGACAAGGCTGGTGTCTTCGATCTGTTTCACTGCCAATATAGGATG
1 CTCCGTTGCAAACTCA-GAAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGCCAATAAAGGAAG
* * * ** * * * *
41098683 ACAAGATCTGCTATCTTCAGTCTACTCTACTGTAAACTCAGGGACGCAAGGTTGGTGTCTTTGAT
65 ACAAGATCCGCTATCTTCACTCTACTCCACTACAAACTCAGGGAAGCAAGGCTAGTGTCTTCGAT
* * *
41098748 CTGCTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTTAGTCTG
130 CTGCTTCGCTGCCAATACAGAAAGACAAGATCTGCTATCTTCAGTCTG
41098796 C-CCTGTTGCAAACTCAAGAAGGCAAG
1 CTCC-GTTGCAAACTC-AGAAGGCAAG
41098822 ACTTGTAACT
Statistics
Matches: 172, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
177 2 0.01
178 167 0.97
179 3 0.02
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.27
Consensus pattern (177 bp):
CTCCGTTGCAAACTCAGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGCCAATAAAGGAAGA
CAAGATCCGCTATCTTCACTCTACTCCACTACAAACTCAGGGAAGCAAGGCTAGTGTCTTCGATC
TGCTTCGCTGCCAATACAGAAAGACAAGATCTGCTATCTTCAGTCTG
Found at i:41099050 original size:177 final size:178
Alignment explanation
Indices: 41098819--41099218 Score: 529
Period size: 177 Copynumber: 2.3 Consensus size: 178
41098809 TCAAGAAGGC
* * *
41098819 AAGACTTGTAACTTTAATTTGCTCCACTGCAACTTCAGGGAGATAGCATTATTGGCTTTAATCTT
1 AAGACTTGTAACTTTAATTCGCTCCACTGCAACTTCAAGGAGATAGCATTATTGGCTTTAATCTA
* * ** * * * * * *
41098884 CTCCATTGCAACTTCAGGGAGATAAGATTTTCCATCTTCTGTCTACCTCACTGCAGCTTTA-GGG
66 CTCCACTGCAACCTCAGGGAGATAAGATTCGCCATATTCAGTCTACCCCACTACAACTTCAGGGG
*
41098948 GATAAGACTTGCTTTCTTCAGTCTACTCCACTGCAACCTT-AGGGATAT
131 GATAAGACTTGCTTTCTTCAGTCTACTCCACTGCAA-CTTCAGGGAGAT
* * *
41098996 AAGACTTGTAACTTTAATTCGCTCCATTGTAACTTCAAGGAGATAGGATTATTGGCTTTAATCTA
1 AAGACTTGTAACTTTAATTCGCTCCACTGCAACTTCAAGGAGATAGCATTATTGGCTTTAATCTA
* *
41099061 CTCCACTGCAACCTCAGGGAGATAAGATTCGCCATATTCAGTCTGCCCCATTACAACTTCAGGGG
66 CTCCACTGCAACCTCAGGGAGATAAGATTCGCCATATTCAGTCTACCCCACTACAACTTCAGGGG
*
41099126 GATAAGACTTGTTTTCTTCAGTCTACTCCACTGCAACTTCAGGGAGAT
131 GATAAGACTTGCTTTCTTCAGTCTACTCCACTGCAACTTCAGGGAGAT
* ** *
41099174 AAGA-TTATTGGCTTTAATAT-GCTCCACTGCAACTTCAGGGAGATA
1 AAGACTT-GTAACTTTAAT-TCGCTCCACTGCAACTTCAAGGAGATA
41099219 AGATTCACCA
Statistics
Matches: 193, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
177 113 0.59
178 79 0.41
179 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (178 bp):
AAGACTTGTAACTTTAATTCGCTCCACTGCAACTTCAAGGAGATAGCATTATTGGCTTTAATCTA
CTCCACTGCAACCTCAGGGAGATAAGATTCGCCATATTCAGTCTACCCCACTACAACTTCAGGGG
GATAAGACTTGCTTTCTTCAGTCTACTCCACTGCAACTTCAGGGAGAT
Found at i:41099212 original size:44 final size:43
Alignment explanation
Indices: 41098830--41099223 Score: 239
Period size: 44 Copynumber: 8.9 Consensus size: 43
41098820 AGACTTGTAA
*
41098830 CTTTAATTTGCTCCACTGCAACTTCAGGGAGAT-AGCATTATTGG
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG-ATT-TTGG
* * *
41098874 CTTTAATCTTCTCCATTGCAACTTCAGGGAGATAAGATTTT-C
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTTGG
* * * *
41098916 CATCT--TCTGTCTACCTCACTGCAGCTTTAGGG-GATAAGACTTGCTT-T
1 C-TTTAATCTG-CT--C-CACTGCAACTTCAGGGAGATAAGA-TT--TTGG
* * * * * **
41098963 CTTCAGTCTACTCCACTGCAACCTT-AGGGATATAAGACTTGTAA
1 CTTTAATCTGCTCCACTGCAA-CTTCAGGGAGATAAGA-TTTTGG
* * * *
41099007 CTTTAAT-TCGCTCCATTGTAACTTCAAGGAGATAGGATTATTGG
1 CTTTAATCT-GCTCCACTGCAACTTCAGGGAGATAAGATT-TTGG
* * * *
41099051 CTTTAATCTACTCCACTGCAACCTCAGGGAGATAAGA-TTCGC
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTTGG
* * * * * **
41099093 CATATTCAGTCTGCCCCATTACAACTTCAGGGGGATAAGACTTGTTTT
1 C-T-TT-AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TT-TTGG
* * *
41099141 CTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGATTATTGG
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-TTGG
*
41099185 CTTTAATATGCTCCACTGCAACTTCAGGGAGATAAGATT
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
41099224 CACCATCTTC
Statistics
Matches: 267, Mismatches: 59, Indels: 48
0.71 0.16 0.13
Matches are distributed among these distances:
41 3 0.01
42 6 0.02
43 13 0.05
44 146 0.55
45 85 0.32
46 2 0.01
47 7 0.03
48 5 0.02
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (43 bp):
CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTTGG
Found at i:41100534 original size:9 final size:9
Alignment explanation
Indices: 41100520--41100545 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
41100510 TCTTTCTTCT
41100520 TTTTTTTGA
1 TTTTTTTGA
41100529 TTTTTTTGA
1 TTTTTTTGA
41100538 TTTTTTTG
1 TTTTTTTG
41100546 TCTCAAGGTA
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:0.08, C:0.00, G:0.12, T:0.81
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:41103086 original size:29 final size:31
Alignment explanation
Indices: 41103050--41103122 Score: 87
Period size: 35 Copynumber: 2.3 Consensus size: 31
41103040 CGACAGAATC
41103050 TTAACATAGTC-G-GTATTAACAGATGATTA
1 TTAACATAGTCGGAGTATTAACAGATGATTA
*
41103079 TTAACATAGTCTGGCAATGTATTAGCAGATGATTA
1 TTAACATAGTC-GG--A-GTATTAACAGATGATTA
41103114 TTAACATAG
1 TTAACATAG
41103123 CTGGTGTAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
29 11 0.30
31 1 0.03
35 25 0.68
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (31 bp):
TTAACATAGTCGGAGTATTAACAGATGATTA
Found at i:41111371 original size:15 final size:15
Alignment explanation
Indices: 41111333--41111371 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
41111323 CAAAACATCT
*
41111333 TAAAAATAAATGGTA
1 TAAAAATAAATAGTA
*
41111348 TATAAAATAGATAGTA
1 TA-AAAATAAATAGTA
41111364 TAAAAATA
1 TAAAAATA
41111372 TTTGCAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (15 bp):
TAAAAATAAATAGTA
Found at i:41111996 original size:23 final size:22
Alignment explanation
Indices: 41111966--41112011 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
41111956 TGAATTAAAT
41111966 TTCTAAGATTACAAAATCATATC
1 TTCTAAGATTAC-AAATCATATC
* *
41111989 TTCTAAGATTGCATATCATATC
1 TTCTAAGATTACAAATCATATC
41112011 T
1 T
41112012 AAGATTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (22 bp):
TTCTAAGATTACAAATCATATC
Found at i:41120235 original size:11 final size:11
Alignment explanation
Indices: 41120219--41120243 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41120209 ATTGAATTGA
41120219 ATTTTTAGTTT
1 ATTTTTAGTTT
41120230 ATTTTTAGTTT
1 ATTTTTAGTTT
41120241 ATT
1 ATT
41120244 ATCATGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (11 bp):
ATTTTTAGTTT
Found at i:41123723 original size:93 final size:93
Alignment explanation
Indices: 41123564--41123749 Score: 309
Period size: 93 Copynumber: 2.0 Consensus size: 93
41123554 AAAGGCAATG
* * * *
41123564 TTTGTTCATTGATCGTTGTAGAGGTGCTACTGCTTTGATCATTGTGTTGTTGTATCCTGGGGGAC
1 TTTGTTCATTAATCGCTGCAGAGGTGCTACTGCTTTGATCATTGTGTTGTTGTATCCTGGGAGAC
*
41123629 ATTCGACCAATATTTCTCCAAGTACCAT
66 ATTCGACCAACATTTCTCCAAGTACCAT
*
41123657 TTTGTTCGTTAATCGCTGCAGAGGTGCTACTGCTTTGATCATTGTGTTGTTGTATCCTGGGAGAC
1 TTTGTTCATTAATCGCTGCAGAGGTGCTACTGCTTTGATCATTGTGTTGTTGTATCCTGGGAGAC
*
41123722 ATTCGACCAACGTTTCTCCAAGTACCAT
66 ATTCGACCAACATTTCTCCAAGTACCAT
41123750 AAGAGTTGTC
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 86 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (93 bp):
TTTGTTCATTAATCGCTGCAGAGGTGCTACTGCTTTGATCATTGTGTTGTTGTATCCTGGGAGAC
ATTCGACCAACATTTCTCCAAGTACCAT
Found at i:41124411 original size:87 final size:86
Alignment explanation
Indices: 41124224--41124617 Score: 325
Period size: 87 Copynumber: 4.5 Consensus size: 86
41124214 CTTTGCTTCC
* * * * * ** *
41124224 AAATTAAAAGTAAATAAAATCAGTTTTGGGATTTCTTGCCGCTGTTCAACGGATTTTATTCCATT
1 AAATTAAAATTAAATAAAATTAGTTTCGGGATTTATTCCCGCCATTCAACGGATTTTATT-CAAT
* ***
41124289 TTTTATTTTATTTCCAAATGGG
65 TTTGATTTTATTTCCAAAAACG
* * *
41124311 AAATTTAAGTTAAATAAAATTCA-TTTCGGGATTTATTCCCGCCATTCAACGAATTTTATTCGAA
1 AAATTAAAATTAAATAAAATT-AGTTTCGGGATTTATTCCCGCCATTCAACGGATTTTATTC-AA
* *
41124375 TTTCGATTTTATTT-CTAAAACG
64 TTTTGATTTTATTTCCAAAAACG
* * * * *
41124397 ATTATTAAAATTAAAATAAAA-TATGTTTCAGGATTTATTCCCGCCGTTCAATGGAGTTTATTCC
1 A-AATTAAAATT-AAATAAAATTA-GTTTCGGGATTTATTCCCGCCATTCAACGGATTTTATT-C
* *
41124461 AAATTTGTTTTTATTTCCAAAAACG
62 AATTTTGATTTTATTTCCAAAAACG
* * *
41124486 AGTATTAAAATTAAA-ATAAATTATGTTTCGGGATTTATTCTCGCCATTTAACGGA-TTTATT-A
1 A-AATTAAAATTAAATA-AAATTA-GTTTCGGGATTTATTCCCGCCATTCAACGGATTTTATTCA
* *
41124548 CATTTTTATTTTGTTTCCAAAAACGAG
63 -ATTTTGATTTTATTTCCAAAAAC--G
** *
41124575 AAATTAAAATTAAATAAAATCT-GTTTCAAGATTTATTCTCGCC
1 AAATTAAAATTAAATAAAAT-TAGTTTCGGGATTTATTCCCGCC
41124618 GTTTGACAAG
Statistics
Matches: 250, Mismatches: 42, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
86 8 0.03
87 108 0.43
88 82 0.33
89 52 0.21
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (86 bp):
AAATTAAAATTAAATAAAATTAGTTTCGGGATTTATTCCCGCCATTCAACGGATTTTATTCAATT
TTGATTTTATTTCCAAAAACG
Found at i:41124460 original size:175 final size:175
Alignment explanation
Indices: 41124224--41124620 Score: 405
Period size: 175 Copynumber: 2.3 Consensus size: 175
41124214 CTTTGCTTCC
* ** * * * *
41124224 AAATTAAAAGTAAATAAAATCA-GTTTTGGGATTTCTTGCCGCTGTTCAACGGATTTTATTCC-A
1 AAATTAAAATTAAATAAAAT-ATGTTTCAGGATTTATTCCCGCCGTTCAACGGAGTTTATTCCAA
* * *** * *
41124287 TTTTTTATTTTATTTCCAAATGGGA-AATTTAAGTT-AAATAAAATTCA-TTTCGGGATTTATTC
65 ATTTGT-TTTTATTTCCAAAAACGAGAATTAAAATTAAAAT-AAATT-AGTTTCGGGATTTATTC
*
41124349 CCGCCATTCAACGAATTTTATT-CGAATTTCGATTTTATTT-CTAAAACGA-
127 CCGCCATTCAACGAA-TTTATTAC--ATTTCGATTTTATTTCCAAAAACGAG
** *
41124398 TTATTAAAATTAAAATAAAATATGTTTCAGGATTTATTCCCGCCGTTCAATGGAGTTTATTCCAA
1 AAATTAAAATT-AAATAAAATATGTTTCAGGATTTATTCCCGCCGTTCAACGGAGTTTATTCCAA
* *
41124463 ATTTGTTTTTATTTCCAAAAACGAGTATTAAAATTAAAATAAATTATGTTTCGGGATTTATTCTC
65 ATTTGTTTTTATTTCCAAAAACGAGAATTAAAATTAAAATAAATTA-GTTTCGGGATTTATTCCC
* * ** *
41124528 GCCATTTAACGGATTTATTACATTTTTATTTTGTTTCCAAAAACGAG
129 GCCATTCAACGAATTTATTACATTTCGATTTTATTTCCAAAAACGAG
* * *
41124575 AAATTAAAATTAAATAAAATCTGTTTCAAGATTTATTCTCGCCGTT
1 AAATTAAAATTAAATAAAATATGTTTCAGGATTTATTCCCGCCGTT
41124621 TGACAAGATT
Statistics
Matches: 183, Mismatches: 30, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
174 9 0.05
175 70 0.38
176 63 0.34
177 41 0.22
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (175 bp):
AAATTAAAATTAAATAAAATATGTTTCAGGATTTATTCCCGCCGTTCAACGGAGTTTATTCCAAA
TTTGTTTTTATTTCCAAAAACGAGAATTAAAATTAAAATAAATTAGTTTCGGGATTTATTCCCGC
CATTCAACGAATTTATTACATTTCGATTTTATTTCCAAAAACGAG
Found at i:41124512 original size:89 final size:87
Alignment explanation
Indices: 41124334--41124617 Score: 322
Period size: 89 Copynumber: 3.2 Consensus size: 87
41124324 ATAAAATTCA
* * * * *
41124334 TTTCGGGATTTATTCCCGCCATTCAACGAATTTTATTCGAATTTCGATTTTATTT-CTAAAACGA
1 TTTCAGGATTTATTCCCGCCATTCAACGGA-TTTATTCAAATTT-GTTTTTATTTCCAAAAACGA
*
41124398 TTATTAAAATTAAAATAAAATATG
64 GTATTAAAATTAAAATAAAATATG
* *
41124422 TTTCAGGATTTATTCCCGCCGTTCAATGGAGTTTATTCCAAATTTGTTTTTATTTCCAAAAACGA
1 TTTCAGGATTTATTCCCGCCATTCAACGGA-TTTATT-CAAATTTGTTTTTATTTCCAAAAACGA
*
41124487 GTATTAAAATTAAAATAAATTATG
64 GTATTAAAATTAAAATAAAATATG
* * * * * *
41124511 TTTCGGGATTTATTCTCGCCATTTAACGGATTTATT-ACATTTTTATTTTGTTTCCAAAAACGAG
1 TTTCAGGATTTATTCCCGCCATTCAACGGATTTATTCAAATTTGT-TTTTATTTCCAAAAACGAG
* *
41124575 AAATTAAAATT-AAATAAAATCTG
65 -TATTAAAATTAAAATAAAATATG
* *
41124598 TTTCAAGATTTATTCTCGCC
1 TTTCAGGATTTATTCCCGCC
41124618 GTTTGACAAG
Statistics
Matches: 169, Mismatches: 23, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
86 6 0.04
87 46 0.27
88 56 0.33
89 61 0.36
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (87 bp):
TTTCAGGATTTATTCCCGCCATTCAACGGATTTATTCAAATTTGTTTTTATTTCCAAAAACGAGT
ATTAAAATTAAAATAAAATATG
Found at i:41124746 original size:157 final size:160
Alignment explanation
Indices: 41124493--41124789 Score: 367
Period size: 161 Copynumber: 1.9 Consensus size: 160
41124483 ACGAGTATTA
*
41124493 AAATTAAAATAAATTATGTTTCGGGATTTATTCTCGCCATTTAACGGATTTATTACATTTTTATT
1 AAATTAAAATAAATTATGTTTCGGGATTTATTCTCGCCATTTAACAGATTTATTACATTTTTATT
* * * * *
41124558 TTGTTTCCAAAAACGAGAAATTAAAATTAAATAAAATCTGTTTCAAGATTTATTCTCGCCGTTTG
66 TTGTTTCC-AAAACGAGAAACTAAAATTAAATAAAATCT-TTTCAAGATTCATTCCCACCGTTTA
41124623 ACAAGATTTTAGTTTGCTTCCAAAGTAGAATT
129 ACAAGATTTTAGTTTGCTTCCAAAGTAGAATT
* **
41124655 AAATT-AAATAATATT-TGTTTCGGGATTTATTCTCG-CAGTTTAACAATATTTTATTTGA-TTT
1 AAATTAAAATAA-ATTATGTTTCGGGATTTATTCTCGCCA-TTTAAC-AGA-TTTATTACATTTT
** **
41124716 TATTTTGTTT-C-AAATTAG-AACT-AAATTAAATAAAATCTTTTCGGGATTCATTCCCACCGTT
62 TATTTTGTTTCCAAAACGAGAAACTAAAATTAAATAAAATCTTTTCAAGATTCATTCCCACCGTT
41124777 TAACAAGATTTTA
127 TAACAAGATTTTA
41124790 TTCGATATTG
Statistics
Matches: 118, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
156 30 0.25
157 16 0.14
158 3 0.03
159 5 0.04
160 2 0.02
161 33 0.28
162 22 0.19
163 7 0.06
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.42
Consensus pattern (160 bp):
AAATTAAAATAAATTATGTTTCGGGATTTATTCTCGCCATTTAACAGATTTATTACATTTTTATT
TTGTTTCCAAAACGAGAAACTAAAATTAAATAAAATCTTTTCAAGATTCATTCCCACCGTTTAAC
AAGATTTTAGTTTGCTTCCAAAGTAGAATT
Found at i:41124780 original size:82 final size:84
Alignment explanation
Indices: 41124627--41124791 Score: 217
Period size: 82 Copynumber: 2.0 Consensus size: 84
41124617 CGTTTGACAA
* * * * * *
41124627 GATTTTAGTTTGCTTCCAAAGTAGAATTAAATTAAATAATATTTGTTTCGGGATTTATTCTCGCA
1 GATTTTAGTTTGCTTCCAAAGTAGAACTAAATTAAATAAAATCTGTTTCGGGATTCATTCCCACA
*
41124692 GTTTAACAATATTTTATTT
66 GTTTAACAAGATTTTATTT
* * * *
41124711 GATTTTATTTTG-TTTCAAATTAGAACTAAATTAAATAAAATCT-TTTCGGGATTCATTCCCACC
1 GATTTTAGTTTGCTTCCAAAGTAGAACTAAATTAAATAAAATCTGTTTCGGGATTCATTCCCACA
41124774 GTTTAACAAGATTTTATT
66 GTTTAACAAGATTTTATT
41124792 CGATATTGTT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
82 33 0.47
83 26 0.37
84 11 0.16
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (84 bp):
GATTTTAGTTTGCTTCCAAAGTAGAACTAAATTAAATAAAATCTGTTTCGGGATTCATTCCCACA
GTTTAACAAGATTTTATTT
Found at i:41126285 original size:50 final size:51
Alignment explanation
Indices: 41126202--41126304 Score: 120
Period size: 50 Copynumber: 2.0 Consensus size: 51
41126192 TTTGAAATTT
* *
41126202 TGGGCCCACATGCCCGTGTGGCCCACATAGCCCAAAATAGCTT-GCCCGTG
1 TGGGCCCACACGCCCGTGTGGCCCACATAGCCCAAAATAGCTTAGACCGTG
* * * * *
41126252 TGGGCCCACACGTCTGTGTGGCCCATACT-GCCCAATATGGCTTAGACCGTG
1 TGGGCCCACACGCCCGTGTGGCCCACA-TAGCCCAAAATAGCTTAGACCGTG
41126303 TG
1 TG
41126305 TCACACACGA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
50 35 0.80
51 9 0.20
ACGTcount: A:0.18, C:0.33, G:0.27, T:0.21
Consensus pattern (51 bp):
TGGGCCCACACGCCCGTGTGGCCCACATAGCCCAAAATAGCTTAGACCGTG
Found at i:41130066 original size:27 final size:27
Alignment explanation
Indices: 41130028--41130082 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
41130018 GCACATTGCG
**
41130028 TGGAATGCATGGTTTACATGAAATGCA
1 TGGAATGCATGGGATACATGAAATGCA
* *
41130055 TGGATTGCATGGGATGCATGAAATGCA
1 TGGAATGCATGGGATACATGAAATGCA
41130082 T
1 T
41130083 TTTTTGCGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (27 bp):
TGGAATGCATGGGATACATGAAATGCA
Found at i:41130071 original size:18 final size:18
Alignment explanation
Indices: 41130022--41130074 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
41130012 CATGCAGCAC
*
41130022 ATTGCGTGGAATGCATGG
1 ATTGCATGGAATGCATGG
* * *
41130040 TTTACATGAAATGCATGG
1 ATTGCATGGAATGCATGG
*
41130058 ATTGCATGGGATGCATG
1 ATTGCATGGAATGCATG
41130075 AAATGCATTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.32, T:0.30
Consensus pattern (18 bp):
ATTGCATGGAATGCATGG
Found at i:41142077 original size:28 final size:28
Alignment explanation
Indices: 41142045--41142138 Score: 161
Period size: 28 Copynumber: 3.4 Consensus size: 28
41142035 CAACATGCAA
41142045 TAACAGTGTGGGCCTTAGCCCGATACAG
1 TAACAGTGTGGGCCTTAGCCCGATACAG
41142073 TAACAGTGTGGGCCTTAGCCCGATACAG
1 TAACAGTGTGGGCCTTAGCCCGATACAG
* *
41142101 GAACAGTGTGGGCCTTAGCCCAATACAG
1 TAACAGTGTGGGCCTTAGCCCGATACAG
*
41142129 TAACAATGTG
1 TAACAGTGTG
41142139 ATAATGCAAC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (28 bp):
TAACAGTGTGGGCCTTAGCCCGATACAG
Found at i:41142213 original size:21 final size:21
Alignment explanation
Indices: 41142163--41142214 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
41142153 CTCAATCCAG
* *
41142163 CCAACACAACGCTTTGTACCG
1 CCAACACACCGCTTTGTACCA
41142184 CCAACACACCGCTTTGTACCA
1 CCAACACACCGCTTTGTACCA
41142205 CCAACACACC
1 CCAACACACC
41142215 ATGTGGGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.44, G:0.10, T:0.15
Consensus pattern (21 bp):
CCAACACACCGCTTTGTACCA
Found at i:41142515 original size:27 final size:27
Alignment explanation
Indices: 41142455--41142682 Score: 275
Period size: 27 Copynumber: 8.4 Consensus size: 27
41142445 AGAGGTATAG
**
41142455 TAGTCATTTTACCCTATGGGGGGTATTT
1 TAGTCATTTTACCCT-TCAGGGGTATTT
** *
41142483 CGGTCATTTTACCCTAT-GGGGGTATTT
1 TAGTCATTTTACCCT-TCAGGGGTATTT
41142510 TAGTCATTTTACCCTTC-GGGAGTATTT
1 TAGTCATTTTACCCTTCAGGG-GTATTT
*
41142537 CAGTCATTTTACCCTTCAGGGGTATTT
1 TAGTCATTTTACCCTTCAGGGGTATTT
*
41142564 TAGTCATTTTACCCTTCAGAGGTATTT
1 TAGTCATTTTACCCTTCAGGGGTATTT
* *
41142591 T-GATTATTTTACCTTTC-GCGGGTATTT
1 TAG-TCATTTTACCCTTCAG-GGGTATTT
* *
41142618 TAGTCATTTTACCCTTTAGAGGTATTT
1 TAGTCATTTTACCCTTCAGGGGTATTT
41142645 TAGTCATTTTACCCTTCAGGGGTATTT
1 TAGTCATTTTACCCTTCAGGGGTATTT
*
41142672 CAGTCATTTTA
1 TAGTCATTTTA
41142683 TTGACCCTAC
Statistics
Matches: 176, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
26 6 0.03
27 150 0.85
28 20 0.11
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.45
Consensus pattern (27 bp):
TAGTCATTTTACCCTTCAGGGGTATTT
Found at i:41143847 original size:13 final size:13
Alignment explanation
Indices: 41143829--41143874 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
41143819 CTACACAGCT
41143829 AGTATAACCAAAA
1 AGTATAACCAAAA
*
41143842 AGTATAATCAAAA
1 AGTATAACCAAAA
*
41143855 AGTATAACCGAAA
1 AGTATAACCAAAA
41143868 AGTATAA
1 AGTATAA
41143875 TCAGCAGCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.20
Consensus pattern (13 bp):
AGTATAACCAAAA
Found at i:41153177 original size:11 final size:11
Alignment explanation
Indices: 41153161--41153205 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
41153151 TATTTCCTTC
41153161 TTTTTTTCAAA
1 TTTTTTTCAAA
*
41153172 TTTTTTTCGAA
1 TTTTTTTCAAA
**
41153183 TTTTTTTTGAA
1 TTTTTTTCAAA
*
41153194 TTTTTTTGAAA
1 TTTTTTTCAAA
41153205 T
1 T
41153206 ACCAATCCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (11 bp):
TTTTTTTCAAA
Found at i:41153677 original size:66 final size:65
Alignment explanation
Indices: 41153595--41153758 Score: 238
Period size: 66 Copynumber: 2.5 Consensus size: 65
41153585 TCAACATATG
* *
41153595 TGATTGGAACATCTATCAGGGCACCTTCATCAATGATTGGAACATCTATCGAGGCAACTTCATCA
1 TGATTGGAACATCTATC-GGGCAACTTCATCAATGATTGGAACATCTATCGAGGCAACTTAATCA
41153660 T
65 T
* * * **
41153661 TGATTGGAACATCTATCGGGCCAGCTTCATCAATGATTGGAACATCTATCGGGGTAGTTTAATCA
1 TGATTGGAACATCTATCGGG-CAACTTCATCAATGATTGGAACATCTATCGAGGCAACTTAATCA
41153726 T
65 T
41153727 TGATTGGAACATCTATCGGTGCAACTTCATCA
1 TGATTGGAACATCTATCGG-GCAACTTCATCA
41153759 TTCTGTTCGA
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
65 3 0.03
66 85 0.96
67 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (65 bp):
TGATTGGAACATCTATCGGGCAACTTCATCAATGATTGGAACATCTATCGAGGCAACTTAATCAT
Found at i:41153759 original size:33 final size:32
Alignment explanation
Indices: 41153595--41153760 Score: 215
Period size: 33 Copynumber: 5.0 Consensus size: 32
41153585 TCAACATATG
* *
41153595 TGATTGGAACATCTATCAGGGCACCTTCATCAA
1 TGATTGGAACATCTATC-GGGCAACTTCATCAT
41153628 TGATTGGAACATCTATCGAGGCAACTTCATCAT
1 TGATTGGAACATCTATCG-GGCAACTTCATCAT
* *
41153661 TGATTGGAACATCTATCGGGCCAGCTTCATCAA
1 TGATTGGAACATCTATCGGG-CAACTTCATCAT
* ** *
41153694 TGATTGGAACATCTATCGGGGTAGTTTAATCAT
1 TGATTGGAACATCTATC-GGGCAACTTCATCAT
41153727 TGATTGGAACATCTATCGGTGCAACTTCATCAT
1 TGATTGGAACATCTATCGG-GCAACTTCATCAT
41153760 T
1 T
41153761 CTGTTCGACT
Statistics
Matches: 117, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
32 5 0.04
33 109 0.93
34 3 0.03
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (32 bp):
TGATTGGAACATCTATCGGGCAACTTCATCAT
Found at i:41159660 original size:27 final size:27
Alignment explanation
Indices: 41159072--41159667 Score: 661
Period size: 27 Copynumber: 22.3 Consensus size: 27
41159062 GAGTATAACA
* *
41159072 GTCATTTTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
41159099 GTCATTTTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
41159126 GTCATTTTACCCTTTAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
41159153 TTCATTTTACCGTATGGGGATATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
41159180 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
41159207 GACACTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * ** *
41159234 GTTATTTTACCCTACGAAGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* **
41159261 GTTATTTTACCCTATGGGGGTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTCG
*
41159288 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
41159315 GTCATTTTACCTTATGAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
*
41159342 GTCA-TTTACCCTATGGGTGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
41159368 GTTATTTTACCTTATGGGGTTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* **
41159395 GTTATTTTACCCTATGGGGGTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
41159422 GTCATTTTACCCTATGAGGGTATTTCT
1 GTCATTTTACCCTATGGGGGTATTTCG
*
41159449 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
41159476 ATCATTCTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
41159503 ATCATTTTACCCTATGGGGGTACTTT-G
1 GTCATTTTACCCTATGGGGGTA-TTTCG
*
41159530 GTCATTTTACCCTATGGGGGTACTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
41159557 ATCATTTTACCCTAT----GTACTTT-G
1 GTCATTTTACCCTATGGGGGTA-TTTCG
* *
41159580 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
41159607 GTCATTTTATCCC-ATGGGGGTATTTCG
1 GTCATTTTA-CCCTATGGGGGTATTTCG
41159634 GTCATTTTA-CCTCATGGGGGTATTTCG
1 GTCATTTTACCCT-ATGGGGGTATTTCG
*
41159661 GTTATTT
1 GTCATTT
41159668 ATTGACCTCT
Statistics
Matches: 491, Mismatches: 66, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
23 18 0.04
24 2 0.00
25 2 0.00
26 26 0.05
27 437 0.89
28 6 0.01
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:41166559 original size:25 final size:24
Alignment explanation
Indices: 41166499--41166586 Score: 92
Period size: 25 Copynumber: 3.6 Consensus size: 24
41166489 GTACATATAG
*
41166499 GCTCATACGAGC-GATAAATGGTAA
1 GCTCATACGAGCTGA-ATATGGTAA
*
41166523 GCTCCT-CTGAGCTGAATATCGGTAA
1 GCTCATAC-GAGCTGAATAT-GGTAA
41166548 GCTCATACGAGCTGTGAAT-TGGTAA
1 GCTCATACGAGC--TGAATATGGTAA
41166573 GCTCATACGAGCTG
1 GCTCATACGAGCTG
41166587 TGGTGAGTTC
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
23 3 0.05
24 12 0.22
25 33 0.60
26 2 0.04
27 5 0.09
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25
Consensus pattern (24 bp):
GCTCATACGAGCTGAATATGGTAA
Found at i:41181012 original size:15 final size:15
Alignment explanation
Indices: 41180992--41181023 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
41180982 AGGGGAAAGG
41180992 TTTTTTGTTTCTATT
1 TTTTTTGTTTCTATT
41181007 TTTTTTGTTTCTATT
1 TTTTTTGTTTCTATT
41181022 TT
1 TT
41181024 CCTTTTTTCT
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:0.06, C:0.06, G:0.06, T:0.81
Consensus pattern (15 bp):
TTTTTTGTTTCTATT
Found at i:41181032 original size:15 final size:15
Alignment explanation
Indices: 41180995--41181033 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
41180985 GGAAAGGTTT
*
41180995 TTTGTTTCTATTTTT
1 TTTGTTTCTATTTTC
41181010 TTTGTTTCTATTTTCC
1 TTTGTTTCTATTTT-C
41181026 TTT-TTTCT
1 TTTGTTTCT
41181034 TCAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.86
16 3 0.14
ACGTcount: A:0.05, C:0.13, G:0.05, T:0.77
Consensus pattern (15 bp):
TTTGTTTCTATTTTC
Found at i:41181232 original size:46 final size:46
Alignment explanation
Indices: 41181177--41181266 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
41181167 ATAAAAAAGA
*
41181177 AAAAGAAAAAGAAAAGCGTTAAAAATGATATTTTTTATTAGTCAGG
1 AAAAGAAAAAGAAAAGCGTTAAAAATGATATTTTTTATCAGTCAGG
*
41181223 AAAAGAAAAAGAAAAGCTTTAAAAATGATATTTTTTATCAGTCA
1 AAAAGAAAAAGAAAAGCGTTAAAAATGATATTTTTTATCAGTCA
41181267 CTATATATGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (46 bp):
AAAAGAAAAAGAAAAGCGTTAAAAATGATATTTTTTATCAGTCAGG
Found at i:41181738 original size:11 final size:11
Alignment explanation
Indices: 41181695--41181746 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
41181685 ATTCAAATAA
41181695 ATTTTA-TTTT
1 ATTTTATTTTT
* *
41181705 ATTTCTCTTTTA
1 ATTT-TATTTTT
*
41181717 ATTTAATTTTT
1 ATTTTATTTTT
41181728 ATTTTATTTTT
1 ATTTTATTTTT
*
41181739 AGTTTATT
1 ATTTTATT
41181747 ATCATGTATT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
10 4 0.12
11 22 0.67
12 7 0.21
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:41188167 original size:22 final size:22
Alignment explanation
Indices: 41188139--41188192 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
41188129 CCTCTCAGTT
*
41188139 TCAGTTTTAGTTAAGACAATTC
1 TCAGTTTCAGTTAAGACAATTC
41188161 TCAGTTTCAGTTAAGACAATTC
1 TCAGTTTCAGTTAAGACAATTC
41188183 TCAGTTTCAG
1 TCAGTTTCAG
41188193 AAAACTTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (22 bp):
TCAGTTTCAGTTAAGACAATTC
Found at i:41188523 original size:27 final size:28
Alignment explanation
Indices: 41188493--41188546 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
41188483 ATCATGTTAA
*
41188493 TTAATC-ATTCGAAAGCTTTCAAAACAT
1 TTAATCTATACGAAAGCTTTCAAAACAT
*
41188520 TTAATCTATACGAAAGCTTTTAAAACA
1 TTAATCTATACGAAAGCTTTCAAAACA
41188547 AATTGTGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (28 bp):
TTAATCTATACGAAAGCTTTCAAAACAT
Found at i:41193273 original size:20 final size:20
Alignment explanation
Indices: 41193248--41193311 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
41193238 TTTCTTAATA
41193248 TTCAAATTTATATTTTTTGT
1 TTCAAATTTATATTTTTTGT
* *
41193268 TTCAAATTTATACTTTTT-A
1 TTCAAATTTATATTTTTTGT
* *
41193287 CTCCAATTT-T-TTTTTTGT
1 TTCAAATTTATATTTTTTGT
41193305 TTCAAAT
1 TTCAAAT
41193312 CCTCATTCTG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
17 5 0.14
18 6 0.17
19 7 0.20
20 17 0.49
ACGTcount: A:0.25, C:0.11, G:0.03, T:0.61
Consensus pattern (20 bp):
TTCAAATTTATATTTTTTGT
Found at i:41193406 original size:19 final size:20
Alignment explanation
Indices: 41193360--41193413 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 20
41193350 CAAAAATTAT
41193360 GAAGTACTGAAAATTTTGAAC
1 GAAGTACT-AAAATTTTGAAC
* *
41193381 G-ATTACTAAAATTTTG-AG
1 GAAGTACTAAAATTTTGAAC
41193399 GAAGTACTAAGAATT
1 GAAGTACTAA-AATT
41193414 ATCCCGAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.07
19 16 0.57
20 9 0.32
21 1 0.04
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (20 bp):
GAAGTACTAAAATTTTGAAC
Found at i:41193455 original size:20 final size:19
Alignment explanation
Indices: 41193426--41193488 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
41193416 CCCGAATACG
41193426 AAAAAACATGAGGGAGTAC
1 AAAAAACATGAGGGAGTAC
* **
41193445 TAAAAACCATGAGAAAGTACC
1 -AAAAAACATGAGGGAGTA-C
* **
41193466 AATAATTATGAGGGAGTAC
1 AAAAAACATGAGGGAGTAC
41193485 AAAA
1 AAAA
41193489 TAGAGAGAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
19 4 0.12
20 28 0.85
21 1 0.03
ACGTcount: A:0.52, C:0.11, G:0.21, T:0.16
Consensus pattern (19 bp):
AAAAAACATGAGGGAGTAC
Found at i:41195231 original size:3 final size:3
Alignment explanation
Indices: 41195225--41195262 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
41195215 TTAATTTAGT
41195225 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
41195263 TATTATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:41195267 original size:3 final size:3
Alignment explanation
Indices: 41195261--41195343 Score: 103
Period size: 3 Copynumber: 27.7 Consensus size: 3
41195251 CATCATCATC
* *
41195261 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** ** *
41195309 ATT ATT ATT GGT ATT ATT GGT ATT ATT ATT TTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
41195344 CAACTTATTT
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:41195740 original size:29 final size:27
Alignment explanation
Indices: 41195702--41195779 Score: 102
Period size: 29 Copynumber: 2.8 Consensus size: 27
41195692 CTCTTTCAAA
41195702 TATTTTAATATCTTTAATTTATTTCAACT
1 TATTTTAATAT-TTTAATTTATTT-AACT
* *
41195731 TATTTCAATATTGTTAATTTATTTAAGT
1 TATTTTAATATT-TTAATTTATTTAACT
*
41195759 TATTTTAACATTTTAATTTAT
1 TATTTTAATATTTTAATTTAT
41195780 ATATATTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.20
28 14 0.32
29 21 0.48
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (27 bp):
TATTTTAATATTTTAATTTATTTAACT
Found at i:41200710 original size:21 final size:21
Alignment explanation
Indices: 41200686--41200731 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
41200676 ATATTTCAAA
*
41200686 AAAATGATGAATAAA-AAAATG
1 AAAATGATGAA-AAAGAAAAAG
41200707 AAAATGATGAAAAAGAAAAAG
1 AAAATGATGAAAAAGAAAAAG
41200728 AAAA
1 AAAA
41200732 AGGAAAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (21 bp):
AAAATGATGAAAAAGAAAAAG
Found at i:41200738 original size:17 final size:17
Alignment explanation
Indices: 41200718--41200752 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
41200708 AAATGATGAA
41200718 AAAGAAAAAGAAAAAGG
1 AAAGAAAAAGAAAAAGG
*
41200735 AAAGGAAAAGAAAAAGG
1 AAAGAAAAAGAAAAAGG
41200752 A
1 A
41200753 GAGGCTAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAAAAGG
Found at i:41202183 original size:44 final size:43
Alignment explanation
Indices: 41202121--41202443 Score: 160
Period size: 44 Copynumber: 7.5 Consensus size: 43
41202111 ATCGAAGAAA
* * *
41202121 CCAATCCTATCTCCCTGAAGTTGTAGTGGAGTGA-ATTAAAAC
1 CCAATCTTATCTCTCTGAAGTTGCAGTGGAGTGAGATTAAAAC
* * *** *
41202163 CACAGATCTTATCTCTCTGAAGTTGCAGTAGAG-CAGA-TCGCAT
1 C-CA-ATCTTATCTCTCTGAAGTTGCAGTGGAGTGAGATTAAAAC
* ** *
41202206 CCAATCTTATCTCCCTGAAGTTGCAGTGGAGT-AGACGAAGAAA
1 CCAATCTTATCTCTCTGAAGTTGCAGTGGAGTGAGATTAA-AAC
* * * * *
41202249 CCAATCATCTCTCTCTAAAGTTGAAGTGGAGCG-GATTAAAAC
1 CCAATCTTATCTCTCTGAAGTTGCAGTGGAGTGAGATTAAAAC
* * * * *** *
41202291 CACAGATCTTATCTCTCTGAAGTTGCAATAGAG-CATA-TCGCAT
1 C-CA-ATCTTATCTCTCTGAAGTTGCAGTGGAGTGAGATTAAAAC
* * * ** *
41202334 CCAGTCTTATCTCTCTGAAGATGCAGTGGAG-CAGACAGAAGAAA
1 CCAATCTTATCTCTCTGAAGTTGCAGTGGAGTGAGA-TTAA-AAC
* * * *
41202378 CCAATCCTATCTCCCTGAAGTTACAGTGGAGCGA-ATTAAAAC
1 CCAATCTTATCTCTCTGAAGTTGCAGTGGAGTGAGATTAAAAC
* *
41202420 CACAGATCTTATCCCTTTGAAGTT
1 C-CA-ATCTTATCTCTCTGAAGTT
41202444 TTAGTAGAGC
Statistics
Matches: 205, Mismatches: 60, Indels: 30
0.69 0.20 0.10
Matches are distributed among these distances:
41 56 0.27
42 11 0.05
43 46 0.22
44 91 0.44
45 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Consensus pattern (43 bp):
CCAATCTTATCTCTCTGAAGTTGCAGTGGAGTGAGATTAAAAC
Found at i:41202224 original size:41 final size:41
Alignment explanation
Indices: 41202168--41202497 Score: 148
Period size: 41 Copynumber: 7.8 Consensus size: 41
41202158 AAAACCACAG
* *
41202168 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAATCCA
* * *
41202209 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGA-CGAAGAAACCA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATC---GAATCCA
* * * * * * * ** *
41202252 ATCATCTCTCTCTAAAGTTGAAGTGGAGCGGATTAAAACCACA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-TCGAATC-CA
* * * *
41202295 GATCTTATCTCTCTGAAGTTGCAATAGAGCATATCGCATCCA
1 -ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAATCCA
* * * * *
41202337 GTCTTATCTCTCTGAAGATGCAGTGGAGCAGACAGA-AGAAACCA
1 ATCTTATCTCCCTGAAGTTGCAGT--AG-AG-CAGATCGAATCCA
* * * ** *
41202381 ATCCTATCTCCCTGAAGTTACAGTGGAGC-GAATTAAAACCACA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAG-A-TCGAATC-CA
* ** * * *
41202424 GATCTTATC-CCTTTGAAGTTTTAGTAGAGCATATCGCATCTA
1 -ATCTTATCTCC-CTGAAGTTGCAGTAGAGCAGATCGAATCCA
*
41202466 GTCTTATCTCCCTGAAGTTGCAG-AGAAGCAGA
1 ATCTTATCTCCCTGAAGTTGCAGTAG-AGCAGA
41202498 CAGAAGAAAC
Statistics
Matches: 211, Mismatches: 58, Indels: 40
0.68 0.19 0.13
Matches are distributed among these distances:
39 1 0.00
40 5 0.02
41 73 0.35
42 13 0.06
43 44 0.21
44 72 0.34
45 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (41 bp):
ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAATCCA
Found at i:41202452 original size:129 final size:128
Alignment explanation
Indices: 41202114--41202510 Score: 580
Period size: 129 Copynumber: 3.1 Consensus size: 128
41202104 AGAACAAATC
* *
41202114 GAAGAAACCAATCCTATCTCCCTGAAGTTGTAGTGGAGTGAATTAAAACCACAGATCTTATCTCT
1 GAAGAAACCAATCCTATCTCCCTGAAGTT-AAGTGGAGCGAATTAAAACCACAGATCTTATCTCT
* * *
41202179 CTGAAGTTGCAGTAGAGCAGATCGCATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGAC-
65 CTGAAGTTGCAGTAGAGCATATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA
* * * * *
41202242 GAAGAAACCAATCATCTCTCTCTAAAGTTGAAGTGGAGCGGATTAAAACCACAGATCTTATCTCT
1 GAAGAAACCAATCCTATCTCCCTGAAGTT-AAGTGGAGCGAATTAAAACCACAGATCTTATCTCT
* * *
41202307 CTGAAGTTGCAATAGAGCATATCGCATCCAGTCTTATCTCTCTGAAGATGCAGTGGAGCAGACA
65 CTGAAGTTGCAGTAGAGCATATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA
*
41202371 GAAGAAACCAATCCTATCTCCCTGAAGTTACAGTGGAGCGAATTAAAACCACAGATCTTATCCCT
1 GAAGAAACCAATCCTATCTCCCTGAAGTTA-AGTGGAGCGAATTAAAACCACAGATCTTATCTCT
* ** * * *
41202436 TTGAAGTTTTAGTAGAGCATATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGAGAAGCAGACA
65 CTGAAGTTGCAGTAGAGCATATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA
41202500 GAAGAAACCAA
1 GAAGAAACCAA
41202511 AAGCAGACAG
Statistics
Matches: 239, Mismatches: 28, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
128 116 0.49
129 123 0.51
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (128 bp):
GAAGAAACCAATCCTATCTCCCTGAAGTTAAGTGGAGCGAATTAAAACCACAGATCTTATCTCTC
TGAAGTTGCAGTAGAGCATATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA
Found at i:41202516 original size:20 final size:20
Alignment explanation
Indices: 41202491--41202530 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
41202481 AGTTGCAGAG
41202491 AAGCAGACAGAAGAAACCAA
1 AAGCAGACAGAAGAAACCAA
41202511 AAGCAGACAGAAGAAACCAA
1 AAGCAGACAGAAGAAACCAA
41202531 TCCTATCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.20, T:0.00
Consensus pattern (20 bp):
AAGCAGACAGAAGAAACCAA
Found at i:41202636 original size:149 final size:149
Alignment explanation
Indices: 41202363--41202656 Score: 464
Period size: 149 Copynumber: 2.0 Consensus size: 149
41202353 GATGCAGTGG
*
41202363 AGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTACAGTGGAGCGAATTAAAACCACAGATC
1 AGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTACAGTGGAGCGAATTAAAACCACAAATC
* * * *
41202428 TTATCCCTTTGAAGTTTTAGTAGAGCATATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGAGAA
66 TTATCCCTCTGAAGTTGTAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGAGAA
*
41202493 GCAGACAGAAGAAACCAAA
131 GCAAACAGAAGAAACCAAA
*
41202512 AGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGC-AGATTAAAACCACAAAT
1 AGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTACAGTGGAGCGA-ATTAAAACCACAAAT
* * * * *
41202576 CTTATCTCTCTGAAGTTGTAGTAGAGCAGATTGCATCCAGTCTTATCTCCCTGAATTTGCAGTGG
65 CTTATCCCTCTGAAGTTGTAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGAGA
41202641 AGCAAACAGAAGAAAC
130 AGCAAACAGAAGAAAC
41202657 TAATCCTATC
Statistics
Matches: 132, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
148 1 0.01
149 131 0.99
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (149 bp):
AGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTACAGTGGAGCGAATTAAAACCACAAATC
TTATCCCTCTGAAGTTGTAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGAGAA
GCAAACAGAAGAAACCAAA
Found at i:41202677 original size:85 final size:85
Alignment explanation
Indices: 41202534--41202992 Score: 275
Period size: 85 Copynumber: 5.3 Consensus size: 85
41202524 AAACCAATCC
** * * * *
41202534 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAAATCTTATCTCTCTGAAGTTGTAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAACAAAACAACAAATCCTATCTCCCTGAAGTTGCAGTA
41202599 GAGCAGATTGCATCCAGTCT
66 GAGCAGATTGCATCCAGTCT
* *
41202619 TATCTCCCTGAATTTGCAGTGGAGCA-AACAGAAGA-AACTAATCCTATCTCCCTGAAGTTGCAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAACA-AA-ACAACAAATCCTATCTCCCTGAAGTTGCAG
* * ** *
41202682 TGGAGTAGATTAAAACCACAGATCT
64 TAGAGCAGATT-GCATC-CAG-TCT
* * * *** * * * * *
41202707 TATCTCTCTGAAGTTGTAGTAGAGCAG---ATTGCATCCAGTCTTATCTCCCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAACAAAACAACAAATCCTATCTCCCTGAAGTTGCAGTA
** * * * *
41202769 GAGCAGACAAAAGAAACCAATCC
66 GAGCAG---ATTGCATCCAGTCT
* * * ** * * * * *
41202792 TATCTCCTTAAAGTTGCAGTGGAGCGGATTAAAACCACATATCTTATCTCTCTGAAGTTGCAATA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAACAAAACAACAAATCCTATCTCCCTGAAGTTGCAGTA
*
41202857 GAGCAGATCGCATCCAGTCT
66 GAGCAGATTGCATCCAGTCT
*** * * *
41202877 TATCTTTTTGAAGTTGCAATGGAGCAG-ACAGAAGA-AACCAATCCTATCTCCCTAAAGTTGCAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAACA-AA-ACAACAAATCCTATCTCCCTGAAGTTGCAG
* ** *
41202940 TAGAGCGGATTAAAACCACAGATCT
64 TAGAGCAGATT-GCATC-CAG-TCT
* *
41202965 TATCTCCTTGAAGTTGCAGTAGAGCAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA
41202993 TCGCATCGAG
Statistics
Matches: 278, Mismatches: 77, Indels: 34
0.71 0.20 0.09
Matches are distributed among these distances:
84 3 0.01
85 175 0.63
86 9 0.03
87 9 0.03
88 82 0.29
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (85 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGAACAAAACAACAAATCCTATCTCCCTGAAGTTGCAGTA
GAGCAGATTGCATCCAGTCT
Found at i:41202747 original size:129 final size:129
Alignment explanation
Indices: 41202512--41203033 Score: 812
Period size: 129 Copynumber: 4.0 Consensus size: 129
41202502 AGAAACCAAA
* *
41202512 AGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAAATC
1 AGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAGATC
* * *
41202577 TTATCTCTCTGAAGTTGTAGTAGAGCAGATTGCATCCAGTCTTATCTCCCTGAATTTGCAGTGG
66 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGG
* * * *
41202641 AGCAAACAGAAGAAACTAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACCACAGATC
1 AGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAGATC
* *
41202706 TTATCTCTCTGAAGTTGTAGTAGAGCAGATTGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGG
66 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGG
* * * *
41202770 AGCAGACAAAAGAAACCAATCCTATCTCCTTAAAGTTGCAGTGGAGCGGATTAAAACCACATATC
1 AGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAGATC
* *** *
41202835 TTATCTCTCTGAAGTTGCAATAGAGCAGATCGCATCCAGTCTTATCTTTTTGAAGTTGCAATGG
66 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGG
* *
41202899 AGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAACCACAGATC
1 AGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAGATC
* *
41202964 TTATCTC-CTTGAAGTTGCAGTAGAGCAGATCGCATCGAGTCTTATCTTCCTGAAGTTGCAGTGG
66 TTATCTCTC-TGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGG
41203028 AGCAGA
1 AGCAGA
41203034 TCCAAATGAT
Statistics
Matches: 363, Mismatches: 29, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
128 1 0.00
129 362 1.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (129 bp):
AGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAGATC
TTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGG
Found at i:41203022 original size:85 final size:84
Alignment explanation
Indices: 41202663--41203094 Score: 302
Period size: 85 Copynumber: 5.1 Consensus size: 84
41202653 AAACTAATCC
* *
41202663 TATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGTAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCT-TGAAGTTGCAGTA
*
41202728 GAGCAGATTGCATCCAGTCT
65 GAGCAGATAGCATCCAGTCT
* ** * *
41202748 TATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAAGAAACCA-ATCCTATCTCCTTAAAGTTGCAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA-CCA-CAGATCTTATCT-CTTGAAGTTGCAG
* * ** * *
41202811 TGGAGCGGATTAAAACCACATATCT
63 TAGAGCAGA-TAGCATC-CA-GTCT
* * * *** * *
41202836 TATCTCTCTGAAGTTGCAATAGAGCAGA-TCGCATC-CAG-TCTTATCTTTTTGAAGTTGCAATG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATC-TCTTGAAGTTGC-A-G
* * * * *
41202898 GAGCAGACAGA-AGAAACCAATCC
63 TAG-AG-CAGATAGCATCCAGTCT
* * *
41202921 TATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAACCACAGATCTTATCTCCTTGAAGTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCT-CTTGAAGTTGCAGTA
* *
41202986 GAGCAGATCGCATCGAGTCT
65 GAGCAGATAGCATCCAGTCT
* ** ** ** * *
41203006 TATCTTCCTGAAGTTGCAGTGGAGCAGATCCAAATGATGGATCTCATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCT-TGAAGTTGCAGTA
* *
41203071 GAGCAGATCGCAT-CAGACT
65 GAGCAGATAGCATCCAGTCT
41203090 TATCT
1 TATCT
41203095 TTAAGTTGTA
Statistics
Matches: 267, Mismatches: 62, Indels: 37
0.73 0.17 0.10
Matches are distributed among these distances:
84 19 0.07
85 167 0.63
86 17 0.06
87 13 0.05
88 48 0.18
89 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.28
Consensus pattern (84 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTTGAAGTTGCAGTAG
AGCAGATAGCATCCAGTCT
Found at i:41203035 original size:41 final size:40
Alignment explanation
Indices: 41202962--41203094 Score: 137
Period size: 41 Copynumber: 3.2 Consensus size: 40
41202952 AAACCACAGA
41202962 TCTTATCTCCTTGAAGTTGCAGTAGAGCAGATCGCATCGAG
1 TCTTATCTCC-TGAAGTTGCAGTAGAGCAGATCGCATCGAG
*
41203003 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATC-CAAAT-GATGG
1 TCTTATC-TCCTGAAGTTGCAGTAGAGCAGATCGC--ATCGA--G
* *
41203046 ATCTCATCTCTCTGAAGTTACAGTAGAGCAGATCGCATC-AG
1 -TCTTATCTC-CTGAAGTTGCAGTAGAGCAGATCGCATCGAG
*
41203087 ACTTATCT
1 TCTTATCT
41203095 TTAAGTTGTA
Statistics
Matches: 77, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
40 7 0.09
41 31 0.40
42 5 0.06
43 6 0.08
44 27 0.35
45 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (40 bp):
TCTTATCTCCTGAAGTTGCAGTAGAGCAGATCGCATCGAG
Found at i:41203947 original size:6 final size:7
Alignment explanation
Indices: 41203931--41203955 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41203921 GCTGCTGTTC
41203931 TTTTTAT
1 TTTTTAT
41203938 TTTTTAT
1 TTTTTAT
41203945 TTTTTAT
1 TTTTTAT
41203952 TTTT
1 TTTT
41203956 GATTGATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:41204596 original size:3 final size:3
Alignment explanation
Indices: 41204588--41204687 Score: 103
Period size: 3 Copynumber: 33.7 Consensus size: 3
41204578 TTAGTTTAAG
* * * *
41204588 ATT ATT ATT AAT -TT AGT ATC ATT ATT ATT ATT ATT ATT ATT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* ** * *
41204635 ACT ATT ATT ATT ATT ATT GGT ATT ATT ATT CTT ATT ATT TTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
41204683 TTT AT
1 ATT AT
41204688 CAACTTATTT
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
2 1 0.01
3 76 0.99
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:41205080 original size:29 final size:28
Alignment explanation
Indices: 41205042--41205118 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 28
41205032 CTCTTTTAAA
*
41205042 TATTTTAATATCTTTAATTTATTTCAACT
1 TATTTTAATAT-TTTAATTTATTTAAACT
* *
41205071 TATTTCAATATTGTTAATTTATTTAAATT
1 TATTTTAATATT-TTAATTTATTTAAACT
*
41205100 TATTTTAACATTTTAATTT
1 TATTTTAATATTTTAATTT
41205119 TTATATATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 8 0.19
29 34 0.81
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.60
Consensus pattern (28 bp):
TATTTTAATATTTTAATTTATTTAAACT
Found at i:41206747 original size:20 final size:20
Alignment explanation
Indices: 41206710--41206747 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41206700 CCAAACTCTT
*
41206710 AAACCTTGAACTTGAACCCC
1 AAACCTTGAACTTAAACCCC
41206730 AAACC-TGAACCTTAAACC
1 AAACCTTGAA-CTTAAACC
41206748 TTAAATCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.39, C:0.34, G:0.08, T:0.18
Consensus pattern (20 bp):
AAACCTTGAACTTAAACCCC
Found at i:41207332 original size:28 final size:28
Alignment explanation
Indices: 41207267--41207344 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
41207257 ATGAAAGCTA
**
41207267 AGAAGAGAAAGAAAAGCAAGAGAAGTTG
1 AGAAGAGAAAGAAAAGCAAGAGAAGCAG
*
41207295 AGGAA-AGAAAGAAAAGCGAGAGAAGCAG
1 A-GAAGAGAAAGAAAAGCAAGAGAAGCAG
*
41207323 AGAAGTGAAAGAAGAA-CAAGAG
1 AGAAGAGAAAGAA-AAGCAAGAG
41207345 GTTGATGAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
27 3 0.07
28 34 0.81
29 5 0.12
ACGTcount: A:0.58, C:0.05, G:0.33, T:0.04
Consensus pattern (28 bp):
AGAAGAGAAAGAAAAGCAAGAGAAGCAG
Found at i:41207357 original size:6 final size:6
Alignment explanation
Indices: 41207348--41207379 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
41207338 ACAAGAGGTT
41207348 GATGAA GATGAA GATGAA GATGAA GATGAA GA
1 GATGAA GATGAA GATGAA GATGAA GATGAA GA
41207380 GAGAAAACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.34, T:0.16
Consensus pattern (6 bp):
GATGAA
Found at i:41207907 original size:28 final size:28
Alignment explanation
Indices: 41207876--41207929 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
41207866 AAGAATCTCA
*
41207876 AACCATGAACCCAAAAC-CTATAACCTTG
1 AACCATAAACCCAAAACTC-ATAACCTTG
* *
41207904 AACCCTAAATCCAAAACTCATAACCT
1 AACCATAAACCCAAAACTCATAACCT
41207930 ATAACCCCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 21 0.95
29 1 0.05
ACGTcount: A:0.44, C:0.33, G:0.04, T:0.19
Consensus pattern (28 bp):
AACCATAAACCCAAAACTCATAACCTTG
Found at i:41208515 original size:28 final size:28
Alignment explanation
Indices: 41208480--41208575 Score: 140
Period size: 28 Copynumber: 3.4 Consensus size: 28
41208470 AAAGCAGAGA
41208480 AGAGAAAGAAAAGCAAAAGAAGAAAATG
1 AGAGAAAGAAAAGCAAAAGAAGAAAATG
*
41208508 AGAGAAAGAAAAGCAAAAGAAGAAGA-G
1 AGAGAAAGAAAAGCAAAAGAAGAAAATG
* * *
41208535 AAGAGAAATAAAACCAAAAGAAGAAAATA
1 -AGAGAAAGAAAAGCAAAAGAAGAAAATG
41208564 AGAGAAAGAAAA
1 AGAGAAAGAAAA
41208576 ATAAGAGGTT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
27 1 0.02
28 59 0.98
ACGTcount: A:0.70, C:0.04, G:0.23, T:0.03
Consensus pattern (28 bp):
AGAGAAAGAAAAGCAAAAGAAGAAAATG
Found at i:41208571 original size:17 final size:17
Alignment explanation
Indices: 41208495--41208582 Score: 58
Period size: 19 Copynumber: 5.0 Consensus size: 17
41208485 AAGAAAAGCA
*
41208495 AAAGAAGAAAATGAGAG
1 AAAGAAGAAAATAAGAG
41208512 AAAGAA-AAGCAA-AAGAAG
1 AAAGAAGAA--AATAAG-AG
* *
41208530 AAGAGAAGAGAAATAAAACCA
1 AA-AGAAGA-AAATAAGA--G
41208551 AAAGAAGAAAATAAGAG
1 AAAGAAGAAAATAAGAG
41208568 AAAG-A-AAAATAAGAG
1 AAAGAAGAAAATAAGAG
41208583 GTTGATCAAG
Statistics
Matches: 57, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
15 10 0.18
16 3 0.05
17 12 0.21
18 6 0.11
19 14 0.25
20 9 0.16
21 3 0.05
ACGTcount: A:0.69, C:0.03, G:0.23, T:0.05
Consensus pattern (17 bp):
AAAGAAGAAAATAAGAG
Found at i:41209726 original size:28 final size:28
Alignment explanation
Indices: 41209704--41209764 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
41209694 GAAAGAAATG
* * * *
41209704 CAAGAGAAGTAGAGTAGAAAAAGAAAAA
1 CAAGAAAAGCAGAGAAGAGAAAGAAAAA
41209732 CAAGAAAAGCAGAGAAGAGAAAGAAAAA
1 CAAGAAAAGCAGAGAAGAGAAAGAAAAA
41209760 CAAGA
1 CAAGA
41209765 GGTTGATGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.66, C:0.07, G:0.25, T:0.03
Consensus pattern (28 bp):
CAAGAAAAGCAGAGAAGAGAAAGAAAAA
Found at i:41210984 original size:28 final size:28
Alignment explanation
Indices: 41210944--41211027 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
41210934 GGAAACGTGA
*
41210944 AAGCAGAGAAGAGAAAGAAAAGCAAGCG
1 AAGCAGAGAAGAGAAAGAAAAGCAAGAG
* *
41210972 AAGTAGAGTAGAGAAAGAAAAGCAAGAG
1 AAGCAGAGAAGAGAAAGAAAAGCAAGAG
* *
41211000 AAGCAGAGAAGAGAAATAAAAACAAGAG
1 AAGCAGAGAAGAGAAAGAAAAGCAAGAG
41211028 GTTGACAAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.60, C:0.07, G:0.30, T:0.04
Consensus pattern (28 bp):
AAGCAGAGAAGAGAAAGAAAAGCAAGAG
Found at i:41211949 original size:28 final size:27
Alignment explanation
Indices: 41211913--41211996 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 27
41211903 ACATGAAAGG
41211913 AGAGAAGAGAAAGAAAAGCAAGAGAAGT
1 AGAGAAGAGAAAGAAAA-CAAGAGAAGT
* *
41211941 AGAGGAGAGAAAGAAACACAAAAGAAGT
1 AGAGAAGAGAAAGAAA-ACAAGAGAAGT
41211969 AGAGAAGAGAAAGAAAAACAAGAGAAGT
1 AGAGAAGAGAAAG-AAAACAAGAGAAGT
41211997 GTAACATCCC
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
28 46 0.92
29 4 0.08
ACGTcount: A:0.62, C:0.05, G:0.30, T:0.04
Consensus pattern (27 bp):
AGAGAAGAGAAAGAAAACAAGAGAAGT
Found at i:41215622 original size:28 final size:28
Alignment explanation
Indices: 41215583--41215685 Score: 107
Period size: 28 Copynumber: 3.7 Consensus size: 28
41215573 ATGAAAGGAG
* *
41215583 AGAAAAGAAAGAAACACAAGAGAAGCAG
1 AGAAGAGAAAGAAACACAAGAGAAGCAA
* * * *
41215611 ATAAGTGAAAGAAAAACAAAAGAAGCAA
1 AGAAGAGAAAGAAACACAAGAGAAGCAA
* * *
41215639 AGGAGAGAAAGAAACGCAAGAGAAACAA
1 AGAAGAGAAAGAAACACAAGAGAAGCAA
* *
41215667 AGCAGAGAAAGAAAAACAA
1 AGAAGAGAAAGAAACACAA
41215686 AAGGTTGATG
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 59 1.00
ACGTcount: A:0.65, C:0.10, G:0.23, T:0.02
Consensus pattern (28 bp):
AGAAGAGAAAGAAACACAAGAGAAGCAA
Found at i:41215662 original size:15 final size:13
Alignment explanation
Indices: 41215637--41215680 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
41215627 CAAAAGAAGC
*
41215637 AAAGGAGAGAAAG
1 AAAGCAGAGAAAG
*
41215650 AAACGCAAGAGAAAC
1 AAA-GC-AGAGAAAG
41215665 AAAGCAGAGAAAG
1 AAAGCAGAGAAAG
41215678 AAA
1 AAA
41215681 AACAAAAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 13 0.50
14 3 0.12
15 10 0.38
ACGTcount: A:0.64, C:0.09, G:0.27, T:0.00
Consensus pattern (13 bp):
AAAGCAGAGAAAG
Found at i:41225324 original size:40 final size:39
Alignment explanation
Indices: 41225268--41225449 Score: 222
Period size: 40 Copynumber: 4.6 Consensus size: 39
41225258 GAAGTATAAA
*
41225268 CAGGGGCACGTATGTGCAATCAGATGTACCGAAATACAAG
1 CAGGGGCACGTATGTGCAATCAG-GGTACCGAAATACAAG
*
41225308 TAGGGGCACGTATGTGCAATCATGGGTACC-AAAGTACAAG
1 CAGGGGCACGTATGTGCAATCA-GGGTACCGAAA-TACAAG
* * *
41225348 TAGGGGCACGTATGTGCAATCAGGGGTATCGAAGTACAAG
1 CAGGGGCACGTATGTGCAATCA-GGGTACCGAAATACAAG
* * * *
41225388 CAGGGGCACATATATGCAATCAGGGATACCGAAGTACAAA
1 CAGGGGCACGTATGTGCAATCAGGG-TACCGAAATACAAG
*
41225428 CAGAGGCACGTATGTGCAATCA
1 CAGGGGCACGTATGTGCAATCA
41225450 TGTATAATTA
Statistics
Matches: 125, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
39 6 0.05
40 116 0.93
41 3 0.02
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (39 bp):
CAGGGGCACGTATGTGCAATCAGGGTACCGAAATACAAG
Found at i:41225393 original size:80 final size:80
Alignment explanation
Indices: 41225259--41225449 Score: 258
Period size: 80 Copynumber: 2.4 Consensus size: 80
41225249 GAAATTACTG
* * * * *
41225259 AAGTATAAACAGGGGCACGTATGTGCAATCAGATGTACCGAAATACAAGTAGGGGCACGTATGTG
1 AAGTACAAACAGGGGCACGTATGTGCAATCAGAGGTACCGAAATACAAGCAGGGGCACATATATG
41225324 CAATCATGGG-TACCA
66 CAATCA-GGGATACCA
** * * *
41225339 AAGTACAAGTAGGGGCACGTATGTGCAATCAGGGGTATCGAAGTACAAGCAGGGGCACATATATG
1 AAGTACAAACAGGGGCACGTATGTGCAATCAGAGGTACCGAAATACAAGCAGGGGCACATATATG
*
41225404 CAATCAGGGATACCG
66 CAATCAGGGATACCA
*
41225419 AAGTACAAACAGAGGCACGTATGTGCAATCA
1 AAGTACAAACAGGGGCACGTATGTGCAATCA
41225450 TGTATAATTA
Statistics
Matches: 96, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
79 3 0.03
80 93 0.97
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (80 bp):
AAGTACAAACAGGGGCACGTATGTGCAATCAGAGGTACCGAAATACAAGCAGGGGCACATATATG
CAATCAGGGATACCA
Found at i:41225944 original size:14 final size:14
Alignment explanation
Indices: 41225910--41225937 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41225900 AACAATTTCA
41225910 ACAAAATTCACCTT
1 ACAAAATTCACCTT
41225924 ACAAAATTCACCTT
1 ACAAAATTCACCTT
41225938 TAAAAATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (14 bp):
ACAAAATTCACCTT
Found at i:41229375 original size:25 final size:25
Alignment explanation
Indices: 41229347--41229403 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
41229337 CTAGAATCAT
41229347 ATCAAACTCACCAAAAGGTAAAAAC
1 ATCAAACTCACCAAAAGGTAAAAAC
41229372 ATCAAACTCACCAAAAGGTAAAAAC
1 ATCAAACTCACCAAAAGGTAAAAAC
41229397 ATCAAAC
1 ATCAAAC
41229404 ATCAAACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.56, C:0.25, G:0.07, T:0.12
Consensus pattern (25 bp):
ATCAAACTCACCAAAAGGTAAAAAC
Found at i:41234958 original size:20 final size:20
Alignment explanation
Indices: 41234933--41235078 Score: 98
Period size: 20 Copynumber: 7.3 Consensus size: 20
41234923 AAAGTATAAA
41234933 CAGGGGCACGTATGTGCAAT
1 CAGGGGCACGTATGTGCAAT
* * * * *
41234953 CAGGGGTACCTAAGTACAAG
1 CAGGGGCACGTATGTGCAAT
*
41234973 CAGGGGCACGTTTGTGCAAT
1 CAGGGGCACGTATGTGCAAT
* * * * *
41234993 CATGGGTATCG-AAGTACAAG
1 CAGGGGCA-CGTATGTGCAAT
* *
41235013 CAGGGGCACGTATGAGGAAT
1 CAGGGGCACGTATGTGCAAT
* * * *
41235033 CAGGGGTACCG-AAGTACAAA
1 CAGGGGCA-CGTATGTGCAAT
*
41235053 CAAGGGCACGTATGTGCAAT
1 CAGGGGCACGTATGTGCAAT
41235073 CAGGGG
1 CAGGGG
41235079 TACCAAGTAC
Statistics
Matches: 86, Mismatches: 36, Indels: 8
0.66 0.28 0.06
Matches are distributed among these distances:
19 4 0.05
20 78 0.91
21 4 0.05
ACGTcount: A:0.30, C:0.18, G:0.34, T:0.17
Consensus pattern (20 bp):
CAGGGGCACGTATGTGCAAT
Found at i:41234979 original size:40 final size:40
Alignment explanation
Indices: 41234924--41235113 Score: 240
Period size: 40 Copynumber: 4.8 Consensus size: 40
41234914 GAAATTACTA
* *
41234924 AAGTATAAACAGGGGCACGTATGTGCAATCAGGGGTACCT
1 AAGTACAAACAGGGGCACGTATGTGCAATCAGGGGTACCG
* * * *
41234964 AAGTACAAGCAGGGGCACGTTTGTGCAATCATGGGTATCG
1 AAGTACAAACAGGGGCACGTATGTGCAATCAGGGGTACCG
* * *
41235004 AAGTACAAGCAGGGGCACGTATGAGGAATCAGGGGTACCG
1 AAGTACAAACAGGGGCACGTATGTGCAATCAGGGGTACCG
*
41235044 AAGTACAAACAAGGGCACGTATGTGCAATCAGGGGTACC-
1 AAGTACAAACAGGGGCACGTATGTGCAATCAGGGGTACCG
* * *
41235083 AAGTACAAA-TGGGGCCCTTTATGTGCAATCA
1 AAGTACAAACAGGGGCAC-GTATGTGCAATCA
41235114 TGTATAATTA
Statistics
Matches: 130, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
38 5 0.04
39 21 0.16
40 104 0.80
ACGTcount: A:0.32, C:0.18, G:0.31, T:0.19
Consensus pattern (40 bp):
AAGTACAAACAGGGGCACGTATGTGCAATCAGGGGTACCG
Found at i:41242178 original size:42 final size:42
Alignment explanation
Indices: 41242130--41242283 Score: 231
Period size: 42 Copynumber: 3.7 Consensus size: 42
41242120 TACACCGGCT
* *
41242130 TTAAGCCTGCTAAACTTATAGT-TCGAATTTATTTCACTGGCA
1 TTAAGCCTGCTAAACGTAAAGTCT-GAATTTATTTCACTGGCA
*
41242172 TTAAGCCTGCTAGACGTAAAGTCTGAATTTATTTCACTGGCA
1 TTAAGCCTGCTAAACGTAAAGTCTGAATTTATTTCACTGGCA
*
41242214 TTAAGCCTGCTAAACGTAAAGTCTGAATTTATTTCACTAGCA
1 TTAAGCCTGCTAAACGTAAAGTCTGAATTTATTTCACTGGCA
*
41242256 TTAAGCATGC-AAGACGTAAAGTCTGAAT
1 TTAAGCCTGCTAA-ACGTAAAGTCTGAAT
41242284 GGTTTCACTG
Statistics
Matches: 104, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
41 2 0.02
42 101 0.97
43 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (42 bp):
TTAAGCCTGCTAAACGTAAAGTCTGAATTTATTTCACTGGCA
Found at i:41248387 original size:12 final size:12
Alignment explanation
Indices: 41248370--41248399 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41248360 GTTCTTAAAG
41248370 GTATGAGGCCAA
1 GTATGAGGCCAA
*
41248382 GTATGAGGCCGA
1 GTATGAGGCCAA
41248394 GTATGA
1 GTATGA
41248400 CTGAGCCGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.13, G:0.37, T:0.20
Consensus pattern (12 bp):
GTATGAGGCCAA
Found at i:41255967 original size:24 final size:24
Alignment explanation
Indices: 41255940--41255991 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41255930 TATTTCTTGC
41255940 TTTTCATTTTAGTTTATTTTCAGT
1 TTTTCATTTTAGTTTATTTTCAGT
** *
41255964 TTTTTTTTTTAGTTTATTTTCTGT
1 TTTTCATTTTAGTTTATTTTCAGT
41255988 TTTT
1 TTTT
41255992 TATCTTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.06, G:0.08, T:0.75
Consensus pattern (24 bp):
TTTTCATTTTAGTTTATTTTCAGT
Found at i:41255992 original size:24 final size:24
Alignment explanation
Indices: 41255946--41255992 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
41255936 TTGCTTTTCA
41255946 TTTTAGTTTATTTTCAGTTTTTTT
1 TTTTAGTTTATTTTCAGTTTTTTT
*
41255970 TTTTAGTTTATTTTCTGTTTTTT
1 TTTTAGTTTATTTTCAGTTTTTT
41255993 ATCTTTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.11, C:0.04, G:0.09, T:0.77
Consensus pattern (24 bp):
TTTTAGTTTATTTTCAGTTTTTTT
Found at i:41256002 original size:24 final size:25
Alignment explanation
Indices: 41255947--41256002 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
41255937 TGCTTTTCAT
* *
41255947 TTTAGTTTATTTTCAGTTTTTT-TT
1 TTTAGTTTATTTTCTGTTTTTTATC
41255971 TTTAGTTTATTTTCTGTTTTTTATC
1 TTTAGTTTATTTTCTGTTTTTTATC
41255996 TTT-GTTT
1 TTTAGTTT
41256003 TTTAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.11, C:0.05, G:0.09, T:0.75
Consensus pattern (25 bp):
TTTAGTTTATTTTCTGTTTTTTATC
Found at i:41261484 original size:21 final size:22
Alignment explanation
Indices: 41261459--41261505 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
41261449 ATAAAATTAA
* *
41261459 TATTATATACTC-ATTCTTATT
1 TATTATATACTCTAATCTAATT
*
41261480 TATTATATTCTCTAATCTAATT
1 TATTATATACTCTAATCTAATT
41261502 TATT
1 TATT
41261506 TAATTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTATATACTCTAATCTAATT
Found at i:41278076 original size:36 final size:36
Alignment explanation
Indices: 41278036--41278105 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
41278026 TTTCGTTAAG
*
41278036 AAATTGATTATAATAATTTGTGTATAATATATAAAT
1 AAATTGATTATAATAATTTGTATATAATATATAAAT
41278072 AAATTGATTATAATAATTTGTATATAATATATAA
1 AAATTGATTATAATAATTTGTATATAATATATAA
41278106 TTAATATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (36 bp):
AAATTGATTATAATAATTTGTATATAATATATAAAT
Found at i:41278517 original size:27 final size:27
Alignment explanation
Indices: 41278484--41278549 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
41278474 TAAAAAATAT
*
41278484 CCAAAATGT-TATAAATTTTTTTATTTA
1 CCAAAATATATAT-AATTTTTTTATTTA
41278511 CCAAAATATATATAATTTTTTTATTTA
1 CCAAAATATATATAATTTTTTTATTTA
41278538 CCAAAATATATA
1 CCAAAATATATA
41278550 AAAAAACAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
27 34 0.92
28 3 0.08
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (27 bp):
CCAAAATATATATAATTTTTTTATTTA
Found at i:41278582 original size:11 final size:11
Alignment explanation
Indices: 41278549--41278575 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41278539 CAAAATATAT
41278549 AAAAAAACAAA
1 AAAAAAACAAA
41278560 AAAAAAACAAA
1 AAAAAAACAAA
41278571 AAAAA
1 AAAAA
41278576 TAAAAAACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:41278662 original size:27 final size:27
Alignment explanation
Indices: 41278623--41278675 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
41278613 TCCCTGGGTG
*
41278623 AAGGGAACACTGTTGGCGGCATCAAAC
1 AAGGGAACACTGTTGGCGGCACCAAAC
*
41278650 AAGGGAACCCTGTTGGCGGCACCAAA
1 AAGGGAACACTGTTGGCGGCACCAAA
41278676 TATTTTGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.32, C:0.25, G:0.30, T:0.13
Consensus pattern (27 bp):
AAGGGAACACTGTTGGCGGCACCAAAC
Found at i:41278721 original size:19 final size:19
Alignment explanation
Indices: 41278674--41278724 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
41278664 GGCGGCACCA
** *
41278674 AATATTTTGGTATTTTTTT
1 AATATTTTATTATTTTTGT
41278693 AATATTTTATTATTTTTGT
1 AATATTTTATTATTTTTGT
*
41278712 AATGTTTTATTAT
1 AATATTTTATTAT
41278725 GGGTTTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (19 bp):
AATATTTTATTATTTTTGT
Found at i:41278812 original size:27 final size:28
Alignment explanation
Indices: 41278762--41278830 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
41278752 AAATAAAAAA
41278762 TTACCAAAATAT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAAC-TTTTTTTAT
41278790 TTACCAAAATATATATAA-TTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
41278817 TTACCAAAATATAT
1 TTACCAAAATATAT
41278831 CAAAAAAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 23 0.57
28 12 0.30
29 5 0.12
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (28 bp):
TTACCAAAATATATATAACTTTTTTTAT
Found at i:41278860 original size:16 final size:17
Alignment explanation
Indices: 41278831--41278863 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41278821 CAAAATATAT
41278831 CAAAAAAAAGTAAAAAA
1 CAAAAAAAAGTAAAAAA
*
41278848 CAAAAAGAA-TAAAAAA
1 CAAAAAAAAGTAAAAAA
41278864 AGGAAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.82, C:0.06, G:0.06, T:0.06
Consensus pattern (17 bp):
CAAAAAAAAGTAAAAAA
Found at i:41279280 original size:26 final size:26
Alignment explanation
Indices: 41279225--41279301 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 26
41279215 TTATTCAAGG
**
41279225 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACA-GGTTCCCTTGTT
41279252 TGGTGCCGCCAACAGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGTTCCCTTGTT
*
41279278 TGGTGCCGCCAATAGTGTTCCCTT
1 TGGTGCCGCCAACAG-GTTCCCTT
41279302 CACCTAGGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 24 0.52
27 22 0.48
ACGTcount: A:0.14, C:0.30, G:0.27, T:0.29
Consensus pattern (26 bp):
TGGTGCCGCCAACAGGTTCCCTTGTT
Found at i:41279351 original size:15 final size:15
Alignment explanation
Indices: 41279331--41279364 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
41279321 TCAGTTCAGG
*
41279331 TTTTTTT-TTTCTAT
1 TTTTTTTATTTTTAT
41279345 TTTTTTTATTTTTAT
1 TTTTTTTATTTTTAT
41279360 TTTTT
1 TTTTT
41279365 GATATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTTATTTTTAT
Found at i:41279400 original size:28 final size:29
Alignment explanation
Indices: 41279366--41279432 Score: 111
Period size: 28 Copynumber: 2.4 Consensus size: 29
41279356 TTATTTTTTG
41279366 ATATATTTTGGTAAAT-AAAAAAATTTAT
1 ATATATTTTGGTAAATAAAAAAAATTTAT
41279394 ATATATTTTGGTAAATAAAAAAAATTTAT
1 ATATATTTTGGTAAATAAAAAAAATTTAT
*
41279423 A-ACATTTTGG
1 ATATATTTTGG
41279433 ATATTTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
28 24 0.65
29 13 0.35
ACGTcount: A:0.48, C:0.01, G:0.09, T:0.42
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAATTTAT
Found at i:41279555 original size:20 final size:19
Alignment explanation
Indices: 41279504--41279555 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
41279494 TTTGATGGGA
*
41279504 TAAAT-TTTAAAAATAATT
1 TAAATATTTAAAAGTAATT
*
41279522 TTAATATATT-AAAGTAAATT
1 TAAATAT-TTAAAAGT-AATT
41279542 TAAATATTTAAAAG
1 TAAATATTTAAAAG
41279556 AGTTATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 4 0.15
19 7 0.26
20 16 0.59
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (19 bp):
TAAATATTTAAAAGTAATT
Found at i:41282358 original size:27 final size:27
Alignment explanation
Indices: 41282320--41282373 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
41282310 GTTGGATGGC
41282320 ATAAACTTTATGATCAGTTCTTTTTAT
1 ATAAACTTTATGATCAGTTCTTTTTAT
41282347 ATAAACTTTATGATCAGTTCTTTTTAT
1 ATAAACTTTATGATCAGTTCTTTTTAT
41282374 CTTTGTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (27 bp):
ATAAACTTTATGATCAGTTCTTTTTAT
Done.