Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 4 of 199
Found at i:1258106 original size:100 final size:104
Alignment explanation
Indices: 1257927--1258176 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
1257917 CTGATAATAC
**
1257927 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
1257992 TCCCAGACATGGTCTTATAGGGGACCTC-TCATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCATCATCTTAAGG
* *
1258029 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
*
1258092 TCCCAGACATGGTCTTACAGGGGACCTCTATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTC-ATCATCTTAAGG
* *
1258133 ATGCCAATGCCATGTCCCAGACATGGTTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGG-TCTTACATGGGACCTCT
1258177 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 48 0.36
101 36 0.27
102 4 0.03
103 1 0.01
104 2 0.02
105 24 0.18
106 16 0.12
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCATCATCTTAAGG
Found at i:1258291 original size:13 final size:13
Alignment explanation
Indices: 1258270--1258301 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1258260 GCTTGGATCA
*
1258270 TCATCAAATAAAT
1 TCATAAAATAAAT
1258283 TCATAAAATAAAT
1 TCATAAAATAAAT
1258296 TCATAA
1 TCATAA
1258302 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:1258540 original size:30 final size:30
Alignment explanation
Indices: 1258506--1258565 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1258496 GCCCTCGACT
*
1258506 CTAAACTTTTTCAAAATTACAATTTTGCCC
1 CTAAACTTTTACAAAATTACAATTTTGCCC
* *
1258536 CTAAACTTTTACATAATTACATTTTTGCCC
1 CTAAACTTTTACAAAATTACAATTTTGCCC
1258566 AAGGCTCGGA
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:0.32, C:0.23, G:0.03, T:0.42
Consensus pattern (30 bp):
CTAAACTTTTACAAAATTACAATTTTGCCC
Found at i:1265598 original size:50 final size:50
Alignment explanation
Indices: 1265474--1265722 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
1265464 GATAATAACA
* * ** * *
1265474 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
1265525 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
1265575 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
1265625 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
1265680 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
1265723 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:1265652 original size:100 final size:104
Alignment explanation
Indices: 1265473--1265722 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
1265463 TGATAATAAC
**
1265473 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
1265538 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
1265575 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
1265638 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
1265680 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1265723 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:1265838 original size:13 final size:13
Alignment explanation
Indices: 1265817--1265848 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1265807 GCTTGGATCA
*
1265817 TCATCAAATAAAT
1 TCATAAAATAAAT
1265830 TCATAAAATAAAT
1 TCATAAAATAAAT
1265843 TCATAA
1 TCATAA
1265849 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:1266094 original size:30 final size:30
Alignment explanation
Indices: 1266060--1266117 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1266050 CCTCGACTCT
*
1266060 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
1266090 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
1266118 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:1273464 original size:91 final size:91
Alignment explanation
Indices: 1273330--1273514 Score: 352
Period size: 91 Copynumber: 2.0 Consensus size: 91
1273320 TAGATGACCT
1273330 TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCAGAGTTATTTCTGACTTA
1 TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCAGAGTTATTTCTGACTTA
1273395 ATCTGGAAAGTCTCTACTTATCTTTG
66 ATCTGGAAAGTCTCTACTTATCTTTG
* *
1273421 TTTTAGCTTATCAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCGGAGTTATTTCTGACTTA
1 TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCAGAGTTATTTCTGACTTA
1273486 ATCTGGAAAGTCTCTACTTATCTTTG
66 ATCTGGAAAGTCTCTACTTATCTTTG
1273512 TTT
1 TTT
1273515 GATGAAGATG
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.46
Consensus pattern (91 bp):
TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCAGAGTTATTTCTGACTTA
ATCTGGAAAGTCTCTACTTATCTTTG
Found at i:1274191 original size:21 final size:21
Alignment explanation
Indices: 1274167--1274228 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
1274157 TGGTGGGAGT
* * *
1274167 GACGAAGAGGATGACGATGAC
1 GACGATGATGATGACGATGAA
**
1274188 GACGATGATGATGGGGATGAA
1 GACGATGATGATGACGATGAA
*
1274209 GATGATGATGATGACGATGA
1 GACGATGATGATGACGATGA
1274229 TGGTGAGGAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.08, G:0.39, T:0.18
Consensus pattern (21 bp):
GACGATGATGATGACGATGAA
Found at i:1274257 original size:15 final size:15
Alignment explanation
Indices: 1274233--1274267 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1274223 CGATGATGGT
*
1274233 GAGGATGAAGAAGAG
1 GAGGACGAAGAAGAG
*
1274248 GAGGACGAAGAAGAT
1 GAGGACGAAGAAGAG
1274263 GAGGA
1 GAGGA
1274268 TGATGAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.46, T:0.06
Consensus pattern (15 bp):
GAGGACGAAGAAGAG
Found at i:1283624 original size:18 final size:18
Alignment explanation
Indices: 1283601--1283640 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1283591 TGCTAAAAAG
*
1283601 AAAAATT-CATAATTGATT
1 AAAAATTCCA-AAATGATT
1283619 AAAAATTCCAAAATGATT
1 AAAAATTCCAAAATGATT
1283637 AAAA
1 AAAA
1283641 TTAGCCCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAAATTCCAAAATGATT
Found at i:1284759 original size:18 final size:19
Alignment explanation
Indices: 1284714--1284759 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
1284704 TATATCAATA
1284714 AAAAAATTATTTAAAAACT
1 AAAAAATTATTTAAAAACT
* **
1284733 -CAATTTTATTTAAAAA-T
1 AAAAAATTATTTAAAAACT
1284750 AAAAAATTAT
1 AAAAAATTAT
1284760 AAAAAATTAA
Statistics
Matches: 20, Mismatches: 6, Indels: 3
0.69 0.21 0.10
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAAATTATTTAAAAACT
Found at i:1289093 original size:46 final size:45
Alignment explanation
Indices: 1289026--1289305 Score: 303
Period size: 46 Copynumber: 6.6 Consensus size: 45
1289016 TTTGAGTACT
* *
1289026 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
1289072 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
1289108 TCTGATCAAGTGAAAAAGTGATAA---GT-G-TTA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
1289144 TATGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
* * *
1289190 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCAGCTATACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
1289236 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
1289281 TCTTATCAAG-G-ACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
1289306 ATCATACGTA
Statistics
Matches: 209, Mismatches: 13, Indels: 27
0.84 0.05 0.11
Matches are distributed among these distances:
36 62 0.30
38 1 0.00
39 2 0.01
40 3 0.01
42 5 0.02
43 15 0.07
44 2 0.01
45 20 0.10
46 98 0.47
47 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:1289108 original size:36 final size:36
Alignment explanation
Indices: 1289062--1289170 Score: 182
Period size: 36 Copynumber: 3.0 Consensus size: 36
1289052 GGTAGCTTTA
*
1289062 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1289098 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
* * *
1289134 GTTATACTTATATGATCAAGTGACAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1289170 G
1 G
1289171 GTAGCTTTAG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:1290598 original size:13 final size:14
Alignment explanation
Indices: 1290573--1290626 Score: 58
Period size: 14 Copynumber: 3.8 Consensus size: 14
1290563 ATAATATATG
1290573 TATAATAATAATAA
1 TATAATAATAATAA
1290587 TATAAT-ATAATAA
1 TATAATAATAATAA
1290600 TA-AATGCTAATAATAA
1 TATAA---TAATAATAA
*
1290616 TATAGTAATAA
1 TATAATAATAA
1290627 ACAATTTAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 2 0.06
13 9 0.26
14 12 0.35
15 1 0.03
16 9 0.26
17 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (14 bp):
TATAATAATAATAA
Found at i:1290612 original size:16 final size:17
Alignment explanation
Indices: 1290574--1290626 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
1290564 TAATATATGT
1290574 ATAATAATAATAATATA
1 ATAATAATAATAATATA
*
1290591 AT-ATAATAATAA-ATG
1 ATAATAATAATAATATA
*
1290606 CTAATAATAAT-ATAGTA
1 ATAATAATAATAATA-TA
1290623 ATAA
1 ATAA
1290627 ACAATTTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 4 0.14
16 19 0.66
17 6 0.21
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (17 bp):
ATAATAATAATAATATA
Found at i:1307006 original size:9 final size:10
Alignment explanation
Indices: 1306984--1307044 Score: 62
Period size: 9 Copynumber: 6.7 Consensus size: 10
1306974 TTTTGGTTAA
1306984 AAATTAACCG
1 AAATTAACCG
1306994 -AATT-ACCG
1 AAATTAACCG
1307002 AAATTAACC-
1 AAATTAACCG
*
1307011 AAATTAATCG
1 AAATTAACCG
*
1307021 -AATTACCCG
1 AAATTAACCG
1307030 -AATTAACCG
1 AAATTAACCG
1307039 -AATTAA
1 AAATTAA
1307045 ATCACTCCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
8 4 0.09
9 37 0.84
10 3 0.07
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.25
Consensus pattern (10 bp):
AAATTAACCG
Found at i:1307007 original size:18 final size:18
Alignment explanation
Indices: 1306985--1307044 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
1306975 TTTGGTTAAA
1306985 AATTAACCGAATT-ACCG
1 AATTAACCGAATTAACCG
* *
1307002 AAATTAACCAAATTAATCG
1 -AATTAACCGAATTAACCG
*
1307021 AATTACCCGAATTAACCG
1 AATTAACCGAATTAACCG
1307039 AATTAA
1 AATTAA
1307045 ATCACTCCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 32 0.91
19 3 0.09
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (18 bp):
AATTAACCGAATTAACCG
Found at i:1307017 original size:27 final size:27
Alignment explanation
Indices: 1306984--1307044 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
1306974 TTTTGGTTAA
1306984 AAATTAACCGAATTA-CCGAAATTAACC
1 AAATTAACCGAATTACCCG-AATTAACC
*
1307011 AAATTAATCGAATTACCCGAATTAACC
1 AAATTAACCGAATTACCCGAATTAACC
*
1307038 GAATTAA
1 AAATTAA
1307045 ATCACTCCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 28 0.90
28 3 0.10
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.25
Consensus pattern (27 bp):
AAATTAACCGAATTACCCGAATTAACC
Found at i:1322261 original size:51 final size:50
Alignment explanation
Indices: 1322200--1322326 Score: 159
Period size: 50 Copynumber: 2.5 Consensus size: 50
1322190 TCAGTTCACA
* *
1322200 TAGTAACCTGCACATAGTACTACACATG-AGGCCATTACCA-TCCAATACACG
1 TAGTAGCCTGCACATAGTACTACACATGCA-ACC--TACCATTCCAATACACG
* **
1322251 TAGTAGCCTGCACATAGTACTACACATGCAACCTATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGCAACCTACCATTCCAATACACG
*
1322301 TAGTAGTCTGCACATAGTACTACACA
1 TAGTAGCCTGCACATAGTACTACACA
1322327 CGTAACCATC
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
49 4 0.06
50 34 0.50
51 29 0.43
52 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGCAACCTACCATTCCAATACACG
Found at i:1354778 original size:24 final size:24
Alignment explanation
Indices: 1354751--1354797 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1354741 GTCTTTATAC
*
1354751 TTTTTGTATATTTAAAATTTAGTA
1 TTTTTATATATTTAAAATTTAGTA
* * *
1354775 TTTTTATTTTTTTTAAATTTAGT
1 TTTTTATATATTTAAAATTTAGT
1354798 TTATCTAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (24 bp):
TTTTTATATATTTAAAATTTAGTA
Found at i:1361141 original size:18 final size:18
Alignment explanation
Indices: 1361118--1361174 Score: 82
Period size: 18 Copynumber: 3.2 Consensus size: 18
1361108 AAATAATTTA
1361118 AAAATTATAGAAATATTC
1 AAAATTATAGAAATATTC
1361136 AAAATTATAGAAATATTC
1 AAAATTATAGAAATATTC
1361154 AAAAGTTCATA-AAAT-TTC
1 AAAA-TT-ATAGAAATATTC
1361172 AAA
1 AAA
1361175 TAAAAAAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
18 28 0.76
19 6 0.16
20 3 0.08
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (18 bp):
AAAATTATAGAAATATTC
Found at i:1364819 original size:27 final size:27
Alignment explanation
Indices: 1364781--1364835 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1364771 CTGCGAATTT
1364781 TGAACAGCATCCAAATTTTGCCCAATA
1 TGAACAGCATCCAAATTTTGCCCAATA
1364808 TGAACAGCATCCAAATTTTGCCCAATA
1 TGAACAGCATCCAAATTTTGCCCAATA
1364835 T
1 T
1364836 TTTTTCTCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.27
Consensus pattern (27 bp):
TGAACAGCATCCAAATTTTGCCCAATA
Found at i:1366313 original size:30 final size:31
Alignment explanation
Indices: 1366252--1366328 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
1366242 TTACAATTTG
1366252 GTCACTGAACTATTAAAAAATTTTCATTTAA
1 GTCACTGAACTATTAAAAAATTTTCATTTAA
* * *
1366283 GTCACTAAACTATTCAAAAGTTTT-ATTTAA
1 GTCACTGAACTATTAAAAAATTTTCATTTAA
*
1366313 GTCATTGAACTATTAA
1 GTCACTGAACTATTAA
1366329 GTTTTTCTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 19 0.47
31 21 0.52
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (31 bp):
GTCACTGAACTATTAAAAAATTTTCATTTAA
Found at i:1374417 original size:26 final size:25
Alignment explanation
Indices: 1374388--1374452 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 25
1374378 CATTATTCAC
1374388 AAGAAAATGGTAATTTTTTTTAAAGT
1 AAGAAAATGGTAATTTTTTTT-AAGT
*
1374414 AAGAAAAT-G--ATTTTTTTTAGGT
1 AAGAAAATGGTAATTTTTTTTAAGT
* *
1374436 AAGATAATGATAATTTT
1 AAGAAAATGGTAATTTT
1374453 AGATATGATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 10 0.30
23 9 0.27
25 6 0.18
26 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (25 bp):
AAGAAAATGGTAATTTTTTTTAAGT
Found at i:1375015 original size:43 final size:43
Alignment explanation
Indices: 1374968--1375067 Score: 148
Period size: 43 Copynumber: 2.3 Consensus size: 43
1374958 AGAGTAATAC
*
1374968 CTTTAGCGGCGTTTTTGGTATAAGCACCGCTATAGA-CTAGGGT
1 CTTTAGCGGCGTTTTTGGTAAAAGCACCGCTATAGATC-AGGGT
* *
1375011 CTTTAGCGACGTTTTTGGTAAAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTTTGGTAAAAGCACCGCTATAGATCAGGGT
*
1375054 CTTTAGTGGCGTTT
1 CTTTAGCGGCGTTT
1375068 GTGACCGAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 50 0.98
44 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTGGTAAAAGCACCGCTATAGATCAGGGT
Found at i:1375468 original size:21 final size:21
Alignment explanation
Indices: 1375439--1375493 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
1375429 TTTGACGCTG
1375439 CTCTGCTTCCCTCGCTTCAGC
1 CTCTGCTTCCCTCGCTTCAGC
* *
1375460 CTCTACTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTTCAGC
1375481 CTCTGCTTCCCTC
1 CTCTGCTTCCCTC
1375494 TTAGCAGCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.05, C:0.47, G:0.11, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTTCAGC
Found at i:1380888 original size:9 final size:9
Alignment explanation
Indices: 1380852--1381279 Score: 203
Period size: 9 Copynumber: 49.8 Consensus size: 9
1380842 AATTGCACGG
1380852 GTAAGTTAT
1 GTAAGTTAT
*
1380861 GT-A-TTGT
1 GTAAGTTAT
*
1380868 GTAAGCTAT
1 GTAAGTTAT
*
1380877 GTAAGTTGT
1 GTAAGTTAT
1380886 GT-A-TTAT
1 GTAAGTTAT
1380893 GTAAGTTAT
1 GTAAGTTAT
1380902 -T-A-TTAT
1 GTAAGTTAT
1380908 GCTTTAAGTTAT
1 G---TAAGTTAT
*
1380920 GTAAGTAAT
1 GTAAGTTAT
1380929 GT-A-TTAT
1 GTAAGTTAT
*
1380936 GTAAGTTGT
1 GTAAGTTAT
*
1380945 GT-A-TAAT
1 GTAAGTTAT
*
1380952 GTTAGTTAT
1 GTAAGTTAT
1380961 GTAAGTTAT
1 GTAAGTTAT
1380970 GTAAGTTAT
1 GTAAGTTAT
1380979 GT-A---A-
1 GTAAGTTAT
1380983 GTAAGTTAT
1 GTAAGTTAT
1380992 GTAAGTTAT
1 GTAAGTTAT
** *
1381001 CAAAGTAAT
1 GTAAGTTAT
*
1381010 GTATGTTAT
1 GTAAGTTAT
1381019 GTAAG-T-T
1 GTAAGTTAT
1381026 GTAAGTTAT
1 GTAAGTTAT
*
1381035 -TATGTATTAT
1 GTAAG--TTAT
*
1381045 GTAAGTTAA
1 GTAAGTTAT
* *
1381054 G-ATGGATTAC
1 GTA-AG-TTAT
1381064 GTAAGTTAT
1 GTAAGTTAT
1381073 GTAAGTTAAAT
1 GTAAGTT--AT
1381084 GT-A-TTAT
1 GTAAGTTAT
1381091 GTAAG-T-T
1 GTAAGTTAT
1381098 GTAAGTTAGAT
1 GTAAGTT--AT
1381109 GT-A-TTAT
1 GTAAGTTAT
1381116 GTAAG-T-T
1 GTAAGTTAT
1381123 GTAAGTTAGAT
1 GTAAGTT--AT
1381134 GT-A-TTAT
1 GTAAGTTAT
1381141 GTAAG-T-T
1 GTAAGTTAT
1381148 GTAAGTTAT
1 GTAAGTTAT
*
1381157 -TATGTATTAT
1 GTAAG--TTAT
1381167 GTAAGTTAT
1 GTAAGTTAT
1381176 GTAAGTTAAAT
1 GTAAGTT--AT
1381187 GT-A-TTAT
1 GTAAGTTAT
1381194 G-AAGGTTAT
1 GTAA-GTTAT
*
1381203 GTAAGTTGT
1 GTAAGTTAT
**
1381212 GTAAGAGAT
1 GTAAGTTAT
*
1381221 TTAAGTTAT
1 GTAAGTTAT
* *
1381230 GTGAGTTTT
1 GTAAGTTAT
1381239 GT-A-TTAT
1 GTAAGTTAT
1381246 GTAAGTTAT
1 GTAAGTTAT
*
1381255 GTAGGTTAT
1 GTAAGTTAT
* *
1381264 TTAGGTTAT
1 GTAAGTTAT
1381273 GTAAGTT
1 GTAAGTT
1381280 TTGAGTTGTT
Statistics
Matches: 318, Mismatches: 45, Indels: 112
0.67 0.09 0.24
Matches are distributed among these distances:
4 2 0.01
5 2 0.01
6 4 0.01
7 65 0.20
8 31 0.10
9 167 0.53
10 20 0.06
11 22 0.07
12 5 0.02
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:1380925 original size:43 final size:42
Alignment explanation
Indices: 1380852--1381025 Score: 148
Period size: 43 Copynumber: 4.2 Consensus size: 42
1380842 AATTGCACGG
* *
1380852 GTAAGTTATGTAT--TGTGTAAGCTATGTAAGTTGTGTATTAT
1 GTAAGTTATGTATAATGT-TAAGTTATGTAAGTTATGTATTAT
* *
1380893 GTAAGTTAT-TATTATGCTTTAAGTTATGTAAGTAATGTATTAT
1 GTAAGTTATGTATAATG--TTAAGTTATGTAAGTTATGTATTAT
*
1380936 GTAAGTTGTGTATAATGTT-AGTTATGTAAGTTATGTAAGTTAT
1 GTAAGTTATGTATAATGTTAAGTTATGTAAGTTATGT-A-TTAT
* ** *
1380979 GTAAG-TAAGT-T-ATG-TAAGTTATCAAAGTAATGTATGTTAT
1 GTAAGTTATGTATAATGTTAAGTTATGTAAGTTATGTA--TTAT
1381019 GTAAGTT
1 GTAAGTT
1381026 GTAAGTTATT
Statistics
Matches: 112, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
39 2 0.02
40 30 0.27
41 27 0.24
42 8 0.07
43 38 0.34
44 7 0.06
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (42 bp):
GTAAGTTATGTATAATGTTAAGTTATGTAAGTTATGTATTAT
Found at i:1380945 original size:59 final size:56
Alignment explanation
Indices: 1380868--1381251 Score: 180
Period size: 53 Copynumber: 7.0 Consensus size: 56
1380858 TATGTATTGT
* *
1380868 GTAAGCTATGTAAGTTGTGTATTATGTAAGTTAT-T-A-TTATGCTTTAAGTTATGTAA
1 GTAAGTTATGTAAGTTGTGTATAATGTAAGTTATGTAAGTTATG---TAAGTTATGTAA
*
1380924 GTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATGTAAGTTATGTAAGTTATGTAA
1 GTAA-G--TTATGTAAGTTGTGTATAATGTAAGTTATGTAAGTTATGTAAGTTATGTAA
* ** * *
1380983 GTAAGTTATGTAAGTTATCAAAGTAATGTATGTTATGTAAG-T-TGTAAGTTAT-TAT
1 GTAAGTTATGTAAGTTGT-GTA-TAATGTAAGTTATGTAAGTTATGTAAGTTATGTAA
* * * *
1381038 GT-A-TTATGTAAGTTAAGATGGATTACGTAAGTTATGTAAGTTA---AA-TGTAT-TAT
1 GTAAGTTATGTAAGTT--G-TGTATAATGTAAGTTATGTAAGTTATGTAAGT-TATGTAA
*
1381091 GTAAG-T-TGTAAGTTAGATGTATTATGTAAG-T-TGTAAGTTAGATGT-A-TTATGTAA
1 GTAAGTTATGTAAGTT-G-TGTATAATGTAAGTTATGTAAGTT--ATGTAAGTTATGTAA
* * * * *
1381145 GT-TG-TAAGTTA-TTATGTATTATGTAAGTTATGTAAGTTAAATGT-A-TTATG-AA
1 GTAAGTTATGTAAGTTGTGTATAATGTAAGTTATGTAAGTT--ATGTAAGTTATGTAA
* * * *
1381197 G---GTTATGTAAGTTGTGTAAGAGATTTAAGTTATGTGAGTTTTGT-A-TTATGTAA
1 GTAAGTTATGTAAGTTGTGT-ATA-ATGTAAGTTATGTAAGTTATGTAAGTTATGTAA
1381250 GT
1 GT
1381252 TATGTAGGTT
Statistics
Matches: 266, Mismatches: 31, Indels: 64
0.74 0.09 0.18
Matches are distributed among these distances:
50 9 0.03
51 19 0.07
52 34 0.13
53 59 0.22
54 43 0.16
55 6 0.02
56 27 0.10
57 3 0.01
58 17 0.06
59 42 0.16
60 1 0.00
61 1 0.00
62 5 0.02
ACGTcount: A:0.33, C:0.01, G:0.22, T:0.45
Consensus pattern (56 bp):
GTAAGTTATGTAAGTTGTGTATAATGTAAGTTATGTAAGTTATGTAAGTTATGTAA
Found at i:1380947 original size:25 final size:26
Alignment explanation
Indices: 1380889--1381279 Score: 274
Period size: 25 Copynumber: 15.1 Consensus size: 26
1380879 AAGTTGTGTA
1380889 TTATGTAAGTT-AT-TATTATGCTTTAAG
1 TTATGTAAGTTAATGTATTATG---TAAG
1380916 TTATGTAAG-TAATGTATTATGTAAG
1 TTATGTAAGTTAATGTATTATGTAAG
*
1380941 TTGTGT-A--TAATGTTAGTTATGTAAG
1 TTATGTAAGTTAATG-TA-TTATGTAAG
1380966 TTATGTAAGTT-ATGTA--A-GTAAG
1 TTATGTAAGTTAATGTATTATGTAAG
* *
1380988 TTATGTAAGTTATCAAAGTA--ATGTATG
1 TTATGTAAG-T-T-AATGTATTATGTAAG
1381015 TTATGTAAGTTGTAA-GTTATTATGT-A-
1 TTATGTAAG-T-TAATG-TATTATGTAAG
* *
1381041 TTATGTAAGTTAAGATGGATTACGTAAG
1 TTATGTAAGTT-A-ATGTATTATGTAAG
1381069 TTATGTAAGTTAAATGTATTATGTAAG
1 TTATGTAAGTT-AATGTATTATGTAAG
1381096 -T-TGTAAGTTAGATGTATTATGTAAG
1 TTATGTAAGTTA-ATGTATTATGTAAG
1381121 -T-TGTAAGTTAGATGTATTATGTAAG
1 TTATGTAAGTTA-ATGTATTATGTAAG
1381146 -T-TGTAAGTTATTATGTATTATGTAAG
1 TTATGTAAGTTA--ATGTATTATGTAAG
1381172 TTATGTAAGTTAAATGTATTATG-AAGG
1 TTATGTAAGTT-AATGTATTATGTAA-G
* ** *
1381199 TTATGTAAGTT-GTGTAAGAGATTTAAG
1 TTATGTAAGTTAATGT-A-TTATGTAAG
* *
1381226 TTATGTGAGTT-TTGTATTATGTAAG
1 TTATGTAAGTTAATGTATTATGTAAG
* *
1381251 TTATGTAGGTT-ATTTAGGTTATGTAAG
1 TTATGTAAGTTAATGTA--TTATGTAAG
1381278 TT
1 TT
1381280 TTGAGTTGTT
Statistics
Matches: 309, Mismatches: 24, Indels: 62
0.78 0.06 0.16
Matches are distributed among these distances:
22 14 0.05
23 7 0.02
24 6 0.02
25 104 0.34
26 48 0.16
27 94 0.30
28 35 0.11
29 1 0.00
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.45
Consensus pattern (26 bp):
TTATGTAAGTTAATGTATTATGTAAG
Found at i:1380986 original size:13 final size:13
Alignment explanation
Indices: 1380970--1380997 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1380960 TGTAAGTTAT
1380970 GTAAGTTATGTAA
1 GTAAGTTATGTAA
1380983 GTAAGTTATGTAA
1 GTAAGTTATGTAA
1380996 GT
1 GT
1380998 TATCAAAGTA
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:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (13 bp):
GTAAGTTATGTAA
Found at i:1380986 original size:22 final size:22
Alignment explanation
Indices: 1380961--1381050 Score: 82
Period size: 22 Copynumber: 4.1 Consensus size: 22
1380951 TGTTAGTTAT
1380961 GTAAGTTATGTAAGTTATGTAA
1 GTAAGTTATGTAAGTTATGTAA
1380983 GTAAGTTATGTAAGTTATCAAAGTAA
1 GTAAGTTATGTAAGTTAT----GTAA
*
1381009 TGTATGTTATGTAAG-T-TGTAA
1 -GTAAGTTATGTAAGTTATGTAA
*
1381030 GTTA-TTATGT-A-TTATGTAA
1 GTAAGTTATGTAAGTTATGTAA
1381049 GT
1 GT
1381051 TAAGATGGAT
Statistics
Matches: 58, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
18 2 0.03
19 13 0.22
20 2 0.03
21 4 0.07
22 18 0.31
25 1 0.02
26 5 0.09
27 13 0.22
ACGTcount: A:0.34, C:0.01, G:0.21, T:0.43
Consensus pattern (22 bp):
GTAAGTTATGTAAGTTATGTAA
Found at i:1381047 original size:19 final size:19
Alignment explanation
Indices: 1381025--1381175 Score: 62
Period size: 19 Copynumber: 8.5 Consensus size: 19
1381015 TTATGTAAGT
1381025 TGTAAGTTATTATGTATTA
1 TGTAAGTTATTATGTATTA
** *
1381044 TGTAAGTTAAGATGGATTA
1 TGTAAGTTATTATGTATTA
*
1381063 CGTAAG---TTATGTA--A
1 TGTAAGTTATTATGTATTA
* *
1381077 -GTTAAATGTATTATGTAAGT-
1 TG-TAAGT-TATTATGT-ATTA
*
1381097 TGTAAGTTA-GATGTATTA
1 TGTAAGTTATTATGTATTA
* *
1381115 TGTAAGTT-GTAAG--TTA
1 TGTAAGTTATTATGTATTA
* *
1381131 -G-ATG-TATTATGTAAGT-
1 TGTAAGTTATTATGT-ATTA
1381147 TGTAAGTTATTATGTATTA
1 TGTAAGTTATTATGTATTA
1381166 TGTAAGTTAT
1 TGTAAGTTAT
1381176 GTAAGTTAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 38
0.62 0.13 0.25
Matches are distributed among these distances:
13 2 0.02
14 9 0.10
15 1 0.01
16 7 0.07
17 4 0.04
18 24 0.26
19 42 0.45
20 4 0.04
21 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (19 bp):
TGTAAGTTATTATGTATTA
Found at i:1381246 original size:43 final size:43
Alignment explanation
Indices: 1381199--1381282 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
1381189 ATTATGAAGG
* *
1381199 TTATGTAAGTTGTGTAAGAGATTTAAGTTATGTGAGTTTTGTA
1 TTATGTAAGTTATGTAAGAGATTTAAGTTATGTAAGTTTTGTA
* ** *
1381242 TTATGTAAGTTATGTAGGTTATTTAGGTTATGTAAGTTTTG
1 TTATGTAAGTTATGTAAGAGATTTAAGTTATGTAAGTTTTG
1381283 AGTTGTTCAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (43 bp):
TTATGTAAGTTATGTAAGAGATTTAAGTTATGTAAGTTTTGTA
Found at i:1381384 original size:19 final size:18
Alignment explanation
Indices: 1381360--1381396 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1381350 AATAATAAAA
*
1381360 TAATATTATATTTAATAAT
1 TAATATAATA-TTAATAAT
1381379 TAATATAATATTAATAAT
1 TAATATAATATTAATAAT
1381397 ATTTAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATATAATATTAATAAT
Found at i:1383895 original size:40 final size:42
Alignment explanation
Indices: 1383846--1383927 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 42
1383836 TTGTCGATTC
*
1383846 CAACTTTTACGGCG-CTT-ACAATCAAACGCCACTAAT-TTTA
1 CAACATTTACGGCGTCTTGACAAT-AAACGCCACTAATATTTA
* *
1383886 CAACATTTACGGCGTTTTGAGAATAAACGCCACTAATATTTA
1 CAACATTTACGGCGTCTTGACAATAAACGCCACTAATATTTA
1383928 ATTCGTCAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 13 0.36
41 15 0.42
42 8 0.22
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.30
Consensus pattern (42 bp):
CAACATTTACGGCGTCTTGACAATAAACGCCACTAATATTTA
Found at i:1384672 original size:39 final size:39
Alignment explanation
Indices: 1384608--1384693 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 39
1384598 AATTCCTAAC
*
1384608 CCAT-AACCCCTAAATCCCCTAAACCCTTAAAGCATAAA
1 CCATAAACCCCTAAATCCCCTAAACCCCTAAAGCATAAA
* * *
1384646 CCATAAACCGCTAAATCTCTCT-AACCCCTAAAGCATAAC
1 CCATAAACCCCTAAATC-CCCTAAACCCCTAAAGCATAAA
*
1384685 CCCTAAACC
1 CCATAAACC
1384694 ATTCCAATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
38 4 0.10
39 34 0.83
40 3 0.07
ACGTcount: A:0.40, C:0.38, G:0.03, T:0.19
Consensus pattern (39 bp):
CCATAAACCCCTAAATCCCCTAAACCCCTAAAGCATAAA
Found at i:1385449 original size:32 final size:31
Alignment explanation
Indices: 1385406--1385480 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
1385396 TAACCCATAT
* * *
1385406 ATAACCCCTAAATCCCCTTTAACCCTTAAAGC
1 ATAACCCCTAAA-CCCCTCTAACCCCTAAACC
* **
1385438 ATAAACCCTAAACTTCTCTAACCCCTAAACC
1 ATAACCCCTAAACCCCTCTAACCCCTAAACC
1385469 ATAACCCCTAAA
1 ATAACCCCTAAA
1385481 AAATTTATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 25 0.69
32 11 0.31
ACGTcount: A:0.39, C:0.37, G:0.01, T:0.23
Consensus pattern (31 bp):
ATAACCCCTAAACCCCTCTAACCCCTAAACC
Found at i:1385778 original size:7 final size:7
Alignment explanation
Indices: 1385750--1385803 Score: 63
Period size: 7 Copynumber: 7.4 Consensus size: 7
1385740 CTTACCGTTC
1385750 AAACCCT
1 AAACCCT
**
1385757 AAACCAA
1 AAACCCT
1385764 AAATCCCT
1 AAA-CCCT
1385772 AAACCCT
1 AAACCCT
1385779 AAACCCT
1 AAACCCT
1385786 AAACCCAT
1 AAACCC-T
*
1385794 AAACCAT
1 AAACCCT
1385801 AAA
1 AAA
1385804 TCTTAACTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
7 29 0.73
8 11 0.28
ACGTcount: A:0.52, C:0.35, G:0.00, T:0.13
Consensus pattern (7 bp):
AAACCCT
Found at i:1385798 original size:15 final size:15
Alignment explanation
Indices: 1385750--1385803 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
1385740 CTTACCGTTC
*
1385750 AAACCCTAAA-CCAA
1 AAACCCTAAACCCAT
1385764 AAATCCCTAAACCC-T
1 AAA-CCCTAAACCCAT
1385779 AAACCCTAAACCCAT
1 AAACCCTAAACCCAT
*
1385794 AAACCATAAA
1 AAACCCTAAA
1385804 TCTTAACTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 13 0.37
15 20 0.57
16 2 0.06
ACGTcount: A:0.52, C:0.35, G:0.00, T:0.13
Consensus pattern (15 bp):
AAACCCTAAACCCAT
Found at i:1386486 original size:114 final size:113
Alignment explanation
Indices: 1386089--1386638 Score: 500
Period size: 114 Copynumber: 4.8 Consensus size: 113
1386079 AATCCCTGAT
* * * * * *
1386089 CATTAGCGGCGCTTTTCTA-AAAGCGCCGCTAAATCCCTCAAAAGCACAGAAAACGACGACGTTG
1 CATTAGCGGCGC-TTTATAGAAAGCGCCGCTAAATCCCT-GAAAGCTCGGGAAACGACGTCGTTG
*
1386153 CGCTTAGTTTTTTTTGCGGCGCTTTCCAAAAAACGCCGCTAAAGA-CTGAA
64 CGCTTAG-TTTTTTTGCGGCGCTTTCCAAAAAACGCCGCTAAAGACCTCAA
* * * * *
1386203 CATTAGCGGCGCTTTA-ACAAAAACGCCGCTAAAATCGCC-GAAAGC-CAGAAAACGGCGTCGTT
1 CATTAGCGGCGCTTTATA-GAAAGCGCCGCT-AAATC-CCTGAAAGCTCGGGAAACGACGTCGTT
* * * * *
1386265 GGGCTTAGGTTTTTTGCGGCGCATT-AACAAAAACGCCGCTAAAGACTTCAA
63 GCGCTTAGTTTTTTTGCGGCGCTTTCCA-AAAAACGCCGCTAAAGACCTCAA
* * *
1386316 CATTAGCGGCGCTTTCT-GTAAAAGCGCCACTAAATCCCTGAAAGCTCGGGAGACGACGTCGTTG
1 CATTAGCGGCGCTTTATAG--AAAGCGCCGCTAAATCCCTGAAAGCTCGGGAAACGACGTCGTTG
* * * *
1386380 CGC-TAGTTTTAAGTAGCGGCGCTTTTCC-AGAAACGCTGCTAAAGACCT-AA
64 CGCTTAGTTTT--TTTGCGGCGC-TTTCCAAAAAACGCCGCTAAAGACCTCAA
* * * *
1386430 CCATTAGCGGCGCTTTATAGAAAGCGCCGCTACATCCCTGAAAGCTCGGGAAACGACATAGTTGG
1 -CATTAGCGGCGCTTTATAGAAAGCGCCGCTAAATCCCTGAAAGCTCGGGAAACGACGTCGTTGC
* * *
1386495 GCTTAGTTATTTTTGCGGCGCTTTCCTAGAAACGCCGCTAAAG-CCTTCAG
65 GCTTAGTT-TTTTTGCGGCGCTTTCCAAAAAACGCCGCTAAAGACC-TCAA
* * * *
1386545 CATTAGCGGCGC-TTACT-GAAAAACGCCGCTAAATCACC-GAATGCTGGGGAAACGGCGTCGTT
1 CATTAGCGGCGCTTTA-TAG-AAAGCGCCGCTAAATC-CCTGAAAGCTCGGGAAACGACGTCGTT
*
1386607 GCGC-TAGGTTTTTTGCGGCGCTTTCTCAAAAA
63 GCGCTTAGTTTTTTTGCGGCGCTTTC-CAAAAA
1386639 TGCCGATAAT
Statistics
Matches: 360, Mismatches: 50, Indels: 53
0.78 0.11 0.11
Matches are distributed among these distances:
111 1 0.00
112 51 0.14
113 79 0.22
114 168 0.47
115 54 0.15
116 7 0.02
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.23
Consensus pattern (113 bp):
CATTAGCGGCGCTTTATAGAAAGCGCCGCTAAATCCCTGAAAGCTCGGGAAACGACGTCGTTGCG
CTTAGTTTTTTTGCGGCGCTTTCCAAAAAACGCCGCTAAAGACCTCAA
Found at i:1386496 original size:228 final size:227
Alignment explanation
Indices: 1386089--1386638 Score: 602
Period size: 228 Copynumber: 2.4 Consensus size: 227
1386079 AATCCCTGAT
* * * * * *
1386089 CATTAGCGGCGCTTT-TCTAAAAGCGCCGCTAAATCCCTCAAAAGCACAGAAAACGACGACGTTG
1 CATTAGCGGCGCTTTCTGTAAAAGCGCCGCTAAATCCCT-GAAAGCTCGGGAAACGACGTCGTTG
** *
1386153 CGCTTAGTTTTTTTTGCGGCGCTTTCCAAAAAACGCCGCTAAAGACTGAACATTAGCGGCGCTTT
65 CGC-TAGTTTTAGTAGCGGCGCTTTCCAAAAAACGCCGCTAAAGACTGAACATTAGCGGCGCTTT
* * *
1386218 AACAAAAACGCCGCTAAAATCGCCGAAAGCCAGAAAACGGCGTCGTTGGGCTTAGGT-TTTTTGC
129 AACAAAAACGCCGCTAAAATCGCCGAAAGCCAGAAAACGACATAGTTGGGCTTAGGTATTTTTGC
1386282 GGCGCATTAAC-AAAAACGCCGCTAAAGACTTCAA
194 GGCGC-TTAACTAAAAACGCCGCTAAAGACTTCAA
* *
1386316 CATTAGCGGCGCTTTCTGTAAAAGCGCCACTAAATCCCTGAAAGCTCGGGAGACGACGTCGTTGC
1 CATTAGCGGCGCTTTCTGTAAAAGCGCCGCTAAATCCCTGAAAGCTCGGGAAACGACGTCGTTGC
* *
1386381 GCTAGTTTTAAGTAGCGGCGCTTTTCC-AGAAACGCTGCTAAAGACCT-AACCATTAGCGGCGCT
66 GCTAGTTTT-AGTAGCGGCGC-TTTCCAAAAAACGCCGCTAAAGA-CTGAA-CATTAGCGGCGCT
* * * * * *
1386444 TTATA-GAAAGCGCCGCT-ACATC-CCTGAAAGCTCGGGAAACGACATAGTTGGGCTTAGTTATT
127 TTA-ACAAAAACGCCGCTAAAATCGCC-GAAAGC-CAGAAAACGACATAGTTGGGCTTAGGTATT
** * * *
1386506 TTTGCGGCGCTTTCCTAGAAACGCCGCTAAAGCCTTCAG
189 TTTGCGGCGCTTAACTAAAAACGCCGCTAAAGACTTCAA
* * * * *
1386545 CATTAGCGGCGCTTACTG-AAAAACGCCGCTAAATCACC-GAATGCTGGGGAAACGGCGTCGTTG
1 CATTAGCGGCGCTTTCTGTAAAAGCGCCGCTAAATC-CCTGAAAGCTCGGGAAACGACGTCGTTG
*
1386608 CGCTAGGTTTT--TTGCGGCGCTTTCTCAAAAA
65 CGCTA-GTTTTAGTAGCGGCGCTTTC-CAAAAA
1386639 TGCCGATAAT
Statistics
Matches: 273, Mismatches: 36, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
225 4 0.01
226 18 0.07
227 75 0.27
228 119 0.44
229 57 0.21
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.23
Consensus pattern (227 bp):
CATTAGCGGCGCTTTCTGTAAAAGCGCCGCTAAATCCCTGAAAGCTCGGGAAACGACGTCGTTGC
GCTAGTTTTAGTAGCGGCGCTTTCCAAAAAACGCCGCTAAAGACTGAACATTAGCGGCGCTTTAA
CAAAAACGCCGCTAAAATCGCCGAAAGCCAGAAAACGACATAGTTGGGCTTAGGTATTTTTGCGG
CGCTTAACTAAAAACGCCGCTAAAGACTTCAA
Found at i:1394921 original size:4 final size:4
Alignment explanation
Indices: 1394912--1394952 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
1394902 ACCCCTATAC
*
1394912 GTAT GTAT GTGT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1394953 CATAGTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:1399932 original size:47 final size:47
Alignment explanation
Indices: 1399879--1399972 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
1399869 AAACTGAGCA
*
1399879 GAAGTATTAATGGATAGATTTGCAAAATAGCTAACAATGAATGCACT
1 GAAGTATTAATGGATAGATCTGCAAAATAGCTAACAATGAATGCACT
1399926 GAAGTATTAATGGATAGATCTGCAAAATAGCTAACAATGAATGCACT
1 GAAGTATTAATGGATAGATCTGCAAAATAGCTAACAATGAATGCACT
1399973 TACTTTCTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.27
Consensus pattern (47 bp):
GAAGTATTAATGGATAGATCTGCAAAATAGCTAACAATGAATGCACT
Found at i:1407293 original size:24 final size:20
Alignment explanation
Indices: 1407248--1407288 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1407238 AACCCCTTAA
1407248 AATAATTTTTTATTTAATTT
1 AATAATTTTTTATTTAATTT
1407268 AATAATTTTTTATTTAATTT
1 AATAATTTTTTATTTAATTT
1407288 A
1 A
1407289 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
AATAATTTTTTATTTAATTT
Found at i:1408991 original size:17 final size:17
Alignment explanation
Indices: 1408969--1409002 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1408959 ATCCACTAAT
*
1408969 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1408986 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1409003 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1413630 original size:17 final size:17
Alignment explanation
Indices: 1413608--1413641 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1413598 ATCCACTAAT
*
1413608 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1413625 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1413642 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1429750 original size:27 final size:28
Alignment explanation
Indices: 1429720--1429773 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
1429710 TAAAATTGAC
*
1429720 TAATTCAA-AAAGTATAGAAGA-TAAAAT
1 TAATTAAATAAAGTATA-AAGACTAAAAT
1429747 TAATTAAATTAAAGTATAAAGACTAAA
1 TAATTAAA-TAAAGTATAAAGACTAAA
1429774 TTCATAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 7 0.30
28 4 0.17
29 12 0.52
ACGTcount: A:0.59, C:0.04, G:0.09, T:0.28
Consensus pattern (28 bp):
TAATTAAATAAAGTATAAAGACTAAAAT
Found at i:1431346 original size:35 final size:34
Alignment explanation
Indices: 1431252--1431363 Score: 145
Period size: 34 Copynumber: 3.2 Consensus size: 34
1431242 AAAATATATC
* *
1431252 AGGGTTTGGAGTTTTTTAAAAAAATTAATTAAGTT
1 AGGGTTTAGAG-TTTTTAAAAAAATTAATTAAATT
* * *
1431287 AGGTTTTATG-GGTTTTAAATAAATTAATTAAATT
1 AGGGTTTA-GAGTTTTTAAAAAAATTAATTAAATT
1431321 AGGGTTTAGAGTTTTTAAAAAAAATTAATTAAATT
1 AGGGTTTAGAGTTTTT-AAAAAAATTAATTAAATT
1431356 AGGGTTTA
1 AGGGTTTA
1431364 TTTTAAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
33 1 0.02
34 32 0.48
35 32 0.48
36 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (34 bp):
AGGGTTTAGAGTTTTTAAAAAAATTAATTAAATT
Found at i:1431741 original size:125 final size:123
Alignment explanation
Indices: 1431452--1431826 Score: 498
Period size: 125 Copynumber: 3.0 Consensus size: 123
1431442 GTAGTTTCAA
* * *
1431452 AAAAATTAATTTTGAGAAGACAGTTCTGAAAAAATGGTGTCAAAAACGCTTTAAGCAGGATGCAC
1 AAAAA-TAATTTTGAGAAGACGGTTCTGAAAAAATGGTGTCAAAAACGCTTCAAGCAAGATGCAC
** * * *
1431517 TGTCAGCAAAAATATTGAAAAAAGCTCTCATATGACGCTTTTTTTCTACATTAGTTCTTG
65 TGTCAGCAAAAATA-TGAAAAAAGCTCTCACGTGGCGCTCTTTTTCTACAGTAGTTCTTG
* * * *
1431577 AAAAATAATTTTGAGAAGACGGTTTTGAAGAAATGGTGTCAAAAATGCTTCAAACAAGATGCACT
1 AAAAATAATTTTGAGAAGACGGTTCTGAAAAAATGGTGTCAAAAACGCTTCAAGCAAGATGCACT
* * *
1431642 GTCAGCAAAAATACTGAAAAAAAACTCCCACGTGGCGCTCTTTTTATACAGTAGTTCTTG
66 GTCAGCAAAAATA-TG-AAAAAAGCTCTCACGTGGCGCTCTTTTTCTACAGTAGTTCTTG
* * * * *
1431702 AAAAATAATTTTGAGAAGATGGTTCTGAACAAATTGTGTCAAAAACACTTCAAGCAAGATGCATT
1 AAAAATAATTTTGAGAAGACGGTTCTGAAAAAATGGTGTCAAAAACGCTTCAAGCAAGATGCACT
* *
1431767 GTTAGCAAAATTGATGAAAAAAGCTCTCACGTGGACGCTCTTTTTCTACAGTAGTTCTTG
66 GTCAGCAAAAAT-ATGAAAAAAGCTCTCACGTGG-CGCTCTTTTTCTACAGTAGTTCTTG
1431827 TTTGGCCTTA
Statistics
Matches: 218, Mismatches: 29, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
124 84 0.39
125 133 0.61
126 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (123 bp):
AAAAATAATTTTGAGAAGACGGTTCTGAAAAAATGGTGTCAAAAACGCTTCAAGCAAGATGCACT
GTCAGCAAAAATATGAAAAAAGCTCTCACGTGGCGCTCTTTTTCTACAGTAGTTCTTG
Found at i:1434888 original size:15 final size:15
Alignment explanation
Indices: 1434850--1434891 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1434840 TTTGTACAAA
*
1434850 TATATTAAAACAATT
1 TATATTAAAATAATT
1434865 TATATTAAAATAATT
1 TATATTAAAATAATT
1434880 TACTA-TAAAATA
1 TA-TATTAAAATA
1434892 TTAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 23 0.92
16 2 0.08
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (15 bp):
TATATTAAAATAATT
Found at i:1435938 original size:7 final size:7
Alignment explanation
Indices: 1435928--1435952 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1435918 TTATATACAT
1435928 AATACTA
1 AATACTA
1435935 AATACTA
1 AATACTA
1435942 AATACTA
1 AATACTA
1435949 AATA
1 AATA
1435953 TGAAATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:1436415 original size:26 final size:27
Alignment explanation
Indices: 1436378--1436429 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1436368 TAAATATATA
1436378 TTTTTTATTTTTTAATTTTAAAATACT
1 TTTTTTATTTTTTAATTTTAAAATACT
*
1436405 TTTTTTATTTTTTATTTTTAAAATA
1 TTTTTTATTTTTTAATTTTAAAATA
1436430 AATTTTTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTTTTATTTTTTAATTTTAAAATACT
Found at i:1436435 original size:27 final size:27
Alignment explanation
Indices: 1436368--1436436 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
1436358 GAATATATAA
*
1436368 TAAATATATATTTTTTATTTTTTAATTT
1 TAAA-ATAAATTTTTTATTTTTTAATTT
** *
1436396 TAAAATACTTTTTTTATTTTTTATTTT
1 TAAAATAAATTTTTTATTTTTTAATTT
1436423 TAAAATAAATTTTT
1 TAAAATAAATTTTT
1436437 GGTGTTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 32 0.89
28 4 0.11
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (27 bp):
TAAAATAAATTTTTTATTTTTTAATTT
Found at i:1441108 original size:24 final size:24
Alignment explanation
Indices: 1441081--1441130 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1441071 ATGGTAAAAC
*
1441081 ATAATGCTAAAATCATAATATATT
1 ATAATACTAAAATCATAATATATT
* *
1441105 ATAATACTAAAATCTTAGTATATT
1 ATAATACTAAAATCATAATATATT
1441129 AT
1 AT
1441131 TTTAATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (24 bp):
ATAATACTAAAATCATAATATATT
Found at i:1452149 original size:9 final size:9
Alignment explanation
Indices: 1452130--1452190 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
1452120 AAAATATTTT
1452130 AAAATTAAAA
1 AAAATT-AAA
1452140 AAAATTAAA
1 AAAATTAAA
*
1452149 AAGTATTTAAA
1 AA--AATTAAA
**
1452160 AAAATTTTA
1 AAAATTAAA
*
1452169 AAATTTAAA
1 AAAATTAAA
*
1452178 AAATTTAAA
1 AAAATTAAA
1452187 AAAA
1 AAAA
1452191 GTATTTTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
9 27 0.66
10 6 0.15
11 8 0.20
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAATTAAA
Found at i:1452152 original size:39 final size:40
Alignment explanation
Indices: 1452080--1452201 Score: 158
Period size: 38 Copynumber: 3.0 Consensus size: 40
1452070 ACCAAAAATT
1452080 TATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAA-AAAAATT-AAAAAAGTATTTTAAAAA
1452124 TATTTTAAAATTAAAAAAAATT-AAAAAGTA-TTTAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
* * *
1452162 AATTTTAAAATTTAAAAAATTTAAAAAAAGTATTTTAAAA
1 TATTTTAAAATTAAAAAAAATT-AAAAAAGTATTTTAAAA
1452202 TTTAAAAAAT
Statistics
Matches: 72, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
38 27 0.38
39 8 0.11
40 8 0.11
41 14 0.19
42 3 0.04
43 6 0.08
44 6 0.08
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:1452197 original size:30 final size:28
Alignment explanation
Indices: 1452139--1452218 Score: 108
Period size: 30 Copynumber: 2.8 Consensus size: 28
1452129 TAAAATTAAA
*
1452139 AAAAATTAAAAAGTATTT-AAAAAAATTTT
1 AAAATTTAAAAA--ATTTAAAAAAAATTTT
1452168 AAAATTTAAAAAATTTAAAAAAAGTATTTT
1 AAAATTTAAAAAATTTAAAAAAA--ATTTT
1452198 AAAATTTAAAAAATTTAAAAA
1 AAAATTTAAAAAATTTAAAAA
1452219 TAAAAATATT
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
27 4 0.09
28 6 0.13
29 11 0.23
30 26 0.55
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATTTAAAAAATTTAAAAAAAATTTT
Found at i:1452211 original size:39 final size:37
Alignment explanation
Indices: 1452098--1452218 Score: 129
Period size: 39 Copynumber: 3.1 Consensus size: 37
1452088 AAATTAAAAC
*
1452098 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAAATTAAAAAAAGTATTTT--AAA-ATTTTAAAATT-TA
*
1452139 AAAAATT--AAAAAGTATTTAAAAAAATTTTAAAATTTA
1 AAAAATTAAAAAAAGTATTT--TAAAATTTTAAAATTTA
*
1452176 AAAAATTTAAAAAAAGTATTTTAAAATTTAAAAAATTTA
1 AAAAA-TTAAAAAAAGTATTTTAAAATTT-TAAAATTTA
1452215 AAAA
1 AAAA
1452219 TAAAAATATT
Statistics
Matches: 70, Mismatches: 4, Indels: 14
0.80 0.05 0.16
Matches are distributed among these distances:
37 6 0.09
38 20 0.29
39 26 0.37
40 11 0.16
41 7 0.10
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (37 bp):
AAAAATTAAAAAAAGTATTTTAAAATTTTAAAATTTA
Found at i:1452219 original size:38 final size:37
Alignment explanation
Indices: 1452098--1452219 Score: 115
Period size: 38 Copynumber: 3.2 Consensus size: 37
1452088 AAATTAAAAC
*
1452098 AAAAA-TTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTTAAAAAAAGTATTTT--AAA-ATTTTAAAATT-T
* *
1452138 AAAAAATT--AAAAAGTATTTAAAAAAATTTTAAAATTT
1 AAAAATTTAAAAAAAGTATTT--TAAAATTTTAAAATTT
*
1452175 AAAAAATTTAAAAAAAGTATTTTAAAATTTAAAAAATTT
1 -AAAAATTTAAAAAAAGTATTTTAAAATTT-TAAAATTT
1452214 AAAAAT
1 AAAAAT
1452220 AAAAATATTT
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
38 31 0.44
39 21 0.30
40 16 0.23
41 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (37 bp):
AAAAATTTAAAAAAAGTATTTTAAAATTTTAAAATTT
Found at i:1463523 original size:17 final size:17
Alignment explanation
Indices: 1463501--1463534 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1463491 ATCCACTAAT
*
1463501 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1463518 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1463535 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1468162 original size:17 final size:17
Alignment explanation
Indices: 1468140--1468173 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1468130 ATCCACTAAT
*
1468140 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1468157 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1468174 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1478654 original size:3 final size:3
Alignment explanation
Indices: 1478646--1478673 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1478636 TTTTCCCTCA
1478646 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1478674 AGCATCCCAA
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:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1480583 original size:15 final size:16
Alignment explanation
Indices: 1480565--1480598 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
1480555 GAAAACTTTG
1480565 AATTTTAAA-ATATTT
1 AATTTTAAATATATTT
1480580 AATTTTAAATTATATTT
1 AATTTTAAA-TATATTT
1480597 AA
1 AA
1480599 AGTGAATCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTTTAAATATATTT
Found at i:1480641 original size:29 final size:29
Alignment explanation
Indices: 1480577--1480641 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
1480567 TTTTAAAATA
* * *
1480577 TTTAATTTTAAATTATATTTAAAGTGAAT
1 TTTATTTTTAAATTAAATTTAAAATGAAT
* *
1480606 CTCATTTTTAAATTAAATTTAAATATG-AT
1 TTTATTTTTAAATTAAATTTAAA-ATGAAT
1480635 TTTATTT
1 TTTATTT
1480642 CCATTAATAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (29 bp):
TTTATTTTTAAATTAAATTTAAAATGAAT
Found at i:1485688 original size:21 final size:21
Alignment explanation
Indices: 1485664--1485706 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1485654 ACCATATCCC
1485664 AAAGGATTAATTTATGTAAGG
1 AAAGGATTAATTTATGTAAGG
1485685 AAAGGATTAATTTATGTAAGG
1 AAAGGATTAATTTATGTAAGG
1485706 A
1 A
1485707 CTTTGTGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (21 bp):
AAAGGATTAATTTATGTAAGG
Found at i:1496669 original size:23 final size:23
Alignment explanation
Indices: 1496643--1496695 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1496633 TAGGATTTAA
1496643 AGTAAGATACGTAAAACAATTTG
1 AGTAAGATACGTAAAACAATTTG
1496666 AGTAAGATACGTAAAACAATTTG
1 AGTAAGATACGTAAAACAATTTG
*
1496689 AATAAGA
1 AGTAAGA
1496696 GGTAAAAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.51, C:0.08, G:0.17, T:0.25
Consensus pattern (23 bp):
AGTAAGATACGTAAAACAATTTG
Found at i:1496840 original size:26 final size:28
Alignment explanation
Indices: 1496785--1496842 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
1496775 AGAATAAATT
*
1496785 TAAAATTTATGTATAAAGCAACTAAAAA
1 TAAAATTTATATATAAAGCAACTAAAAA
* *
1496813 TAAAA-TTATATATAAA-TAACTTAAAA
1 TAAAATTTATATATAAAGCAACTAAAAA
1496839 TAAA
1 TAAA
1496843 TCATTTGCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 12 0.44
27 10 0.37
28 5 0.19
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.31
Consensus pattern (28 bp):
TAAAATTTATATATAAAGCAACTAAAAA
Found at i:1497009 original size:40 final size:39
Alignment explanation
Indices: 1496950--1497032 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 39
1496940 AATAACATAT
1496950 AAAAAAAATTAAACTAAATAATATAT-ATACATATATAA
1 AAAAAAAATTAAACTAAATAATATATAATACATATATAA
*
1496988 AAAAAACAATTTAAACTAAATAATATATACATACATATATTA
1 AAAAAA-AA-TTAAACTAAATAATATATA-ATACATATATAA
1497030 AAA
1 AAA
1497033 TAGGTGCTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
38 6 0.15
39 2 0.05
40 18 0.45
42 14 0.35
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (39 bp):
AAAAAAAATTAAACTAAATAATATATAATACATATATAA
Found at i:1527429 original size:14 final size:14
Alignment explanation
Indices: 1527406--1527442 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1527396 TACAATATCC
*
1527406 AAATAATAACAACA
1 AAATAGTAACAACA
1527420 AAATAGTAACAACA
1 AAATAGTAACAACA
*
1527434 TAATAGTAA
1 AAATAGTAA
1527443 AATGGTACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.65, C:0.11, G:0.05, T:0.19
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:1527494 original size:61 final size:61
Alignment explanation
Indices: 1527423--1527546 Score: 196
Period size: 61 Copynumber: 2.0 Consensus size: 61
1527413 AACAACAAAA
*
1527423 TAGTAACAACATAATAGTAAAATGGTACCAAAATAAG-GAGAAAACAATAAGAAAATAATAT
1 TAGTAACAACATAATAGTAAAATGGTACCAAAAT-AGTGAGAAAAAAATAAGAAAATAATAT
* * *
1527484 TAGTAGCAACATAATAGTAAAATGGTAGCAAAATAGTGAGAAAAAAATAAGAAAATACTAT
1 TAGTAACAACATAATAGTAAAATGGTACCAAAATAGTGAGAAAAAAATAAGAAAATAATAT
1527545 TA
1 TA
1527547 AAAACAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
60 2 0.03
61 56 0.97
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.21
Consensus pattern (61 bp):
TAGTAACAACATAATAGTAAAATGGTACCAAAATAGTGAGAAAAAAATAAGAAAATAATAT
Found at i:1529142 original size:17 final size:17
Alignment explanation
Indices: 1529117--1529156 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1529107 TTTAAGCTTG
* *
1529117 TTTTAATTTTTTTAATA
1 TTTTAATTTTATTAAAA
*
1529134 TTTTTATTTTATTAAAA
1 TTTTAATTTTATTAAAA
1529151 TTTTAA
1 TTTTAA
1529157 ACATAGATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAATTTTATTAAAA
Found at i:1532055 original size:17 final size:17
Alignment explanation
Indices: 1532033--1532069 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1532023 TTTTAACCGT
1532033 AAGTTTGTAATTTTGAA
1 AAGTTTGTAATTTTGAA
1532050 AAGTTTGTAATTTTGAA
1 AAGTTTGTAATTTTGAA
1532067 AAG
1 AAG
1532070 GAACAAGACT
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:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (17 bp):
AAGTTTGTAATTTTGAA
Found at i:1537375 original size:30 final size:30
Alignment explanation
Indices: 1537339--1537399 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1537329 AAAAAATTAG
1537339 GTAATTTTTTAAAAATATATAGATCTCATT
1 GTAATTTTTTAAAAATATATAGATCTCATT
1537369 GTAATTTTTTAAAAATATATAGATCTCATT
1 GTAATTTTTTAAAAATATATAGATCTCATT
1537399 G
1 G
1537400 AGGAATGTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (30 bp):
GTAATTTTTTAAAAATATATAGATCTCATT
Found at i:1541711 original size:46 final size:47
Alignment explanation
Indices: 1541511--1541731 Score: 203
Period size: 47 Copynumber: 4.6 Consensus size: 47
1541501 GACCATGGTT
* *
1541511 GGATCATGGCAGCA-TGTGAAATGTGATTTCCGTATAAGACCATAGCTG
1 GGAT-ATGGCATCAGTGTGATATGTGA-TTCCGTATAAGACCATAGCTG
* * * * * *
1541559 GGCTATGGCTTCGGAGAAATGTGATTTGTGCTTCCGTATAAGACCATATCCG
1 GGATATGGCATC--AG---TGTGATATGTGATTCCGTATAAGACCATAGCTG
* * * * *
1541611 GGATATGGCATCGGTGTGATATGTGCTACTGTATAAGACCATATCTG
1 GGATATGGCATCAGTGTGATATGTGATTCCGTATAAGACCATAGCTG
*
1541658 GGATATGGCATCAGTGTGATATGTGATT-CGTATAAGACCATGGCTG
1 GGATATGGCATCAGTGTGATATGTGATTCCGTATAAGACCATAGCTG
* *
1541704 GGCTATGGCCTCAGTATGTGATATGTGA
1 GGATATGGCATCAG--TGTGATATGTGA
1541732 CTATGTGCAA
Statistics
Matches: 142, Mismatches: 23, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
46 27 0.19
47 60 0.42
48 15 0.11
49 1 0.01
50 1 0.01
52 29 0.20
53 9 0.06
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (47 bp):
GGATATGGCATCAGTGTGATATGTGATTCCGTATAAGACCATAGCTG
Found at i:1543990 original size:22 final size:22
Alignment explanation
Indices: 1543965--1544007 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1543955 TCTCCCTATT
1543965 TTGCTACCATTTTACTGTTATG
1 TTGCTACCATTTTACTGTTATG
** *
1543987 TTGCTATTATTTTGCTGTTAT
1 TTGCTACCATTTTACTGTTAT
1544008 TGTTTGGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.56
Consensus pattern (22 bp):
TTGCTACCATTTTACTGTTATG
Found at i:1552053 original size:20 final size:20
Alignment explanation
Indices: 1552028--1552065 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1552018 GCGTGTTTGT
*
1552028 CTTCATTATTCCTTTTGTTG
1 CTTCATTACTCCTTTTGTTG
*
1552048 CTTCATTCCTCCTTTTGT
1 CTTCATTACTCCTTTTGT
1552066 ATCTCTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.08, C:0.26, G:0.08, T:0.58
Consensus pattern (20 bp):
CTTCATTACTCCTTTTGTTG
Found at i:1558788 original size:19 final size:20
Alignment explanation
Indices: 1558749--1558788 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1558739 ATTTCTTTTG
*
1558749 TTTTTAAAATATTTTTATAA
1 TTTTTAAAATATTTATATAA
*
1558769 TTTTTAAATTATTTAT-TAA
1 TTTTTAAAATATTTATATAA
1558788 T
1 T
1558789 ATAGCATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTAAAATATTTATATAA
Found at i:1570466 original size:15 final size:16
Alignment explanation
Indices: 1570441--1570474 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1570431 AAATTGTAAT
1570441 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
1570457 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
1570472 TTT
1 TTT
1570475 TAAAAGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:1573946 original size:21 final size:22
Alignment explanation
Indices: 1573936--1573978 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 22
1573926 TCTTTAATTA
1573936 TAAAAT-ATTATTTTATACATT
1 TAAAATAATTATTTTATACATT
1573957 TAAAATAATTATATTTAATACA
1 TAAAATAATTAT-TTT-ATACA
1573979 AATATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 3 0.16
24 5 0.26
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAAATAATTATTTTATACATT
Found at i:1574016 original size:22 final size:23
Alignment explanation
Indices: 1573971--1574017 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
1573961 ATAATTATAT
* *
1573971 TTAATACAAATATATAAATTAAA
1 TTAATAAAAATATATAAATAAAA
*
1573994 TTAATAAAAAT-TATATATAAAA
1 TTAATAAAAATATATAAATAAAA
1574016 TT
1 TT
1574018 TGATGATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAATAAAAATATATAAATAAAA
Found at i:1574824 original size:24 final size:24
Alignment explanation
Indices: 1574773--1574827 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
1574763 ACTCAAAAAA
* **
1574773 TAAATAAACTATACTAATAAATGT
1 TAAATATACTATACTAATAAATAC
*
1574797 TAAATATATTATACTAATAAATAC
1 TAAATATACTATACTAATAAATAC
1574821 TAAATAT
1 TAAATAT
1574828 TCTAGAAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (24 bp):
TAAATATACTATACTAATAAATAC
Found at i:1577965 original size:23 final size:23
Alignment explanation
Indices: 1577939--1578014 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
1577929 ATAAGCGCAA
*
1577939 CACTGATATGTAGCCGAAGCTAT
1 CACTGATATGTAGCCGAAGCTAC
*
1577962 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
1577985 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1578008 CACTGAT
1 CACTGAT
1578015 CAACAACACT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:1579387 original size:24 final size:24
Alignment explanation
Indices: 1579360--1579412 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1579350 TTAGTAAGTC
*
1579360 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1579384 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1579408 AAATA
1 AAATA
1579413 TTCTAGAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1579413 original size:24 final size:24
Alignment explanation
Indices: 1579368--1579413 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1579358 TCAAATAAAC
*
1579368 TATACTAATAAATGCTAAATATAT
1 TATACTAATAAATACTAAATATAT
1579392 TATACTAATAAATACTAAATAT
1 TATACTAATAAATACTAAATAT
1579414 TCTAGAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (24 bp):
TATACTAATAAATACTAAATATAT
Found at i:1580028 original size:11 final size:11
Alignment explanation
Indices: 1579993--1580032 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
1579983 GATTGAATCG
*
1579993 ATTTTTTTAT-
1 ATTTTTTAATA
1580003 ATTTTTTAA-A
1 ATTTTTTAATA
1580013 A-TTTTTAATA
1 ATTTTTTAATA
1580023 ATTTTTTAAT
1 ATTTTTTAAT
1580033 CGAACTGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
9 7 0.27
10 11 0.42
11 8 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTTTTTAATA
Found at i:1587143 original size:13 final size:12
Alignment explanation
Indices: 1587122--1587153 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
1587112 TGCAATTCTC
1587122 AAAAAAAAAAAG
1 AAAAAAAAAAAG
1587134 AAAAAGAAAAAAG
1 AAAAA-AAAAAAG
1587147 AAAAAAA
1 AAAAAAA
1587154 CAGTAGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:1601959 original size:41 final size:41
Alignment explanation
Indices: 1601882--1602073 Score: 252
Period size: 41 Copynumber: 4.8 Consensus size: 41
1601872 AAATATATTT
*
1601882 ATTTTTTTAAATTTTAAAATATTTTT-ACATACTTTTTT-A
1 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTAA
*
1601921 ATTTTTTTAAATTTTTAAATATTTTTAAAATACTTTTTTAA
1 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTAA
* *
1601962 ATTTTTTT-AATTTTAAAATAATTTTAAAATACTTTTTTTTA
1 ATTTTTTTAAATTTTAAAATATTTTTAAAATAC-TTTTTTAA
*
1602003 ATTTTTTT-AATTTTAAAATATTTTTAAAATA-TTTTTAAA
1 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTAA
* *
1602042 ATACTTTTTTAATTTTTTAAA-ATTTTTAAAAT
1 AT--TTTTTTAAATTTTAAAATATTTTTAAAAT
1602074 GTTTTAATAT
Statistics
Matches: 137, Mismatches: 10, Indels: 10
0.87 0.06 0.06
Matches are distributed among these distances:
39 33 0.24
40 33 0.24
41 63 0.46
42 8 0.06
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (41 bp):
ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTAA
Found at i:1602067 original size:8 final size:9
Alignment explanation
Indices: 1601884--1602080 Score: 63
Period size: 9 Copynumber: 19.8 Consensus size: 9
1601874 ATATATTTAT
*
1601884 TTTTTTAAA
1 TTTTTAAAA
*
1601893 TTTTAAAATA
1 TTTTTAAA-A
*
1601903 TTTTTACATAC
1 TTTTTA-A-AA
* *
1601914 TTTTTTAAT
1 TTTTTAAAA
*
1601923 TTTTTTAAA
1 TTTTTAAAA
1601932 TTTTTAAATA
1 TTTTTAAA-A
1601942 TTTTTAAAATA
1 TTTTT-AAA-A
*
1601953 CTTTTTTAAA
1 -TTTTTAAAA
**
1601963 TTTTTTTAA
1 TTTTTAAAA
1601972 -TTTTAAAA
1 TTTTTAAAA
1601980 TAATTTTAAAATA
1 T--TTTT-AAA-A
**
1601993 CTTTTTTTTAA
1 --TTTTTAAAA
**
1602004 TTTTTTTAA
1 TTTTTAAAA
*
1602013 TTTTAAAATA
1 TTTTTAAA-A
1602023 TTTTTAAAATA
1 TTTTT-AAA-A
1602034 TTTTTAAAATA
1 TTTTT-AAA-A
* *
1602045 CTTTTTTAAT
1 -TTTTTAAAA
1602055 TTTTTAAAA
1 TTTTTAAAA
1602064 TTTTTAAAA
1 TTTTTAAAA
1602073 TGTTTTAA
1 T-TTTTAA
1602081 TATTCAAGAA
Statistics
Matches: 149, Mismatches: 22, Indels: 33
0.73 0.11 0.16
Matches are distributed among these distances:
8 6 0.04
9 61 0.41
10 25 0.17
11 36 0.24
12 15 0.10
13 5 0.03
15 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.60
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:1602069 original size:52 final size:51
Alignment explanation
Indices: 1601972--1602078 Score: 153
Period size: 52 Copynumber: 2.1 Consensus size: 51
1601962 ATTTTTTTAA
*
1601972 TTTTAAAATAATTTTAAAATACTTTTTTTTAATTTTTTTAATTTTAAAATAT
1 TTTTAAAATAATTTTAAAATAC-TTTTTTTAATTTTTTAAATTTTAAAATAT
* *
1602024 TTTTAAAATATTTTTAAAATAC-TTTTTTAATTTTTTAAAATTTTTAAAATGT
1 TTTTAAAATAATTTTAAAATACTTTTTTTAATTTTTT-AAA-TTTTAAAATAT
1602076 TTT
1 TTT
1602079 AATATTCAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
50 14 0.28
51 2 0.04
52 34 0.68
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (51 bp):
TTTTAAAATAATTTTAAAATACTTTTTTTAATTTTTTAAATTTTAAAATAT
Found at i:1602078 original size:11 final size:10
Alignment explanation
Indices: 1601893--1602080 Score: 76
Period size: 11 Copynumber: 18.6 Consensus size: 10
1601883 TTTTTTTAAA
1601893 TTTTAAAATAT
1 TTTTAAAAT-T
*
1601904 TTTTACATACTT
1 TTTTA-A-AATT
1601916 TTTT--AATT
1 TTTTAAAATT
*
1601924 TTTTTAAA-T
1 TTTTAAAATT
1601933 TTTT-AAATAT
1 TTTTAAAAT-T
1601943 TTTTAAAATACT
1 TTTTAAAAT--T
*
1601955 TTTTTAAATT
1 TTTTAAAATT
*
1601965 TTTT-TAA--
1 TTTTAAAATT
1601972 TTTTAAAATAAT
1 TTTTAAAAT--T
*
1601984 TTTAAAATACTT
1 TTTTAAA-A-TT
**
1601996 TTTTTTAATT
1 TTTTAAAATT
*
1602006 TTTT-TAA--
1 TTTTAAAATT
1602013 TTTTAAAATAT
1 TTTTAAAAT-T
1602024 TTTTAAAATAT
1 TTTTAAAAT-T
1602035 TTTTAAAATACT
1 TTTTAAAAT--T
*
1602047 TTTT-TAATT
1 TTTTAAAATT
1602056 TTTTAAAA-T
1 TTTTAAAATT
*
1602065 TTTTAAAATG
1 TTTTAAAATT
1602075 TTTTAA
1 TTTTAA
1602081 TATTCAAGAA
Statistics
Matches: 140, Mismatches: 15, Indels: 45
0.70 0.08 0.22
Matches are distributed among these distances:
7 8 0.06
8 14 0.10
9 24 0.17
10 26 0.19
11 33 0.24
12 31 0.22
13 3 0.02
14 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.60
Consensus pattern (10 bp):
TTTTAAAATT
Found at i:1608384 original size:51 final size:50
Alignment explanation
Indices: 1608215--1608439 Score: 182
Period size: 51 Copynumber: 4.4 Consensus size: 50
1608205 TTCAGTGGTT
* * * * * **
1608215 TGCACATAGTACCACCCACGTGACCATTGTCATCCGATACATGTAGTAGCC
1 TGCACATAGTACTACACACGTGACCA-AGCCATCCGGTACACATAGTAGCC
* * ** * * * *
1608266 TACACATAGTACTACACACGTGATCAAGCTTTCCGGTTCACGTAGTAACT
1 TGCACATAGTACTACACACGTGACCAAGCCATCCGGTACACATAGTAGCC
*
1608316 TGCACATAGTACTACACACGTGACCAAGGCCATCTGGTACACATAGTAGCC
1 TGCACATAGTACTACACACGTGACCAA-GCCATCCGGTACACATAGTAGCC
* * * * * *
1608367 TGCATATAGTACTACACATGTGACCATTATCTAT-CGATACACGTAGTAGCC
1 TGCACATAGTACTACACACGTGACCA--AGCCATCCGGTACACATAGTAGCC
* * *
1608418 TGCACTTTGTACTACATACGTG
1 TGCACATAGTACTACACACGTG
1608440 CTCATAGGTA
Statistics
Matches: 137, Mismatches: 34, Indels: 6
0.77 0.19 0.03
Matches are distributed among these distances:
50 40 0.29
51 93 0.68
52 3 0.02
53 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (50 bp):
TGCACATAGTACTACACACGTGACCAAGCCATCCGGTACACATAGTAGCC
Found at i:1610279 original size:101 final size:101
Alignment explanation
Indices: 1610100--1610416 Score: 438
Period size: 101 Copynumber: 3.1 Consensus size: 101
1610090 AATTATTAAA
* * * *
1610100 ACGTAAGACTATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAACTAGACTATGGCATTC
1 ACGTAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTC
* * *
1610165 TGATGATATGACCATAGCTGGGTTATAACACTATGG
66 TGATGATAAGACCATAACTGGGTTATAGCACTATGG
* * *
1610201 ACGTAAGACCATGGTTAGACCACGACAGTGTTTATATGTAAGACCATAGTTGGGCTATGGCATTC
1 ACGTAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTC
* * * *
1610266 TGATGACAAGACCATAACTGAGTTATGGCACCATGG
66 TGATGATAAGACCATAACTGGGTTATAGCACTATGG
* *
1610302 ACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGACATTC
1 ACGTAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTC
* * *
1610367 TGATGATAAGACCACAATTGGGTTATAGCACTA-CG
66 TGATGATAAGACCATAACTGGGTTATAGCACTATGG
*
1610402 ACTGTAAGACTATGG
1 AC-GTAAGACCATGG
1610417 CAGGGCAATG
Statistics
Matches: 188, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
100 3 0.02
101 185 0.98
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (101 bp):
ACGTAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTC
TGATGATAAGACCATAACTGGGTTATAGCACTATGG
Found at i:1615746 original size:42 final size:42
Alignment explanation
Indices: 1615699--1615823 Score: 115
Period size: 42 Copynumber: 3.0 Consensus size: 42
1615689 AAGGCTGCAT
* * *
1615699 GGAAGCACATAAGTGCTAAATGGAAACCTATAAGGGTTAAAC
1 GGAAGCACATAAGAGCTAAACGGAAACCCATAAGGGTTAAAC
* * * * *
1615741 GGAAGCTCATAGGAGCTGAACGGAAACCCATAATGGTTAATC
1 GGAAGCACATAAGAGCTAAACGGAAACCCATAAGGGTTAAAC
* * * * ** *
1615783 TGAAACTCAGAAGAGCTAAACTAAAACCCATTAGGGTTAAA
1 GGAAGCACATAAGAGCTAAACGGAAACCCATAAGGGTTAAA
1615824 TTGAAACTCA
Statistics
Matches: 65, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (42 bp):
GGAAGCACATAAGAGCTAAACGGAAACCCATAAGGGTTAAAC
Found at i:1620200 original size:35 final size:35
Alignment explanation
Indices: 1620161--1620230 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1620151 TTAGTTTTGA
1620161 GGGCCAATAAATAGGAAGGTTCCATCCCCAGTTGT
1 GGGCCAATAAATAGGAAGGTTCCATCCCCAGTTGT
1620196 GGGCCAATAAATAGGAAGGTTCCATCCCCAGTTGT
1 GGGCCAATAAATAGGAAGGTTCCATCCCCAGTTGT
1620231 ACATACTTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (35 bp):
GGGCCAATAAATAGGAAGGTTCCATCCCCAGTTGT
Found at i:1620858 original size:22 final size:24
Alignment explanation
Indices: 1620812--1620858 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
1620802 AAGATTATAG
* *
1620812 ATAAGTTATCAAACTTTTAAATAA
1 ATAAGTTAACAAACTTTCAAATAA
1620836 ATAAGTTAAC-AA-TTTCAAATAA
1 ATAAGTTAACAAACTTTCAAATAA
1620858 A
1 A
1620859 CAAATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 2 0.10
24 9 0.43
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (24 bp):
ATAAGTTAACAAACTTTCAAATAA
Found at i:1621506 original size:34 final size:33
Alignment explanation
Indices: 1621442--1621509 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 33
1621432 TAATAATTTT
*
1621442 TATTTTTTAAAATTTTAAAATTATAATTTTTTAG
1 TATTTTTTAAAAATTTAAAATTAT-ATTTTTTAG
* *
1621476 TATTTTTTAATAAATTTATAAGTTATTTTTTTTA
1 TATTTTTTAA-AAATTTA-AAATTATATTTTTTA
1621510 TAAAATTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 10 0.34
35 13 0.45
36 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (33 bp):
TATTTTTTAAAAATTTAAAATTATATTTTTTAG
Found at i:1621703 original size:16 final size:15
Alignment explanation
Indices: 1621677--1621706 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1621667 ATAATAATAT
1621677 TTAATTTAAATTTAG
1 TTAATTTAAATTTAG
1621692 TTAATATTAAATTTA
1 TTAAT-TTAAATTTA
1621707 AAAATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTAATTTAAATTTAG
Found at i:1626368 original size:129 final size:132
Alignment explanation
Indices: 1626068--1626406 Score: 305
Period size: 129 Copynumber: 2.6 Consensus size: 132
1626058 TTCCGGAGAG
* * * * * * * *
1626068 ATATTCGATTATCTTG-GACAAACGGGAGATTGCAGCCCAGCACGATAGGGTACTATTCCCCGAA
1 ATATTCGATTATTTTGAG-CAAACGAGAAATTGCAACCCAACACGATAGGGCACGATTCCCCAAA
* * * **
1626132 CTGCCAAACATCGAACACTTCTTTCGTTTTAAAAGGTTTTTAGAAAACGTGAATGAAATTTCTAA
65 CTGCCAAACATCGAACACTCCTTTCGTATTAAAAGGTTTTTAGAAAACATGAATGAAATACCTAA
1626197 GGA
130 GGA
* * * * * * ** *
1626200 ATCTTCGATTGTTTAGAACAAATGAAAAAGCGCAACCCAACACGATAGGGCACGA-TCCTCAAA-
1 ATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGATAGGGCACGATTCCCCAAAC
* *
1626263 TCGCCAAACATCGAACA-TCCTTT-GTATTGAAAGGTTTTTA-ATAAACATGAGTGAAA-ACCTA
66 T-GCCAAACATCGAACACTCCTTTCGTATTAAAAGGTTTTTAGA-AAACATGAATGAAATACCT-
1626324 AAGGA
128 AAGGA
* * * * * * *
1626329 ATATTCGATTATTTTGAGCAAACGAGAAATTGCACCCCAACATGTTAGGGCACTATTCCGCGAAT
1 ATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGATAGGGCACGATTCCCCAAAC
*
1626394 TGCCAAATATCGA
66 TGCCAAACATCGA
1626407 GTCTCGTCTT
Statistics
Matches: 162, Mismatches: 39, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
128 3 0.02
129 75 0.46
130 23 0.14
131 22 0.14
132 39 0.24
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (132 bp):
ATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGATAGGGCACGATTCCCCAAAC
TGCCAAACATCGAACACTCCTTTCGTATTAAAAGGTTTTTAGAAAACATGAATGAAATACCTAAG
GA
Found at i:1626743 original size:14 final size:15
Alignment explanation
Indices: 1626712--1626757 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1626702 TGATATAATA
*
1626712 AGTATAATAAATAAT
1 AGTATAATAAAAAAT
*
1626727 AGTGTAA-AAAAAAT
1 AGTATAATAAAAAAT
*
1626741 AGTATAATAAATAAT
1 AGTATAATAAAAAAT
1626756 AG
1 AG
1626758 GAAAATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (15 bp):
AGTATAATAAAAAAT
Found at i:1628803 original size:219 final size:221
Alignment explanation
Indices: 1628458--1629429 Score: 1054
Period size: 219 Copynumber: 4.4 Consensus size: 221
1628448 GCCAAATACA
* * * * * *
1628458 GGAAGGCAAGATCTGCAATCTTCAATCTACTTCCTACCAATATAGGAAGACAGGACCTGCTATCT
1 GGAAGACAAGACCTGCTATCTTCGATCTACTTCCTACCAATATAGGAAGACAAGATCTGCTATCT
* * * * * *
1628523 TCGATCTACTTCATGCCAATACATGAAGACAAGATTTACTTTCTTCGATCCACTCCCTACCAATA
66 TCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCCACTTCCTACCAATA
* * * *
1628588 TAGGGAGACAGGACCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC-AT
131 TAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
* * * *
1628652 CTTG-GATCCACTTC-CTATCAATATA
196 C-TGCGATCTACTTCGCCACCAATATG
* * * * * *
1628677 GGAAGATAGGACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTTTC
1 GGAAGACAAGACCTGCTATCTTCGATCTACTTC-CTACCAATATAGGAAGACAAGATCTGCTATC
* * **
1628741 TTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCCTACCAA
65 TTCGATCTACTTC-ACGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCCACTTCCTACCAA
* * * *
1628805 TATAGAAAGATAGGATCTGCTATCCTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGCT
129 TATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCT
1628870 TTCTGCGATCTACTTCGCCACCAATATG
194 TTCTGCGATCTACTTCGCCACCAATATG
* * * *
1628898 GGAAGACAAGACCTGTTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATC
1 GGAAGACAAGACCTGCTATCTTCGATCTACTTC-CTACCAATATAGGAAGACAAGATCTGCTATC
* **
1628962 TTCGATCTACTTCGC-CCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCCTACCAAT
65 TTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCCACTTCCTACCAAT
* *
1629025 ATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
130 ATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1629090 TCTGCGATCTACTTCGCCACCAATATG
195 TCTGCGATCTACTTCGCCACCAATATG
* * * * *
1629117 GGAAGACAAGATCTG-TATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCT
1 GGAAGACAAGACCTGCTATCTTCGATCTACTTCCTACCAATATAGGAAGACAAGATCTGCTATCT
* * * * * *
1629181 TCGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAAT
66 TCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCCACTTC-CTACCAAT
* * * * * * * * *
1629246 ATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGATAGGATCTACT
130 ATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCT
** * * * **
1629309 ACCTTCGATCTACTTC-ACGCCAATACA
194 TTCTGCGATCTACTTCGCCACCAATATG
* * * * * *
1629336 TGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATC
1 GGAAGACAAGACCTGCTATCTTCGATCTACTTC-CTACCAATATAGGAAGACAAGATCTGCTATC
* * * *
1629400 TTTGATCCACTTC-CTACCAATATAGGAAGA
65 TTCGATCTACTTCAC-GCCAATACAGGAAGA
1629430 TAGGACCTAT
Statistics
Matches: 640, Mismatches: 99, Indels: 27
0.84 0.13 0.04
Matches are distributed among these distances:
217 23 0.04
218 30 0.05
219 336 0.52
220 131 0.20
221 99 0.15
222 21 0.03
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (221 bp):
GGAAGACAAGACCTGCTATCTTCGATCTACTTCCTACCAATATAGGAAGACAAGATCTGCTATCT
TCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCCACTTCCTACCAATA
TAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
CTGCGATCTACTTCGCCACCAATATG
Found at i:1628806 original size:132 final size:132
Alignment explanation
Indices: 1628422--1629434 Score: 1026
Period size: 132 Copynumber: 7.7 Consensus size: 132
1628412 GGGAGGTAAA
* * ** * * * * *
1628422 ATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
1 ATCTGCTATCTTCGATCTACTTC-CCACC-AATATAGGAAGACAAGATCTGCTATCTTCGATCCA
* *
1628487 CTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCATGCCAATACATGAAGA
64 CTTCCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCCTGCCAATACATGAAGA
1628552 CAAG
129 CAAG
* * * * * * * * *
1628556 ATTTACTTTCTTCGATCCAC-TCCCTACCAATATAGGGAGACAGGACCTGTTATCTTCGATCTAC
1 ATCTGCTATCTTCGATCTACTTCCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCCAC
* * * * * * ** * *
1628620 TTCAC-GCCAATACATGAAGACAAGATCTGC-ATCTTGGATCCACTTCCTATCAATATAGGAAGA
65 TTC-CTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCCTGCCAATACATGAAGA
* *
1628683 TAGG
129 CAAG
* * * * * * *
1628687 ACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACT
1 ATCTGCTATCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCCACT
* * * * * *
1628752 TCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCCTACCAATATA-GAAAGA
66 TC-CTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCCTGCCAATACATG-AAGA
* *
1628815 TAGG
129 CAAG
* *** * * * * *
1628819 ATCTGCTATCCTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACT
1 ATCTGCTATCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCCACT
* * * * * * ** ***
1628884 TCGCCACCAATATGGGAAGACAAGACCTGTTTTCTTCGATCTACTTCGCCACCAATATGGGAAGA
66 TC-CTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTC-CTGCCAATACATGAAGA
1628949 CAAG
129 CAAG
* *
1628953 ATCTGC-ATCTTCGATCTACTTCGC-CCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACT
1 ATCTGCTATCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCCACT
* *
1629015 TCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCAC-GCCAATACATGAAGAC
66 TCCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTC-CTGCCAATACATGAAGAC
1629079 AAG
130 AAG
* * *
1629082 ATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTG-TATCTTCGATCCAC
1 ATCTGCTATCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCCAC
* * *
1629146 TTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCATGCCAATACATGAAGAC
65 TTCCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCCTGCCAATACATGAAGAC
1629211 AAG
130 AAG
* * *
1629214 ATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCAC
1 ATCTGCTATCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCCAC
* * *
1629278 TTCCTACCAATATAGGAAGATAGGATCTACTACCTTCGATCTACTTCAC-GCCAATACATGAAGA
65 TTCCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTC-CTGCCAATACATGAAGA
1629342 CAAG
129 CAAG
* * * *
1629346 ATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTTGATCCAC
1 ATCTGCTATCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCCAC
*
1629410 TTCCTACCAATATAGGAAGATAGGA
65 TTCCTACCAATATAGGAAGACAGGA
1629435 CCTATTTACG
Statistics
Matches: 772, Mismatches: 92, Indels: 32
0.86 0.10 0.04
Matches are distributed among these distances:
129 21 0.03
130 51 0.07
131 93 0.12
132 537 0.70
133 34 0.04
134 35 0.05
135 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (132 bp):
ATCTGCTATCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCCACT
TCCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCCTGCCAATACATGAAGACA
AG
Found at i:1629110 original size:351 final size:350
Alignment explanation
Indices: 1628562--1629396 Score: 1291
Period size: 351 Copynumber: 2.4 Consensus size: 350
1628552 CAAGATTTAC
* *
1628562 TTTCTTCGATCCAC-TCCCTACCAATATAGGG-AGACAGGACCTGTTATCTTCGATCTACTTCAC
1 TTTCTTCGATCCACTTCCC-ACCAATAT-GGGAAGACAGGATCTG-CATCTTCGATCTACTTCAC
* * *
1628625 GCCAATACATGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACC
63 GCCAATACATGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATC
* *
1628690 TGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCG
128 TGCTACCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCG
1628755 CCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGA
193 CCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGA
1628820 TCTGCTATCC-TCGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACT
258 TCTGCTA-CCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACT
1628884 TCGCCACCAATATGGGAAGACAAGACCTG
322 TCGCCACCAATATGGGAAGACAAGACCTG
* * *
1628913 TTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCTACTTCGC-
1 -TTTCTTCGATCCACTTC-CCACCAATATGGGAAGACAGGATCTGCATCTTCGATCTACTTCACG
***
1628977 CCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCT
64 CCAATACATGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCT
1629042 GCTACCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGC
129 GCTACCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGC
* *
1629107 CACCAATATGGGAAGACAAGATCTGTATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGAT
194 CACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGAT
1629172 CTGCTACCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
259 CTGCTACCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
*
1629237 GCCACCAATATGGGAAGACAAGATCTG
324 GCCACCAATATGGGAAGACAAGACCTG
** * * * * *
1629264 CATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTACTACCTTCGATCTACTTCACGC
1 TTTCTTCGATCCACTTCCCACCAATATGGGAAGACAGGATCTGC-ATCTTCGATCTACTTCACGC
* * * * * * *
1629329 CAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATC
65 CAATACATGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGATAGGATC
1629394 TGC
128 TGC
1629397 ATCTTTGATC
Statistics
Matches: 439, Mismatches: 36, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
349 22 0.05
350 32 0.07
351 294 0.67
352 46 0.10
353 43 0.10
354 2 0.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (350 bp):
TTTCTTCGATCCACTTCCCACCAATATGGGAAGACAGGATCTGCATCTTCGATCTACTTCACGCC
AATACATGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGC
TACCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCA
CCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGATCT
GCTACCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGC
CACCAATATGGGAAGACAAGACCTG
Found at i:1634788 original size:266 final size:266
Alignment explanation
Indices: 1634314--1634845 Score: 1010
Period size: 266 Copynumber: 2.0 Consensus size: 266
1634304 GCGGATACAT
* *
1634314 ATACGGCTTTGCCCTCATATGCGGAGACATTCGATCATTTTCTTCGTTCGAGCGTTAAGATAAGT
1 ATACGGCTTTGCCCTCATATGCGGAGACATTCGATCATTTTCTTCATTCGAACGTTAAGATAAGT
*
1634379 CTCACGAACTCTTCAAAAGGGACGTATCTTATATCTCCTTTTTACTCAATCCGGGTCGTGACTCG
66 CTCACGAACTCTTCAAAAGGGACGTATCTTATATCTCCTTTTTACTCAATCCGGGCCGTGACTCG
*
1634444 TTGCTCACTAAAACTCATGGTGCTCGTTGGCTTCTCTTTTAAAAAAGTTCAGCGGCTCTCGAATA
131 TTGCTCACTAAAACTCATGGTGCTCGTTGGCTTCTCTTTTAAAAAAGTTCAGCGGCTCTCAAATA
1634509 ATCCTTGTCACATTAAATTCTCGGGCCACGGAGCAATGGTTGTGTGGTCCTCCATTAAACTATCA
196 ATCCTTGTCACATTAAATTCTCGGGCCACGGAGCAATGGTTGTGTGGTCCTCCATTAAACTATCA
1634574 TCCTTC
261 TCCTTC
1634580 ATACGGCTTTGCCCTCATATGCGGAGACATTCGATCATTTTCTTCATTCGAACGTTAAGATAAGT
1 ATACGGCTTTGCCCTCATATGCGGAGACATTCGATCATTTTCTTCATTCGAACGTTAAGATAAGT
1634645 CTCACGAACTCTTCAAAAGGGACGTATCTTATATCTCCTTTTTACTCAATCCGGGCCGTGACTCG
66 CTCACGAACTCTTCAAAAGGGACGTATCTTATATCTCCTTTTTACTCAATCCGGGCCGTGACTCG
* *
1634710 TTGCTCACTAAACCTCATGGTGCTCGTTGGCTTCTCTTTTAAGAAAGTTCAGCGGCTCTCAAATA
131 TTGCTCACTAAAACTCATGGTGCTCGTTGGCTTCTCTTTTAAAAAAGTTCAGCGGCTCTCAAATA
1634775 ATCCTTGTCACATTAAATTCTCGGGCCACGGAGCAATGGTTGTGTGGTCCTCCATTAAACTATCA
196 ATCCTTGTCACATTAAATTCTCGGGCCACGGAGCAATGGTTGTGTGGTCCTCCATTAAACTATCA
1634840 TCCTTC
261 TCCTTC
1634846 TCTTATCACG
Statistics
Matches: 260, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
266 260 1.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.33
Consensus pattern (266 bp):
ATACGGCTTTGCCCTCATATGCGGAGACATTCGATCATTTTCTTCATTCGAACGTTAAGATAAGT
CTCACGAACTCTTCAAAAGGGACGTATCTTATATCTCCTTTTTACTCAATCCGGGCCGTGACTCG
TTGCTCACTAAAACTCATGGTGCTCGTTGGCTTCTCTTTTAAAAAAGTTCAGCGGCTCTCAAATA
ATCCTTGTCACATTAAATTCTCGGGCCACGGAGCAATGGTTGTGTGGTCCTCCATTAAACTATCA
TCCTTC
Found at i:1636389 original size:129 final size:132
Alignment explanation
Indices: 1636156--1636459 Score: 296
Period size: 129 Copynumber: 2.3 Consensus size: 132
1636146 GAGATTGCAG
* * * * *
1636156 CCCAGCACGATAGGGCACTATTCCCCGAACTGCCAAACATCGAACACTTCTTTCGTTTTAAAAGG
1 CCCAACACGATAGGGCACGATTCCCCAAACTGCCAAACATCGAACACTCCTTTCGTATTAAAAGG
* ** * * * *
1636221 TTTTTAGAAAACGTGAATGAAATTTCGAAGGAATCTTCGATTGTTTAGAACAAATGAAAAAACGC
66 TTTTTAGAAAACATGAATGAAACCTCAAAGGAATATTCGATTATTTAGAACAAACGAAAAAACGC
1636286 AA
131 AA
* *
1636288 CCCAACACGATAGGGCACGA-TCCTCAAA-TCGCCAAACATCGAACA-TCCTTT-GTATTGAAAG
1 CCCAACACGATAGGGCACGATTCCCCAAACT-GCCAAACATCGAACACTCCTTTCGTATTAAAAG
* * * * *
1636349 GTTTTTA-ATAAACATGAGTGAAAACCT-AAAGGAATATTCGATTATTTTGAGCAAACGAGAAAT
65 GTTTTTAGA-AAACATGAATG-AAACCTCAAAGGAATATTCGATTATTTAGAACAAACGAAAAAA
*
1636412 TGCAA
128 CGCAA
* * * * * * *
1636417 CCCAACATGTTAGGGCACTATTCCGCGAATTGCCAAATATCGA
1 CCCAACACGATAGGGCACGATTCCCCAAACTGCCAAACATCGA
1636460 GTCTCGTCTT
Statistics
Matches: 141, Mismatches: 26, Indels: 12
0.79 0.15 0.07
Matches are distributed among these distances:
128 1 0.01
129 73 0.52
130 27 0.19
131 22 0.16
132 18 0.13
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (132 bp):
CCCAACACGATAGGGCACGATTCCCCAAACTGCCAAACATCGAACACTCCTTTCGTATTAAAAGG
TTTTTAGAAAACATGAATGAAACCTCAAAGGAATATTCGATTATTTAGAACAAACGAAAAAACGC
AA
Found at i:1636796 original size:14 final size:15
Alignment explanation
Indices: 1636765--1636810 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1636755 TGATATAATA
*
1636765 AGTATAATAAATAAT
1 AGTATAATAAAAAAT
*
1636780 AGTGTAA-AAAAAAT
1 AGTATAATAAAAAAT
*
1636794 AGTATAATAAATAAT
1 AGTATAATAAAAAAT
1636809 AG
1 AG
1636811 GAAAATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (15 bp):
AGTATAATAAAAAAT
Found at i:1640297 original size:23 final size:23
Alignment explanation
Indices: 1640271--1640368 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
1640261 ATAAGTGCCA
1640271 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1640294 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
1640317 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1640339 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1640362 CACTGAT
1 CACTGAT
1640369 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:1640336 original size:45 final size:45
Alignment explanation
Indices: 1640278--1640366 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
1640268 CCACACTGAT
* *
1640278 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
1640323 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1640367 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:1666317 original size:41 final size:41
Alignment explanation
Indices: 1666272--1666362 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
1666262 AAATGGGGTA
1666272 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
1 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
*
1666313 TGGGAGTGGCTTAGATACAAAAGGGTCTGTGCCTCAGGTGT
1 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
*
1666354 TGGGGGTGG
1 TGGGAGTGG
1666363 AGAGTTTGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.21, C:0.13, G:0.41, T:0.25
Consensus pattern (41 bp):
TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
Found at i:1672810 original size:20 final size:20
Alignment explanation
Indices: 1672785--1672822 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1672775 GATAGTAATG
* *
1672785 AGATATCTATATCTATATCT
1 AGATATATATATATATATCT
1672805 AGATATATATATATATAT
1 AGATATATATATATATAT
1672823 ATGAGAAGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (20 bp):
AGATATATATATATATATCT
Found at i:1675393 original size:29 final size:30
Alignment explanation
Indices: 1675361--1675431 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 30
1675351 CAAATAGAGT
* *
1675361 TTCATGTGTATAATTGCAC-CAAATTAAAG
1 TTCATGTATATAATTGCACACAAATCAAAG
* *
1675390 TTCATGTATATAATTTCACATTAAATCAAAG
1 TTCATGTATATAATTGCACA-CAAATCAAAG
1675421 TTCATGTATAT
1 TTCATGTATAT
1675432 TTTTTATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 17 0.47
31 19 0.53
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (30 bp):
TTCATGTATATAATTGCACACAAATCAAAG
Found at i:1675867 original size:20 final size:22
Alignment explanation
Indices: 1675834--1675877 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1675824 GTTTTTAATG
1675834 TTTTAATGTGTTTG-ATAATCA
1 TTTTAATGTGTTTGCATAATCA
* *
1675855 TTTTAA-GTTTTTGCCTAATCA
1 TTTTAATGTGTTTGCATAATCA
1675876 TT
1 TT
1675878 ATTCCATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.09, G:0.11, T:0.55
Consensus pattern (22 bp):
TTTTAATGTGTTTGCATAATCA
Found at i:1677558 original size:13 final size:13
Alignment explanation
Indices: 1677540--1677567 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1677530 TTTAGACTGA
1677540 TTTTTTTAAAATT
1 TTTTTTTAAAATT
1677553 TTTTTTTAAAATT
1 TTTTTTTAAAATT
1677566 TT
1 TT
1677568 AATGATTTAT
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:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTTTAAAATT
Found at i:1677696 original size:7 final size:7
Alignment explanation
Indices: 1677684--1677708 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1677674 ATCTGTTTTT
1677684 TTTTTAA
1 TTTTTAA
1677691 TTTTTAA
1 TTTTTAA
1677698 TTTTTAA
1 TTTTTAA
1677705 TTTT
1 TTTT
1677709 CAATCAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTAA
Found at i:1693113 original size:21 final size:21
Alignment explanation
Indices: 1693089--1693140 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1693079 AGCTCGTTTG
1693089 AGCTTCTGTTCAGCTCTTACA
1 AGCTTCTGTTCAGCTCTTACA
* * **
1693110 AGCTTCTGCTCAGCTTTTATG
1 AGCTTCTGTTCAGCTCTTACA
1693131 AGCTTCTGTT
1 AGCTTCTGTT
1693141 AACGATGTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.42
Consensus pattern (21 bp):
AGCTTCTGTTCAGCTCTTACA
Found at i:1694792 original size:31 final size:31
Alignment explanation
Indices: 1694754--1694819 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
1694744 ACAGGCTGAG
* *
1694754 ACACGGCCGTGTGTTCTTATTTCCAATGTCC
1 ACACGGCCGTGTGTTCCTATTTCAAATGTCC
1694785 ACACGGCCGTGTGTTCCTATTTCAAATGTCC
1 ACACGGCCGTGTGTTCCTATTTCAAATGTCC
1694816 ACAC
1 ACAC
1694820 CGCCTAAGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.32
Consensus pattern (31 bp):
ACACGGCCGTGTGTTCCTATTTCAAATGTCC
Found at i:1697107 original size:2 final size:2
Alignment explanation
Indices: 1697100--1697125 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1697090 TATGTTCATA
1697100 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
1697126 CTCGCATTGG
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:1711850 original size:32 final size:32
Alignment explanation
Indices: 1711792--1711856 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
1711782 CACTTTTCAC
**
1711792 GCTTCTGGTTTAGTCCTGGACCATCTTTTTAG
1 GCTTCTGGTTTAGTCCTAAACCATCTTTTTAG
*
1711824 GCTTCTGGTTTAGAT-CTAAACGATCTTTTTAG
1 GCTTCTGGTTTAG-TCCTAAACCATCTTTTTAG
1711856 G
1 G
1711857 TTTGAAGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (32 bp):
GCTTCTGGTTTAGTCCTAAACCATCTTTTTAG
Found at i:1727160 original size:35 final size:35
Alignment explanation
Indices: 1727121--1727231 Score: 95
Period size: 32 Copynumber: 3.1 Consensus size: 35
1727111 AAGAACAAAC
1727121 AAAAACATATGAAAAGGAATATTTGTTAAACAACAA
1 AAAAACATAT-AAAAGGAATATTTGTTAAACAACAA
** *
1727157 AAAAACATA-AAAA--AA-AAGTGTTAGAAGAACAA
1 AAAAACATATAAAAGGAATATTTGTTA-AACAACAA
* *
1727189 ACAAAAAATTATAAAAAAGGAATATTTGTTAAACAACGA
1 A-AAAACA-TAT--AAAAGGAATATTTGTTAAACAACAA
1727228 AAAA
1 AAAA
1727232 CAAACAAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
31 6 0.10
32 10 0.17
33 5 0.09
34 6 0.10
36 9 0.16
37 4 0.07
38 3 0.05
39 9 0.16
40 6 0.10
ACGTcount: A:0.63, C:0.07, G:0.11, T:0.19
Consensus pattern (35 bp):
AAAAACATATAAAAGGAATATTTGTTAAACAACAA
Done.