Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 4 of 284
Found at i:1000899 original size:15 final size:15
Alignment explanation
Indices: 1000879--1000911 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1000869 ACAAAATAAC
1000879 ATAAAAGCA-ATAAAA
1 ATAAAA-CACATAAAA
1000894 ATAAAACACATAAAA
1 ATAAAACACATAAAA
1000909 ATA
1 ATA
1000912 TGTCCATGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.73, C:0.09, G:0.03, T:0.15
Consensus pattern (15 bp):
ATAAAACACATAAAA
Found at i:1004059 original size:30 final size:30
Alignment explanation
Indices: 1004025--1004085 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1004015 CATTTAATAC
*
1004025 AAACTTTGGAAAAATTATACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
* * *
1004055 AAACTTTTGCATAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
1004085 A
1 A
1004086 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACACTTTTGCCCCT
Found at i:1006660 original size:18 final size:19
Alignment explanation
Indices: 1006627--1006662 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1006617 TTAAATTTAG
*
1006627 TAAATTAATTGAATTATGT
1 TAAATTAAATGAATTATGT
1006646 TAAATTAAATG-ATTATG
1 TAAATTAAATGAATTATG
1006663 GTGCCAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (19 bp):
TAAATTAAATGAATTATGT
Found at i:1007208 original size:50 final size:50
Alignment explanation
Indices: 1007081--1007271 Score: 206
Period size: 49 Copynumber: 3.8 Consensus size: 50
1007071 GCTAGGTCGT
* ** ** * *
1007081 ATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGAGA-ACTTCGATCAC
1 ATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CC-AGATAGATAGGTCAC
* *
1007132 ATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAGCTAGGTCAC
1 ATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGATAGGTCAC
* * * * *
1007182 GTGTGTAGTACTAAGTGCACGCTACTACGTGTACCGGATA-ATTGGTCGC
1 ATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGATAGGTCAC
* *
1007231 ATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAG
1 ATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
1007272 TTTGGCTACA
Statistics
Matches: 118, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
49 44 0.37
50 44 0.37
51 30 0.25
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (50 bp):
ATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGATAGGTCAC
Found at i:1007271 original size:99 final size:101
Alignment explanation
Indices: 1007082--1007271 Score: 267
Period size: 99 Copynumber: 1.9 Consensus size: 101
1007072 CTAGGTCGTA
* *
1007082 TGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGAGAACTTCGATCACATGTGTAGTACTAAG
1 TGTGTAGTACTAAGTGCACGCTACTACGCATACCCGAGAACTTCGATCACATGTGTAGTACTAAG
* *
1007147 TGCAGGCTACTACGTGTATCAGATAGCTAGGTCACG
66 TGCAGGCTACTACGCGTACCAGATAGCTAGGTCACG
** * * * *
1007183 TGTGTAGTACTAAGTGCACGCTACTACGTGTACCGGATAA-TT-GGTCGCATGTGTAGTACTAAG
1 TGTGTAGTACTAAGTGCACGCTACTACGCATACCCGAGAACTTCGATCACATGTGTAGTACTAAG
*
1007246 TGCAGGCTACTATGCGTACCAGATAG
66 TGCAGGCTACTACGCGTACCAGATAG
1007272 TTTGGCTACA
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
99 42 0.54
100 2 0.03
101 34 0.44
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (101 bp):
TGTGTAGTACTAAGTGCACGCTACTACGCATACCCGAGAACTTCGATCACATGTGTAGTACTAAG
TGCAGGCTACTACGCGTACCAGATAGCTAGGTCACG
Found at i:1017789 original size:41 final size:41
Alignment explanation
Indices: 1017715--1017989 Score: 283
Period size: 40 Copynumber: 6.8 Consensus size: 41
1017705 ATGTTTTTTA
* * * *
1017715 CGGCGCTTTTTCAAAAATGCAGCTAAAGA--CCGAGCATTAG
1 CGGCGCCTTTTCAAAAACGCCGCTAAA-ACCCCTAGCATTAG
* *
1017755 CGGCGCCTTTTCACAAACGCCGCTAAAACCCCGAGCATTAG
1 CGGCGCCTTTTCAAAAACGCCGCTAAAACCCCTAGCATTAG
* * * * * * *
1017796 CTGC-ACTTTTCCAAAAACGCTGTTAAAGCTCCTAGCACTAG
1 CGGCGCCTTTT-CAAAAACGCCGCTAAAACCCCTAGCATTAG
* *
1017837 CGGCG-CTATCCAAAAACGCCGCTAAAACCCCTAGCATTAG
1 CGGCGCCTTTTCAAAAACGCCGCTAAAACCCCTAGCATTAG
* * *
1017877 CGGCGCATTTGCAAAACCG-CGCTAAAACCCCTAGCATTAG
1 CGGCGCCTTTTCAAAAACGCCGCTAAAACCCCTAGCATTAG
* * *
1017917 CGGCGCTTTTTCAAAAACGTCGCTAAAACCCCAAGCATTAG
1 CGGCGCCTTTTCAAAAACGCCGCTAAAACCCCTAGCATTAG
*
1017958 CGGCG-CTTTCTCAAAAACGCCGCTAAAGCCCC
1 CGGCGCCTTT-TCAAAAACGCCGCTAAAACCCC
1017990 AAAAGGTGAC
Statistics
Matches: 196, Mismatches: 32, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
39 1 0.01
40 98 0.50
41 97 0.49
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.20
Consensus pattern (41 bp):
CGGCGCCTTTTCAAAAACGCCGCTAAAACCCCTAGCATTAG
Found at i:1017855 original size:81 final size:80
Alignment explanation
Indices: 1017715--1017989 Score: 277
Period size: 81 Copynumber: 3.4 Consensus size: 80
1017705 ATGTTTTTTA
* * * * * * *
1017715 CGGCGCTTTTTCAAAAATGCAGCTAAAG-ACCGAGCATTAGCGGCGCCTT-TTCACAAACGCCGC
1 CGGCGC-TTTCCAAAAACGC-GCTAAAGCCCCTAGCACTAGCGGCG-CTTATCCAAAAACGCCGC
*
1017778 TAAAACCCCGAGCATTAG
63 TAAAACCCCAAGCATTAG
* * * *
1017796 CTGCACTTTTCCAAAAACGCTGTTAAAGCTCCTAGCACTAGCGGCGC-TATCCAAAAACGCCGCT
1 CGGCGC-TTTCCAAAAACGC-GCTAAAGCCCCTAGCACTAGCGGCGCTTATCCAAAAACGCCGCT
*
1017860 AAAACCCCTAGCATTAG
64 AAAACCCCAAGCATTAG
* * * * * * *
1017877 CGGCGCATTTGCAAAACCGCGCTAAAACCCCTAGCATTAGCGGCGCTTTTTCAAAAACGTCGCTA
1 CGGCGC-TTTCCAAAAACGCGCTAAAGCCCCTAGCACTAGCGGCGCTTATCCAAAAACGCCGCTA
1017942 AAACCCCAAGCATTAG
65 AAACCCCAAGCATTAG
1017958 CGGCGCTTTCTCAAAAACGCCGCTAAAGCCCC
1 CGGCGCTTTC-CAAAAACG-CGCTAAAGCCCC
1017990 AAAAGGTGAC
Statistics
Matches: 161, Mismatches: 28, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
80 26 0.16
81 110 0.68
82 25 0.16
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.20
Consensus pattern (80 bp):
CGGCGCTTTCCAAAAACGCGCTAAAGCCCCTAGCACTAGCGGCGCTTATCCAAAAACGCCGCTAA
AACCCCAAGCATTAG
Found at i:1017991 original size:41 final size:40
Alignment explanation
Indices: 1017715--1017989 Score: 295
Period size: 41 Copynumber: 6.8 Consensus size: 40
1017705 ATGTTTTTTA
* * *
1017715 CGGCGCTTTTTCAAAAATGCAGCTAAAGA--CCGAGCATTAG
1 CGGCGC-TTTTCAAAAACGCCGCTAAA-ACCCCTAGCATTAG
* *
1017755 CGGCGCCTTTTCACAAACGCCGCTAAAACCCCGAGCATTAG
1 CGGCG-CTTTTCAAAAACGCCGCTAAAACCCCTAGCATTAG
* * * * * * *
1017796 CTGCACTTTTCCAAAAACGCTGTTAAAGCTCCTAGCACTAG
1 CGGCGCTTTT-CAAAAACGCCGCTAAAACCCCTAGCATTAG
* *
1017837 CGGCGCTATCCAAAAACGCCGCTAAAACCCCTAGCATTAG
1 CGGCGCTTTTCAAAAACGCCGCTAAAACCCCTAGCATTAG
* *
1017877 CGGCGCATTTGCAAAACCG-CGCTAAAACCCCTAGCATTAG
1 CGGCGC-TTTTCAAAAACGCCGCTAAAACCCCTAGCATTAG
* *
1017917 CGGCGCTTTTTCAAAAACGTCGCTAAAACCCCAAGCATTAG
1 CGGCGC-TTTTCAAAAACGCCGCTAAAACCCCTAGCATTAG
*
1017958 CGGCGCTTTCTCAAAAACGCCGCTAAAGCCCC
1 CGGCGCTTT-TCAAAAACGCCGCTAAAACCCC
1017990 AAAAGGTGAC
Statistics
Matches: 198, Mismatches: 30, Indels: 13
0.82 0.12 0.05
Matches are distributed among these distances:
39 1 0.01
40 98 0.49
41 99 0.50
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.20
Consensus pattern (40 bp):
CGGCGCTTTTCAAAAACGCCGCTAAAACCCCTAGCATTAG
Found at i:1018087 original size:27 final size:27
Alignment explanation
Indices: 1018035--1018085 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1018025 AAAAACGCCG
*
1018035 CTAATGCTCTTTTTAGTGGCGATTTCT
1 CTAATGCTCTTTTTAGCGGCGATTTCT
1018062 CTAATGCTCTTTTTAGCGGC-ATTT
1 CTAATGCTCTTTTTAGCGGCGATTT
1018086 TCCATAAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.47
Consensus pattern (27 bp):
CTAATGCTCTTTTTAGCGGCGATTTCT
Found at i:1018153 original size:12 final size:12
Alignment explanation
Indices: 1018136--1018170 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
1018126 TTTGTCCAAA
1018136 TGCCGCTAAAAG
1 TGCCGCTAAAAG
1018148 TGCCGCTAAAAG
1 TGCCGCTAAAAG
1018160 TGCCGCTAAAA
1 TGCCGCTAAAA
1018171 ACCAGTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (12 bp):
TGCCGCTAAAAG
Found at i:1040912 original size:27 final size:27
Alignment explanation
Indices: 1040882--1041059 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
1040872 ATATTGAGTC
* * * *
1040882 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
1040909 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
1040936 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
1040964 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
1040991 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
1041018 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
1041045 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1041060 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:1041021 original size:82 final size:81
Alignment explanation
Indices: 1040903--1041058 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
1040893 TGCTATATAA
* *
1040903 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
1040968 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
1040985 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
1041049 CACTTAGTGC
65 CACTTAGTGC
1041059 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:1043955 original size:45 final size:45
Alignment explanation
Indices: 1043891--1043977 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
1043881 GCCTGTACCT
1043891 TAGATTTCAAATCTGTTAAAGATTTTGAGAGTTTCCATTGTTGAA
1 TAGATTTCAAATCTGTTAAAGATTTTGAGAGTTTCCATTGTTGAA
*
1043936 TAGATTTCGAATCTGTTAAAGATTTTGAGAGTTTCCATTGTT
1 TAGATTTCAAATCTGTTAAAGATTTTGAGAGTTTCCATTGTT
1043978 TAACCTATGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (45 bp):
TAGATTTCAAATCTGTTAAAGATTTTGAGAGTTTCCATTGTTGAA
Found at i:1055506 original size:50 final size:49
Alignment explanation
Indices: 1055340--1055563 Score: 261
Period size: 48 Copynumber: 4.5 Consensus size: 49
1055330 CTAGTACGCA
* * * *
1055340 TAGTAGCCTACACATAGTACTACACATGTGACCAATTATCCGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
1055389 TAGTAGCCTGCACTTAGTACTACACACG-GACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
* ** * *
1055437 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACACG
* * * ** * *
1055487 TAGTATCCTGCACTTAGTACTACACACGTGATCACAGTTTTTGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATCCGGTACACG
*
1055538 TAGTAGCCTTCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
1055564 TGCGACCTCA
Statistics
Matches: 149, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
48 46 0.31
49 29 0.19
50 41 0.28
51 32 0.21
52 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
Found at i:1055561 original size:101 final size:98
Alignment explanation
Indices: 1055333--1055571 Score: 300
Period size: 101 Copynumber: 2.4 Consensus size: 98
1055323 AAGCTATCTA
* ** * *
1055333 GTACGCATAGTAGCCTACACATAGTACTACACATGTGACC-AATTATCCGGTACATGTAGTAGCC
1 GTACGCATAGTAGCCTACACTTAGTACTACACATGTGACCTAACCATCCGATACACGTAGTAGCC
1055397 TGCACTTAGTACTACACACGGACCAATTATCCG
66 TGCACTTAGTACTACACACGGACCAATTATCCG
* * * * *
1055430 GTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGATACACGTAGTATCC
1 GTACGCATAGTAGCCTACACTTAGTACTACACATGTGACCTAACCATCCGATACACGTAGTAGCC
* * **
1055495 TGCACTTAGTACTACACACGTGATCACAGTTTTTGG
66 TGCACTTAGTACTACACACG-GA-C-CAATTATCCG
* *
1055531 GTACGCATAGTAGCCTTCACTTAGTACTACACATGCGACCT
1 GTACGCATAGTAGCCTACACTTAGTACTACACATGTGACCT
1055572 CACAATAGAT
Statistics
Matches: 120, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
97 36 0.30
98 38 0.32
99 2 0.02
100 1 0.01
101 43 0.36
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (98 bp):
GTACGCATAGTAGCCTACACTTAGTACTACACATGTGACCTAACCATCCGATACACGTAGTAGCC
TGCACTTAGTACTACACACGGACCAATTATCCG
Found at i:1080887 original size:24 final size:24
Alignment explanation
Indices: 1080835--1080900 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 24
1080825 AGAAACAATC
*
1080835 ATAAAAATAAAATATAGTTAAAAAG
1 ATAAAAA-AAAATATAGCTAAAAAG
1080860 ATAAAAAAAAATA-AGACTAAGAAA-
1 ATAAAAAAAAATATAG-CTAA-AAAG
1080884 ATAACAATAAAAATATA
1 ATAA-AA-AAAAATATA
1080901 AATATAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
23 2 0.06
24 13 0.37
25 12 0.34
26 7 0.20
27 1 0.03
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (24 bp):
ATAAAAAAAAATATAGCTAAAAAG
Found at i:1090569 original size:43 final size:43
Alignment explanation
Indices: 1090512--1090646 Score: 128
Period size: 43 Copynumber: 3.1 Consensus size: 43
1090502 CCTACATGTT
* * *
1090512 ATCAC-ATATCGATGCCACTATCCCAGATAGGGTCTTACAGGAA
1 ATCACAATAT-GATGCCAATATCCCAGACAGGGTCTTACACGAA
* * * * *
1090555 ATCATAATATGATGCCAATGTCCTAGACATGGTCTTACACGTA
1 ATCACAATATGATGCCAATATCCCAGACAGGGTCTTACACGAA
* * * * * *
1090598 ATCACAATATGACGCCAATGTCTCAGACATGGTCTTACAAGTA
1 ATCACAATATGATGCCAATATCCCAGACAGGGTCTTACACGAA
1090641 ATCACA
1 ATCACA
1090647 TCTCGGTAAC
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 74 0.95
44 4 0.05
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (43 bp):
ATCACAATATGATGCCAATATCCCAGACAGGGTCTTACACGAA
Found at i:1102152 original size:46 final size:46
Alignment explanation
Indices: 1102083--1102180 Score: 178
Period size: 46 Copynumber: 2.1 Consensus size: 46
1102073 ATGGTAGAAA
1102083 ATGAAAGATTATTGAAAGATAAACAACTTTTACAAAGTGATTTTTG
1 ATGAAAGATTATTGAAAGATAAACAACTTTTACAAAGTGATTTTTG
* *
1102129 ATGAAAGATTGTTGAAAGGTAAACAACTTTTACAAAGTGATTTTTG
1 ATGAAAGATTATTGAAAGATAAACAACTTTTACAAAGTGATTTTTG
1102175 ATGAAA
1 ATGAAA
1102181 ACATGATTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (46 bp):
ATGAAAGATTATTGAAAGATAAACAACTTTTACAAAGTGATTTTTG
Found at i:1102225 original size:20 final size:20
Alignment explanation
Indices: 1102200--1102244 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1102190 AGGGACTAAA
* *
1102200 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
1102220 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
1102240 ATGAA
1 ATGAA
1102245 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:1105324 original size:20 final size:21
Alignment explanation
Indices: 1105283--1105331 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
1105273 AAAAATAACT
*
1105283 ACTAAAATATAACTTTGCTAA
1 ACTAAAATATAACTATGCTAA
1105304 ACTAAAA-ATAA-TATGCATAA
1 ACTAAAATATAACTATGC-TAA
1105324 AC-AAAATA
1 ACTAAAATA
1105332 AAAGCAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 8 0.32
20 10 0.40
21 7 0.28
ACGTcount: A:0.57, C:0.12, G:0.04, T:0.27
Consensus pattern (21 bp):
ACTAAAATATAACTATGCTAA
Found at i:1105515 original size:5 final size:5
Alignment explanation
Indices: 1105505--1105536 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
1105495 TAATCAAATA
1105505 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
1105537 TGAACAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1105898 original size:5 final size:5
Alignment explanation
Indices: 1105888--1105912 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1105878 GTTGAAGAAG
1105888 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
1105913 TGGGGTTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1106598 original size:21 final size:22
Alignment explanation
Indices: 1106563--1106604 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
1106553 AGTAGTACCT
1106563 TGTTCCAAGCCTTAATTTGGTG
1 TGTTCCAAGCCTTAATTTGGTG
1106585 TGTTCCAA-CCTTAATTTGGT
1 TGTTCCAAGCCTTAATTTGGT
1106605 ATGGTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (22 bp):
TGTTCCAAGCCTTAATTTGGTG
Found at i:1113660 original size:40 final size:41
Alignment explanation
Indices: 1113567--1113675 Score: 114
Period size: 40 Copynumber: 2.7 Consensus size: 41
1113557 CGCTGACTCA
* *
1113567 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGCCT
1 AAAAGCCCTTCGAAACCAAGCTCGGATTATGACACTGGCCT
* * * * * *
1113608 GAAGGCCTTTCGAAACTAGGTTCGG-TTATGACACTGG-CT
1 AAAAGCCCTTCGAAACCAAGCTCGGATTATGACACTGGCCT
*
1113647 CAAAAGCCCTTCGAGACCAAGCTCGGATT
1 -AAAAGCCCTTCGAAACCAAGCTCGGATT
1113676 TAAACCCCAA
Statistics
Matches: 51, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
39 2 0.04
40 29 0.57
41 20 0.39
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.23
Consensus pattern (41 bp):
AAAAGCCCTTCGAAACCAAGCTCGGATTATGACACTGGCCT
Found at i:1128513 original size:30 final size:30
Alignment explanation
Indices: 1128479--1128539 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1128469 TCCTTAACTC
1128479 AAACTTTAGAAAAATTACAATTTTGCCCCT
1 AAACTTTAGAAAAATTACAATTTTGCCCCT
* * * * *
1128509 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTAGAAAAATTACAATTTTGCCCCT
1128539 A
1 A
1128540 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.38
Consensus pattern (30 bp):
AAACTTTAGAAAAATTACAATTTTGCCCCT
Found at i:1130762 original size:31 final size:31
Alignment explanation
Indices: 1130719--1130790 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
1130709 AGGCCAAGTT
*
1130719 GGGCGTGTGGGCTCACATGGGCAAGCCACAC
1 GGGCATGTGGGCTCACATGGGCAAGCCACAC
1130750 GGGCATGTGGGCTCACATGGGCAAGCCACAC
1 GGGCATGTGGGCTCACATGGGCAAGCCACAC
*
1130781 AGGCATGTGG
1 GGGCATGTGG
1130791 ACCCAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.21, C:0.26, G:0.39, T:0.14
Consensus pattern (31 bp):
GGGCATGTGGGCTCACATGGGCAAGCCACAC
Found at i:1131977 original size:14 final size:14
Alignment explanation
Indices: 1131941--1131977 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1131931 TTCTACCATT
*
1131941 TTACTATTATATTG
1 TTACTATTTTATTG
*
1131955 CTACTATTTTATTG
1 TTACTATTTTATTG
1131969 TTACTATTT
1 TTACTATTT
1131978 GGATATTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.24, C:0.11, G:0.05, T:0.59
Consensus pattern (14 bp):
TTACTATTTTATTG
Found at i:1136703 original size:40 final size:40
Alignment explanation
Indices: 1136609--1136793 Score: 198
Period size: 40 Copynumber: 4.6 Consensus size: 40
1136599 TATTCGAATG
*
1136609 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTA-GTGACT
* * * *
1136650 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
*
1136690 ATATCCGGGCTAAGA-CCTGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCC-GAAGGCATTTGTGCTAGTGACT
* * *
1136730 ATATCCGGGCTATG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* *
1136770 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
1136794 CTTGCGCAAG
Statistics
Matches: 120, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
39 3 0.03
40 85 0.71
41 31 0.26
42 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:1136782 original size:80 final size:81
Alignment explanation
Indices: 1136611--1136793 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 81
1136601 TTCGAATGAT
* * *
1136611 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGCAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGCAT
* * *
1136676 TCGTGCGAGTTGCTAT
66 TCATGCGAGTTGCCAC
* * * *
1136692 ATCCGGGCTAAGACCTGAAGGCATTTGTGCTA-GCGACTATATCCGGGCTATG-TCCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGAT-CCGAAGGCA
* *
1136755 TTTATGCTAG-TGACCAC
65 TTCATGCGAGTTG-CCAC
1136772 ATCCGGGCTAAGACCCGAAGGC
1 ATCCGGGCTAAGACCCGAAGGC
1136794 CTTGCGCAAG
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
79 3 0.03
80 55 0.63
81 29 0.33
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (81 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGCAT
TCATGCGAGTTGCCAC
Found at i:1145523 original size:40 final size:40
Alignment explanation
Indices: 1145458--1145537 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
1145448 TAAATACCTA
* ** *
1145458 AGGGAAATGAAACCTAAGATGGATCTTGTTATTATTATCT
1 AGGGAAATGAAACCTAAAACAGATCTTGTTATAATTATCT
*
1145498 AGGGGAATGAAACCTAAAACAGATCTTGTTATAATTATCT
1 AGGGAAATGAAACCTAAAACAGATCTTGTTATAATTATCT
1145538 GAATTGTATG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33
Consensus pattern (40 bp):
AGGGAAATGAAACCTAAAACAGATCTTGTTATAATTATCT
Found at i:1152636 original size:9 final size:9
Alignment explanation
Indices: 1152619--1152649 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1152609 GTTGTGAATT
1152619 GGCCAAATG
1 GGCCAAATG
*
1152628 GGCCGAATG
1 GGCCAAATG
1152637 GGCCAAATG
1 GGCCAAATG
1152646 GGCC
1 GGCC
1152650 CGATGGGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.39, T:0.10
Consensus pattern (9 bp):
GGCCAAATG
Found at i:1152656 original size:18 final size:18
Alignment explanation
Indices: 1152614--1152649 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1152604 CTTGGGTTGT
*
1152614 GAATTGGCCAAATGGGCC
1 GAATGGGCCAAATGGGCC
1152632 GAATGGGCCAAATGGGCC
1 GAATGGGCCAAATGGGCC
1152650 CGATGGGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.22, G:0.36, T:0.14
Consensus pattern (18 bp):
GAATGGGCCAAATGGGCC
Found at i:1152775 original size:28 final size:29
Alignment explanation
Indices: 1152735--1152814 Score: 110
Period size: 28 Copynumber: 2.8 Consensus size: 29
1152725 ACTGTAAATG
*
1152735 TGATTTGGGCCTAGT-GGCCATATGAATC
1 TGATTTGGGCCTAGTGGGCCATATGAAAC
* *
1152763 TGATTTGGGCCTAATGGGCCATATGAAAG
1 TGATTTGGGCCTAGTGGGCCATATGAAAC
*
1152792 AGA-TTGGGCCTAGTGGGCCATAT
1 TGATTTGGGCCTAGTGGGCCATAT
1152815 ATATATAGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 33 0.72
29 13 0.28
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (29 bp):
TGATTTGGGCCTAGTGGGCCATATGAAAC
Found at i:1161387 original size:30 final size:30
Alignment explanation
Indices: 1161343--1161431 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
1161333 CAAAGATAAT
1161343 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
1161372 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
1161402 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
1161432 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:1161391 original size:15 final size:15
Alignment explanation
Indices: 1161343--1161422 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
1161333 CAAAGATAAT
*
1161343 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
1161357 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
1161372 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
1161387 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
1161402 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
1161417 AAGAAA
1 AAGAAA
1161423 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:1161431 original size:15 final size:15
Alignment explanation
Indices: 1161354--1161431 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
1161344 AGAAAACCGA
1161354 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
1161369 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
1161383 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
1161398 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
1161414 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
1161429 ATA
1 ATA
1161432 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:1175299 original size:28 final size:27
Alignment explanation
Indices: 1175255--1175309 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
1175245 CCACGTCTTT
* *
1175255 CCCTACTACTAGTAGTTATAAGTCAAA
1 CCCTACTACTAGCAGTTATAAATCAAA
*
1175282 NCCCTACTGCTAGCAGTTATAAATCAAA
1 -CCCTACTACTAGCAGTTATAAATCAAA
1175310 ATAAATAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.27
Consensus pattern (27 bp):
CCCTACTACTAGCAGTTATAAATCAAA
Found at i:1177183 original size:15 final size:15
Alignment explanation
Indices: 1177165--1177195 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1177155 CATATTCATC
*
1177165 TTATCAAAAATTCAA
1 TTATAAAAAATTCAA
1177180 TTATAAAAAATTCAA
1 TTATAAAAAATTCAA
1177195 T
1 T
1177196 CACATATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (15 bp):
TTATAAAAAATTCAA
Found at i:1177447 original size:38 final size:38
Alignment explanation
Indices: 1177404--1177480 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
1177394 TTTCAAATTA
1177404 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
* * *
1177442 ACATGTTTAACTGTGGTATATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
1177480 A
1 A
1177481 ATGAACCAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (38 bp):
ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
Found at i:1177549 original size:80 final size:84
Alignment explanation
Indices: 1177416--1177604 Score: 289
Period size: 80 Copynumber: 2.3 Consensus size: 84
1177406 ATGTATAACC
* *
1177416 GTGGCATATCCACTTAGCACCACGTTACATGTTTAACTGTGGTATATCCACTTAGCACCACGTTA
1 GTGGCATATCCACTTAGCACCACGGT--ATGTTTAACCGTGGTATATCCACTTAGCACCACGTTA
1177481 ATGAACCAATATATGTAA-TT
64 ATGAACCAATATATGTAACTT
1177501 GTGGCATATCCACTTAGCACCA-GGT-T-TTTAACCGTGGTATATCCACTTAGCACCACGTTAAT
1 GTGGCATATCCACTTAGCACCACGGTATGTTTAACCGTGGTATATCCACTTAGCACCACGTTAAT
*
1177563 GAATCAATATATGTAACTT
66 GAACCAATATATGTAACTT
*
1177582 -TGGCATATCCACTTAGCAGCACG
1 GTGGCATATCCACTTAGCACCACG
1177605 TTACATGTAT
Statistics
Matches: 98, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
80 70 0.71
81 4 0.04
84 2 0.02
85 22 0.22
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (84 bp):
GTGGCATATCCACTTAGCACCACGGTATGTTTAACCGTGGTATATCCACTTAGCACCACGTTAAT
GAACCAATATATGTAACTT
Found at i:1177640 original size:48 final size:47
Alignment explanation
Indices: 1177533--1177662 Score: 172
Period size: 48 Copynumber: 2.7 Consensus size: 47
1177523 GGTTTTTAAC
*
1177533 CGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATGTAA
1 CGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATGTAA
* * * *
1177579 CTTTGGCATATCCACTTAGCAGCACGTTACATGTATCAATATGTGTAA
1 C-GTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATGTAA
* *
1177627 TCGTGGTACATCCACTTAGCACCACGTTACACGTAT
1 -CGTGGTATATCCACTTAGCACCACGTTACATGTAT
1177663 AACCATGGTA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
46 1 0.01
47 24 0.34
48 45 0.63
49 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (47 bp):
CGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATGTAA
Found at i:1179398 original size:27 final size:27
Alignment explanation
Indices: 1179339--1179399 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
1179329 ATATATATAC
* *
1179339 ATCACATAGGGGCAAAACAGTCATCTT
1 ATCATATAAGGGCAAAACAGTCATCTT
* *
1179366 ACCATATAAGGGCAAAATAGTCAT-TT
1 ATCATATAAGGGCAAAACAGTCATCTT
1179392 AATCATAT
1 -ATCATAT
1179400 GTAAGGGGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (27 bp):
ATCATATAAGGGCAAAACAGTCATCTT
Found at i:1187269 original size:25 final size:25
Alignment explanation
Indices: 1187241--1187291 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1187231 CTTTTATGAT
1187241 TTAGTCCTTTTCACTTAATTAACTA
1 TTAGTCCTTTTCACTTAATTAACTA
1187266 TTAGTCCTTTTCACTTAATTAACTA
1 TTAGTCCTTTTCACTTAATTAACTA
1187291 T
1 T
1187292 CTAAATGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (25 bp):
TTAGTCCTTTTCACTTAATTAACTA
Found at i:1191880 original size:25 final size:25
Alignment explanation
Indices: 1191846--1191894 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1191836 TAAATTAAAT
*
1191846 TATAAAAACTCAAGCAAAACATAAC
1 TATAAAAACTCAAGAAAAACATAAC
*
1191871 TATAAAAACTTAAGAAAAACATAA
1 TATAAAAACTCAAGAAAAACATAA
1191895 TAAAAATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.63, C:0.14, G:0.04, T:0.18
Consensus pattern (25 bp):
TATAAAAACTCAAGAAAAACATAAC
Found at i:1193305 original size:26 final size:26
Alignment explanation
Indices: 1193225--1193321 Score: 83
Period size: 26 Copynumber: 3.8 Consensus size: 26
1193215 TCTCATCCCT
* *
1193225 ATTTTA-CCCTAGCAAAATTTTGACT
1 ATTTTACCCCTAGTAAAATTTTGACA
**
1193250 ATTTTACCCCT-GATAAACA-TTAAACA
1 ATTTTACCCCTAG-TAAA-ATTTTGACA
* *
1193276 ATTTTACCCCTGGTAAAATTTTGACG
1 ATTTTACCCCTAGTAAAATTTTGACA
* *
1193302 ATTTTGCCACTAGTAAAATT
1 ATTTTACCCCTAGTAAAATT
1193322 CGAAAAAATA
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
25 8 0.14
26 47 0.82
27 2 0.04
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (26 bp):
ATTTTACCCCTAGTAAAATTTTGACA
Found at i:1195258 original size:20 final size:20
Alignment explanation
Indices: 1195210--1195250 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1195200 ATTTGTAGTA
1195210 TCCATTTCATCAACAATGCT
1 TCCATTTCATCAACAATGCT
*
1195230 TCCATTTCATCAATAATGCT
1 TCCATTTCATCAACAATGCT
1195250 T
1 T
1195251 TCTCTTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.39
Consensus pattern (20 bp):
TCCATTTCATCAACAATGCT
Found at i:1196895 original size:20 final size:19
Alignment explanation
Indices: 1196872--1196930 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
1196862 ATTTTAACCT
*
1196872 TTTTATATATTTTTTTTGAAT
1 TTTT-TATATTTTTTTT-AAA
*
1196893 TTTTTAAATTTTTTTTAAA
1 TTTTTATATTTTTTTTAAA
* *
1196912 TTTTTATAATTTATTTAAA
1 TTTTTATATTTTTTTTAAA
1196931 AATATAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 18 0.55
20 11 0.33
21 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTATATTTTTTTTAAA
Found at i:1196928 original size:11 final size:10
Alignment explanation
Indices: 1196871--1196928 Score: 55
Period size: 11 Copynumber: 5.6 Consensus size: 10
1196861 AATTTTAACC
1196871 TTTTTATATAT
1 TTTTTATA-AT
*
1196882 TTTTTTTGAAT
1 TTTTTAT-AAT
1196893 TTTTTA-AAT
1 TTTTTATAAT
* *
1196902 TTTTTTTAAA
1 TTTTTATAAT
1196912 TTTTTATAAT
1 TTTTTATAAT
1196922 TTATTTA
1 TT-TTTA
1196929 AAAATATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 8 0.21
10 12 0.32
11 17 0.45
12 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:1196970 original size:28 final size:27
Alignment explanation
Indices: 1196939--1196992 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
1196929 AAAATATAAA
*
1196939 TTTAGAAATT-TTTATAAATATTTTGAAT
1 TTTAAAAATTATTT-TAAAT-TTTTGAAT
*
1196967 TTTAAAAATTATTTTGAATTTTTGAA
1 TTTAAAAATTATTTTAAATTTTTGAA
1196993 AATTATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 13 0.57
29 3 0.13
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (27 bp):
TTTAAAAATTATTTTAAATTTTTGAAT
Found at i:1197009 original size:20 final size:20
Alignment explanation
Indices: 1196945--1197008 Score: 89
Period size: 19 Copynumber: 3.4 Consensus size: 20
1196935 TAAATTTAGA
*
1196945 AATTTTTATAAA-TATTTTG
1 AATTTTTAAAAATTATTTTG
1196964 AA-TTTTAAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
*
1196983 AATTTTTGAAAATTATTTT-
1 AATTTTTAAAAATTATTTTG
1197002 AATTTTT
1 AATTTTT
1197009 TTTGTAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.20
19 18 0.44
20 15 0.37
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:1198468 original size:19 final size:19
Alignment explanation
Indices: 1198444--1198487 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1198434 ATTAAGAACT
1198444 TTTAAATTT-TAAAAAATA
1 TTTAAATTTATAAAAAATA
*
1198462 TTATAAATTTATAAAAATTA
1 TT-TAAATTTATAAAAAATA
1198482 TTTAAA
1 TTTAAA
1198488 AAATAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 11 0.48
20 10 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTAAATTTATAAAAAATA
Found at i:1200612 original size:44 final size:44
Alignment explanation
Indices: 1200525--1200614 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 44
1200515 GTTGAAATAA
* * *
1200525 AATAGAAGTTATGATAATTATACATCTAAAAGAAGTTATAATTT
1 AATAGAAGTTATGATAATTACACATCTAAAAGAAATTAGAATTT
* *
1200569 AATAGAATTTATGATAATTACACATTTAAAA-ATAATTAGAATTT
1 AATAGAAGTTATGATAATTACACATCTAAAAGA-AATTAGAATTT
1200613 AA
1 AA
1200615 ATTATAATCA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 1 0.03
44 39 0.98
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (44 bp):
AATAGAAGTTATGATAATTACACATCTAAAAGAAATTAGAATTT
Found at i:1200622 original size:18 final size:18
Alignment explanation
Indices: 1200582--1200615 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1200572 AGAATTTATG
1200582 ATAATTACACATTTAAAA
1 ATAATTACACATTTAAAA
*
1200600 ATAATTAGA-ATTTAAA
1 ATAATTACACATTTAAA
1200616 TTATAATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAATTACACATTTAAAA
Found at i:1201713 original size:11 final size:10
Alignment explanation
Indices: 1201681--1201718 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
1201671 AATCTCTGAT
1201681 AATCTTGCCA
1 AATCTTGCCA
1201691 AATCCTTG-CA
1 AAT-CTTGCCA
1201701 AATCTTGCCCA
1 AATCTTG-CCA
1201712 AATCTTG
1 AATCTTG
1201719 ATACCAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.16
10 8 0.32
11 13 0.52
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.32
Consensus pattern (10 bp):
AATCTTGCCA
Found at i:1212904 original size:41 final size:40
Alignment explanation
Indices: 1212771--1212994 Score: 308
Period size: 40 Copynumber: 5.6 Consensus size: 40
1212761 AACCCAAGTA
* * * *
1212771 CCTTCGGGATTTA-ACCGGATATAG-CAAATCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
1212810 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
1212850 CCTTCGAGACTTAGCCCGGATATAGTCACTAGCACAAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC-AAATG
* *
1212891 CCTTCGGGTCTTAGCCCGGATATCGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
1212931 CCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAAGTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAA-TG
*
1212972 CCTTCGGGTCTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
1212995 CATCCGAATA
Statistics
Matches: 166, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
39 12 0.07
40 94 0.57
41 60 0.36
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:1212995 original size:81 final size:80
Alignment explanation
Indices: 1212771--1212995 Score: 328
Period size: 81 Copynumber: 2.8 Consensus size: 80
1212761 AACCCAAGTA
* * * * *
1212771 CCTTCGGGATTTAA-CCGGATATAG-CAAATCGCACAAATGCCTTCGGGACTTAGCCCGGATATA
1 CCTTCGGGACTTAACCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATC
*
1212834 GTAACTCGCACAAATG
65 GTAACTAGCACAAATG
* *
1212850 CCTTCGAGACTTAGCCCGGATATAGTCACTAGCACAAAATGCCTTCGGGTCTTAGCCCGGATATC
1 CCTTCGGGACTTAACCCGGATATAGTCACTAGCAC-AAATGCCTTCGGGTCTTAGCCCGGATATC
*
1212915 GTCACTAGCACAAATG
65 GTAACTAGCACAAATG
1212931 CCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAAGTGCCTTCGGGTCTTAGCCCGGATATC
1 CCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAA-TGCCTTCGGGTCTTAGCCCGGATATC
1212996 ATCCGAATAA
Statistics
Matches: 131, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
79 11 0.08
80 19 0.15
81 101 0.77
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATCG
TAACTAGCACAAATG
Found at i:1216974 original size:37 final size:37
Alignment explanation
Indices: 1216924--1217002 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
1216914 TTATTACGAA
* * *
1216924 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
1216961 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
1216998 GTCTT
1 GTCTT
1217003 TAGAGCTCAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:1217208 original size:47 final size:47
Alignment explanation
Indices: 1217165--1218113 Score: 1817
Period size: 47 Copynumber: 20.1 Consensus size: 47
1217155 TTGGCCACTC
* * *
1217165 GGCCTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217212 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217259 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217306 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217353 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217400 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217447 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217494 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217541 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217588 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217635 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217682 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217729 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217776 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217823 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217870 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217917 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1217964 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
*
1218011 GGCCTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTA
1 GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
* * *
1218058 GGCCCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTA
1 GGCCTTATCAC--GTATATACACTTTTACATTCATCACATCGGCCATTA
1218107 GGCCTTA
1 GGCCTTA
1218114 CTATCATTTC
Statistics
Matches: 893, Mismatches: 7, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
47 852 0.95
49 41 0.05
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.34
Consensus pattern (47 bp):
GGCCTTATCACGTATATACACTTTTACATTCATCACATCGGCCATTA
Found at i:1224619 original size:41 final size:41
Alignment explanation
Indices: 1224562--1224804 Score: 278
Period size: 41 Copynumber: 6.0 Consensus size: 41
1224552 GTTATATGAC
*
1224562 TTTTAGCGGTGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
1224603 TTTTAGCGGCGTTTTACCAAAAGCGCCGGTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
1224644 TTTTAGCGGCGTTTTACCAAAAGCGTCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
** * *
1224685 TTTTAGCGGCGTTTTACTGAAGGCGCCGCTAATGCTCT-AT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* * * **
1224725 TTTTAGCGGCATTTTTTACTAAAA-CGCCGTTGTTGCTCT-GT
1 TTTTAGCGGC--GTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* * * * *
1224766 TTTTAGTGGCATTTTTCTTAAAA-CGCCGCTATTGCTCTG
1 TTTTAGCGGCGTTTTAC-CAAAAGCGCCGCTAATGCTCTG
1224805 TATTTTAAAA
Statistics
Matches: 177, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
39 5 0.03
40 29 0.16
41 134 0.76
42 9 0.05
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
Found at i:1226363 original size:52 final size:51
Alignment explanation
Indices: 1226240--1226417 Score: 247
Period size: 52 Copynumber: 3.5 Consensus size: 51
1226230 ACTAGTGACT
*
1226240 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAG-AGATAGC-TTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGTCA
1226289 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGATAGCTTTGGTCA
* * * *
1226341 CAAGTGTGGTACCATGTCAAGGCCACTTTGTGAAGAAGGTAGCTTT-GACTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGTC-A
*
1226392 CAAG-GTTGGTACTATGTGCAGGCCAC
1 CAAGTG-TGGTACTATGTGAAGGCCAC
1226418 CGGGTATCCG
Statistics
Matches: 116, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
49 34 0.29
50 3 0.03
51 39 0.34
52 40 0.34
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (51 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGTCA
Found at i:1250655 original size:76 final size:73
Alignment explanation
Indices: 1250558--1250714 Score: 170
Period size: 73 Copynumber: 2.1 Consensus size: 73
1250548 TGTGACACAC
* * * * * *
1250558 GGCCATGTGTCCCCTGTATCTATTAAATTGAGCAAAACAAAACGTTCACACGATCTAGCACATGG
1 GGCCGTGTGACCCCTGCATCTATT---TTGAGCAAAACAAAACGCTCACACGACCTAGCACACGG
1250623 GCGTGTGGCTT
63 GCGTGTGGCTT
* ** ** * *
1250634 GTCCGTGTGACCCCTGCATCTATTTTTTGCAAGTCAATACGCTCACACGGCCTAGCACACGGGCG
1 GGCCGTGTGACCCCTGCATCTATTTTGAGCAAAACAAAACGCTCACACGACCTAGCACACGGGCG
1250699 TGTGGCTT
66 TGTGGCTT
1250707 GGCCGTGT
1 GGCCGTGT
1250715 AACCTAAGCC
Statistics
Matches: 67, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
73 47 0.70
76 20 0.30
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.27
Consensus pattern (73 bp):
GGCCGTGTGACCCCTGCATCTATTTTGAGCAAAACAAAACGCTCACACGACCTAGCACACGGGCG
TGTGGCTT
Found at i:1263737 original size:48 final size:48
Alignment explanation
Indices: 1263664--1263938 Score: 210
Period size: 48 Copynumber: 5.8 Consensus size: 48
1263654 TTCAGTTATG
* *** *
1263664 TATTGGCACTTGGTGTGCAAAATTGAAATAGCTTCGGCTATATATATA
1 TATTGGCACTTAGTGTGCGTGATTGAGATAGCTTCGGCTATATATATA
* * * *
1263712 TATTGGCACTTAGTGTGCGTTATTGAGGTAGCTCCAGCTATATATATA
1 TATTGGCACTTAGTGTGCGTGATTGAGATAGCTTCGGCTATATATATA
* * * *
1263760 TATTGGCAGTTAGTGCGCGTGATTGAGATAGCTCCGTCTATATATATATATATA
1 TATTGGCACTTAGTGTGCGTGATTGAGATAGCTTCGGC------TATATATATA
* ** *
1263814 TATTGGCACATAGTGTGCGAT-ACCGAGATAGCTTCGGC--TACATAT-
1 TATTGGCACTTAGTGTGCG-TGATTGAGATAGCTTCGGCTATATATATA
*
1263859 T-TTGGCACTTAGTATGCGTGATTGAGATAGC-TCTGGC----TATATA
1 TATTGGCACTTAGTGTGCGTGATTGAGATAGCTTC-GGCTATATATATA
* ** *
1263902 TATTGGCACTTAGTGTGCGAGATCAATATAGCTTCGG
1 TATTGGCACTTAGTGTGCGTGATTGAGATAGCTTCGG
1263939 TTGTTTATTT
Statistics
Matches: 183, Mismatches: 32, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
42 4 0.02
43 4 0.02
44 54 0.30
45 3 0.02
46 6 0.03
48 72 0.39
54 39 0.21
55 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (48 bp):
TATTGGCACTTAGTGTGCGTGATTGAGATAGCTTCGGCTATATATATA
Found at i:1263882 original size:98 final size:101
Alignment explanation
Indices: 1263702--1263904 Score: 259
Period size: 102 Copynumber: 2.0 Consensus size: 101
1263692 TAGCTTCGGC
* * ** * *
1263702 TATATATATATATTGGCACTTAGTGTGCGTTATTGAGGTAGCTCCAGCTATATATATATATTGGC
1 TATATATATATATTGGCACATAGTGTGCGATACCGAGATAGCTCCAGC-ATACATATATATTGGC
* * *
1263767 AGTTAGTGCGCGTGATTGAGATAGCTCCGTCTATATA
65 ACTTAGTACGCGTGATTGAGATAGCTCCGGCTATATA
* *
1263804 TATATATATATATTGGCACATAGTGTGCGATACCGAGATAGCTTCGGC-TACATAT-T-TTGGCA
1 TATATATATATATTGGCACATAGTGTGCGATACCGAGATAGCTCCAGCATACATATATATTGGCA
* *
1263866 CTTAGTATGCGTGATTGAGATAGCTCTGGCTATATA
66 CTTAGTACGCGTGATTGAGATAGCTCCGGCTATATA
1263902 TAT
1 TAT
1263905 TGGCACTTAG
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
98 40 0.45
99 1 0.01
100 6 0.07
102 41 0.47
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.36
Consensus pattern (101 bp):
TATATATATATATTGGCACATAGTGTGCGATACCGAGATAGCTCCAGCATACATATATATTGGCA
CTTAGTACGCGTGATTGAGATAGCTCCGGCTATATA
Found at i:1263886 original size:44 final size:44
Alignment explanation
Indices: 1263811--1263938 Score: 141
Period size: 44 Copynumber: 2.9 Consensus size: 44
1263801 ATATATATAT
* * * *
1263811 ATATATTGGCACATAGTGTGCGATACCGAGATAGCTTCGGCTAC
1 ATATATTGGCACTTAGTATGCGAGATCGAGATAGCTTCGGCTAC
* * * *
1263855 ATATTTTGGCACTTAGTATGCGTGATTGAGATAGC-TCTGGCTAT
1 ATATATTGGCACTTAGTATGCGAGATCGAGATAGCTTC-GGCTAC
* * *
1263899 ATATATTGGCACTTAGTGTGCGAGATCAATATAGCTTCGG
1 ATATATTGGCACTTAGTATGCGAGATCGAGATAGCTTCGG
1263939 TTGTTTATTT
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
43 2 0.03
44 64 0.94
45 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (44 bp):
ATATATTGGCACTTAGTATGCGAGATCGAGATAGCTTCGGCTAC
Found at i:1265445 original size:46 final size:46
Alignment explanation
Indices: 1265395--1266396 Score: 1714
Period size: 46 Copynumber: 21.7 Consensus size: 46
1265385 TGGTTGAGCA
1265395 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1265441 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1265487 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1265533 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1265579 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1265625 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1265671 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1265717 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1265763 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1265809 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1265855 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1265901 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1265947 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1265993 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1266039 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1266085 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1266131 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
1266177 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
1266222 CATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
1266270 TCCGAACTCATTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
1266315 CATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
1266363 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
1266397 GGGGCGGGTT
Statistics
Matches: 913, Mismatches: 25, Indels: 36
0.94 0.03 0.04
Matches are distributed among these distances:
42 4 0.00
43 7 0.01
45 6 0.01
46 825 0.90
47 55 0.06
48 6 0.01
50 6 0.01
51 4 0.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:1266246 original size:47 final size:47
Alignment explanation
Indices: 1266177--1266345 Score: 211
Period size: 47 Copynumber: 3.6 Consensus size: 47
1266167 GATGCGAATG
*
1266177 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
* * * * *
1266224 TCCGAACTCATTGAGTTGAGTCCGAGTTCACT--TATG-GA-TACGAA
1 TCCGAACTCATTGAGTTGAGTCCGAGTTC-GTGAAATGTAACTAGGCA
1266268 TGTCCGAACTCATTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
1 --TCCGAACTCATTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
* *
1266317 TCCAAACTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCATTGAGTTGAGTCCGAGTTC
1266346 ACTTATGGAT
Statistics
Matches: 102, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
44 4 0.04
45 2 0.02
46 32 0.31
47 58 0.57
48 2 0.02
49 4 0.04
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (47 bp):
TCCGAACTCATTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
Found at i:1271056 original size:49 final size:49
Alignment explanation
Indices: 1270984--1271080 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
1270974 ATTAAGCTTA
*
1270984 TGCTAGCAATAATTCAACCTAGGGTTCATATTTGGAAAAATAGCCATAT
1 TGCTAGCAATAATTCAACCTAGGGTTCATATTTGGAAAAATACCCATAT
1271033 TGCTAGCAATAATTCAACCTAGGGTTCATATTTGGAAAAATACCCATA
1 TGCTAGCAATAATTCAACCTAGGGTTCATATTTGGAAAAATACCCATA
1271081 GGTGAAATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (49 bp):
TGCTAGCAATAATTCAACCTAGGGTTCATATTTGGAAAAATACCCATAT
Found at i:1271487 original size:38 final size:38
Alignment explanation
Indices: 1271445--1271519 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
1271435 AGGAAAACTG
*
1271445 AAATTCGGGCTAAAATGGAAAAATACCAAGTTGTGGAT
1 AAATTCGGGCTAAAATGAAAAAATACCAAGTTGTGGAT
1271483 AAATTCGGGCTAAAATGAAAAAATACCAAGTTGTGGA
1 AAATTCGGGCTAAAATGAAAAAATACCAAGTTGTGGA
1271520 CGAAATGGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.23
Consensus pattern (38 bp):
AAATTCGGGCTAAAATGAAAAAATACCAAGTTGTGGAT
Found at i:1271881 original size:46 final size:46
Alignment explanation
Indices: 1271831--1272187 Score: 578
Period size: 46 Copynumber: 7.7 Consensus size: 46
1271821 TGGTTGAGCA
1271831 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1271877 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1271923 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1271969 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1272015 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
1272061 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
1272106 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
1272154 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
1272188 GGGGCGGGTT
Statistics
Matches: 291, Mismatches: 11, Indels: 18
0.91 0.03 0.06
Matches are distributed among these distances:
42 2 0.01
43 4 0.01
45 3 0.01
46 245 0.84
47 29 0.10
48 3 0.01
50 3 0.01
51 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:1274342 original size:20 final size:20
Alignment explanation
Indices: 1274303--1274343 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1274293 TGCATATGGC
1274303 TTATGTTATGTGATTAAGGT
1 TTATGTTATGTGATTAAGGT
1274323 TTATGTTATGTGATTAAGGT
1 TTATGTTATGTGATTAAGGT
1274343 T
1 T
1274344 GGATTCATTA
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:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (20 bp):
TTATGTTATGTGATTAAGGT
Found at i:1276758 original size:39 final size:39
Alignment explanation
Indices: 1276336--1276746 Score: 671
Period size: 39 Copynumber: 10.5 Consensus size: 39
1276326 ACAAAGCATG
* * *
1276336 CGGGACTTTAAGCCCGGATGTAATACCAGCAC-AAAGCCTT
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
1276376 CAGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
1276415 CGGGACTTAGCCCGGGTATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
1276454 TGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
1276493 CGGGACTTAGCCCGGGTATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
1276532 TGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
1276571 CGGGACTTAGCCCGGGTATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
1276610 TGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
1276649 CGGGACTTAGCCCGAATTTAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
1276688 CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
1276727 CGGGAATTAGCCCGGATATA
1 CGGGACTTAGCCCGGATATA
1276747 TATCTCACAC
Statistics
Matches: 347, Mismatches: 23, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
38 20 0.06
39 322 0.93
40 5 0.01
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:1280194 original size:31 final size:31
Alignment explanation
Indices: 1280156--1280217 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1280146 TCTCTATGTT
*
1280156 TCCTACAAAAATTTTGAAATCTTTTCCCTAC
1 TCCTACAAAAATTTTGAAATCTTATCCCTAC
1280187 TCCTACAAAAATTTTGAAATCTTATCCCTAC
1 TCCTACAAAAATTTTGAAATCTTATCCCTAC
1280218 ATAATTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (31 bp):
TCCTACAAAAATTTTGAAATCTTATCCCTAC
Found at i:1289578 original size:21 final size:20
Alignment explanation
Indices: 1289554--1289602 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1289544 GCTTTTCCAC
1289554 AAAACAAATTAAAAAAATTAA
1 AAAACAAATTAAAAAAA-TAA
* * * *
1289575 AAAATATATTAGAAAAATAC
1 AAAACAAATTAAAAAAATAA
1289595 AAAACAAA
1 AAAACAAA
1289603 CTTTATATTT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.18
Consensus pattern (20 bp):
AAAACAAATTAAAAAAATAA
Found at i:1292359 original size:17 final size:17
Alignment explanation
Indices: 1292334--1292374 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1292324 AGTTAAGAGA
*
1292334 CTGGTATTAAGGCCTAT
1 CTGGAATTAAGGCCTAT
1292351 CTGGAATTAAGGCCTAT
1 CTGGAATTAAGGCCTAT
1292368 CTGGAAT
1 CTGGAAT
1292375 GGAAACTCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (17 bp):
CTGGAATTAAGGCCTAT
Found at i:1299202 original size:41 final size:42
Alignment explanation
Indices: 1299140--1299223 Score: 152
Period size: 41 Copynumber: 2.0 Consensus size: 42
1299130 GGTGTGTTTG
*
1299140 TACACTACTTAACATTCTCTTTTGTTATTTAATAAATTCTAA
1 TACACTACTTAACATTCTCTTTTCTTATTTAATAAATTCTAA
1299182 TACACTACTT-ACATTCTCTTTTCTTATTTAATAAATTCTAA
1 TACACTACTTAACATTCTCTTTTCTTATTTAATAAATTCTAA
1299223 T
1 T
1299224 TTTCTAGAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 31 0.76
42 10 0.24
ACGTcount: A:0.32, C:0.18, G:0.01, T:0.49
Consensus pattern (42 bp):
TACACTACTTAACATTCTCTTTTCTTATTTAATAAATTCTAA
Found at i:1310772 original size:43 final size:44
Alignment explanation
Indices: 1310703--1310788 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 44
1310693 TATCCTAGAA
*
1310703 AAAAAAAGAATTTAAAAAGAGAAGAAGATAATCTTGGGTTGTTG
1 AAAAAAAGAATTTAAAAAAAGAAGAAGATAATCTTGGGTTGTTG
* *
1310747 AAAAAAA-ATTTTAAAAAAAGGAGAAGATAATCTTGGGTTGTT
1 AAAAAAAGAATTTAAAAAAAGAAGAAGATAATCTTGGGTTGTT
1310789 AGATTTATCC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 32 0.82
44 7 0.18
ACGTcount: A:0.50, C:0.02, G:0.21, T:0.27
Consensus pattern (44 bp):
AAAAAAAGAATTTAAAAAAAGAAGAAGATAATCTTGGGTTGTTG
Found at i:1312156 original size:19 final size:20
Alignment explanation
Indices: 1312134--1312171 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1312124 TCATTAATAA
1312134 ATTTATT-AATTTTTAACCG
1 ATTTATTGAATTTTTAACCG
*
1312153 ATTTATTGATTTTTTAACC
1 ATTTATTGAATTTTTAACC
1312172 TTAATCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.55
Consensus pattern (20 bp):
ATTTATTGAATTTTTAACCG
Found at i:1314642 original size:12 final size:12
Alignment explanation
Indices: 1314625--1314652 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1314615 ATAATTTACG
1314625 AAAATTTTAATA
1 AAAATTTTAATA
1314637 AAAATTTTAATA
1 AAAATTTTAATA
1314649 AAAA
1 AAAA
1314653 AAAGAGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAATTTTAATA
Found at i:1315107 original size:21 final size:21
Alignment explanation
Indices: 1315061--1315108 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1315051 AATATAAATT
* * *
1315061 ATATGATACATTTATTTATTT
1 ATATAATACATTTAGTTATTG
*
1315082 TTATAATACATTTAGTTATTG
1 ATATAATACATTTAGTTATTG
1315103 ATATAA
1 ATATAA
1315109 AAGATGATAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (21 bp):
ATATAATACATTTAGTTATTG
Found at i:1321620 original size:49 final size:49
Alignment explanation
Indices: 1321531--1321656 Score: 146
Period size: 49 Copynumber: 2.6 Consensus size: 49
1321521 GATGCTGACA
* * *
1321531 CCATGTCCTAGACATGGTCTTACACTGACTTTCATATATCGAG-GCCGATG
1 CCATGTCCCAGACA-GGTCTTACACTGACTCTCATATATCG-GTGCCAATG
* * * * * *
1321581 CCGTGTCCCAGATAGGTCTTGCACTGGCTCTCATCTATCGGTGTCAATG
1 CCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCGGTGCCAATG
1321630 CCATGTCCCAGACAGGTCTTACACTGA
1 CCATGTCCCAGACAGGTCTTACACTGA
1321657 GACACAATAA
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
48 1 0.02
49 50 0.81
50 11 0.18
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (49 bp):
CCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCGGTGCCAATG
Found at i:1321817 original size:46 final size:45
Alignment explanation
Indices: 1321719--1321821 Score: 111
Period size: 46 Copynumber: 2.2 Consensus size: 45
1321709 TCTCGAGGTT
* *
1321719 GATGCATATCCCAGACATGTCTTACACTAGCTCTCGTCTTAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTC-TCATAATGCC
* * *
1321765 GCTGCATGTCTCAGACATGTCTTACACTGGCTCT-T-ATAATGTGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCTCATAA--T-GCC
1321811 GATGCATGTCC
1 GATGCATGTCC
1321822 TACACTAACA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
43 3 0.06
44 1 0.02
45 1 0.02
46 42 0.89
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.31
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTCTCTCATAATGCC
Found at i:1323120 original size:25 final size:26
Alignment explanation
Indices: 1323075--1323125 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
1323065 AAAAGAAAAA
1323075 GAAAAGAAAGAGATAGTAAATAAAATT
1 GAAAAGAAAGAGATAG-AAATAAAATT
1323102 GAAAAGAAAGATGA-A-AAATAAAAT
1 GAAAAGAAAGA-GATAGAAATAAAAT
1323126 AAAAAAGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 9 0.39
27 12 0.52
28 2 0.09
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.16
Consensus pattern (26 bp):
GAAAAGAAAGAGATAGAAATAAAATT
Found at i:1327408 original size:4 final size:4
Alignment explanation
Indices: 1327399--1327427 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1327389 CCCTTTTCTA
1327399 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1327428 CACGTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:1333538 original size:12 final size:11
Alignment explanation
Indices: 1333514--1333543 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1333504 CATTTTGTTC
1333514 TTTAGTTTCTTT
1 TTTA-TTTCTTT
1333526 TTTATTTCTTT
1 TTTATTTCTTT
1333537 TTTATTT
1 TTTATTT
1333544 TTGTTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTATTTCTTT
Found at i:1334501 original size:20 final size:22
Alignment explanation
Indices: 1334463--1334502 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1334453 TTTTCAAATA
*
1334463 CTTTTGTATATTATCATTATCT
1 CTTTTATATATTATCATTATCT
1334485 CTTTTATATA-TAT-ATTAT
1 CTTTTATATATTATCATTAT
1334503 ATTAGGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 3 0.18
22 9 0.53
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.60
Consensus pattern (22 bp):
CTTTTATATATTATCATTATCT
Found at i:1342656 original size:47 final size:47
Alignment explanation
Indices: 1342547--1342657 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
1342537 CCGGGATAAG
*
1342547 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
1342594 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
1342641 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
1342658 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:1343430 original size:4 final size:4
Alignment explanation
Indices: 1343421--1343445 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1343411 CCCTTTTCTA
1343421 TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC T
1343446 CACGTTTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:1343489 original size:14 final size:14
Alignment explanation
Indices: 1343470--1343500 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1343460 GTAACTTTTC
1343470 TATTCTTTACTCAT
1 TATTCTTTACTCAT
*
1343484 TATTCTTTATTCAT
1 TATTCTTTACTCAT
1343498 TAT
1 TAT
1343501 ACTATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTCTTTACTCAT
Found at i:1345570 original size:20 final size:22
Alignment explanation
Indices: 1345532--1345571 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1345522 TTTTCAAATA
*
1345532 CTTTTGTATATTATCATTATCT
1 CTTTTATATATTATCATTATCT
1345554 CTTTTATATA-TAT-ATTAT
1 CTTTTATATATTATCATTAT
1345572 ATTAGGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 3 0.18
22 9 0.53
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.60
Consensus pattern (22 bp):
CTTTTATATATTATCATTATCT
Found at i:1348231 original size:24 final size:21
Alignment explanation
Indices: 1348204--1348276 Score: 78
Period size: 24 Copynumber: 3.3 Consensus size: 21
1348194 TTTCTTTCCT
1348204 TTGCATTCATCCCATGCATTTGCA
1 TTGCATTCAT--CATGCA-TTGCA
1348228 TTGCATTGCATCATGTGCATTGCA
1 TTGCATT-CATCA--TGCATTGCA
1348252 TTGCA-TCAT-ATGCATTGCA
1 TTGCATTCATCATGCATTGCA
1348271 TTGCAT
1 TTGCAT
1348277 CATTTGCATT
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
19 14 0.31
21 1 0.02
22 3 0.07
23 3 0.07
24 17 0.38
25 7 0.16
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.38
Consensus pattern (21 bp):
TTGCATTCATCATGCATTGCA
Found at i:1348233 original size:5 final size:5
Alignment explanation
Indices: 1348218--1348276 Score: 63
Period size: 5 Copynumber: 12.0 Consensus size: 5
1348208 ATTCATCCCA
1348218 TGCATT TGCAT TGCAT TGCA- T-CAT GTGCAT TGCAT TGCA- T-CAT ATGCAT
1 TGCA-T TGCAT TGCAT TGCAT TGCAT -TGCAT TGCAT TGCAT TGCAT -TGCAT
1348267 TGCAT TGCAT
1 TGCAT TGCAT
1348277 CATTTGCATT
Statistics
Matches: 47, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
3 4 0.09
4 2 0.04
5 31 0.66
6 10 0.21
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (5 bp):
TGCAT
Found at i:1348246 original size:19 final size:19
Alignment explanation
Indices: 1348224--1348286 Score: 108
Period size: 19 Copynumber: 3.3 Consensus size: 19
1348214 CCCATGCATT
*
1348224 TGCATTGCATTGCATCATG
1 TGCATTGCATTGCATCATA
1348243 TGCATTGCATTGCATCATA
1 TGCATTGCATTGCATCATA
*
1348262 TGCATTGCATTGCATCATT
1 TGCATTGCATTGCATCATA
1348281 TGCATT
1 TGCATT
1348287 AGATTTTCCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (19 bp):
TGCATTGCATTGCATCATA
Found at i:1350543 original size:47 final size:47
Alignment explanation
Indices: 1350274--1350544 Score: 266
Period size: 47 Copynumber: 5.8 Consensus size: 47
1350264 CACATTATGA
* * * *
1350274 GAGCCAATGTAAGACCATGTTTGGGACATGGCATTGGCATTGAGACGA-
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGAC-TTGAGA-TAT
* * * * **
1350322 GAGCTAATGTAAGA-CATGTCTGGGACAT-GCATTGGCCTCGAGACGT
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCA-TCGACTTGAGATAT
* * * *
1350368 TAGCCAATGTAAGA-CATGTCTGGGACA-AGCAGCGGCTTCGAGATGAT
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGACTT-GAGAT-AT
* * * * *
1350415 -AGTCAGTGTAAAACCATGTCAGGGACATGGCATCAACTTGAGATAT
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATAT
*
1350461 GAGCCATTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATAT
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATAT
*
1350508 GAGCCATTGTAAGACCATGTCTGGGACATGGCATCGA
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGA
1350545 TACCTTACCC
Statistics
Matches: 187, Mismatches: 28, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
45 3 0.02
46 52 0.28
47 112 0.60
48 20 0.11
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (47 bp):
GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATAT
Found at i:1364087 original size:24 final size:24
Alignment explanation
Indices: 1364057--1364107 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
1364047 ATTTGCTAAT
1364057 AAAGTAGAATGGCTAAAGTAATAA
1 AAAGTAGAATGGCTAAAGTAATAA
1364081 AAAGTAGAATGGCTAAAGTAATAA
1 AAAGTAGAATGGCTAAAGTAATAA
1364105 AAA
1 AAA
1364108 TCGAGTGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.57, C:0.04, G:0.20, T:0.20
Consensus pattern (24 bp):
AAAGTAGAATGGCTAAAGTAATAA
Found at i:1366576 original size:16 final size:16
Alignment explanation
Indices: 1366555--1366606 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
1366545 TTTGGTTCGC
1366555 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1366571 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
1366587 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
1366603 TGTA
1 TGTA
1366607 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:1366653 original size:45 final size:44
Alignment explanation
Indices: 1366587--1366681 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
1366577 GGATTAGAGG
* *
1366587 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
1366632 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
1366676 TGTAAT
1 TGTAAT
1366682 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:1367055 original size:47 final size:46
Alignment explanation
Indices: 1367004--1367164 Score: 140
Period size: 47 Copynumber: 3.6 Consensus size: 46
1366994 GATTTAATAA
1367004 AATTTAAAATAATTATAACTAATAAATTATCTTATATGAATTTGTAT
1 AATTTAAAATAATTATAA-TAATAAATTATCTTATATGAATTTGTAT
* * * * *
1367051 AATTTAAAATAATTATTATTACATATAAT-TTA-AT-AA---GATAT
1 AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTG-TAT
* * * *
1367092 AATTTCATAA-AATTATTGATAATAAATTTTCTTATATGAATTTATAT
1 AATTT-AAAATAATTA-TAATAATAAATTATCTTATATGAATTTGTAT
1367139 AATTTAAAATAATT-TATATAATAAAT
1 AATTTAAAATAATTATA-ATAATAAAT
1367165 CTATTGTATA
Statistics
Matches: 88, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
40 1 0.01
41 13 0.15
42 11 0.12
43 5 0.06
44 4 0.05
45 6 0.07
46 19 0.22
47 29 0.33
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (46 bp):
AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTGTAT
Found at i:1372112 original size:46 final size:45
Alignment explanation
Indices: 1371931--1372193 Score: 183
Period size: 46 Copynumber: 5.6 Consensus size: 45
1371921 TTTGTTTGTG
* * * * * *
1371931 AGCTAGTGTAAGACATGTCTGGGACATGCGTAGGC-CACATTATGAG
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGACTC-GA-GATGAC
* * * *
1371977 AGCTAGTATAAGACCATGTTTGGGACATGGCATCTGAATTGAGATGAC
1 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATC-GACTCGAGATGAC
* *
1372025 AGCTAGTGTAAGACATGGCTGGGACATGCATCGGCCTCGAGATGTA-
1 AGCTAGTGTAAGACATGTCTGGGACATGCATC-GACTCGAGATG-AC
* *
1372071 AGCCAGTGTAAGACATGTCTGGGACATGCATCGACTACGAGATGAT
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGACT-CGAGATGAC
* * * * *
1372117 AGTTGGTGTAAGACTATGT-TAGTGACATGGCATCGACTTGAGAT-ATA
1 AGCTAGTGTAAGAC-ATGTCT-GGGACAT-GCATCGACTCGAGATGA-C
* *
1372164 AGCCATTTGTAAGACCATGTCTGGGACATG
1 AGCTA-GTGTAAGA-CATGTCTGGGACATG
1372194 GCATTGACAC
Statistics
Matches: 172, Mismatches: 31, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
45 4 0.02
46 75 0.44
47 44 0.26
48 45 0.26
49 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (45 bp):
AGCTAGTGTAAGACATGTCTGGGACATGCATCGACTCGAGATGAC
Found at i:1375954 original size:293 final size:292
Alignment explanation
Indices: 1375418--1376641 Score: 1748
Period size: 293 Copynumber: 4.2 Consensus size: 292
1375408 GTCCGCCAAT
*
1375418 TTTCAAAACCATGATGTGGGCAAGAACTTAACAAATCTTTGAAACATTACTACTATGAGGAAGAT
1 TTTCAAAACCATGATGTGGGCAAGAACTTAACAAATCTTTGAAACATTACTACTATAAGGAAGAT
* * *
1375483 TGGACAATCTGATATATCCCAATATCAAAATTCATGGAAAGGCCCTAAATTGAAGTGGAAGGGGA
66 TGAATAATCTGATACATCCCAATATCAAAATTCATGGAAAGGCCCTAAATTGAAGTGGAAGGGGA
* * * *
1375548 AAAAGGTTGTGACAACAAGGGAAATTATGCAACAACACTCTGATGCTATTC-AAAAAATGAGGGG
131 AAAAGGCTGTGACAACAAGGCAAATTATGCAACAACACTCTAATGCTATTCGAAAGAAT-AGGGG
* *
1375612 AAAACCTTATAAATAAGTGCAAATAGGGACACAAGAAAGCCAAATAGATTCTATTATAATTGATG
195 AAAACCTTCTAAA-AAGTGCAAATAGGGACACAAGAAAGCCAAATAGATTCTATTATAATAGATG
* *
1375677 ATTGAAATGCAAATTGATGCTATATTACTTTTAA
259 ATTGAAGTGCAAATTGATGCTAGATTACTTTTAA
*
1375711 TTTCAAAACCATGATGTGGGCAAGAACTTAACAAATCTTTGAAAAATTACTACTATAAGGAAGAT
1 TTTCAAAACCATGATGTGGGCAAGAACTTAACAAATCTTTGAAACATTACTACTATAAGGAAGAT
* *
1375776 TGAATAATCTGATACATCCCAATATCAACATTCATGGAAAGGCCCTAAATTGAAGTGGGAGGGGA
66 TGAATAATCTGATACATCCCAATATCAAAATTCATGGAAAGGCCCTAAATTGAAGTGGAAGGGGA
* ** * *
1375841 AAAAGGCTGTGACAACAAGGCAAATTATGAAACAACACTCTAATATTGTTCGATAGAATAGGGGA
131 AAAAGGCTGTGACAACAAGGCAAATTATGCAACAACACTCTAATGCTATTCGAAAGAATAGGGGA
* * * * * * *
1375906 AAACCTTCTAAACAAGTGTAGATAGGGACACAAGCAAGCTAGATAGATTCTATTATAATATATTA
196 AAACCTTCTAAA-AAGTGCAAATAGGGACACAAGAAAGCCAAATAGATTCTATTATAATAGATGA
* *
1375971 TTGAAGTGCAAATTGATGCTAGCTTAGTTTTAA
260 TTGAAGTGCAAATTGATGCTAGATTACTTTTAA
* * * *
1376004 TTTCAAAACCATGATGTGGGCAAGAACTCAAGAAATATTTGAAACATTACTACTGTAAGGAAGAT
1 TTTCAAAACCATGATGTGGGCAAGAACTTAACAAATCTTTGAAACATTACTACTATAAGGAAGAT
* * * * *
1376069 TGGATAATCTGATACATCCCAATATCAAAATTCATGAAAAGGCCCTAGATTGAAATGGAAGGGCA
66 TGAATAATCTGATACATCCCAATATCAAAATTCATGGAAAGGCCCTAAATTGAAGTGGAAGGGGA
*
1376134 AAAAGGCTGTGACAACAAGGCAAATTATGCAACAACACTCTAATGCTATTCGAAAGAAAAGGGGA
131 AAAAGGCTGTGACAACAAGGCAAATTATGCAACAACACTCTAATGCTATTCGAAAGAATAGGGGA
* * * *
1376199 AAACCTTTTAAAAAGTGCAAATAGGGACACAAGAAAGCCAAACAGATTTTTTTTATAATAGATGA
196 AAACCTTCTAAAAAGTGCAAATAGGGACACAAGAAAGCCAAATAGA-TTCTATTATAATAGATGA
1376264 TTGAAGTGCAAATTGATGCTAGATTACTTTTAA
260 TTGAAGTGCAAATTGATGCTAGATTACTTTTAA
* * * *
1376297 TTTCAAAACCATGATGTAGGCAAGAACTTAACAAATCTTTGAAACATTACTATTGTAAGGAATAT
1 TTTCAAAACCATGATGTGGGCAAGAACTTAACAAATCTTTGAAACATTACTACTATAAGGAAGAT
* * * * * *
1376362 TGAATAATTTGATACATCTCAATATCAACATTCATGGAAAGGCACTAGATTGAAGTGGGAGGGGA
66 TGAATAATCTGATACATCCCAATATCAAAATTCATGGAAAGGCCCTAAATTGAAGTGGAAGGGGA
** * * * * *
1376427 AAAAGGCTAAGACAACAAGGCAAATTATGCAGCAACACTCTAATGTTGTTCTAAAGAAGAGGGGA
131 AAAAGGCTGTGACAACAAGGCAAATTATGCAACAACACTCTAATGCTATTCGAAAGAATAGGGGA
* ** * * * * * *
1376492 AAACCTTCTAAAAAAGTGTAGGTAGGGACAAAAGCAACCCAAAAAGATTCTACTATCATAGATGA
196 AAACCTTCT-AAAAAGTGCAAATAGGGACACAAGAAAGCCAAATAGATTCTATTATAATAGATGA
*
1376557 TTGAAGTGCAAATTGATGCTAGCTTACTTTTAA
260 TTGAAGTGCAAATTGATGCTAGATTACTTTTAA
* *
1376590 TTTTAAAACCATGATGTGGCCAAGAACTTAACAAATCTTTGAAACATTACTA
1 TTTCAAAACCATGATGTGGGCAAGAACTTAACAAATCTTTGAAACATTACTA
1376642 ATGTAACAAC
Statistics
Matches: 829, Mismatches: 99, Indels: 6
0.89 0.11 0.01
Matches are distributed among these distances:
292 28 0.03
293 766 0.92
294 35 0.04
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (292 bp):
TTTCAAAACCATGATGTGGGCAAGAACTTAACAAATCTTTGAAACATTACTACTATAAGGAAGAT
TGAATAATCTGATACATCCCAATATCAAAATTCATGGAAAGGCCCTAAATTGAAGTGGAAGGGGA
AAAAGGCTGTGACAACAAGGCAAATTATGCAACAACACTCTAATGCTATTCGAAAGAATAGGGGA
AAACCTTCTAAAAAGTGCAAATAGGGACACAAGAAAGCCAAATAGATTCTATTATAATAGATGAT
TGAAGTGCAAATTGATGCTAGATTACTTTTAA
Found at i:1376542 original size:586 final size:585
Alignment explanation
Indices: 1375418--1376647 Score: 1933
Period size: 586 Copynumber: 2.1 Consensus size: 585
1375408 GTCCGCCAAT
* *
1375418 TTTCAAAACCATGATGTGGGCAAGAACTTAACAAATCTTTGAAACATTACTACTATGAGGAAGAT
1 TTTCAAAACCATGATGTGGGCAAGAACTTAACAAATCTTTGAAACATTACTACTGTAAGGAAGAT
* * * *
1375483 TGGACAATCTGATATATCCCAATATCAAAATTCATGGAAAGGCCCTAAATTGAAGTGGAAGGGGA
66 TGGACAATCTGATACATCCCAATATCAAAATTCATGAAAAGGCCCTAAATTGAAATGGAAGGGCA
* * *
1375548 AAAAGGTTGTGACAACAAGGGAAATTATGCAACAACACTCTGATGCTATTCAAAAAATGAGGGGA
131 AAAAGGCTGTGACAACAAGGCAAATTATGCAACAACACTCTAATGCTATTCAAAAAA-GAGGGGA
* *
1375613 AAACCTTATAAATAAGTGCAAATAGGGACACAAGAAAGCCAAATAGATTCTATTATAATTGATGA
195 AAACCTTATAAATAAGTGCAAATAGGGACACAAGAAAGCCAAACAGATTCTATTATAATAGATGA
* *
1375678 TTGAAATGCAAATTGATGCTATATTACTTTTAATTTCAAAACCATGATGTGGGCAAGAACTTAAC
260 TTGAAATGCAAATTGATGCTAGATTACTTTTAATTTCAAAACCATGATGTAGGCAAGAACTTAAC
1375743 AAATCTTTGAAAAATTACTACTATAAGGAAGATTGAATAATCTGATACATCCCAATATCAACATT
325 AAATCTTTGAAAAATTACTACTATAAGGAAGATTGAATAATCTGATACATCCCAATATCAACATT
* **
1375808 CATGGAAAGGCCCTAAATTGAAGTGGGAGGGGAAAAAGGCTGTGACAACAAGGCAAATTATGAAA
390 CATGGAAAGGCACTAAATTGAAGTGGGAGGGGAAAAAGGCTAAGACAACAAGGCAAATTATGAAA
* * * *
1375873 CAACACTCTAATATTGTTCGATAGAATAGGGGAAAACCTTCTAAACAAGTGTAGATAGGGACACA
455 CAACACTCTAATATTGTTCGAAAGAAGAGGGGAAAACCTTCTAAAAAAGTGTAGATAGGGACAAA
* * * * * * * *
1375938 AGCAAGCTAGATAGATTCTATTATAATATATTATTGAAGTGCAAATTGATGCTAGCTTAGTTTTA
520 AGCAACCCAAAAAGATTCTACTATAATAGATGATTGAAGTGCAAATTGATGCTAGCTTACTTTTA
1376003 A
585 A
* * *
1376004 TTTCAAAACCATGATGTGGGCAAGAACTCAAGAAATATTTGAAACATTACTACTGTAAGGAAGAT
1 TTTCAAAACCATGATGTGGGCAAGAACTTAACAAATCTTTGAAACATTACTACTGTAAGGAAGAT
* *
1376069 TGGATAATCTGATACATCCCAATATCAAAATTCATGAAAAGGCCCTAGATTGAAATGGAAGGGCA
66 TGGACAATCTGATACATCCCAATATCAAAATTCATGAAAAGGCCCTAAATTGAAATGGAAGGGCA
1376134 AAAAGGCTGTGACAACAAGGCAAATTATGCAACAACACTCTAATGCTATTCGAAAGAAA-AGGGG
131 AAAAGGCTGTGACAACAAGGCAAATTATGCAACAACACTCTAATGCTATTC-AAA-AAAGAGGGG
* * *
1376198 AAAACCTTTTAAA-AAGTGCAAATAGGGACACAAGAAAGCCAAACAGATTTTTTTTATAATAGAT
194 AAAACCTTATAAATAAGTGCAAATAGGGACACAAGAAAGCCAAACAGA-TTCTATTATAATAGAT
*
1376262 GATTGAAGTGCAAATTGATGCTAGATTACTTTTAATTTCAAAACCATGATGTAGGCAAGAACTTA
258 GATTGAAATGCAAATTGATGCTAGATTACTTTTAATTTCAAAACCATGATGTAGGCAAGAACTTA
* * * * * *
1376327 ACAAATCTTTGAAACATTACTATTGTAAGGAATATTGAATAATTTGATACATCTCAATATCAACA
323 ACAAATCTTTGAAAAATTACTACTATAAGGAAGATTGAATAATCTGATACATCCCAATATCAACA
* *
1376392 TTCATGGAAAGGCACTAGATTGAAGTGGGAGGGGAAAAAGGCTAAGACAACAAGGCAAATTATGC
388 TTCATGGAAAGGCACTAAATTGAAGTGGGAGGGGAAAAAGGCTAAGACAACAAGGCAAATTATGA
* * * *
1376457 AGCAACACTCTAATGTTGTTCTAAAGAAGAGGGGAAAACCTTCTAAAAAAGTGTAGGTAGGGACA
453 AACAACACTCTAATATTGTTCGAAAGAAGAGGGGAAAACCTTCTAAAAAAGTGTAGATAGGGACA
*
1376522 AAAGCAACCCAAAAAGATTCTACTATCATAGATGATTGAAGTGCAAATTGATGCTAGCTTACTTT
518 AAAGCAACCCAAAAAGATTCTACTATAATAGATGATTGAAGTGCAAATTGATGCTAGCTTACTTT
1376587 TAA
583 TAA
* * *
1376590 TTTTAAAACCATGATGTGGCCAAGAACTTAACAAATCTTTGAAACATTACTAATGTAA
1 TTTCAAAACCATGATGTGGGCAAGAACTTAACAAATCTTTGAAACATTACTACTGTAA
1376648 CAACCTGTTT
Statistics
Matches: 585, Mismatches: 56, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
585 33 0.06
586 546 0.93
587 3 0.01
588 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (585 bp):
TTTCAAAACCATGATGTGGGCAAGAACTTAACAAATCTTTGAAACATTACTACTGTAAGGAAGAT
TGGACAATCTGATACATCCCAATATCAAAATTCATGAAAAGGCCCTAAATTGAAATGGAAGGGCA
AAAAGGCTGTGACAACAAGGCAAATTATGCAACAACACTCTAATGCTATTCAAAAAAGAGGGGAA
AACCTTATAAATAAGTGCAAATAGGGACACAAGAAAGCCAAACAGATTCTATTATAATAGATGAT
TGAAATGCAAATTGATGCTAGATTACTTTTAATTTCAAAACCATGATGTAGGCAAGAACTTAACA
AATCTTTGAAAAATTACTACTATAAGGAAGATTGAATAATCTGATACATCCCAATATCAACATTC
ATGGAAAGGCACTAAATTGAAGTGGGAGGGGAAAAAGGCTAAGACAACAAGGCAAATTATGAAAC
AACACTCTAATATTGTTCGAAAGAAGAGGGGAAAACCTTCTAAAAAAGTGTAGATAGGGACAAAA
GCAACCCAAAAAGATTCTACTATAATAGATGATTGAAGTGCAAATTGATGCTAGCTTACTTTTAA
Found at i:1377968 original size:22 final size:22
Alignment explanation
Indices: 1377940--1378000 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 22
1377930 AGCTCGAAAG
1377940 AGCTTACTGTTTATCTCAATAA
1 AGCTTACTGTTTATCTCAATAA
* * * *
1377962 AGCTTACCGTTTTCAGCTTAATAG
1 AGCTTACTG-TTT-ATCTCAATAA
1377986 AGCTTACTGTTTATC
1 AGCTTACTGTTTATC
1378001 AGCTCATGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
22 10 0.32
23 6 0.19
24 15 0.48
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (22 bp):
AGCTTACTGTTTATCTCAATAA
Found at i:1377984 original size:24 final size:25
Alignment explanation
Indices: 1377957--1378004 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
1377947 TGTTTATCTC
1377957 AATAAAGCTTACCGTTT-TCAGCTT
1 AATAAAGCTTACCGTTTATCAGCTT
* *
1377981 AATAGAGCTTACTGTTTATCAGCT
1 AATAAAGCTTACCGTTTATCAGCT
1378005 CATGAAGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (25 bp):
AATAAAGCTTACCGTTTATCAGCTT
Found at i:1383842 original size:47 final size:46
Alignment explanation
Indices: 1383732--1383956 Score: 206
Period size: 47 Copynumber: 4.8 Consensus size: 46
1383722 TGGGTAAGGT
* **
1383732 GCCGATGACATGTCCCAGACATGGTCTTACACTGGCTCAT-ATC-TCAA
1 GCCGATG-CATGTCCCAGACA-GGTCTTACACTAGCTC-TCATCTTGTA
* * * * * *
1383779 GTCGATACCATATCCCAGATAGGGTCTTACA-TTGACTATCATCTTGTA
1 GCCGAT-GCATGTCCCAGACA-GGTCTTACACTAG-CTCTCATCTTGTA
* *
1383827 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTT-AA
1 GCCGATGCATGTCCCAGACAGGTCTTACACTAGCTCTCATCTTGTA
** *
1383872 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTG
1 -GCCGATG-CATGTCCCAGACA-GGTCTTACACTAGCTCTCATCTTGTA
*
1383921 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTC
1 GCCGATGCATGTCCCAGACAGGTCTTACACTAGCTC
1383957 ACACACAAAT
Statistics
Matches: 146, Mismatches: 23, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
45 1 0.01
46 42 0.29
47 69 0.47
48 34 0.23
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.28
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACAGGTCTTACACTAGCTCTCATCTTGTA
Found at i:1383899 original size:94 final size:93
Alignment explanation
Indices: 1383732--1383957 Score: 285
Period size: 94 Copynumber: 2.4 Consensus size: 93
1383722 TGGGTAAGGT
* *
1383732 GCCGATGACATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAAGTCGATACCATATCCCAG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCATATCTCAAGCCGATACCATATCCCAG
* * **
1383797 ATAGGGTCTTACA-TTGACTATCATCTTGTA
64 ACAGGGTCTTACACTAG-CTATCATAATGTA
* * *
1383827 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTC-TCATCTTAATGCCGATGCCATGTCCCAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCAT-ATCTCAA-GCCGATACCATATCCCAG
* * *
1383891 ACATGGTCTTACACTAGCTCTCATAATGTG
64 ACAGGGTCTTACACTAGCTATCATAATGTA
1383921 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCA
1383958 CACACAAATG
Statistics
Matches: 115, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
92 1 0.01
93 20 0.17
94 85 0.74
95 9 0.08
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (93 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCATATCTCAAGCCGATACCATATCCCAGAC
AGGGTCTTACACTAGCTATCATAATGTA
Found at i:1388868 original size:47 final size:46
Alignment explanation
Indices: 1388758--1388975 Score: 165
Period size: 47 Copynumber: 4.6 Consensus size: 46
1388748 TGGGTAGGGT
* * * *
1388758 GCCGATGACATGTCCTAGACATGGTCTTACACTGGCTCGT-ATCTCA-A
1 GCCGATG-CATGTCCCAGACA-GGTCTTACATTGACTC-TCATCTTATA
* * * *
1388805 GTCGATACCATATCCCAGACAGGGTCTTACATTGACTATCATCTTATA
1 GCCGAT-GCATGTCCCAGACA-GGTCTTACATTGACTCTCATCTTATA
* * *
1388853 ACCGATGCATGTCCCAGACATGTCTTACACT-AGCTCTCATCTTA-A
1 GCCGATGCATGTCCCAGACAGGTCTTACATTGA-CTCTCATCTTATA
* * ** * *
1388898 TGCCGATGCCATGTCCCAAACATGGTCTTACATTGGCTCTCATAATGTG
1 -GCCGATG-CATGTCCCAGACA-GGTCTTACATTGACTCTCATCTTATA
*
1388947 GCCGATGCATGTCCCAGACATGTCTTACA
1 GCCGATGCATGTCCCAGACAGGTCTTACA
1388976 CTAGCTCACA
Statistics
Matches: 135, Mismatches: 27, Indels: 19
0.75 0.15 0.10
Matches are distributed among these distances:
45 2 0.01
46 34 0.25
47 70 0.52
48 29 0.21
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACAGGTCTTACATTGACTCTCATCTTATA
Found at i:1388927 original size:94 final size:93
Alignment explanation
Indices: 1388759--1388982 Score: 270
Period size: 94 Copynumber: 2.4 Consensus size: 93
1388749 GGGTAGGGTG
* * * *
1388759 CCGATGACATGTCCTAGACATGGTCTTACACTGGCTCGTATCTCAAGTCGATACCATATCCCAGA
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCGTATCTCAAGCCGATACCATATCCCAAA
**
1388824 CAGGGTCTTACATTGACTATCATCTTATAA
64 CAGGGTCTTACATTGACTATCATAATATAA
* * *
1388854 CCGATGCATGTCCCAGACATGTCTTACACTAGCTC-TCATCTTAATGCCGATGCCATGTCCCAAA
1 CCGATGCATGTCCCAGACATGTCTTACACTAGCTCGT-ATCTCAA-GCCGATACCATATCCCAAA
* * * * **
1388918 CATGGTCTTACATTGGCTCTCATAATGTGG
64 CAGGGTCTTACATTGACTATCATAATATAA
1388948 CCGATGCATGTCCCAGACATGTCTTACACTAGCTC
1 CCGATGCATGTCCCAGACATGTCTTACACTAGCTC
1388983 ACACACAAAT
Statistics
Matches: 112, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
92 1 0.01
93 20 0.18
94 85 0.76
95 6 0.05
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (93 bp):
CCGATGCATGTCCCAGACATGTCTTACACTAGCTCGTATCTCAAGCCGATACCATATCCCAAACA
GGGTCTTACATTGACTATCATAATATAA
Found at i:1393404 original size:23 final size:23
Alignment explanation
Indices: 1393378--1393504 Score: 134
Period size: 23 Copynumber: 5.4 Consensus size: 23
1393368 ATAGCTCGTA
*
1393378 AGAGCTTACTGTTTCAGCTCACT
1 AGAGCTTACTGTTTCAGCTCAAT
* *
1393401 AGAGCTTACCGATTCAGCTCGAA-
1 AGAGCTTACTGTTTCAGCTC-AAT
1393424 AGAGCTTACTG-TTCAGCTCAAT
1 AGAGCTTACTGTTTCAGCTCAAT
1393446 AGAGCTTACCAT-TTTCAGCTCAAT
1 AGAGCTTA-C-TGTTTCAGCTCAAT
* *
1393470 AGAGCGTACTGTTTATCAGCTCATT
1 AGAGCTTACTG-TT-TCAGCTCAAT
1393495 AAGAGCTTAC
1 -AGAGCTTAC
1393505 CGACCATGTC
Statistics
Matches: 88, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
21 2 0.02
22 17 0.19
23 30 0.34
24 22 0.25
25 9 0.10
26 8 0.09
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (23 bp):
AGAGCTTACTGTTTCAGCTCAAT
Found at i:1393463 original size:46 final size:46
Alignment explanation
Indices: 1393370--1393524 Score: 165
Period size: 46 Copynumber: 3.3 Consensus size: 46
1393360 AACTCACCAT
* *
1393370 AGCTCGTAAGAGCTTACTGTTTCAGCTCACTAGAGCTTACCGATTC
1 AGCTCGAAAGAGCTTACTGTTTCAGCTCAATAGAGCTTACCGATTC
1393416 AGCTCGAAAGAGCTTACTG-TTCAGCTCAATAGAGCTTACC-ATTTTC
1 AGCTCGAAAGAGCTTACTGTTTCAGCTCAATAGAGCTTACCGA--TTC
* * *
1393462 AGCTC-AATAGAGCGTACTGTTTATCAGCTCATTAAGAGCTTACCGA-CC
1 AGCTCGAA-AGAGCTTACTG-TT-TCAGCTCAAT-AGAGCTTACCGATTC
1393510 ATGTCTCGAAAGAGC
1 A-G-CTCGAAAGAGC
1393525 ATGTATGATG
Statistics
Matches: 93, Mismatches: 5, Indels: 18
0.80 0.04 0.16
Matches are distributed among these distances:
44 1 0.01
45 22 0.24
46 36 0.39
48 3 0.03
49 10 0.11
50 18 0.19
51 3 0.03
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (46 bp):
AGCTCGAAAGAGCTTACTGTTTCAGCTCAATAGAGCTTACCGATTC
Found at i:1393467 original size:24 final size:24
Alignment explanation
Indices: 1393389--1393505 Score: 109
Period size: 24 Copynumber: 4.9 Consensus size: 24
1393379 GAGCTTACTG
*
1393389 TTTCAGCTCACTAGAGCTTACCGA-
1 TTTCAGCTCAATAGAGCTTACC-AT
1393413 -TTCAGCTCGAA-AGAGCTTA-C-T
1 TTTCAGCTC-AATAGAGCTTACCAT
*
1393434 GTTCAGCTCAATAGAGCTTACCAT
1 TTTCAGCTCAATAGAGCTTACCAT
* **
1393458 TTTCAGCTCAATAGAGCGTACTGT
1 TTTCAGCTCAATAGAGCTTACCAT
*
1393482 TTATCAGCTCATTAAGAGCTTACC
1 TT-TCAGCTCAAT-AGAGCTTACC
1393506 GACCATGTCT
Statistics
Matches: 77, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.03
22 17 0.22
23 17 0.22
24 24 0.31
25 9 0.12
26 8 0.10
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (24 bp):
TTTCAGCTCAATAGAGCTTACCAT
Found at i:1398493 original size:23 final size:23
Alignment explanation
Indices: 1398467--1398511 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1398457 TAGGAAAGAA
1398467 ATGGTTG-ATTGATATGTGTTTGG
1 ATGGTTGAATTGATATGT-TTTGG
*
1398490 ATGGTTGAATTGGTATGTTTTG
1 ATGGTTGAATTGATATGTTTTG
1398512 AAAGTAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (23 bp):
ATGGTTGAATTGATATGTTTTGG
Found at i:1404557 original size:28 final size:30
Alignment explanation
Indices: 1404518--1404587 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
1404508 ATAAATATCA
* *
1404518 AATT-TATACATG-AACTTTGA-TTGGTGC
1 AATTATATACATGAAACATTGATTTGATGC
*
1404545 AATTATATACATGAAACATTGATTTTGATTC
1 AATTATATACATGAAACATTGA-TTTGATGC
1404576 AATTATATACAT
1 AATTATATACAT
1404588 ATATTTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 4 0.11
28 8 0.22
29 7 0.19
31 17 0.47
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.41
Consensus pattern (30 bp):
AATTATATACATGAAACATTGATTTGATGC
Found at i:1405875 original size:20 final size:20
Alignment explanation
Indices: 1405818--1405869 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1405808 GGAAATATTA
*
1405818 TAAAATCTATCTAAATTATTTTT
1 TAAAATCTATCT---TTACTTTT
1405841 TAAAATCTATCTTTACTTTT
1 TAAAATCTATCTTTACTTTT
1405861 TAAAA-CTAT
1 TAAAATCTAT
1405870 GTTTTAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 4 0.14
20 12 0.43
23 12 0.43
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAAATCTATCTTTACTTTT
Found at i:1406053 original size:17 final size:18
Alignment explanation
Indices: 1406021--1406054 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1406011 AACAAATTCC
*
1406021 TTATTTTTAATTATTTTT
1 TTATTTTTAATAATTTTT
1406039 TTATTTTT-ATAATTTT
1 TTATTTTTAATAATTTT
1406055 GCGGCAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATTTTTAATAATTTTT
Found at i:1408395 original size:14 final size:14
Alignment explanation
Indices: 1408376--1408403 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1408366 CTTGATAAGT
1408376 GAAGAATCTTCAAG
1 GAAGAATCTTCAAG
1408390 GAAGAATCTTCAAG
1 GAAGAATCTTCAAG
1408404 TTATTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
GAAGAATCTTCAAG
Found at i:1408959 original size:28 final size:27
Alignment explanation
Indices: 1408926--1408981 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 27
1408916 ATGAACTGGA
*
1408926 TCTTTTGCAATATTGATGGTCGTTTAG
1 TCTTTTGCAATATTGATGGTCGCTTAG
1408953 TNCTTTTGCAATATTGATGGTCGCTTAG
1 T-CTTTTGCAATATTGATGGTCGCTTAG
1408981 T
1 T
1408982 TATCACATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.18, C:0.12, G:0.21, T:0.46
Consensus pattern (27 bp):
TCTTTTGCAATATTGATGGTCGCTTAG
Found at i:1421981 original size:18 final size:17
Alignment explanation
Indices: 1421937--1421986 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
1421927 AATAAGTTGA
1421937 AAAGATAAAAGTAAATAAT
1 AAAGA-AAAA-TAAATAAT
* *
1421956 TAACAAAAATAAATCAAT
1 AAAGAAAAATAAAT-AAT
1421974 AAAGAAAAATAAA
1 AAAGAAAAATAAA
1421987 CCTCGGGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 5 0.19
18 18 0.69
19 3 0.12
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (17 bp):
AAAGAAAAATAAATAAT
Found at i:1428514 original size:36 final size:35
Alignment explanation
Indices: 1428474--1428543 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
1428464 ATTCTAAAAA
1428474 TAATATTATTTTAATAGT-TTAATATTAAATTTAATT
1 TAATATTATTTTAATAGTATT-ATATT-AATTTAATT
*
1428510 TAATATTATTTTAATAGTATTTTATTAATTTAAT
1 TAATATTATTTTAATAGTATTATATTAATTTAAT
1428544 AATGAAGTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 8 0.25
36 22 0.69
37 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (35 bp):
TAATATTATTTTAATAGTATTATATTAATTTAATT
Found at i:1428522 original size:11 final size:11
Alignment explanation
Indices: 1428474--1428533 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
1428464 ATTCTAAAAA
1428474 TAATATTATTT
1 TAATATTATTT
*
1428485 TAATAGTTTAATAT
1 TAATA--TT-ATTT
*
1428499 TAA-ATTTAATT
1 TAATA-TTATTT
1428510 TAATATTATTT
1 TAATATTATTT
*
1428521 TAATAGTATTT
1 TAATATTATTT
1428532 TA
1 TA
1428534 TTAATTTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
11 27 0.68
12 4 0.10
13 3 0.08
14 6 0.15
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (11 bp):
TAATATTATTT
Found at i:1435088 original size:42 final size:42
Alignment explanation
Indices: 1435041--1435146 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
1435031 CCGAGATTCT
* * **
1435041 ATATAAGACCATATCTGGGATATGGTATCGGTATG-TGATTTC
1 ATATAAGACCATATCAGGGATATGGCATCCATATGAT-ATTTC
* * *
1435083 ATATAAGACCATGTCAGGGACATGGCGTCCATATGATATTTC
1 ATATAAGACCATATCAGGGATATGGCATCCATATGATATTTC
* *
1435125 ATGTAAGACCATATCCGGGATA
1 ATATAAGACCATATCAGGGATA
1435147 CTGCATTGAT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 51 0.98
43 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (42 bp):
ATATAAGACCATATCAGGGATATGGCATCCATATGATATTTC
Found at i:1442897 original size:19 final size:19
Alignment explanation
Indices: 1442871--1442912 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
1442861 AAATTCAAAG
1442871 AAATATATAAAAAAAATACAT
1 AAATAT-TAAAAAAAA-ACAT
*
1442892 AAATATTTAAAAAAAACAT
1 AAATATTAAAAAAAAACAT
1442911 AA
1 AA
1442913 TAAAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 8 0.40
21 6 0.30
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATATTAAAAAAAAACAT
Done.