Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 1 of 185
Found at i:599 original size:31 final size:32
Alignment explanation
Indices: 563--627 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
553 TTCTTAATAA
563 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
594 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
626 TT
1 TT
628 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:5231 original size:3 final size:3
Alignment explanation
Indices: 5225--5252 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5215 GGAGGAGGAG
5225 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
5253 CCTGGGTGTT
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:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:10390 original size:13 final size:13
Alignment explanation
Indices: 10372--10396 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10362 TAATATTTTA
10372 ATTTTTCGTGTTG
1 ATTTTTCGTGTTG
10385 ATTTTTCGTGTT
1 ATTTTTCGTGTT
10397 TTGAATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.08, G:0.20, T:0.64
Consensus pattern (13 bp):
ATTTTTCGTGTTG
Found at i:25749 original size:58 final size:58
Alignment explanation
Indices: 25659--25777 Score: 238
Period size: 58 Copynumber: 2.1 Consensus size: 58
25649 GAATAACTGT
25659 TATTCATACACATACATTTTTCATCATTTACAAAGAAAGAATACTTACCTTATACAAA
1 TATTCATACACATACATTTTTCATCATTTACAAAGAAAGAATACTTACCTTATACAAA
25717 TATTCATACACATACATTTTTCATCATTTACAAAGAAAGAATACTTACCTTATACAAA
1 TATTCATACACATACATTTTTCATCATTTACAAAGAAAGAATACTTACCTTATACAAA
25775 TAT
1 TAT
25778 AAAATAAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.35
Consensus pattern (58 bp):
TATTCATACACATACATTTTTCATCATTTACAAAGAAAGAATACTTACCTTATACAAA
Found at i:29365 original size:17 final size:17
Alignment explanation
Indices: 29320--29366 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
29310 ATGCTTAACA
29320 AAAGAGTTCGCC-AACC
1 AAAGAGTTCGCCAAACC
* *
29336 ATAGA-TCTCGCCAAAGC
1 AAAGAGT-TCGCCAAACC
29353 AAAGAGTTCGCCAA
1 AAAGAGTTCGCCAA
29367 TTGGCATAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 1 0.04
16 9 0.36
17 14 0.56
18 1 0.04
ACGTcount: A:0.38, C:0.28, G:0.19, T:0.15
Consensus pattern (17 bp):
AAAGAGTTCGCCAAACC
Found at i:30180 original size:12 final size:13
Alignment explanation
Indices: 30161--30192 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
30151 AAGAGAGAGA
30161 GAGAGGGGGAGGG
1 GAGAGGGGGAGGG
30174 G-GAGGGGGAGGG
1 GAGAGGGGGAGGG
30186 GAGAGGG
1 GAGAGGG
30193 AGAGAGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.22, C:0.00, G:0.78, T:0.00
Consensus pattern (13 bp):
GAGAGGGGGAGGG
Found at i:30181 original size:7 final size:6
Alignment explanation
Indices: 30163--30192 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
30153 GAGAGAGAGA
30163 GAGGGG GAGGGG GAGGGG GAGGGG AGAGGG
1 GAGGGG GAGGGG GAGGGG GAGGGG -GAGGG
30193 AGAGAGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (6 bp):
GAGGGG
Found at i:30964 original size:27 final size:27
Alignment explanation
Indices: 30926--30982 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
30916 ATGTACCAGT
30926 TTGCAAATGAGTCTCTGAAAACTCCTA
1 TTGCAAATGAGTCTCTGAAAACTCCTA
30953 TTGCAAATGAGTCTCTGAAAACTCCTA
1 TTGCAAATGAGTCTCTGAAAACTCCTA
30980 TTG
1 TTG
30983 ACACGCCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (27 bp):
TTGCAAATGAGTCTCTGAAAACTCCTA
Found at i:33155 original size:43 final size:42
Alignment explanation
Indices: 33090--33176 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 42
33080 AAAGTAATGG
* *
33090 CAGAATTGTCAGCTAAACTAAAACTGATTCCACAAATTAAGT
1 CAGAATTGACAGCTAAACTAAAACTGATTCCACAAATCAAGT
*
33132 CAGAATTGACAGGCTTAACTAAAACTGATTCCACAAATCAAGT
1 CAGAATTGACA-GCTAAACTAAAACTGATTCCACAAATCAAGT
33175 CA
1 CA
33177 AAGGGGAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 10 0.24
43 31 0.76
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.24
Consensus pattern (42 bp):
CAGAATTGACAGCTAAACTAAAACTGATTCCACAAATCAAGT
Found at i:34856 original size:29 final size:30
Alignment explanation
Indices: 34800--34856 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
34790 CAAGTTGACT
* *
34800 TAAATTTTGAAATATGAAAAGTACAAAGGC
1 TAAATTTTCAAATATGAAAAGGACAAAGGC
34830 TAAA-TTTCAAATATGTAAAAGGA-AAAG
1 TAAATTTTCAAATATG-AAAAGGACAAAG
34857 CTAGAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (30 bp):
TAAATTTTCAAATATGAAAAGGACAAAGGC
Found at i:37574 original size:20 final size:20
Alignment explanation
Indices: 37549--37588 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
37539 GACTATATCA
* *
37549 GAAAAATTTGGAAATTTTAG
1 GAAAAATTTGAAAAATTTAG
37569 GAAAAATTTGAAAAATTTAG
1 GAAAAATTTGAAAAATTTAG
37589 ACTGCAAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (20 bp):
GAAAAATTTGAAAAATTTAG
Found at i:41667 original size:9 final size:10
Alignment explanation
Indices: 41651--41697 Score: 51
Period size: 9 Copynumber: 4.5 Consensus size: 10
41641 TATATAGGAG
41651 TATATATTTT
1 TATATATTTT
41661 T-TATATTTT
1 TATATATTTT
41670 TATATATTTAT
1 TATATATTT-T
*
41681 ATACATACTTTT
1 -TATATA-TTTT
41693 TATAT
1 TATAT
41698 TTTATGATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 9 0.29
10 8 0.26
11 5 0.16
12 6 0.19
13 3 0.10
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (10 bp):
TATATATTTT
Found at i:42400 original size:109 final size:109
Alignment explanation
Indices: 42203--42410 Score: 337
Period size: 109 Copynumber: 1.9 Consensus size: 109
42193 AAATGTTTCC
*
42203 AAATAAGGCAATATGTTGCGTTTGGAAATTCGAGGAATGTGCCCTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATGTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* *
42268 CTCGTTCGACCAAATAGCTAAATATCCTTTTGAAAACTTTTCAA
66 CTCGTTCAACCAAATAGCTAAATATCCTATTGAAAACTTTTCAA
* *
42312 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATGTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* *
42377 CTCGTTTAACCAAATTG-TCAAATATCCTATTGAA
66 CTCGTTCAACCAAATAGCT-AAATATCCTATTGAA
42411 TTTAAACTCA
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
108 1 0.01
109 90 0.99
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (109 bp):
AAATAAGGCAATATGTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
CTCGTTCAACCAAATAGCTAAATATCCTATTGAAAACTTTTCAA
Found at i:43810 original size:19 final size:20
Alignment explanation
Indices: 43770--43813 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
43760 GTCTCTTTAG
* *
43770 GCATT-CATTTCATGCATCT
1 GCATTACATTGCATGCATAT
43789 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
43808 GCATTA
1 GCATTA
43814 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:46461 original size:7 final size:8
Alignment explanation
Indices: 46440--46469 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
46430 TCTCATGAAT
46440 TCAAAAAA
1 TCAAAAAA
46448 TCAAAAAA
1 TCAAAAAA
46456 TCAAAAAAA
1 TC-AAAAAA
46465 TCAAA
1 TCAAA
46470 GTCAAAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.73, C:0.13, G:0.00, T:0.13
Consensus pattern (8 bp):
TCAAAAAA
Found at i:48769 original size:88 final size:88
Alignment explanation
Indices: 48620--49397 Score: 1065
Period size: 88 Copynumber: 8.9 Consensus size: 88
48610 ATGAAGTTAC
* * * *
48620 AGATCTTGCCTTCCTGCATTGATAGTGAAGCAGGTCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
48685 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
48708 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
48773 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
*
48796 AGATCTTGCTTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
48861 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
48884 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
48949 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
48972 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
49037 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* *
49060 AGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
*
49125 TGATAGAGCTGGTTGAAGACAAAA
66 TGATGGAGCTGGTTGAAGAC-AAA
* * * * * ** *
49149 AAATCTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAA-A-ACAAGCCTTGCGTCCATCGATTG
1 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
* * **
49212 -CAGTGGAGCTGGTTAAAGA-AGC
66 TGA-TGGAGCTGGTTGAAGACAAA
* * * * * ** *
49234 AGATCTTACCTTCCTACATTAATAGCGAAGCAGATCGAA-A-ACAAAGCCCTGCATCCATCGATT
1 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCTTTCGGTT
* * * **
49297 G-CAGTGGAGCTAGTTAAAGA-AGC
65 GTGA-TGGAGCTGGTTGAAGACAAA
* * * * **
49320 AGATCTTGCCTTCCTGCATTAACAGCAAAGCAGATC-AA-AAACAAAGCCTTGCCTCCATCGGTT
1 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCTTTCGGTT
*
49383 G-CATTGGAGCTGGTT
65 GTGA-TGGAGCTGGTT
49398 AAAGGTTACA
Statistics
Matches: 645, Mismatches: 41, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
85 42 0.07
86 103 0.16
87 32 0.05
88 429 0.67
89 39 0.06
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.25
Consensus pattern (88 bp):
AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
TGATGGAGCTGGTTGAAGACAAA
Found at i:49646 original size:43 final size:44
Alignment explanation
Indices: 49546--49651 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 44
49536 GATCTTGTCC
* * *
49546 CCCTGAAGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCT
1 CCCTGAAGTTACAGTGGAGCAGATCGAAGACAGAGATCCTATCT
* * **
49590 CCCCG-AGATTACAGCGGAGCAGATCGAAGACA-CTATCCTATCT
1 CCCTGAAG-TTACAGTGGAGCAGATCGAAGACAGAGATCCTATCT
49633 CCCTGAAGTTACAGTGGAG
1 CCCTGAAGTTACAGTGGAG
49652 TGGGTTAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
43 24 0.47
44 27 0.53
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (44 bp):
CCCTGAAGTTACAGTGGAGCAGATCGAAGACAGAGATCCTATCT
Found at i:51966 original size:109 final size:109
Alignment explanation
Indices: 51769--51976 Score: 337
Period size: 109 Copynumber: 1.9 Consensus size: 109
51759 AAATGTTTCC
*
51769 AAATAAGGCAATATGTTGCGTTTGGAAATTCGAGGAATGTGCCCTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATGTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* *
51834 CTCGTTCGACCAAATAGCTAAATATCCTTTTGAAAACTTTTCAA
66 CTCGTTCAACCAAATAGCTAAATATCCTATTGAAAACTTTTCAA
* *
51878 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATGTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* *
51943 CTCGTTTAACCAAATTG-TCAAATATCCTATTGAA
66 CTCGTTCAACCAAATAGCT-AAATATCCTATTGAA
51977 TTTAAACTCA
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
108 1 0.01
109 90 0.99
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (109 bp):
AAATAAGGCAATATGTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
CTCGTTCAACCAAATAGCTAAATATCCTATTGAAAACTTTTCAA
Found at i:56007 original size:15 final size:16
Alignment explanation
Indices: 55987--56017 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
55977 ATCTCGCTTC
55987 CTTTTCTTT-TTTTCT
1 CTTTTCTTTATTTTCT
56002 CTTTTCTTTATTTTCT
1 CTTTTCTTTATTTTCT
56018 GTCGATTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (16 bp):
CTTTTCTTTATTTTCT
Found at i:57672 original size:31 final size:31
Alignment explanation
Indices: 57634--57702 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
57624 CTTAACAACC
*
57634 CAGTAACTTAAATAAAAACTTTTAAATAATT
1 CAGTAACTTAAATAAAAACTTTCAAATAATT
* *
57665 CAGTAACTTAAATGAAAACTTTCAAATAGTT
1 CAGTAACTTAAATAAAAACTTTCAAATAATT
57696 CAGTAAC
1 CAGTAAC
57703 CATTTTGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (31 bp):
CAGTAACTTAAATAAAAACTTTCAAATAATT
Found at i:66982 original size:71 final size:72
Alignment explanation
Indices: 66902--67034 Score: 182
Period size: 70 Copynumber: 1.9 Consensus size: 72
66892 TTATATGTTT
* *
66902 TTTAATTAAAAGTATGTTTATGATATTTA-GGTTTAGGTG-TGTGTCTTTATTTA-TTATTTTAC
1 TTTAATT-AAAGTATCTTTATGATA-TTAGGGTTTAGGTGTTGTGTCTTTATTTACTTAGTTTAC
66964 TAAGAGATC
64 TAAGAGATC
* * *
66973 TTTAATTAAAGTATCTTTATGGTATTAGGGTTTAGGTGTTTTTTCTTTATTTACTTAGTTTA
1 TTTAATTAAAGTATCTTTATGATATTAGGGTTTAGGTGTTGTGTCTTTATTTACTTAGTTTA
67035 AGACTCGATC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
69 3 0.06
70 25 0.46
71 19 0.35
72 7 0.13
ACGTcount: A:0.26, C:0.05, G:0.17, T:0.53
Consensus pattern (72 bp):
TTTAATTAAAGTATCTTTATGATATTAGGGTTTAGGTGTTGTGTCTTTATTTACTTAGTTTACTA
AGAGATC
Found at i:73966 original size:2 final size:2
Alignment explanation
Indices: 73959--73984 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
73949 ATTAGCATTA
73959 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
73985 ATAAGTCTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:98947 original size:21 final size:22
Alignment explanation
Indices: 98921--98967 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
98911 CTCTGCTCAA
*
98921 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
98942 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
98964 ACTC
1 ACTC
98968 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:102073 original size:15 final size:16
Alignment explanation
Indices: 102053--102093 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
102043 ATTCAGATTT
102053 TTTTTAAATATTAG-A
1 TTTTTAAATATTAGTA
102068 TTTTT--ATATTAGTA
1 TTTTTAAATATTAGTA
102082 TTTTTAAA-ATTA
1 TTTTTAAATATTA
102094 AAAAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.30
14 6 0.26
15 9 0.39
16 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTTTAAATATTAGTA
Found at i:108012 original size:9 final size:9
Alignment explanation
Indices: 107998--108034 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
107988 TATAGTTTGA
107998 TATTCGAAT
1 TATTCGAAT
108007 TATTCGAAT
1 TATTCGAAT
*
108016 TATTCGAGT
1 TATTCGAAT
108025 TATTCGAAT
1 TATTCGAAT
108034 T
1 T
108035 CGAAAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:111821 original size:8 final size:8
Alignment explanation
Indices: 111808--111832 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
111798 TGAAAGGTTC
111808 ACAAAAGG
1 ACAAAAGG
111816 ACAAAAGG
1 ACAAAAGG
111824 ACAAAAGG
1 ACAAAAGG
111832 A
1 A
111833 AGTGCTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.24, T:0.00
Consensus pattern (8 bp):
ACAAAAGG
Found at i:117799 original size:19 final size:18
Alignment explanation
Indices: 117775--117816 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
117765 TATTAAACCC
117775 TTTTAAAATTTAAAAATT
1 TTTTAAAATTTAAAAATT
*
117793 ATTTTAAAATTTATAAATT
1 -TTTTAAAATTTAAAAATT
117812 TTTTA
1 TTTTA
117817 TTAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTAAAATTTAAAAATT
Found at i:119240 original size:49 final size:49
Alignment explanation
Indices: 119184--119280 Score: 194
Period size: 49 Copynumber: 2.0 Consensus size: 49
119174 TTCACTTGTG
119184 ACATTCATAGTGTGGCATACCTAAATCCTGAGTGGATGATGGACTATGC
1 ACATTCATAGTGTGGCATACCTAAATCCTGAGTGGATGATGGACTATGC
119233 ACATTCATAGTGTGGCATACCTAAATCCTGAGTGGATGATGGACTATG
1 ACATTCATAGTGTGGCATACCTAAATCCTGAGTGGATGATGGACTATG
119281 TATGTGTGTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (49 bp):
ACATTCATAGTGTGGCATACCTAAATCCTGAGTGGATGATGGACTATGC
Found at i:123454 original size:21 final size:21
Alignment explanation
Indices: 123430--123471 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
123420 GCAACCATCA
*
123430 ACGCATCACCACCGTGAACCG
1 ACGCATCACCACCATGAACCG
123451 ACGCATCACCACCATGAACCG
1 ACGCATCACCACCATGAACCG
123472 CTACCTCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.43, G:0.17, T:0.10
Consensus pattern (21 bp):
ACGCATCACCACCATGAACCG
Found at i:128823 original size:19 final size:20
Alignment explanation
Indices: 128796--128843 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
128786 GTTGGTAAAT
*
128796 ACATGTGTA-ATAATAATAA
1 ACATATGTATATAATAATAA
*
128815 ACATATGTATTTAATAATAA
1 ACATATGTATATAATAATAA
128835 A-ATATGTAT
1 ACATATGTAT
128844 TGCTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (20 bp):
ACATATGTATATAATAATAA
Found at i:128844 original size:19 final size:20
Alignment explanation
Indices: 128806--128844 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
128796 ACATGTGTAA
128806 TAATAATAAACATATGTATT
1 TAATAATAAACATATGTATT
128826 TAATAATAAA-ATATGTATT
1 TAATAATAAACATATGTATT
128845 GCTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TAATAATAAACATATGTATT
Found at i:129681 original size:24 final size:24
Alignment explanation
Indices: 129654--129700 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
129644 ATTGAAATGG
129654 ATTG-ATTTAATATGTGA-TGAATTT
1 ATTGAATTT-ATAT-TGATTGAATTT
129678 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
129701 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 14 0.67
25 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:129980 original size:40 final size:40
Alignment explanation
Indices: 129861--129998 Score: 149
Period size: 40 Copynumber: 3.5 Consensus size: 40
129851 CTTTGAGTCA
* *
129861 ATGAGACACTGGGTGTCAATTTATTACTT-AGGATTAATTCG
1 ATGAGACACTGGGTGTCAAATTATTACTTCA-GATTAA-CCG
* * * *
129902 ATGAGGCACTGGGTGTC-AA-T-TTACTTCGGTTTAGCCG
1 ATGAGACACTGGGTGTCAAATTATTACTTCAGATTAACCG
*
129939 ATGAGACACTGGGTGTCAAATTATTACTTCAAATTAACCG
1 ATGAGACACTGGGTGTCAAATTATTACTTCAGATTAACCG
* *
129979 ATGAGGCACTGGGTGCCAAA
1 ATGAGACACTGGGTGTCAAA
129999 CTGGTGTGTT
Statistics
Matches: 80, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
37 18 0.22
38 12 0.15
39 2 0.03
40 32 0.40
41 16 0.20
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (40 bp):
ATGAGACACTGGGTGTCAAATTATTACTTCAGATTAACCG
Found at i:135792 original size:19 final size:19
Alignment explanation
Indices: 135744--135799 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
135734 AAAGAATAAA
*
135744 TAATGATTTTTCAGAATTTT
1 TAAT-ATTTTTTAGAATTTT
135764 TAATATTTTTTAGAATTTT
1 TAATATTTTTTAGAATTTT
*
135783 TTAT-TCTTTTTAGAATT
1 TAATAT-TTTTTAGAATT
135800 ATTGTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 1 0.03
19 28 0.85
20 4 0.12
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.61
Consensus pattern (19 bp):
TAATATTTTTTAGAATTTT
Found at i:136460 original size:25 final size:25
Alignment explanation
Indices: 136414--136462 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
136404 ATTATATATT
* * **
136414 AAATATATTTTTTTTATTTTTAATC
1 AAATATAATTTTTTAAAATTTAATC
136439 AAATATAATTTTTTAAAATTTAAT
1 AAATATAATTTTTTAAAATTTAAT
136463 ATGCTATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
AAATATAATTTTTTAAAATTTAATC
Found at i:144867 original size:22 final size:22
Alignment explanation
Indices: 144842--144889 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
144832 AACAAGCTCT
144842 AATACCAATTGTTAGGCCTAAA
1 AATACCAATTGTTAGGCCTAAA
144864 AATA-CAATTGTTAGGCCTAAA
1 AATACCAATTGTTAGGCCTAAA
144885 AATAC
1 AATAC
144890 TAAGATAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (22 bp):
AATACCAATTGTTAGGCCTAAA
Found at i:144898 original size:20 final size:20
Alignment explanation
Indices: 144854--144898 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
144844 TACCAATTGT
*
144854 TAGGCCTAAAAATACAATTGT
1 TAGGCCTAAAAATACAA-TGA
144875 TAGGCCTAAAAATACTAA-GA
1 TAGGCCTAAAAATAC-AATGA
144895 TAGG
1 TAGG
144899 GTGAATTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 15 0.68
22 2 0.09
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.24
Consensus pattern (20 bp):
TAGGCCTAAAAATACAATGA
Found at i:145547 original size:22 final size:21
Alignment explanation
Indices: 145522--145565 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
145512 TTTATTTCAC
*
145522 ACATTTAACAATATGTCTCGAG
1 ACATATAACAAT-TGTCTCGAG
**
145544 ACATATAACCCTTGTCTCGAG
1 ACATATAACAATTGTCTCGAG
145565 A
1 A
145566 TAGGAAGAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (21 bp):
ACATATAACAATTGTCTCGAG
Found at i:173581 original size:21 final size:19
Alignment explanation
Indices: 173538--173595 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 19
173528 TAAATAAAAC
*
173538 AAAAAATAATATAATATTTTT
1 AAAAAAAAAT-TAAT-TTTTT
173559 AAATAAAAAATTAATTTTATT
1 AAA-AAAAAATTAATTTT-TT
*
173580 AAAATAATAATTAATT
1 AAAA-AAAAATTAATT
173596 ATAAATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 4 0.12
21 22 0.69
22 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAAAAAAATTAATTTTTT
Found at i:173590 original size:17 final size:18
Alignment explanation
Indices: 173541--173591 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
173531 ATAAAACAAA
* *
173541 AAATAATATAATATTTTT
1 AAATAAAATAATAATTTT
173559 AAATAAAA-AATTAATTTT
1 AAATAAAATAA-TAATTTT
*
173577 -ATTAAAATAATAATT
1 AAATAAAATAATAATT
173592 AATTATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAAAATAATAATTTT
Found at i:182998 original size:12 final size:12
Alignment explanation
Indices: 182981--183019 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
182971 AAGATGACCA
*
182981 TTAGAGTTAGAG
1 TTAGAGTTAAAG
*
182993 TTAGAGATAAAG
1 TTAGAGTTAAAG
*
183005 TTAAAGTTAAAG
1 TTAGAGTTAAAG
183017 TTA
1 TTA
183020 AGGTTTTCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (12 bp):
TTAGAGTTAAAG
Found at i:184319 original size:25 final size:25
Alignment explanation
Indices: 184291--184342 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
184281 CATAACTTAC
184291 CTCAATAACAATTTAATATGATAAG
1 CTCAATAACAATTTAATATGATAAG
184316 CTCAATAACAATTTAATATGATAAG
1 CTCAATAACAATTTAATATGATAAG
184341 CT
1 CT
184343 ACTAGCTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (25 bp):
CTCAATAACAATTTAATATGATAAG
Found at i:196896 original size:40 final size:40
Alignment explanation
Indices: 196852--196932 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
196842 TTCTTAGGTT
* *
196852 TTAATGAGCCATATTATCTACCAATAGATATCCAAAGGGA
1 TTAATGAGCCACATTATCTACCAATAGACATCCAAAGGGA
** * *
196892 TTAATGAGGTACATTATCTACCAATGGACATCCTAAGGGA
1 TTAATGAGCCACATTATCTACCAATAGACATCCAAAGGGA
196932 T
1 T
196933 CAAGATAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (40 bp):
TTAATGAGCCACATTATCTACCAATAGACATCCAAAGGGA
Found at i:208780 original size:11 final size:13
Alignment explanation
Indices: 208752--208796 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 13
208742 TTTTACATTC
208752 AATTAAAAATATA
1 AATTAAAAATATA
208765 AATTAAAAA-A-A
1 AATTAAAAATATA
*
208776 AATTAAAAACTATC
1 AATTAAAAA-TATA
208790 AATTAAA
1 AATTAAA
208797 TTTTATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 10 0.36
12 1 0.04
13 10 0.36
14 7 0.25
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (13 bp):
AATTAAAAATATA
Found at i:211109 original size:59 final size:59
Alignment explanation
Indices: 211011--211122 Score: 143
Period size: 59 Copynumber: 1.9 Consensus size: 59
211001 ACTTCCTTAA
* * * * *
211011 AAGAAGAATTGTTCAAACTTATAAAATGTACTAAGAGAATCTAAACAACCCAACAAATG
1 AAGAAGAATTATTCAAACTTATAAAATATACTAAAAGAATCAAAACAAACCAACAAATG
* * * *
211070 AAGAAGAATTATTCGAACTTGTAAAGTATCCTAAAAGAATCAAAACAAACCAA
1 AAGAAGAATTATTCAAACTTATAAAATATACTAAAAGAATCAAAACAAACCAA
211123 AAAAACAAGA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 44 1.00
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.21
Consensus pattern (59 bp):
AAGAAGAATTATTCAAACTTATAAAATATACTAAAAGAATCAAAACAAACCAACAAATG
Found at i:222115 original size:17 final size:17
Alignment explanation
Indices: 222093--222126 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
222083 TTACAAAATT
*
222093 AAATCTTATAGGATTAC
1 AAATCTTATAAGATTAC
*
222110 AAATCTTCTAAGATTAC
1 AAATCTTATAAGATTAC
222127 TTTCCTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (17 bp):
AAATCTTATAAGATTAC
Found at i:222812 original size:10 final size:11
Alignment explanation
Indices: 222783--222823 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
222773 TTTATAATTT
222783 TAAATTTTTTG
1 TAAATTTTTTG
222794 TAAATTTTTTG
1 TAAATTTTTTG
*
222805 TAAATTTTTTA
1 TAAATTTTTTG
222816 T-AATTTTT
1 TAAATTTTT
222824 ATGGTCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 7 0.24
11 22 0.76
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (11 bp):
TAAATTTTTTG
Found at i:234511 original size:11 final size:11
Alignment explanation
Indices: 234497--234536 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
234487 CTAAAAAAAC
234497 TTAAAAAATTA
1 TTAAAAAATTA
234508 TTAAAAATATATA
1 TTAAAAA-AT-TA
234521 TT-AAAAATTA
1 TTAAAAAATTA
234531 TTAAAA
1 TTAAAA
234537 TATTCATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 4 0.15
11 12 0.46
12 6 0.23
13 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TTAAAAAATTA
Found at i:237579 original size:28 final size:28
Alignment explanation
Indices: 237531--237586 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
237521 CAAATGTTTA
*
237531 TTTTCGTAATTAATCTGTTTTTCATATT
1 TTTTCGTAATTAATCTGTTTTTAATATT
* *
237559 TTTTTGTAATTAAT-TATTTTTTAATATT
1 TTTTCGTAATTAATCT-GTTTTTAATATT
237587 ATTTATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.64
Consensus pattern (28 bp):
TTTTCGTAATTAATCTGTTTTTAATATT
Found at i:242445 original size:21 final size:20
Alignment explanation
Indices: 242407--242446 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
242397 TTCAAATTTT
* *
242407 ATTTTTTATATAGTTAATAA
1 ATTTATTATATAGATAATAA
242427 ATTTATTATCATAGATAATA
1 ATTTATTAT-ATAGATAATA
242447 TATATAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
ATTTATTATATAGATAATAA
Found at i:248150 original size:28 final size:28
Alignment explanation
Indices: 248114--248245 Score: 113
Period size: 28 Copynumber: 4.7 Consensus size: 28
248104 GAATTCGCAC
* * *
248114 GTAAAAGTTTGTATGAATTATCTTTCAA
1 GTAAGAGTTTGTATGGATTATCTTCCAA
* * * * * *
248142 GCACGAGTTTGTACGGATTTTCATCCAG
1 GTAAGAGTTTGTATGGATTATCTTCCAA
* ** * *
248170 GTAAGAGTCTACATGAATTATCTTTCAA
1 GTAAGAGTTTGTATGGATTATCTTCCAA
*
248198 G-AACGAGTTTGTATGGATTTTCTTCCAA
1 GTAA-GAGTTTGTATGGATTATCTTCCAA
248226 GTAAGAGTTTGTATGGATTA
1 GTAAGAGTTTGTATGGATTA
248246 GATTTCGAAC
Statistics
Matches: 75, Mismatches: 27, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
27 2 0.03
28 71 0.95
29 2 0.03
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (28 bp):
GTAAGAGTTTGTATGGATTATCTTCCAA
Found at i:248186 original size:56 final size:56
Alignment explanation
Indices: 248126--248233 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 56
248116 AAAAGTTTGT
* *
248126 ATGAATTATCTTTCAAGCACGAGTTTGTACGGATTTTCATCCAGGTAAGAGTCTAC
1 ATGAATTATCTTTCAAGAACGAGTTTGTACGGATTTTCATCCAAGTAAGAGTCTAC
* *
248182 ATGAATTATCTTTCAAGAACGAGTTTGTATGGATTTTCTTCCAAGTAAGAGT
1 ATGAATTATCTTTCAAGAACGAGTTTGTACGGATTTTCATCCAAGTAAGAGT
248234 TTGTATGGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (56 bp):
ATGAATTATCTTTCAAGAACGAGTTTGTACGGATTTTCATCCAAGTAAGAGTCTAC
Found at i:248431 original size:26 final size:26
Alignment explanation
Indices: 248395--248447 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
248385 CGAATATAAG
248395 TTTGCACCATTATAAAATCGCATGCA
1 TTTGCACCATTATAAAATCGCATGCA
248421 TTTGCACCATTATAAAATCGCATGCA
1 TTTGCACCATTATAAAATCGCATGCA
248447 T
1 T
248448 GAAGTCACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (26 bp):
TTTGCACCATTATAAAATCGCATGCA
Found at i:251832 original size:27 final size:28
Alignment explanation
Indices: 251800--251859 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
251790 AATTTATAAA
*
251800 ATTTTA-AATT-AATAATTATAAAATTAT
1 ATTTTATAATTCAA-AATAATAAAATTAT
**
251827 ATTTTATTTTTCAAAATAATAAAATTAT
1 ATTTTATAATTCAAAATAATAAAATTAT
251855 ATTTT
1 ATTTT
251860 TACTATCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.21
28 20 0.71
29 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
ATTTTATAATTCAAAATAATAAAATTAT
Found at i:251875 original size:28 final size:28
Alignment explanation
Indices: 251817--251875 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
251807 ATTAATAATT
* *
251817 ATAAAATTATATTTTATTTTTCAAAATA
1 ATAAAATTATATTTTATCTATCAAAATA
251845 ATAAAATTATATTTT-TACTATCATAAA-A
1 ATAAAATTATATTTTAT-CTATCA-AAATA
251873 ATA
1 ATA
251876 TATAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.04
28 23 0.85
29 3 0.11
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (28 bp):
ATAAAATTATATTTTATCTATCAAAATA
Found at i:259998 original size:58 final size:58
Alignment explanation
Indices: 259928--260047 Score: 231
Period size: 58 Copynumber: 2.1 Consensus size: 58
259918 CCTTTTTGCA
259928 GGGTATTCTTGTTGGCATTGAAATATTAATTTCATGTGTGCTTAATTTTTTCATTTAT
1 GGGTATTCTTGTTGGCATTGAAATATTAATTTCATGTGTGCTTAATTTTTTCATTTAT
*
259986 GGGTATTCTTGTTGGCATTGAAATATTAATTTCATGTGTGCTTACTTTTTTCATTTAT
1 GGGTATTCTTGTTGGCATTGAAATATTAATTTCATGTGTGCTTAATTTTTTCATTTAT
260044 GGGT
1 GGGT
260048 GTGGGGTCTT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (58 bp):
GGGTATTCTTGTTGGCATTGAAATATTAATTTCATGTGTGCTTAATTTTTTCATTTAT
Found at i:260287 original size:25 final size:25
Alignment explanation
Indices: 260253--260307 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
260243 AGGCATTGAG
*
260253 TTCTGGTTCCTTAGAACTGTCTTTT
1 TTCTGGTTCCATAGAACTGTCTTTT
260278 TTCTGGTTCCATAGAACTGTCTTTT
1 TTCTGGTTCCATAGAACTGTCTTTT
260303 TTCTG
1 TTCTG
260308 ACATATAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.13, C:0.20, G:0.16, T:0.51
Consensus pattern (25 bp):
TTCTGGTTCCATAGAACTGTCTTTT
Found at i:263391 original size:12 final size:12
Alignment explanation
Indices: 263374--263400 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
263364 GGCAAATCTC
263374 TTTTCTTTTTTT
1 TTTTCTTTTTTT
263386 TTTTCTTTTTTT
1 TTTTCTTTTTTT
263398 TTT
1 TTT
263401 CTAAGCACTT
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:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:268378 original size:24 final size:24
Alignment explanation
Indices: 268351--268402 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
268341 TTAGTAAGTC
*
268351 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
268375 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
268399 AAAT
1 AAAT
268403 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:286290 original size:23 final size:23
Alignment explanation
Indices: 286264--286312 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
286254 TATTACAAGT
*
286264 ATATTATTTTA-AAATTATAAAAA
1 ATATTATTTAATAAATTA-AAAAA
*
286287 ATATTATTTAATAAATTAAACAA
1 ATATTATTTAATAAATTAAAAAA
286310 ATA
1 ATA
286313 AACATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATTATTTAATAAATTAAAAAA
Found at i:295231 original size:42 final size:41
Alignment explanation
Indices: 295068--295261 Score: 165
Period size: 44 Copynumber: 4.5 Consensus size: 41
295058 ATGGCATTAC
* *
295068 ATGATTTCGTATAAGACCATAGCTGGGCTATGACATCGATAT
1 ATGA-TTCGTGTAAGACCATAGCTGGGCTATGGCATCGATAT
* * * *
295110 ATGAGACTTTGTGTAAGACCATATCTAGGATATGGCATCGATAT
1 AT--GA-TTCGTGTAAGACCATAGCTGGGCTATGGCATCGATAT
* * *
295154 ATGTGATTACGTGTAAGACTATATCTGGAAC-ATTGGCATCGATAT
1 A--TGATT-CGTGTAAGACCATAGCTGG-GCTA-TGGCATCGATAT
*
295199 ATGATTCGTGTAAGACCATAGCTGGGCTATTGGCACCGATAT
1 ATGATTCGTGTAAGACCATAGCTGGGCTA-TGGCATCGATAT
* * *
295241 GTGATAACATGTAAGACCATA
1 ATGAT-TCGTGTAAGACCATA
295262 TGTGGGATAT
Statistics
Matches: 124, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.01
42 36 0.29
43 20 0.16
44 53 0.43
45 13 0.10
46 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.30
Consensus pattern (41 bp):
ATGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATAT
Found at i:295254 original size:85 final size:87
Alignment explanation
Indices: 295101--295262 Score: 204
Period size: 85 Copynumber: 1.9 Consensus size: 87
295091 TGGGCTATGA
* * * * *
295101 CATCGATATATGAGACTTTGTGTAAGACCATATCTAGGATATGGCATCGATATATGTGATTACGT
1 CATCGATATAT-AGACTTCGTGTAAGACCATAGCTAGGATATGGCACCGA-ATATGTGATAACAT
*
295166 GTAAGACTATATCTGGAACATTGG
64 GTAAGACCATATCTGGAACATTGG
* *
295190 CATCGATATAT-GA-TTCGTGTAAGACCATAGCTGGGCTATTGGCACCG-ATATGTGATAACATG
1 CATCGATATATAGACTTCGTGTAAGACCATAGCTAGGATA-TGGCACCGAATATGTGATAACATG
295252 TAAGACCATAT
65 TAAGACCATAT
295263 GTGGGATATG
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
85 23 0.36
86 21 0.33
87 9 0.14
89 11 0.17
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (87 bp):
CATCGATATATAGACTTCGTGTAAGACCATAGCTAGGATATGGCACCGAATATGTGATAACATGT
AAGACCATATCTGGAACATTGG
Found at i:302503 original size:54 final size:54
Alignment explanation
Indices: 302389--302509 Score: 152
Period size: 54 Copynumber: 2.2 Consensus size: 54
302379 TACAGTCTAT
* * * * ** *
302389 TGATTTATGATCATGACCTTTTACTTACGAGATTTTATTAATCTCACGGTCCGC
1 TGATTTACGATCATGACATTTTACTTACAAGATTTTATGAATCTCACAATCAGC
* * *
302443 TAATTTACGATCATGACATTTTACTTACAAGATTTTATGAATCTCGCAATTAGC
1 TGATTTACGATCATGACATTTTACTTACAAGATTTTATGAATCTCACAATCAGC
302497 TGATTTACGATCA
1 TGATTTACGATCA
302510 CAAAATTTAA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (54 bp):
TGATTTACGATCATGACATTTTACTTACAAGATTTTATGAATCTCACAATCAGC
Found at i:302583 original size:54 final size:54
Alignment explanation
Indices: 302509--302620 Score: 217
Period size: 54 Copynumber: 2.1 Consensus size: 54
302499 ATTTACGATC
302509 ACAA-AATTTAACTTTCTTATAATCCACTAATTTACAATCACAACATTTTACTT
1 ACAATAATTTAACTTTCTTATAATCCACTAATTTACAATCACAACATTTTACTT
302562 ACAATAATTTAACTTTCTTATAATCCACTAATTTACAATCACAACATTTTACTT
1 ACAATAATTTAACTTTCTTATAATCCACTAATTTACAATCACAACATTTTACTT
302616 ACAAT
1 ACAAT
302621 TTGCAATAGT
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 4 0.07
54 54 0.93
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.39
Consensus pattern (54 bp):
ACAATAATTTAACTTTCTTATAATCCACTAATTTACAATCACAACATTTTACTT
Found at i:312030 original size:28 final size:28
Alignment explanation
Indices: 311984--312107 Score: 142
Period size: 28 Copynumber: 4.4 Consensus size: 28
311974 TGACTTTTGA
311984 CACTAAGTGTGCGAA-TTTAATTGTAAAG
1 CACTAAGTGTGC-AAGTTTAATTGTAAAG
* *
312012 CACTAATTGTGCAAGTTTAATTGAAAAG
1 CACTAAGTGTGCAAGTTTAATTGTAAAG
* *
312040 CACTAAGTGTGCGAGTTTAATGGTAAAG
1 CACTAAGTGTGCAAGTTTAATTGTAAAG
** * * **
312068 CACTAAGTGTGTGAGTTTGATTATTGAG
1 CACTAAGTGTGCAAGTTTAATTGTAAAG
312096 CACTAAGTGTGC
1 CACTAAGTGTGC
312108 GAACTTATTA
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
27 2 0.02
28 80 0.98
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.32
Consensus pattern (28 bp):
CACTAAGTGTGCAAGTTTAATTGTAAAG
Found at i:312070 original size:56 final size:56
Alignment explanation
Indices: 311984--312110 Score: 166
Period size: 56 Copynumber: 2.3 Consensus size: 56
311974 TGACTTTTGA
* *
311984 CACTAAGTGTGCGAATTTAATTGTAAAGCACTAATTGTGCAAGTTTAATTGA-AAAG
1 CACTAAGTGTGCGAATTTAATGGTAAAGCACTAAGTGTGCAAGTTTAATT-ATAAAG
* ** * **
312040 CACTAAGTGTGCGAGTTTAATGGTAAAGCACTAAGTGTGTGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAATTTAATGGTAAAGCACTAAGTGTGCAAGTTTAATTATAAAG
312096 CACTAAGTGTGCGAA
1 CACTAAGTGTGCGAA
312111 CTTATTAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
55 1 0.02
56 60 0.98
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.31
Consensus pattern (56 bp):
CACTAAGTGTGCGAATTTAATGGTAAAGCACTAAGTGTGCAAGTTTAATTATAAAG
Found at i:317895 original size:52 final size:48
Alignment explanation
Indices: 317876--318078 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
317866 TGACAAGTGG
* *
317876 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
317922 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
317974 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
318020 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
318066 AAAGTGATAAGTG
1 AAAGTGATAAGTG
318079 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:317931 original size:98 final size:98
Alignment explanation
Indices: 317810--318078 Score: 448
Period size: 98 Copynumber: 2.7 Consensus size: 98
317800 TTTGAGTACT
* *
317810 TCTGATCAAGTGACAAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
317875 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
317908 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
317973 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
318006 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
318071 GATAAGTG
65 GAAAAGTG
318079 GCTACACTTA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 148 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:318086 original size:37 final size:37
Alignment explanation
Indices: 318042--318187 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
318032 GATAGCTTTA
*
318042 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
318079 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
318116 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
318153 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
318188 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:322321 original size:16 final size:16
Alignment explanation
Indices: 322288--322321 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
322278 TTTATATGTT
* *
322288 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
322304 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
322320 AA
1 AA
322322 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:325140 original size:21 final size:21
Alignment explanation
Indices: 325114--325154 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
325104 AGACGAGCAA
* *
325114 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
325135 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
325155 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:334388 original size:21 final size:21
Alignment explanation
Indices: 334362--334402 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
334352 AGACGAGCAA
* *
334362 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
334383 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
334403 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:343470 original size:23 final size:23
Alignment explanation
Indices: 343444--343492 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
343434 TATTACAAGT
*
343444 ATATTATTTTA-AAATTATAAAAA
1 ATATTATTTAATAAATTA-AAAAA
*
343467 ATATTATTTAATAAATTAAACAA
1 ATATTATTTAATAAATTAAAAAA
343490 ATA
1 ATA
343493 AACATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATTATTTAATAAATTAAAAAA
Found at i:344419 original size:18 final size:18
Alignment explanation
Indices: 344392--344484 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
344382 TACGACCGTT
*
344392 TACGGTACTATTTACGTA
1 TACGGTACTATTCACGTA
*
344410 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
344428 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
344446 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
344464 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
344482 TAC
1 TAC
344485 AGTAGTTGGG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 69 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:344439 original size:36 final size:36
Alignment explanation
Indices: 344392--344484 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
344382 TACGACCGTT
*
344392 TACGGTACTATTTACGTATACGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACGTA
344428 TACGGTACTATTCACGTATACGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACGTA
*
344464 TACGGTACTGTTCACGTATAC
1 TACGGTACTATTCACGTATAC
344485 AGTAGTTGGG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACGGCACTATTCACGTA
Found at i:350734 original size:23 final size:23
Alignment explanation
Indices: 350708--350753 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
350698 TGTCAAATGC
350708 AAATTTTGCATTTTGATATCAAG
1 AAATTTTGCATTTTGATATCAAG
350731 AAATTTTGCATTTTGATATCAAG
1 AAATTTTGCATTTTGATATCAAG
350754 CCGCACAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (23 bp):
AAATTTTGCATTTTGATATCAAG
Found at i:357725 original size:42 final size:41
Alignment explanation
Indices: 357562--357755 Score: 174
Period size: 44 Copynumber: 4.5 Consensus size: 41
357552 ATGGCATTAC
* *
357562 ATGATTTCGTATAAGACCATAGCTGGGCTATGACATCGATAT
1 ATGA-TTCGTGTAAGACCATAGCTGGGCTATGGCATCGATAT
* * * *
357604 ATGAGACTTTGTGTAAGACCATATCTAGGATATGGCATCGATAT
1 AT--GA-TTCGTGTAAGACCATAGCTGGGCTATGGCATCGATAT
* *
357648 ATGTGATTACGTGTAAGACCATATCTGGAAC-ATTGGCATCGATAT
1 A--TGATT-CGTGTAAGACCATAGCTGG-GCTA-TGGCATCGATAT
*
357693 ATGATTCGTGTAAGACCATAGCTGGGCTATTGGCACCGATAT
1 ATGATTCGTGTAAGACCATAGCTGGGCTA-TGGCATCGATAT
* * *
357735 GTGATAACATGTAAGACCATA
1 ATGAT-TCGTGTAAGACCATA
357756 TGTGGGATAT
Statistics
Matches: 126, Mismatches: 17, Indels: 17
0.79 0.11 0.11
Matches are distributed among these distances:
41 1 0.01
42 37 0.29
43 20 0.16
44 54 0.43
45 13 0.10
46 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (41 bp):
ATGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATAT
Found at i:357748 original size:85 final size:87
Alignment explanation
Indices: 357595--357756 Score: 213
Period size: 85 Copynumber: 1.9 Consensus size: 87
357585 TGGGCTATGA
* * * * *
357595 CATCGATATATGAGACTTTGTGTAAGACCATATCTAGGATATGGCATCGATATATGTGATTACGT
1 CATCGATATAT-AGACTTCGTGTAAGACCATAGCTAGGATATGGCACCGA-ATATGTGATAACAT
357660 GTAAGACCATATCTGGAACATTGG
64 GTAAGACCATATCTGGAACATTGG
* *
357684 CATCGATATAT-GA-TTCGTGTAAGACCATAGCTGGGCTATTGGCACCG-ATATGTGATAACATG
1 CATCGATATATAGACTTCGTGTAAGACCATAGCTAGGATA-TGGCACCGAATATGTGATAACATG
357746 TAAGACCATAT
65 TAAGACCATAT
357757 GTGGGATATG
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
85 24 0.37
86 21 0.32
87 9 0.14
89 11 0.17
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (87 bp):
CATCGATATATAGACTTCGTGTAAGACCATAGCTAGGATATGGCACCGAATATGTGATAACATGT
AAGACCATATCTGGAACATTGG
Found at i:378662 original size:38 final size:38
Alignment explanation
Indices: 378594--378670 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
378584 CTTTTACTTA
* * *
378594 CGAGATTTTATTAATCTCACAGTCCGCTAATTTACGAT
1 CGAGATTTTATGAATCTCACAATCCACTAATTTACGAT
* *
378632 CGAGATTTTATGAATCTCGCAATTCACTAATTTACGAT
1 CGAGATTTTATGAATCTCACAATCCACTAATTTACGAT
378670 C
1 C
378671 ACAACCTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (38 bp):
CGAGATTTTATGAATCTCACAATCCACTAATTTACGAT
Found at i:382609 original size:21 final size:21
Alignment explanation
Indices: 382568--382609 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
382558 CAATGACAGC
* *
382568 AAAATTTAAATTTATCTTATA
1 AAAATATAAATTTATCATATA
382589 AAAATATAAATTATAT-ATATA
1 AAAATATAAATT-TATCATATA
382610 CATAATAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATATAAATTTATCATATA
Found at i:387976 original size:33 final size:33
Alignment explanation
Indices: 387905--387980 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
387895 ACAGGGGAAA
*
387905 GTGATGTTGAAAGAGTAGAAGTTGATAGAAAGG
1 GTGATGTTGAAAGAGTAAAAGTTGATAGAAAGG
* * * * **
387938 ATGATGTTGAAGGGGTAAAAGTTGATGGGGAGG
1 GTGATGTTGAAAGAGTAAAAGTTGATAGAAAGG
387971 GTGATGTTGA
1 GTGATGTTGA
387981 TGGGAAGGGT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.33, C:0.00, G:0.41, T:0.26
Consensus pattern (33 bp):
GTGATGTTGAAAGAGTAAAAGTTGATAGAAAGG
Found at i:387981 original size:18 final size:18
Alignment explanation
Indices: 387958--388003 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
387948 AGGGGTAAAA
*
387958 GTTGATGGGGAGGGTGAT
1 GTTGATGGGGAGGGTAAT
*
387976 GTTGATGGGAAGGGTAAT
1 GTTGATGGGGAGGGTAAT
387994 GTTGATGGGG
1 GTTGATGGGG
388004 TAGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.52, T:0.28
Consensus pattern (18 bp):
GTTGATGGGGAGGGTAAT
Found at i:388051 original size:33 final size:33
Alignment explanation
Indices: 388012--388133 Score: 102
Period size: 33 Copynumber: 3.7 Consensus size: 33
388002 GGTAGATTTA
* *
388012 GATGGGGAAGGTGTTGTAGAAGGGGTACAAGTT
1 GATGGGGAAGGTGATGTAGAAGGGGTACAAGCT
* * * * *
388045 GTTGGGGAATGTGATGTTGAAAGGGTAGAAGCT
1 GATGGGGAAGGTGATGTAGAAGGGGTACAAGCT
* * *
388078 GATGGGTAGGGTGATGTAGAAGGCGTACGAA-CT
1 GATGGGGAAGGTGATGTAGAAGGGGTAC-AAGCT
* ** *
388111 TATGAAGAGGGTGATGTAGAAGG
1 GATGGGGAAGGTGATGTAGAAGG
388134 TGTAAAAGTT
Statistics
Matches: 69, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
33 67 0.97
34 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.43, T:0.24
Consensus pattern (33 bp):
GATGGGGAAGGTGATGTAGAAGGGGTACAAGCT
Found at i:388785 original size:11 final size:11
Alignment explanation
Indices: 388769--388819 Score: 93
Period size: 11 Copynumber: 4.6 Consensus size: 11
388759 TACACAAGGC
*
388769 TGCCTTTGCAT
1 TGCCTTCGCAT
388780 TGCCTTCGCAT
1 TGCCTTCGCAT
388791 TGCCTTCGCAT
1 TGCCTTCGCAT
388802 TGCCTTCGCAT
1 TGCCTTCGCAT
388813 TGCCTTC
1 TGCCTTC
388820 ATTCTTAAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.08, C:0.35, G:0.18, T:0.39
Consensus pattern (11 bp):
TGCCTTCGCAT
Found at i:399910 original size:22 final size:23
Alignment explanation
Indices: 399876--399919 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
399866 ACCATCAATG
399876 TATTTAAATAA-TTAATTTTATA
1 TATTTAAATAATTTAATTTTATA
399898 TATTTATAA-AATTTTAATTTTA
1 TATTTA-AATAA-TTTAATTTTA
399920 ATTTTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.42
23 2 0.11
24 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTTAAATAATTTAATTTTATA
Found at i:405723 original size:196 final size:196
Alignment explanation
Indices: 405384--405773 Score: 602
Period size: 196 Copynumber: 2.0 Consensus size: 196
405374 CCTTGTAGGA
* *
405384 CTTTCTGTATAAAAAGACACTCTTGTGGTTGAGTTTGATTCACTTAAAACTTCTTTGTGCTCTAG
1 CTTTCTGTATAAAAAGACACTCTTGTGGTTGAGTTTAATTCACTTAAAACTTCTTTGTGCTCAAG
* *
405449 GGATGGAGAGGGAACACATACTAAATGCACCATGACGTAATTTCTTGGAAGGATATCTTATATTA
66 GGATGGAGAGAGAACACATACTAAATGCACCATGACATAATTTCTTGGAAGGATATCTTATATTA
* * *
405514 CTAATTATTATAGGTCAAGTTGTGTCGGATTGAAACCACTTGAGATGAAAATGGAATGTGCTTGT
131 CTAATTATTATAGGTCAAATTGCGTCGGATTGAAACCACTTGAAATGAAAATGGAATGTGCTTGT
405579 G
196 G
* * * * * *
405580 CTTTTTGTATAAAAGGACATTCTTGTGGTTGTGTTTAATTCACTTTAAGCTTAC-TTGTGCTCAA
1 CTTTCTGTATAAAAAGACACTCTTGTGGTTGAGTTTAATTCACTTAAAACTT-CTTTGTGCTCAA
* * * *
405644 GGGATGGAGAGATAACACATACTAAATGTACCTTGACATGATTTCTTGGAAGGATATCTTATATT
65 GGGATGGAGAGAGAACACATACTAAATGCACCATGACATAATTTCTTGGAAGGATATCTTATATT
*
405709 ACTAATTATTATAGGTCAAATTGCGTTGGATTGAAACCACTTGAAATGAAAATGGAATGTGCTTG
130 ACTAATTATTATAGGTCAAATTGCGTCGGATTGAAACCACTTGAAATGAAAATGGAATGTGCTTG
405774 CACTTTTTAA
Statistics
Matches: 175, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
196 174 0.99
197 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (196 bp):
CTTTCTGTATAAAAAGACACTCTTGTGGTTGAGTTTAATTCACTTAAAACTTCTTTGTGCTCAAG
GGATGGAGAGAGAACACATACTAAATGCACCATGACATAATTTCTTGGAAGGATATCTTATATTA
CTAATTATTATAGGTCAAATTGCGTCGGATTGAAACCACTTGAAATGAAAATGGAATGTGCTTGT
G
Found at i:409174 original size:14 final size:14
Alignment explanation
Indices: 409155--409182 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
409145 ATCACTCAAC
409155 GAGGTCAACTGGTT
1 GAGGTCAACTGGTT
409169 GAGGTCAACTGGTT
1 GAGGTCAACTGGTT
409183 AAATTTGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.36, T:0.29
Consensus pattern (14 bp):
GAGGTCAACTGGTT
Found at i:413654 original size:3 final size:3
Alignment explanation
Indices: 413646--413718 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
413636 TTTGTTACTG
* * * *
413646 TTA TTA TTA TCA TTA TAA TTA -AA TT- TCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
413692 TTA CTA TTG TTA CTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
413719 CCGCTTTGTG
Statistics
Matches: 52, Mismatches: 16, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:415455 original size:20 final size:19
Alignment explanation
Indices: 415424--415482 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
415414 ACTTGTTTAA
*
415424 AAACAATTTTAACATGATTG
1 AAACAGTTTTAAC-TGATTG
*
415444 AAA-ATGTTTTAACTCAATTG
1 AAACA-GTTTTAACT-GATTG
415464 AAACAGTTTTAACTTGATT
1 AAACAGTTTTAAC-TGATT
415483 TTATCATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (19 bp):
AAACAGTTTTAACTGATTG
Found at i:415534 original size:22 final size:24
Alignment explanation
Indices: 415507--415550 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
415497 ATTTTGTTCA
415507 ACTTTAATTT-TTAT-TCAAAAAC
1 ACTTTAATTTGTTATATCAAAAAC
415529 ACTTTAATTTGTTATATCAAAA
1 ACTTTAATTTGTTATATCAAAA
415551 CATATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.45
Consensus pattern (24 bp):
ACTTTAATTTGTTATATCAAAAAC
Found at i:418082 original size:31 final size:29
Alignment explanation
Indices: 418047--418131 Score: 91
Period size: 31 Copynumber: 2.9 Consensus size: 29
418037 CAACAAATAC
* *
418047 TTATAATTTAAGAACTCAATTAAAACATTAT
1 TTATAATTTAAAAACTCAATTAAAA-AAT-T
* *
418078 TTATAGTTCAAAAACTCAATTAAAAAATT
1 TTATAATTTAAAAACTCAATTAAAAAATT
*
418107 TTAAAATTTAAAAACT-AAGTTAAAA
1 TTATAATTTAAAAACTCAA-TTAAAA
418132 TTTTTTAGAG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.04
29 20 0.43
30 2 0.04
31 22 0.48
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (29 bp):
TTATAATTTAAAAACTCAATTAAAAAATT
Found at i:421550 original size:16 final size:17
Alignment explanation
Indices: 421516--421566 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
421506 TAGAAATTAT
*
421516 ATAAAAA-ATAAATATAA
1 ATAAAAATATTAATA-AA
421533 ATAAAAATATTAA-AAA
1 ATAAAAATATTAATAAA
* *
421549 ATAATAATCTTAATAAA
1 ATAAAAATATTAATAAA
421566 A
1 A
421567 ACAACAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 13 0.45
17 12 0.41
18 4 0.14
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAAAAATATTAATAAA
Found at i:421554 original size:13 final size:14
Alignment explanation
Indices: 421513--421554 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
421503 TTCTAGAAAT
421513 TATATAAAAAATAA
1 TATATAAAAAATAA
421527 -ATATAAATAAA-AA
1 TATATAAA-AAATAA
421540 TAT-TAAAAAATAA
1 TATATAAAAAATAA
421553 TA
1 TA
421555 ATCTTAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.12
13 17 0.68
14 5 0.20
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TATATAAAAAATAA
Found at i:439200 original size:32 final size:32
Alignment explanation
Indices: 439155--439215 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
439145 GAAATAAAAC
* * * *
439155 AACTTTAATTAAAAATAGCTTAAAATAAACTG
1 AACTTAAAGTAAAAATAACGTAAAATAAACTG
*
439187 AACTTAAAGTAAAAGTAACGTAAAATAAA
1 AACTTAAAGTAAAAATAACGTAAAATAAA
439216 AAGTAAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.26
Consensus pattern (32 bp):
AACTTAAAGTAAAAATAACGTAAAATAAACTG
Found at i:459311 original size:23 final size:22
Alignment explanation
Indices: 459268--459342 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
459258 CTGGCCTGAA
*
459268 TTATATAT-TAAATATATATATT
1 TTATATATATCAA-ATATATATT
* *
459290 TTATTTTTAATCAAATATATATT
1 TTATATAT-ATCAAATATATATT
*
459313 TTATATATATTAAATATATATAT
1 TTATATATATCAAATATATAT-T
459336 TTA-ATAT
1 TTATATAT
459343 GAGTCAGGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
22 22 0.50
23 19 0.43
24 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATATATATCAAATATATATT
Found at i:459814 original size:13 final size:14
Alignment explanation
Indices: 459796--459824 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
459786 CCAGCCTGTC
459796 TATATAATTT-TTT
1 TATATAATTTATTT
459809 TATATAATTTATTT
1 TATATAATTTATTT
459823 TA
1 TA
459825 AAAAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATATAATTTATTT
Found at i:460317 original size:22 final size:19
Alignment explanation
Indices: 460275--460317 Score: 50
Period size: 22 Copynumber: 2.1 Consensus size: 19
460265 TGAAAAAATC
*
460275 TATTTTTTATTAATATTAA
1 TATTTTTTATTAATATAAA
460294 TATTTTTATAATTAAATATAAA
1 TATTTTT-T-ATT-AATATAAA
460316 TA
1 TA
460318 AAAATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 3 0.15
22 9 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTTTTTATTAATATAAA
Found at i:462715 original size:16 final size:17
Alignment explanation
Indices: 462678--462714 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
462668 TAGTTTTTTG
462678 TTTTTAATTTAATTTAA
1 TTTTTAATTTAATTTAA
*
462695 TTTTTACTTT-ATTT-A
1 TTTTTAATTTAATTTAA
462710 TTTTT
1 TTTTT
462715 TCAGATAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 4 0.21
17 9 0.47
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTAATTTAATTTAA
Found at i:464422 original size:215 final size:216
Alignment explanation
Indices: 464009--464441 Score: 562
Period size: 215 Copynumber: 2.0 Consensus size: 216
463999 CTTTAGCTAA
* * * * * *
464009 ATGGTATATTAAGAGTTTTATTAATGCAATTGACGTGGGTTTAAATCCCATCATATGCATATTTT
1 ATGGTAAATTAAAAGTTTTACTAATGCAATTGACATGGGTTCAAATCCCACCATATGCATATTTT
** * * *
464074 TATTGGATTTTTTAAAATGAAAAGACTAAAATACCCTCGATTAATGTTACTTATTTTAATTACGA
66 TATTGGATTTTTTAAAATGAAAAGACTAAAATACCCTAAAATAATATTAATTATTTTAATTACGA
* *** *
464139 AAATACATTTTTGTAACTCCCTAACTGAGTTGGTGACCTGGTTAAGGGTGACACCGACTCAATCA
131 AAAGACATTCCCGTAACTCCCTAACCGAGTTGGTGACCTGGTTAAGGGTGACACCGACTCAATCA
*
464204 GGAACTTAAATAATATTATAG
196 GGAACTTAAATAATAGTATAG
* *
464225 ATGGTAAATTAAAAGTTTTACTAATGCAATTGGCATGGGTTCAAATCTCACCATATGCATATTTT
1 ATGGTAAATTAAAAGTTTTACTAATGCAATTGACATGGGTTCAAATCCCACCATATGCATATTTT
* * * * * * *
464290 TATTGGTTTTTTTAAAGT-AAAAGACTAACATACCCTAAAATAATATTAATTGTTTTGATTATGG
66 TATTGGATTTTTTAAAATGAAAAGACTAAAATACCCTAAAATAATATTAATTATTTTAATTACGA
* * * * * * *
464354 AAGGACATTCCCGTAACTTCCTAACCGAGTTGGTGACCTGGTTGAGGGTGACGCCGATTTAGTCA
131 AAAGACATTCCCGTAACTCCCTAACCGAGTTGGTGACCTGGTTAAGGGTGACACCGACTCAATCA
464419 GGAACTTAAATAATAGTATAG
196 GGAACTTAAATAATAGTATAG
464440 AT
1 AT
464442 ATACAATTGA
Statistics
Matches: 184, Mismatches: 33, Indels: 1
0.84 0.15 0.00
Matches are distributed among these distances:
215 111 0.60
216 73 0.40
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (216 bp):
ATGGTAAATTAAAAGTTTTACTAATGCAATTGACATGGGTTCAAATCCCACCATATGCATATTTT
TATTGGATTTTTTAAAATGAAAAGACTAAAATACCCTAAAATAATATTAATTATTTTAATTACGA
AAAGACATTCCCGTAACTCCCTAACCGAGTTGGTGACCTGGTTAAGGGTGACACCGACTCAATCA
GGAACTTAAATAATAGTATAG
Found at i:465298 original size:17 final size:19
Alignment explanation
Indices: 465276--465312 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
465266 GTCTTTTACC
*
465276 AAAATATTA-CAAAA-AAT
1 AAAATAATATCAAAATAAT
465293 AAAATAATATCAAAATAAT
1 AAAATAATATCAAAATAAT
465312 A
1 A
465313 TAAACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATAATATCAAAATAAT
Found at i:465449 original size:19 final size:19
Alignment explanation
Indices: 465422--465458 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
465412 TAGAGGCGGC
465422 ACCAATTGTTCGTATTTTG
1 ACCAATTGTTCGTATTTTG
*
465441 ACCATTTGTTCGTATTTT
1 ACCAATTGTTCGTATTTT
465459 TTTCTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (19 bp):
ACCAATTGTTCGTATTTTG
Found at i:465510 original size:16 final size:16
Alignment explanation
Indices: 465466--465513 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
465456 TTTTTTCTTG
465466 AATTTTATTACTTTTAA
1 AATTTTATTA-TTTTAA
* * * *
465483 AAATATACTATTTTAT
1 AATTTTATTATTTTAA
465499 AATTTTATTATTTTA
1 AATTTTATTATTTTA
465514 CATTATTTTA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTTTATTATTTTAA
Found at i:465818 original size:152 final size:151
Alignment explanation
Indices: 465434--466013 Score: 754
Period size: 152 Copynumber: 3.9 Consensus size: 151
465424 CAATTGTTCG
* ***
465434 TATTTTGACCATTTGTTCGTATTTTTTTCTTGAATTTTATTACTTTT--AAAAATATACTATTTT
1 TATTTCGACCATTTGTTCGTATTTTTTTCCCCAATTTTATTACTTTTAAAAAAATATACTATTTT
* * * *
465497 ATAATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTTAGTGTGTTTT
66 ATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTTTTTT
465562 TAAATAAATTTTAAAAAAACTCT
131 TAAATAAA-TTTAAAAAAAC-CT
* * * *
465585 TATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTT
1 TATTTCGACCATTTGTTCGTATTTTTTTCCCCAATTTTATTACTTTTAA-AAAAATATACTATTT
* * * **
465650 TCGT-ATTTTATCATTTTACATTATTTTAGTACATCATGTTTGAAATGTATTAATTTACACTTTT
65 T-ATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTTTT
465714 TTTAAATAAA-TTAAAAAAACCCT
129 TTTAAATAAATTTAAAAAAA-CCT
* * *
465737 TATTTCGACCCTTTGTTCGTATTTTTTTCCCCAGAGTTAATTACTTTTAAAAAAATATACTATTT
1 TATTTCGACCATTTGTTCGTATTTTTTTCCCCA-ATTTTATTACTTTTAAAAAAATATACTATTT
*
465802 TCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTCTTT
65 TATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGT-TTT
465867 TTTAAATAAATTTAAAAAAA---
129 TTTAAATAAATTTAAAAAAACCT
* * * * *
465887 -A--AC-ACCCTATGTTCGTATTTTTTT-CCCATATTTTCTTACTTTTAAAAAAA-ATATTATTT
1 TATTTCGACCATTTGTTCGTATTTTTTTCCCCA-ATTTTATTACTTTTAAAAAAATATACTATTT
*
465946 TATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTTTTT
65 TATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTTTTT
466011 TTA
130 TTA
466014 TTGAAAGTAA
Statistics
Matches: 384, Mismatches: 36, Indels: 26
0.86 0.08 0.06
Matches are distributed among these distances:
143 7 0.02
144 67 0.17
145 22 0.06
146 20 0.05
147 1 0.00
149 1 0.00
151 43 0.11
152 109 0.28
153 27 0.07
154 86 0.22
155 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.52
Consensus pattern (151 bp):
TATTTCGACCATTTGTTCGTATTTTTTTCCCCAATTTTATTACTTTTAAAAAAATATACTATTTT
ATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTTTTTT
TAAATAAATTTAAAAAAACCT
Found at i:466164 original size:152 final size:150
Alignment explanation
Indices: 466008--466503 Score: 761
Period size: 152 Copynumber: 3.3 Consensus size: 150
465998 ATTTAGTGTT
466008 TTTTTATTGAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGATTTTTTT
1 TTTTT-TTGAAAGTAATAAAATTCGGG-AAAAAATACGAACAAAGGGCCGAAATAAGATTTTTTT
* **
466073 AAATTTATTTAAAAGCACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGCGAAAT
64 AAATTTATTTAAAAGCACACTAAATGAATACATTTCAAATATAATGTACTAAAATAATGTAAAAT
466138 AATAAAATTATAAAATAGTATA
129 AATAAAATTATAAAATAGTATA
*
466160 TTTTTTT-AAAGTAATAAAATCTAGGGAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTTTT
1 TTTTTTTGAAAGTAATAAAAT-TCGGGAAAAAATACGAACAAAGGGCCGAAATAAGA--TTTTTT
*
466224 TAAATTTATTTAAAAACACACTAAATGAATACATTTCAAATATAATGTACTAAAATAATGTAAAA
63 TAAATTTATTTAAAAGCACACTAAATGAATACATTTCAAATATAATGTACTAAAATAATGTAAAA
466289 TAATAAAATTATAAAATAGTATA
128 TAATAAAATTATAAAATAGTATA
466312 TTTTTATTGAAAGTAATAAAA-TCAGGGAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTT
1 TTTTT-TTGAAAGTAATAAAATTC-GGGAAAAAATACGAACAAAGGGCCGAAATAA-GATTTTTT
* *
466376 T-AATTTATTTAAAAAAG-ACACTAAATTAATACATTTCAAATATAATGTACGAAAATAATGTAA
63 TAAATTTATTT--AAAAGCACACTAAATGAATACATTTCAAATATAATGTACTAAAATAATGTAA
*
466439 AATAA-AAAATTAAAAAATAGTATA
126 AATAATAAAATTATAAAATAGTATA
* * *
466463 TTTTTTAG-AAGTAATAAACTTCGGAAAAAAATACGAACAAA
1 TTTTTTTGAAAGTAATAAAATTCGGGAAAAAATACGAACAAA
466504 ATGCCAAAAT
Statistics
Matches: 321, Mismatches: 13, Indels: 23
0.90 0.04 0.06
Matches are distributed among these distances:
149 28 0.09
150 47 0.15
151 38 0.12
152 157 0.49
153 37 0.12
154 14 0.04
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (150 bp):
TTTTTTTGAAAGTAATAAAATTCGGGAAAAAATACGAACAAAGGGCCGAAATAAGATTTTTTTAA
ATTTATTTAAAAGCACACTAAATGAATACATTTCAAATATAATGTACTAAAATAATGTAAAATAA
TAAAATTATAAAATAGTATA
Found at i:466640 original size:18 final size:19
Alignment explanation
Indices: 466609--466651 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
466599 AAATAAAAAA
466609 ATTTATATTATTTTAGTATT
1 ATTT-TATTATTTTAGTATT
* *
466629 -TTTTATTTTTTTTGTATT
1 ATTTTATTATTTTAGTATT
466647 ATTTT
1 ATTTT
466652 GGCAGAAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (19 bp):
ATTTTATTATTTTAGTATT
Found at i:469536 original size:21 final size:21
Alignment explanation
Indices: 469510--469554 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
469500 TTACTTGCCT
469510 ATACACATGGTAAGTCTTCCA
1 ATACACATGGTAAGTCTTCCA
469531 ATACACATGGTAAGTCTTCCA
1 ATACACATGGTAAGTCTTCCA
469552 ATA
1 ATA
469555 AAATTAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (21 bp):
ATACACATGGTAAGTCTTCCA
Found at i:470105 original size:18 final size:18
Alignment explanation
Indices: 470082--470120 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
470072 CGTAAATTTT
470082 TTATTATATCCCAACTGC
1 TTATTATATCCCAACTGC
470100 TTATTATATCCCAACTGC
1 TTATTATATCCCAACTGC
470118 TTA
1 TTA
470121 ATTAATTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.05, T:0.41
Consensus pattern (18 bp):
TTATTATATCCCAACTGC
Found at i:471100 original size:29 final size:30
Alignment explanation
Indices: 471043--471104 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
471033 ATACATTTTA
471043 ATCACAATCAAAGTTTCATGCCTATAATTGC
1 ATCACAATCAAAGTTTCATG-CTATAATTGC
471074 ATCA-AATCAAAG-TTCATG-TATCAAATTGC
1 ATCACAATCAAAGTTTCATGCTAT--AATTGC
471103 AT
1 AT
471105 ATTAAATCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 3 0.10
29 14 0.48
30 8 0.28
31 4 0.14
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (30 bp):
ATCACAATCAAAGTTTCATGCTATAATTGC
Found at i:471869 original size:12 final size:12
Alignment explanation
Indices: 471852--471876 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
471842 TTGACCTGAA
471852 GAGTGAACTGTT
1 GAGTGAACTGTT
471864 GAGTGAACTGTT
1 GAGTGAACTGTT
471876 G
1 G
471877 TTCCTCCACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.36, T:0.32
Consensus pattern (12 bp):
GAGTGAACTGTT
Found at i:473447 original size:10 final size:9
Alignment explanation
Indices: 473407--473457 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
473397 ATTGTTATTG
473407 AATTAATA-
1 AATTAATAT
*
473415 ATTTAATAT
1 AATTAATAT
473424 AAATATAAATAT
1 -AAT-T-AATAT
473436 AATTATATAT
1 AATTA-ATAT
473446 AATTAATAT
1 AATTAATAT
473455 AAT
1 AAT
473458 ATTTTTATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
8 7 0.19
9 8 0.22
10 12 0.33
11 4 0.11
12 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AATTAATAT
Found at i:473774 original size:3 final size:3
Alignment explanation
Indices: 473766--473798 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
473756 CAACTCTTTC
*
473766 ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
473799 TATTTTACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:475816 original size:129 final size:129
Alignment explanation
Indices: 475586--475843 Score: 516
Period size: 129 Copynumber: 2.0 Consensus size: 129
475576 CCTCGCTCCT
475586 TTCCATCCTTCATACCCAGCAAAGCTTAGGAGTTTCGTGTATGCTTAAGTGTAATGCACTTGTCT
1 TTCCATCCTTCATACCCAGCAAAGCTTAGGAGTTTCGTGTATGCTTAAGTGTAATGCACTTGTCT
475651 CGTAGATGTCTAGAAAATAAATTGGTCTAACTTGAAATATAGATTTTAATGTGACACTAGATAA
66 CGTAGATGTCTAGAAAATAAATTGGTCTAACTTGAAATATAGATTTTAATGTGACACTAGATAA
475715 TTCCATCCTTCATACCCAGCAAAGCTTAGGAGTTTCGTGTATGCTTAAGTGTAATGCACTTGTCT
1 TTCCATCCTTCATACCCAGCAAAGCTTAGGAGTTTCGTGTATGCTTAAGTGTAATGCACTTGTCT
475780 CGTAGATGTCTAGAAAATAAATTGGTCTAACTTGAAATATAGATTTTAATGTGACACTAGATAA
66 CGTAGATGTCTAGAAAATAAATTGGTCTAACTTGAAATATAGATTTTAATGTGACACTAGATAA
475844 GGGTTAGACA
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 129 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (129 bp):
TTCCATCCTTCATACCCAGCAAAGCTTAGGAGTTTCGTGTATGCTTAAGTGTAATGCACTTGTCT
CGTAGATGTCTAGAAAATAAATTGGTCTAACTTGAAATATAGATTTTAATGTGACACTAGATAA
Found at i:481710 original size:7 final size:7
Alignment explanation
Indices: 481698--481729 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
481688 AAAAGGGGTC
481698 AAAAATG
1 AAAAATG
481705 AAAAATG
1 AAAAATG
481712 AAAAATG
1 AAAAATG
481719 AAAAATG
1 AAAAATG
481726 AAAA
1 AAAA
481730 GCAATTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:489244 original size:24 final size:24
Alignment explanation
Indices: 489174--489247 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
489164 ATAATTATAC
* * *
489174 GTATATATAATATA-TTTTACAAT
1 GTATATATTATAAACTTTTACATT
* * *
489197 CT-TATATTATATAAC-CTTATATT
1 GTATATATTATA-AACTTTTACATT
489220 GTATATATTATAAACTTTTACATT
1 GTATATATTATAAACTTTTACATT
489244 GTAT
1 GTAT
489248 CATAAATGTC
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
22 8 0.21
23 11 0.29
24 19 0.50
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (24 bp):
GTATATATTATAAACTTTTACATT
Found at i:490209 original size:22 final size:23
Alignment explanation
Indices: 490179--490258 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 23
490169 GTTAAAATTG
490179 TAGACAATTGTAGACAATGCAAC
1 TAGACAATTGTAGACAATGCAAC
* *
490202 TAGA-AATTGCAGTTAAAATTGCCAAC
1 TAGACAATTGTAG--ACAA-TG-CAAC
* *
490228 -AGATAATCGTAGACAATGCAAC
1 TAGACAATTGTAGACAATGCAAC
490250 TAGA-AATTG
1 TAGACAATTG
490259 CAGTTTAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
22 15 0.33
23 9 0.20
24 6 0.13
25 5 0.11
26 10 0.22
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (23 bp):
TAGACAATTGTAGACAATGCAAC
Found at i:490835 original size:43 final size:43
Alignment explanation
Indices: 490788--491102 Score: 185
Period size: 43 Copynumber: 7.3 Consensus size: 43
490778 TCAGGGTCTT
* * *
490788 TAGCGGCGTTTTTTTCTCAAACGCCGCAATAGACCCTGATCTA
1 TAGCGGCGCTTTCTCCTCAAACGCCGCAATAGACCCTGATCTA
** * * * * *
490831 TAGCGGCGCTTTGACCACAAACGCCACTAA-AGAACCTAATCTT
1 TAGCGGCGCTTTCTCCTCAAACGCCGC-AATAGACCCTGATCTA
*
490874 TAGCGGCGCTTTCTCCTAAAACGCCGCAATAGACCCTGATCTA
1 TAGCGGCGCTTTCTCCTCAAACGCCGCAATAGACCCTGATCTA
* * * * * * *
490917 TAGCGGCAC-TTCGACCACAAAACGCCACTAA-AGAACCTAATCTT
1 TAGCGGCGCTTTC-TCCTC-AAACGCCGC-AATAGACCCTGATCTA
* * * * * *
490961 TAGCGGCGC-TTCGACCACAAAACGCCACTAA-AGAACCTAATCTT
1 TAGCGGCGCTTTC-TCCTC-AAACGCCGC-AATAGACCCTGATCTA
* ** * *
491005 TAGCGGCGCTTTCCCCAAAAACGCCGCTAA-AGACCATGATCTT
1 TAGCGGCGCTTTCTCCTCAAACGCCGC-AATAGACCCTGATCTA
* * * * * *
491048 TAGTGGCGCTTTTTCCACAAACGCCGCTAA-AGACTCTTATCTT
1 TAGCGGCGCTTTCTCCTCAAACGCCGC-AATAGACCCTGATCTA
491091 TAGCGGCGCTTT
1 TAGCGGCGCTTT
491103 GACCAAAAAT
Statistics
Matches: 226, Mismatches: 40, Indels: 12
0.81 0.14 0.04
Matches are distributed among these distances:
42 5 0.02
43 141 0.62
44 75 0.33
45 5 0.02
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (43 bp):
TAGCGGCGCTTTCTCCTCAAACGCCGCAATAGACCCTGATCTA
Found at i:491121 original size:43 final size:43
Alignment explanation
Indices: 490826--491122 Score: 321
Period size: 43 Copynumber: 6.9 Consensus size: 43
490816 ATAGACCCTG
* *
490826 ATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGAACCTA
1 ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGAACCTA
** * * * *
490869 ATCTTTAGCGGCGCTTTCTCCTAAAACGCCGC-AATAGACCCTG
1 ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAA-AGAACCTA
* * *
490912 ATCTATAGCGGCACTTCGACCACAAAACGCCACTAAAGAACCTA
1 ATCTTTAGCGGCGCTTTGACCA-AAAACGCCACTAAAGAACCTA
*
490956 ATCTTTAGCGGCGCTTCGACCACAAAACGCCACTAAAGAACCTA
1 ATCTTTAGCGGCGCTTTGACCA-AAAACGCCACTAAAGAACCTA
** * *
491000 ATCTTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAG-ACCATG
1 ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGAACC-TA
* ** * * *
491043 ATCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAAG-ACTCTT
1 ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGAAC-CTA
*
491086 ATCTTTAGCGGCGCTTTGACCAAAAATGCCACTAAAG
1 ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAG
491123 GCCAACACCT
Statistics
Matches: 214, Mismatches: 35, Indels: 10
0.83 0.14 0.04
Matches are distributed among these distances:
42 5 0.02
43 130 0.61
44 77 0.36
45 2 0.01
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (43 bp):
ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGAACCTA
Found at i:491147 original size:86 final size:86
Alignment explanation
Indices: 490784--491122 Score: 371
Period size: 86 Copynumber: 3.9 Consensus size: 86
490774 TAGATCAGGG
* * * *
490784 TCTTTAGCGGCGTTTTTTTCTCAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCAC
1 TCTTTAGCGGCGCTTTTTCCACAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCAA
*
490849 AAACGCCACTAAAGAACCTAA
66 AAACGCCACTAAAGAACCAAA
* * *
490870 TCTTTAGCGGCGCTTTCTCCTA-AAACGCCGCAATAGACCCTGATCTATAGCGGCACTTCGACCA
1 TCTTTAGCGGCGCTTTTTCC-ACAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCA
*
490934 CAAAACGCCACTAAAGAACCTAA
65 -AAAACGCCACTAAAGAACCAAA
*** * * * * **
490957 TCTTTAGCGGCGCTTCGACCACAAAACGCCACTAA-AGAACCTAATCTTTAGCGGCGCTTTCCCC
1 TCTTTAGCGGCGCTTTTTCCAC-AAACGCCGC-AATAGACCCTGATCTATAGCGGCGCTTTGACC
* *
491021 AAAAACGCCGCTAAAG-ACCATGA
64 AAAAACGCCACTAAAGAACCA-AA
* * * *
491044 TCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAA-AGACTCTTATCTTTAGCGGCGCTTTGACCA
1 TCTTTAGCGGCGCTTTTTCCACAAACGCCGC-AATAGACCCTGATCTATAGCGGCGCTTTGACCA
*
491108 AAAATGCCACTAAAG
65 AAAACGCCACTAAAG
491123 GCCAACACCT
Statistics
Matches: 214, Mismatches: 33, Indels: 12
0.83 0.13 0.05
Matches are distributed among these distances:
86 110 0.51
87 71 0.33
88 31 0.14
89 2 0.01
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (86 bp):
TCTTTAGCGGCGCTTTTTCCACAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCAA
AAACGCCACTAAAGAACCAAA
Found at i:491497 original size:21 final size:21
Alignment explanation
Indices: 491468--491560 Score: 96
Period size: 21 Copynumber: 4.4 Consensus size: 21
491458 TTTGACGCTG
*
491468 CTCTACTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
**
491489 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
491510 CTCTGCTTCCCTCACTACAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * * *
491531 CTGTACTTCTCTAGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
491552 CTCTGCTTC
1 CTCTGCTTC
491561 TCTTACTGCC
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.09, C:0.44, G:0.14, T:0.33
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:491662 original size:66 final size:66
Alignment explanation
Indices: 491590--491720 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 66
491580 TTAAGCTGCT
* * * *
491590 GCTGGAGTTCTTCATA-CTTTCGTTGAACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTTAGTTG
1 GCTGGAGTTCTTCATATCTTT-GTTGAACCTCAACTTCTCTCGATGCTGCATCCGCTTTAAGTTG
491654 TA
65 TA
* * *
491656 GCTGGAGTTCTTCATATCTTTTTTGAACCTCAACTTCTCTCGATGTTGCCTCCGCTTTAAGTTGT
1 GCTGGAGTTCTTCATATCTTTGTTGAACCTCAACTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
491721 GTAATTTGCT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 53 0.93
67 4 0.07
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.42
Consensus pattern (66 bp):
GCTGGAGTTCTTCATATCTTTGTTGAACCTCAACTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
A
Done.