Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 143 of 335
Found at i:42133434 original size:31 final size:31
Alignment explanation
Indices: 42133396--42133490 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
42133386 CCTTTTCATA
*
42133396 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
42133427 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
42133458 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
42133489 TT
1 TT
42133491 ACTGTAAACG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATATTACTGGGCCGAAGCCT
Found at i:42133733 original size:24 final size:24
Alignment explanation
Indices: 42133682--42133824 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
42133672 GCTTTATCAT
*
42133682 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
42133707 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
42133731 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
42133754 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
42133778 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
42133802 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
42133825 TCACTTCCTC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 76 0.68
25 12 0.11
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:42133761 original size:47 final size:48
Alignment explanation
Indices: 42133682--42133823 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 48
42133672 GCTTTATCAT
* *
42133682 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTCA
**
42133731 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
*
42133778 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTT
42133824 TTCACTTCCT
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 44 0.51
48 31 0.36
49 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:42133782 original size:71 final size:72
Alignment explanation
Indices: 42133681--42133824 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
42133671 TGCTTTATCA
*
42133681 TATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
1 TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
42133746 GCCCTTT
66 GCCCTTT
* * **
42133753 TATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA
1 TATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
42133816 AGCCCTTT
65 AGCCCTTT
42133824 T
1 T
42133825 TCACTTCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 53 0.80
72 13 0.20
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (72 bp):
TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
GCCCTTT
Found at i:42133900 original size:20 final size:20
Alignment explanation
Indices: 42133875--42133934 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
42133865 TATGATTACC
42133875 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
* *
42133895 TCATGTGCATAGCATACATT
1 TCATGTGCATATCATACATA
42133915 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
42133935 CCATATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:42134009 original size:25 final size:25
Alignment explanation
Indices: 42133977--42134024 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42133967 ATACATAAAC
* * *
42133977 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
42134002 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
42134025 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:42135208 original size:26 final size:27
Alignment explanation
Indices: 42135179--42135242 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
42135169 GGGCATATTC
42135179 GTCATTTTACCATACAGGGG-TTTACG
1 GTCATTTTACCATACAGGGGCTTTACG
* * *
42135205 GTCACTTTACCCTATAGGGGCTTTACG
1 GTCATTTTACCATACAGGGGCTTTACG
*
42135232 GTCTTTTTACC
1 GTCATTTTACC
42135243 TTTTAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 17 0.53
27 15 0.47
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.38
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGCTTTACG
Found at i:42135240 original size:27 final size:26
Alignment explanation
Indices: 42135179--42135252 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 26
42135169 GGGCATATTC
*
42135179 GTCATTTTACCATACAGGGGTTTACG
1 GTCATTTTACCATATAGGGGTTTACG
* *
42135205 GTCACTTTACCCTATAGGGGCTTTACG
1 GTCATTTTACCATATAGGGG-TTTACG
* * *
42135232 GTCTTTTTACCTTTTAGGGGT
1 GTCATTTTACCATATAGGGGT
42135253 ATTTTAGTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 18 0.45
27 22 0.55
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (26 bp):
GTCATTTTACCATATAGGGGTTTACG
Found at i:42135326 original size:27 final size:26
Alignment explanation
Indices: 42135296--42135351 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
42135286 GTAAATCAAC
*
42135296 AAACCAAAGGTATTTC-AGTAATTTTGT
1 AAACCAAAGGTACTTCTA-TAATTTT-T
*
42135323 AAACCAATGGTACTTCTATAATTTTT
1 AAACCAAAGGTACTTCTATAATTTTT
42135349 AAA
1 AAA
42135352 AAGTCAAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 21 0.81
28 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (26 bp):
AAACCAAAGGTACTTCTATAATTTTT
Found at i:42135392 original size:27 final size:27
Alignment explanation
Indices: 42135304--42135442 Score: 95
Period size: 27 Copynumber: 5.0 Consensus size: 27
42135294 ACAAACCAAA
* * **
42135304 GGTATTTCAGTAATTTTGTAAACCAAT
1 GGTATTTCTGTAATTTTGTAAATCAGG
* * *
42135331 GGTACTTCTATAATTTT-TAAAAAGTCAAG
1 GGTATTTCTGTAATTTTGT--AAA-TCAGG
*
42135360 GGTATTTCTGTAACTTTGTAAATCAGG
1 GGTATTTCTGTAATTTTGTAAATCAGG
** *
42135387 GGTATTT-TGGTAATTTTACAAAT-TGAG
1 GGTATTTCT-GTAATTTTGTAAATCAG-G
*
42135414 GGTATTTCGGTAATTTTGTAAATCGAGG
1 GGTATTTCTGTAATTTTGTAAATC-AGG
42135442 G
1 G
42135443 TAAAACAGTA
Statistics
Matches: 86, Mismatches: 17, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
26 3 0.03
27 56 0.65
28 8 0.09
29 18 0.21
30 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
GGTATTTCTGTAATTTTGTAAATCAGG
Found at i:42135752 original size:27 final size:27
Alignment explanation
Indices: 42135421--42135741 Score: 414
Period size: 27 Copynumber: 11.9 Consensus size: 27
42135411 GAGGGTATTT
* *
42135421 CGGTAATTTTGTAAATCGAGGGTAAAA
1 CGGTAATTCTATAAATCGAGGGTAAAA
* * *
42135448 CAGTAATTCTGTAAATCAAGGGTAAAA
1 CGGTAATTCTATAAATCGAGGGTAAAA
*
42135475 CAGTAATTCTATAAATCGAGGGTAAAA
1 CGGTAATTCTATAAATCGAGGGTAAAA
*
42135502 CGGTAATTCTGTAAATCGAGGGTAAAA
1 CGGTAATTCTATAAATCGAGGGTAAAA
* *
42135529 CGGTAATTCTGTAAGTCGAGGGTAAAA
1 CGGTAATTCTATAAATCGAGGGTAAAA
* * *
42135556 CGATAATTATGTAAATC-AGGGGTAAAA
1 CGGTAATTCTATAAATCGA-GGGTAAAA
* * *
42135583 CGGTAATTATGTAAAT-TAGGGGTAAAA
1 CGGTAATTCTATAAATCGA-GGGTAAAA
42135610 CGGTAATTCTATAAATCGAGGGTAAAA
1 CGGTAATTCTATAAATCGAGGGTAAAA
** *
42135637 TAGTAATTCTGTAAA-CTGAGGGTAAAA
1 CGGTAATTCTATAAATC-GAGGGTAAAA
42135664 CGGTAATTCTATAAATCGAGGGTAAAA
1 CGGTAATTCTATAAATCGAGGGTAAAA
* *
42135691 CGGTAATTTTACAAATCGAGGGTAAAA
1 CGGTAATTCTATAAATCGAGGGTAAAA
42135718 CGGTAATTCTATAAATCGAGGGTA
1 CGGTAATTCTATAAATCGAGGGTA
42135742 CTTTGGTAAT
Statistics
Matches: 264, Mismatches: 25, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
26 2 0.01
27 260 0.98
28 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (27 bp):
CGGTAATTCTATAAATCGAGGGTAAAA
Found at i:42135763 original size:27 final size:26
Alignment explanation
Indices: 42135692--42135943 Score: 186
Period size: 27 Copynumber: 9.4 Consensus size: 26
42135682 AGGGTAAAAC
****
42135692 GGTAATTTTACAAATCGAGGGTAAAAC
1 GGTAATTTTAC-AATCGAGGGTATTTT
*
42135719 GGTAATTCTATA-AATCGAGGGTACTTT
1 GGTAATT-T-TACAATCGAGGGTATTTT
*
42135746 GGTAATTTTACAAGTCGAGGGTATTTC
1 GGTAATTTTACAA-TCGAGGGTATTTT
** * *
42135773 AATAATTTTACAGGTCGAGGGTATTTC
1 GGTAATTTTACA-ATCGAGGGTATTTT
* * *
42135800 AGTAATTTCACAAAT-TAGGGGTATTTT
1 GGTAATTTTAC-AATCGA-GGGTATTTT
* *
42135827 GGTAATTTTACAAACTAGGGGTATTTT
1 GGTAATTTTACAATCGA-GGGTATTTT
* * *
42135854 GATAATTTTACAAACTAGGGGTATTTT
1 GGTAATTTTACAATCGA-GGGTATTTT
* *
42135881 GGTAATTTTACAAACTAGGGGTATTTT
1 GGTAATTTTACAATCGA-GGGTATTTT
* *
42135908 AGTAATTTTACAA-AGCAGGGTATTTT
1 GGTAATTTTACAATCG-AGGGTATTTT
42135934 GGTAATTTTA
1 GGTAATTTTA
42135944 TAAACCAAAG
Statistics
Matches: 193, Mismatches: 23, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
25 2 0.01
26 24 0.12
27 163 0.84
28 2 0.01
29 2 0.01
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (26 bp):
GGTAATTTTACAATCGAGGGTATTTT
Found at i:42135876 original size:81 final size:82
Alignment explanation
Indices: 42135737--42135948 Score: 236
Period size: 81 Copynumber: 2.6 Consensus size: 82
42135727 TATAAATCGA
* * * ** ** *
42135737 GGGTACTTTGGTAATTTTAC-AAGTCGAGGGTATTTCAATAATTTTAC-AGGTCGAGGGTATTTC
1 GGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTTGATAATTTTACAAACTAGAGGGTATTTC
*
42135800 AGTAATTTCACAAATTAG
65 AGTAATTTCACAAACTAG
**
42135818 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGATAATTTTACAAACTAG-GGGTATTTTG
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGATAATTTTACAAACTAGAGGGTATTTCA
*
42135882 GTAATTTTACAAACTAG
66 GTAATTTCACAAACTAG
* * *
42135899 GGGTATTTTAGTAATTTTACAAAGC-A-GGGTATTTTGGTAATTTTATAAAC
1 GGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGATAATTTTACAAAC
42135949 CAAAGTATTT
Statistics
Matches: 113, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
80 22 0.19
81 83 0.73
82 8 0.07
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (82 bp):
GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGATAATTTTACAAACTAGAGGGTATTTCA
GTAATTTCACAAACTAG
Found at i:42135959 original size:26 final size:27
Alignment explanation
Indices: 42135791--42135948 Score: 230
Period size: 27 Copynumber: 5.9 Consensus size: 27
42135781 TACAGGTCGA
** * *
42135791 GGGTATTTCAGTAATTTCACAAATTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
42135818 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
*
42135845 GGGTATTTTGATAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
42135872 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
*
42135899 GGGTATTTTAGTAATTTTACAAAGC-A-
1 GGGTATTTTGGTAATTTTACAAA-CTAG
*
42135925 GGGTATTTTGGTAATTTTATAAAC
1 GGGTATTTTGGTAATTTTACAAAC
42135949 CAAAGTATTT
Statistics
Matches: 121, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
25 1 0.01
26 21 0.17
27 98 0.81
28 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTAG
Found at i:42139329 original size:35 final size:35
Alignment explanation
Indices: 42139283--42139352 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
42139273 TAAACTTGGG
42139283 GAAACAATCTAAAAATTTTTAATTTTCCAAAAATC
1 GAAACAATCTAAAAATTTTTAATTTTCCAAAAATC
*
42139318 GAAACAATCTAAAATTTTTTAATTTTCCAAAAATC
1 GAAACAATCTAAAAATTTTTAATTTTCCAAAAATC
42139353 AACTTATCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.36
Consensus pattern (35 bp):
GAAACAATCTAAAAATTTTTAATTTTCCAAAAATC
Found at i:42140253 original size:68 final size:68
Alignment explanation
Indices: 42140144--42140280 Score: 229
Period size: 68 Copynumber: 2.0 Consensus size: 68
42140134 TATTGGTGTA
* * ***
42140144 CACGGCCATGTTGCACGGCCGTGTCAATCTTCATTCACCTCTCCTGTGCCCGTGTATGTAGGCAC
1 CACGGCCATGTTGCACGACCATGTCAATCTTCATTCACCTCTCCCACGCCCGTGTATGTAGGCAC
42140209 ACG
66 ACG
42140212 CACGGCCATGTTGCACGACCATGTCAATCTTCATTCACCTCTCCCACGCCCGTGTATGTAGGCAC
1 CACGGCCATGTTGCACGACCATGTCAATCTTCATTCACCTCTCCCACGCCCGTGTATGTAGGCAC
42140277 ACG
66 ACG
42140280 C
1 C
42140281 CCGTGTTCTT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.18, C:0.36, G:0.21, T:0.25
Consensus pattern (68 bp):
CACGGCCATGTTGCACGACCATGTCAATCTTCATTCACCTCTCCCACGCCCGTGTATGTAGGCAC
ACG
Found at i:42145443 original size:29 final size:30
Alignment explanation
Indices: 42145399--42145463 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
42145389 CGAGGCTATC
*
42145399 CCTTTTCATAATTTGACGGTTGTCACCA-T
1 CCTTTTCATAATTTGACGGTCGTCACCATT
*
42145428 CCTTTTCTATAA-TTGATGGTCGTCACCATT
1 CCTTTTC-ATAATTTGACGGTCGTCACCATT
42145458 CCTTTT
1 CCTTTT
42145464 TGTAATCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 21 0.66
30 11 0.34
ACGTcount: A:0.18, C:0.25, G:0.12, T:0.45
Consensus pattern (30 bp):
CCTTTTCATAATTTGACGGTCGTCACCATT
Found at i:42150993 original size:17 final size:18
Alignment explanation
Indices: 42150961--42150994 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42150951 GAAATTTTAA
*
42150961 TTTAAAAACAATAAATAG
1 TTTAAAAACAACAAATAG
42150979 TTTAAAAA-AACAAATA
1 TTTAAAAACAACAAATA
42150995 AAAGTCCAAA
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:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
TTTAAAAACAACAAATAG
Found at i:42151005 original size:20 final size:20
Alignment explanation
Indices: 42150964--42151005 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
42150954 ATTTTAATTT
**
42150964 AAAAACAATAAATAGTTTAA
1 AAAAACAATAAATAGTCCAA
42150984 AAAAACAAATAAA-AGTCCAA
1 AAAAAC-AATAAATAGTCCAA
42151004 AA
1 AA
42151006 CAAAGCAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.69, C:0.10, G:0.05, T:0.17
Consensus pattern (20 bp):
AAAAACAATAAATAGTCCAA
Found at i:42155642 original size:21 final size:21
Alignment explanation
Indices: 42155585--42155648 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
42155575 ATGCTTTTTA
*
42155585 TAGCAAAT-ACAGACCATGCT
1 TAGCAAATAACAGATCATGCT
*
42155605 TAGCAAATAACATATCATGCT
1 TAGCAAATAACAGATCATGCT
** * *
42155626 TAGCTTATAATAGATCACGCT
1 TAGCAAATAACAGATCATGCT
42155647 TA
1 TA
42155649 ACATATGACA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 8 0.22
21 28 0.78
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.28
Consensus pattern (21 bp):
TAGCAAATAACAGATCATGCT
Found at i:42157538 original size:40 final size:40
Alignment explanation
Indices: 42157411--42157540 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
42157401 ATGCTGGAAA
* *
42157411 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
42157451 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
42157491 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
42157531 TTATATCCGG
1 TTATATCCGG
42157541 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:42165380 original size:40 final size:40
Alignment explanation
Indices: 42165253--42165382 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
42165243 ATGCTGGAAA
* *
42165253 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
42165293 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
42165333 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
42165373 TTATATCCGG
1 TTATATCCGG
42165383 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:42170655 original size:15 final size:15
Alignment explanation
Indices: 42170635--42170664 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42170625 ACTTAATTCC
*
42170635 ATTAGTTTTATTTAA
1 ATTAGTTATATTTAA
42170650 ATTAGTTATATTTAA
1 ATTAGTTATATTTAA
42170665 CTTCTATAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
ATTAGTTATATTTAA
Found at i:42175578 original size:18 final size:19
Alignment explanation
Indices: 42175555--42175594 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
42175545 TGTTTTAAAG
42175555 TTTATAG-T-TTAATTTTAT
1 TTTATAGTTATTAATTTT-T
42175573 TTTATAGTTATTAATTTTT
1 TTTATAGTTATTAATTTTT
42175592 TTT
1 TTT
42175595 TGTCTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 5 0.25
20 8 0.40
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTATAGTTATTAATTTTT
Found at i:42180585 original size:17 final size:17
Alignment explanation
Indices: 42180526--42180585 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
42180516 TAATAAATTT
42180526 AAAATATAATATATAATAA
1 AAAATATAAT-TAT-ATAA
42180545 AAAATAT-ATT-TAT-A
1 AAAATATAATTATATAA
*
42180559 AGAATAATAATTATATAA
1 AAAAT-ATAATTATATAA
42180577 AAAATATAA
1 AAAATATAA
42180586 AATATATTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 4 0.11
17 8 0.23
18 7 0.20
19 7 0.20
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATATAATTATATAA
Found at i:42184688 original size:35 final size:35
Alignment explanation
Indices: 42184630--42184817 Score: 295
Period size: 35 Copynumber: 5.3 Consensus size: 35
42184620 AATCATATCT
42184630 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
42184667 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
* *
42184702 TCTAAGATTGTATCATATCTAATATTGCAATGATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
42184737 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
* * * *
42184772 TCTAAGATTGTATTATATCTAGGATTGCATCTCACA
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCATA
42184808 TCTAAGATTG
1 TCTAAGATTG
42184818 CATATCATTA
Statistics
Matches: 142, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
35 118 0.83
36 14 0.10
37 10 0.07
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:42185530 original size:205 final size:205
Alignment explanation
Indices: 42185168--42185854 Score: 1104
Period size: 205 Copynumber: 3.4 Consensus size: 205
42185158 TTCATCGAAC
* * * * *
42185168 ACAGATATGCCAAATCATCTTAGATTTGCTTTAACGTAAGCACGTGAAAGCCAAATTAGCTATGT
1 ACAGAGATGACAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCTATGT
* * *
42185233 CTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCTGCTTCAACATAAACAT
66 CTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTTGGATCTGCTTCAGCATAAACAT
* * *
42185298 CTGAAGGTGAGATCTGCCATGTATCTGCTCTCCATTGAAGTGGAGATGCCAGACTTCGATTTGTT
131 CTGAAGGTGAGATCTGCTATGTATCTGCTCTCTATTGAAGTAGAGATGCCAGACTTCGATTTGTT
*
42185363 CTCTAACACT
196 CTCTGACACT
* *
42185373 ACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAATACGTGAAAGCCAAATCAGCTATGT
1 ACAGAGATGACAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCTATGT
42185438 CTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTTGGATCTGCTTCAGCATAAACAT
66 CTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTTGGATCTGCTTCAGCATAAACAT
* *
42185503 TTGAAGGTGAGATCTGCTATGTATCTGCTCTCTATTGAAGTAGAGATGCCAGACTTAGATTTGTT
131 CTGAAGGTGAGATCTGCTATGTATCTGCTCTCTATTGAAGTAGAGATGCCAGACTTCGATTTGTT
42185568 CTCTGACACT
196 CTCTGACACT
* * * * *
42185578 ACAGAGACGACAAATCATCTTATATTTGCTTTAACGTAAGCAGGTGAAAGCCAAATCAGCTATGT
1 ACAGAGATGACAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCTATGT
* * * *
42185643 CTTCGATTTGTTCATTGTAAGCACAATGATACCAAACCATCTTGGATCTGCTTTAGCATAAACGT
66 CTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTTGGATCTGCTTCAGCATAAACAT
*
42185708 CTGAAGGTGAGATCTCCTATGTATCTGCTCTCTATTGAAGTAGAGATGCCAGACTTCGATTTGTT
131 CTGAAGGTGAGATCTGCTATGTATCTGCTCTCTATTGAAGTAGAGATGCCAGACTTCGATTTGTT
*
42185773 CTCTGACAAT
196 CTCTGACACT
* * *
42185783 ACAGAGATGAAAAATCATCTTAGATTTGCTTCATCGTAAATACGTGAAAGCCAAATCAGCTATGT
1 ACAGAGATGACAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCTATGT
42185848 CTTCGAT
66 CTTCGAT
42185855 CTGCTCTCCG
Statistics
Matches: 443, Mismatches: 39, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
205 443 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (205 bp):
ACAGAGATGACAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCTATGT
CTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTTGGATCTGCTTCAGCATAAACAT
CTGAAGGTGAGATCTGCTATGTATCTGCTCTCTATTGAAGTAGAGATGCCAGACTTCGATTTGTT
CTCTGACACT
Found at i:42185903 original size:44 final size:44
Alignment explanation
Indices: 42185847--42185930 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
42185837 ATCAGCTATG
*
42185847 TCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGGTA
1 TCTTCGATCTGCTCTCCGACAATACAGAGATGCCAAATCTGGTA
* *
42185891 TCTTCGATCTGCTCTCTGACAATACAGAGATGCCGAATCT
1 TCTTCGATCTGCTCTCCGACAATACAGAGATGCCAAATCT
42185931 ACTGTCTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (44 bp):
TCTTCGATCTGCTCTCCGACAATACAGAGATGCCAAATCTGGTA
Found at i:42185939 original size:44 final size:44
Alignment explanation
Indices: 42185845--42185939 Score: 136
Period size: 44 Copynumber: 2.2 Consensus size: 44
42185835 AAATCAGCTA
* **
42185845 TGTCTTCGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGG
1 TGTCTTCGATCTGCTCTCCGACAATACAGAGATGCCAAATCTAC
* * *
42185889 TATCTTCGATCTGCTCTCTGACAATACAGAGATGCCGAATCTAC
1 TGTCTTCGATCTGCTCTCCGACAATACAGAGATGCCAAATCTAC
42185933 TGTCTTC
1 TGTCTTC
42185940 AATTTGTTCC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (44 bp):
TGTCTTCGATCTGCTCTCCGACAATACAGAGATGCCAAATCTAC
Found at i:42186070 original size:44 final size:44
Alignment explanation
Indices: 42185870--42186458 Score: 400
Period size: 44 Copynumber: 13.4 Consensus size: 44
42185860 CTCCGCCAAT
* * * * * *
42185870 ACAGAGATGCCAAATCTGGTATCTTCGATCTGCTCTCTGA-CAAT
1 ACAGGGATGCCAAATCTGCTATCTTCGATCTGTTCCCT-ATAAAC
* * * * * * *
42185914 ACAGAGATGCCGAATCTACTGTCTTCAATTTGTTCCCTATAAAA
1 ACAGGGATGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
* ** * * *
42185958 ACAGGGATACC--ATGCTGAAATCTTCGATCTGCTTCGCTGTAAGC
1 ACAGGGATGCCAAAT-CTGCTATCTTCGATCTG-TTCCCTATAAAC
* * ** *
42186002 ACA-GGAGTGTCAGATCTATTATCTTCGATCTGTTCCATATAAAC
1 ACAGGGA-TGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
* *
42186046 ACAGGGATGCCAAATCTGCTATCTTC-AACTTGTTCCCTACAAAC
1 ACAGGGATGCCAAATCTGCTATCTTCGATC-TGTTCCCTATAAAC
** * * * **
42186090 ACAGGGATGCC--ATGCTGAAATCCTCGATCTGTTTCGCTGTAATT
1 ACAGGGATGCCAAAT-CTGCTATCTTCGATCTG-TTCCCTATAAAC
* * *
42186134 ACA-GGAGTGTCAGATCTGTTATCTTCGATCTGTTCCCTATAAAC
1 ACAGGGA-TGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
* *
42186178 ACAGGGATGCCAAATCTGCTATCTT-TAACTTGTTCCCTATAAAC
1 ACAGGGATGCCAAATCTGCTATCTTCGATC-TGTTCCCTATAAAC
** * * *
42186222 ACAGGGATGCC--ATGCTGAAATCCTT-GATCTGCTTCGCTGTAAGC
1 ACAGGGATGCCAAAT-CTGCTAT-CTTCGATCTG-TTCCCTATAAAC
* * * *
42186266 ACA-GGAGTGTCAGATCTGTTATCTTCGATCTATTCCCTATAAAC
1 ACAGGGA-TGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
* *
42186310 ACAGGGATGCCAAATCCGCTATCTTC-AACTTGTTCCCTATAAAC
1 ACAGGGATGCCAAATCTGCTATCTTCGATC-TGTTCCCTATAAAC
** * * *
42186354 ACAGGGATGCC--ATGCTGAAATCTTCGATCTGCTTCACTGTAAGC
1 ACAGGGATGCCAAAT-CTGCTATCTTCGATCTG-TTCCCTATAAAC
* * * *
42186398 ACAGGAATGTCAGATCTTCTATCTTCGATCTGTTCCCTATAAAC
1 ACAGGGATGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
42186442 ACAGGGATGCCAAATCT
1 ACAGGGATGCCAAATCT
42186459 TGTTTCTTTG
Statistics
Matches: 417, Mismatches: 98, Indels: 60
0.73 0.17 0.10
Matches are distributed among these distances:
42 8 0.02
43 54 0.13
44 286 0.69
45 61 0.15
46 8 0.02
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (44 bp):
ACAGGGATGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
Found at i:42186126 original size:132 final size:132
Alignment explanation
Indices: 42185883--42186458 Score: 886
Period size: 132 Copynumber: 4.4 Consensus size: 132
42185873 GAGATGCCAA
* * * * * * * * * *
42185883 ATCTGGTATCTTCGATCTGCTCTCTGA-CAATACAGAGATGCCGAATCTACTGTCTTCAATTTGT
1 ATCTGTTATCTTCGATCTGTTCCCT-ATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGT
* * *
42185947 TCCCTATAAAAACAGGGATACCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACAGGAGTGT
65 TCCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAGGAGTGT
42186012 CAG
130 CAG
* *
42186015 ATCTATTATCTTCGATCTGTTCCATATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
1 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
* * **
42186080 CCCTACAAACACAGGGATGCCATGCTGAAATCCTCGATCTGTTTCGCTGTAATTACAGGAGTGTC
66 CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAGGAGTGTC
42186145 AG
131 AG
*
42186147 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTTAACTTGTT
1 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
*
42186212 CCCTATAAACACAGGGATGCCATGCTGAAATCCTTGATCTGCTTCGCTGTAAGCACAGGAGTGTC
66 CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAGGAGTGTC
42186277 AG
131 AG
* *
42186279 ATCTGTTATCTTCGATCTATTCCCTATAAACACAGGGATGCCAAATCCGCTATCTTCAACTTGTT
1 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
* * *
42186344 CCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTC
66 CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAGGAGTGTC
42186409 AG
131 AG
42186411 ATCT-TCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCT
1 ATCTGT-TATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCT
42186459 TGTTTCTTTG
Statistics
Matches: 406, Mismatches: 36, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
131 2 0.00
132 404 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.31
Consensus pattern (132 bp):
ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAGGAGTGTC
AG
Found at i:42187372 original size:21 final size:19
Alignment explanation
Indices: 42187348--42187418 Score: 74
Period size: 18 Copynumber: 3.7 Consensus size: 19
42187338 TTGGCCTCTC
42187348 TATTTTTCTTTTTTCTCTTTT
1 TATTTTTCTTTTTT-T-TTTT
42187369 TATTTTTCTTTTTATTTTTT
1 TATTTTTCTTTTT-TTTTTT
* *
42187389 TATTTAT-TTTTTTATTTT
1 TATTTTTCTTTTTTTTTTT
*
42187407 TCTTTTT-TTTTT
1 TATTTTTCTTTTT
42187419 GAAATAGAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
18 15 0.33
19 5 0.11
20 10 0.22
21 14 0.31
22 1 0.02
ACGTcount: A:0.08, C:0.07, G:0.00, T:0.85
Consensus pattern (19 bp):
TATTTTTCTTTTTTTTTTT
Found at i:42187380 original size:12 final size:12
Alignment explanation
Indices: 42187358--42187418 Score: 62
Period size: 12 Copynumber: 5.4 Consensus size: 12
42187348 TATTTTTCTT
42187358 TTTTCTCTTTTTA
1 TTTT-TCTTTTTA
42187371 TTTTTCTTTTTA
1 TTTTTCTTTTTA
42187383 ---TT-TTTTTA
1 TTTTTCTTTTTA
42187391 TTTATT-TTTTTA
1 TTT-TTCTTTTTA
42187403 TTTTTCTTTTT-
1 TTTTTCTTTTTA
42187414 TTTTT
1 TTTTT
42187419 GAAATAGAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
8 6 0.14
9 2 0.05
11 7 0.16
12 24 0.56
13 4 0.09
ACGTcount: A:0.08, C:0.07, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTCTTTTTA
Found at i:42187380 original size:20 final size:18
Alignment explanation
Indices: 42187351--42187418 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 18
42187341 GCCTCTCTAT
*
42187351 TTTTCTTTTTTCTCTTTTTA
1 TTTT-TTTTTT-TATTTTTA
*
42187371 TTTTTCTTTTTATTTTTTTA
1 TTTTT-TTTTT-TATTTTTA
* *
42187391 TTTATTTTTTTATTTTTC
1 TTTTTTTTTTTATTTTTA
42187409 TTTTTTTTTT
1 TTTTTTTTTT
42187419 GAAATAGAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.37
19 6 0.15
20 20 0.49
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTTTTTTTATTTTTA
Found at i:42189460 original size:28 final size:28
Alignment explanation
Indices: 42189412--42189494 Score: 139
Period size: 28 Copynumber: 2.9 Consensus size: 28
42189402 GTGACAGAGT
* *
42189412 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCAGGGC
42189441 CACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGGGC
42189469 CACCAGAACAGATAATTTGTGGCAGG
1 CACCAGAACAGATAATTTGTGGCAGG
42189495 ACGCTTCCTC
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
28 45 0.87
29 7 0.13
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGGGC
Found at i:42189642 original size:28 final size:28
Alignment explanation
Indices: 42189599--42189661 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
42189589 AAATTAACCC
*
42189599 TAGGGGTATAACGGTAATTTTGTATACA
1 TAGGGGTATAACGGTAATTTTGCATACA
*
42189627 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAACGGTAATTTTGCATACA
42189655 TAGGGGT
1 TAGGGGT
42189662 TTTCTAGTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.30, C:0.06, G:0.29, T:0.35
Consensus pattern (28 bp):
TAGGGGTATAACGGTAATTTTGCATACA
Found at i:42197344 original size:28 final size:28
Alignment explanation
Indices: 42197296--42197386 Score: 132
Period size: 28 Copynumber: 3.2 Consensus size: 28
42197286 GTGACAGAGT
*
42197296 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCAGTGC
42197325 CACCAGAACAGATAATTTGTGGCAAG-GC
1 CACCAGAACAGATAATTTGTGGC-AGTGC
42197353 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGATAATTTGTGGCAGT-GC
42197381 CACCAG
1 CACCAG
42197387 GACGCTTCCT
Statistics
Matches: 58, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
27 1 0.02
28 48 0.83
29 9 0.16
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGTGC
Found at i:42197534 original size:28 final size:28
Alignment explanation
Indices: 42197491--42197555 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
42197481 AAATTAACCC
42197491 TAGGGGTATAACGGTAATTTTGCATACA
1 TAGGGGTATAACGGTAATTTTGCATACA
*
42197519 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAACGGTAATTTTGCATACA
42197547 TAGGGGTAT
1 TAGGGGTAT
42197556 TCTAGTACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAACGGTAATTTTGCATACA
Found at i:42203939 original size:23 final size:22
Alignment explanation
Indices: 42203911--42203962 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
42203901 TTTGGGTATG
*
42203911 TGATGACGTTATCTT-ATAAATA
1 TGATGAAGTTATCTTGA-AAATA
*
42203933 TGCATGAATTTATCTTGAAAATA
1 TG-ATGAAGTTATCTTGAAAATA
42203956 TGATGAA
1 TGATGAA
42203963 TTGGTTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 7 0.27
23 18 0.69
24 1 0.04
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (22 bp):
TGATGAAGTTATCTTGAAAATA
Found at i:42203964 original size:22 final size:23
Alignment explanation
Indices: 42203919--42203964 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
42203909 TGTGATGACG
42203919 TTATCTTATAAATATGCATGAAT
1 TTATCTTATAAATATGCATGAAT
42203942 TTATCTTGA-AAATATG-ATGAAT
1 TTATCTT-ATAAATATGCATGAAT
42203964 T
1 T
42203965 GGTTTGGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.32
23 14 0.64
24 1 0.05
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (23 bp):
TTATCTTATAAATATGCATGAAT
Found at i:42209044 original size:21 final size:21
Alignment explanation
Indices: 42208979--42209044 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
42208969 TATAAGAGAT
* *
42208979 ACAGATCGTGCTTAGA-AAATA
1 ACAGATCATGCTTA-ACATATA
* * * * *
42209000 ACATATCATACTTAGCTTAAA
1 ACAGATCATGCTTAACATATA
42209021 ACAGATCATGCTTAACATATA
1 ACAGATCATGCTTAACATATA
42209042 ACA
1 ACA
42209045 TATTAACCAC
Statistics
Matches: 32, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (21 bp):
ACAGATCATGCTTAACATATA
Found at i:42209758 original size:14 final size:14
Alignment explanation
Indices: 42209739--42209765 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42209729 ATTTTTGGGG
42209739 AAAAAATAAAAATA
1 AAAAAATAAAAATA
42209753 AAAAAATAAAAAT
1 AAAAAATAAAAAT
42209766 CAGTATATAT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAAAATAAAAATA
Found at i:42213012 original size:48 final size:48
Alignment explanation
Indices: 42212952--42213083 Score: 167
Period size: 48 Copynumber: 2.8 Consensus size: 48
42212942 TCAATCAATA
* * * *
42212952 AGTAGCTATACCATCGCCTGAAGCCAAATCAAGGTAACTTATCCCCAG-
1 AGTACCTATACCATGGCCCGAAGCCAAATCAAGGTAACTCAT-CCCAGT
* * *
42213000 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCTGT
1 AGTACCTATACCATGGCCCGAAGCCAAATCAAGGTAACTCATCCCAGT
* *
42213048 AATACCTATACCATGGCCCGAAGCGAAATCAAGGTA
1 AGTACCTATACCATGGCCCGAAGCCAAATCAAGGTA
42213084 TAATTCGCAC
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
47 3 0.04
48 70 0.96
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.21
Consensus pattern (48 bp):
AGTACCTATACCATGGCCCGAAGCCAAATCAAGGTAACTCATCCCAGT
Found at i:42216043 original size:26 final size:26
Alignment explanation
Indices: 42216013--42216064 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
42216003 GCTAAGGGAA
42216013 AGAAAAAAAGTCGACTAAGTCTTCGG
1 AGAAAAAAAGTCGACTAAGTCTTCGG
42216039 AGAAAAAAAGTCGACTAAGTCTTCGG
1 AGAAAAAAAGTCGACTAAGTCTTCGG
42216065 TTCCACCTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (26 bp):
AGAAAAAAAGTCGACTAAGTCTTCGG
Found at i:42224282 original size:25 final size:25
Alignment explanation
Indices: 42224248--42224300 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
42224238 AAAAAAATCA
42224248 TGATTAAAGAAATAGTGAATTTACC
1 TGATTAAAGAAATAGTGAATTTACC
42224273 TGATTAAAGAAATAGTGAATTTACC
1 TGATTAAAGAAATAGTGAATTTACC
42224298 TGA
1 TGA
42224301 GAGATAGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (25 bp):
TGATTAAAGAAATAGTGAATTTACC
Found at i:42225217 original size:21 final size:21
Alignment explanation
Indices: 42225193--42225236 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
42225183 GTTCTGCTCT
42225193 GCCTCCCTCGCTGCTGCCTCC
1 GCCTCCCTCGCTGCTGCCTCC
* *
42225214 GCCTCCCTTGTTGCTGCCTCC
1 GCCTCCCTCGCTGCTGCCTCC
42225235 GC
1 GC
42225237 TCTAAGTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.52, G:0.20, T:0.27
Consensus pattern (21 bp):
GCCTCCCTCGCTGCTGCCTCC
Found at i:42229395 original size:53 final size:49
Alignment explanation
Indices: 42229320--42229425 Score: 131
Period size: 53 Copynumber: 2.1 Consensus size: 49
42229310 GTGAGTTATG
* ** *
42229320 TAATTTATTTAAGTAATGATCAATATTGATACTATTTTGATAAAAATTAGTTA
1 TAATATATTTAAAAAATGATCAATATTG-T--TATATTGAT-AAAATTAGTTA
*
42229373 TAATATATTTAAAAAATGATCAATATTGTTATATTGATAAAATTATTTA
1 TAATATATTTAAAAAATGATCAATATTGTTATATTGATAAAATTAGTTA
42229422 TAAT
1 TAAT
42229426 TGACCCTTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
49 14 0.29
50 8 0.17
52 1 0.02
53 25 0.52
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (49 bp):
TAATATATTTAAAAAATGATCAATATTGTTATATTGATAAAATTAGTTA
Found at i:42230024 original size:7 final size:7
Alignment explanation
Indices: 42230012--42230042 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
42230002 AGACATTTAA
42230012 AAATATT
1 AAATATT
42230019 AAATATT
1 AAATATT
42230026 AAATATT
1 AAATATT
42230033 AAATATT
1 AAATATT
42230040 AAA
1 AAA
42230043 ATCAAACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAATATT
Found at i:42231172 original size:7 final size:7
Alignment explanation
Indices: 42231160--42231197 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
42231150 AGACATTTAA
42231160 AAATATT
1 AAATATT
42231167 AAATATT
1 AAATATT
42231174 AAATATT
1 AAATATT
42231181 AAATATT
1 AAATATT
42231188 AAATATT
1 AAATATT
42231195 AAA
1 AAA
42231198 ATCAATTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAATATT
Found at i:42232088 original size:20 final size:20
Alignment explanation
Indices: 42232026--42232090 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
42232016 TGAAATAAGC
42232026 TTAAAAATTTAGGAATGTAA
1 TTAAAAATTTAGGAATGTAA
* **
42232046 TT-TAAATGTTAGGAA-AAACA
1 TTAAAAAT-TTAGGAATGTA-A
*
42232066 TTAAAAATTAAGGAATGTAA
1 TTAAAAATTTAGGAATGTAA
42232086 TTAAA
1 TTAAA
42232091 TGTTAATTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
19 5 0.15
20 24 0.71
21 5 0.15
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.32
Consensus pattern (20 bp):
TTAAAAATTTAGGAATGTAA
Found at i:42234902 original size:15 final size:15
Alignment explanation
Indices: 42234876--42234907 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42234866 AAATAATAAT
*
42234876 TTATATATATTTATC
1 TTATATACATTTATC
42234891 TTATATACATTTATC
1 TTATATACATTTATC
42234906 TT
1 TT
42234908 CTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATACATTTATC
Found at i:42235986 original size:41 final size:41
Alignment explanation
Indices: 42235929--42236106 Score: 286
Period size: 41 Copynumber: 4.4 Consensus size: 41
42235919 GTTATATGAC
*
42235929 TTTTAGCGGCGTTTTACCAAAAGCACCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* * *
42235970 TTTTAGCGGTGTTTTACCAAAAGTGCCGCTAATGCTCTAGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
42236011 TTTTAGCGGCGTTTTACCAAAAGCGTCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
42236052 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCT-TTGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
42236092 TTTTAGTGGCGTTTT
1 TTTTAGCGGCGTTTT
42236107 TTAAAACGCC
Statistics
Matches: 126, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 17 0.13
41 109 0.87
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.37
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
Found at i:42238846 original size:21 final size:21
Alignment explanation
Indices: 42238822--42238871 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
42238812 GCTCGCGAGC
42238822 TGCTCAAATCAAGTAATAAGG
1 TGCTCAAATCAAGTAATAAGG
42238843 TGCTCAAATCAAGTAATAAGG
1 TGCTCAAATCAAGTAATAAGG
*
42238864 TACTCAAA
1 TGCTCAAA
42238872 CATGGCTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (21 bp):
TGCTCAAATCAAGTAATAAGG
Found at i:42252051 original size:12 final size:12
Alignment explanation
Indices: 42252034--42252060 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
42252024 ATAAATGGAC
42252034 TTTATTTTTTTA
1 TTTATTTTTTTA
42252046 TTTATTTTTTTA
1 TTTATTTTTTTA
42252058 TTT
1 TTT
42252061 TAGTTTAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:42252315 original size:44 final size:44
Alignment explanation
Indices: 42252259--42252484 Score: 362
Period size: 44 Copynumber: 5.1 Consensus size: 44
42252249 ACAAAGATGA
* * *
42252259 CAAATCTACTATCTTTGATCTACTCTCTGACAATATAGGGACGC
1 CAAATCTACTATCTTTGATCTGCTCTCTGACAATACAGAGACGC
* *
42252303 CAAATCTACTATCTTTGATCTGCTCTCTGACAATATAGAGATGC
1 CAAATCTACTATCTTTGATCTGCTCTCTGACAATACAGAGACGC
*
42252347 CAAATCTGCTATCTTTGATCTGCTCTCTGACAATACAGAGACGC
1 CAAATCTACTATCTTTGATCTGCTCTCTGACAATACAGAGACGC
*
42252391 CAAATCTACTATCTTTGATCCGCTCTCTGACAATACAGAGACGC
1 CAAATCTACTATCTTTGATCTGCTCTCTGACAATACAGAGACGC
* * *
42252435 CAAATCTACTATCTTCGATCTTCTCTCTGACAATACAGAGATGC
1 CAAATCTACTATCTTTGATCTGCTCTCTGACAATACAGAGACGC
42252479 CAAATC
1 CAAATC
42252485 ATCTTGGATC
Statistics
Matches: 170, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 170 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.31
Consensus pattern (44 bp):
CAAATCTACTATCTTTGATCTGCTCTCTGACAATACAGAGACGC
Found at i:42252525 original size:54 final size:54
Alignment explanation
Indices: 42252438--42252552 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
42252428 GAGACGCCAA
* ** *
42252438 ATCTACTATCTTCGATCTTCTCTCTGACAATACAGAGATGCCAAATCATCTTGG
1 ATCTGCTATCTTCGATCTTCTCTCTGACAATACAGAGACACCAAATCATCTTAG
*
42252492 ATCTGCTATCTTTGATCTAT-TCTCTGACAATACAGAGACACCAAATCATCTTAG
1 ATCTGCTATCTTCGATCT-TCTCTCTGACAATACAGAGACACCAAATCATCTTAG
*
42252546 ATTTGCT
1 ATCTGCT
42252553 TTAACGTAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 53 0.98
55 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (54 bp):
ATCTGCTATCTTCGATCTTCTCTCTGACAATACAGAGACACCAAATCATCTTAG
Found at i:42252673 original size:44 final size:44
Alignment explanation
Indices: 42252572--42252714 Score: 187
Period size: 44 Copynumber: 3.2 Consensus size: 44
42252562 ACACGTGAAA
* * * *
42252572 GCCAAATCAGCTATGTCTTCGATCTGTTCCCTGTCGAATACAGAGAT
1 GCCAAATCTGCTA--TCTTCGATCTGTTCTCTGAC-AATACAGAGAC
* * *
42252619 GCCAAATCTGCTATCTTCGATCTATTCTCTGACAATATAGAGGC
1 GCCAAATCTGCTATCTTCGATCTGTTCTCTGACAATACAGAGAC
*
42252663 GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGAC
1 GCCAAATCTGCTATCTTCGATCTGTTCTCTGACAATACAGAGAC
42252707 GCCAAATC
1 GCCAAATC
42252715 ATCTTAGATT
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
44 56 0.66
45 17 0.20
47 12 0.14
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (44 bp):
GCCAAATCTGCTATCTTCGATCTGTTCTCTGACAATACAGAGAC
Found at i:42255647 original size:44 final size:44
Alignment explanation
Indices: 42255564--42256159 Score: 349
Period size: 44 Copynumber: 13.6 Consensus size: 44
42255554 GGGCTGTCAC
* * * *
42255564 ATGCCAAATCTG-TTTCTTTGATTTGTTCTCTGACAATACAGAG
1 ATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
**
42255607 ATGCCAAATCTGCTATCTTCGATCTGCTCTCTGATTATACAGAG
1 ATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
* * * * * *
42255651 ACGCCAAATC-G---TCTTAGATTTGGTTCAACTTA-AATACATGA-
1 ATGCCAAATCTGCTATCTTCGATCT-GCTC-TCTGACAATACA-GAG
* * * * **
42255692 AAGCCAAATCAGCTATGTCTTTGATCTGCTCCCTGTAGGATACAGAG
1 ATGCCAAATCTGCTA--TCTTCGATCTGCTCTCTG-ACAATACAGAG
* * * * *
42255739 ATGCCAAATCTG-TTTCTTCAATTTGTTCTCTGACAATATAGAG
1 ATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
*
42255782 ACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
1 ATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
* * * * * *
42255826 ACGCCAAA--T-C-ATCTTAGATTTGCT-TC-AACATAAACACGTG
1 ATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACA-ATACA-GAG
* * *
42255866 AAAGCCAAAT-TAGCTATGTCTTCGATCTGCTCCCTGTCGAATACAGAG
1 -ATGCCAAATCT-GCTA--TCTTCGATCTGCTCTCTGAC-AATACAGAG
* * * *
42255914 ATGCCAAATCTG-TTTCTTCGATTTGTTCTCTGACAATACTGAG
1 ATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
** * * *
42255957 ACACCAAATCTGCTATCTTCGATCTTCTCTCTGACAATATAGAT
1 ATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
* * * *
42256001 ATGCCAAA--T-C-ATCTTAGATTTGCT-TC-AACGTAA-ACACGTG
1 ATGCCAAATCTGCTATCTTCGATCTGCTCTCTGAC--AATACA-GAG
* * * *
42256041 AAAGCCAAATCAGCTATGTCTTCGATCTGCTCCCTGTCGAATACAGAG
1 -ATGCCAAATCTGCTA--TCTTCGATCTGCTCTCTGAC-AATACAGAG
* * * *
42256089 ATGCCAAATCTG-TTTCTTCGATTTGTTCTCTGAAAATACAGAG
1 ATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
*
42256132 ACGCCAAATCTGCTATCTTCGATCTGCT
1 ATGCCAAATCTGCTATCTTCGATCTGCT
42256160 TCAGTGTAAA
Statistics
Matches: 415, Mismatches: 96, Indels: 83
0.70 0.16 0.14
Matches are distributed among these distances:
38 5 0.01
39 10 0.02
40 36 0.09
41 33 0.08
42 9 0.02
43 70 0.17
44 156 0.38
45 4 0.01
46 9 0.02
47 64 0.15
48 9 0.02
49 9 0.02
50 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (44 bp):
ATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
Found at i:42255870 original size:175 final size:175
Alignment explanation
Indices: 42255564--42256159 Score: 985
Period size: 175 Copynumber: 3.4 Consensus size: 175
42255554 GGGCTGTCAC
* *
42255564 ATGCCAAATCTGTTTCTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGA
1 ATGCCAAATCTGTTTCTTCGATTTGTTCTCTGACAATACAGAGACGCCAAATCTGCTATCTTCGA
** * * * * *
42255629 TCTGCTCTCTGATTATACAGAGACGCCAAATCGTCTTAGATTTGGTTCAACTTAAATACATGAAA
66 TCTGCTCTCTGACAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACATAAACACGTGAAA
* * *
42255694 GCCAAATCAGCTATGTCTTTGATCTGCTCCCTGTAGGATACAGAG
131 GCCAAATCAGCTATGTCTTCGATCTGCTCCCTGTCGAATACAGAG
* *
42255739 ATGCCAAATCTGTTTCTTCAATTTGTTCTCTGACAATATAGAGACGCCAAATCTGCTATCTTCGA
1 ATGCCAAATCTGTTTCTTCGATTTGTTCTCTGACAATACAGAGACGCCAAATCTGCTATCTTCGA
42255804 TCTGCTCTCTGACAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACATAAACACGTGAAA
66 TCTGCTCTCTGACAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACATAAACACGTGAAA
*
42255869 GCCAAATTAGCTATGTCTTCGATCTGCTCCCTGTCGAATACAGAG
131 GCCAAATCAGCTATGTCTTCGATCTGCTCCCTGTCGAATACAGAG
* *
42255914 ATGCCAAATCTGTTTCTTCGATTTGTTCTCTGACAATACTGAGACACCAAATCTGCTATCTTCGA
1 ATGCCAAATCTGTTTCTTCGATTTGTTCTCTGACAATACAGAGACGCCAAATCTGCTATCTTCGA
* * * * *
42255979 TCTTCTCTCTGACAATATAGATATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAA
66 TCTGCTCTCTGACAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACATAAACACGTGAAA
42256044 GCCAAATCAGCTATGTCTTCGATCTGCTCCCTGTCGAATACAGAG
131 GCCAAATCAGCTATGTCTTCGATCTGCTCCCTGTCGAATACAGAG
*
42256089 ATGCCAAATCTGTTTCTTCGATTTGTTCTCTGAAAATACAGAGACGCCAAATCTGCTATCTTCGA
1 ATGCCAAATCTGTTTCTTCGATTTGTTCTCTGACAATACAGAGACGCCAAATCTGCTATCTTCGA
42256154 TCTGCT
66 TCTGCT
42256160 TCAGTGTAAA
Statistics
Matches: 392, Mismatches: 29, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
175 392 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (175 bp):
ATGCCAAATCTGTTTCTTCGATTTGTTCTCTGACAATACAGAGACGCCAAATCTGCTATCTTCGA
TCTGCTCTCTGACAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACATAAACACGTGAAA
GCCAAATCAGCTATGTCTTCGATCTGCTCCCTGTCGAATACAGAG
Found at i:42263659 original size:20 final size:20
Alignment explanation
Indices: 42263636--42263678 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
42263626 AGTTTGGGAC
42263636 CAAGCTTAGATCTTTGGCAT
1 CAAGCTTAGATCTTTGGCAT
42263656 CAAGCTTAGATCTTTGGCAT
1 CAAGCTTAGATCTTTGGCAT
42263676 CAA
1 CAA
42263679 CTCCATGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (20 bp):
CAAGCTTAGATCTTTGGCAT
Found at i:42266242 original size:46 final size:46
Alignment explanation
Indices: 42266175--42266303 Score: 231
Period size: 46 Copynumber: 2.8 Consensus size: 46
42266165 TGTAACCCGC
* * *
42266175 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
42266221 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
42266267 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
42266304 TGCCCAAATA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:42268725 original size:29 final size:29
Alignment explanation
Indices: 42268686--42268773 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
42268676 CAAAGATAAC
*
42268686 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
42268715 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
42268744 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
42268774 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:42268744 original size:15 final size:15
Alignment explanation
Indices: 42268686--42268764 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
42268676 CAAAGATAAC
*
42268686 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
42268700 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
42268715 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
42268729 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
42268744 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
42268759 AAGAAA
1 AAGAAA
42268765 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:42268773 original size:15 final size:15
Alignment explanation
Indices: 42268697--42268773 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
42268687 AGAAAACCGA
42268697 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
42268712 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
42268726 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
42268740 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
42268756 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
42268771 ATA
1 ATA
42268774 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:42271790 original size:93 final size:93
Alignment explanation
Indices: 42271678--42271849 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
42271668 GCCCATAAGT
* *
42271678 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42271743 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
42271771 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42271836 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
42271850 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:42271845 original size:46 final size:46
Alignment explanation
Indices: 42271670--42271845 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
42271660 TGTAACCCGC
* * *
42271670 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
42271716 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
42271766 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
42271809 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
42271846 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:42274681 original size:34 final size:34
Alignment explanation
Indices: 42274628--42274695 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
42274618 GCACAGTTAA
* *
42274628 ACAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGAGCCTAAGCCCATTTCAGTA-CAGTG
*
42274663 ACAGT-TTGAGCCTTAGCCCATTTCAGTACAGTG
1 ACAGTCTTGAGCCTAAGCCCATTTCAGTACAGTG
42274696 TCAAAAATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (34 bp):
ACAGTCTTGAGCCTAAGCCCATTTCAGTACAGTG
Found at i:42277795 original size:25 final size:25
Alignment explanation
Indices: 42277761--42277811 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
42277751 TACAGAAAAA
42277761 TGTTGAGTTTGTTTGGTCCAATAAG
1 TGTTGAGTTTGTTTGGTCCAATAAG
42277786 TGTTGAGTTTGTTTGGTCCAATAAG
1 TGTTGAGTTTGTTTGGTCCAATAAG
42277811 T
1 T
42277812 TCCAACAAAG
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:0.20, C:0.08, G:0.27, T:0.45
Consensus pattern (25 bp):
TGTTGAGTTTGTTTGGTCCAATAAG
Found at i:42281745 original size:30 final size:30
Alignment explanation
Indices: 42281690--42281820 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
42281680 ATAGTGAATC
*
42281690 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
42281719 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
42281749 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AACT
* * * *
42281777 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAACT
42281807 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42281821 CAATCTTGTC
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 19 0.21
30 48 0.52
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAACT
Found at i:42281800 original size:58 final size:58
Alignment explanation
Indices: 42281689--42281820 Score: 176
Period size: 58 Copynumber: 2.3 Consensus size: 58
42281679 TATAGTGAAT
* * * * *
42281689 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGC
1 CCGCACACTTAGTGCTATATA-TATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
* *
42281748 TCGCACACTTAGTGCTATATA-ATCAAACTCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATATATATC-AACTCGCACACTTAGTGCTATACAATTTTAAAC
42281806 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
42281821 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 2 0.03
58 42 0.66
59 20 0.31
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (58 bp):
CCGCACACTTAGTGCTATATATATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
Found at i:42284330 original size:21 final size:21
Alignment explanation
Indices: 42284306--42284521 Score: 177
Period size: 21 Copynumber: 10.4 Consensus size: 21
42284296 TTTTACTTTT
*
42284306 TGTTCAGCTCTTACGAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
42284327 TGTT---CTCTTATGAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
* * * *
42284345 TATTCAACTCTTTTGAGTTTC
1 TGTTCAGCTCTTATGAGCTTC
*
42284366 TGTTTAGCTCTTATGAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
* * *
42284387 TATTTAGCTCTTATGAGTTTC
1 TGTTCAGCTCTTATGAGCTTC
* * *
42284408 TGTTTAGCTCTTATGAGTTTT
1 TGTTCAGCTCTTATGAGCTTC
* * * *
42284429 TATTTAACTCTTATGAGTTTC
1 TGTTCAGCTCTTATGAGCTTC
* ** *
42284450 TGTTCAACTCTTACCAGCTGC
1 TGTTCAGCTCTTATGAGCTTC
* * *
42284471 TATTCAACTCTTATGAGTTTC
1 TGTTCAGCTCTTATGAGCTTC
**
42284492 TGTTCAGCTCTTACCAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
*
42284513 TATTCAGCT
1 TGTTCAGCT
42284522 TTGAAGCTTC
Statistics
Matches: 159, Mismatches: 33, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
18 16 0.10
21 143 0.90
ACGTcount: A:0.18, C:0.21, G:0.14, T:0.47
Consensus pattern (21 bp):
TGTTCAGCTCTTATGAGCTTC
Found at i:42284384 original size:42 final size:42
Alignment explanation
Indices: 42284331--42284518 Score: 250
Period size: 42 Copynumber: 4.5 Consensus size: 42
42284321 AGCTTCTGTT
* *
42284331 CTCTTATGAGCTTCTATTCAACTCTTTTGAGTTTCTGTTTAG
1 CTCTTATGAGCTTCTATTCAACTCTTATGAGTTTCTGTTCAG
* * *
42284373 CTCTTATGAGCTTCTATTTAGCTCTTATGAGTTTCTGTTTAG
1 CTCTTATGAGCTTCTATTCAACTCTTATGAGTTTCTGTTCAG
* * * *
42284415 CTCTTATGAGTTTTTATTTAACTCTTATGAGTTTCTGTTCAA
1 CTCTTATGAGCTTCTATTCAACTCTTATGAGTTTCTGTTCAG
** *
42284457 CTCTTACCAGCTGCTATTCAACTCTTATGAGTTTCTGTTCAG
1 CTCTTATGAGCTTCTATTCAACTCTTATGAGTTTCTGTTCAG
**
42284499 CTCTTACCAGCTTCTATTCA
1 CTCTTATGAGCTTCTATTCA
42284519 GCTTTGAAGC
Statistics
Matches: 130, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 130 1.00
ACGTcount: A:0.19, C:0.21, G:0.13, T:0.47
Consensus pattern (42 bp):
CTCTTATGAGCTTCTATTCAACTCTTATGAGTTTCTGTTCAG
Found at i:42284449 original size:84 final size:84
Alignment explanation
Indices: 42284308--42284518 Score: 257
Period size: 84 Copynumber: 2.5 Consensus size: 84
42284298 TTACTTTTTG
* * *
42284308 TTCAGCTCTTACGAGCTTCTG-TT--CTCTTATGAGCTTCTATTCAACTCTTTTGAGTTTCTGTT
1 TTCAGCTCTTATGAGTTTCTGTTTAGCTCTTATGAGCTTCTATTCAACTCTTATGAGTTTCTGTT
* * ** *
42284370 TAGCTCTTATGAGCTTCTA
66 CAACTCTTACCAGCTGCTA
* * * *
42284389 TTTAGCTCTTATGAGTTTCTGTTTAGCTCTTATGAGTTTTTATTTAACTCTTATGAGTTTCTGTT
1 TTCAGCTCTTATGAGTTTCTGTTTAGCTCTTATGAGCTTCTATTCAACTCTTATGAGTTTCTGTT
42284454 CAACTCTTACCAGCTGCTA
66 CAACTCTTACCAGCTGCTA
* * **
42284473 TTCAACTCTTATGAGTTTCTGTTCAGCTCTTACCAGCTTCTATTCA
1 TTCAGCTCTTATGAGTTTCTGTTTAGCTCTTATGAGCTTCTATTCA
42284519 GCTTTGAAGC
Statistics
Matches: 107, Mismatches: 20, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
81 18 0.17
82 2 0.02
84 87 0.81
ACGTcount: A:0.18, C:0.21, G:0.14, T:0.47
Consensus pattern (84 bp):
TTCAGCTCTTATGAGTTTCTGTTTAGCTCTTATGAGCTTCTATTCAACTCTTATGAGTTTCTGTT
CAACTCTTACCAGCTGCTA
Found at i:42290563 original size:9 final size:9
Alignment explanation
Indices: 42290549--42290578 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
42290539 TCATGTTTTA
42290549 TTTTTATTT
1 TTTTTATTT
42290558 TTTTTATTT
1 TTTTTATTT
42290567 TTTTTATCTT
1 TTTTTAT-TT
42290577 TT
1 TT
42290579 CTTCTCCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTATTT
Found at i:42293870 original size:47 final size:47
Alignment explanation
Indices: 42293812--42293929 Score: 148
Period size: 47 Copynumber: 2.5 Consensus size: 47
42293802 CTGAGTTGAT
* **
42293812 GAACAGTAAGCTCTATTGAGCTGAAATTGTAAGCTCTGACGAGCTGA
1 GAACAGTAAGCTCTATTGAGCTGAAACTGTAAGCTCCAACGAGCTGA
* * *
42293859 GAACAGTAAGCTCTAATGAGATAAAACTGTAAGCTCCAACGAGCTGA
1 GAACAGTAAGCTCTATTGAGCTGAAACTGTAAGCTCCAACGAGCTGA
* *
42293906 AAACAGTAAACTCT-TATGAGCTGA
1 GAACAGTAAGCTCTAT-TGAGCTGA
42293930 TATATCGGTA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (47 bp):
GAACAGTAAGCTCTATTGAGCTGAAACTGTAAGCTCCAACGAGCTGA
Found at i:42293871 original size:24 final size:24
Alignment explanation
Indices: 42293813--42293929 Score: 112
Period size: 24 Copynumber: 5.0 Consensus size: 24
42293803 TGAGTTGATG
*
42293813 AACAGTAAGCTCTATTGAGCTG-A
1 AACAGTAAGCTCTAATGAGCTGAA
** * * *
42293836 AATTGTAAGCTCTGACGAGCTGAG
1 AACAGTAAGCTCTAATGAGCTGAA
*
42293860 AACAGTAAGCTCTAATGAGAT-AA
1 AACAGTAAGCTCTAATGAGCTGAA
* * *
42293883 AACTGTAAGCTCCAACGAGCTGAA
1 AACAGTAAGCTCTAATGAGCTGAA
* *
42293907 AACAGTAAACTCTTATGAGCTGA
1 AACAGTAAGCTCTAATGAGCTGA
42293930 TATATCGGTA
Statistics
Matches: 71, Mismatches: 21, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
23 35 0.49
24 36 0.51
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (24 bp):
AACAGTAAGCTCTAATGAGCTGAA
Found at i:42293952 original size:50 final size:47
Alignment explanation
Indices: 42293813--42293953 Score: 115
Period size: 47 Copynumber: 2.9 Consensus size: 47
42293803 TGAGTTGATG
* * * * ** *
42293813 AACAGTAAGCTCTATTGAGCTGAAATTGTAAGCTC-TGACGAGCTGAG
1 AACAGTAAACTCTAATGAGATAAAACGGTAAGCTCAT-ACGAGCTGAA
* *
42293860 AACAGTAAGCTCTAATGAGATAAAACTGTAAGCTCCA-ACGAGCTGAA
1 AACAGTAAACTCTAATGAGATAAAACGGTAAGCT-CATACGAGCTGAA
* * *
42293907 AACAGTAAACTCTTATGAGCTGATATATCGGTAAGCTCATACGAGCT
1 AACAGTAAACTCTAATGA---GATAAAACGGTAAGCTCATACGAGCT
42293954 ACGGTGAGTC
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
47 55 0.71
48 1 0.01
49 2 0.03
50 20 0.26
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (47 bp):
AACAGTAAACTCTAATGAGATAAAACGGTAAGCTCATACGAGCTGAA
Found at i:42300475 original size:23 final size:23
Alignment explanation
Indices: 42300439--42300499 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
42300429 CTAGATATAT
*
42300439 TATATTTTATTATATAACAT-TTA
1 TATATATTA-TATATAACATGTTA
**
42300462 TATATATATATATATTTCATGTTA
1 TATATAT-TATATATAACATGTTA
*
42300486 TGTATATTATATAT
1 TATATATTATATAT
42300500 TATCTATCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 21 0.66
24 11 0.34
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (23 bp):
TATATATTATATATAACATGTTA
Found at i:42300502 original size:16 final size:16
Alignment explanation
Indices: 42300459--42300543 Score: 52
Period size: 16 Copynumber: 5.1 Consensus size: 16
42300449 TATATAACAT
42300459 TTATATATATATATATA
1 TTATATAT-TATATATA
* *
42300476 TT-TCATGTTATGTATA
1 TTAT-ATATTATATATA
42300492 TTATATATTATCTATCATA
1 TTATATATTA--TAT-ATA
*
42300511 TTATATATGT-TTTATA
1 TTATATAT-TATATATA
42300527 TTACT-TATTATAT-TA
1 TTA-TATATTATATATA
42300542 TT
1 TT
42300544 TAATTTTAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
15 5 0.09
16 26 0.48
17 9 0.17
18 2 0.04
19 11 0.20
20 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.58
Consensus pattern (16 bp):
TTATATATTATATATA
Found at i:42300509 original size:28 final size:26
Alignment explanation
Indices: 42300459--42300529 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 26
42300449 TATATAACAT
*
42300459 TTATATATA-TATATA-TATTTCATG
1 TTATATATATTATATATTATTTCATA
*
42300483 TTATGTATATTATATATTATCTATCATA
1 TTATATATATTATATATTAT-T-TCATA
* *
42300511 TTATATATGTTTTATATTA
1 TTATATATATTATATATTA
42300530 CTTATTATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
24 8 0.21
25 6 0.16
26 3 0.08
27 1 0.03
28 20 0.53
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.56
Consensus pattern (26 bp):
TTATATATATTATATATTATTTCATA
Found at i:42303906 original size:14 final size:16
Alignment explanation
Indices: 42303887--42303923 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
42303877 CGATATCCTT
42303887 TTTGCAT-TCAT-GCA
1 TTTGCATCTCATAGCA
42303901 TTTGCATCTCATAGCA
1 TTTGCATCTCATAGCA
42303917 TTT-CATC
1 TTTGCATC
42303924 ACATCGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (16 bp):
TTTGCATCTCATAGCA
Found at i:42303923 original size:15 final size:15
Alignment explanation
Indices: 42303887--42303936 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
42303877 CGATATCCTT
42303887 TTTGCAT-TCATGCA
1 TTTGCATCTCATGCA
42303901 TTTGCATCTCATAGCA
1 TTTGCATCTCAT-GCA
* *
42303917 TTT-CATCACAT-CG
1 TTTGCATCTCATGCA
42303930 TTTGCAT
1 TTTGCAT
42303937 TCAAGTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 4 0.13
14 10 0.32
15 11 0.35
16 6 0.19
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (15 bp):
TTTGCATCTCATGCA
Found at i:42312805 original size:12 final size:13
Alignment explanation
Indices: 42312783--42312812 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
42312773 CCTTGAAACC
42312783 AAATGAAATAAAT
1 AAATGAAATAAAT
42312796 AAAT-AAATAAAT
1 AAATGAAATAAAT
42312808 AAATG
1 AAATG
42312813 TTTATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (13 bp):
AAATGAAATAAAT
Found at i:42314260 original size:24 final size:23
Alignment explanation
Indices: 42314220--42314283 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
42314210 TTCCTAGATA
*
42314220 TATTATATTTTATTATATAACAT-T
1 TATTATATTATA-TATAT-ACATGT
*
42314244 TATTATATATATATATATTCATGT
1 TATTATAT-TATATATATACATGT
42314268 TATGTATATTATATAT
1 TAT-TATATTATATAT
42314284 TATCTATCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 3 0.09
24 24 0.69
25 8 0.23
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (23 bp):
TATTATATTATATATATACATGT
Found at i:42314293 original size:28 final size:29
Alignment explanation
Indices: 42314244--42314313 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
42314234 ATATAACATT
* *
42314244 TATTATATATATATATATTCATGTTATGTA
1 TATTATATAT-TATATATTCATATTATATA
*
42314274 TATTATATATTATCTA-TCATATTATATA
1 TATTATATATTATATATTCATATTATATA
* *
42314302 TGTTTTATATTA
1 TATTATATATTA
42314314 CTCATTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 20 0.57
29 5 0.14
30 10 0.29
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (29 bp):
TATTATATATTATATATTCATATTATATA
Found at i:42321974 original size:7 final size:6
Alignment explanation
Indices: 42321962--42322043 Score: 55
Period size: 6 Copynumber: 13.3 Consensus size: 6
42321952 ATAAATTTTA
*
42321962 TTATAT GTTATAT TTTTAT TATATAT ATTATAT TTATAT TT-TA- TTATAT
1 TTATAT -TTATAT TTATAT T-TATAT -TTATAT TTATAT TTATAT TTATAT
* *
42322011 GTTATAT ATT-T-T TTACTAT ATATAT ATATAT TT
1 -TTATAT -TTATAT TTA-TAT TTATAT TTATAT TT
42322044 TACTATATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
4 4 0.06
5 5 0.08
6 26 0.42
7 26 0.42
8 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.63
Consensus pattern (6 bp):
TTATAT
Found at i:42321979 original size:27 final size:26
Alignment explanation
Indices: 42321925--42322058 Score: 84
Period size: 27 Copynumber: 5.1 Consensus size: 26
42321915 TATATGAAAA
* * *
42321925 ATAATATATATTATTATATACATCTTT
1 ATAATATATATTA-TATTTATATTTTT
*
42321952 ATAA-ATTTTATTATATGTTATATTTTT
1 ATAATA-TATATTATAT-TTATATTTTT
*
42321979 ATTATATATATTATATTTATA-TTTT
1 ATAATATATATTATATTTATATTTTT
*
42322004 AT--TATATGTTATA--TAT-TTTTT
1 ATAATATATATTATATTTATATTTTT
*
42322025 ACTATATATATATATATTTTACTATATTTTT
1 A-TA-ATATATAT-TATATT--TATATTTTT
42322056 ATA
1 ATA
42322059 TGTAAAATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 25
0.71 0.08 0.21
Matches are distributed among these distances:
21 8 0.10
22 1 0.01
23 10 0.12
25 12 0.14
26 12 0.14
27 29 0.35
28 1 0.01
30 5 0.06
31 6 0.07
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (26 bp):
ATAATATATATTATATTTATATTTTT
Found at i:42321992 original size:20 final size:22
Alignment explanation
Indices: 42321963--42322045 Score: 75
Period size: 22 Copynumber: 3.8 Consensus size: 22
42321953 TAAATTTTAT
*
42321963 TATATGTTATAT-TTTTATTA-
1 TATATATTATATATTTTATTAC
* *
42321983 TATATATTATAT-TTATATTTTAT
1 TATATATTATATATT-T-TATTAC
*
42322006 TATATGTTATATATTTT-TTAC
1 TATATATTATATATTTTATTAC
42322027 TATATATATATATATTTTA
1 TATATAT-TATATATTTTA
42322046 CTATATTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
20 13 0.25
21 10 0.19
22 15 0.29
23 12 0.23
24 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (22 bp):
TATATATTATATATTTTATTAC
Found at i:42321997 original size:18 final size:17
Alignment explanation
Indices: 42321958--42322042 Score: 66
Period size: 18 Copynumber: 4.8 Consensus size: 17
42321948 CTTTATAAAT
*
42321958 TTTAT-TATATGTTATA
1 TTTATATATATATTATA
42321974 TTTTTATTATATATATTATA
1 --TTTA-TATATATATTATA
*
42321994 TTTATAT-TTTATTATA
1 TTTATATATATATTATA
* *
42322010 TGTTATATATTTTTTACTA
1 T-TTATATATATATTA-TA
*
42322029 TATATATATATATT
1 TTTATATATATATT
42322043 TTACTATATT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
16 9 0.16
17 9 0.16
18 24 0.43
19 4 0.07
20 10 0.18
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTATATATATATTATA
Found at i:42322010 original size:43 final size:41
Alignment explanation
Indices: 42321951--42322059 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 41
42321941 TATACATCTT
*
42321951 TATAAATTTTATTATATGTTATAT-TTTTATTA-TATATATTA
1 TATATATTTTATTATATGTTATATATTTT-TTACTATATA-TA
42321992 TATTTATATTTTATTATATGTTATATATTTTTTACTATATATA
1 TA--TATATTTTATTATATGTTATATATTTTTTACTATATATA
* *
42322035 TATATATTTTACTATAT-TTTTATAT
1 TATATATTTTATTATATGTTATATAT
42322060 GTAAAATTAC
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
40 7 0.11
41 16 0.26
43 28 0.46
44 10 0.16
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (41 bp):
TATATATTTTATTATATGTTATATATTTTTTACTATATATA
Found at i:42322058 original size:20 final size:20
Alignment explanation
Indices: 42321985--42322059 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
42321975 TTTTATTATA
* *
42321985 TATATTATATTTATATTTTAT
1 TATATT-TATATATATTTTAC
*
42322006 TATATGTTATATATTTTTTAC
1 TATAT-TTATATATATTTTAC
*
42322027 TATATATATATATATTTTAC
1 TATATTTATATATATTTTAC
*
42322047 TATATTTTTATAT
1 TATATTTATATAT
42322060 GTAAAATTAC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
20 24 0.52
21 21 0.46
22 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (20 bp):
TATATTTATATATATTTTAC
Found at i:42322425 original size:16 final size:16
Alignment explanation
Indices: 42322406--42322440 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
42322396 AAACATCTTT
*
42322406 ATTTTTATTTTATTTG
1 ATTTTTATTTTATATG
42322422 ATTTTTATTTTATATG
1 ATTTTTATTTTATATG
42322438 ATT
1 ATT
42322441 ATAATTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
ATTTTTATTTTATATG
Found at i:42324455 original size:31 final size:32
Alignment explanation
Indices: 42324396--42324464 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
42324386 CCAAAGGCCC
* * *
42324396 GCCCGAAAAATGGGAGGTTTGGGTAAAAATATAG
1 GCCCGAAAAAT-GGAGGCTTGGGCAAAAA-AAAG
42324430 GCCCGAAAAAT-G-GGCTTGGGCAAAAAAAAG
1 GCCCGAAAAATGGAGGCTTGGGCAAAAAAAAG
42324460 GCCCG
1 GCCCG
42324465 TTTAGAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 8 0.25
31 12 0.38
32 1 0.03
34 11 0.34
ACGTcount: A:0.38, C:0.16, G:0.32, T:0.14
Consensus pattern (32 bp):
GCCCGAAAAATGGAGGCTTGGGCAAAAAAAAG
Found at i:42324635 original size:35 final size:33
Alignment explanation
Indices: 42324587--42324651 Score: 78
Period size: 35 Copynumber: 1.9 Consensus size: 33
42324577 TAACCATTTT
*
42324587 TTATTATATTATCAATTTGTGTA-TTGTTTTAAGAA
1 TTATTATAGTATC-ATTT-T-TATTTGTTTTAAGAA
*
42324622 TTATTTTAGTATCATTTTTATTTGTTTTAA
1 TTATTATAGTATCATTTTTATTTGTTTTAA
42324652 TATTTGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 2 0.07
33 10 0.37
34 4 0.15
35 11 0.41
ACGTcount: A:0.28, C:0.03, G:0.09, T:0.60
Consensus pattern (33 bp):
TTATTATAGTATCATTTTTATTTGTTTTAAGAA
Found at i:42324706 original size:25 final size:26
Alignment explanation
Indices: 42324661--42324711 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
42324651 ATATTTGTTT
*
42324661 TTATGTTTTTAAATATATTTTATTTA
1 TTATATTTTTAAATATATTTTATTTA
*
42324687 TTATATTTTTAAA-ATTTTTTATTTA
1 TTATATTTTTAAATATATTTTATTTA
42324712 ATGAAATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (26 bp):
TTATATTTTTAAATATATTTTATTTA
Found at i:42325658 original size:26 final size:29
Alignment explanation
Indices: 42325603--42325656 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
42325593 GAGATGGGAG
42325603 AATATTGATTGAATTAGTAAAAAATAAAT
1 AATATTGATTGAATTAGTAAAAAATAAAT
* *
42325632 AATATTTATTTAA-TAG-AAAAAATAA
1 AATATTGATTGAATTAGTAAAAAATAA
42325657 TATTCTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
28 3 0.13
29 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (29 bp):
AATATTGATTGAATTAGTAAAAAATAAAT
Found at i:42326676 original size:2 final size:2
Alignment explanation
Indices: 42326669--42326698 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
42326659 ATGTAAAATT
42326669 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42326699 TTTGAGCCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:42336357 original size:2 final size:2
Alignment explanation
Indices: 42336350--42336382 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
42336340 ATGTAAAATT
42336350 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42336383 GTATTTTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42355109 original size:21 final size:21
Alignment explanation
Indices: 42355085--42355137 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
42355075 CCTAATATTG
42355085 AAATCCTAAATCCTAAACATA
1 AAATCCTAAATCCTAAACATA
* * *
42355106 AAATCCTAAACCCTAAACCTT
1 AAATCCTAAATCCTAAACATA
*
42355127 AAACCCTAAAT
1 AAATCCTAAAT
42355138 TAATTAGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATCCTAAATCCTAAACATA
Found at i:42358412 original size:33 final size:33
Alignment explanation
Indices: 42358375--42358441 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
42358365 CGTGTTTCGA
42358375 TAGAGCGCAAGAAACCATGGGTGTATGGACTCC
1 TAGAGCGCAAGAAACCATGGGTGTATGGACTCC
42358408 TAGAGCGCAAGAAACCATGGGTGTATGGACTCC
1 TAGAGCGCAAGAAACCATGGGTGTATGGACTCC
42358441 T
1 T
42358442 TTAGCCTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.19
Consensus pattern (33 bp):
TAGAGCGCAAGAAACCATGGGTGTATGGACTCC
Found at i:42373538 original size:25 final size:25
Alignment explanation
Indices: 42373500--42373547 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
42373490 TTGAGATTTG
42373500 TATATTTTAATTGAC-ATCTTTTGAC
1 TATATTTTAATTGACTAT-TTTTGAC
**
42373525 TATATTTTTTTTGACTATTTTTG
1 TATATTTTAATTGACTATTTTTG
42373548 TCCAACTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.60
Consensus pattern (25 bp):
TATATTTTAATTGACTATTTTTGAC
Found at i:42380889 original size:24 final size:24
Alignment explanation
Indices: 42380861--42380915 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 24
42380851 TATGTTTTTT
*
42380861 TTGCTAAATTCTTTATGTGACCGA
1 TTGCTAAATTCTTTATGTGACCAA
42380885 TTGCTAAATTCTTTATGTGACCAA
1 TTGCTAAATTCTTTATGTGACCAA
42380909 TTAGCTA
1 TT-GCTA
42380916 GTAGTAGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (24 bp):
TTGCTAAATTCTTTATGTGACCAA
Found at i:42383522 original size:126 final size:126
Alignment explanation
Indices: 42383321--42383828 Score: 768
Period size: 126 Copynumber: 4.0 Consensus size: 126
42383311 TTTCTGCAAG
* * * *
42383321 AATAATTCTAAGCAGACGTTTCTGGAA-AAATAGTGTCGGAAAATGTTTCAAGCAGGATGCACTG
1 AATAATTCTAAGTAGACGTTTCT-GAACAAATAGTG-CCGAAAACGCTTCAAGCAGGATGCACTG
* * *
42383385 TCAGCAAAATTTCTGGAATAAA-CTCCCACGTGGACGCTCTTTCGCTACAGTAGTTTGTGGAAA
64 TCAGCAAAATTTATGGAA-AAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
* * *
42383448 AATAATTCTAAGTAGACGTTTCTGAACAAATAGTGCCTAAAACACTTCAAGCAGGATGCACTGTT
1 AATAATTCTAAGTAGACGTTTCTGAACAAATAGTGCCGAAAACGCTTCAAGCAGGATGCACTGTC
* *
42383513 TGAAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
66 AGCAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
* * * *
42383574 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAATGCTTCAAGCAGGATACACTGTC
1 AATAATTCTAAGTAGACGTTTCTGAACAAATAGTGCCGAAAACGCTTCAAGCAGGATGCACTGTC
* *
42383639 AGCAAAATTTCTGGAAAAAGCTCCTACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
66 AGCAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
* * *
42383700 AATAATTCTGAGTAGACGTTTTTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTC
1 AATAATTCTAAGTAGACGTTTCTGAACAAATAGTGCCGAAAACGCTTCAAGCAGGATGCACTGTC
* *
42383765 AGCAAAATTTATGGAAAAAGCTCCCACGTAGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
66 AGCAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
42383826 AAT
1 AAT
42383829 GAGGCTATAA
Statistics
Matches: 349, Mismatches: 30, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
125 3 0.01
126 316 0.91
127 30 0.09
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (126 bp):
AATAATTCTAAGTAGACGTTTCTGAACAAATAGTGCCGAAAACGCTTCAAGCAGGATGCACTGTC
AGCAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
Found at i:42387338 original size:18 final size:18
Alignment explanation
Indices: 42387312--42387354 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
42387302 GACTAGGAAA
*
42387312 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGTT
42387330 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGTT
42387348 AGGATAC
1 AGGATAC
42387355 TCACCTGGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.42, C:0.07, G:0.28, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGTT
Found at i:42389164 original size:15 final size:14
Alignment explanation
Indices: 42389139--42389171 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
42389129 ATCGGATTTT
*
42389139 TTAATTTAAAAAAA
1 TTAAATTAAAAAAA
42389153 TTAAATTAAAAAAA
1 TTAAATTAAAAAAA
42389167 TTAAA
1 TTAAA
42389172 CAAAGAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TTAAATTAAAAAAA
Found at i:42391638 original size:28 final size:29
Alignment explanation
Indices: 42391586--42391649 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
42391576 TGACATTCAC
* * * *
42391586 TCTCCCAAATATTTCACATACAAAAA-AA
1 TCTCTCAAATATTTCAAAAAAAAAAATAA
42391614 TCTCTCAAATATTTCAAAAAAAAAAATTAA
1 TCTCTCAAATATTTCAAAAAAAAAAA-TAA
42391644 TCTCTC
1 TCTCTC
42391650 CAAAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 22 0.73
30 8 0.27
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (29 bp):
TCTCTCAAATATTTCAAAAAAAAAAATAA
Found at i:42392532 original size:19 final size:20
Alignment explanation
Indices: 42392495--42392532 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
42392485 CCTTTAAAAT
42392495 AATAAGATTATTAACAATAA
1 AATAAGATTATTAACAATAA
42392515 AATAAG-TT-TTATACAATA
1 AATAAGATTATTA-ACAATA
42392533 TCCAAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 8 0.47
20 6 0.35
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (20 bp):
AATAAGATTATTAACAATAA
Found at i:42392565 original size:14 final size:13
Alignment explanation
Indices: 42392546--42392575 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
42392536 AAACAATAAC
42392546 AATAAAATAGTAGA
1 AATAAAATAGTA-A
42392560 AATAAAATAGTAA
1 AATAAAATAGTAA
42392573 AAT
1 AAT
42392576 GGTAGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (13 bp):
AATAAAATAGTAA
Found at i:42405379 original size:21 final size:21
Alignment explanation
Indices: 42405355--42405409 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
42405345 CTTACAAATT
42405355 TTTATTATATATACATTTTAC
1 TTTATTATATATACATTTTAC
**
42405376 TTTA-TATATTATTTATTTTAC
1 TTTATTATA-TATACATTTTAC
*
42405397 TATATTTATATAT
1 TTTA-TTATATAT
42405410 GTAAATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 4 0.14
21 17 0.61
22 3 0.11
23 4 0.14
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATTATATATACATTTTAC
Found at i:42405468 original size:24 final size:26
Alignment explanation
Indices: 42405388--42405468 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 26
42405378 TATATATTAT
*
42405388 TTATTTTACTATATTTATATATGTA-AA
1 TTATTATAC-ATATTTAT-TATGTATAA
* *
42405415 TTATTATACATTATTATATTAT-TTTTA
1 TTATTATACA-TATT-TATTATGTATAA
42405442 TTATTA-AC-TATTTATTATGTATAA
1 TTATTATACATATTTATTATGTATAA
42405466 TTA
1 TTA
42405469 ACATTTTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
23 6 0.13
24 10 0.22
26 4 0.09
27 22 0.49
28 3 0.07
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (26 bp):
TTATTATACATATTTATTATGTATAA
Found at i:42409703 original size:40 final size:39
Alignment explanation
Indices: 42409658--42409787 Score: 152
Period size: 40 Copynumber: 3.3 Consensus size: 39
42409648 CGGAATATAA
42409658 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** *
42409698 CCGGATAGAATGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * * * *
42409738 CCGGATGTAGCTACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
42409778 CCGGATATAA
1 CCGGATATAA
42409788 TTTCCAGCAT
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 73 0.99
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:42415828 original size:40 final size:39
Alignment explanation
Indices: 42415762--42415926 Score: 147
Period size: 40 Copynumber: 4.2 Consensus size: 39
42415752 AAATTGAATG
* *
42415762 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-TGCTGGAGATT
* * * **
42415801 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-TGCTGGAGATT
* *
42415841 ACATCCGGGCTAAGACCCGAAGGC-ATTCG-TGCGAGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTTGCTG-GAGATT
* * ** *
42415879 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-TGCTGGAGATT
42415919 ATATCCGG
1 ATATCCGG
42415927 TTATATTCCG
Statistics
Matches: 98, Mismatches: 23, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
37 1 0.01
38 26 0.27
39 18 0.18
40 53 0.54
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTTGCTGGAGATT
Found at i:42415894 original size:38 final size:38
Alignment explanation
Indices: 42415763--42415910 Score: 149
Period size: 40 Copynumber: 3.8 Consensus size: 38
42415753 AATTGAATGA
* * * *
42415763 TATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATTA
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGATTC
* * *
42415802 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGAT-TC
42415840 TACATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGATTC
1 T--ATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGATTC
*
42415880 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
42415911 ACGTGATTAT
Statistics
Matches: 91, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
37 1 0.01
38 28 0.31
39 17 0.19
40 44 0.48
41 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (38 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGATTC
Found at i:42415925 original size:78 final size:78
Alignment explanation
Indices: 42415762--42415926 Score: 192
Period size: 78 Copynumber: 2.1 Consensus size: 78
42415752 AAATTGAATG
*
42415762 ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCAA
1 ATATCCGGGCTAAGCCCGAAGACAATTATGC-GGAAATTATATCCGGGCTAAGACCCGAAGGCAA
*
42415827 TTGTGCTAGTGGCT
65 TTGTGCTAGTGACT
* * * * *
42415841 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGATTCTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAG-CCCGAAGACAATT-ATGCGGAAATTATATCCGGGCTAAGACCCGAAGGCA
* *
42415904 TTTGTGC-ACGTGATT
64 ATTGTGCTA-GTGACT
42415919 ATATCCGG
1 ATATCCGG
42415927 TTATATTCCG
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
77 1 0.01
78 45 0.62
79 16 0.22
80 11 0.15
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (78 bp):
ATATCCGGGCTAAGCCCGAAGACAATTATGCGGAAATTATATCCGGGCTAAGACCCGAAGGCAAT
TGTGCTAGTGACT
Found at i:42423790 original size:40 final size:40
Alignment explanation
Indices: 42423724--42423874 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
42423714 AAATTGAATG
* *
42423724 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
* * ****
42423763 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
* *
42423803 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GAAATT
* *
42423843 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
42423875 ACATGGTTAT
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
39 16 0.18
40 72 0.80
41 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
Found at i:42423858 original size:80 final size:79
Alignment explanation
Indices: 42423726--42423874 Score: 203
Period size: 80 Copynumber: 1.9 Consensus size: 79
42423716 ATTGAATGAT
*
42423726 ATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCAATT
1 ATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAATT
42423791 GTGCTAGTGGCTAC
66 GTGCTAGTGGCTAC
* * * *
42423805 ATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATTCTATCCGGGCTAAGACCCGAAGGCA
1 ATCCGGGCTAAG-CCCGAAGACAATT-ATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGGCA
*
42423868 TTTGTGC
63 ATTGTGC
42423875 ACATGGTTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
79 16 0.26
80 45 0.74
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (79 bp):
ATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAATT
GTGCTAGTGGCTAC
Found at i:42423889 original size:80 final size:79
Alignment explanation
Indices: 42423724--42423890 Score: 196
Period size: 80 Copynumber: 2.1 Consensus size: 79
42423714 AAATTGAATG
*
42423724 ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCAA
1 ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAA
*
42423789 TTGTGCTAGTGGCT
66 TTGTGCTAATGGCT
* * * * *
42423803 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATTCTATCCGGGCTAAGACCCGAAGG
1 ATATCCGGGCTAAG-CCCGAAGACAATT-ATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGG
* *
42423866 CATTTGTGC-ACATGGTT
63 CAATTGTGCTA-ATGGCT
42423883 ATATCCGG
1 ATATCCGG
42423891 TTATATTCCG
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
79 18 0.24
80 56 0.76
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (79 bp):
ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCTAATGGCT
Found at i:42426496 original size:48 final size:48
Alignment explanation
Indices: 42426422--42426597 Score: 334
Period size: 48 Copynumber: 3.7 Consensus size: 48
42426412 AGATAAATAT
* *
42426422 ATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGGAATATGTATGAG
42426470 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGGAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGGAATATGTATGAG
42426518 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGGAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGGAATATGTATGAG
42426566 ATATGTATATGTGGTAAAGCCGAATGGCTAAT
1 ATATGTATATGTGGTAAAGCCGAATGGCTAAT
42426598 ATGTATATGT
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 126 1.00
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGGAATATGTATGAG
Found at i:42426602 original size:30 final size:30
Alignment explanation
Indices: 42426566--42426627 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
42426556 TATGTATGAG
*
42426566 ATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATATGTATATGTGGTAAAGCCGAATGGATA
42426596 ATATGTATATGTGGTAAAGCCGAATGGATA
1 ATATGTATATGTGGTAAAGCCGAATGGATA
42426626 AT
1 AT
42426628 GTGAAATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.31
Consensus pattern (30 bp):
ATATGTATATGTGGTAAAGCCGAATGGATA
Found at i:42426611 original size:78 final size:78
Alignment explanation
Indices: 42426518--42426675 Score: 298
Period size: 78 Copynumber: 2.0 Consensus size: 78
42426508 TATGTATGAG
* *
42426518 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGGAATATGTATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATATGTATGAGATATGTATATGTGGTAA
42426583 AGCCGAATGGCTA
66 AGCCGAATGGCTA
42426596 ATATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATATGTATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATATGTATGAGATATGTATATGTGGTAA
42426661 AGCCGAATGGCTA
66 AGCCGAATGGCTA
42426674 AT
1 AT
42426676 GTGAAATATA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (78 bp):
ATATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATATGTATGAGATATGTATATGTGGTAA
AGCCGAATGGCTA
Done.