Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 35 of 172
Found at i:11012243 original size:16 final size:16
Alignment explanation
Indices: 11012199--11012246 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
11012189 TATATATTTA
11012199 AATAAAT-TTATTTTTT
1 AATAAATATT-TTTTTT
*
11012215 AACAAATAAATTTTTTTT
1 AATAAAT--ATTTTTTTT
11012233 AATAAATATTTTTT
1 AATAAATATTTTTT
11012247 ATTTTCTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 13 0.48
18 12 0.44
19 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
AATAAATATTTTTTTT
Found at i:11012246 original size:18 final size:18
Alignment explanation
Indices: 11012204--11012251 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
11012194 ATTTAAATAA
*
11012204 ATTTATTTTTTAACAAAT
1 ATTTTTTTTTTAACAAAT
** *
11012222 AAATTTTTTTTAATAAAT
1 ATTTTTTTTTTAACAAAT
11012240 ATTTTTTATTTT
1 ATTTTTT-TTTT
11012252 CTAATTAATC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTTTTTTTAACAAAT
Found at i:11012602 original size:21 final size:23
Alignment explanation
Indices: 11012556--11012605 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
11012546 TAAAATATTG
11012556 AAATATTACAAAAATCATATTTA
1 AAATATTACAAAAATCATATTTA
*
11012579 AAATTTTA-AAAAAT-A-ATTTCA
1 AAATATTACAAAAATCATATTT-A
11012600 AAATAT
1 AAATAT
11012606 ATATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 4 0.17
21 7 0.29
22 6 0.25
23 7 0.29
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATATTACAAAAATCATATTTA
Found at i:11012627 original size:20 final size:22
Alignment explanation
Indices: 11012593--11012634 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
11012583 TTTAAAAAAT
*
11012593 AATTTCAAAATATATAT-TTAA
1 AATTTCAAAAAATATATATTAA
11012614 AATTT-AAAAAATATATATTAA
1 AATTTCAAAAAATATATATTAA
11012635 TAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTTCAAAAAATATATATTAA
Found at i:11012644 original size:33 final size:33
Alignment explanation
Indices: 11012556--11012626 Score: 101
Period size: 34 Copynumber: 2.2 Consensus size: 33
11012546 TAAAATATTG
*
11012556 AAAT-ATTACAAAA-ATCATATTTAAAATTTTAAA
1 AAATAATTTCAAAATAT-ATATTTAAAA-TTTAAA
11012589 AAATAATTTCAAAATATATATTTAAAATTTAAA
1 AAATAATTTCAAAATATATATTTAAAATTTAAA
11012622 AAATA
1 AAATA
11012627 TATATTAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
33 15 0.43
34 18 0.51
35 2 0.06
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (33 bp):
AAATAATTTCAAAATATATATTTAAAATTTAAA
Found at i:11012655 original size:25 final size:25
Alignment explanation
Indices: 11012584--11012657 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 25
11012574 ATTTAAAATT
11012584 TTAA-AAAATAATTTCAAAATATATA
1 TTAATAAAAT-ATTTCAAAATATATA
**
11012609 TT--TAAAAT-TTAAAAAATATATA
1 TTAATAAAATATTTCAAAATATATA
11012631 TTAATAAAATATTTCAAAATATATA
1 TTAATAAAATATTTCAAAATATATA
11012656 TT
1 TT
11012658 TCAAAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
22 14 0.34
24 11 0.27
25 16 0.39
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (25 bp):
TTAATAAAATATTTCAAAATATATA
Found at i:11012658 original size:14 final size:14
Alignment explanation
Indices: 11012581--11012664 Score: 55
Period size: 13 Copynumber: 6.7 Consensus size: 14
11012571 CATATTTAAA
* *
11012581 ATTTTAAAAAATA-
1 ATTTCAAAATATAT
11012594 ATTTCAAAATATAT
1 ATTTCAAAATATAT
11012608 ATTT-AAAAT-T-T
1 ATTTCAAAATATAT
*
11012619 A---AAAAATATAT
1 ATTTCAAAATATAT
11012630 A-TT-AATAA-A-AT
1 ATTTCAA-AATATAT
11012641 ATTTCAAAATATAT
1 ATTTCAAAATATAT
11012655 ATTTCAAAAT
1 ATTTCAAAAT
11012665 TTTTAAAATT
Statistics
Matches: 58, Mismatches: 2, Indels: 21
0.72 0.02 0.26
Matches are distributed among these distances:
9 5 0.09
10 1 0.02
11 7 0.12
12 8 0.14
13 21 0.36
14 16 0.28
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (14 bp):
ATTTCAAAATATAT
Found at i:11012673 original size:48 final size:48
Alignment explanation
Indices: 11012584--11012690 Score: 139
Period size: 47 Copynumber: 2.2 Consensus size: 48
11012574 ATTTAAAATT
11012584 TTAA-AAAATAATTTCAAAATATATATTTAAAATTTAAAAAA-T-ATATA
1 TTAATAAAAT-ATTTCAAAATATATATTTAAAATTTAAAAAATTAATA-A
**
11012631 TTAATAAAATATTTCAAAATATATATTTCAAAATTTTTAAAATTAATAA
1 TTAATAAAATATTTCAAAATATATATTT-AAAATTTAAAAAATTAATAA
*
11012680 TAAATAAAATA
1 TTAATAAAATA
11012691 AATAAAATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
47 22 0.42
48 16 0.30
49 12 0.23
50 3 0.06
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (48 bp):
TTAATAAAATATTTCAAAATATATATTTAAAATTTAAAAAATTAATAA
Found at i:11012690 original size:9 final size:9
Alignment explanation
Indices: 11012678--11012710 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
11012668 TAAAATTAAT
11012678 AATAAATAA
1 AATAAATAA
11012687 AATAAATAA
1 AATAAATAA
11012696 AATAAA-ATA
1 AATAAATA-A
11012705 AATAAA
1 AATAAA
11012711 GACAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 1 0.04
9 22 0.96
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AATAAATAA
Found at i:11012698 original size:48 final size:47
Alignment explanation
Indices: 11012588--11012699 Score: 120
Period size: 48 Copynumber: 2.3 Consensus size: 47
11012578 AAAATTTTAA
* *
11012588 AAAATAATTTCAAAATATATATTTAAAATTTAAAAAATATATATTAAT
1 AAAATAA-ATCAAAATATATATTTAAAATTTAAAAAATATATATAAAT
** **
11012636 AAAATATTTCAAAATATATATTTCAAAATTTTTAAAAT-TAATAATAAAT
1 AAAATAAATCAAAATATATATTT-AAAATTTAAAAAATAT-AT-ATAAAT
11012685 AAAATAAAT-AAAATA
1 AAAATAAATCAAAATA
11012700 AAATAAATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
47 17 0.31
48 26 0.47
49 12 0.22
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (47 bp):
AAAATAAATCAAAATATATATTTAAAATTTAAAAAATATATATAAAT
Found at i:11012700 original size:14 final size:14
Alignment explanation
Indices: 11012681--11012710 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
11012671 AATTAATAAT
11012681 AAATAAAATAAATA
1 AAATAAAATAAATA
11012695 AAATAAAATAAATA
1 AAATAAAATAAATA
11012709 AA
1 AA
11012711 GACAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAAAATAAATA
Found at i:11016587 original size:78 final size:78
Alignment explanation
Indices: 11016458--11016610 Score: 279
Period size: 78 Copynumber: 2.0 Consensus size: 78
11016448 TTAACTTAAC
*
11016458 CATAGTGAAATACAAAAAGAACATCACAGGCATCGGCCTTCTCTATATTAGGAGTGAATTCGATT
1 CATAGTGAAATACAAAAAGAACATCACAGGCATCGACCTTCTCTATATTAGGAGTGAATTCGATT
11016523 TGATTTTGGTAAT
66 TGATTTTGGTAAT
* *
11016536 CATAGTGAAATACAAAAAGAACATCATAGGCATCGATCTTCTCTATATTAGGAGTGAATTCGATT
1 CATAGTGAAATACAAAAAGAACATCACAGGCATCGACCTTCTCTATATTAGGAGTGAATTCGATT
11016601 TGATTTTGGT
66 TGATTTTGGT
11016611 TTTTTCATAT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (78 bp):
CATAGTGAAATACAAAAAGAACATCACAGGCATCGACCTTCTCTATATTAGGAGTGAATTCGATT
TGATTTTGGTAAT
Found at i:11020275 original size:14 final size:14
Alignment explanation
Indices: 11020251--11020289 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
11020241 CAAAATGTAC
11020251 AATAT-AATTAAAT
1 AATATAAATTAAAT
11020264 AATATAAATTAAAT
1 AATATAAATTAAAT
* *
11020278 AAAATAATTTAA
1 AATATAAATTAA
11020290 TTAACTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATATAAATTAAAT
Found at i:11027361 original size:50 final size:50
Alignment explanation
Indices: 11027286--11027381 Score: 183
Period size: 50 Copynumber: 1.9 Consensus size: 50
11027276 CTACTACCTG
11027286 TAAAGGAAAATAAAAATGAAATATGCTGGCTAGGAGTAAATGCATGAGAT
1 TAAAGGAAAATAAAAATGAAATATGCTGGCTAGGAGTAAATGCATGAGAT
*
11027336 TAAAGGAAAATGAAAATGAAATATGCTGGCTAGGAGTAAATGCATG
1 TAAAGGAAAATAAAAATGAAATATGCTGGCTAGGAGTAAATGCATG
11027382 GCAGCTGTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.47, C:0.06, G:0.25, T:0.22
Consensus pattern (50 bp):
TAAAGGAAAATAAAAATGAAATATGCTGGCTAGGAGTAAATGCATGAGAT
Found at i:11027547 original size:17 final size:16
Alignment explanation
Indices: 11027525--11027560 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
11027515 AAAGTCTATC
*
11027525 ATCCTCTTAAAACTCAT
1 ATCCTCTCAAAACTC-T
11027542 ATCCTCTCAAAACTCT
1 ATCCTCTCAAAACTCT
11027558 ATC
1 ATC
11027561 AAATTCTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (16 bp):
ATCCTCTCAAAACTCT
Found at i:11031577 original size:49 final size:50
Alignment explanation
Indices: 11031505--11031607 Score: 190
Period size: 49 Copynumber: 2.1 Consensus size: 50
11031495 TGAGAAAATG
*
11031505 AATATTGCATATAACATTGCAATATTTATAATGATTTTTAAAAATTTAAT
1 AATATTGCATATAACATTACAATATTTATAATGATTTTTAAAAATTTAAT
11031555 AATATTGCA-ATAACATTACAATATTTATAATGATTTTTAAAAATTTAAT
1 AATATTGCATATAACATTACAATATTTATAATGATTTTTAAAAATTTAAT
11031604 AATA
1 AATA
11031608 AGTATAATAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 43 0.83
50 9 0.17
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.43
Consensus pattern (50 bp):
AATATTGCATATAACATTACAATATTTATAATGATTTTTAAAAATTTAAT
Found at i:11032303 original size:16 final size:16
Alignment explanation
Indices: 11032282--11032314 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
11032272 ATTTGCAGGG
11032282 TTTGAATTTGTACGTT
1 TTTGAATTTGTACGTT
11032298 TTTGAATTTGTACGTT
1 TTTGAATTTGTACGTT
11032314 T
1 T
11032315 AATATATTTA
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:0.18, C:0.06, G:0.18, T:0.58
Consensus pattern (16 bp):
TTTGAATTTGTACGTT
Found at i:11033266 original size:18 final size:18
Alignment explanation
Indices: 11033227--11033268 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
11033217 TAATTCTTAA
11033227 ATTAAAAATAAATAAATTT
1 ATTAAAAATAAATAAA-TT
*
11033246 ATTAAAAAGTATATAAA-T
1 ATTAAAAA-TAAATAAATT
11033264 ATTAA
1 ATTAA
11033269 TTAACATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 8 0.38
20 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
ATTAAAAATAAATAAATT
Found at i:11035185 original size:19 final size:19
Alignment explanation
Indices: 11035163--11035211 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
11035153 TGATAAGCTT
11035163 TATCCAATTTGTAAAGTTG
1 TATCCAATTTGTAAAGTTG
11035182 TATCCAATTTGTAAAGTTG
1 TATCCAATTTGTAAAGTTG
11035201 TATCCAATTTG
1 TATCCAATTTG
11035212 AAAACCAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (19 bp):
TATCCAATTTGTAAAGTTG
Found at i:11042999 original size:279 final size:279
Alignment explanation
Indices: 11042499--11043052 Score: 1072
Period size: 279 Copynumber: 2.0 Consensus size: 279
11042489 GGACACGACG
11042499 AGCACTGCTCTTACTTGGTTCACTTGGCTGGTTTCCAAGCATCCAATAGTGGAAACAAGATCATA
1 AGCACTGCTCTTACTTGGTTCACTTGGCTGGTTTCCAAGCATCCAATAGTGGAAACAAGATCATA
11042564 GAAGAACTTGAATCAAAAATACCTATAGGTGAAACCAAATGGAGGCTTCTATTCAATGTCGATGA
66 GAAGAACTTGAATCAAAAATACCTATAGGTGAAACCAAATGGAGGCTTCTATTCAATGTCGATGA
11042629 GGTAAAGAATTTGGTTTATCTCCATGGAGCATTGTGTGAGGCATTAAGGTTGTATCCACCAGTCC
131 GGTAAAGAATTTGGTTTATCTCCATGGAGCATTGTGTGAGGCATTAAGGTTGTATCCACCAGTCC
* * *
11042694 CTTTCAATCATAAGGAACCTGTCAAACCAGACATAGTTCCTAGCGGGCATCTAGTTCATCCAAAG
196 CTTTCAATCATAAGGAACCTGTCAAACCAGACATACTTCCAAGCGGGCATCCAGTTCATCCAAAG
11042759 ACAAAAATCTTGTTTTGTA
261 ACAAAAATCTTGTTTTGTA
11042778 AGCACTGCTCTTACTTGGTTCACTTGGCTGGTTTCCAAGCATCCAATAGTGGAAACAAGATCATA
1 AGCACTGCTCTTACTTGGTTCACTTGGCTGGTTTCCAAGCATCCAATAGTGGAAACAAGATCATA
11042843 GAAGAACTTGAATCAAAAATACCTATAGGTGAAACCAAATGGAGGCTTCTATTCAATGTCGATGA
66 GAAGAACTTGAATCAAAAATACCTATAGGTGAAACCAAATGGAGGCTTCTATTCAATGTCGATGA
11042908 GGTAAAGAATTTGGTTTATCTCCATGGAGCATTGTGTGAGGCATTAAGGTTGTATCCACCAGTCC
131 GGTAAAGAATTTGGTTTATCTCCATGGAGCATTGTGTGAGGCATTAAGGTTGTATCCACCAGTCC
*
11042973 CTTTCAATCATAAGGAACCTGTCAAACCTGACATACTTCCAAGCGGGCATCCAGTTCATCCAAAG
196 CTTTCAATCATAAGGAACCTGTCAAACCAGACATACTTCCAAGCGGGCATCCAGTTCATCCAAAG
11043038 ACAAAAATCTTGTTT
261 ACAAAAATCTTGTTT
11043053 AGTGTGTATT
Statistics
Matches: 271, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
279 271 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (279 bp):
AGCACTGCTCTTACTTGGTTCACTTGGCTGGTTTCCAAGCATCCAATAGTGGAAACAAGATCATA
GAAGAACTTGAATCAAAAATACCTATAGGTGAAACCAAATGGAGGCTTCTATTCAATGTCGATGA
GGTAAAGAATTTGGTTTATCTCCATGGAGCATTGTGTGAGGCATTAAGGTTGTATCCACCAGTCC
CTTTCAATCATAAGGAACCTGTCAAACCAGACATACTTCCAAGCGGGCATCCAGTTCATCCAAAG
ACAAAAATCTTGTTTTGTA
Found at i:11044756 original size:21 final size:22
Alignment explanation
Indices: 11044732--11044775 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
11044722 GTTCAAAATT
11044732 GATTCAACTA-TTAGTTCAACC
1 GATTCAACTACTTAGTTCAACC
* *
11044753 GATTTAATTAGCTTAGTTCAACC
1 GATTCAACTA-CTTAGTTCAACC
11044776 AATCCGTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.36
Consensus pattern (22 bp):
GATTCAACTACTTAGTTCAACC
Found at i:11045634 original size:17 final size:16
Alignment explanation
Indices: 11045604--11045638 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
11045594 TATTATGTGT
*
11045604 TATAAATTAAATAATA
1 TATAAAATAAATAATA
11045620 TATAAAATAACATAATA
1 TATAAAATAA-ATAATA
11045637 TA
1 TA
11045639 AAACATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
TATAAAATAAATAATA
Found at i:11046002 original size:28 final size:29
Alignment explanation
Indices: 11045969--11046041 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 29
11045959 AATTATAGGG
* *
11045969 AATAGATCAAATTA-TCTCTCTATTATTA
1 AATAGATCAAATTAGTCCCTATATTATTA
11045997 AATAGATCAAATTAGTCCCTATATTATTA
1 AATAGATCAAATTAGTCCCTATATTATTA
* *
11046026 AA-AAATCAAATAAGTC
1 AATAGATCAAATTAGTC
11046042 TAAATTATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 26 0.65
29 14 0.35
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (29 bp):
AATAGATCAAATTAGTCCCTATATTATTA
Found at i:11046245 original size:18 final size:21
Alignment explanation
Indices: 11046201--11046245 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 21
11046191 TTTTAAAGAG
11046201 TTGGCCTTAATTGATTCTTTT
1 TTGGCCTTAATTGATTCTTTT
*
11046222 TAGGCC-TAA-TGATT-TTTT
1 TTGGCCTTAATTGATTCTTTT
11046240 TTGGCC
1 TTGGCC
11046246 CTCCAAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 9 0.41
19 5 0.23
20 3 0.14
21 5 0.23
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.51
Consensus pattern (21 bp):
TTGGCCTTAATTGATTCTTTT
Found at i:11046480 original size:29 final size:28
Alignment explanation
Indices: 11046448--11046510 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
11046438 TTTAATTAAT
11046448 TTTTTAAAACTTAAAAAT-ATTTTTTATA
1 TTTTTAAAACTTAAAAATAATTTTTT-TA
***
11046476 CTTTTTAATTTTTAAAAATAATTTTTTTA
1 -TTTTTAAAACTTAAAAATAATTTTTTTA
11046505 TTTTTA
1 TTTTTA
11046511 TAATTTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 6 0.20
29 17 0.57
30 7 0.23
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTTAAAACTTAAAAATAATTTTTTTA
Found at i:11046500 original size:30 final size:30
Alignment explanation
Indices: 11046458--11046529 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
11046448 TTTTTAAAAC
11046458 TTAAAAAT-ATTTTTTATACTTTT-TAATTT
1 TTAAAAATAATTTTTT-TACTTTTATAATTT
*
11046487 TTAAAAATAATTTTTTTATTTTTATAATTT
1 TTAAAAATAATTTTTTTACTTTTATAATTT
11046517 TTAAAAACTAATT
1 TTAAAAA-TAATT
11046530 AAATGTTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 14 0.36
30 20 0.51
31 5 0.13
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (30 bp):
TTAAAAATAATTTTTTTACTTTTATAATTT
Found at i:11046657 original size:24 final size:23
Alignment explanation
Indices: 11046629--11046685 Score: 82
Period size: 21 Copynumber: 2.5 Consensus size: 23
11046619 GATTTGGTAA
11046629 AAAAAATTTAAGAACTAAAAACAAC
1 AAAAAA-TTAA-AACTAAAAACAAC
11046654 AAAAAATT--AACTAAAAACAAC
1 AAAAAATTAAAACTAAAAACAAC
11046675 AAAAAATTAAA
1 AAAAAATTAAA
11046686 TTAAGGACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 21 0.70
23 1 0.03
24 2 0.07
25 6 0.20
ACGTcount: A:0.72, C:0.11, G:0.02, T:0.16
Consensus pattern (23 bp):
AAAAAATTAAAACTAAAAACAAC
Found at i:11046667 original size:21 final size:21
Alignment explanation
Indices: 11046641--11046684 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
11046631 AAAATTTAAG
11046641 AACTAAAAACAACAAAAAATT
1 AACTAAAAACAACAAAAAATT
11046662 AACTAAAAACAACAAAAAATT
1 AACTAAAAACAACAAAAAATT
11046683 AA
1 AA
11046685 ATTAAGGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.73, C:0.14, G:0.00, T:0.14
Consensus pattern (21 bp):
AACTAAAAACAACAAAAAATT
Found at i:11047215 original size:13 final size:13
Alignment explanation
Indices: 11047199--11047226 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
11047189 TAAAACTAAA
11047199 GTTATGTAGATAT
1 GTTATGTAGATAT
11047212 GTTATGTAGATAT
1 GTTATGTAGATAT
11047225 GT
1 GT
11047227 ACTGTTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (13 bp):
GTTATGTAGATAT
Found at i:11052137 original size:9 final size:9
Alignment explanation
Indices: 11052096--11052137 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
11052086 TTTATACAAA
11052096 TAATTTGGT
1 TAATTTGGT
*
11052105 TAATTCGGT
1 TAATTTGGT
* *
11052114 TAATTCGAT
1 TAATTTGGT
11052123 TAATTTGGT
1 TAATTTGGT
11052132 TAATTT
1 TAATTT
11052138 TATACTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.26, C:0.05, G:0.17, T:0.52
Consensus pattern (9 bp):
TAATTTGGT
Found at i:11058271 original size:7 final size:7
Alignment explanation
Indices: 11058229--11058269 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
11058219 ATACTCTTTT
11058229 AAAATTA
1 AAAATTA
11058236 AAAATTA
1 AAAATTA
11058243 AAAATTA
1 AAAATTA
11058250 AAAATTA
1 AAAATTA
*
11058257 AAAATTC
1 AAAATTA
11058264 AAAATT
1 AAAATT
11058270 CAGTCTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAATTA
Found at i:11058560 original size:33 final size:32
Alignment explanation
Indices: 11058498--11058597 Score: 105
Period size: 33 Copynumber: 3.0 Consensus size: 32
11058488 AAATAAGAAC
* * *
11058498 ATAAAAAAT-GAAAATTTTAAATTTTAAAAAA
1 ATAAAAAATAAAAAATTTTAAAATTCAAAAAA
11058529 ATAAAAAATAAAAAATCTTTAAAATTCAAAAAA
1 ATAAAAAATAAAAAAT-TTTAAAATTCAAAAAA
*
11058562 AT-AAAAATAAAAATTATTTTAACAATTTAAACAAA
1 ATAAAAAATAAAAA--ATTTTAA-AATTCAAA-AAA
11058597 A
1 A
11058598 ATTCCAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
31 9 0.15
32 16 0.27
33 21 0.36
34 9 0.15
35 4 0.07
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (32 bp):
ATAAAAAATAAAAAATTTTAAAATTCAAAAAA
Found at i:11058761 original size:30 final size:32
Alignment explanation
Indices: 11058718--11058782 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 32
11058708 TTTTATTTTC
11058718 ATTTTTAAAAAAATTAAAATATTATT-TTTAA
1 ATTTTTAAAAAAATTAAAATATTATTATTTAA
* *
11058749 ATTTTT-AAAAAATTATAATATTTTTATTTAA
1 ATTTTTAAAAAAATTAAAATATTATTATTTAA
11058780 ATT
1 ATT
11058783 ATAAAACAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
ATTTTTAAAAAAATTAAAATATTATTATTTAA
Found at i:11058788 original size:30 final size:30
Alignment explanation
Indices: 11058721--11058793 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
11058711 TATTTTCATT
11058721 TTTA-AAAAAATTAAAATATTATTTTTAAA
1 TTTATAAAAAATTAAAATATTATTTTTAAA
* * *
11058750 TTTTTAAAAAATTATAATATTTTTATTTAAA
1 TTTATAAAAAATTAAAATATTATT-TTTAAA
11058781 -TTATAAAACAATT
1 TTTATAAAA-AATT
11058794 TATTTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 3 0.08
30 24 0.65
31 10 0.27
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (30 bp):
TTTATAAAAAATTAAAATATTATTTTTAAA
Found at i:11058818 original size:18 final size:18
Alignment explanation
Indices: 11058795--11058831 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11058785 AAAACAATTT
* *
11058795 ATTTTTTTTTATTTTTAA
1 ATTTTTATTTAATTTTAA
11058813 ATTTTTATTTAATTTTAA
1 ATTTTTATTTAATTTTAA
11058831 A
1 A
11058832 AGGTAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTTATTTAATTTTAA
Found at i:11059782 original size:29 final size:29
Alignment explanation
Indices: 11059735--11059811 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
11059725 ACATTTAATT
* *
11059735 AATTTTCTAAAA-CTTAAAAAT-GTTTTTA
1 AATTTT-TAAAATTTTAAAAATAATTTTTA
* *
11059763 TACTTTTT-AATTTTTAAAAATAATTTTTA
1 -AATTTTTAAAATTTTAAAAATAATTTTTA
11059792 AATTTTTAAAATTTTAAAAA
1 AATTTTTAAAATTTTAAAAA
11059812 ACTAATTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 2 0.05
28 15 0.38
29 22 0.56
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (29 bp):
AATTTTTAAAATTTTAAAAATAATTTTTA
Found at i:11062629 original size:16 final size:17
Alignment explanation
Indices: 11062604--11062640 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
11062594 TGCTACAAGA
*
11062604 AATATTGTTAATTTT-T
1 AATATAGTTAATTTTAT
11062620 AATATAGTTAATTTTAT
1 AATATAGTTAATTTTAT
11062637 AATA
1 AATA
11062641 GTTAGCTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
AATATAGTTAATTTTAT
Found at i:11065849 original size:15 final size:17
Alignment explanation
Indices: 11065816--11065848 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
11065806 ACAATCATAC
11065816 TTTTGACATAATATATA
1 TTTTGACATAATATATA
11065833 TTTTGACATAATATAT
1 TTTTGACATAATATAT
11065849 TAAGCTCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (17 bp):
TTTTGACATAATATATA
Found at i:11066546 original size:10 final size:11
Alignment explanation
Indices: 11066521--11066550 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
11066511 TTAAAAATAA
11066521 AAAAATATTTT
1 AAAAATATTTT
11066532 AAAAATATTTT
1 AAAAATATTTT
11066543 AAAAATAT
1 AAAAATAT
11066551 AAAAATTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:11067004 original size:14 final size:14
Alignment explanation
Indices: 11066985--11067014 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11066975 TTTTATAATG
*
11066985 TTTAATATTTTATT
1 TTTAATAATTTATT
11066999 TTTAATAATTTATT
1 TTTAATAATTTATT
11067013 TT
1 TT
11067015 CTTTGAGCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTAATAATTTATT
Found at i:11084774 original size:35 final size:35
Alignment explanation
Indices: 11084735--11084805 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
11084725 GCTTTTCTTT
*
11084735 TTTCTTTGCTGAGTTTTTCAACCTTGTGTGCTCTA
1 TTTCTTTGCTGAGTTCTTCAACCTTGTGTGCTCTA
*
11084770 TTTCTTTGCTGAGTTCTTCAGCCTTGTGTGCTCTA
1 TTTCTTTGCTGAGTTCTTCAACCTTGTGTGCTCTA
11084805 T
1 T
11084806 CAACTAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.10, C:0.21, G:0.18, T:0.51
Consensus pattern (35 bp):
TTTCTTTGCTGAGTTCTTCAACCTTGTGTGCTCTA
Found at i:11093752 original size:25 final size:24
Alignment explanation
Indices: 11093713--11093794 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 24
11093703 TGCTCATACA
* *
11093713 AGCTATGAATTGGTATGCTCGCTCG
1 AGCTAT-AATCGGTATGCTCGCACG
* *
11093738 AGCTATAGATCGGTATTCTCTCACG
1 AGCTATA-ATCGGTATGCTCGCACG
* * **
11093763 AGCTGTAATCAGTATGCTCTTACG
1 AGCTATAATCGGTATGCTCGCACG
11093787 AGCTATAA
1 AGCTATAA
11093795 ATCAATATGC
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
24 22 0.47
25 25 0.53
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (24 bp):
AGCTATAATCGGTATGCTCGCACG
Found at i:11093803 original size:25 final size:25
Alignment explanation
Indices: 11093725--11093806 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
11093715 CTATGAATTG
* * * *
11093725 GTATGCTCGCTCGAGCTATAGATCG
1 GTATGCTCTCACGAGCTATAAATCA
* *
11093750 GTATTCTCTCACGAGCTGT-AATCA
1 GTATGCTCTCACGAGCTATAAATCA
*
11093774 GTATGCTCTTACGAGCTATAAATCA
1 GTATGCTCTCACGAGCTATAAATCA
*
11093799 ATATGCTC
1 GTATGCTC
11093807 ACACAAGATA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
24 19 0.41
25 27 0.59
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (25 bp):
GTATGCTCTCACGAGCTATAAATCA
Found at i:11100941 original size:27 final size:26
Alignment explanation
Indices: 11100885--11100941 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
11100875 CAACCTTAAC
* *
11100885 CCTAGGGGTATATCAGTAATTTTACT
1 CCTAGGGGTAAATCAGTAATTTTACA
* *
11100911 CCTAGGGGTAAATCTGTAAATTTTCCA
1 CCTAGGGGTAAATCAGT-AATTTTACA
11100938 CCTA
1 CCTA
11100942 TAAAGGTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (26 bp):
CCTAGGGGTAAATCAGTAATTTTACA
Found at i:11105346 original size:22 final size:22
Alignment explanation
Indices: 11105318--11105361 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
11105308 CAACGAGTTA
*
11105318 AGTAATCTTCCTTTGATTCTTT
1 AGTAATCTTCCTTTCATTCTTT
*
11105340 AGTAATCTTCTTTTCATTCTTT
1 AGTAATCTTCCTTTCATTCTTT
11105362 GAGTTCTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.18, G:0.07, T:0.57
Consensus pattern (22 bp):
AGTAATCTTCCTTTCATTCTTT
Found at i:11107411 original size:20 final size:20
Alignment explanation
Indices: 11107358--11107401 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
11107348 ACAAGATTGT
* *
11107358 ACTTTGGTGACTTTGTTTGC
1 ACTTCGGTGACTCTGTTTGC
11107378 ACTTCGGTGACTCTGTTTGC
1 ACTTCGGTGACTCTGTTTGC
11107398 ACTT
1 ACTT
11107402 GGATGCCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.45
Consensus pattern (20 bp):
ACTTCGGTGACTCTGTTTGC
Found at i:11111197 original size:44 final size:43
Alignment explanation
Indices: 11111052--11111256 Score: 215
Period size: 44 Copynumber: 4.7 Consensus size: 43
11111042 AAAGCTCGTA
*
11111052 CAATGCCAACGTCCCAGACGTGGTCTTACATGT-AATCGAATA-T
1 CAATGCCAACGTCCCAGACGTGGTCTTACACGTAAATC-AA-AGT
** **
11111095 TGATGCC-ACTGTCCCAGACAG-GGTCTTACAC--AAACTCAAAAA
1 CAATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAA-TCAAAGT
11111137 CAATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCATAAGT
1 CAATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCA-AAGT
*
11111181 CAATACCAACGTCCCAGACGTGGTCTTACACGTAAATCATAAGT
1 CAATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCA-AAGT
** * *
11111225 TGATACCAACGTCACAGACGTGGTCTTACACG
1 CAATGCCAACGTCCCAGACGTGGTCTTACACG
11111257 ATAACACATA
Statistics
Matches: 140, Mismatches: 12, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
41 2 0.01
42 30 0.21
43 30 0.21
44 78 0.56
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.22
Consensus pattern (43 bp):
CAATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCAAAGT
Found at i:11112220 original size:2 final size:2
Alignment explanation
Indices: 11112206--11112261 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
11112196 ATTTCTTTCT
*
11112206 TC TC TC T- TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
11112247 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
11112262 TTTACAATAA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:11112981 original size:9 final size:9
Alignment explanation
Indices: 11112957--11112987 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
11112947 TTAATGTGAA
11112957 AAATAAAAT
1 AAATAAAAT
11112966 AAAATAAAAT
1 -AAATAAAAT
11112976 AAATAAAAT
1 AAATAAAAT
11112985 AAA
1 AAA
11112988 GATAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:11113001 original size:6 final size:5
Alignment explanation
Indices: 11112956--11112999 Score: 63
Period size: 5 Copynumber: 8.6 Consensus size: 5
11112946 CTTAATGTGA
11112956 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAAGAT AAAGAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAA-AT AAA
11113000 GAACACACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
4 4 0.11
5 22 0.59
6 11 0.30
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:11118077 original size:12 final size:11
Alignment explanation
Indices: 11118032--11118109 Score: 57
Period size: 12 Copynumber: 6.4 Consensus size: 11
11118022 TAAGTTTAAG
11118032 AAAATAAAAAAA
1 AAAAT-AAAAAA
*
11118044 AAGCAACTAAAACA
1 AA--AA-TAAAAAA
*
11118058 AAATTAAAAAGA
1 AAAATAAAAA-A
*
11118070 AAGATAAATAAA
1 AAAATAAA-AAA
11118082 AAAATAAAATAA
1 AAAATAAAA-AA
11118094 AAAATAAAACAA
1 AAAATAAAA-AA
11118106 AAAA
1 AAAA
11118110 ATAATAAACT
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
11 6 0.11
12 35 0.66
13 2 0.04
14 9 0.17
15 1 0.02
ACGTcount: A:0.79, C:0.05, G:0.04, T:0.12
Consensus pattern (11 bp):
AAAATAAAAAA
Found at i:11118093 original size:13 final size:13
Alignment explanation
Indices: 11118075--11118113 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
11118065 AAAGAAAGAT
11118075 AAATAAAAAAATA
1 AAATAAAAAAATA
11118088 AAAT-AAAAAATA
1 AAATAAAAAAATA
*
11118100 AAACAAAAAAATA
1 AAATAAAAAAATA
11118113 A
1 A
11118114 TAAACTCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.13
Consensus pattern (13 bp):
AAATAAAAAAATA
Found at i:11118100 original size:20 final size:20
Alignment explanation
Indices: 11118075--11118113 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
11118065 AAAGAAAGAT
11118075 AAATAAAA-AAATAAAATAAA
1 AAATAAAACAAA-AAAATAAA
11118095 AAATAAAACAAAAAAATAA
1 AAATAAAACAAAAAAATAA
11118114 TAAACTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.13
Consensus pattern (20 bp):
AAATAAAACAAAAAAATAAA
Found at i:11128975 original size:11 final size:11
Alignment explanation
Indices: 11128952--11128986 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
11128942 ATTGTTTCAT
*
11128952 AAAAA-TATTA
1 AAAAATTATAA
11128962 AAAAATTATAA
1 AAAAATTATAA
11128973 AAAAATTATAA
1 AAAAATTATAA
11128984 AAA
1 AAA
11128987 TTCAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:11129044 original size:29 final size:28
Alignment explanation
Indices: 11128963--11129053 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 28
11128953 AAAATATTAA
* * *
11128963 AAAATTATAAAAAAATTATA-AAAATT-C
1 AAAATTAT-TAAAAATTATATAAACTTAT
* *
11128990 AAAA-TATTAAAATTTATATATACTTATT
1 AAAATTATTAAAAATTATATAAACTTA-T
11129018 AAAATTATTAAAAATTATA-AAAGCTTAT
1 AAAATTATTAAAAATTATATAAA-CTTAT
11129046 AAATATTA
1 AAA-ATTA
11129054 AGGTTAAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
25 9 0.18
26 7 0.14
27 4 0.08
28 10 0.20
29 21 0.41
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (28 bp):
AAAATTATTAAAAATTATATAAACTTAT
Found at i:11129763 original size:18 final size:18
Alignment explanation
Indices: 11129742--11129802 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 18
11129732 AATTTGGAAT
*
11129742 TTTTATAAA-TATTTTGAC
1 TTTTA-AAAGTATTTTGAA
11129760 TTTTAAAAGTTATTTTGAA
1 TTTTAAAAG-TATTTTGAA
11129779 TTTTTGAAAA-TGATTTTGAA
1 -TTTT-AAAAGT-ATTTTGAA
11129799 TTTT
1 TTTT
11129803 TTTTGTAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 3 0.08
18 5 0.14
19 13 0.35
20 12 0.32
21 4 0.11
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.56
Consensus pattern (18 bp):
TTTTAAAAGTATTTTGAA
Found at i:11129794 original size:20 final size:18
Alignment explanation
Indices: 11129733--11129803 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 18
11129723 AAAATATAAA
*
11129733 ATTTGGAATTTTTATAAAT
1 ATTTTGAATTTTTA-AAAT
*
11129752 ATTTTG-ACTTTTAAAAGTT
1 ATTTTGAATTTTTAAAA--T
11129771 ATTTTGAATTTTTGAAAAT
1 ATTTTGAATTTTT-AAAAT
11129790 GATTTTGAATTTTT
1 -ATTTTGAATTTTT
11129804 TTTGTAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
17 3 0.07
18 6 0.14
19 13 0.30
20 18 0.41
21 4 0.09
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.55
Consensus pattern (18 bp):
ATTTTGAATTTTTAAAAT
Found at i:11130904 original size:29 final size:30
Alignment explanation
Indices: 11130872--11130932 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
11130862 TTTAAATATC
11130872 TTTTTATTAAT-TTTAT-AATTTAT-TAGAT
1 TTTTTA-TAATATTTATAAATTTATATAGAT
*
11130900 TTTTTATAATATTTATAAATTTATATATAT
1 TTTTTATAATATTTATAAATTTATATAGAT
11130930 TTT
1 TTT
11130933 AATATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 4 0.14
28 11 0.38
29 7 0.24
30 7 0.24
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (30 bp):
TTTTTATAATATTTATAAATTTATATAGAT
Found at i:11130942 original size:40 final size:37
Alignment explanation
Indices: 11130874--11130948 Score: 96
Period size: 40 Copynumber: 1.9 Consensus size: 37
11130864 TAAATATCTT
* *
11130874 TTTATTAATTTTATAATTTATTAGATTTTTTATAATA
1 TTTATAAATTTTATAATTTAATAGATTTTTTATAATA
*
11130911 TTTATAAATTTATATATATTTTAATATATTTTTTATAA
1 TTTATAAATTT-TATA-A-TTTAATAGATTTTTTATAA
11130949 AAAAAATTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 10 0.31
38 4 0.12
39 1 0.03
40 17 0.53
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (37 bp):
TTTATAAATTTTATAATTTAATAGATTTTTTATAATA
Found at i:11132168 original size:56 final size:56
Alignment explanation
Indices: 11132108--11132221 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
11132098 GGTCGATGAG
* *
11132108 ATAAATTTAATTTTGGATTTGTTCGGTTCAGTTTATATTATTATTTATTAAAATCT
1 ATAAATTTAACTTTGGATTTGTTCGGTTCAGTTTATATTATTATTTATTAAAACCT
11132164 ATAAATTTAACTTTGGATTTGTTCGGTTCAGTTTATATTATTATTTATTAAAACCT
1 ATAAATTTAACTTTGGATTTGTTCGGTTCAGTTTATATTATTATTTATTAAAACCT
11132220 AT
1 AT
11132222 TTTTATTTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.52
Consensus pattern (56 bp):
ATAAATTTAACTTTGGATTTGTTCGGTTCAGTTTATATTATTATTTATTAAAACCT
Found at i:11134415 original size:8 final size:8
Alignment explanation
Indices: 11134399--11134444 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
11134389 AAACATTCCC
*
11134399 TTTTCTCT
1 TTTTTTCT
11134407 TTTTTTCT
1 TTTTTTCT
*
11134415 TTCTTTCT
1 TTTTTTCT
*
11134423 TTCTTTCT
1 TTTTTTCT
11134431 TTTCTTTCT
1 TTT-TTTCT
11134440 TTTTT
1 TTTTT
11134445 ATTGAAAGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
8 26 0.76
9 8 0.24
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTCT
Found at i:11134419 original size:4 final size:4
Alignment explanation
Indices: 11134404--11134441 Score: 58
Period size: 4 Copynumber: 9.2 Consensus size: 4
11134394 TTCCCTTTTC
*
11134404 TCTT TTTT TCTT TCTT TCTT TCTT TCTTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TC-TT TCTT TCTT T
11134442 TTTATTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TCTT
Found at i:11135055 original size:23 final size:24
Alignment explanation
Indices: 11135015--11135069 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
11135005 AAATACTGAC
11135015 AAAT-AAAACCAAGCCCAA-AACAA
1 AAATCAAAACCAAGCCCAAGAA-AA
11135038 AAATCAAAACCAAG-CCAAGAAAA
1 AAATCAAAACCAAGCCCAAGAAAA
*
11135061 AAACCAAAA
1 AAATCAAAA
11135070 AATTGAAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.67, C:0.24, G:0.05, T:0.04
Consensus pattern (24 bp):
AAATCAAAACCAAGCCCAAGAAAA
Found at i:11136901 original size:14 final size:14
Alignment explanation
Indices: 11136882--11136948 Score: 71
Period size: 14 Copynumber: 4.7 Consensus size: 14
11136872 GTTTGCAGGT
*
11136882 AAAATGTTTTCCGG
1 AAAATGATTTCCGG
*
11136896 AAAATGATTTCTGG
1 AAAATGATTTCCGG
* *
11136910 AAAATAATTTCTTGG
1 AAAATGATTTC-CGG
* *
11136925 AAAATAATTTCTGG
1 AAAATGATTTCCGG
11136939 AAAATGATTT
1 AAAATGATTT
11136949 ACTTTTCTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
14 34 0.71
15 14 0.29
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCCGG
Found at i:11136927 original size:15 final size:14
Alignment explanation
Indices: 11136889--11136948 Score: 84
Period size: 14 Copynumber: 4.2 Consensus size: 14
11136879 GGTAAAATGT
* *
11136889 TTTCCGGAAAATGA
1 TTTCTGGAAAATAA
11136903 TTTCTGGAAAATAA
1 TTTCTGGAAAATAA
11136917 TTTCTTGGAAAATAA
1 TTTC-TGGAAAATAA
*
11136932 TTTCTGGAAAATGA
1 TTTCTGGAAAATAA
11136946 TTT
1 TTT
11136949 ACTTTTCTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
14 28 0.67
15 14 0.33
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (14 bp):
TTTCTGGAAAATAA
Found at i:11141441 original size:18 final size:18
Alignment explanation
Indices: 11141418--11141457 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
11141408 GTTGAATTTT
11141418 ATAATTTGAATAAG-TCAA
1 ATAATTTGAAT-AGTTCAA
11141436 ATAATTTGAATAGTTCAA
1 ATAATTTGAATAGTTCAA
11141454 ATAA
1 ATAA
11141458 CGAATTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (18 bp):
ATAATTTGAATAGTTCAA
Found at i:11141614 original size:20 final size:19
Alignment explanation
Indices: 11141539--11141605 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
11141529 CTTACAAAAT
* *
11141539 AATTCGAAATAATTTTTAAA
1 AATTCAAAATAAATTTT-AA
11141559 AATTCAAAATAAATTTTAA
1 AATTCAAAATAAATTTTAA
11141578 AATTCAAAATAAATTTTAA
1 AATTCAAAATAAATTTTAA
11141597 AATTCAAAA
1 AATTCAAAA
11141606 AATTATTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 30 0.67
20 15 0.33
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.36
Consensus pattern (19 bp):
AATTCAAAATAAATTTTAA
Found at i:11142477 original size:21 final size:20
Alignment explanation
Indices: 11142453--11142499 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
11142443 GAACAATTTC
*
11142453 ATTTGA-TTCGACTTGACTTG
1 ATTTGATTTC-ACTTGACTAG
*
11142473 AATTTTATTTCACTTGACTAG
1 -ATTTGATTTCACTTGACTAG
11142494 ATTTGA
1 ATTTGA
11142500 AAAAATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.23
21 14 0.64
22 3 0.14
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.47
Consensus pattern (20 bp):
ATTTGATTTCACTTGACTAG
Found at i:11147491 original size:49 final size:50
Alignment explanation
Indices: 11147425--11147570 Score: 170
Period size: 51 Copynumber: 2.9 Consensus size: 50
11147415 TAGCCAAAGC
* * * * *
11147425 TATCTGGTACGCATAGTAGCCTACACATAGTACTACCCATGCGACCAA-T
1 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAGT
* * * * *
11147474 TATTC-GGTACACGTAGTAGCCTGCACTTAGTACTGCACACGTGATCGAAGT
1 TA-TCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAAGT
11147525 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACC
11147571 TCACAATAGA
Statistics
Matches: 79, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
49 33 0.42
50 8 0.10
51 38 0.48
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (50 bp):
TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAGT
Found at i:11148178 original size:84 final size:84
Alignment explanation
Indices: 11148037--11148204 Score: 318
Period size: 84 Copynumber: 2.0 Consensus size: 84
11148027 CCAGAAACGG
* *
11148037 CAATTTACCATTTTAGTCCATAATCTTGTATTTTCCCGATTTAAGCCCGAATCTCGATTTTCTTC
1 CAATTTACCATTTTAGTCCATAACCTTGTATTTTCCCGATTTAAGCCCGAATCTCGATTTCCTTC
11148102 ATCTATAATATCACATTTA
66 ATCTATAATATCACATTTA
11148121 CAATTTACCATTTTAGTCCATAACCTTGTATTTTCCCGATTTAAGCCCGAATCTCGATTTCCTTC
1 CAATTTACCATTTTAGTCCATAACCTTGTATTTTCCCGATTTAAGCCCGAATCTCGATTTCCTTC
11148186 ATCTATAATATCACATTTA
66 ATCTATAATATCACATTTA
11148205 GCCTAATAAT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.42
Consensus pattern (84 bp):
CAATTTACCATTTTAGTCCATAACCTTGTATTTTCCCGATTTAAGCCCGAATCTCGATTTCCTTC
ATCTATAATATCACATTTA
Found at i:11149088 original size:20 final size:21
Alignment explanation
Indices: 11149056--11149096 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
11149046 TTCAGGTTTA
11149056 AAATGTTTATTTA-TTTATTT
1 AAATGTTTATTTATTTTATTT
11149076 AAAT-TTTATTTTATTTTATTT
1 AAATGTTTA-TTTATTTTATTT
11149097 TTATTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 8 0.42
21 7 0.37
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
AAATGTTTATTTATTTTATTT
Found at i:11149090 original size:16 final size:16
Alignment explanation
Indices: 11149065--11149102 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
11149055 AAAATGTTTA
11149065 TTTA-TTTATTTAAAT
1 TTTATTTTATTTAAAT
* *
11149080 TTTATTTTATTTTATT
1 TTTATTTTATTTAAAT
11149096 TTTATTT
1 TTTATTT
11149103 CAAAACCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTTTATTTAAAT
Found at i:11155506 original size:23 final size:23
Alignment explanation
Indices: 11155476--11155562 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
11155466 GCTTTACTGA
* * *
11155476 TCAGGCACTTTATATGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
11155499 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
11155520 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
11155542 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
11155563 ACTGATCAGG
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
21 35 0.65
22 2 0.04
23 17 0.31
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:11157274 original size:15 final size:15
Alignment explanation
Indices: 11157254--11157288 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
11157244 CCTAGAGATG
11157254 AAAACTTTATTAATA
1 AAAACTTTATTAATA
11157269 AAAACTTTATTAATA
1 AAAACTTTATTAATA
11157284 AAAAC
1 AAAAC
11157289 AATTGTCTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAACTTTATTAATA
Found at i:11166248 original size:16 final size:17
Alignment explanation
Indices: 11166217--11166249 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11166207 TTCATAAGTA
11166217 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
11166234 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
11166250 GCTCTATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:11170231 original size:46 final size:47
Alignment explanation
Indices: 11170169--11170301 Score: 155
Period size: 46 Copynumber: 2.9 Consensus size: 47
11170159 TTTGACATGA
* * * **
11170169 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATGTCACAT
* ** *
11170215 TGCTATGGTATCTTTCAACCATGGTCTTGTTCA-TTTCATGTTACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATGTCACAT
*
11170261 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTT-ATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATGT
11170302 AACACCTCAA
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
45 4 0.06
46 65 0.90
47 3 0.04
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.44
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATGTCACAT
Found at i:11172625 original size:46 final size:46
Alignment explanation
Indices: 11172562--11172711 Score: 282
Period size: 46 Copynumber: 3.3 Consensus size: 46
11172552 TCGGAGCGTT
* *
11172562 ACATTTTATATCCTGTTGCCATGGTATCTTTCAACCATGGTCTTAC
1 ACATTTCATATCTTGTTGCCATGGTATCTTTCAACCATGGTCTTAC
11172608 ACATTTCATATCTTGTTGCCATGGTATCTTTCAACCATGGTCTTAC
1 ACATTTCATATCTTGTTGCCATGGTATCTTTCAACCATGGTCTTAC
11172654 ACATTTCATATCTTGTTGCCATGGTATCTTTCAACCATGGTCTTAC
1 ACATTTCATATCTTGTTGCCATGGTATCTTTCAACCATGGTCTTAC
11172700 ACATTTCATATC
1 ACATTTCATATC
11172712 AGAGAGCACA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 102 1.00
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (46 bp):
ACATTTCATATCTTGTTGCCATGGTATCTTTCAACCATGGTCTTAC
Found at i:11176376 original size:12 final size:12
Alignment explanation
Indices: 11176359--11176384 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11176349 ATGACTTGAT
11176359 TTCGCTTAATTA
1 TTCGCTTAATTA
11176371 TTCGCTTAATTA
1 TTCGCTTAATTA
11176383 TT
1 TT
11176385 TGAGAAAAAT
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:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (12 bp):
TTCGCTTAATTA
Found at i:11181004 original size:37 final size:37
Alignment explanation
Indices: 11180949--11181038 Score: 126
Period size: 37 Copynumber: 2.4 Consensus size: 37
11180939 TTCTGATCAG
* *
11180949 TGACAAGTGATAAGTGGTAGCCTCAGCTATACTTATC
1 TGACCAGTGATAAGTGGTAGCCTCAGCTACACTTATC
* *
11180986 TGACCAGTGATAAGTGGTAGCTTTAGCTACACTTATC
1 TGACCAGTGATAAGTGGTAGCCTCAGCTACACTTATC
* *
11181023 TGATCAGTGACAAGTG
1 TGACCAGTGATAAGTG
11181039 ATAAGTGATA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (37 bp):
TGACCAGTGATAAGTGGTAGCCTCAGCTACACTTATC
Found at i:11181070 original size:51 final size:51
Alignment explanation
Indices: 11180991--11181093 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
11180981 TTATCTGACC
11180991 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGATA
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGATA
*
11181042 AGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCAGTGACAAGTGATA
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGATA
11181093 A
1 A
11181094 ATGTGATCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (51 bp):
AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGATA
Found at i:11190297 original size:21 final size:22
Alignment explanation
Indices: 11190273--11190315 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
11190263 GTGTCAGAAC
* *
11190273 TGTTTTAAT-AATTTTTATTTT
1 TGTTTAAATAAATTATTATTTT
11190294 TGTTTAAATAAATTATTATTTT
1 TGTTTAAATAAATTATTATTTT
11190316 GAAATCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (22 bp):
TGTTTAAATAAATTATTATTTT
Found at i:11192151 original size:43 final size:43
Alignment explanation
Indices: 11192099--11192182 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
11192089 GATAAGATAT
** * *
11192099 TCAATCTTTAGTCTGCTTTCTTGCTACCTCAGAA-AGATAAGAC
1 TCAATCTTTAACCTGCTCTCTTACTACCTCA-AAGAGATAAGAC
11192142 TCAATCTTTAACCTGCTCTCTTACTACCTCAAAGAGATAAG
1 TCAATCTTTAACCTGCTCTCTTACTACCTCAAAGAGATAAG
11192183 GCTTGAGGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 2 0.06
43 34 0.94
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (43 bp):
TCAATCTTTAACCTGCTCTCTTACTACCTCAAAGAGATAAGAC
Found at i:11192157 original size:177 final size:177
Alignment explanation
Indices: 11191830--11192229 Score: 507
Period size: 177 Copynumber: 2.3 Consensus size: 177
11191820 GGAAATAGGA
* * ** *
11191830 CTAGTGACTTAAATCTGCTCCATTGCCAATACATGGAGATAAGATTTGCCATCCTCAATCTGCTC
1 CTAGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCCTCAATCTACTC
* * * *
11191895 CACAACTACTTTAGGGAAATAGATCTTCAATCTTCAGTCTACTTCCTTTCTACCTCAGGAAGATA
66 CACAACCACTTTAGGGAAATAGATATTCAATCTTCAGTCTACTTCCTTGCTACCTCAGAAAGATA
* * *
11191960 AGACTAAAATCGCCAACCTGCTCTCTTGCTACTTCAGAGAGATAAGG
131 AGACTAAAATCGCCAACCTGCTCTCTTACTACCTCAAAGAGATAAGG
* * * *
11192007 CTAGTGGCTAAAATCTGCTCCATTGCCGGTACATGGAGATAAGATTCACCATCTTCGATCTACTC
1 CTAGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCCTCAATCTACTC
* * * * * *
11192072 CACTACCGC-TTAGGGGAGATAAGATATTCAATCTTTAGTCTGCTTTCTTGCTACCTCAGAAAGA
66 CACAACCACTTTA-GGGAAAT-AGATATTCAATCTTCAGTCTACTTCCTTGCTACCTCAGAAAGA
* ***
11192136 TAAGACT-CAATCTTTAACCTGCTCTCTTACTACCTCAAAGAGATAAGG
129 TAAGACTAAAATCGCCAACCTGCTCTCTTACTACCTCAAAGAGATAAGG
* * *
11192184 CTTGAGGCTTAAATCTGCTCCATTGTCGATACATGGAGATAAGATT
1 CTAGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATT
11192230 TGCCTCTTCC
Statistics
Matches: 190, Mismatches: 31, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
176 3 0.02
177 143 0.75
178 44 0.23
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (177 bp):
CTAGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCCTCAATCTACTC
CACAACCACTTTAGGGAAATAGATATTCAATCTTCAGTCTACTTCCTTGCTACCTCAGAAAGATA
AGACTAAAATCGCCAACCTGCTCTCTTACTACCTCAAAGAGATAAGG
Found at i:11192364 original size:147 final size:141
Alignment explanation
Indices: 11192097--11192490 Score: 541
Period size: 147 Copynumber: 2.8 Consensus size: 141
11192087 GAGATAAGAT
* * *
11192097 ATTCAATCTTTAGTCTGCTTTCTTGCTACCTCAGAAAGATAAGAC-TCAATCTTTAACCTGCTCT
1 ATTCAATC-TTAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTCAATCTTCAACCTGCTCT
* * **
11192161 CTTACTACCTCAAAGAGATAAGGCTTGAGGCTTAAATCTGCTCCATTGTCGATACATGGAGATAA
65 CTTGCTACCTCAGAGAGATAAGGCTTGAGGCTTAAATCTGCTCCATTACCGATACATGGAGATAA
11192226 GATTTGCCTCTTCCA
130 GATTTG-C-C-TCCA
* * *
11192241 ATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTCAATATTGAACCAGCT
1 A--TTCAATCTT-AGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTCAATCTTCAACCTGCT
*
11192306 TTCTTGCTACCTCAGAGAGATAAGGCTTGAGGCTTAAATCTGCTCCATTACCGATACATGGAGAT
63 CTCTTGCTACCTCAGAGAGATAAGGCTTGAGGCTTAAATCTGCTCCATTACCGATACATGGAGAT
11192371 AAGATTTGCCTCCA
128 AAGATTTGCCTCCA
11192385 A-TC--T-TTAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTCAATCTTCAACCTGCTCTC
1 ATTCAATCTTAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTCAATCTTCAACCTGCTCTC
* * *
11192446 TTGCTACCTTAGAGAGATAAGGC-TGATGG-TAAAATCTGCTTCATT
66 TTGCTACCTCAGAGAGATAAGGCTTGA-GGCTTAAATCTGCTCCATT
11192491 GTCGATACTA
Statistics
Matches: 228, Mismatches: 17, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
136 17 0.07
137 75 0.33
138 2 0.01
139 1 0.00
141 2 0.01
144 6 0.03
145 3 0.01
146 40 0.18
147 82 0.36
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (141 bp):
ATTCAATCTTAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTCAATCTTCAACCTGCTCTC
TTGCTACCTCAGAGAGATAAGGCTTGAGGCTTAAATCTGCTCCATTACCGATACATGGAGATAAG
ATTTGCCTCCA
Found at i:11192442 original size:44 final size:44
Alignment explanation
Indices: 11192243--11192454 Score: 139
Period size: 44 Copynumber: 4.7 Consensus size: 44
11192233 CTCTTCCAAT
*
11192243 CTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGA
1 CTTCAATCTTCAATCTGCTTCCTTGCTACCTCAGGAAGATAAGA
* * * * * *
11192287 CTTCAATATTGAACCAGCTTTCTTGCTACCTCA-GAGAGATAAGG
1 CTTCAATCTTCAATCTGCTTCCTTGCTACCTCAGGA-AGATAAGA
* ** * *
11192331 CTTGAGGCTTAAATCTGC-TCCAT--TACCGATACATGG-AGATAAGA
1 CTTCAATCTTCAATCTGCTTCCTTGCTACC--T-CA-GGAAGATAAGA
* * *
11192375 TTTGCCTCCAATCTTTAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGA
1 -----CTTCAATCTTCAATCTGCTTCCTTGCTACCTCAGGAAGATAAGA
*
11192424 CTTCAATCTTCAACCTGC-TCTCTTGCTACCT
1 CTTCAATCTTCAATCTGCTTC-CTTGCTACCT
11192455 TAGAGAGATA
Statistics
Matches: 124, Mismatches: 28, Indels: 32
0.67 0.15 0.17
Matches are distributed among these distances:
41 4 0.03
43 8 0.06
44 78 0.63
46 1 0.01
48 2 0.02
49 22 0.18
50 5 0.04
52 4 0.03
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.32
Consensus pattern (44 bp):
CTTCAATCTTCAATCTGCTTCCTTGCTACCTCAGGAAGATAAGA
Found at i:11194551 original size:30 final size:30
Alignment explanation
Indices: 11194506--11194565 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
11194496 ATTTAATACG
*
11194506 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* *
11194536 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
11194566 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:11199763 original size:45 final size:45
Alignment explanation
Indices: 11199668--11199835 Score: 165
Period size: 45 Copynumber: 3.7 Consensus size: 45
11199658 CAATTCGCAA
* * * * * **
11199668 CTATGAATCTTCTTTTTATAAATTTGCATGTATGAGCCCTTCATGG
1 CTATGAATCTTC-TTCTATGAATTTGCATGTATAAGTCCGTCATAT
* *
11199714 CTATGAATCTTCTTCTATGAATTTGCATGTATTATTCCGTCATAT
1 CTATGAATCTTCTTCTATGAATTTGCATGTATAAGTCCGTCATAT
* *** *
11199759 CTATGAAGCTTCTTCTATGAATTCATATGTATAAGTCCGCCATAT
1 CTATGAATCTTCTTCTATGAATTTGCATGTATAAGTCCGTCATAT
* * * *
11199804 CTATGAATCTTCTTATACGATTTTGAATGTAT
1 CTATGAATCTTCTTCTATGAATTTGCATGTAT
11199836 GAGTTCGCAT
Statistics
Matches: 100, Mismatches: 22, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
45 88 0.88
46 12 0.12
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (45 bp):
CTATGAATCTTCTTCTATGAATTTGCATGTATAAGTCCGTCATAT
Found at i:11202953 original size:15 final size:15
Alignment explanation
Indices: 11202933--11202966 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
11202923 GACATTATGA
*
11202933 ATTTCTGGTGATGTC
1 ATTTCTGGTAATGTC
*
11202948 ATTTCTTGTAATGTC
1 ATTTCTGGTAATGTC
11202963 ATTT
1 ATTT
11202967 GGATTAACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.53
Consensus pattern (15 bp):
ATTTCTGGTAATGTC
Found at i:11206770 original size:45 final size:45
Alignment explanation
Indices: 11206710--11206810 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 45
11206700 CACAGTTCAC
* * * * * *
11206710 ATCTATAAATATTCTTTTATAAATCTGCATGTATGAGTATATCAT
1 ATCTATGAATCTTCTTCTAAAAATCTGCATGTATAAGTATACCAT
* * *
11206755 ATCTATGAATCTTCTTCTAAAAATTTGCATGTATAAGTCTGCCAT
1 ATCTATGAATCTTCTTCTAAAAATCTGCATGTATAAGTATACCAT
11206800 ATCTATGAATC
1 ATCTATGAATC
11206811 CGTATGTATG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.42
Consensus pattern (45 bp):
ATCTATGAATCTTCTTCTAAAAATCTGCATGTATAAGTATACCAT
Found at i:11206819 original size:31 final size:31
Alignment explanation
Indices: 11206783--11206841 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
11206773 AAAAATTTGC
*
11206783 ATGTATAAGTCTGCCATATCTATGAATCCGT
1 ATGTATAAGTCTGCCATATCTATAAATCCGT
* *
11206814 ATGTATGAGTCTGTCATATCTATAAATC
1 ATGTATAAGTCTGCCATATCTATAAATC
11206842 TTCTTTTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (31 bp):
ATGTATAAGTCTGCCATATCTATAAATCCGT
Found at i:11206844 original size:76 final size:76
Alignment explanation
Indices: 11206738--11206886 Score: 192
Period size: 76 Copynumber: 2.0 Consensus size: 76
11206728 ATAAATCTGC
* * *
11206738 ATGTATGAGTATATCATATCTATGAATCTTCTTCTAAAAATTTGCATGTATAAGT-CTGCCATAT
1 ATGTATGAGTATATCATATCTATAAATCTTCTTCTAAAAATTTGCATGTATAACTCCT-ACATAT
11206802 CTATGAATCCGT
65 CTATGAATCCGT
* * * ** * *
11206814 ATGTATGAGTCTGTCATATCTATAAATCTTCTTTTATGAATTTGCCTGTATGACTCCTACATATC
1 ATGTATGAGTATATCATATCTATAAATCTTCTTCTAAAAATTTGCATGTATAACTCCTACATATC
11206879 TATGAATC
66 TATGAATC
11206887 TTCTTCTACA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
76 60 0.97
77 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (76 bp):
ATGTATGAGTATATCATATCTATAAATCTTCTTCTAAAAATTTGCATGTATAACTCCTACATATC
TATGAATCCGT
Found at i:11209623 original size:27 final size:27
Alignment explanation
Indices: 11209585--11209637 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
11209575 TTGTGGCATG
11209585 TATATAGGTGCCTTAAATGTATAAAAT
1 TATATAGGTGCCTTAAATGTATAAAAT
11209612 TATATAGGTGCCTTAAATGTATAAAA
1 TATATAGGTGCCTTAAATGTATAAAA
11209638 GTGTTTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.36
Consensus pattern (27 bp):
TATATAGGTGCCTTAAATGTATAAAAT
Found at i:11209811 original size:21 final size:20
Alignment explanation
Indices: 11209782--11209824 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
11209772 TATAAATGAC
11209782 ATTTGACAAAGAATTGAACTG
1 ATTTGACAAAGAATTGAA-TG
* * *
11209803 ATTTTACAATGACTTGAATG
1 ATTTGACAAAGAATTGAATG
11209823 AT
1 AT
11209825 GGCCTTGGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (20 bp):
ATTTGACAAAGAATTGAATG
Found at i:11215983 original size:39 final size:39
Alignment explanation
Indices: 11215929--11216007 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
11215919 CCAACAATAA
*
11215929 TAACGAATAAGAAGAAATAACTCCCAACACCTACGTGCT
1 TAACGAATAAGAAGAAATAACTCCCAAAACCTACGTGCT
11215968 TAACGAATAAGAAGAAATAACTCCCAAAACCTACGTGCT
1 TAACGAATAAGAAGAAATAACTCCCAAAACCTACGTGCT
11216007 T
1 T
11216008 CACATTCAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.24, G:0.13, T:0.19
Consensus pattern (39 bp):
TAACGAATAAGAAGAAATAACTCCCAAAACCTACGTGCT
Found at i:11220051 original size:16 final size:15
Alignment explanation
Indices: 11219987--11220052 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 15
11219977 AAAAAATAGT
11219987 AGAAGAAGAAAATGAGG
1 AGAAGAAGAAAA--AGG
* * * * *
11220004 AGGAGGAGGAAGAGA
1 AGAAGAAGAAAAAGG
11220019 AGAAGAAGAAAAAGG
1 AGAAGAAGAAAAAGG
*
11220034 AGAAGAGGAAAAATGG
1 AGAAGAAGAAAAA-GG
11220050 AGA
1 AGA
11220053 TGCCTGAAGT
Statistics
Matches: 37, Mismatches: 11, Indels: 3
0.73 0.22 0.06
Matches are distributed among these distances:
15 24 0.65
16 5 0.14
17 8 0.22
ACGTcount: A:0.58, C:0.00, G:0.39, T:0.03
Consensus pattern (15 bp):
AGAAGAAGAAAAAGG
Found at i:11221344 original size:21 final size:21
Alignment explanation
Indices: 11221317--11221366 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
11221307 GCAGCTTGTT
11221317 GAGTTGGGGTACCCTCTTGCC
1 GAGTTGGGGTACCCTCTTGCC
* * * *
11221338 GATTTGGGGTAGCCTGTTGCT
1 GAGTTGGGGTACCCTCTTGCC
11221359 GAGTTGGG
1 GAGTTGGG
11221367 ACACCAACTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.18, G:0.40, T:0.32
Consensus pattern (21 bp):
GAGTTGGGGTACCCTCTTGCC
Found at i:11239017 original size:175 final size:175
Alignment explanation
Indices: 11238726--11239077 Score: 704
Period size: 175 Copynumber: 2.0 Consensus size: 175
11238716 TATGGAGGAG
11238726 ATGTCACTGAATAACTATCAATGGCAAGTCATGAGGACAAAGCCAACGAAAATAGCAGGCATTTA
1 ATGTCACTGAATAACTATCAATGGCAAGTCATGAGGACAAAGCCAACGAAAATAGCAGGCATTTA
11238791 TAACGTCGATTCGGTCACTATGCTCTCTAATCAGGTAGAACTCTTGAATAAAAAGATTGATGGTT
66 TAACGTCGATTCGGTCACTATGCTCTCTAATCAGGTAGAACTCTTGAATAAAAAGATTGATGGTT
11238856 TTCTTAGTTCTTCACAGGTTCACCAAGTAATGCAATGCGAAGTAA
131 TTCTTAGTTCTTCACAGGTTCACCAAGTAATGCAATGCGAAGTAA
11238901 ATGTCACTGAATAACTATCAATGGCAAGTCATGAGGACAAAGCCAACGAAAATAGCAGGCATTTA
1 ATGTCACTGAATAACTATCAATGGCAAGTCATGAGGACAAAGCCAACGAAAATAGCAGGCATTTA
11238966 TAACGTCGATTCGGTCACTATGCTCTCTAATCAGGTAGAACTCTTGAATAAAAAGATTGATGGTT
66 TAACGTCGATTCGGTCACTATGCTCTCTAATCAGGTAGAACTCTTGAATAAAAAGATTGATGGTT
11239031 TTCTTAGTTCTTCACAGGTTCACCAAGTAATGCAATGCGAAGTAA
131 TTCTTAGTTCTTCACAGGTTCACCAAGTAATGCAATGCGAAGTAA
11239076 AT
1 AT
11239078 AGCGGTGGAA
Statistics
Matches: 177, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 177 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (175 bp):
ATGTCACTGAATAACTATCAATGGCAAGTCATGAGGACAAAGCCAACGAAAATAGCAGGCATTTA
TAACGTCGATTCGGTCACTATGCTCTCTAATCAGGTAGAACTCTTGAATAAAAAGATTGATGGTT
TTCTTAGTTCTTCACAGGTTCACCAAGTAATGCAATGCGAAGTAA
Found at i:11243398 original size:17 final size:17
Alignment explanation
Indices: 11243376--11243410 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
11243366 ATTTAGGATA
*
11243376 AATTTTAATTGATTTAT
1 AATTTTAATTGATATAT
*
11243393 AATTTTGATTGATATAT
1 AATTTTAATTGATATAT
11243410 A
1 A
11243411 TTGAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (17 bp):
AATTTTAATTGATATAT
Found at i:11246557 original size:40 final size:40
Alignment explanation
Indices: 11246512--11246611 Score: 164
Period size: 40 Copynumber: 2.5 Consensus size: 40
11246502 AACGCGATCG
11246512 CACTGCATGCATATTAAAAAATAGGCAACACACCAACAAT
1 CACTGCATGCATATTAAAAAATAGGCAACACACCAACAAT
* **
11246552 CACTGCATGCATATTCAAAAATATTCAACACACCAACAAT
1 CACTGCATGCATATTAAAAAATAGGCAACACACCAACAAT
*
11246592 CAATGCATGCATATTAAAAA
1 CACTGCATGCATATTAAAAA
11246612 GCATTCACTA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.47, C:0.24, G:0.08, T:0.21
Consensus pattern (40 bp):
CACTGCATGCATATTAAAAAATAGGCAACACACCAACAAT
Found at i:11246673 original size:17 final size:18
Alignment explanation
Indices: 11246651--11246690 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
11246641 ATATGAAGTT
11246651 AGAATATAGGCATCAG-A
1 AGAATATAGGCATCAGAA
11246668 AGAATATAGGCATCAGAA
1 AGAATATAGGCATCAGAA
11246686 AGAAT
1 AGAAT
11246691 CTTTACCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.50, C:0.10, G:0.23, T:0.17
Consensus pattern (18 bp):
AGAATATAGGCATCAGAA
Found at i:11248298 original size:15 final size:15
Alignment explanation
Indices: 11248278--11248306 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11248268 ATGCATCACT
11248278 ATCACTACCAGACAC
1 ATCACTACCAGACAC
11248293 ATCACTACCAGACA
1 ATCACTACCAGACA
11248307 TGTTTTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.38, G:0.07, T:0.14
Consensus pattern (15 bp):
ATCACTACCAGACAC
Found at i:11248683 original size:64 final size:64
Alignment explanation
Indices: 11248614--11248819 Score: 367
Period size: 64 Copynumber: 3.2 Consensus size: 64
11248604 TAGGTGCTTG
*
11248614 GATACAAAAAATAACAGATATACACAATAAACATCAGTTTGATAATGGCATTCATACAATGGCA
1 GATACAAATAATAACAGATATACACAATAAACATCAGTTTGATAATGGCATTCATACAATGGCA
*
11248678 GATACAAATAATTACAGATATACACAATAAACATCAGTTTGATAATGGCATTCATACAATGGCA
1 GATACAAATAATAACAGATATACACAATAAACATCAGTTTGATAATGGCATTCATACAATGGCA
**
11248742 GATACAAATAATGGCAGATATACACAATAAACATCAGTTTGATAATGGCATTCATACAATGGCA
1 GATACAAATAATAACAGATATACACAATAAACATCAGTTTGATAATGGCATTCATACAATGGCA
*
11248806 GATACAAACAATAA
1 GATACAAATAATAA
11248820 ACATCATGCA
Statistics
Matches: 135, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 135 1.00
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (64 bp):
GATACAAATAATAACAGATATACACAATAAACATCAGTTTGATAATGGCATTCATACAATGGCA
Found at i:11248735 original size:34 final size:34
Alignment explanation
Indices: 11248697--11248799 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 34
11248687 AATTACAGAT
11248697 ATACACAATAAACATCAGTTTGATAATGGCATTC
1 ATACACAATAAACATCAGTTTGATAATGGCATTC
** * * *
11248731 AT--ACAATGGCAGATACA----AATAATGGCAGAT-
1 ATACACAAT-AAACAT-CAGTTTGATAATGGCA-TTC
11248761 ATACACAATAAACATCAGTTTGATAATGGCATTC
1 ATACACAATAAACATCAGTTTGATAATGGCATTC
11248795 ATACA
1 ATACA
11248800 ATGGCAGATA
Statistics
Matches: 49, Mismatches: 10, Indels: 20
0.62 0.13 0.25
Matches are distributed among these distances:
30 13 0.27
31 4 0.08
32 10 0.20
33 4 0.08
34 18 0.37
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.26
Consensus pattern (34 bp):
ATACACAATAAACATCAGTTTGATAATGGCATTC
Found at i:11248981 original size:18 final size:18
Alignment explanation
Indices: 11248930--11249004 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
11248920 AAGTAACCCT
11248930 AAATCGAAATCAAAATCA-
1 AAATCGAAATCAAAAT-AG
* * * *
11248948 AATTCTAATTCTAAATAG
1 AAATCGAAATCAAAATAG
* *
11248966 AGATCGAAATCAAAATTG
1 AAATCGAAATCAAAATAG
*
11248984 AAATCGAAATCTAAATCAG
1 AAATCGAAATCAAAAT-AG
11249003 AA
1 AA
11249005 TCAGTGAGTG
Statistics
Matches: 42, Mismatches: 13, Indels: 3
0.72 0.22 0.05
Matches are distributed among these distances:
17 1 0.02
18 38 0.90
19 3 0.07
ACGTcount: A:0.53, C:0.13, G:0.09, T:0.24
Consensus pattern (18 bp):
AAATCGAAATCAAAATAG
Found at i:11248999 original size:12 final size:12
Alignment explanation
Indices: 11248930--11249006 Score: 50
Period size: 12 Copynumber: 6.4 Consensus size: 12
11248920 AAGTAACCCT
11248930 AAATCGAAATCA
1 AAATCGAAATCA
*
11248942 AAATC-AAATTCT
1 AAATCGAAA-TCA
* *
11248954 AATTCTAAAT-A
1 AAATCGAAATCA
*
11248965 GAGATCGAAATCA
1 -AAATCGAAATCA
* *
11248978 AAATTGAAATCG
1 AAATCGAAATCA
*
11248990 AAATCTAAATCA
1 AAATCGAAATCA
*
11249002 GAATC
1 AAATC
11249007 AGTGAGTGTT
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
11 3 0.06
12 41 0.85
13 4 0.08
ACGTcount: A:0.52, C:0.14, G:0.09, T:0.25
Consensus pattern (12 bp):
AAATCGAAATCA
Found at i:11249047 original size:24 final size:24
Alignment explanation
Indices: 11249020--11249065 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
11249010 GAGTGTTTCA
* *
11249020 AAATTATAATCAAAATCGAAATAG
1 AAATTAAAATCAAAATCAAAATAG
11249044 AAATTAAAATCAAAATCAAAAT
1 AAATTAAAATCAAAATCAAAAT
11249066 TAAAATTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.63, C:0.09, G:0.04, T:0.24
Consensus pattern (24 bp):
AAATTAAAATCAAAATCAAAATAG
Found at i:11249052 original size:18 final size:18
Alignment explanation
Indices: 11249031--11249076 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
11249021 AATTATAATC
11249031 AAAATCGAAAT-AGAAATT
1 AAAATCGAAATCA-AAATT
*
11249049 AAAATCAAAATCAAAATT
1 AAAATCGAAATCAAAATT
*
11249067 AAAATTGAAA
1 AAAATCGAAA
11249077 CTGAAACTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.22
Consensus pattern (18 bp):
AAAATCGAAATCAAAATT
Found at i:11249059 original size:12 final size:12
Alignment explanation
Indices: 11249017--11249072 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
11249007 AGTGAGTGTT
*
11249017 TCAAAATTATAA
1 TCAAAATTAAAA
**
11249029 TCAAAATCGAAA
1 TCAAAATTAAAA
11249041 T-AGAAATTAAAA
1 TCA-AAATTAAAA
*
11249053 TCAAAATCAAAA
1 TCAAAATTAAAA
*
11249065 TTAAAATT
1 TCAAAATT
11249073 GAAACTGAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
11 1 0.03
12 32 0.94
13 1 0.03
ACGTcount: A:0.61, C:0.09, G:0.04, T:0.27
Consensus pattern (12 bp):
TCAAAATTAAAA
Found at i:11249071 original size:24 final size:23
Alignment explanation
Indices: 11249019--11249072 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
11249009 TGAGTGTTTC
* *
11249019 AAAATTATAATCAAAATCGAAAT
1 AAAATTAAAATCAAAATCAAAAT
11249042 AGAAATTAAAATCAAAATCAAAATT
1 A-AAATTAAAATCAAAATCAAAA-T
11249067 AAAATT
1 AAAATT
11249073 GAAACTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 1 0.04
24 24 0.89
25 2 0.07
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (23 bp):
AAAATTAAAATCAAAATCAAAAT
Found at i:11254337 original size:17 final size:17
Alignment explanation
Indices: 11254315--11254351 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
11254305 AGACCTTAAA
11254315 GGACAGAATGAAACAGC
1 GGACAGAATGAAACAGC
11254332 GGACAGAATGAAACAGC
1 GGACAGAATGAAACAGC
11254349 GGA
1 GGA
11254352 TTGATAGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.16, G:0.32, T:0.05
Consensus pattern (17 bp):
GGACAGAATGAAACAGC
Found at i:11255462 original size:16 final size:16
Alignment explanation
Indices: 11255429--11255462 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11255419 AACAAATGTT
* *
11255429 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
11255445 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
11255461 AA
1 AA
11255463 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:11258287 original size:21 final size:21
Alignment explanation
Indices: 11258261--11258301 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11258251 AGACGAGCAA
* *
11258261 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
11258282 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
11258302 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:11260240 original size:16 final size:16
Alignment explanation
Indices: 11260207--11260240 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11260197 GGAGATTGTT
* *
11260207 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
11260223 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
11260239 AA
1 AA
11260241 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:11263553 original size:3 final size:3
Alignment explanation
Indices: 11263545--11263608 Score: 82
Period size: 3 Copynumber: 22.3 Consensus size: 3
11263535 ATTAATTAAG
*
11263545 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TAA TTGA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
11263590 -TA TTA -TA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
11263609 GAAGTAAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 6 0.11
3 47 0.87
4 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:11263871 original size:3 final size:3
Alignment explanation
Indices: 11263865--11263892 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
11263855 TATTATGAAA
11263865 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
11263893 AATTAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:11264015 original size:15 final size:16
Alignment explanation
Indices: 11263989--11264018 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11263979 TCGCATAGGG
11263989 AGAAAGAAAAAGGGAA
1 AGAAAGAAAAAGGGAA
11264005 AGAAA-AAAAAGGGA
1 AGAAAGAAAAAGGGA
11264019 GAAATTAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAAAGGGAA
Found at i:11264412 original size:17 final size:18
Alignment explanation
Indices: 11264390--11264425 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11264380 TAAATGAGTT
11264390 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
11264407 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
11264425 A
1 A
11264426 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:11266198 original size:10 final size:10
Alignment explanation
Indices: 11266179--11266228 Score: 68
Period size: 10 Copynumber: 5.0 Consensus size: 10
11266169 TAAAATTCTA
11266179 AAAGATAAAT
1 AAAGATAAAT
11266189 ACAA-ATAAAT
1 A-AAGATAAAT
11266199 AAAGATAAAT
1 AAAGATAAAT
11266209 AAAGATAAAT
1 AAAGATAAAT
11266219 GAAA-ATAAAT
1 -AAAGATAAAT
11266229 CCTAGAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 2 0.05
10 30 0.81
11 5 0.14
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:11267014 original size:96 final size:97
Alignment explanation
Indices: 11266876--11267062 Score: 279
Period size: 96 Copynumber: 1.9 Consensus size: 97
11266866 ATTTTATTTA
* * * *
11266876 TTTATTTTTACTTAGGAATATATTGAACCTTTTGACGTGAAGAGAGATAACAGCCAAACACC-CT
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATAACAGCCAAACACCTC-
11266940 ACCCCGGTTACTAAACCCAACACATTCCTAATT
65 ACCCCGGTTACTAAACCCAACACATTCCTAATT
*
11266973 TTTATTTTT-CTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAACACCTCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATAACAGCCAAACACCTCA
* * *
11267037 CCCCTGTTACTCAGCCCAACACATTC
66 CCCCGGTTACTAAACCCAACACATTC
11267063 TTAAAAATTA
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
96 71 0.88
97 10 0.12
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (97 bp):
TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATAACAGCCAAACACCTCA
CCCCGGTTACTAAACCCAACACATTCCTAATT
Found at i:11267803 original size:5 final size:5
Alignment explanation
Indices: 11267788--11267840 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
11267778 TCAACATCCA
*
11267788 AAAAT -AAAT AAAAT AAAAT --AAT AAATAGT AAAAT AAAAT CAAAT AAAA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-A-T AAAAT AAAAT AAAAT AAAAT
11267836 AAAAT
1 AAAAT
11267841 TAGGCTGCCT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
3 3 0.08
4 8 0.20
5 23 0.57
6 2 0.05
7 4 0.10
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (5 bp):
AAAAT
Done.