Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, whole genome shotgun sequence
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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 23 of 64
Found at i:3334151 original size:12 final size:12
Alignment explanation
Indices: 3334132--3334206 Score: 73
Period size: 12 Copynumber: 6.0 Consensus size: 12
3334122 AAAGGTATCC
3334132 AAAAAAAAAAA-
1 AAAAAAAAAAAG
3334143 AAAAGAAAAAAAG
1 AAAA-AAAAAAAG
*
3334156 AAAAAGAAAAAG
1 AAAAAAAAAAAG
*
3334168 CAAAAAAAAAAG
1 AAAAAAAAAAAG
3334180 AAACAAGAAAAAA-
1 AAA-AA-AAAAAAG
3334193 AATGAAAAAAAAAG
1 AA--AAAAAAAAAG
3334207 TGACAAAGGA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
11 4 0.08
12 26 0.49
13 14 0.26
14 8 0.15
15 1 0.02
ACGTcount: A:0.85, C:0.03, G:0.11, T:0.01
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:3334165 original size:28 final size:29
Alignment explanation
Indices: 3334132--3334206 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
3334122 AAAGGTATCC
3334132 AAAAAAAAAAAAAAAGAA-AAA-AAGAAA
1 AAAAAAAAAAAAAAAGAAGAAACAAGAAA
3334159 AAGAAAAAGCAAAAAAAA-AAGAAACAAGAAA
1 AA-AAAAA--AAAAAAAAGAAGAAACAAGAAA
*
3334190 AAAAATGAAAAAAAAAG
1 AAAAA-AAAAAAAAAAG
3334207 TGACAAAGGA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
27 2 0.05
28 5 0.12
29 10 0.25
30 14 0.35
31 9 0.22
ACGTcount: A:0.85, C:0.03, G:0.11, T:0.01
Consensus pattern (29 bp):
AAAAAAAAAAAAAAAGAAGAAACAAGAAA
Found at i:3334173 original size:35 final size:35
Alignment explanation
Indices: 3334133--3334201 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
3334123 AAGGTATCCA
* *
3334133 AAAAAAAAAAAAAAGAAAAAAAGAAAAAGAAAAAGC
1 AAAAAAAAAAGAAACAAAAAAA-AAAAAGAAAAAGC
* *
3334169 AAAAAAAAAAGAAACAAGAAAAAAAATGAAAAA
1 AAAAAAAAAAGAAACAAAAAAAAAAAAGAAAAA
3334202 AAAAGTGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 10 0.34
36 19 0.66
ACGTcount: A:0.86, C:0.03, G:0.10, T:0.01
Consensus pattern (35 bp):
AAAAAAAAAAGAAACAAAAAAAAAAAAGAAAAAGC
Found at i:3334176 original size:31 final size:29
Alignment explanation
Indices: 3334132--3334206 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 29
3334122 AAAGGTATCC
3334132 AAAAAA-AAAAAAAAAGA-AAAAAAGAAAA
1 AAAAAAGAAAAAAAAAGAGAAAAAAG-AAA
*
3334160 AGAAAAAGCAAAAAAAAA-AGAAACAAGAAA
1 A-AAAAAG-AAAAAAAAAGAGAAAAAAGAAA
*
3334190 AAAAATGAAAAAAAAAG
1 AAAAAAGAAAAAAAAAG
3334207 TGACAAAGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 10 0.25
29 10 0.25
30 5 0.12
31 15 0.38
ACGTcount: A:0.85, C:0.03, G:0.11, T:0.01
Consensus pattern (29 bp):
AAAAAAGAAAAAAAAAGAGAAAAAAGAAA
Found at i:3336053 original size:120 final size:120
Alignment explanation
Indices: 3335918--3336228 Score: 333
Period size: 120 Copynumber: 2.6 Consensus size: 120
3335908 CTCAGTACTA
* * * *
3335918 GTCACTTTATCTTTTTGACTCATGATTTTGTCCCGATCATTTGATCTTGGTTTCATCCAAATCAT
1 GTCACTTTATCTTTTTGACTCATGATTTTATCCCG-TCATTTGATCTCGGTTTCATCTAGATCAT
* * * * *
3335983 TTTCTTGA-TTCGTGATTTCATCCCAATAAGTCATATTCAACCTCGACTTGGGCTTG
65 TTTCCTGACTT-GCGATTCCATCCCAATAAGTCATATTCAACCTCGACTCGAGCTTG
** * * *
3336039 GTTGCTTTAT-TTTTTGACTCACGATTTTATCCCTGTCATTCTG-TCTCAGTTCCATCTAGATCA
1 GTCACTTTATCTTTTTGACTCATGATTTTATCCC-GTCATT-TGATCTCGGTTTCATCTAGATCA
* * * * * *
3336102 -TTTCCTGACTTGCGATTCCATCCCAATTAGTTATATTCGACTTTGACTCGATCTTG
64 TTTTCCTGACTTGCGATTCCATCCCAATAAGTCATATTCAACCTCGACTCGAGCTTG
* * * *
3336158 GTCACTTTATCTTTTTAACTCTTGATTTTATCCCGGTTATTTGATCTCGATTTCATCTAGATCAT
1 GTCACTTTATCTTTTTGACTCATGATTTTATCCC-GTCATTTGATCTCGGTTTCATCTAGATCAT
3336223 TTTCCT
65 TTTCCT
3336229 AATTTATGAT
Statistics
Matches: 154, Mismatches: 30, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
119 52 0.34
120 85 0.55
121 17 0.11
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (120 bp):
GTCACTTTATCTTTTTGACTCATGATTTTATCCCGTCATTTGATCTCGGTTTCATCTAGATCATT
TTCCTGACTTGCGATTCCATCCCAATAAGTCATATTCAACCTCGACTCGAGCTTG
Found at i:3336562 original size:3 final size:3
Alignment explanation
Indices: 3336554--3336597 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3336544 ACCATACTGC
3336554 ATT 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 ATT AT
3336598 CATCATCATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3337276 original size:26 final size:26
Alignment explanation
Indices: 3337247--3337298 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
3337237 TGTTTGAGGG
3337247 TCTAGAGAGAAAAA-GC-AAAGGCATCA
1 TCTAG-GAGAAAAATGCTAAAGG-ATCA
*
3337273 TCTAGGATAAAAATGCTAAAGGATCA
1 TCTAGGAGAAAAATGCTAAAGGATCA
3337299 CTTTTATACC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 7 0.30
26 11 0.48
27 5 0.22
ACGTcount: A:0.48, C:0.13, G:0.21, T:0.17
Consensus pattern (26 bp):
TCTAGGAGAAAAATGCTAAAGGATCA
Found at i:3337489 original size:22 final size:22
Alignment explanation
Indices: 3337431--3337491 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
3337421 CTTTTTCATT
*
3337431 TTATTTTTATTTTTTGATTTTA
1 TTATTTTTATCTTTTGATTTTA
*
3337453 TT-TTTTTATGGTTTT-ATTTATA
1 TTATTTTTAT-CTTTTGATTT-TA
3337475 TTATTTTTATCTTTTGA
1 TTATTTTTATCTTTTGA
3337492 AAATATATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 11 0.33
22 14 0.42
23 8 0.24
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.74
Consensus pattern (22 bp):
TTATTTTTATCTTTTGATTTTA
Found at i:3338797 original size:58 final size:58
Alignment explanation
Indices: 3338693--3338840 Score: 156
Period size: 58 Copynumber: 2.5 Consensus size: 58
3338683 TTTTGTTATA
* * * * *
3338693 AGTTTGTTGAAACTTATTTGAGTTTTAGTTGCCAATGTATTAAGTTTTT-TTGGTTAGTT
1 AGTTTGTTGAAATTTATTTAAGTTTTGGTTACCAATGTATTAAGTTTTTGTTAGTT--TT
* * *
3338752 A-TTTGTTGAAATTTATTTAAGTTTTGGTTACCAATTTGTTGAGTTTTTGTTAGTTTT
1 AGTTTGTTGAAATTTATTTAAGTTTTGGTTACCAATGTATTAAGTTTTTGTTAGTTTT
* * *
3338809 ATGTTTGTTGAAATCTGTTTAGGTTTTGGTTA
1 A-GTTTGTTGAAATTTATTTAAGTTTTGGTTA
3338841 TATATTTGTT
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
57 3 0.04
58 40 0.53
59 32 0.43
ACGTcount: A:0.21, C:0.04, G:0.20, T:0.55
Consensus pattern (58 bp):
AGTTTGTTGAAATTTATTTAAGTTTTGGTTACCAATGTATTAAGTTTTTGTTAGTTTT
Found at i:3339788 original size:19 final size:20
Alignment explanation
Indices: 3339755--3339793 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3339745 AGATAATTTT
3339755 GTTTAGTATAGCAAT-AATA
1 GTTTAGTATAGCAATCAATA
3339774 GTTTA-TATAGTCAATCAATA
1 GTTTAGTATAG-CAATCAATA
3339794 AAAATGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (20 bp):
GTTTAGTATAGCAATCAATA
Found at i:3340401 original size:18 final size:18
Alignment explanation
Indices: 3340363--3340401 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3340353 CTACTGAGTA
* * *
3340363 TAGTGAATGATATATTGC
1 TAGTAAATGATAAATTAC
3340381 TAGTAAATGATAAATTAC
1 TAGTAAATGATAAATTAC
3340399 TAG
1 TAG
3340402 AAAACTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (18 bp):
TAGTAAATGATAAATTAC
Found at i:3341676 original size:17 final size:17
Alignment explanation
Indices: 3341654--3341695 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
3341644 AAAATTATGC
3341654 TTGAAGTTGTGAATTAT
1 TTGAAGTTGTGAATTAT
* *
3341671 TTGAAGTTGTTAATTGT
1 TTGAAGTTGTGAATTAT
*
3341688 TTAAAGTT
1 TTGAAGTT
3341696 TCGATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (17 bp):
TTGAAGTTGTGAATTAT
Found at i:3346741 original size:12 final size:12
Alignment explanation
Indices: 3346724--3346750 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3346714 TAGACTAACA
3346724 TAATCAATTAAT
1 TAATCAATTAAT
3346736 TAATCAATTAAT
1 TAATCAATTAAT
3346748 TAA
1 TAA
3346751 CGACAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATCAATTAAT
Found at i:3348003 original size:21 final size:22
Alignment explanation
Indices: 3347958--3348008 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
3347948 ATATCGAGAG
3347958 AAATGATTTTTCACATTTCTAA
1 AAATGATTTTTCACATTTCTAA
3347980 AAATGATTTTTCACATTTCTAA
1 AAATGATTTTTCACATTTCTAA
3348002 AAATGAT
1 AAATGAT
3348009 AACTTTTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (22 bp):
AAATGATTTTTCACATTTCTAA
Found at i:3349503 original size:18 final size:18
Alignment explanation
Indices: 3349472--3349517 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
3349462 AATATTAATT
3349472 TAATAAAAATAATAAATA
1 TAATAAAAATAATAAATA
3349490 TAATATAAAA-AATAAATA
1 TAATA-AAAATAATAAATA
*
3349508 TAACAAAAAT
1 TAATAAAAAT
3349518 GAAAATGCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
TAATAAAAATAATAAATA
Found at i:3349671 original size:2 final size:2
Alignment explanation
Indices: 3349664--3349702 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
3349654 GGCATCCATG
3349664 TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3349703 CAATGTATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3350016 original size:24 final size:24
Alignment explanation
Indices: 3349971--3350017 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
3349961 TTATATTAGT
**
3349971 AATATATAAAATAATTGCATATTA
1 AATATATAAAATAATTAAATATTA
**
3349995 AATATATATCATAATTAAATATT
1 AATATATAAAATAATTAAATATT
3350018 TAAAATAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
AATATATAAAATAATTAAATATTA
Found at i:3350069 original size:57 final size:56
Alignment explanation
Indices: 3349991--3350111 Score: 149
Period size: 57 Copynumber: 2.2 Consensus size: 56
3349981 ATAATTGCAT
* * *
3349991 ATTAAA-TATATATCATAATTAAATATTTAAAATA-ATTTTATATGA-TTATATTAA
1 ATTAAATTATGTATTATAATTAAAAATTTAAAATATATTTTATAT-ATTTATATTAA
* *
3350045 ATATATAATTATGTATTATAATTAAAAATTTTAAATATTTTTTATATATTTATATTAA
1 AT-TA-AATTATGTATTATAATTAAAAATTTAAAATATATTTTATATATTTATATTAA
3350103 ATTAAATTA
1 ATTAAATTA
3350112 AATATAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
54 2 0.04
55 2 0.04
56 7 0.12
57 27 0.47
58 19 0.33
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (56 bp):
ATTAAATTATGTATTATAATTAAAAATTTAAAATATATTTTATATATTTATATTAA
Found at i:3350648 original size:16 final size:15
Alignment explanation
Indices: 3350627--3350676 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
3350617 CAAATTAAAC
3350627 TAAATTAAAAATAACT
1 TAAATTAAAAATAA-T
*
3350643 TAAATTTAAAATAATT
1 TAAATTAAAAATAA-T
* *
3350659 TAAACTCAAAATAAT
1 TAAATTAAAAATAAT
3350674 TAA
1 TAA
3350677 TACTCAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 4 0.13
16 26 0.87
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAATTAAAAATAAT
Found at i:3350685 original size:15 final size:15
Alignment explanation
Indices: 3350634--3350689 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
3350624 AACTAAATTA
* *
3350634 AAAATAACTTAAATTT
1 AAAATAA-TTAAACTC
3350650 AAAATAATTTAAACTC
1 AAAATAA-TTAAACTC
3350666 AAAATAATTAATACTC
1 AAAATAATTAA-ACTC
3350682 -AAATAATT
1 AAAATAATT
3350690 CAATCTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.33
16 24 0.67
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAATAATTAAACTC
Found at i:3351553 original size:29 final size:27
Alignment explanation
Indices: 3351521--3351581 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 27
3351511 GTTAAATTAA
3351521 TAATTTTAAATTA-AAATAATATATAATTT
1 TAATTTTAAATTACAAAT--TATAT-ATTT
3351550 TAATTTTTAAATTACAAATTATATATTT
1 TAA-TTTTAAATTACAAATTATATATTT
3351578 TAAT
1 TAAT
3351582 CTTTTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 1 0.03
28 7 0.23
29 8 0.27
30 10 0.33
31 4 0.13
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
TAATTTTAAATTACAAATTATATATTT
Found at i:3351586 original size:29 final size:29
Alignment explanation
Indices: 3351524--3351589 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 29
3351514 AAATTAATAA
3351524 TTTTAAATTAAAATAATATATAATTTTAAT
1 TTTTAAATTAAAAT-ATATATAATTTTAAT
3351554 TTTTAAATTACAAAT-TATAT-ATTTTAAT
1 TTTTAAATTA-AAATATATATAATTTTAAT
3351582 CTTTTAAA
1 -TTTTAAA
3351590 ATCTGATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
28 8 0.24
29 12 0.35
30 10 0.29
31 4 0.12
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTTAAATTAAAATATATATAATTTTAAT
Found at i:3354812 original size:18 final size:18
Alignment explanation
Indices: 3354781--3354826 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
3354771 AACATTAATT
3354781 TAATAAAAATAATAAATA
1 TAATAAAAATAATAAATA
3354799 TAATATAAAA-AATAAATA
1 TAATA-AAAATAATAAATA
*
3354817 TAACAAAAAT
1 TAATAAAAAT
3354827 GAAAACTCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
TAATAAAAATAATAAATA
Found at i:3355333 original size:26 final size:28
Alignment explanation
Indices: 3355296--3355393 Score: 85
Period size: 28 Copynumber: 3.4 Consensus size: 28
3355286 AATATATATC
3355296 ATAATTAAATATTTAAAATAATTTTTA-T
1 ATAATT-AATATTTAAAATAATTTTTATT
* * *
3355324 ATGATT-ATATTAAATATATAATTGTGTATT
1 ATAATTAATATTTAA-A-ATAATT-TTTATT
*
3355354 ATAATTAAAATTTAAAATAATTTTT-TT
1 ATAATTAATATTTAAAATAATTTTTATT
*
3355381 ATATATTTATATT
1 ATA-ATTAATATT
3355394 AAATTAAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
26 7 0.13
27 6 0.11
28 20 0.36
29 9 0.16
30 7 0.13
31 6 0.11
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (28 bp):
ATAATTAATATTTAAAATAATTTTTATT
Found at i:3355944 original size:16 final size:16
Alignment explanation
Indices: 3355920--3355965 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
3355910 AATTAAATTG
3355920 AATTAAAAATAATTTA
1 AATTAAAAATAATTTA
* *
3355936 AATTTAAAATGATTTA
1 AATTAAAAATAATTTA
*
3355952 AATTCAAAATAATT
1 AATTAAAAATAATT
3355966 CATACTCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
AATTAAAAATAATTTA
Found at i:3355991 original size:15 final size:16
Alignment explanation
Indices: 3355925--3355991 Score: 59
Period size: 16 Copynumber: 4.3 Consensus size: 16
3355915 AATTGAATTA
*
3355925 AAAATAATTTAAATTT
1 AAAATAATTTAAATCT
*
3355941 AAAATGATTTAAAT-T
1 AAAATAATTTAAATCT
* *
3355956 CAAAATAATTCATA-CT
1 -AAAATAATTTAAATCT
*
3355972 CAAATAATTT-AATCT
1 AAAATAATTTAAATCT
3355987 AAAAT
1 AAAAT
3355992 TAAAATAACA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
14 1 0.03
15 15 0.38
16 24 0.60
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.37
Consensus pattern (16 bp):
AAAATAATTTAAATCT
Found at i:3356493 original size:33 final size:33
Alignment explanation
Indices: 3356450--3356519 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
3356440 TGCATTTTTT
3356450 ATTTAAATTTTAGGAA-ATATA-AATAATTTTATA
1 ATTTAAATTTT--GAACATATATAATAATTTTATA
* * *
3356483 ATTTATATTTTGAACTTTTATAATAATTTTATA
1 ATTTAAATTTTGAACATATATAATAATTTTATA
3356516 ATTT
1 ATTT
3356520 TATAATAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 3 0.09
32 3 0.09
33 26 0.81
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (33 bp):
ATTTAAATTTTGAACATATATAATAATTTTATA
Found at i:3356841 original size:23 final size:23
Alignment explanation
Indices: 3356808--3356858 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
3356798 TGTAAATGAG
3356808 TTAAATT--AATAATAT-TAAATT
1 TTAAATTAAAATAATATAT-AATT
*
3356829 TTGAATTAAAATAATATATAATT
1 TTAAATTAAAATAATATATAATT
3356852 TTAAATT
1 TTAAATT
3356859 TTAAATTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 6 0.24
23 18 0.72
24 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAAATTAAAATAATATATAATT
Found at i:3356889 original size:29 final size:28
Alignment explanation
Indices: 3356843--3356907 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
3356833 ATTAAAATAA
* *
3356843 TATATAATTTTAAATTTTAAATTGCAAAT
1 TATAT-ATTTTAAATTTTAAAATCCAAAT
* *
3356872 TATATATTTTAATCTTTTAAAATCCAATT
1 TATATATTTTAA-ATTTTAAAATCCAAAT
3356901 TATATAT
1 TATATAT
3356908 ATATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 7 0.23
29 24 0.77
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.51
Consensus pattern (28 bp):
TATATATTTTAAATTTTAAAATCCAAAT
Found at i:3358248 original size:23 final size:21
Alignment explanation
Indices: 3358222--3358273 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
3358212 CAATATCATT
**
3358222 TTTTTGAAATCAAATTATTTTA
1 TTTTTGAAAT-AAACCATTTTA
*
3358244 ATTTTGAAAATAAACCATTTTA
1 TTTTTG-AAATAAACCATTTTA
3358266 TTTTTGAA
1 TTTTTGAA
3358274 TTTTTTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 2 0.08
22 19 0.76
23 4 0.16
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (21 bp):
TTTTTGAAATAAACCATTTTA
Found at i:3360336 original size:19 final size:21
Alignment explanation
Indices: 3360309--3360349 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3360299 GACTTTAAGG
3360309 TTGAGTTTTGGCT-TTTTTCT
1 TTGAGTTTTGGCTATTTTTCT
*
3360329 TTGA-TTTTTGCTATTTTTCT
1 TTGAGTTTTGGCTATTTTTCT
3360349 T
1 T
3360350 GATCAACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.07, C:0.10, G:0.15, T:0.68
Consensus pattern (21 bp):
TTGAGTTTTGGCTATTTTTCT
Found at i:3367675 original size:2 final size:2
Alignment explanation
Indices: 3367668--3367697 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3367658 CTTTTATCTC
3367668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3367698 CTTCTCAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3368149 original size:86 final size:86
Alignment explanation
Indices: 3368058--3368220 Score: 204
Period size: 86 Copynumber: 1.9 Consensus size: 86
3368048 TCTCTAGCAT
* * * *
3368058 TCTCAAACTTAGCATCAAATAACCAAAATAAAAAATAT-CTATCAAACTCAAATTTAACAGAAAA
1 TCTCAAACTCAGCATCAAATAACCAAAAT-AAAAATATGAT-TCAAACTCAAATATAACAAAAAA
*
3368122 -TAAGCTAAAAATTTTTAAAAAA
64 GTAAGCCAAAAATTTTTAAAAAA
** * * *
3368144 TCTCAAACTCATTATCAAATAACCCAAATAAAAATATGATTCAAATTCAAATATAATAAAAAAGT
1 TCTCAAACTCAGCATCAAATAACCAAAATAAAAATATGATTCAAACTCAAATATAACAAAAAAGT
3368209 AAGCCAAAAATT
66 AAGCCAAAAATT
3368221 AAAAAAAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
85 27 0.42
86 38 0.58
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (86 bp):
TCTCAAACTCAGCATCAAATAACCAAAATAAAAATATGATTCAAACTCAAATATAACAAAAAAGT
AAGCCAAAAATTTTTAAAAAA
Found at i:3368422 original size:20 final size:21
Alignment explanation
Indices: 3368397--3368438 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3368387 AAGGAACAAC
3368397 AAAAGAAAGA-AGAAAAAATA
1 AAAAGAAAGAGAGAAAAAATA
3368417 AAAAGAAAGAGAGAAAAAATA
1 AAAAGAAAGAGAGAAAAAATA
3368438 A
1 A
3368439 GGATGGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (21 bp):
AAAAGAAAGAGAGAAAAAATA
Found at i:3371546 original size:19 final size:19
Alignment explanation
Indices: 3371510--3371546 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3371500 TTCAAATGTC
* *
3371510 CATCCTATTAGAGTAAGAA
1 CATCCTATTAAAGCAAGAA
3371529 CATCCTATTAAAGCAAGA
1 CATCCTATTAAAGCAAGA
3371547 TACTTTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (19 bp):
CATCCTATTAAAGCAAGAA
Found at i:3371576 original size:21 final size:21
Alignment explanation
Indices: 3371548--3371593 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3371538 AAAGCAAGAT
3371548 ACTT-TGATAACTACTATAGA
1 ACTTATGATAACTACTATAGA
** *
3371568 ACTTATGATAGTTACTATATA
1 ACTTATGATAACTACTATAGA
3371589 ACTTA
1 ACTTA
3371594 AGTATTAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (21 bp):
ACTTATGATAACTACTATAGA
Found at i:3374913 original size:2 final size:2
Alignment explanation
Indices: 3374906--3374976 Score: 81
Period size: 2 Copynumber: 35.0 Consensus size: 2
3374896 GTTAAAATCA
* * * *
3374906 AT AT AT AT AT AT AT AT AT AT AT AT AT TT GCT -T TT GAA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT AT AT
3374949 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3374977 TAGATGTTCC
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
1 1 0.02
2 59 0.97
3 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3376005 original size:286 final size:286
Alignment explanation
Indices: 3375493--3376066 Score: 1006
Period size: 286 Copynumber: 2.0 Consensus size: 286
3375483 TTAAAATAAT
*
3375493 TGTTTAAAATTTAATAATGTTAATTAAAATTTAAAACCATTTCATTTTAATTTTTAACAATTTTG
1 TGTTTAAAATTTAATAATATTAATTAAAATTTAAAACCATTTCATTTTAATTTTTAACAATTTTG
* *
3375558 CATCAAATGTAGAGCTTAAAATAAGTATACAAATTAATTTGAAAATCTTATAGATGTTGAAGATC
66 CATCAAATGTAAAGCTTAAAATAAGTATACAAATTAATTTGAAAATCTTATAGATATTGAAGATC
*
3375623 AAGATATCAATAAAACTCATTAAAAAAATACATGCGAATAAGTTATCATGCATATTATTTAAACA
131 AAGATATCAATAAAACTCATTAAAAAAATACATGCGAATAAGTTATCATGCATATTATTTAAAAA
*
3375688 TTTAAAATCATTATTATTTTTAAATAAATAAAACTTATTTTAAAATTATATACACTTGTAGGTGT
196 TTTAAAATCATTATTATTTTTAAATAAATAAAACTTATTTTAAAATTATATACACTTGCAGGTGT
*
3375753 GCAAAAAAGATTACACAAGATGAAAA
261 ACAAAAAAGATTACACAAGATGAAAA
* *
3375779 TGTTTAAAATTTAATAATATTAATTAAAATTTAAAACTATTTCATTTTAGTTTTTAACAATTTTG
1 TGTTTAAAATTTAATAATATTAATTAAAATTTAAAACCATTTCATTTTAATTTTTAACAATTTTG
*
3375844 CATCAAATGTAAAGCTTAAAATAAGTATACAAATTAATTTGAAAATCTTATAGATATTGAAGATT
66 CATCAAATGTAAAGCTTAAAATAAGTATACAAATTAATTTGAAAATCTTATAGATATTGAAGATC
* *
3375909 AAGATATCATTAAAACTCATTAAAAAAATACATGTGAATAAGTTATCATGCATATTATTTAAAAA
131 AAGATATCAATAAAACTCATTAAAAAAATACATGCGAATAAGTTATCATGCATATTATTTAAAAA
*
3375974 TTTAAAATCATTATT-TTCTTTAAATAAATAAACCTTATTTTAAAATTATATACACTTGCAGGTG
196 TTTAAAATCATTATTATT-TTTAAATAAATAAAACTTATTTTAAAATTATATACACTTGCAGGTG
**
3376038 TATGAAAAAGATTACACAAGATGAAAA
260 TACAAAAAAGATTACACAAGATGAAAA
3376065 TG
1 TG
3376067 AAACAAATTG
Statistics
Matches: 273, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
285 2 0.01
286 271 0.99
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (286 bp):
TGTTTAAAATTTAATAATATTAATTAAAATTTAAAACCATTTCATTTTAATTTTTAACAATTTTG
CATCAAATGTAAAGCTTAAAATAAGTATACAAATTAATTTGAAAATCTTATAGATATTGAAGATC
AAGATATCAATAAAACTCATTAAAAAAATACATGCGAATAAGTTATCATGCATATTATTTAAAAA
TTTAAAATCATTATTATTTTTAAATAAATAAAACTTATTTTAAAATTATATACACTTGCAGGTGT
ACAAAAAAGATTACACAAGATGAAAA
Found at i:3378405 original size:54 final size:54
Alignment explanation
Indices: 3378312--3378430 Score: 145
Period size: 53 Copynumber: 2.2 Consensus size: 54
3378302 GGTTTGGGCA
* * *
3378312 ATTTAGGGTTTTGGGTAGGTTTTAAGGTTTGGTTGGTTTAAG-GTTTTCATGTAAG
1 ATTTAGGGTTTTGAGTAGGTTTTAAGGTTTGGTTAGTTT-AGTG-TTTCAAGTAAG
*
3378367 ATTTAGGGTTTTGAG-AGGTTTTAAGGTTTAGG-TAGTTTAGTGTTTCAAGTAGG
1 ATTTAGGGTTTTGAGTAGGTTTTAAGGTTT-GGTTAGTTTAGTGTTTCAAGTAAG
*
3378420 GTTTAGGGTTT
1 ATTTAGGGTTT
3378431 GGATAATACG
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
53 21 0.37
54 20 0.35
55 16 0.28
ACGTcount: A:0.19, C:0.02, G:0.33, T:0.46
Consensus pattern (54 bp):
ATTTAGGGTTTTGAGTAGGTTTTAAGGTTTGGTTAGTTTAGTGTTTCAAGTAAG
Found at i:3378465 original size:17 final size:17
Alignment explanation
Indices: 3378440--3378477 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3378430 TGGATAATAC
*
3378440 GGTTTATGGTAGTTTAG
1 GGTTAATGGTAGTTTAG
*
3378457 GGTTAATGGTATTTTAG
1 GGTTAATGGTAGTTTAG
3378474 GGTT
1 GGTT
3378478 TTAATTTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.47
Consensus pattern (17 bp):
GGTTAATGGTAGTTTAG
Found at i:3385116 original size:21 final size:22
Alignment explanation
Indices: 3385061--3385116 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
3385051 TATTAATTTC
* *
3385061 AATAATCTCATTAATTTTTTAT
1 AATAATATAATTAATTTTTTAT
*
3385083 AATAA-ATAGTTAATTTTTT-T
1 AATAATATAATTAATTTTTTAT
*
3385103 AATAATGTAATTAA
1 AATAATATAATTAA
3385117 GAGATATAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 6 0.21
21 17 0.61
22 5 0.18
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (22 bp):
AATAATATAATTAATTTTTTAT
Found at i:3389442 original size:24 final size:23
Alignment explanation
Indices: 3389415--3389471 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 23
3389405 TTTATGACAT
3389415 TATTTTGATACTTTTAAACTTA-TA
1 TATTTTGAT--TTTTAAACTTATTA
*
3389439 TA-TTTGATTTTTAAAGTTATTA
1 TATTTTGATTTTTAAACTTATTA
3389461 TATATTT-ATTT
1 TAT-TTTGATTT
3389472 GGTAGTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 10 0.34
22 4 0.14
23 10 0.34
24 5 0.17
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.60
Consensus pattern (23 bp):
TATTTTGATTTTTAAACTTATTA
Found at i:3391855 original size:22 final size:22
Alignment explanation
Indices: 3391827--3391874 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
3391817 ATGAAAGTCA
*
3391827 ACTCCACCCGGTCATATGCTTT
1 ACTCCACCCGGTCATATACTTT
3391849 ACTCCACCCGGTCATATACTTT
1 ACTCCACCCGGTCATATACTTT
3391871 ACTC
1 ACTC
3391875 ATATCTAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.38, G:0.10, T:0.31
Consensus pattern (22 bp):
ACTCCACCCGGTCATATACTTT
Found at i:3396331 original size:18 final size:17
Alignment explanation
Indices: 3396300--3396333 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3396290 CTACGACCTT
3396300 TTGAGTTTTGACCTCTG
1 TTGAGTTTTGACCTCTG
*
3396317 TTGATGTTTTTACCTCT
1 TTGA-GTTTTGACCTCT
3396334 ATTCTTTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.12, C:0.18, G:0.18, T:0.53
Consensus pattern (17 bp):
TTGAGTTTTGACCTCTG
Found at i:3399095 original size:12 final size:12
Alignment explanation
Indices: 3399078--3399118 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
3399068 ATGTTTCAAT
*
3399078 TATATATACAAA
1 TATATACACAAA
3399090 TATATACACAAA
1 TATATACACAAA
*
3399102 TGTATACACAAA
1 TATATACACAAA
3399114 TATAT
1 TATAT
3399119 GTCACACATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (12 bp):
TATATACACAAA
Found at i:3400815 original size:67 final size:67
Alignment explanation
Indices: 3400716--3400846 Score: 199
Period size: 67 Copynumber: 2.0 Consensus size: 67
3400706 GATGAAGAGG
* * * *
3400716 ATAAAAAGGATAATGTATTTTTGGACTTGTTTAGTCAAGGATTATCTGAATACTAGCAATGAAAC
1 ATAAAAAGGATAATGTAATTTTGGACTTGTTTAGTCAAGCATCATCTAAATACTAGCAATGAAAC
3400781 AT
66 AT
* * *
3400783 ATAAAAATGATAATGTAATTTTGTACTTGTTTAGTCAATCATCATCTAAATACTAGCAATGAAA
1 ATAAAAAGGATAATGTAATTTTGGACTTGTTTAGTCAAGCATCATCTAAATACTAGCAATGAAA
3400847 TATGTTTTCA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (67 bp):
ATAAAAAGGATAATGTAATTTTGGACTTGTTTAGTCAAGCATCATCTAAATACTAGCAATGAAAC
AT
Found at i:3401284 original size:41 final size:41
Alignment explanation
Indices: 3401230--3401312 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
3401220 TCTTTTTAGT
3401230 AAAAATTGATTATTATTGATAGGTCTTGTATATTTAAGAAA
1 AAAAATTGATTATTATTGATAGGTCTTGTATATTTAAGAAA
3401271 AAAAATTGATTATTATTGATAGGTCTTGTATATTTAAGAAA
1 AAAAATTGATTATTATTGATAGGTCTTGTATATTTAAGAAA
3401312 A
1 A
3401313 TTAGTGAGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.41
Consensus pattern (41 bp):
AAAAATTGATTATTATTGATAGGTCTTGTATATTTAAGAAA
Found at i:3409539 original size:6 final size:7
Alignment explanation
Indices: 3409522--3409546 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3409512 CATAATAGAG
3409522 TTTTTAA
1 TTTTTAA
3409529 TTTTTAA
1 TTTTTAA
3409536 TTTTTAA
1 TTTTTAA
3409543 TTTT
1 TTTT
3409547 CTTTTTCCTT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTAA
Found at i:3418513 original size:12 final size:12
Alignment explanation
Indices: 3418496--3418537 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
3418486 AGAAAATGCC
3418496 AAAACAAAAAAA
1 AAAACAAAAAAA
3418508 AAAACAAAAAACA
1 AAAACAAAAAA-A
*
3418521 AAACCCAAAAAAA
1 AAA-ACAAAAAAA
3418534 AAAA
1 AAAA
3418538 ATTGTTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 11 0.42
13 8 0.31
14 7 0.27
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAACAAAAAAA
Found at i:3418927 original size:17 final size:18
Alignment explanation
Indices: 3418888--3418929 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
3418878 AAAAAAAAAC
3418888 AAAAAAAAAGCAAGCAAA
1 AAAAAAAAAGCAAGCAAA
*
3418906 AAAAAAAAAG-AAGGAAA
1 AAAAAAAAAGCAAGCAAA
3418923 GAAAAAA
1 -AAAAAA
3418930 TGAATGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGCAAGCAAA
Found at i:3420244 original size:32 final size:31
Alignment explanation
Indices: 3420217--3420275 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
3420207 GAAAAATTTT
3420217 ATATCACTTGCATTTGCATAAAAAAAAAAAA
1 ATATCACTTGCATTTGCATAAAAAAAAAAAA
* *
3420248 AGA-CATTTGCATTTGCATAAAAAAAAAA
1 ATATCACTTGCATTTGCATAAAAAAAAAA
3420276 GACATTTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.25
Consensus pattern (31 bp):
ATATCACTTGCATTTGCATAAAAAAAAAAAA
Found at i:3420277 original size:27 final size:28
Alignment explanation
Indices: 3420224--3420292 Score: 113
Period size: 27 Copynumber: 2.4 Consensus size: 28
3420214 TTTATATCAC
3420224 TTGCATTTGCATAAAAAAAAAAAAAGACAT
1 TTGCATTTGCAT--AAAAAAAAAAAGACAT
3420254 TTGCATTTGCAT-AAAAAAAAAAGACAT
1 TTGCATTTGCATAAAAAAAAAAAGACAT
3420281 TTGCATTTGCAT
1 TTGCATTTGCAT
3420293 CAGTTGCATT
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 27 0.69
30 12 0.31
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.29
Consensus pattern (28 bp):
TTGCATTTGCATAAAAAAAAAAAGACAT
Found at i:3420365 original size:44 final size:43
Alignment explanation
Indices: 3420254--3420428 Score: 186
Period size: 42 Copynumber: 4.2 Consensus size: 43
3420244 AAAAAGACAT
* * * *
3420254 TTGCATTTGCAT-AAAAAAAAAAGACATTTGCATTTGCATCAG
1 TTGCATTTGTATCATAAGAAAAAGACATTTGCATTTGCATCAC
** *
3420296 TTGCATTTACATCAT--G--AAAGA-ATTTGCATTTGCATCCC
1 TTGCATTTGTATCATAAGAAAAAGACATTTGCATTTGCATCAC
* *
3420334 TTGCATTTGTATCATAAGGAAAAAGATATTTGCATTTGCATCTC
1 TTGCATTTGTATCATAA-GAAAAAGACATTTGCATTTGCATCAC
*
3420378 TTGTATTTGTATC--AAGAAAAAGGACATTTGCATTTGCATCAC
1 TTGCATTTGTATCATAAGAAAAA-GACATTTGCATTTGCATCAC
3420420 TTGCATTTG
1 TTGCATTTG
3420429 CACTTGTATC
Statistics
Matches: 113, Mismatches: 12, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
38 28 0.25
39 5 0.04
41 7 0.06
42 39 0.35
43 6 0.05
44 28 0.25
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (43 bp):
TTGCATTTGTATCATAAGAAAAAGACATTTGCATTTGCATCAC
Found at i:3421307 original size:67 final size:68
Alignment explanation
Indices: 3421160--3421307 Score: 217
Period size: 67 Copynumber: 2.2 Consensus size: 68
3421150 CAAAACCTCT
* *
3421160 GATTTGTAAAACATTTTAAATTTTTAAAGTTTCATGGCCTCTAATTGGAAGAGCATTCAAGGTTT
1 GATTTGTAAAACATTTTAAA-TTTTAAAGTTTCATGGCCTCTAATTGGAAGAGCATTCAAAGATT
3421225 TTGA
65 TTGA
* * * *
3421229 GATTTGCAAAACATTTTAAA-TTTAAAGTTTCATGGCCTCTGATTGGAGGAGCATTTAAAGATTT
1 GATTTGTAAAACATTTTAAATTTTAAAGTTTCATGGCCTCTAATTGGAAGAGCATTCAAAGATTT
3421293 TGA
66 TGA
*
3421296 GATTTATAAAAC
1 GATTTGTAAAAC
3421308 TTCATGGTAT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
67 52 0.73
69 19 0.27
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.39
Consensus pattern (68 bp):
GATTTGTAAAACATTTTAAATTTTAAAGTTTCATGGCCTCTAATTGGAAGAGCATTCAAAGATTT
TGA
Found at i:3421395 original size:75 final size:76
Alignment explanation
Indices: 3421263--3421411 Score: 221
Period size: 75 Copynumber: 2.0 Consensus size: 76
3421253 AAGTTTCATG
* *
3421263 GCCTCTGATTGGAGGAGCATTTAAAGATTTTGAGATTTATAAAACTTCATGGTATAATCTC-AAG
1 GCCTCTGATTGGAGGAGCATTTAAAGATTTTGAGATTTATAAAACCTCATGGCATAATCTCTAAG
3421327 ACATTCGGGTA
66 ACATTCGGGTA
* * *
3421338 GCCTCTGATTGGATGAGCATTTAAAGATTTTGAGATTTGTAAGACCTC-TAGGCATAATCTCTAA
1 GCCTCTGATTGGAGGAGCATTTAAAGATTTTGAGATTTATAAAACCTCAT-GGCATAATCTCTAA
*
3421402 GACTTTCGGG
65 GACATTCGGG
3421412 CATAATTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
74 1 0.02
75 54 0.82
76 11 0.17
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.34
Consensus pattern (76 bp):
GCCTCTGATTGGAGGAGCATTTAAAGATTTTGAGATTTATAAAACCTCATGGCATAATCTCTAAG
ACATTCGGGTA
Found at i:3421521 original size:127 final size:126
Alignment explanation
Indices: 3421345--3421721 Score: 562
Period size: 127 Copynumber: 3.0 Consensus size: 126
3421335 GTAGCCTCTG
* *
3421345 ATTGGATGAGCATTTAAAGATTTTGAGATTTGTAAGACCTCTAGGCATAATCTCTAAGACTTTCG
1 ATTGGAGGAGCATTTAAAGATTTTGAGATTTGTAAGACCT-TTGGCATAATCTCTAAGACTTTCG
3421410 GGCATAATTTTCAAGACCTTTGGGCAAAACATTTTTAAATTTTTAAAGTTTCATGGCCTCAT
65 GGCATAATTTTCAAGACCTTTGGGCAAAACATTTTTAAATTTTTAAAGTTTCATGGCCTCAT
3421472 ATTGGAGGAGCATTTAAAGATTTTGAGATTTGTAAGACCTTTGGTCATAATCTCTAAGACTTTCG
1 ATTGGAGGAGCATTTAAAGATTTTGAGATTTGTAAGACCTTTGG-CATAATCTCTAAGACTTTCG
* * * *
3421537 GGCATAATTTTGAAGA-CTTCTGGGTAAAACATTTTAAAATTTTTAAAGTTTCATGGCCTCTT
65 GGCATAATTTTCAAGACCTT-TGGGCAAAACATTTTTAAATTTTTAAAGTTTCATGGCCTCAT
* * * * *
3421599 ATTGGGGGAGCATTCAAAGATTTTAAGATTTGTAAAACCTTTAGGCATAATCTCTAATATCTTT-
1 ATTGGAGGAGCATTTAAAGATTTTGAGATTTGTAAGACCTTT-GGCATAATCTCTAAGA-CTTTC
* * *
3421663 GGGCATAATTTTCAAGACCTCTGAGCAAAACA-TTTTAAATTTTCAAAGTTTCATGGCCT
64 GGGCATAATTTTCAAGACCTTTGGGCAAAACATTTTTAAATTTTTAAAGTTTCATGGCCT
3421722 TTGATTAGAG
Statistics
Matches: 228, Mismatches: 17, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
126 31 0.14
127 189 0.83
128 8 0.04
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (126 bp):
ATTGGAGGAGCATTTAAAGATTTTGAGATTTGTAAGACCTTTGGCATAATCTCTAAGACTTTCGG
GCATAATTTTCAAGACCTTTGGGCAAAACATTTTTAAATTTTTAAAGTTTCATGGCCTCAT
Found at i:3421775 original size:33 final size:33
Alignment explanation
Indices: 3421704--3421780 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
3421694 ATTTTAAATT
* * *
3421704 TTCAAAGTTTCATGGCCTTTGATTAGAGGACCA
1 TTCAAAGTTTCATAGCCTCTGATTAGAAGACCA
* *
3421737 CTCAAAGTTTCATAGCCTCTGATTAGAAGAGCA
1 TTCAAAGTTTCATAGCCTCTGATTAGAAGACCA
3421770 TTCAAAAGTTT
1 TTC-AAAGTTT
3421781 TTTTGATTCC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 30 0.81
34 7 0.19
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (33 bp):
TTCAAAGTTTCATAGCCTCTGATTAGAAGACCA
Found at i:3421823 original size:68 final size:67
Alignment explanation
Indices: 3421738--3421925 Score: 243
Period size: 68 Copynumber: 2.7 Consensus size: 67
3421728 AGAGGACCAC
* *
3421738 TCAAAGTTTCATAGCCTCTGATTAGAAGAGCATTCAAAAGTTTTTTTGATTCCAAGAATTTTTAA
1 TCAAAGTTTCATGGCCTCT-ATTAGAAGAGCATTCAAAAGTTTTTATGATTCCAAGAATTTTTAA
3421803 TTT
65 TTT
* * *
3421806 TCTAAGTTTCATGGCCTCTTACTA-AAGGAGCATTCAAAAGTTTTTATGATTCCAAGCATTTTTA
1 TCAAAGTTTCATGGCCTC-TATTAGAA-GAGCATTCAAAAGTTTTTATGATTCCAAGAATTTTTA
3421870 ATTT
64 ATTT
* * * *
3421874 TCAAAGTTTTATGGCTTCTAGTTAGAGGAGCATTCAAAAAGTTTTTGTGATT
1 TCAAAGTTTCATGGCCTCTA-TTAGAAGAGCATTC-AAAAGTTTTTATGATT
3421926 TAATCTTTAA
Statistics
Matches: 104, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
67 4 0.04
68 83 0.80
69 17 0.16
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (67 bp):
TCAAAGTTTCATGGCCTCTATTAGAAGAGCATTCAAAAGTTTTTATGATTCCAAGAATTTTTAAT
TT
Found at i:3439644 original size:12 final size:12
Alignment explanation
Indices: 3439627--3439652 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3439617 AACTTGGACA
3439627 TAATTTATCGGT
1 TAATTTATCGGT
3439639 TAATTTATCGGT
1 TAATTTATCGGT
3439651 TA
1 TA
3439653 TCGAGTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (12 bp):
TAATTTATCGGT
Found at i:3443760 original size:20 final size:22
Alignment explanation
Indices: 3443710--3443761 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
3443700 AAATTTAAGA
3443710 ATTCTCAACTTAAAGTTCAGAAG
1 ATTCTCAA-TTAAAGTTCAGAAG
*
3443733 -TTCGCAATTAAA-TTCA-AAG
1 ATTCTCAATTAAAGTTCAGAAG
3443752 ATTCTCAATT
1 ATTCTCAATT
3443762 TGAATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 3 0.12
20 12 0.46
21 5 0.19
22 6 0.23
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (22 bp):
ATTCTCAATTAAAGTTCAGAAG
Found at i:3443870 original size:17 final size:18
Alignment explanation
Indices: 3443828--3443874 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
3443818 AATAAATTGA
3443828 ATTCAAAGATTCGCAAAAG
1 ATTC-AAGATTCGCAAAAG
*
3443847 ATTCAAGATTCTCAAAA-
1 ATTCAAGATTCGCAAAAG
*
3443864 CTTCAAGATTC
1 ATTCAAGATTC
3443875 ATAAAATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 10 0.38
18 12 0.46
19 4 0.15
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.28
Consensus pattern (18 bp):
ATTCAAGATTCGCAAAAG
Found at i:3443990 original size:18 final size:18
Alignment explanation
Indices: 3443960--3444037 Score: 59
Period size: 18 Copynumber: 4.3 Consensus size: 18
3443950 CAAAGATTTA
3443960 AGATTCAAAAATTCGCAAG
1 AGATTC-AAAATTCGCAAG
*
3443979 AGATTCAAAATTTGCAA-
1 AGATTCAAAATTCGCAAG
* ** *
3443996 AAATTCAAAGATTCATAAA
1 AGATTCAAA-ATTCGCAAG
* * *
3444015 AGATTCAAGATTTGTAAG
1 AGATTCAAAATTCGCAAG
3444033 AGATT
1 AGATT
3444038 TAAAGATTCA
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
17 8 0.17
18 26 0.55
19 13 0.28
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.28
Consensus pattern (18 bp):
AGATTCAAAATTCGCAAG
Found at i:3444061 original size:37 final size:36
Alignment explanation
Indices: 3443962--3444085 Score: 117
Period size: 36 Copynumber: 3.4 Consensus size: 36
3443952 AAGATTTAAG
* ** *
3443962 ATTCAAAAATTCGCAAGAGATTCAAAATTTGCAAAA
1 ATTCAAAGATTCATAAGAGATTCAAGATTTGCAAAA
* * *
3443998 ATTCAAAGATTCATAAAAGATTCAAGATTTGTAAGAG
1 ATTCAAAGATTCATAAGAGATTCAAGATTTGCAA-AA
* *
3444035 ATTTAAAGATTCATAAGAGATACAAGA-TT-CACAAA
1 ATTCAAAGATTCATAAGAGATTCAAGATTTGCA-AAA
* *
3444070 ATTTAAAAATTCATAA
1 ATTCAAAGATTCATAA
3444086 AAGTTAAAAA
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
35 17 0.23
36 31 0.42
37 25 0.34
ACGTcount: A:0.50, C:0.10, G:0.11, T:0.28
Consensus pattern (36 bp):
ATTCAAAGATTCATAAGAGATTCAAGATTTGCAAAA
Found at i:3444063 original size:18 final size:18
Alignment explanation
Indices: 3444003--3444065 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
3443993 CAAAAATTCA
* *
3444003 AAGATTCATAAAAGATTC
1 AAGATTCATAAGAGATAC
**
3444021 AAGATTTGTAAGAGATTTA-
1 AAGATTCATAAGAGA--TAC
3444040 AAGATTCATAAGAGATAC
1 AAGATTCATAAGAGATAC
3444058 AAGATTCA
1 AAGATTCA
3444066 CAAAATTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
17 2 0.06
18 20 0.56
19 13 0.36
20 1 0.03
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.29
Consensus pattern (18 bp):
AAGATTCATAAGAGATAC
Found at i:3444097 original size:18 final size:17
Alignment explanation
Indices: 3444061--3444103 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
3444051 GAGATACAAG
*
3444061 ATTCACAAAATTTAAAA
1 ATTCACAAAATTAAAAA
*
3444078 ATTCATAAAAGTTAAAAA
1 ATTCACAAAA-TTAAAAA
*
3444096 ATTTACAA
1 ATTCACAA
3444104 GTTTCAAGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.30
Consensus pattern (17 bp):
ATTCACAAAATTAAAAA
Found at i:3444167 original size:25 final size:24
Alignment explanation
Indices: 3444122--3444196 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 24
3444112 ATTTGCTTCT
* *
3444122 GATTCAAAATTCGTAAAAATTTAA
1 GATTCAAAATTCGCAATAATTTAA
3444146 GATTCAAATATTCGCAATAATTTAA
1 GATTCAAA-ATTCGCAATAATTTAA
* *
3444171 GATTCAAAGATTTGCAAGTGATTTAA
1 GATTCAAA-ATTCGCAA-TAATTTAA
3444197 AAATTCACAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
24 8 0.18
25 29 0.66
26 7 0.16
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (24 bp):
GATTCAAAATTCGCAATAATTTAA
Found at i:3444611 original size:17 final size:17
Alignment explanation
Indices: 3444579--3444679 Score: 125
Period size: 18 Copynumber: 5.8 Consensus size: 17
3444569 TCGCATTAAG
3444579 GATTCA-AAGAATTTTTA
1 GATTCATAAGAA-TTTTA
*
3444596 GATTCGTAAGAATTTTTA
1 GATTCATAAGAA-TTTTA
3444614 GATTCATAAGAATTTTA
1 GATTCATAAGAATTTTA
*
3444631 -ACTTCATAAGAATTATA
1 GA-TTCATAAGAATTTTA
*
3444648 AACTTCATAAGAATTTTA
1 GA-TTCATAAGAATTTTA
3444666 GATTCATAAGAATT
1 GATTCATAAGAATT
3444680 CACAAGACTT
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
16 1 0.01
17 36 0.47
18 39 0.51
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (17 bp):
GATTCATAAGAATTTTA
Found at i:3444630 original size:35 final size:35
Alignment explanation
Indices: 3444579--3444679 Score: 127
Period size: 35 Copynumber: 2.9 Consensus size: 35
3444569 TCGCATTAAG
* *
3444579 GATTCA-AAGAATTTTTAGATTCGTAAGAATTTTTA
1 GATTCATAAGAA-TTTTAGATTCATAAGAATTTATA
3444614 GATTCATAAGAATTTTA-ACTTCATAAGAA-TTATA
1 GATTCATAAGAATTTTAGA-TTCATAAGAATTTATA
*
3444648 AACTTCATAAGAATTTTAGATTCATAAGAATT
1 GA-TTCATAAGAATTTTAGATTCATAAGAATT
3444680 CACAAGACTT
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
34 6 0.10
35 45 0.78
36 7 0.12
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (35 bp):
GATTCATAAGAATTTTAGATTCATAAGAATTTATA
Found at i:3444758 original size:18 final size:18
Alignment explanation
Indices: 3444697--3444844 Score: 71
Period size: 18 Copynumber: 8.7 Consensus size: 18
3444687 CTTTTTCAAT
*
3444697 TTCGCAAGAA-TTTCAGC
1 TTCGCAAGAATTTTCAGA
* * *
3444714 TTTGCAAGAATTATCAAA
1 TTCGCAAGAATTTTCAGA
** *
3444732 TTCATAAGAATTTTTAGA
1 TTCGCAAGAATTTTCAGA
3444750 TTCGCAAGAA--TTCA-A
1 TTCGCAAGAATTTTCAGA
* * *
3444765 TTCTCAAGGATTTT-AGG
1 TTCGCAAGAATTTTCAGA
*
3444782 TTCACAAGAA-TTT--GA
1 TTCGCAAGAATTTTCAGA
** *
3444797 TTTTCAAGGA-TTTCAGA
1 TTCGCAAGAATTTTCAGA
* * *
3444814 TTCACAGGAATTTTCAAA
1 TTCGCAAGAATTTTCAGA
*
3444832 TTCGTAAGAATTT
1 TTCGCAAGAATTT
3444845 CTTAGTGATT
Statistics
Matches: 94, Mismatches: 30, Indels: 13
0.69 0.22 0.09
Matches are distributed among these distances:
15 20 0.21
16 7 0.07
17 27 0.29
18 40 0.43
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (18 bp):
TTCGCAAGAATTTTCAGA
Found at i:3444790 original size:32 final size:32
Alignment explanation
Indices: 3444743--3444825 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
3444733 TCATAAGAAT
*
3444743 TTTTAGATTCGCAAGAATTCAATTCTCAAGGA
1 TTTTAGATTCACAAGAATTCAATTCTCAAGGA
* ** *
3444775 TTTTAGGTTCACAAGAATTTGATTTTCAAGGA
1 TTTTAGATTCACAAGAATTCAATTCTCAAGGA
* *
3444807 TTTCAGATTCACAGGAATT
1 TTTTAGATTCACAAGAATT
3444826 TTCAAATTCG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
TTTTAGATTCACAAGAATTCAATTCTCAAGGA
Found at i:3446614 original size:7 final size:7
Alignment explanation
Indices: 3446593--3446667 Score: 59
Period size: 7 Copynumber: 11.0 Consensus size: 7
3446583 TCAATTTGAG
3446593 TATTTTT
1 TATTTTT
*
3446600 TCTCTTTT
1 TAT-TTTT
3446608 TATTTTT
1 TATTTTT
3446615 CT-TTTTT
1 -TATTTTT
**
3446622 T-TTTCG
1 TATTTTT
3446628 TA-TTTT
1 TATTTTT
*
3446634 CA-TTTT
1 TATTTTT
3446640 TATTTTT
1 TATTTTT
3446647 TATTTTT
1 TATTTTT
3446654 TATTTTT
1 TATTTTT
*
3446661 CATTTTT
1 TATTTTT
3446668 ATACTTCATT
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
6 13 0.24
7 35 0.64
8 7 0.13
ACGTcount: A:0.11, C:0.08, G:0.01, T:0.80
Consensus pattern (7 bp):
TATTTTT
Found at i:3446615 original size:14 final size:13
Alignment explanation
Indices: 3446604--3446669 Score: 64
Period size: 13 Copynumber: 5.0 Consensus size: 13
3446594 ATTTTTTCTC
*
3446604 TTTTTATTTTTCT
1 TTTTTATTTTTAT
3446617 TTTTT-TTTTCGTA-
1 TTTTTATTTT--TAT
*
3446630 TTTTCATTTTTAT
1 TTTTTATTTTTAT
3446643 TTTTTATTTTTTAT
1 TTTTTA-TTTTTAT
*
3446657 TTTTCATTTTTAT
1 TTTTTATTTTTAT
3446670 ACTTCATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
12 6 0.14
13 21 0.48
14 17 0.39
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:3446631 original size:20 final size:21
Alignment explanation
Indices: 3446611--3446667 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
3446601 CTCTTTTTAT
3446611 TTTTC-TTTTT-TTTTTCGTA
1 TTTTCATTTTTATTTTTCGTA
3446630 TTTTCATTTTTATTTTT--TA
1 TTTTCATTTTTATTTTTCGTA
*
3446649 TTTTTTATTTTTCATTTTT
1 -TTTTCATTTTT-ATTTTT
3446668 ATACTTCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 7 0.21
20 15 0.45
21 11 0.33
ACGTcount: A:0.11, C:0.07, G:0.02, T:0.81
Consensus pattern (21 bp):
TTTTCATTTTTATTTTTCGTA
Found at i:3446640 original size:27 final size:27
Alignment explanation
Indices: 3446593--3446669 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
3446583 TCAATTTGAG
* * *
3446593 TATTTTTTCTCTTTTTATTTTTCTTTTT
1 TATTTTTTAT-TTTTCATTTTTATTTTT
*
3446621 T-TTTTCGTA-TTTTCATTTTTATTTTT
1 TATTTT-TTATTTTTCATTTTTATTTTT
3446647 TATTTTTTATTTTTCATTTTTAT
1 TATTTTTTATTTTTCATTTTTAT
3446670 ACTTCATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
26 18 0.44
27 21 0.51
28 2 0.05
ACGTcount: A:0.12, C:0.08, G:0.01, T:0.79
Consensus pattern (27 bp):
TATTTTTTATTTTTCATTTTTATTTTT
Found at i:3446652 original size:6 final size:6
Alignment explanation
Indices: 3446604--3446669 Score: 60
Period size: 6 Copynumber: 10.2 Consensus size: 6
3446594 ATTTTTTCTC
* * *
3446604 TTTTTA TTTTTC TTTTTT TTTTCGTA TTTTCA TTTTTA TTTTTTA TTTTTTA
1 TTTTTA TTTTTA TTTTTA TTTT--TA TTTTTA TTTTTA -TTTTTA -TTTTTA
3446656 TTTTTCA TTTTTA T
1 TTTTT-A TTTTTA T
3446670 ACTTCATTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
6 27 0.53
7 19 0.37
8 5 0.10
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:3446668 original size:13 final size:13
Alignment explanation
Indices: 3446630--3446684 Score: 65
Period size: 13 Copynumber: 4.1 Consensus size: 13
3446620 TTTTTTCGTA
3446630 TTTTCATTTTTAT
1 TTTTCATTTTTAT
*
3446643 TTTTTATTTTTTAT
1 TTTTCA-TTTTTAT
3446657 TTTTCATTTTTAT
1 TTTTCATTTTTAT
**
3446670 ACTTCATTTATTAT
1 TTTTCATTT-TTAT
3446684 T
1 T
3446685 GATATCTCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
13 19 0.54
14 16 0.46
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTCATTTTTAT
Found at i:3446678 original size:27 final size:27
Alignment explanation
Indices: 3446630--3446684 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3446620 TTTTTTCGTA
** * *
3446630 TTTTCATTTTTATTTTTTATTTTTTAT
1 TTTTCATTTTTATACTTCATTTATTAT
3446657 TTTTCATTTTTATACTTCATTTATTAT
1 TTTTCATTTTTATACTTCATTTATTAT
3446684 T
1 T
3446685 GATATCTCCT
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:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTTCATTTTTATACTTCATTTATTAT
Found at i:3450938 original size:94 final size:97
Alignment explanation
Indices: 3450758--3450946 Score: 267
Period size: 94 Copynumber: 2.0 Consensus size: 97
3450748 TAACTCAGAG
* * * *
3450758 ATTTAAATATTCCAATCATTTGGTAGGATTAAAAAATTATTTTTACTTTAAAATTCATTATGAAA
1 ATTTAAATATTCCAATCATTTAGCAGGATTAAAAAATTAATTTTAC--TAAAATTCAATATGAAA
*
3450823 TTCTCCAATCGTTTGGGAGAATTCATAATTCGAT
64 TTCTCCAATAGTTTGGGAGAATTCATAATTCGAT
* *
3450857 ATTTAAATCTTCCAATCATTTAGCAGGA-TGAAAAATTAATTTT-C-AAAATTCAATATGAAATT
1 ATTTAAATATTCCAATCATTTAGCAGGATTAAAAAATTAATTTTACTAAAATTCAATATGAAATT
*
3450919 CTCCAATAGTTTGGTAGAATTCATAATT
66 CTCCAATAGTTTGGGAGAATTCATAATT
3450947 TAAAGATTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
94 43 0.52
97 1 0.01
98 13 0.16
99 25 0.30
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40
Consensus pattern (97 bp):
ATTTAAATATTCCAATCATTTAGCAGGATTAAAAAATTAATTTTACTAAAATTCAATATGAAATT
CTCCAATAGTTTGGGAGAATTCATAATTCGAT
Found at i:3459693 original size:17 final size:18
Alignment explanation
Indices: 3459666--3459699 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3459656 CTGATTCATC
3459666 TTTTAAGATTAAATTTTT
1 TTTTAAGATTAAATTTTT
3459684 TTTTAA-ATTAAATTTT
1 TTTTAAGATTAAATTTT
3459700 AAATCAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTAAGATTAAATTTTT
Found at i:3459803 original size:33 final size:34
Alignment explanation
Indices: 3459764--3459847 Score: 93
Period size: 33 Copynumber: 2.5 Consensus size: 34
3459754 TTTAATATGA
3459764 TATATATAATTATTT-TTTAATTATT-TATTTA-AT
1 TATATATAA-TATTTATTTAATT-TTATATTTATAT
*
3459797 TATATATTATATTTATTTAATTTTATATTTATAT
1 TATATATAATATTTATTTAATTTTATATTTATAT
* *
3459831 TAAAAAATAATATTTAT
1 T-ATATATAATATTTAT
3459848 ATTTATAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
32 7 0.16
33 21 0.49
34 3 0.07
35 12 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATAATATTTATTTAATTTTATATTTATAT
Found at i:3459811 original size:21 final size:22
Alignment explanation
Indices: 3459785--3459831 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3459775 ATTTTTTAAT
3459785 TATTTATTTAATTATATA-TTA
1 TATTTATTTAATTATATATTTA
*
3459806 TATTTATTTAATTTTATATTTA
1 TATTTATTTAATTATATATTTA
3459828 TATT
1 TATT
3459832 AAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTTATTTAATTATATATTTA
Found at i:3459822 original size:16 final size:16
Alignment explanation
Indices: 3459774--3459833 Score: 61
Period size: 16 Copynumber: 3.7 Consensus size: 16
3459764 TATATATAAT
3459774 TATTT-TTTAATTATT-
1 TATTTATTTAATT-TTA
* *
3459789 TATTTAATTATATATTA
1 TATTTATTTA-ATTTTA
3459806 TATTTATTTAATTTTA
1 TATTTATTTAATTTTA
3459822 TATTTATATTAA
1 TATTTAT-TTAA
3459834 AAAATAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
15 5 0.14
16 17 0.46
17 15 0.41
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTATTTAATTTTA
Found at i:3459845 original size:19 final size:19
Alignment explanation
Indices: 3459821--3459871 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
3459811 ATTTAATTTT
3459821 ATATTTATATTAAAAAATA
1 ATATTTATATTAAAAAATA
*
3459840 ATATTTATATTTATAAAATA
1 ATATTTATA-TTAAAAAATA
3459860 ATATTT-TATTAA
1 ATATTTATATTAA
3459872 TTTTAAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 3 0.10
19 11 0.38
20 15 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATATTAAAAAATA
Found at i:3460521 original size:2 final size:2
Alignment explanation
Indices: 3460516--3460546 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3460506 TCATATTCAC
3460516 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3460547 CACTCCATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3462539 original size:2 final size:2
Alignment explanation
Indices: 3462532--3462570 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3462522 TGTGAGAAAG
3462532 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3462571 CCCAATACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3466413 original size:12 final size:12
Alignment explanation
Indices: 3466396--3466448 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
3466386 TAAAACTCTA
3466396 AAATGAAACCCT
1 AAATGAAACCCT
*
3466408 AAATGAAACTCT
1 AAATGAAACCCT
* *
3466420 AAAAGCAAAACCTT
1 AAATG--AAACCCT
3466434 AAATGAAA-CCT
1 AAATGAAACCCT
3466445 AAAT
1 AAAT
3466449 CTTAGGTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
11 6 0.18
12 18 0.55
14 9 0.27
ACGTcount: A:0.55, C:0.19, G:0.08, T:0.19
Consensus pattern (12 bp):
AAATGAAACCCT
Found at i:3466437 original size:26 final size:25
Alignment explanation
Indices: 3466388--3466447 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
3466378 TAAATTTTTA
3466388 AAACTCTAAAATGAAACCCTAAATG
1 AAACTCTAAAATGAAACCCTAAATG
*
3466413 AAACTCTAAAA-GCAAAACCTTAAATG
1 AAACTCTAAAATG--AAACCCTAAATG
3466439 AAAC-CTAAA
1 AAACTCTAAA
3466448 TCTTAGGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 1 0.03
25 16 0.50
26 15 0.47
ACGTcount: A:0.55, C:0.20, G:0.07, T:0.18
Consensus pattern (25 bp):
AAACTCTAAAATGAAACCCTAAATG
Found at i:3466472 original size:38 final size:39
Alignment explanation
Indices: 3466425--3466526 Score: 102
Period size: 39 Copynumber: 2.6 Consensus size: 39
3466415 ACTCTAAAAG
3466425 CAAAA-CCTTAAATGAAACCT-AAA-TCTTAGGTAAAACT
1 CAAAACCCTTAAATGAAACCTAAAATTC-TAGGTAAAACT
* * *
3466462 CAAAACCCTTAAATAAAATCTAAAATTCTAGGTGAAACT
1 CAAAACCCTTAAATGAAACCTAAAATTCTAGGTAAAACT
** * *
3466501 TTAAACCCTAAAAATGAAACCCAAAA
1 CAAAACCCT-TAAATGAAACCTAAAA
3466527 CCCTAACGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
37 5 0.10
38 13 0.25
39 20 0.38
40 14 0.27
ACGTcount: A:0.51, C:0.20, G:0.07, T:0.23
Consensus pattern (39 bp):
CAAAACCCTTAAATGAAACCTAAAATTCTAGGTAAAACT
Found at i:3484714 original size:3 final size:3
Alignment explanation
Indices: 3484706--3484734 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3484696 TTAGCAGTTA
3484706 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3484735 ATGTTAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3490742 original size:13 final size:13
Alignment explanation
Indices: 3490724--3490749 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3490714 GAAACTAGTC
3490724 TGAGCTTACAAAT
1 TGAGCTTACAAAT
3490737 TGAGCTTACAAAT
1 TGAGCTTACAAAT
3490750 AGTTGCCAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGAGCTTACAAAT
Found at i:3495536 original size:13 final size:13
Alignment explanation
Indices: 3495518--3495546 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3495508 TCACTGGAGC
3495518 AAAGTAAACTCTA
1 AAAGTAAACTCTA
3495531 AAAGTAAACTCTA
1 AAAGTAAACTCTA
3495544 AAA
1 AAA
3495547 ACCGATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (13 bp):
AAAGTAAACTCTA
Found at i:3497134 original size:12 final size:12
Alignment explanation
Indices: 3497117--3497145 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3497107 GAAAAAAAAT
3497117 TCCAAGTAGATC
1 TCCAAGTAGATC
3497129 TCCAAGTAGATC
1 TCCAAGTAGATC
3497141 TCCAA
1 TCCAA
3497146 TTGGAAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (12 bp):
TCCAAGTAGATC
Found at i:3499079 original size:6 final size:6
Alignment explanation
Indices: 3499070--3499135 Score: 54
Period size: 6 Copynumber: 11.7 Consensus size: 6
3499060 ATATTATTTT
*
3499070 TAAATA TAAATA TAAA-A TTAA-A TAAATA TAAA-A -AATATA TAAATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAA-ATA TAAATA
*
3499115 TAAA-A TTAA-A TAAATAA TAAA
1 TAAATA TAAATA TAAAT-A TAAA
3499136 ACATATTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
4 2 0.04
5 18 0.36
6 23 0.46
7 7 0.14
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
TAAATA
Found at i:3499096 original size:16 final size:16
Alignment explanation
Indices: 3499075--3499136 Score: 88
Period size: 16 Copynumber: 3.8 Consensus size: 16
3499065 ATTTTTAAAT
3499075 ATAAATATAAAATTAA
1 ATAAATATAAAATTAA
* *
3499091 ATAAATATAAAAAATAT
1 ATAAATAT-AAAATTAA
3499108 ATAAATATAAAATTAA
1 ATAAATATAAAATTAA
3499124 ATAAATAATAAAA
1 ATAAAT-ATAAAA
3499137 CATATTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
16 20 0.50
17 20 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAATATAAAATTAA
Found at i:3499111 original size:17 final size:16
Alignment explanation
Indices: 3499073--3499141 Score: 75
Period size: 16 Copynumber: 4.1 Consensus size: 16
3499063 TTATTTTTAA
*
3499073 ATATAAATATAAAATT
1 ATATAAATATAAAAAT
*
3499089 AAATAAATATAAAAAAT
1 ATATAAATAT-AAAAAT
*
3499106 ATATAAATATAAAATT
1 ATATAAATATAAAAAT
*
3499122 AAATAAATAATAAAACAT
1 ATATAAAT-ATAAAA-AT
3499140 AT
1 AT
3499142 TTTATATATA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
16 21 0.49
17 20 0.47
18 2 0.05
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.30
Consensus pattern (16 bp):
ATATAAATATAAAAAT
Found at i:3499115 original size:33 final size:34
Alignment explanation
Indices: 3499073--3499141 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 34
3499063 TTATTTTTAA
3499073 ATATAAATATAAAATTAAATAAAT-ATAAAAAAT
1 ATATAAATATAAAATTAAATAAATAATAAAAAAT
*
3499106 ATATAAATATAAAATTAAATAAATAATAAAACAT
1 ATATAAATATAAAATTAAATAAATAATAAAAAAT
3499140 AT
1 AT
3499142 TTTATATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 24 0.71
34 10 0.29
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.30
Consensus pattern (34 bp):
ATATAAATATAAAATTAAATAAATAATAAAAAAT
Found at i:3503216 original size:15 final size:15
Alignment explanation
Indices: 3503198--3503227 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3503188 TTTACCACTA
*
3503198 GGTTGCAAATCAATT
1 GGTTGCAAATAAATT
3503213 GGTTGCAAATAAATT
1 GGTTGCAAATAAATT
3503228 TTAAAAATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (15 bp):
GGTTGCAAATAAATT
Found at i:3511985 original size:23 final size:24
Alignment explanation
Indices: 3511961--3512007 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
3511951 ATATGGCTCA
*
3511961 GTCTTTTAAAATTATATATAACAG
1 GTCTTTTAAAATTATACATAACAG
*
3511985 TGTCTTTTAAAGTTATACATAAC
1 -GTCTTTTAAAATTATACATAAC
3512008 CGAATCTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.43
Consensus pattern (24 bp):
GTCTTTTAAAATTATACATAACAG
Found at i:3512015 original size:25 final size:25
Alignment explanation
Indices: 3511962--3512016 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
3511952 TATGGCTCAG
* **
3511962 TCTTTTAAAATTATATATAACAGTG
1 TCTTTTAAAATTATACATAACAGAA
* *
3511987 TCTTTTAAAGTTATACATAACCGAA
1 TCTTTTAAAATTATACATAACAGAA
3512012 TCTTT
1 TCTTT
3512017 CAGAGGGAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (25 bp):
TCTTTTAAAATTATACATAACAGAA
Found at i:3521670 original size:14 final size:14
Alignment explanation
Indices: 3521651--3521726 Score: 73
Period size: 14 Copynumber: 5.3 Consensus size: 14
3521641 AAAAGTCAGT
*
3521651 AAAATAAAAAACTA
1 AAAATAAAAAAATA
** *
3521665 AAAATAAAATTACA
1 AAAATAAAAAAATA
*
3521679 AAATATAAAGTAAATA
1 AAA-ATAAA-AAAATA
3521695 AAAATAAATAAAAT-
1 AAAATAAA-AAAATA
3521709 AAAATAAAAAAATA
1 AAAATAAAAAAATA
3521723 AAAA
1 AAAA
3521727 CCTGTGATCG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 5 0.10
14 25 0.51
15 14 0.29
16 5 0.10
ACGTcount: A:0.78, C:0.03, G:0.01, T:0.18
Consensus pattern (14 bp):
AAAATAAAAAAATA
Found at i:3521701 original size:15 final size:14
Alignment explanation
Indices: 3521624--3521726 Score: 63
Period size: 14 Copynumber: 7.4 Consensus size: 14
3521614 TTATTTAACA
3521624 AAAAATAAATAAAT
1 AAAAATAAATAAAT
* * * *
3521638 AATAA-AAGTCAGT
1 AAAAATAAATAAAT
3521651 -AAAATAAA-AAACT
1 AAAAATAAATAAA-T
*
3521664 AAAAATAAAATTACA-
1 AAAAAT-AAA-TAAAT
*
3521679 AAATATAAAGTAAAT
1 AAAAATAAA-TAAAT
3521694 AAAAATAAATAAA-
1 AAAAATAAATAAAT
*
3521707 ATAAAATAAAAAAAT
1 A-AAAATAAATAAAT
3521722 AAAAA
1 AAAAA
3521727 CCTGTGATCG
Statistics
Matches: 66, Mismatches: 14, Indels: 18
0.67 0.14 0.18
Matches are distributed among these distances:
12 4 0.06
13 9 0.14
14 34 0.52
15 17 0.26
17 2 0.03
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (14 bp):
AAAAATAAATAAAT
Found at i:3521710 original size:24 final size:23
Alignment explanation
Indices: 3521651--3521726 Score: 63
Period size: 24 Copynumber: 3.4 Consensus size: 23
3521641 AAAAGTCAGT
*
3521651 AAAATAAAAAACT--AA-AAATA
1 AAAATAAAAAAATAAAATAAATA
* * *
3521671 AAATTACAAAATATAAAGTAAATA
1 AAAATA-AAAAAATAAAATAAATA
3521695 AAAATAAATAAAATAAAAT-AA-A
1 AAAATAAA-AAAATAAAATAAATA
3521717 AAAATAAAAA
1 AAAATAAAAA
3521727 CCTGTGATCG
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
20 5 0.11
21 7 0.16
22 9 0.20
23 5 0.11
24 18 0.41
ACGTcount: A:0.78, C:0.03, G:0.01, T:0.18
Consensus pattern (23 bp):
AAAATAAAAAAATAAAATAAATA
Found at i:3522416 original size:3 final size:3
Alignment explanation
Indices: 3522408--3522603 Score: 192
Period size: 3 Copynumber: 66.3 Consensus size: 3
3522398 ATGAAAATGA
* * * *
3522408 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAC AAC AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
3522456 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
3522504 AAT GA- AAT -AT AGCAT AAT AA- ATAT TAT ACT AAT -AT ACT -AT ACT
1 AAT AAT AAT AAT A--AT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
*
3522547 -AT ACT -AT ACCAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3522592 AAT AAT -AT AAT A
1 AAT AAT AAT AAT A
3522604 TCATACTATA
Statistics
Matches: 164, Mismatches: 16, Indels: 26
0.80 0.08 0.13
Matches are distributed among these distances:
2 11 0.07
3 147 0.90
5 6 0.04
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3539294 original size:13 final size:13
Alignment explanation
Indices: 3539278--3539330 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
3539268 AATTTAAATT
*
3539278 TATTATTTTTATA
1 TATTATTTTAATA
3539291 TATTATTTTAATA
1 TATTATTTTAATA
**
3539304 TAAAATTTTAATA
1 TATTATTTTAATA
3539317 -A--ATTTTAATA
1 TATTATTTTAATA
3539327 TATT
1 TATT
3539331 TTGATATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
12 1 0.03
13 23 0.68
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATTTTAATA
Found at i:3539310 original size:33 final size:32
Alignment explanation
Indices: 3539273--3539354 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 32
3539263 TTTTAAATTT
3539273 AAATTTATTATTTTTATATATTATTTTAATATA
1 AAATTTATTATTTTTATATA-TATTTTAATATA
* * *
3539306 AAATTTTAATAAATTTTA-ATATATTTTGATATA
1 AAA-TTT-ATTATTTTTATATATATTTTAATATA
*
3539339 AAA-TAATTATTTTTAT
1 AAATTTATTATTTTTAT
3539355 TTTATAAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
30 8 0.20
31 1 0.03
33 17 0.43
34 6 0.15
35 8 0.20
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (32 bp):
AAATTTATTATTTTTATATATATTTTAATATA
Found at i:3539708 original size:30 final size:29
Alignment explanation
Indices: 3539672--3539738 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
3539662 CTGAGAATTT
3539672 TTTATTTCAAAT-AAGTTGAATCTTTAAATA
1 TTTATTTC-AATCAA-TTGAATCTTTAAATA
* *
3539702 TTTATTTTCATTCAATTGAGTCTTTAAATA
1 TTTA-TTTCAATCAATTGAATCTTTAAATA
*
3539732 TCTATTT
1 TTTATTT
3539739 TCACTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 3 0.09
30 23 0.72
31 6 0.19
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.52
Consensus pattern (29 bp):
TTTATTTCAATCAATTGAATCTTTAAATA
Found at i:3540128 original size:26 final size:26
Alignment explanation
Indices: 3540082--3540131 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
3540072 ATAAAGCCGC
3540082 TGTGTGTATAAATGGTATCAGAGCTA
1 TGTGTGTATAAATGGTATCAGAGCTA
3540108 TGTGTGTATAAATGGTATCAGAGC
1 TGTGTGTATAAATGGTATCAGAGC
3540132 CTAACAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.34
Consensus pattern (26 bp):
TGTGTGTATAAATGGTATCAGAGCTA
Found at i:3547237 original size:23 final size:24
Alignment explanation
Indices: 3547207--3547254 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
3547197 TACCTGTCGT
3547207 TATGTGTAT-AATGGTATCAGAGC
1 TATGTGTATAAATGGTATCAGAGC
3547230 TATGTGTATAAATGGTATCAGAGC
1 TATGTGTATAAATGGTATCAGAGC
3547254 T
1 T
3547255 GGGAAAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.35
Consensus pattern (24 bp):
TATGTGTATAAATGGTATCAGAGC
Found at i:3551704 original size:15 final size:14
Alignment explanation
Indices: 3551680--3551718 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3551670 AGGCTCAAAG
*
3551680 TTTTTGTTTTCCTT
1 TTTTTGTTTTTCTT
*
3551694 TTTTTGTTTTTTTT
1 TTTTTGTTTTTCTT
3551708 TTGTTTGTTTT
1 TT-TTTGTTTT
3551719 GTTAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (14 bp):
TTTTTGTTTTTCTT
Found at i:3551831 original size:12 final size:12
Alignment explanation
Indices: 3551804--3551842 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
3551794 GTATTTATCC
3551804 TTTTTTTGTTTCTG
1 TTTTTTTG-TT-TG
3551818 TTTTTTTGTTTG
1 TTTTTTTGTTTG
*
3551830 TTTTTTTTTTTG
1 TTTTTTTGTTTG
3551842 T
1 T
3551843 GGTTGGTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 14 0.58
13 2 0.08
14 8 0.33
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.85
Consensus pattern (12 bp):
TTTTTTTGTTTG
Found at i:3551935 original size:6 final size:6
Alignment explanation
Indices: 3551924--3551948 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3551914 AATAGTGATA
3551924 AGCTCG AGCTCG AGCTCG AGCTCG A
1 AGCTCG AGCTCG AGCTCG AGCTCG A
3551949 CTCACAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.16
Consensus pattern (6 bp):
AGCTCG
Found at i:3553537 original size:110 final size:110
Alignment explanation
Indices: 3553371--3553570 Score: 278
Period size: 110 Copynumber: 1.8 Consensus size: 110
3553361 ATGCCGTAAC
* * * *
3553371 TACAGAATCGACTGTGATAACACCGCAAGTCAAAAAATAAGAAATCAGTTGGGATAACACCGTAA
1 TACAGAATCGACTGTGATAACACCGCAAGTCAAAAAATAAGAAATCAGTCGAGATAAAACCGCAA
3553436 ATCAAAATTATGCCTGAAGGTCTTAGAAATCATGCCTAGAAGTTT
66 ATCAAAATTATGCCTGAAGGTCTTAGAAATCATGCCTAGAAGTTT
* * *
3553481 TACAGAATTGACTGTGATAACACTGCAAGTCAAAAAATAA-AGAATC-GATCGAGATAAAATCGC
1 TACAGAATCGACTGTGATAACACCGCAAGTCAAAAAATAAGA-AATCAG-TCGAGATAAAACCGC
* * *
3553544 GAATCAAAATTATGTCTGGAGGTCTTA
64 AAATCAAAATTATGCCTGAAGGTCTTA
3553571 CAAAATCGAC
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
109 2 0.03
110 76 0.97
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.24
Consensus pattern (110 bp):
TACAGAATCGACTGTGATAACACCGCAAGTCAAAAAATAAGAAATCAGTCGAGATAAAACCGCAA
ATCAAAATTATGCCTGAAGGTCTTAGAAATCATGCCTAGAAGTTT
Found at i:3553627 original size:198 final size:197
Alignment explanation
Indices: 3553371--3553773 Score: 521
Period size: 198 Copynumber: 2.0 Consensus size: 197
3553361 ATGCCGTAAC
* * * *
3553371 TACAGAATCGACTGTGATAACACCGCAAGTCAAAAAATAAGAAATCAGTTGGGATAACACCGTAA
1 TACAAAATCGACTGGGATAACACCGCAAGTCAAAAAATAAGAAATCAGTTGAGATAACACCGCAA
* * *
3553436 ATCAAAATTATGC-CTGAAGGTCTTAGAAATCATGCCTAG-AAGTTTTACAGAATTGACTGTGAT
66 ATCAAAATTATGCTC-GAAGGTCTTAGAAATCATGCC-AGAAAGTCTTACAGAATCGACTGGGAT
* * * *
3553499 AACACTGCAAGTCAAAAAATAA-AGAATCGATCGAGATAAAATCGCGAATCAAAATTATGTCTGG
129 AACACCGCAAGT-AAAAAATAAGA-AATCGATCGAGATAAAACCGCGAATCAAAATTATGTCCGA
3553563 AGGTCT
192 AGGTCT
* *
3553569 TACAAAATCGACTGGGATAACACCGTAAGTCAAAAAATAA-AGAATC-GATTGAGATAACATCGC
1 TACAAAATCGACTGGGATAACACCGCAAGTCAAAAAATAAGA-AATCAG-TTGAGATAACACCGC
* * * * *
3553632 GAATCGAAATTATGCTCGGAGGTCTTAGAAATCATGCCCGAAAGTCTTATAGAATCGACTGGGAT
64 AAATCAAAATTATGCTCGAAGGTCTTAGAAATCATGCCAGAAAGTCTTACAGAATCGACTGGGAT
* *
3553697 AACACCGCAAGTTAAAAATAAGAAATCGATCGAGATAACACCGCGAATCAAAATTATGTCCGAAG
129 AACACCGCAAGTAAAAAATAAGAAATCGATCGAGATAAAACCGCGAATCAAAATTATGTCCGAAG
*
3553762 GTTT
194 GTCT
3553766 TA-AAAATC
1 TACAAAATC
3553774 ATGCCTGGAG
Statistics
Matches: 179, Mismatches: 21, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
196 6 0.03
197 54 0.30
198 118 0.66
199 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (197 bp):
TACAAAATCGACTGGGATAACACCGCAAGTCAAAAAATAAGAAATCAGTTGAGATAACACCGCAA
ATCAAAATTATGCTCGAAGGTCTTAGAAATCATGCCAGAAAGTCTTACAGAATCGACTGGGATAA
CACCGCAAGTAAAAAATAAGAAATCGATCGAGATAAAACCGCGAATCAAAATTATGTCCGAAGGT
CT
Found at i:3553631 original size:88 final size:88
Alignment explanation
Indices: 3553480--3553658 Score: 270
Period size: 88 Copynumber: 2.0 Consensus size: 88
3553470 CCTAGAAGTT
* * * *
3553480 TTACAGAATTGACTGTGATAACACTGCAAGTCAAAAAATAAAGAATCGATCGAGATAAAATCGCG
1 TTACAAAATCGACTGGGATAACACCGCAAGTCAAAAAATAAAGAATCGATCGAGATAAAATCGCG
3553545 AATCAAAATTATG-TCTGGAGGTC
66 AATCAAAATTATGCTC-GGAGGTC
* * *
3553568 TTACAAAATCGACTGGGATAACACCGTAAGTCAAAAAATAAAGAATCGATTGAGATAACATCGCG
1 TTACAAAATCGACTGGGATAACACCGCAAGTCAAAAAATAAAGAATCGATCGAGATAAAATCGCG
*
3553633 AATCGAAATTATGCTCGGAGGTC
66 AATCAAAATTATGCTCGGAGGTC
3553656 TTA
1 TTA
3553659 GAAATCATGC
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
88 80 0.98
89 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (88 bp):
TTACAAAATCGACTGGGATAACACCGCAAGTCAAAAAATAAAGAATCGATCGAGATAAAATCGCG
AATCAAAATTATGCTCGGAGGTC
Found at i:3553773 original size:109 final size:109
Alignment explanation
Indices: 3553565--3553883 Score: 408
Period size: 109 Copynumber: 2.9 Consensus size: 109
3553555 ATGTCTGGAG
* * *
3553565 GTCTTACAAAATCGACTGGGATAACACCGTAAGTCAAAAAATAA-AGAATCGATTGAGATAACAT
1 GTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAAAAATAAGA-AATCGATCGAGATAACAT
* *
3553629 CGCGAATCGAAATTATGCTCGGAGGTCTTAGAAATCATGCCCGAAA
65 CGCGAATCAAAATTATGC-CGGAGGTCTTAAAAATCATGCCCGAAA
* * *
3553675 GTCTTATAGAATCGACTGGGATAACACCGCAAGT-TAAAAATAAGAAATCGATCGAGATAACACC
1 GTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAAAAATAAGAAATCGATCGAGATAACATC
* * * * *
3553739 GCGAATCAAAATTATGTCCGAAGGTTTTAAAAATCATGCCTGGAG
66 GCGAATCAAAATTATG-CCGGAGGTCTTAAAAATCATGCCCGAAA
* * * * *
3553784 GTCTTACAGAATCGACTGGGATAACACTGCAACTCGAAAGATAAGGAATCGATCGAGATAACATC
1 GTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAAAAATAAGAAATCGATCGAGATAACATC
*
3553849 GTGAATCAAAATTATGCCCGGAGGTCTTACAAAAT
66 GCGAATCAAAATTATG-CCGGAGGTCTTA-AAAAT
3553884 TGACTAAGAT
Statistics
Matches: 181, Mismatches: 24, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
109 92 0.51
110 84 0.46
111 5 0.03
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.22
Consensus pattern (109 bp):
GTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAAAAATAAGAAATCGATCGAGATAACATC
GCGAATCAAAATTATGCCGGAGGTCTTAAAAATCATGCCCGAAA
Found at i:3553864 original size:110 final size:109
Alignment explanation
Indices: 3553549--3553883 Score: 429
Period size: 110 Copynumber: 3.0 Consensus size: 109
3553539 ATCGCGAATC
* * * * *
3553549 AAAATTATGTCTGGAGGTCTTACAAAATCGACTGGGATAACACCGTAAGTCAAAAAATAAAGAAT
1 AAAATCATGCCTGGAGGTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAAAAATAAGGAAT
* *
3553614 CGATTGAGATAACATCGCGAATCGAAATTATGCTCGGAGGTCTTA
66 CGATCGAGATAACATCGCGAATCAAAATTATGC-CGGAGGTCTTA
* * * * * * *
3553659 GAAATCATGCCCGAAAGTCTTATAGAATCGACTGGGATAACACCGCAAGT-TAAAAATAAGAAAT
1 AAAATCATGCCTGGAGGTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAAAAATAAGGAAT
* * *
3553723 CGATCGAGATAACACCGCGAATCAAAATTATGTCCGAAGGTTTTA
66 CGATCGAGATAACATCGCGAATCAAAATTATG-CCGGAGGTCTTA
* * * *
3553768 AAAATCATGCCTGGAGGTCTTACAGAATCGACTGGGATAACACTGCAACTCGAAAGATAAGGAAT
1 AAAATCATGCCTGGAGGTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAAAAATAAGGAAT
*
3553833 CGATCGAGATAACATCGTGAATCAAAATTATGCCCGGAGGTCTTA
66 CGATCGAGATAACATCGCGAATCAAAATTATG-CCGGAGGTCTTA
3553878 CAAAAT
1 -AAAAT
3553884 TGACTAAGAT
Statistics
Matches: 190, Mismatches: 32, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
109 92 0.48
110 93 0.49
111 5 0.03
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (109 bp):
AAAATCATGCCTGGAGGTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAAAAATAAGGAAT
CGATCGAGATAACATCGCGAATCAAAATTATGCCGGAGGTCTTA
Found at i:3553868 original size:197 final size:197
Alignment explanation
Indices: 3553660--3554080 Score: 467
Period size: 197 Copynumber: 2.1 Consensus size: 197
3553650 GAGGTCTTAG
* * * ** * *
3553660 AAATCATGCCCGAAAGTCTTATAGAATCGACTGGGATAACACCGCAAGTTAAAA-ATAAGAAATC
1 AAATTATGCCCGAAAGTCTTACAAAATCGACTAAGATAACACCGCAAATCAAAAGATAAGAAAT-
* * * * *
3553724 GATCGAGATAACACCGCGAATC-AAAATTATG-TCCGAAGGTTTTAAAAATCATG-CCTGGAGGT
65 GATCAAGATAACACCACGAATCGAAAA-TATGCT-CGAAAGTCTTAAAAATCATGTCC-GAAGGT
* * *
3553786 CTTACAGAATCGACTGGGATAACA-CTGCAACTCGAAAGATAAGGAATCGATCGAGATAACATCG
127 CTTACAGAATCGACTAGGATAACATC-GCAACTCGAAAGATAAGGAATCGATCGAGACAACACCG
**
3553850 TGAATCA
191 CAAATCA
* * * * *
3553857 AAATTATGCCCGGAGGTCTTACAAAATTGACTAAGATAACACCGTAAATCAAAAGATAAGGAATG
1 AAATTATGCCCGAAAGTCTTACAAAATCGACTAAGATAACACCGCAAATCAAAAGATAAGAAATG
** *
3553922 ATCAAGATAACATTATGAATCGAAAATATGCTCGAAAGTCTTAAAAATCATGTCCGAAGGTCTTA
66 ATCAAGATAACACCACGAATCGAAAATATGCTCGAAAGTCTTAAAAATCATGTCCGAAGGTCTTA
* * * *
3553987 CAGAATCGACTAGGATGACATCGCAAGTCGAAAGATAAGGAATTGATCGGGACAACACCGCAAAT
131 CAGAATCGACTAGGATAACATCGCAACTCGAAAGATAAGGAATCGATCGAGACAACACCGCAAAT
3554052 CA
196 CA
* * *
3554054 AAATTATGTCCGGAGGTCTTA-AAAATC
1 AAATTATGCCCGAAAGTCTTACAAAATC
3554081 ATGCTCGGAG
Statistics
Matches: 188, Mismatches: 31, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
196 5 0.03
197 167 0.89
198 16 0.09
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22
Consensus pattern (197 bp):
AAATTATGCCCGAAAGTCTTACAAAATCGACTAAGATAACACCGCAAATCAAAAGATAAGAAATG
ATCAAGATAACACCACGAATCGAAAATATGCTCGAAAGTCTTAAAAATCATGTCCGAAGGTCTTA
CAGAATCGACTAGGATAACATCGCAACTCGAAAGATAAGGAATCGATCGAGACAACACCGCAAAT
CA
Found at i:3553895 original size:88 final size:88
Alignment explanation
Indices: 3553768--3553970 Score: 232
Period size: 88 Copynumber: 2.3 Consensus size: 88
3553758 GAAGGTTTTA
* * * ** * * *
3553768 AAAATCATGCCTGGAGGTCTTACAGAATCGACTGGGATAACACTGCAACTCGAAAGATAAGGAAT
1 AAAATTATGCCCGGAGGTCTTACAAAATCGACTAAGATAACACCGCAAATCAAAAGATAAGGAAT
* *
3553833 CGATCGAGATAACATCGTGAATC-
66 -GATCAAGATAACATCATGAATCG
* *
3553856 AAAATTATGCCCGGAGGTCTTACAAAATTGACTAAGATAACACCGTAAATCAAAAGATAAGGAAT
1 AAAATTATGCCCGGAGGTCTTACAAAATCGACTAAGATAACACCGCAAATCAAAAGATAAGGAAT
*
3553921 GATCAAGATAACATTATGAATCG
66 GATCAAGATAACATCATGAATCG
* * *
3553944 AAAA-TATGCTCGAAAGTCTTA-AAAATC
1 AAAATTATGCCCGGAGGTCTTACAAAATC
3553971 ATGTCCGAAG
Statistics
Matches: 97, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
86 5 0.05
87 33 0.34
88 59 0.61
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (88 bp):
AAAATTATGCCCGGAGGTCTTACAAAATCGACTAAGATAACACCGCAAATCAAAAGATAAGGAAT
GATCAAGATAACATCATGAATCG
Found at i:3554046 original size:307 final size:307
Alignment explanation
Indices: 3553371--3554103 Score: 936
Period size: 307 Copynumber: 2.4 Consensus size: 307
3553361 ATGCCGTAAC
* * * *
3553371 TACAGAATCGACTGTGATAACACCGCAAGTCAAAAAATAA-GAAATCAGTTGGGATAACACCGTA
1 TACAGAATCGACTG-GATAACACCGCAAGTCAAAAAATAAGGAATTGA-TCGGGATAACACCGCA
* * * * * *
3553435 AATCAAAATTATG-CCTGAAGGTCTTAGAAATCATGCCTAGAAGTTTTACAGAATTGACTGTGAT
64 AATCAAAATTATGTCC-GAAGGTCTTAAAAATCATGCCTGGAGGTCTTACAGAATCGACTGGGAT
* * *
3553499 AACACTGCAAGTCAAAAAATAAAGAATCGATCGAGATAAAATCGCGAATCAAAATTATGTCTGGA
128 AACACTGCAACTCAAAAAATAAAGAATCGATCGAGATAAAATCGCGAATCAAAATTATGCCCGGA
** * **
3553564 GGTCTTACAAAATCGACTGGGATAACACCGTAAGTCAAAAAATAAAGAATCGATTGAGATAACAT
193 GGTCTTACAAAATCGACTAAGATAACACCGTAAATCAAAAAATAAAGAATCGATCAAGATAACAT
* * * * *
3553629 CGCGAATCGAAATTATGCTCGGAGGTCTTAGAAATCATGCCCGAAAGTCT
258 CACGAATCGAAAATATGCTCGAAAGTCTTAAAAATCATGCCCGAAAGTCT
* * * * * *
3553679 TATAGAATCGACTGGGATAACACCGCAAGT-TAAAAATAAGAAATCGATCGAGATAACACCGCGA
1 TACAGAATCGACT-GGATAACACCGCAAGTCAAAAAATAAGGAATTGATCGGGATAACACCGCAA
*
3553743 ATCAAAATTATGTCCGAAGGTTTTAAAAATCATGCCTGGAGGTCTTACAGAATCGACTGGGATAA
65 ATCAAAATTATGTCCGAAGGTCTTAAAAATCATGCCTGGAGGTCTTACAGAATCGACTGGGATAA
* * * * *
3553808 CACTGCAACTCGAAAGATAAGGAATCGATCGAGATAACATCGTGAATCAAAATTATGCCCGGAGG
130 CACTGCAACTCAAAAAATAAAGAATCGATCGAGATAAAATCGCGAATCAAAATTATGCCCGGAGG
* * * *
3553873 TCTTACAAAATTGACTAAGATAACACCGTAAATCAAAAGATAAGGAAT-GATCAAGATAACATTA
195 TCTTACAAAATCGACTAAGATAACACCGTAAATCAAAAAATAAAGAATCGATCAAGATAACATCA
* * *
3553937 TGAATCGAAAATATGCTCGAAAGTCTTAAAAATCATGTCCGAAGGTCT
260 CGAATCGAAAATATGCTCGAAAGTCTTAAAAATCATGCCCGAAAGTCT
* * * * *
3553985 TACAGAATCGACTAGGATGACATCGCAAGTCGAAAGATAAGGAATTGATCGGGACAACACCGCAA
1 TACAGAATCGACT-GGATAACACCGCAAGTCAAAAAATAAGGAATTGATCGGGATAACACCGCAA
* *
3554050 ATCAAAATTATGTCCGGAGGTCTTAAAAATCATG-CTCGGAGGTCTTACAAAATC
65 ATCAAAATTATGTCCGAAGGTCTTAAAAATCATGCCT-GGAGGTCTTACAGAATC
3554104 ATGTCCAGAA
Statistics
Matches: 364, Mismatches: 56, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
306 81 0.22
307 250 0.69
308 32 0.09
309 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.23
Consensus pattern (307 bp):
TACAGAATCGACTGGATAACACCGCAAGTCAAAAAATAAGGAATTGATCGGGATAACACCGCAAA
TCAAAATTATGTCCGAAGGTCTTAAAAATCATGCCTGGAGGTCTTACAGAATCGACTGGGATAAC
ACTGCAACTCAAAAAATAAAGAATCGATCGAGATAAAATCGCGAATCAAAATTATGCCCGGAGGT
CTTACAAAATCGACTAAGATAACACCGTAAATCAAAAAATAAAGAATCGATCAAGATAACATCAC
GAATCGAAAATATGCTCGAAAGTCTTAAAAATCATGCCCGAAAGTCT
Found at i:3554089 original size:22 final size:23
Alignment explanation
Indices: 3554064--3554106 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
3554054 AAATTATGTC
3554064 CGGAGGTCTTA-AAAATCATGCT
1 CGGAGGTCTTACAAAATCATGCT
3554086 CGGAGGTCTTACAAAATCATG
1 CGGAGGTCTTACAAAATCATG
3554107 TCCAGAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (23 bp):
CGGAGGTCTTACAAAATCATGCT
Done.