Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 127 of 349
Found at i:40547786 original size:27 final size:27
Alignment explanation
Indices: 40547752--40547929 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40547742 TAAATTGTAC
40547752 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
40547779 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40547805 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
40547833 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
40547861 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40547888 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40547915 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40547930 GACTTAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:40547866 original size:82 final size:81
Alignment explanation
Indices: 40547753--40547908 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40547743 AAATTGTACA
* *
40547753 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
40547817 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
40547834 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
40547899 TGCGAGTTGA
65 TGCGAATTGA
40547909 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40547920 original size:82 final size:81
Alignment explanation
Indices: 40547749--40547929 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
40547739 GGTTAAATTG
* *
40547749 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
40547814 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
40547830 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
40547894 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
40547912 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40547930 GACTTAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:40555251 original size:27 final size:27
Alignment explanation
Indices: 40555217--40555394 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40555207 TAAATTGTAC
40555217 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
40555244 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40555270 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
40555298 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
40555326 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40555353 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40555380 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40555395 GACTTAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:40555331 original size:82 final size:81
Alignment explanation
Indices: 40555218--40555373 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40555208 AAATTGTACA
* *
40555218 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
40555282 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
40555299 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
40555364 TGCGAGTTGA
65 TGCGAATTGA
40555374 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40555385 original size:82 final size:81
Alignment explanation
Indices: 40555214--40555394 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
40555204 GGTTAAATTG
* *
40555214 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
40555279 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
40555295 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
40555359 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
40555377 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40555395 GACTTAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:40557275 original size:8 final size:8
Alignment explanation
Indices: 40557262--40557286 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
40557252 AGTATTAGGG
40557262 GTAATTTT
1 GTAATTTT
40557270 GTAATTTT
1 GTAATTTT
40557278 GTAATTTT
1 GTAATTTT
40557286 G
1 G
40557287 CATAAATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (8 bp):
GTAATTTT
Found at i:40559460 original size:45 final size:45
Alignment explanation
Indices: 40559144--40559500 Score: 208
Period size: 45 Copynumber: 7.9 Consensus size: 45
40559134 ATGATCGGAG
* ** * * *
40559144 GGTGCCATGGTGTCTTTCAACCGTGGTCTTATTTATTCTCGACT-T
1 GGTGCCATAGTGTCTTTCAACTATGGTCTTATTCATT-TCCAGTAT
* * * *
40559189 GATGCCATAATGTCTTTCAACCATAGTCTTATTCATTTTCCA-TCAT
1 GGTGCCATAGTGTCTTTCAACTATGGTCTTATTCA-TTTCCAGT-AT
* * * * *
40559235 GTTGCCATAGTTTCTTTCAACTATGGTATTTTTCATTTTCC-GTCGT
1 GGTGCCATAGTGTCTTTCAACTATGGTCTTATTCA-TTTCCAGT-AT
* * * ** * * *
40559281 GTTGCCATAGTATCTGTCAACTATGGTCTTATTGGTTT-GATTCGT
1 GGTGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGT-AT
* * * * *
40559326 GATGCCATAGTGTCTTTTAGCTATGGTCTTACTTGA--T--AGAAT
1 GGTGCCATAGTGTCTTTCAACTATGGTCTTA-TTCATTTCCAGTAT
** * * * * *
40559368 CGTGATGCCATAACGTCTTTTAGCTATGGTCTTACTCGTTTCTAGTAT
1 -G-G-TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGTAT
*
40559416 GGTGCCATAGTGTCTTTCAACTATGGTCTTATTTATTTCCAGTAT
1 GGTGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGTAT
* * * *
40559461 AGTACCATAGTGTCTTTCAACTATAGTCTTAATCATTTCC
1 GGTGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCC
40559501 TTCAAGCCAA
Statistics
Matches: 247, Mismatches: 52, Indels: 26
0.76 0.16 0.08
Matches are distributed among these distances:
42 1 0.00
43 2 0.01
44 3 0.01
45 162 0.66
46 74 0.30
47 1 0.00
48 4 0.02
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (45 bp):
GGTGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGTAT
Found at i:40559485 original size:24 final size:23
Alignment explanation
Indices: 40559420--40559488 Score: 61
Period size: 24 Copynumber: 3.0 Consensus size: 23
40559410 TAGTATGGTG
*
40559420 CCATAGTGTCTTTCAACTATGGT
1 CCATAGTGTCTTTCAACTATAGT
* * * * *
40559443 -CTTA-TTTATTTCCAGTATAGT
1 CCATAGTGTCTTTCAACTATAGT
40559464 ACCATAGTGTCTTTCAACTATAGT
1 -CCATAGTGTCTTTCAACTATAGT
40559488 C
1 C
40559489 TTAATCATTT
Statistics
Matches: 32, Mismatches: 11, Indels: 6
0.65 0.22 0.12
Matches are distributed among these distances:
21 12 0.38
22 3 0.09
23 4 0.12
24 13 0.41
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (23 bp):
CCATAGTGTCTTTCAACTATAGT
Found at i:40565013 original size:93 final size:93
Alignment explanation
Indices: 40564905--40565075 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
40564895 GCCCATAAGT
* * *
40564905 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40564970 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
40564998 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40565063 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40565076 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:40565072 original size:46 final size:46
Alignment explanation
Indices: 40564897--40565072 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
40564887 TGTAACCCGC
* * * *
40564897 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
40564943 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * *
40564993 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
40565036 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40565073 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 63 0.58
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:40565532 original size:30 final size:30
Alignment explanation
Indices: 40565498--40565557 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
40565488 ATTTAATACG
40565498 AACTTTGGA-AAAATTACACTTTTGCCCCTA
1 AACTTT-GACAAAATTACACTTTTGCCCCTA
* *
40565528 AACTTTTACATAATTACACTTTTGCCCCTA
1 AACTTTGACAAAATTACACTTTTGCCCCTA
40565558 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTGACAAAATTACACTTTTGCCCCTA
Found at i:40568718 original size:49 final size:49
Alignment explanation
Indices: 40568550--40568774 Score: 279
Period size: 49 Copynumber: 4.5 Consensus size: 49
40568540 TGAGGTCGCA
* * * * *
40568550 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-T-TGGTCACG
* * * **
40568601 TGTGTAGTACTAAGTGCAGGCTACCACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GGTCACG
* *
40568651 TGTGTAGTACTAACTGCAGGCTACTACATGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
* * *
40568700 TATGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
*
40568749 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
40568775 TACGTACCAG
Statistics
Matches: 150, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
49 76 0.51
50 42 0.28
51 32 0.21
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
Found at i:40568731 original size:99 final size:100
Alignment explanation
Indices: 40568543--40568782 Score: 295
Period size: 99 Copynumber: 2.4 Consensus size: 100
40568533 TCTATTGTGA
* ** *
40568543 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACGTGTGTAG
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACACGTACCCGAAAACTGTGATCACGTATGTAG
* **
40568608 TACTAAGTGCAGGCTACCACGTGTATCAGATGGTT
66 TACTAAGTGCAGGCTACCACGTGTACCAGATAATT
* * * * * *
40568643 AGGTCACGTGTGTAGTACTAACTGCAGGCTACTACATGTACCGGATAA-T-TGGTCACGTATGTA
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACACGTACCCGAAAACTGTGATCACGTATGTA
* *
40568706 GTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
65 GTACTAAGTGCAGGCTACCACGTGTACCAGATAATT
* * *
40568742 GGTCGCATGTGTAGTACTATGTGCAGGCTACTATACGTACC
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACACGTACC
40568783 AGATAGCTTT
Statistics
Matches: 118, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
98 35 0.30
99 43 0.36
100 1 0.01
101 39 0.33
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (100 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACACGTACCCGAAAACTGTGATCACGTATGTAG
TACTAAGTGCAGGCTACCACGTGTACCAGATAATT
Found at i:40572364 original size:13 final size:13
Alignment explanation
Indices: 40572346--40572370 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40572336 AATATCTTAG
40572346 AAAATAAATAATA
1 AAAATAAATAATA
40572359 AAAATAAATAAT
1 AAAATAAATAAT
40572371 TTTTCATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAAATAATA
Found at i:40573398 original size:17 final size:17
Alignment explanation
Indices: 40573376--40573408 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40573366 TTTATATAAA
40573376 TAAATAACTTTT-TCAAG
1 TAAATAA-TTTTCTCAAG
40573393 TAAATAATTTTCTCAA
1 TAAATAATTTTCTCAA
40573409 CCCGATTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAATAATTTTCTCAAG
Found at i:40581953 original size:41 final size:41
Alignment explanation
Indices: 40581893--40582042 Score: 196
Period size: 41 Copynumber: 3.7 Consensus size: 41
40581883 TTGGGGTTTA
*
40581893 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTTTCGAAGGGCTTTTGAGCCAGTGTCAT
40581934 AATCCGAGCTTGGTTTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTTTCGAAGGGCTTTTGAGCCAGTGTCAT
* * * * * * *
40581975 AA-CCGAACCTAGTTTCGAAGGGCCTTCGGGCCAATGTCAT
1 AATCCGAGCTTGGTTTCGAAGGGCTTTTGAGCCAGTGTCAT
*
40582015 ATTCCGAGCTTGGTCTT-GAAGGGCTTTT
1 AATCCGAGCTTGGT-TTCGAAGGGCTTTT
40582043 TGAGTCAGCA
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
40 32 0.34
41 59 0.63
42 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (41 bp):
AATCCGAGCTTGGTTTCGAAGGGCTTTTGAGCCAGTGTCAT
Found at i:40582013 original size:40 final size:41
Alignment explanation
Indices: 40581908--40582021 Score: 149
Period size: 40 Copynumber: 2.8 Consensus size: 41
40581898 GAGCTTGGTC
* * *
40581908 TCGAAGGGCTTTTGAGCCAGTGTCATAATCCGAGCTTGGTT
1 TCGAAGGGCTTTTGAGCCAGTGTCATAATCCGAACCTAGTT
40581949 TCGAAGGGCTTTTGAGCCAGTGTCATAA-CCGAACCTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGTCATAATCCGAACCTAGTT
* * * * *
40581989 TCGAAGGGCCTTCGGGCCAATGTCATATTCCGA
1 TCGAAGGGCTTTTGAGCCAGTGTCATAATCCGA
40582022 GCTTGGTCTT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 32 0.50
41 32 0.50
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (41 bp):
TCGAAGGGCTTTTGAGCCAGTGTCATAATCCGAACCTAGTT
Found at i:40594137 original size:6 final size:6
Alignment explanation
Indices: 40594122--40594186 Score: 94
Period size: 6 Copynumber: 10.8 Consensus size: 6
40594112 TAAAGACAAA
* * *
40594122 ATAAAC ATAAAA ATAAAA ATAAAC ATAAAC ATAAAA ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
*
40594170 ATAAAC ATAAAG ATAAA
1 ATAAAC ATAAAC ATAAA
40594187 TGGACTCAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.17
Consensus pattern (6 bp):
ATAAAC
Found at i:40594142 original size:18 final size:18
Alignment explanation
Indices: 40594119--40594186 Score: 109
Period size: 18 Copynumber: 3.8 Consensus size: 18
40594109 ATATAAAGAC
*
40594119 AAAATAAACATAAAAATA
1 AAAATAAACATAAACATA
40594137 AAAATAAACATAAACATA
1 AAAATAAACATAAACATA
40594155 AAAATAAACATAAACATA
1 AAAATAAACATAAACATA
* *
40594173 AACATAAAGATAAA
1 AAAATAAACATAAA
40594187 TGGACTCAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.74, C:0.09, G:0.01, T:0.16
Consensus pattern (18 bp):
AAAATAAACATAAACATA
Found at i:40595915 original size:14 final size:14
Alignment explanation
Indices: 40595896--40595922 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40595886 AAACAAAGTA
40595896 AAATAATAATAAAG
1 AAATAATAATAAAG
40595910 AAATAATAATAAA
1 AAATAATAATAAA
40595923 AAGAGTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
AAATAATAATAAAG
Found at i:40604548 original size:3 final size:3
Alignment explanation
Indices: 40604540--40604566 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40604530 GGATGTTTTA
40604540 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
40604567 TAGTATGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:40606888 original size:40 final size:40
Alignment explanation
Indices: 40606807--40607028 Score: 340
Period size: 40 Copynumber: 5.6 Consensus size: 40
40606797 AACCCAAGTA
* * *
40606807 CCTTCGAGAATTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* * *
40606846 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
40606886 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAGG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
40606926 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
40606966 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAGG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
40607006 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
40607029 CATCCGAATA
Statistics
Matches: 167, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
39 11 0.07
40 155 0.93
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:40608925 original size:6 final size:6
Alignment explanation
Indices: 40608916--40608979 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
40608906 CAAATTTATA
* * *
40608916 TTTTTC TTTTTC TTTTT- TTTTTC ATTTTCTC TTCTTC TATTT- TTCTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC -TTTT-TC TTTTTC TTTTTC TTTTTC
* *
40608964 TTCTTG TTTTTC TTTT
1 TTTTTC TTTTTC TTTT
40608980 CTCCCCTATA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
5 8 0.17
6 29 0.63
7 7 0.15
8 2 0.04
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:40608981 original size:17 final size:18
Alignment explanation
Indices: 40608916--40608979 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 18
40608906 CAAATTTATA
*
40608916 TTTTTCTTTTTCTT-TTT
1 TTTTTCTTTTTCTTCTTC
40608933 TTTTTCATTTTCTCTTCTTC
1 TTTTTC-TTTT-TCTTCTTC
* * *
40608953 TATTT-TTCTTCTTCTTG
1 TTTTTCTTTTTCTTCTTC
40608970 TTTTTCTTTT
1 TTTTTCTTTT
40608980 CTCCCCTATA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
17 17 0.46
18 10 0.27
19 4 0.11
20 6 0.16
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTCTTTTTCTTCTTC
Found at i:40610300 original size:20 final size:20
Alignment explanation
Indices: 40610257--40610304 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
40610247 GCTATTTTGT
40610257 TATGGGCCAACTGTATTGAA
1 TATGGGCCAACTGTATTGAA
*
40610277 -ATGGGCCCAACTGTGTT-AA
1 TATGGG-CCAACTGTATTGAA
40610296 TAT-GGCCAA
1 TATGGGCCAA
40610305 GGCCCAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 4 0.16
19 9 0.36
20 12 0.48
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (20 bp):
TATGGGCCAACTGTATTGAA
Found at i:40613160 original size:16 final size:16
Alignment explanation
Indices: 40613141--40613171 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40613131 CTTCTTCACT
40613141 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
40613157 TACTTACTTACTTAA
1 TACTCACTTACTTAA
40613172 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:40613177 original size:20 final size:20
Alignment explanation
Indices: 40613138--40613177 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
40613128 AAACTTCTTC
* *
40613138 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
40613158 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
40613178 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:40613553 original size:55 final size:53
Alignment explanation
Indices: 40613431--40613617 Score: 171
Period size: 55 Copynumber: 3.5 Consensus size: 53
40613421 GCCATGTCCC
* * *
40613431 GACATGGTCTTACATGGTATCCTTGCCTTATGATCTCACCAATGCCATGCCTT
1 GACATGGTCTTACATGGGATCCTTGCCTCATGAACTCACCAATGCCATGCCTT
* * * * * *
40613484 GGCCTGGTCTTACATGGGA-CCTTTGCCTCATAGTAACTTATCAATGTCATGTCTT
1 GACATGGTCTTACATGGGATCC-TTGCCTCAT-G-AACTCACCAATGCCATGCCTT
* *
40613539 GACATGGTCTTACATGGTATCCTTGCCTTA-GAAACCTCACCAATTGCCATGCCTT
1 GACATGGTCTTACATGGGATCCTTGCCTCATG-AA-CTCACCAA-TGCCATGCCTT
* * * *
40613594 GGCATGATCTCACATGGTATCCTT
1 GACATGGTCTTACATGGGATCCTT
40613618 AAACCCTAAT
Statistics
Matches: 107, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
52 2 0.02
53 27 0.25
54 7 0.07
55 69 0.64
56 2 0.02
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (53 bp):
GACATGGTCTTACATGGGATCCTTGCCTCATGAACTCACCAATGCCATGCCTT
Found at i:40617359 original size:29 final size:29
Alignment explanation
Indices: 40617324--40617397 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
40617314 GTTGTGAGAT
* *
40617324 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
40617353 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
40617382 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
40617398 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:40621670 original size:26 final size:26
Alignment explanation
Indices: 40621641--40621690 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
40621631 TCTCATTCCT
40621641 ATTTTACCCCT-AGTAAAATTTTGACG
1 ATTTTACCCCTGA-TAAAATTTTGACG
40621667 ATTTTACCCCTGATAAAATTTTGA
1 ATTTTACCCCTGATAAAATTTTGA
40621691 GAAAAAAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (26 bp):
ATTTTACCCCTGATAAAATTTTGACG
Found at i:40621845 original size:6 final size:6
Alignment explanation
Indices: 40621834--40621876 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
40621824 TGCAAATGGA
* * * *
40621834 CCATTT CCATTT ACATTA CCATTA CCATTA CCATTT CCATTT C
1 CCATTT CCATTT CCATTT CCATTT CCATTT CCATTT CCATTT C
40621877 TAGTTTTGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.42
Consensus pattern (6 bp):
CCATTT
Found at i:40623971 original size:13 final size:13
Alignment explanation
Indices: 40623953--40623977 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40623943 AAAGTAACAA
40623953 TTAGTAAATTAAG
1 TTAGTAAATTAAG
40623966 TTAGTAAATTAA
1 TTAGTAAATTAA
40623978 ATTTAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
TTAGTAAATTAAG
Found at i:40625814 original size:17 final size:18
Alignment explanation
Indices: 40625782--40625815 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40625772 AACTTTGATT
40625782 TGAAGAAATAAGAAGAAG
1 TGAAGAAATAAGAAGAAG
*
40625800 TGAAGAAGT-AGAAGAA
1 TGAAGAAATAAGAAGAA
40625816 CAGAGGCGTT
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:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (18 bp):
TGAAGAAATAAGAAGAAG
Found at i:40627973 original size:101 final size:101
Alignment explanation
Indices: 40627796--40628061 Score: 424
Period size: 101 Copynumber: 2.6 Consensus size: 101
40627786 TTGCATTCGC
* * * * *
40627796 ACGTAAGACCATGGTTGGACGATGGCAGTGTTTATATGTAAGACCATAGCTGAGCTATGGAATTT
1 ACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGATGGGCTATGGCATTC
40627861 TGATGACAAGACCAAAACTGAGTTATGGCACTATGG
66 TGATGACAAGACCAAAACTGAGTTATGGCACTATGG
*
40627897 ACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGTTGGGCTATGGCATTC
1 ACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGATGGGCTATGGCATTC
* * * *
40627962 TGATGATAAGACCATAACTGGGTTATGGTACTATGG
66 TGATGACAAGACCAAAACTGAGTTATGGCACTATGG
* *
40627998 AGGTAAGATCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGATGGGCTATGGCATT
1 ACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGATGGGCTATGGCATT
40628062 GTGACAGCCC
Statistics
Matches: 153, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 153 1.00
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (101 bp):
ACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGATGGGCTATGGCATTC
TGATGACAAGACCAAAACTGAGTTATGGCACTATGG
Found at i:40628058 original size:35 final size:34
Alignment explanation
Indices: 40627798--40628060 Score: 115
Period size: 33 Copynumber: 7.8 Consensus size: 34
40627788 GCATTCGCAC
* * * *
40627798 GTAAGACCATGGTTGGACGATGGCAGTGTTTATAT
1 GTAAGACCATAGTTGGGCTATGGCA-TGTTTAGAT
* * *
40627833 GTAAGACCATAGCTGAGCTATGGAAT-TTT-GAT
1 GTAAGACCATAGTTGGGCTATGGCATGTTTAGAT
* * ** * * * * * *
40627865 GACAAGACCAAAACTGAGTTATGGCA-CTATGGAC
1 G-TAAGACCATAGTTGGGCTATGGCATGTTTAGAT
* * * *
40627899 GTAAGACCATGGTTGGACCATGGCAGTGTTTATAT
1 GTAAGACCATAGTTGGGCTATGGCA-TGTTTAGAT
*
40627934 GTAAGACCATAGTTGGGCTATGGCAT-TCT-GAT
1 GTAAGACCATAGTTGGGCTATGGCATGTTTAGAT
** * * * * * *
40627966 GATAAGACCATAACTGGGTTATGGTA-CTATGGAG
1 G-TAAGACCATAGTTGGGCTATGGCATGTTTAGAT
* * * * *
40628000 GTAAGATCATGGTTGGACCATGGCAGTGTTTATAT
1 GTAAGACCATAGTTGGGCTATGGCA-TGTTTAGAT
*
40628035 GTAAGACCATAGATGGGCTATGGCAT
1 GTAAGACCATAGTTGGGCTATGGCAT
40628061 TGTGACAGCC
Statistics
Matches: 161, Mismatches: 57, Indels: 21
0.67 0.24 0.09
Matches are distributed among these distances:
32 6 0.04
33 79 0.49
34 9 0.06
35 67 0.42
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (34 bp):
GTAAGACCATAGTTGGGCTATGGCATGTTTAGAT
Found at i:40629766 original size:39 final size:40
Alignment explanation
Indices: 40629719--40629889 Score: 258
Period size: 39 Copynumber: 4.3 Consensus size: 40
40629709 AGACTAAGAT
40629719 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-C
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGTC
40629758 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-C
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGTC
* *
40629797 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGTC
* * * *
40629837 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAT-TCCGGGCTAAGTC
40629877 CCGAAGGCATTTG
1 CCGAAGGCATTTG
40629890 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
39 76 0.62
40 47 0.38
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGTC
Found at i:40629920 original size:79 final size:79
Alignment explanation
Indices: 40629719--40629922 Score: 218
Period size: 79 Copynumber: 2.6 Consensus size: 79
40629709 AGACTAAGAT
** * * * *
40629719 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCT-AAGCCCGAAGGCATTTGTGCGAGATACTA
1 CCGAAGGCATTTGAACGAGTTACTAAATCCGGGCTAAATCCCGAAGGCAATTGTGCGAGATACTA
*
40629783 ATTCCGGGCTAAGC
66 ATACCGGGCTAAGC
** * *
40629797 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT-
1 CCGAAGGCATTTGAACGAGTTACTAAATCCGGGCTAAATCCCGAAGGCAATTGTGCGAGATACTA
*
40629861 ATAACCGGGCTATGTC
66 AT-ACCGGGCTAAG-C
* * *
40629877 CCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTTA-CTAAATCCGGGCTAAATCCCGAAGG
40629923 TACGTGATTT
Statistics
Matches: 108, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
78 35 0.32
79 48 0.44
80 25 0.23
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTTACTAAATCCGGGCTAAATCCCGAAGGCAATTGTGCGAGATACTA
ATACCGGGCTAAGC
Found at i:40632463 original size:41 final size:41
Alignment explanation
Indices: 40632404--40632501 Score: 169
Period size: 41 Copynumber: 2.4 Consensus size: 41
40632394 AGATCCATAT
*
40632404 GGCTAGACACACTGGCGTGTGACTTGGCCGTGTGAGACACAC
1 GGCTAG-CACACGGGCGTGTGACTTGGCCGTGTGAGACACAC
*
40632446 GGCTAGTACACGGGCGTGTGACTTGGCCGTGTGAGACACAC
1 GGCTAGCACACGGGCGTGTGACTTGGCCGTGTGAGACACAC
40632487 GGCTAGCACACGGGC
1 GGCTAGCACACGGGC
40632502 ATGCGAAACC
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 47 0.89
42 6 0.11
ACGTcount: A:0.20, C:0.27, G:0.36, T:0.17
Consensus pattern (41 bp):
GGCTAGCACACGGGCGTGTGACTTGGCCGTGTGAGACACAC
Found at i:40633310 original size:13 final size:14
Alignment explanation
Indices: 40633292--40633329 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
40633282 TATTAGTTAT
40633292 TAAATTAATTTAA-
1 TAAATTAATTTAAC
*
40633305 TAAATTAAATTAAC
1 TAAATTAATTTAAC
40633319 TAAATTAATTT
1 TAAATTAATTT
40633330 CTCACTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAATTAATTTAAC
Found at i:40633328 original size:18 final size:18
Alignment explanation
Indices: 40633290--40633328 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40633280 AATATTAGTT
* *
40633290 ATTAAATTAATTTAATAA
1 ATTAAATTAACTAAATAA
*
40633308 ATTAAATTAACTAAATTA
1 ATTAAATTAACTAAATAA
40633326 ATT
1 ATT
40633329 TCTCACTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTAAATTAACTAAATAA
Found at i:40644575 original size:13 final size:13
Alignment explanation
Indices: 40644557--40644582 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40644547 AAATGTACAT
40644557 GTTCTATCAAAAG
1 GTTCTATCAAAAG
40644570 GTTCTATCAAAAG
1 GTTCTATCAAAAG
40644583 ACTCTAGTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
GTTCTATCAAAAG
Found at i:40646036 original size:22 final size:22
Alignment explanation
Indices: 40646011--40646069 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 22
40646001 CAGTTTTCAA
*
40646011 TTATATAAATTAT-TACAATATC
1 TTAT-TAAATTATATAAAATATC
*
40646033 TTATTTAATTATATAAAATA--
1 TTATTAAATTATATAAAATATC
* *
40646053 TTATTCAATTACATAAA
1 TTATTAAATTATATAAA
40646070 TTATTACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 15 0.47
21 7 0.22
22 10 0.31
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (22 bp):
TTATTAAATTATATAAAATATC
Found at i:40646062 original size:20 final size:20
Alignment explanation
Indices: 40646033--40646075 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
40646023 TTACAATATC
* *
40646033 TTATTTAATTATATAAAATA
1 TTATTCAATTACATAAAATA
*
40646053 TTATTCAATTACATAAATTA
1 TTATTCAATTACATAAAATA
40646073 TTA
1 TTA
40646076 CAAATTTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTCAATTACATAAAATA
Found at i:40648928 original size:23 final size:23
Alignment explanation
Indices: 40648896--40648942 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
40648886 TATAAAAAGG
*
40648896 ATAGCGTAAGTAATGCCATTTTT
1 ATAGCATAAGTAATGCCATTTTT
40648919 ATAGCATAAGTAATGCCATTTTT
1 ATAGCATAAGTAATGCCATTTTT
40648942 A
1 A
40648943 ATTTACTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (23 bp):
ATAGCATAAGTAATGCCATTTTT
Found at i:40674185 original size:14 final size:14
Alignment explanation
Indices: 40674166--40674196 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40674156 ATATATTTAC
*
40674166 ATAATAAATATATA
1 ATAATAAATAAATA
40674180 ATAATAAATAAATA
1 ATAATAAATAAATA
40674194 ATA
1 ATA
40674197 TAATAATATG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATAAATAAATA
Found at i:40674197 original size:19 final size:18
Alignment explanation
Indices: 40674168--40674204 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
40674158 ATATTTACAT
40674168 AATAAATATATAATAATA
1 AATAAATATATAATAATA
40674186 AATAAATAATATAATAATA
1 AATAAAT-ATATAATAATA
40674205 TGAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATATATAATAATA
Found at i:40674259 original size:60 final size:63
Alignment explanation
Indices: 40674179--40674312 Score: 170
Period size: 62 Copynumber: 2.2 Consensus size: 63
40674169 ATAAATATAT
* * * *
40674179 AATAATAAATAAATAATATAATAAT-ATGAAACAT-AA-CTCAAATTAATTAAATTAATAG-AA
1 AATAATAAAAAAACAATATAAAAATAATGAAA-ATAAAGCTCAAATTAATTAAATTAACAGTAA
* *
40674239 AATAATAAAAAAACAATATAAAAATAATGAGAATAAAGCTCAAATTAATTAATTTAACAGTAA
1 AATAATAAAAAAACAATATAAAAATAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAA
40674302 AATAA-AAAAAA
1 AATAATAAAAAA
40674313 TAAAAAAAAG
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
60 24 0.38
61 7 0.11
62 26 0.41
63 7 0.11
ACGTcount: A:0.64, C:0.05, G:0.04, T:0.26
Consensus pattern (63 bp):
AATAATAAAAAAACAATATAAAAATAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAA
Found at i:40674642 original size:37 final size:37
Alignment explanation
Indices: 40674592--40674662 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
40674582 ATAACAAGTA
40674592 GGGTGATGGAGGTAGTGGATGGTTTAGTAGGGTGTGG
1 GGGTGATGGAGGTAGTGGATGGTTTAGTAGGGTGTGG
40674629 GGGTGATGGAGGTAGTGGATGGTTTAGTAGGGTG
1 GGGTGATGGAGGTAGTGGATGGTTTAGTAGGGTG
40674663 ATGGAGTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.17, C:0.00, G:0.54, T:0.30
Consensus pattern (37 bp):
GGGTGATGGAGGTAGTGGATGGTTTAGTAGGGTGTGG
Found at i:40674682 original size:29 final size:29
Alignment explanation
Indices: 40674629--40674691 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
40674619 TAGGGTGTGG
*
40674629 GGGTGATGGAGGTAGTGGATGGTTTAGTA
1 GGGTGATGGAGGTAGTGGATAGTTTAGTA
* *
40674658 GGGTGATGGAGTTAGTGG-TCAGTTTAGTG
1 GGGTGATGGAGGTAGTGGAT-AGTTTAGTA
40674687 GGGTG
1 GGGTG
40674692 TTTAATTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 1 0.03
29 29 0.97
ACGTcount: A:0.17, C:0.02, G:0.49, T:0.32
Consensus pattern (29 bp):
GGGTGATGGAGGTAGTGGATAGTTTAGTA
Found at i:40675133 original size:133 final size:133
Alignment explanation
Indices: 40674893--40675506 Score: 908
Period size: 133 Copynumber: 4.6 Consensus size: 133
40674883 CACAGAGATG
** ** *
40674893 TGATCTGCTTTACTCCTGCTCAGTAAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCCTGCT
1 TGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTA--TTTAGCCTGCTCCACTCCTGCT
* ** * *
40674958 CAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATTGCCGATACATGGAGATAAGATTCATCA
64 CAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCA
40675023 AAATT
129 AAATT
* * * *
40675028 TGATCTTCTTTGCTCCTGCTCAGCGAAGATAAGATCTAGTATATAGACTGCTCCACTCCTGCTCA
1 TGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTGCTCA
*
40675093 GTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAATATTCACCAAA
66 GTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCAAA
40675158 ATT
131 ATT
* * *
40675161 TGATCTGCTCCGCTCCTACTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCTTGCTCA
1 TGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTGCTCA
* * *
40675226 GTGAAGATAAGGCTGGTGGCTGAAATCTACTCCATTGTCGATACATGGAGATAAGACTT-GCCAA
66 GTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGA-TTCACCAA
40675290 AATT
130 AATT
* * *
40675294 TGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCCTGCT
1 TGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTA--TTTAGCCTGCTCCACTCCTGCT
*
40675359 CAGTGAAGATAAGGCTAGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCA
64 CAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCA
40675424 AAATT
129 AAATT
* * *
40675429 TGATTTGCTCCGCTCCTGTTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTGCTCA
1 TGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTGCTCA
*
40675494 GTG-GGATAAGGCT
66 GTGAAGATAAGGCT
40675507 TGCCGAAATA
Statistics
Matches: 434, Mismatches: 41, Indels: 11
0.89 0.08 0.02
Matches are distributed among these distances:
132 9 0.02
133 266 0.61
134 4 0.01
135 155 0.36
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (133 bp):
TGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTGCTCA
GTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCAAA
ATT
Found at i:40675406 original size:268 final size:265
Alignment explanation
Indices: 40674918--40675506 Score: 912
Period size: 268 Copynumber: 2.2 Consensus size: 265
40674908 CTGCTCAGTA
* * *
40674918 AAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGG
1 AAGATAAGATCTAGTA--TTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGACTGA
* * **
40674983 AATCTGCTCCATTGCCGATACATGGAGATAAGATTCATCAAAATTTGATCTTCTTTGCTCCTGCT
64 AATCTACTCCATTGCCGATACATGGAGATAAGATTCA-CAAAATTTGATCTGCTTCACTCCTGCT
*
40675048 CAGCGAAGATAAGATCTAGTATATAGACTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGC
128 CAGCGAAGATAAGATCTAGTATATAGACTGCTCCACTCCTGCTCAGTGAAGATAAGGCTAGTGGC
*
40675113 TGAAATCTGCTCCATTGCCGATACATGGAGATAATATTCACCAAAATTTGATCTGCTCCGCTCCT
193 TGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCAAAATTTGATCTGCTCCGCTCCT
40675178 ACTCAGCG
258 ACTCAGCG
* * *
40675186 AAGATAAGATCTAGTATTTAGCCTGCTCCACTCTTGCTCAGTGAAGATAAGGCTGGTGGCTGAAA
1 AAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGACTGAAA
*
40675251 TCTACTCCATTGTCGATACATGGAGATAAGACTTGC-CAAAATTTGATCTGCTTCACTCCTGCTC
66 TCTACTCCATTGCCGATACATGGAGATAAGA-TT-CACAAAATTTGATCTGCTTCACTCCTGCTC
* * * *
40675315 AGTGAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTAGTGG
129 AGCGAAGATAAGATCTAGTA--TATAGACTGCTCCACTCCTGCTCAGTGAAGATAAGGCTAGTGG
*
40675380 CTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCAAAATTTGATTTGCTCCGCTCC
192 CTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCAAAATTTGATCTGCTCCGCTCC
**
40675445 TGTTCAGCG
257 TACTCAGCG
*
40675454 AAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTGCTCAGTG-GGATAAGGCT
1 AAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCT
40675507 TGCCGAAATA
Statistics
Matches: 295, Mismatches: 22, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
266 116 0.39
267 11 0.04
268 168 0.57
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (265 bp):
AAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGACTGAAA
TCTACTCCATTGCCGATACATGGAGATAAGATTCACAAAATTTGATCTGCTTCACTCCTGCTCAG
CGAAGATAAGATCTAGTATATAGACTGCTCCACTCCTGCTCAGTGAAGATAAGGCTAGTGGCTGA
AATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCAAAATTTGATCTGCTCCGCTCCTACT
CAGCG
Found at i:40676792 original size:26 final size:26
Alignment explanation
Indices: 40676763--40676845 Score: 98
Period size: 27 Copynumber: 3.1 Consensus size: 26
40676753 TCTCCTTTGC
40676763 TTTTCTTT-TTTTTCTCTTTTTTTTGT
1 TTTTCTTTCTTTTTCTCTTTTTTTT-T
*
40676789 TTTTCTCTTCTTTTTC-CTTTTCCTTTT
1 TTTTCT-TTCTTTTTCTCTTTT-TTTTT
*
40676816 TTCTCTTTCCTTTTTCTCTTTTTTTTT
1 TTTTCTTT-CTTTTTCTCTTTTTTTTT
40676843 TTT
1 TTT
40676846 GAAAGTTAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
26 8 0.17
27 26 0.54
28 14 0.29
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (26 bp):
TTTTCTTTCTTTTTCTCTTTTTTTTT
Found at i:40676818 original size:14 final size:14
Alignment explanation
Indices: 40676788--40676836 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 14
40676778 CTTTTTTTTG
40676788 TTTTTCTC-TT-CT
1 TTTTTCTCTTTCCT
*
40676800 TTTTCCT-TTTCCT
1 TTTTTCTCTTTCCT
40676813 TTTTTCTCTTTCC-
1 TTTTTCTCTTTCCT
40676826 TTTTTCTCTTT
1 TTTTTCTCTTT
40676837 TTTTTTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 8 0.25
13 19 0.59
14 5 0.16
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTTCTCTTTCCT
Found at i:40679442 original size:21 final size:21
Alignment explanation
Indices: 40679418--40679458 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40679408 GCTGACTTAT
40679418 CATGTTGT-TCTGGGATTCTAA
1 CATG-TGTCTCTGGGATTCTAA
40679439 CATGTGTCTCTGGGATTCTA
1 CATGTGTCTCTGGGATTCTA
40679459 GCATCTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.41
Consensus pattern (21 bp):
CATGTGTCTCTGGGATTCTAA
Found at i:40681277 original size:13 final size:12
Alignment explanation
Indices: 40681244--40681294 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
40681234 CTAACCATAT
*
40681244 ATAAATAATAAAA
1 ATAATTAAT-AAA
40681257 ATAA-TAATAATA
1 ATAATTAATAA-A
*
40681269 GTAATTAATAGAA
1 ATAATTAATA-AA
40681282 ATAATTAATAAA
1 ATAATTAATAAA
40681294 A
1 A
40681295 CAACAGTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 11 0.33
13 19 0.58
14 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
ATAATTAATAAA
Found at i:40681624 original size:17 final size:14
Alignment explanation
Indices: 40681590--40681642 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
40681580 GCTTAAAAGT
*
40681590 ATATATAGAT-ATAT
1 ATATATA-ATAATAA
*
40681604 ATATTTACATAATAA
1 ATATATA-ATAATAA
40681619 ATATATAATAATAA
1 ATATATAATAATAA
*
40681633 ATAAATAATA
1 ATATATAATA
40681643 TAATAATATG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
14 24 0.73
15 9 0.27
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (14 bp):
ATATATAATAATAA
Found at i:40681643 original size:19 final size:18
Alignment explanation
Indices: 40681614--40681650 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
40681604 ATATTTACAT
40681614 AATAAATATATAATAATA
1 AATAAATATATAATAATA
40681632 AATAAATAATATAATAATA
1 AATAAAT-ATATAATAATA
40681651 TGAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATATATAATAATA
Found at i:40682088 original size:37 final size:37
Alignment explanation
Indices: 40682037--40682107 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
40682027 ATAACAAGTA
40682037 GGGTGATGGAGGTAGTGGATGGTTTAATAGGGTGTGG
1 GGGTGATGGAGGTAGTGGATGGTTTAATAGGGTGTGG
* *
40682074 GGGTGATGGTGGTAGTGGATGGTTTAGTAGGGTG
1 GGGTGATGGAGGTAGTGGATGGTTTAATAGGGTG
40682108 ATGGAGTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.17, C:0.00, G:0.52, T:0.31
Consensus pattern (37 bp):
GGGTGATGGAGGTAGTGGATGGTTTAATAGGGTGTGG
Found at i:40682290 original size:18 final size:18
Alignment explanation
Indices: 40682263--40682299 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40682253 TGTACTAATA
40682263 TTTTCACACATACACCCT
1 TTTTCACACATACACCCT
* *
40682281 TTTTCCCACATACCCCCT
1 TTTTCACACATACACCCT
40682299 T
1 T
40682300 CCTTATGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.43, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTTCACACATACACCCT
Found at i:40691306 original size:13 final size:13
Alignment explanation
Indices: 40691285--40691318 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
40691275 ACGATTAAAT
*
40691285 TTTCGTACGAAAC
1 TTTCATACGAAAC
40691298 TTTCATACGAAAC
1 TTTCATACGAAAC
40691311 TTTCATAC
1 TTTCATAC
40691319 ATACTAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (13 bp):
TTTCATACGAAAC
Found at i:40691864 original size:18 final size:18
Alignment explanation
Indices: 40691841--40691885 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
40691831 AAGCTTAAGA
*
40691841 CTATTCTGAATCAGGCTC
1 CTATTCTGAATCAAGCTC
*
40691859 CTATTCTGACTCAAGCTC
1 CTATTCTGAATCAAGCTC
*
40691877 CTGTTCTGA
1 CTATTCTGA
40691886 TATAACCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.36
Consensus pattern (18 bp):
CTATTCTGAATCAAGCTC
Found at i:40702099 original size:93 final size:97
Alignment explanation
Indices: 40701942--40702148 Score: 235
Period size: 93 Copynumber: 2.1 Consensus size: 97
40701932 ATAGTAAAAC
** *
40701942 TATGGTCTTGCACATAGTCACATATCACATACCGAGGCCATAGCCCAGCCATGGTCTTACACGG-
1 TATGGTCTTATACATAGTCACATATCACA-ACCGAGGCCATAGCCCAGACATGGTCTTACACGGA
* * *
40702006 ATCACATATCACA-CT-GATGCCATATCCCAGA
65 AGCACATATCACATCTCGAAGCCATAGCCCAGA
* * * *
40702037 TATGGTCTTATACAGTAG-CACATATCAC-ACCGATGCCATATCCCAGATATGGTCTTATACGGA
1 TATGGTCTTATACA-TAGTCACATATCACAACCGAGGCCATAGCCCAGACATGGTCTTACACGGA
*
40702100 AGCACATATCACATTTCTCCGAAGCCATAGCCCAGC
65 AGCACATATCACA--TCT-CGAAGCCATAGCCCAGA
40702136 TATGGTCTTATAC
1 TATGGTCTTATAC
40702149 GGAAATCACA
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
93 29 0.31
94 12 0.13
95 22 0.23
96 3 0.03
97 2 0.02
99 26 0.28
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (97 bp):
TATGGTCTTATACATAGTCACATATCACAACCGAGGCCATAGCCCAGACATGGTCTTACACGGAA
GCACATATCACATCTCGAAGCCATAGCCCAGA
Found at i:40702143 original size:52 final size:49
Alignment explanation
Indices: 40701960--40702152 Score: 209
Period size: 47 Copynumber: 4.0 Consensus size: 49
40701950 TGCACATAGT
* ** * *
40701960 CACATATCACA-TACCGAGGCCATAGCCCAGCCATGGTCTTACACGG-AT
1 CACATATCACACT-CCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* * *
40702008 CACATATCACACT--GATGCCATATCCCAGATATGGTCTTATACAGTAG
1 CACATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
*
40702055 CACATATCACA--CCGATGCCATATCCCAGATATGGTCTTATACGGAAG
1 CACATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* *
40702102 CACATATCACATTTCTCCGAAGCCATAGCCCAGCTATGGTCTTATACGGAA
1 CACATATCACA---CTCCGATGCCATAGCCCAGATATGGTCTTATACGGAA
40702153 ATCACATTTC
Statistics
Matches: 124, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
46 25 0.20
47 55 0.44
48 11 0.09
49 1 0.01
52 32 0.26
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (49 bp):
CACATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
Found at i:40702646 original size:19 final size:19
Alignment explanation
Indices: 40702622--40702663 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
40702612 TTCACCCATA
40702622 AATTGAACTAATTTTTCTT
1 AATTGAACTAATTTTTCTT
40702641 AATTGAACTAATTTTTCTT
1 AATTGAACTAATTTTTCTT
40702660 AATT
1 AATT
40702664 AACACTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (19 bp):
AATTGAACTAATTTTTCTT
Found at i:40710958 original size:18 final size:18
Alignment explanation
Indices: 40710937--40710975 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
40710927 TTTAAATTGT
40710937 TGTTATTATTATTATATG
1 TGTTATTATTATTATATG
*
40710955 TGTTTTTATTATTATATG
1 TGTTATTATTATTATATG
40710973 TGT
1 TGT
40710976 ATGGAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (18 bp):
TGTTATTATTATTATATG
Found at i:40718722 original size:13 final size:13
Alignment explanation
Indices: 40718704--40718728 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40718694 AACCTTGTTT
40718704 AAAAAAAGAAAAG
1 AAAAAAAGAAAAG
40718717 AAAAAAAGAAAA
1 AAAAAAAGAAAA
40718729 CATTGTTCAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:40724290 original size:23 final size:23
Alignment explanation
Indices: 40724264--40724310 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
40724254 AGAACAAAAA
40724264 AAATGGGAGAGTAAAAGAGTGAG
1 AAATGGGAGAGTAAAAGAGTGAG
40724287 AAATGGGAGAGTAAAAGAGTGAG
1 AAATGGGAGAGTAAAAGAGTGAG
40724310 A
1 A
40724311 GTATGAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.38, T:0.13
Consensus pattern (23 bp):
AAATGGGAGAGTAAAAGAGTGAG
Found at i:40729450 original size:26 final size:26
Alignment explanation
Indices: 40729421--40729528 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
40729411 TGGTACAAAT
40729421 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
40729447 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40729473 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
40729499 TGATAATGGTTTAGATAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40729525 TGAT
1 TGAT
40729529 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:40730718 original size:8 final size:8
Alignment explanation
Indices: 40730705--40730734 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
40730695 AGATCGGCAC
40730705 AAGCCGAA
1 AAGCCGAA
40730713 AAGCCGAA
1 AAGCCGAA
*
40730721 ATGCCGAA
1 AAGCCGAA
40730729 AAGCCG
1 AAGCCG
40730735 GTATTTTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.27, G:0.27, T:0.03
Consensus pattern (8 bp):
AAGCCGAA
Found at i:40731162 original size:27 final size:27
Alignment explanation
Indices: 40731122--40731206 Score: 93
Period size: 27 Copynumber: 3.1 Consensus size: 27
40731112 AGGAAGCGTC
40731122 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTATGCCACAATTATCTGAT
* *
40731149 CTGGTGGCTTTGCCAC-ATATATCTGTT
1 CTGGTGGCTATGCCACAAT-TATCTGAT
* * *
40731176 CTGGCGGCTCTGTCACAA-TATCTGTAT
1 CTGGTGGCTATGCCACAATTATCTG-AT
40731203 CTGG
1 CTGG
40731207 AGACTTCGTC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
26 8 0.16
27 40 0.82
28 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTATGCCACAATTATCTGAT
Found at i:40731217 original size:27 final size:27
Alignment explanation
Indices: 40731135--40731226 Score: 91
Period size: 27 Copynumber: 3.4 Consensus size: 27
40731125 GTGGCTATGC
* * *
40731135 CACAATTATCTG-ATCTGGTGGCTTTGC
1 CACAA-TATCTGTATCTGGAGGCTTCGT
*
40731162 CACATATATCTGT-TCTGGCGGC-TCTGT
1 CACA-ATATCTGTATCTGGAGGCTTC-GT
*
40731189 CACAATATCTGTATCTGGAGACTTCGT
1 CACAATATCTGTATCTGGAGGCTTCGT
40731216 CACAATATCTG
1 CACAATATCTG
40731227 GCAGCCTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
26 9 0.16
27 43 0.78
28 3 0.05
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (27 bp):
CACAATATCTGTATCTGGAGGCTTCGT
Found at i:40732543 original size:40 final size:39
Alignment explanation
Indices: 40732487--40732563 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 39
40732477 TAAGATATTC
*
40732487 ATAACAAATATAAAATTTTAAAA-AATAAAAATATATAAA
1 ATAACAAATATAAAA-TTAAAAATAATAAAAATATATAAA
* *
40732526 ATAACTAAATATCAAATTAAAAATAATATAAATATATA
1 ATAAC-AAATATAAAATTAAAAATAATAAAAATATATA
40732564 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 11 0.33
40 22 0.67
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (39 bp):
ATAACAAATATAAAATTAAAAATAATAAAAATATATAAA
Found at i:40734605 original size:13 final size:13
Alignment explanation
Indices: 40734587--40734612 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40734577 GGGCCACCCC
40734587 CAAAACCCAATAA
1 CAAAACCCAATAA
40734600 CAAAACCCAATAA
1 CAAAACCCAATAA
40734613 ACCAAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.31, G:0.00, T:0.08
Consensus pattern (13 bp):
CAAAACCCAATAA
Found at i:40734834 original size:16 final size:16
Alignment explanation
Indices: 40734813--40734851 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
40734803 CTCCATGCGT
40734813 CTGACACCACCCACAC
1 CTGACACCACCCACAC
40734829 CTGACACCACCCACAC
1 CTGACACCACCCACAC
40734845 CTGACAC
1 CTGACAC
40734852 ACCTGTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.31, C:0.54, G:0.08, T:0.08
Consensus pattern (16 bp):
CTGACACCACCCACAC
Found at i:40739018 original size:48 final size:48
Alignment explanation
Indices: 40738957--40739054 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
40738947 AATGTTTCCC
*
40738957 AACAAATTGAAAATAAATGAAAAAATATATGTATACTTAAATAACATT
1 AACAAATTAAAAATAAATGAAAAAATATATGTATACTTAAATAACATT
*
40739005 AACAAATTAAAAATAAATTAAAAAATATATGTATACTTAAATAACATT
1 AACAAATTAAAAATAAATGAAAAAATATATGTATACTTAAATAACATT
40739053 AA
1 AA
40739055 GATATGTGCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (48 bp):
AACAAATTAAAAATAAATGAAAAAATATATGTATACTTAAATAACATT
Found at i:40739151 original size:14 final size:14
Alignment explanation
Indices: 40739128--40739162 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
40739118 TACAATATCC
*
40739128 AAATAATAACAACA
1 AAATAGTAACAACA
40739142 AAATAGTAACAACA
1 AAATAGTAACAACA
*
40739156 TAATAGT
1 AAATAGT
40739163 GAAATATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:40739227 original size:25 final size:25
Alignment explanation
Indices: 40739174--40739226 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
40739164 AAATATTAGC
* *
40739174 AAAATAGTGAAAAAAAAATAACAAG
1 AAAATAGTCAAAAAAAAAGAACAAG
*
40739199 AAAATAG-CAAAAAAAAAGAAGAAG
1 AAAATAGTCAAAAAAAAAGAACAAG
40739223 AAAA
1 AAAA
40739227 AACAACAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.75, C:0.04, G:0.13, T:0.08
Consensus pattern (25 bp):
AAAATAGTCAAAAAAAAAGAACAAG
Found at i:40739942 original size:22 final size:22
Alignment explanation
Indices: 40739917--40739958 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
40739907 TTAGAATTAT
40739917 AATTGTAATTATGTT-TAATTGA
1 AATTGTAATTAT-TTATAATTGA
*
40739939 AATTTTAATTATTTATAATT
1 AATTGTAATTATTTATAATT
40739959 CAGTACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
AATTGTAATTATTTATAATTGA
Found at i:40740975 original size:24 final size:24
Alignment explanation
Indices: 40740948--40741012 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
40740938 AAAAACTAAG
*
40740948 TGGCACTATGTGTGCGA-GACTACA
1 TGGCACTATGTGTGCGAGGA-AACA
* *
40740972 TGGCACTCTGTGTGCGAGGAAACG
1 TGGCACTATGTGTGCGAGGAAACA
40740996 TGGCACTATGTGTGCGA
1 TGGCACTATGTGTGCGA
40741013 ATAAGTAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
24 34 0.94
25 2 0.06
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.25
Consensus pattern (24 bp):
TGGCACTATGTGTGCGAGGAAACA
Found at i:40743790 original size:16 final size:17
Alignment explanation
Indices: 40743765--40743797 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
40743755 TCTCAATTTA
40743765 ATATATTTTTTTGAATT
1 ATATATTTTTTTGAATT
40743782 ATATA-TTTTTTGAATT
1 ATATATTTTTTTGAATT
40743798 TTTGTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (17 bp):
ATATATTTTTTTGAATT
Found at i:40743805 original size:17 final size:17
Alignment explanation
Indices: 40743766--40743818 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
40743756 CTCAATTTAA
*
40743766 TATATTTTTTTGAA-TTA
1 TATA-TTTTTTGAATTTT
40743783 TATATTTTTTGAATTTT
1 TATATTTTTTGAATTTT
* *
40743800 TGTATTTTCTTAAATTTT
1 TATATTTT-TTGAATTTT
40743818 T
1 T
40743819 TGAATTCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 9 0.29
17 13 0.42
18 9 0.29
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.68
Consensus pattern (17 bp):
TATATTTTTTGAATTTT
Found at i:40743817 original size:18 final size:17
Alignment explanation
Indices: 40743785--40743818 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40743775 TTGAATTATA
*
40743785 TATTTTTTGAATTTTTG
1 TATTTTTTAAATTTTTG
40743802 TATTTTCTTAAATTTTT
1 TATTTT-TTAAATTTTT
40743819 TGAATTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.71
Consensus pattern (17 bp):
TATTTTTTAAATTTTTG
Found at i:40759874 original size:31 final size:29
Alignment explanation
Indices: 40759830--40759887 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 29
40759820 ATTTATCTAC
40759830 AAGATAAACTTTAA-ATTAATATTAATATT
1 AAGATAAACTTTAATATTAA-ATTAATATT
40759859 AAGATAATCACTTTAATATTAAATTAATA
1 AAGATAA--ACTTTAATATTAAATTAATA
40759888 AAATACTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 7 0.27
31 14 0.54
32 5 0.19
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (29 bp):
AAGATAAACTTTAATATTAAATTAATATT
Found at i:40759886 original size:20 final size:17
Alignment explanation
Indices: 40759840--40759930 Score: 66
Period size: 17 Copynumber: 5.4 Consensus size: 17
40759830 AAGATAAACT
40759840 TTAAATTAATATTAATA
1 TTAAATTAATATTAATA
40759857 TTAAGA-TAATCACTTTAATA
1 TTAA-ATTAAT-A--TTAATA
*
40759877 TTAAATTAATA-AAATA
1 TTAAATTAATATTAATA
* *
40759893 CT--ATTAACA-TAACTA
1 TTAAATTAATATTAA-TA
*
40759908 TTAAATTAATTTTAATA
1 TTAAATTAATATTAATA
40759925 TTAAAT
1 TTAAAT
40759931 GTATTAAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
14 8 0.14
15 3 0.05
16 5 0.09
17 21 0.36
18 5 0.09
19 2 0.03
20 14 0.24
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (17 bp):
TTAAATTAATATTAATA
Found at i:40769168 original size:20 final size:19
Alignment explanation
Indices: 40769135--40769172 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
40769125 ATTCCGAAAA
*
40769135 TAATATTATTTTAATAATT
1 TAATATTATCTTAATAATT
40769154 TAATACTTATCTTAATAAT
1 TAATA-TTATCTTAATAAT
40769173 ATTTTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATATTATCTTAATAATT
Found at i:40769279 original size:12 final size:12
Alignment explanation
Indices: 40769259--40769292 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
40769249 TATTATTTTA
*
40769259 ATAAGATTTAAT
1 ATAATATTTAAT
40769271 ATAATATTTAAT
1 ATAATATTTAAT
40769283 ATAATATTTA
1 ATAATATTTA
40769293 TTTTGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (12 bp):
ATAATATTTAAT
Found at i:40769280 original size:62 final size:59
Alignment explanation
Indices: 40769204--40769320 Score: 146
Period size: 62 Copynumber: 1.9 Consensus size: 59
40769194 AATGATTATC
* * *
40769204 TTAATATTAAATTTAATTTAACATTTATCTTGTAGATAAACATTCTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATATAACATTTAT-TT-T-GATAAACATTATATTAATTTAATAAGAT
* *
40769266 TTAATA-TAATATTTAATATAATATTTATTTTGATAAATATTATATTAATTTAATA
1 TTAATATTAA-ATTTAATATAACATTTATTTTGATAAACATTATATTAATTTAATA
40769321 TTAAAGTGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
59 21 0.43
60 1 0.02
61 5 0.10
62 22 0.45
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (59 bp):
TTAATATTAAATTTAATATAACATTTATTTTGATAAACATTATATTAATTTAATAAGAT
Found at i:40769320 original size:16 final size:16
Alignment explanation
Indices: 40769264--40769323 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
40769254 TTTTAATAAG
*
40769264 ATTTAATATAATATTTA
1 ATTTAATATTATA-TTA
* * *
40769281 ATATAATATTTATTTTG
1 ATTTAATA-TTATATTA
*
40769298 A-TAAATATTATATTA
1 ATTTAATATTATATTA
40769313 ATTTAATATTA
1 ATTTAATATTA
40769324 AAGTGATTAA
Statistics
Matches: 32, Mismatches: 9, Indels: 5
0.70 0.20 0.11
Matches are distributed among these distances:
15 7 0.22
16 12 0.38
17 10 0.31
18 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTTAATATTATATTA
Found at i:40773034 original size:16 final size:17
Alignment explanation
Indices: 40773010--40773042 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40773000 TACTTATTGA
40773010 ATATAATTAAT-TTTTT
1 ATATAATTAATATTTTT
*
40773026 ATATGATTAATATTTTT
1 ATATAATTAATATTTTT
40773043 TTCAATATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
ATATAATTAATATTTTT
Found at i:40785834 original size:31 final size:31
Alignment explanation
Indices: 40785799--40785874 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
40785789 AAAAAAACTT
* * *
40785799 AATAGCCTAGTGACTTAAAT-AAGAACTTTTG
1 AATAGCTTAGTGACTTAAATGAA-AACGTTCG
*
40785830 AATAG-TTCATTGACTTAAATGAAAACGTTCG
1 AATAGCTT-AGTGACTTAAATGAAAACGTTCG
40785861 AATAGCTTAGTGAC
1 AATAGCTTAGTGAC
40785875 CAAATTGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
30 1 0.03
31 32 0.86
32 4 0.11
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (31 bp):
AATAGCTTAGTGACTTAAATGAAAACGTTCG
Found at i:40789629 original size:30 final size:29
Alignment explanation
Indices: 40789595--40789658 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
40789585 TTAATAAAAG
* *
40789595 TAAAATTGTACTTTAACCTTTTTAAAATTA
1 TAAAATT-TAATTTAACCTTTTAAAAATTA
*
40789625 TAAAAATTTAATTTAATCTTTTAAAAATTA
1 T-AAAATTTAATTTAACCTTTTAAAAATTA
40789655 TAAA
1 TAAA
40789659 GATATAAGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 3 0.10
30 21 0.70
31 6 0.20
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (29 bp):
TAAAATTTAATTTAACCTTTTAAAAATTA
Found at i:40793652 original size:26 final size:26
Alignment explanation
Indices: 40793605--40793705 Score: 82
Period size: 26 Copynumber: 3.9 Consensus size: 26
40793595 TATAAGTAAT
*
40793605 ATATAACTAGTAATATCAAAATATATAC
1 ATATAA-TA-TAATATAAAAATATATAC
**
40793633 ATGATAATAT-ATATAAAAATATATGT
1 AT-ATAATATAATATAAAAATATATAC
* *
40793659 ATATAATGTAATATGAAAATATAT--
1 ATATAATATAATATAAAAATATATAC
* * *
40793683 ATGTAGTATAATATTAAAATATA
1 ATATAATATAATATAAAAATATA
40793706 ATAATACAAC
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
24 19 0.31
25 6 0.10
26 28 0.45
27 1 0.02
28 4 0.06
29 4 0.06
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (26 bp):
ATATAATATAATATAAAAATATATAC
Found at i:40793745 original size:32 final size:32
Alignment explanation
Indices: 40793693--40793773 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 32
40793683 ATGTAGTATA
*
40793693 ATAT-TAAAATATAATAATACAACATTAAAAAT
1 ATATATAACATATAA-AATACAACATTAAAAAT
* * *
40793725 ATATGAT-ATATATAAAATACAATATTAAAAGT
1 ATAT-ATAACATATAAAATACAACATTAAAAAT
40793757 ATATATAACATATAAAA
1 ATATATAACATATAAAA
40793774 ATATATATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
31 2 0.05
32 32 0.76
33 7 0.17
34 1 0.02
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.32
Consensus pattern (32 bp):
ATATATAACATATAAAATACAACATTAAAAAT
Found at i:40795972 original size:12 final size:12
Alignment explanation
Indices: 40795956--40796001 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
40795946 TATTATTATC
40795956 ATATTATATTTA
1 ATATTATATTTA
* *
40795968 GTATTA-CTTTA
1 ATATTATATTTA
40795979 ATATTATA-TTA
1 ATATTATATTTA
40795990 ACTATTATATTT
1 A-TATTATATTT
40796002 TATTATTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
11 13 0.48
12 12 0.44
13 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (12 bp):
ATATTATATTTA
Found at i:40796021 original size:17 final size:17
Alignment explanation
Indices: 40795938--40796042 Score: 81
Period size: 17 Copynumber: 5.9 Consensus size: 17
40795928 TTTGTACTGC
40795938 ATTATAATTATTATTATCAT
1 ATTAT-ATTATTATTA-C-T
*
40795958 ATTATATTTAGTATTACT
1 ATTATA-TTATTATTACT
40795976 -TTAATATTA-TATTAACT
1 ATT-ATATTATTATT-ACT
40795993 ATTATATTTTATTATTACT
1 ATTATA--TTATTATTACT
* *
40796012 ATTACATTATTAGTAC-
1 ATTATATTATTATTACT
*
40796028 ATTATTTTATTATTA
1 ATTATATTATTATTA
40796043 TTTTTATTGT
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
16 16 0.22
17 20 0.28
18 6 0.08
19 13 0.18
20 17 0.24
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTATATTATTATTACT
Found at i:40796064 original size:15 final size:14
Alignment explanation
Indices: 40796054--40796086 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
40796044 TTTTATTGTA
40796054 AATATTATTATTCT
1 AATATTATTATTCT
*
40796068 AATATTATT-TTAT
1 AATATTATTATTCT
40796081 AATATT
1 AATATT
40796087 TTTCATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
AATATTATTATTCT
Found at i:40796151 original size:12 final size:13
Alignment explanation
Indices: 40796123--40796155 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
40796113 TTATTTATTC
*
40796123 TTATATATGTCAT
1 TTATTTATGTCAT
40796136 TTATTTATGT-AT
1 TTATTTATGTCAT
40796148 TTATTTAT
1 TTATTTAT
40796156 TTTATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (13 bp):
TTATTTATGTCAT
Found at i:40797542 original size:26 final size:26
Alignment explanation
Indices: 40797495--40797595 Score: 82
Period size: 26 Copynumber: 3.9 Consensus size: 26
40797485 TATAAGTAAT
*
40797495 ATATAACTAGTAATATCAAAATATATAC
1 ATATAA-TA-TAATATAAAAATATATAC
**
40797523 ATGATAATAT-ATATAAAAATATATGT
1 AT-ATAATATAATATAAAAATATATAC
* *
40797549 ATATAATGTAATATGAAAATATAT--
1 ATATAATATAATATAAAAATATATAC
* * *
40797573 ATGTAGTATAATATTAAAATATA
1 ATATAATATAATATAAAAATATA
40797596 ATAATACAAC
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
24 19 0.31
25 6 0.10
26 28 0.45
27 1 0.02
28 4 0.06
29 4 0.06
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (26 bp):
ATATAATATAATATAAAAATATATAC
Found at i:40797635 original size:32 final size:32
Alignment explanation
Indices: 40797583--40797663 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 32
40797573 ATGTAGTATA
*
40797583 ATAT-TAAAATATAATAATACAACATTAAAAAT
1 ATATATAACATATAA-AATACAACATTAAAAAT
* * *
40797615 ATATGAT-ATATATAAAATACAATATTAAAAGT
1 ATAT-ATAACATATAAAATACAACATTAAAAAT
40797647 ATATATAACATATAAAA
1 ATATATAACATATAAAA
40797664 ATATATATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
31 2 0.05
32 32 0.76
33 7 0.17
34 1 0.02
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.32
Consensus pattern (32 bp):
ATATATAACATATAAAATACAACATTAAAAAT
Found at i:40799887 original size:12 final size:12
Alignment explanation
Indices: 40799871--40799916 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
40799861 TATTATTATC
40799871 ATATTATATTTA
1 ATATTATATTTA
* *
40799883 GTATTA-CTTTA
1 ATATTATATTTA
40799894 ATATTATA-TTA
1 ATATTATATTTA
40799905 ACTATTATATTT
1 A-TATTATATTT
40799917 TATTATTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
11 13 0.48
12 12 0.44
13 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (12 bp):
ATATTATATTTA
Found at i:40799936 original size:17 final size:17
Alignment explanation
Indices: 40799853--40799957 Score: 81
Period size: 17 Copynumber: 5.9 Consensus size: 17
40799843 TTTGTACTGC
40799853 ATTATAATTATTATTATCAT
1 ATTAT-ATTATTATTA-C-T
*
40799873 ATTATATTTAGTATTACT
1 ATTATA-TTATTATTACT
40799891 -TTAATATTA-TATTAACT
1 ATT-ATATTATTATT-ACT
40799908 ATTATATTTTATTATTACT
1 ATTATA--TTATTATTACT
* *
40799927 ATTACATTATTAGTAC-
1 ATTATATTATTATTACT
*
40799943 ATTATTTTATTATTA
1 ATTATATTATTATTA
40799958 TTTTTATTGT
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
16 16 0.22
17 20 0.28
18 6 0.08
19 13 0.18
20 17 0.24
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTATATTATTATTACT
Found at i:40800008 original size:14 final size:13
Alignment explanation
Indices: 40799945--40800009 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
40799935 ATTAGTACAT
*
40799945 TATTTTATTATTA
1 TATTTTATTATAA
*
40799958 T-TTTTATTGTAAA
1 TATTTTATTAT-AA
*
40799971 TATTATTATTCTAA
1 TATT-TTATTATAA
*
40799985 TATTATATTATAA
1 TATTTTATTATAA
40799998 TATTTTCATTAT
1 TATTTT-ATTAT
40800010 TTGTATCATT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
12 8 0.19
13 15 0.36
14 13 0.31
15 6 0.14
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.62
Consensus pattern (13 bp):
TATTTTATTATAA
Found at i:40800065 original size:12 final size:13
Alignment explanation
Indices: 40800037--40800069 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
40800027 TTATTTATTC
*
40800037 TTATATATGTCAT
1 TTATTTATGTCAT
40800050 TTATTTATGT-AT
1 TTATTTATGTCAT
40800062 TTATTTAT
1 TTATTTAT
40800070 TTTATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (13 bp):
TTATTTATGTCAT
Found at i:40803965 original size:18 final size:18
Alignment explanation
Indices: 40803942--40804005 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
40803932 TCATTGTGAT
40803942 CTGAAGCCCGAAGTCTAA
1 CTGAAGCCCGAAGTCTAA
**
40803960 CTGAAGCACATAAGTGCTAAA
1 CTGAAGC-CCGAAGT-CT-AA
* *
40803981 CGGAAGCCCGAAGGCTAA
1 CTGAAGCCCGAAGTCTAA
40803999 CTGAAGC
1 CTGAAGC
40804006 TCATCAGAGC
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 15 0.42
19 7 0.19
20 6 0.17
21 8 0.22
ACGTcount: A:0.36, C:0.25, G:0.25, T:0.14
Consensus pattern (18 bp):
CTGAAGCCCGAAGTCTAA
Found at i:40815001 original size:44 final size:45
Alignment explanation
Indices: 40814937--40815441 Score: 231
Period size: 44 Copynumber: 11.5 Consensus size: 45
40814927 AGCCTTAACC
* * *
40814937 CCCTAAGCAGTAGGGTAACAGGCT-GAATTTACAAGATCTTATCA
1 CCCTAAGCAGTAGGGGAACAGGATCGAAATTACAAGATCTTATCA
* * ** * *
40814981 CCCTAAGCAGTAGGGGAACA-GATCGAAGATGAC-GGGCCTTAACC
1 CCCTAAGCAGTAGGGGAACAGGATCGAA-ATTACAAGATCTTATCA
* * * * *
40815025 CCCTAAGCAGTAGGGTAACAGGTTGGAAATTA-TAGATCTTATCT
1 CCCTAAGCAGTAGGGGAACAGGATCGAAATTACAAGATCTTATCA
* * *** * *
40815069 CCCTAAGCAGTAGTGGAGCA-GATCGAAGACGGCGAG-CCTTAATC-
1 CCCTAAGCAGTAGGGGAACAGGATCGAA-ATTACAAGATCTT-ATCA
* * * *
40815113 CCCTAAGCAGTAGGGTAGCAGGCT-GAATTTACAAGATCTTATCA
1 CCCTAAGCAGTAGGGGAACAGGATCGAAATTACAAGATCTTATCA
* * * * ** *
40815157 CCTTAAGCAGTAAGGGAACA-GATCGAAAATGAC-GGGCCTTAAC-
1 CCCTAAGCAGTAGGGGAACAGGATCG-AAATTACAAGATCTTATCA
* * * * * *
40815200 CCCATAAGCAGTAGAGTAACATGTTGGAAATTAC-AGATCTTATCT
1 CCC-TAAGCAGTAGGGGAACAGGATCGAAATTACAAGATCTTATCA
** * * ** * * * *
40815245 CCCTAAGCAGTATTGGAGCA-GATTGAAGACGACGAG-CCTTAACC
1 CCCTAAGCAGTAGGGGAACAGGATCGAA-ATTACAAGATCTTATCA
* * * *
40815289 CCCTAAGTAGTAGGGTAAAAGG--CTAAATTTACAAGATCTTATCA
1 CCCTAAGCAGTAGGGGAACAGGATCGAAA-TTACAAGATCTTATCA
* * ** * * *
40815333 CCCTAAGCAGTGGGGGAACA-GATCGAAGATGATGAG-CCTTAACC
1 CCCTAAGCAGTAGGGGAACAGGATCGAA-ATTACAAGATCTTATCA
* * *
40815377 CCCTAAGTAGTAGGGTAACA-GAT-TAAATTTACAAGATCTTATCA
1 CCCTAAGCAGTAGGGGAACAGGATCGAAA-TTACAAGATCTTATCA
40815421 CCCTAAGCAGTAGGGGAACAG
1 CCCTAAGCAGTAGGGGAACAG
40815442 ATAGAAGATG
Statistics
Matches: 328, Mismatches: 107, Indels: 51
0.67 0.22 0.10
Matches are distributed among these distances:
42 2 0.01
43 35 0.11
44 254 0.77
45 36 0.11
46 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.22
Consensus pattern (45 bp):
CCCTAAGCAGTAGGGGAACAGGATCGAAATTACAAGATCTTATCA
Found at i:40815062 original size:88 final size:89
Alignment explanation
Indices: 40814911--40815679 Score: 907
Period size: 88 Copynumber: 8.7 Consensus size: 89
40814901 TTCCTAAGAG
* * * *
40814911 CAGATCGAAGACGGCGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCT-GAATTTACAAGATC
1 CAGATCGAAGATGACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAAGATC
40814975 TTATCACCCTAAGCAGTAGGGGAA
66 TTATCACCCTAAGCAGTAGGGGAA
* *
40814999 CAGATCGAAGATGACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTGGAAATTA-TAGATC
1 CAGATCGAAGATGACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAAGATC
* * *
40815063 TTATCTCCCTAAGCAGTAGTGGAG
66 TTATCACCCTAAGCAGTAGGGGAA
* * * * * *
40815087 CAGATCGAAGACGGCGAGCCTTAATCCCCTAAGCAGTAGGGTAGCAGGCT-GAATTTACAAGATC
1 CAGATCGAAGATGACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAAGATC
* *
40815151 TTATCACCTTAAGCAGTAAGGGAA
66 TTATCACCCTAAGCAGTAGGGGAA
* * * * *
40815175 CAGATCGAAAATGACGGGCCTTAACCCCATAAGCAGTAGAGTAACATGTTGGAAATTAC-AGATC
1 CAGATCGAAGATGACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAAGATC
* ** *
40815239 TTATCTCCCTAAGCAGTATTGGAG
66 TTATCACCCTAAGCAGTAGGGGAA
* * * * *
40815263 CAGATTGAAGACGACGAGCCTTAACCCCCTAAGTAGTAGGGTAAAAGGCT--AAATTTACAAGAT
1 CAGATCGAAGATGACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAA-TTACAAGAT
*
40815326 CTTATCACCCTAAGCAGTGGGGGAA
65 CTTATCACCCTAAGCAGTAGGGGAA
* * * * *
40815351 CAGATCGAAGATGATGAGCCTTAACCCCCTAAGTAGTAGGGTAACA-GAT-TAAATTTACAAGAT
1 CAGATCGAAGATGACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAA-TTACAAGAT
40815414 CTTATCACCCTAAGCAGTAGGGGAA
65 CTTATCACCCTAAGCAGTAGGGGAA
* * *
40815439 CAGATAGAAGATGATGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGC-GGAAGATTA-TAGAT
1 CAGATCGAAGATGACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAA-ATTACAAGAT
* * *
40815502 CTTGTCTCCCTAAGCAGTAGTGGAA
65 CTTATCACCCTAAGCAGTAGGGGAA
* * * * * * * *
40815527 CAAACCGAAGACGATGGGCCTTAACCCCTTAAGCAGTAGGGTAACAGACTGAAAATTA-TAGATC
1 CAGATCGAAGATGACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAAGATC
* * * *
40815591 TTATCATCTTAAGCAGGAGGGGAG
66 TTATCACCCTAAGCAGTAGGGGAA
*
40815615 CAGATCGAAGATGACGGGACC-TAACTCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAA-AT
1 CAGATCGAAGATGACGGG-CCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAAGAT
40815678 CT
65 CT
40815680 CATCTCCTTG
Statistics
Matches: 578, Mismatches: 91, Indels: 24
0.83 0.13 0.03
Matches are distributed among these distances:
86 3 0.01
87 12 0.02
88 537 0.93
89 25 0.04
90 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (89 bp):
CAGATCGAAGATGACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAAGATC
TTATCACCCTAAGCAGTAGGGGAA
Found at i:40815137 original size:176 final size:176
Alignment explanation
Indices: 40814845--40815679 Score: 1043
Period size: 176 Copynumber: 4.8 Consensus size: 176
40814835 TGGTGAATTC
* *
40814845 ACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTGGAAATTACAGATCTTGTCTTCCT----
1 ACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTGGAAATTACAGATCTTATCTCCCTAAGC
*
40814906 A--A---GAGCAGATCGAAGACGGCGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATT
66 AGTAGGGGAGCAGATCGAAGACGACGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATT
40814966 TACAAGATCTTATCACCCTAAGCAGTAGGGGAACAGATCGAAGATG
131 TACAAGATCTTATCACCCTAAGCAGTAGGGGAACAGATCGAAGATG
*
40815012 ACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTGGAAATTATAGATCTTATCTCCCTAAGC
1 ACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTGGAAATTACAGATCTTATCTCCCTAAGC
* * * *
40815077 AGTAGTGGAGCAGATCGAAGACGGCGAGCCTTAATCCCCTAAGCAGTAGGGTAGCAGGCTGAATT
66 AGTAGGGGAGCAGATCGAAGACGACGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATT
* * *
40815142 TACAAGATCTTATCACCTTAAGCAGTAAGGGAACAGATCGAAAATG
131 TACAAGATCTTATCACCCTAAGCAGTAGGGGAACAGATCGAAGATG
* * *
40815188 ACGGGCCTTAACCCCATAAGCAGTAGAGTAACATGTTGGAAATTACAGATCTTATCTCCCTAAGC
1 ACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTGGAAATTACAGATCTTATCTCCCTAAGC
** * * * *
40815253 AGTATTGGAGCAGATTGAAGACGACGAGCCTTAACCCCCTAAGTAGTAGGGTAAAAGGCTAAATT
66 AGTAGGGGAGCAGATCGAAGACGACGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATT
*
40815318 TACAAGATCTTATCACCCTAAGCAGTGGGGGAACAGATCGAAGATG
131 TACAAGATCTTATCACCCTAAGCAGTAGGGGAACAGATCGAAGATG
* * * * *
40815364 ATGAGCCTTAACCCCCTAAGTAGTAGGGTAACAGATT--AAATTTACAAGATCTTATCACCCTAA
1 ACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTGGAAA-TTAC-AGATCTTATCTCCCTAA
* * * * * *
40815427 GCAGTAGGGGAACAGATAGAAGATGATGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCGGAA
64 GCAGTAGGGGAGCAGATCGAAGACGACGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAA
* * * * * * * *
40815492 GATTA-TAGATCTTGTCTCCCTAAGCAGTAGTGGAACAAACCGAAGACG
129 -TTTACAAGATCTTATCACCCTAAGCAGTAGGGGAACAGATCGAAGATG
* * ** * * *
40815540 ATGGGCCTTAACCCCTTAAGCAGTAGGGTAACAGACTGAAAATTATAGATCTTATCAT-CTTAAG
1 ACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTGGAAATTACAGATCTTATC-TCCCTAAG
* * * *
40815604 CAGGAGGGGAGCAGATCGAAGATGACGGGACC-TAACTCCCTAAGCAGTAGGGTAACAGGCTGGA
65 CAGTAGGGGAGCAGATCGAAGACGACGAG-CCTTAACCCCCTAAGCAGTAGGGTAACAGGCT-GA
*
40815668 AATTACAA-ATCT
128 ATTTACAAGATCT
40815680 CATCTCCTTG
Statistics
Matches: 584, Mismatches: 66, Indels: 27
0.86 0.10 0.04
Matches are distributed among these distances:
167 58 0.10
171 1 0.00
173 1 0.00
174 3 0.01
175 4 0.01
176 502 0.86
177 12 0.02
178 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (176 bp):
ACGGGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTGGAAATTACAGATCTTATCTCCCTAAGC
AGTAGGGGAGCAGATCGAAGACGACGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAATT
TACAAGATCTTATCACCCTAAGCAGTAGGGGAACAGATCGAAGATG
Found at i:40815924 original size:28 final size:28
Alignment explanation
Indices: 40815877--40815934 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
40815867 AGTTGCATGA
* *
40815877 AGTGGATCAAAGTAACAAGACGAAGTGG
1 AGTGGATCAAAGCAAAAAGACGAAGTGG
* *
40815905 AGTGGATCAAAGCAAAAAGATGCAGTGG
1 AGTGGATCAAAGCAAAAAGACGAAGTGG
40815933 AG
1 AG
40815935 CAGACTGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.10, G:0.33, T:0.14
Consensus pattern (28 bp):
AGTGGATCAAAGCAAAAAGACGAAGTGG
Found at i:40816062 original size:41 final size:44
Alignment explanation
Indices: 40816005--40816109 Score: 137
Period size: 41 Copynumber: 2.5 Consensus size: 44
40815995 AATCACAGAT
* *
40816005 CTTATCTCTCTGAAGTTGCAGTAGAGCA-GAT-CA-AAACAAAC
1 CTTATCTCTCTGAAGTTACAGTAGAGCAGGATGAAGAAACAAAC
* *
40816046 CTTATCTCTCTGAAGTTACAGTGGAGCAGGTTGAAGAAACAAAC
1 CTTATCTCTCTGAAGTTACAGTAGAGCAGGATGAAGAAACAAAC
40816090 CTTATCTC-CTTGAAGTTACA
1 CTTATCTCTC-TGAAGTTACA
40816110 ATGGAGTAGG
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
41 26 0.46
42 2 0.04
43 2 0.04
44 26 0.46
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (44 bp):
CTTATCTCTCTGAAGTTACAGTAGAGCAGGATGAAGAAACAAAC
Found at i:40816104 original size:44 final size:44
Alignment explanation
Indices: 40816005--40816214 Score: 173
Period size: 44 Copynumber: 4.8 Consensus size: 44
40815995 AATCACAGAT
* * *
40816005 CTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T-CA-AAACAAAC
1 CTTATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGAAACAAAC
*
40816046 CTTATCTCTCTGAAGTTACAGTGGAGCAGGTTGAAGAAACAAAC
1 CTTATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGAAACAAAC
* * * * *
40816090 CTTATCTC-CTTGAAGTTACAATGGAGTAGGTTG-A-AATCAGAAGT
1 CTTATCTCTC-TGAAGTTACAGTGGAGCAGATTGAAGAAACA-AA-C
* * * * ** *
40816134 CTTATC-CCCTTGAAGTTGCAGTGGGGCAGACTGAAGTTACGAAC
1 CTTATCTCTC-TGAAGTTACAGTGGAGCAGATTGAAGAAACAAAC
* *
40816178 CTTATCTCTCTGAAGTTGCAGTGGAGCACATTGAAGA
1 CTTATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGA
40816215 TACATGAAAG
Statistics
Matches: 135, Mismatches: 24, Indels: 17
0.77 0.14 0.10
Matches are distributed among these distances:
41 27 0.20
42 5 0.04
43 6 0.04
44 91 0.67
45 5 0.04
46 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (44 bp):
CTTATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGAAACAAAC
Found at i:40816212 original size:88 final size:86
Alignment explanation
Indices: 40816005--40816212 Score: 206
Period size: 88 Copynumber: 2.4 Consensus size: 86
40815995 AATCACAGAT
* * *
40816005 CTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCAAAACAAACCTTATCTCTCTGAAGTTACAGTG
1 CTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAAACAAACCTTATCCCTCTGAAGTTACAGTG
**
40816069 GAGCAGGTTGAAGAAACAAAC
66 GAGCAGACTGAAGAAACAAAC
* * * * * * *
40816090 CTTATCTC-CTTGAAGTTACAATGGAGTAGGTTGAAATCAGAAGTCTTATCCC-CTTGAAGTTGC
1 CTTATCTCTC-TGAAGTTGCAGTGGAGCAGATTGAAAACA-AA-CCTTATCCCTC-TGAAGTTAC
* ** *
40816153 AGTGGGGCAGACTGAAGTTACGAAC
62 AGTGGAGCAGACTGAAGAAACAAAC
*
40816178 CTTATCTCTCTGAAGTTGCAGTGGAGCACATTGAA
1 CTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAA
40816213 GATACATGAA
Statistics
Matches: 96, Mismatches: 21, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
84 1 0.01
85 23 0.24
86 6 0.06
87 3 0.03
88 62 0.65
89 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (86 bp):
CTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAAACAAACCTTATCCCTCTGAAGTTACAGTG
GAGCAGACTGAAGAAACAAAC
Found at i:40822318 original size:46 final size:46
Alignment explanation
Indices: 40822153--40822325 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
40822143 TGTAACCCGC
* * * * *
40822153 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* * * * *
40822199 CCATGAGTGAACTCGGACTCAACTCATCGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
*
40822249 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
*
40822292 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC
40822326 AGATGCTCAA
Statistics
Matches: 103, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 57 0.55
47 28 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:40822323 original size:93 final size:93
Alignment explanation
Indices: 40822160--40822331 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
40822150 CGCCCATAAG
* * *
40822160 CGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
* *
40822225 TCGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCAGATGCCTAGTTACATCTCA
* * *
40822253 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40822318 ACGAGTTCAGATGC
66 ACGAGTTCAGATGC
40822332 TCAACCATCC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCAGATGCCTAGTTACATCTCA
Found at i:40822347 original size:46 final size:45
Alignment explanation
Indices: 40822204--40822347 Score: 109
Period size: 46 Copynumber: 3.1 Consensus size: 45
40822194 CGCATCCATG
* *
40822204 AGTGAACTCGGACTCAACTCATCGAGTTCGGATGC-CTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCTC-A---ACCATCT
* * * * *
40822251 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTC--AGATGCT-CAACCATCT
40822297 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCAT-CT
40822343 AGTGA
1 AGTGA
40822348 CATGTCACTT
Statistics
Matches: 75, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
44 9 0.12
45 2 0.03
46 31 0.41
47 28 0.37
48 1 0.01
49 3 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCATCT
Found at i:40831356 original size:22 final size:24
Alignment explanation
Indices: 40831297--40831357 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 24
40831287 GTATGTACAC
40831297 CAAATAAT-AATAATATATAAGTGA
1 CAAA-AATGAATAATATATAAGTGA
*
40831321 CAATAATGAA-AATA-ATAAGT-A
1 CAAAAATGAATAATATATAAGTGA
*
40831342 TAAAAATGAATAATAT
1 CAAAAATGAATAATAT
40831358 GATATACGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 9 0.29
22 10 0.32
23 7 0.23
24 5 0.16
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (24 bp):
CAAAAATGAATAATATATAAGTGA
Found at i:40831743 original size:26 final size:25
Alignment explanation
Indices: 40831666--40831774 Score: 73
Period size: 26 Copynumber: 4.4 Consensus size: 25
40831656 GGGACAGTAT
**
40831666 AAAATATATACATGGAA-ATATATA
1 AAAATATATACATATAATATATATA
* * * *
40831690 AGTAATATATA-A-CTAGTA-ATATC
1 A-AAATATATACATATAATATATATA
40831713 AAAATATATACATGATAATATATATA
1 AAAATATATACAT-ATAATATATATA
** * *
40831739 AAAATATATGTATATAATGTAGTATG
1 AAAATATATACATATAATATA-TATA
40831765 AAAATATATA
1 AAAATATATA
40831775 TGTAGTATAA
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
22 8 0.12
23 7 0.11
24 3 0.05
25 19 0.30
26 27 0.42
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.34
Consensus pattern (25 bp):
AAAATATATACATATAATATATATA
Found at i:40831792 original size:24 final size:23
Alignment explanation
Indices: 40831706--40831829 Score: 69
Period size: 24 Copynumber: 5.1 Consensus size: 23
40831696 ATATAACTAG
*
40831706 TAATATCAAAATATATACATG-ATA
1 TAATATTAAAATATAT--ATGTATA
40831730 -ATATATATAAAA-ATATATGTATA
1 TA-ATAT-TAAAATATATATGTATA
40831753 TAATGTAGTATGAAAATATATATGTAGTA
1 TAA--TA-T-T-AAAATATATATGTA-TA
*
40831782 TAATATTAAAATATA-AT-AATA
1 TAATATTAAAATATATATGTATA
* * *
40831803 CAACATTAAAATATATGATATATA
1 TAATATTAAAATATAT-ATGTATA
40831827 TAA
1 TAA
40831830 AATACAATAT
Statistics
Matches: 81, Mismatches: 6, Indels: 26
0.72 0.05 0.23
Matches are distributed among these distances:
21 15 0.19
22 4 0.05
23 9 0.11
24 22 0.27
25 7 0.09
26 4 0.05
27 6 0.07
28 9 0.11
29 5 0.06
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.36
Consensus pattern (23 bp):
TAATATTAAAATATATATGTATA
Found at i:40831860 original size:32 final size:32
Alignment explanation
Indices: 40831778--40831863 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 32
40831768 ATATATATGT
40831778 AGTATAATATTAAAATATAATAATACAACATTAAA
1 AGTAT-ATA-TAAAATATAA-AATACAACATTAAA
* *
40831813 A-TATATGAT-ATATATAAAATACAATATTAAA
1 AGTATAT-ATAAAATATAAAATACAACATTAAA
*
40831844 AGTATATATAACATATAAAA
1 AGTATATATAAAATATAAAA
40831864 ATATATATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
31 16 0.36
32 21 0.47
33 3 0.07
34 4 0.09
35 1 0.02
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (32 bp):
AGTATATATAAAATATAAAATACAACATTAAA
Found at i:40834094 original size:12 final size:12
Alignment explanation
Indices: 40834078--40834123 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
40834068 TATTATTATC
40834078 ATATTATATTTA
1 ATATTATATTTA
* *
40834090 GTATTA-CTTTA
1 ATATTATATTTA
40834101 ATATTATA-TTA
1 ATATTATATTTA
40834112 ACTATTATATTT
1 A-TATTATATTT
40834124 TATTATTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
11 13 0.48
12 12 0.44
13 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (12 bp):
ATATTATATTTA
Done.