Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 82 of 103
Found at i:30506949 original size:8 final size:8
Alignment explanation
Indices: 30506933--30506962 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
30506923 GAGTTACATT
*
30506933 TTATATAA
1 TTATTTAA
30506941 TTATTTAA
1 TTATTTAA
30506949 TTATTTAA
1 TTATTTAA
30506957 TTATTT
1 TTATTT
30506963 TTAATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTATTTAA
Found at i:30506967 original size:18 final size:20
Alignment explanation
Indices: 30506944--30506989 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
30506934 TATATAATTA
30506944 TTTAATTATT-TAA-TTATT
1 TTTAATTATTATAATTTATT
30506962 TTTAATTTATTATAATTTTATT
1 TTTAA-TTATTATAA-TTTATT
30506984 TTTAAT
1 TTTAAT
30506990 CATCTACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.21
19 5 0.21
20 3 0.12
21 1 0.04
22 10 0.42
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTAATTATTATAATTTATT
Found at i:30527682 original size:14 final size:14
Alignment explanation
Indices: 30527663--30527708 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
30527653 AGGTGTGGTA
30527663 TTATATCTTAAAAT
1 TTATATCTTAAAAT
*
30527677 TTATATTTTATAAAT
1 TTATATCTTA-AAAT
*
30527692 GTATTATCTTAAAAT
1 TTA-TATCTTAAAAT
30527707 TT
1 TT
30527709 GATAAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 9 0.35
15 11 0.42
16 6 0.23
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.54
Consensus pattern (14 bp):
TTATATCTTAAAAT
Found at i:30531187 original size:54 final size:54
Alignment explanation
Indices: 30531105--30531212 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
30531095 TGCAACATCC
*
30531105 TAGAATACACGGCAAAGAGAAATGTTTGATACACGCCTTTTCTTTCTTTTTGCT
1 TAGAATACACGGCAAAGAGAAATGTTTGATACACACCTTTTCTTTCTTTTTGCT
30531159 TAGAATACACGGCAAAGAGAAATGTTTGATACACACCTTTTCTTTCTTTTTGCT
1 TAGAATACACGGCAAAGAGAAATGTTTGATACACACCTTTTCTTTCTTTTTGCT
30531213 GCAGTCTATA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (54 bp):
TAGAATACACGGCAAAGAGAAATGTTTGATACACACCTTTTCTTTCTTTTTGCT
Found at i:30537687 original size:2 final size:2
Alignment explanation
Indices: 30537680--30537740 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
30537670 ACTAAGTTTC
**
30537680 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT AN CT -T CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
30537721 CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
30537741 TCAATTCTCT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:30542932 original size:14 final size:13
Alignment explanation
Indices: 30542904--30542942 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
30542894 TTTGTAGATA
*
30542904 TAAAATTTTTAAT
1 TAAATTTTTTAAT
30542917 TAAATTTTTATAAT
1 TAAATTTTT-TAAT
*
30542931 TAAGTTTTTTAA
1 TAAATTTTTTAA
30542943 ATATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (13 bp):
TAAATTTTTTAAT
Found at i:30543626 original size:24 final size:21
Alignment explanation
Indices: 30543586--30543634 Score: 53
Period size: 24 Copynumber: 2.2 Consensus size: 21
30543576 TTTTTATTTA
*
30543586 TATATATATTTAATATAATTAAT
1 TATATATAATTAATATAA--AAT
*
30543609 TATACTATAATTATTATAAAAT
1 TATA-TATAATTAATATAAAAT
30543631 TATA
1 TATA
30543635 AATCTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 4 0.17
24 12 0.52
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TATATATAATTAATATAAAAT
Found at i:30547268 original size:15 final size:16
Alignment explanation
Indices: 30547238--30547272 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
30547228 ATAAAATATT
30547238 ATGTTTTTCAATTAAA
1 ATGTTTTTCAATTAAA
* *
30547254 ATGTTTTTTAATAAAA
1 ATGTTTTTCAATTAAA
30547270 ATG
1 ATG
30547273 AGATTTATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.49
Consensus pattern (16 bp):
ATGTTTTTCAATTAAA
Found at i:30547757 original size:129 final size:129
Alignment explanation
Indices: 30547523--30547779 Score: 435
Period size: 129 Copynumber: 2.0 Consensus size: 129
30547513 TATTAAACGG
* *
30547523 TCACTTCAGTGGTGGGGGTTTCCGTGGACTGCCTATGAGAGGGGCACGGTAACCTAATTATATAT
1 TCACTGCAGTGGTGGGGGTTTCCGTGGACTGCCTATGAGAGGAGCACGGTAACCTAATTATATAT
* *
30547588 TTACCTCCGGGGGGAGATGTTGGATGAAGTATCTCTTGAGGTAAGATTTGAATGCACCTCACGA
66 TTACCTCCGAGGGGAGATGTTGGATGAAGTATCTCCTGAGGTAAGATTTGAATGCACCTCACGA
30547652 TCACTGCAGTGGTGGGGGTTTCCGTGGACTGCCTATGAGAGGAGCACGGTAA-CTCAATTATATA
1 TCACTGCAGTGGTGGGGGTTTCCGTGGACTGCCTATGAGAGGAGCACGGTAACCT-AATTATATA
* * *
30547716 TTTACCTCCGAGGGGAGATGTTGGGTGAAGTATCTCCTGAGGTATGATTTGAGTGCACCTCACG
65 TTTACCTCCGAGGGGAGATGTTGGATGAAGTATCTCCTGAGGTAAGATTTGAATGCACCTCACG
30547780 TTCGGGCCAC
Statistics
Matches: 120, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
128 2 0.02
129 118 0.98
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (129 bp):
TCACTGCAGTGGTGGGGGTTTCCGTGGACTGCCTATGAGAGGAGCACGGTAACCTAATTATATAT
TTACCTCCGAGGGGAGATGTTGGATGAAGTATCTCCTGAGGTAAGATTTGAATGCACCTCACGA
Found at i:30548894 original size:10 final size:10
Alignment explanation
Indices: 30548879--30548919 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
30548869 AATTTGATTT
30548879 TTTATTTTCA
1 TTTATTTTCA
*
30548889 TTTATTTTTA
1 TTTATTTTCA
30548899 TTT-TTTTC-
1 TTTATTTTCA
*
30548907 TATATTTTCA
1 TTTATTTTCA
30548917 TTT
1 TTT
30548920 TCCTTTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
8 2 0.08
9 9 0.36
10 14 0.56
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTATTTTCA
Found at i:30548901 original size:28 final size:28
Alignment explanation
Indices: 30548865--30548919 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
30548855 AATATTAAAG
30548865 TTTTAATTTGATTTT-T-TATTTTCATTTA
1 TTTTAATTT--TTTTCTATATTTTCATTTA
*
30548893 TTTTTATTTTTTTCTATATTTTCATTT
1 TTTTAATTTTTTTCTATATTTTCATTT
30548920 TCCTTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.17
27 1 0.04
28 19 0.79
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (28 bp):
TTTTAATTTTTTTCTATATTTTCATTTA
Found at i:30548904 original size:18 final size:18
Alignment explanation
Indices: 30548865--30548902 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
30548855 AATATTAAAG
30548865 TTTTAATTTGATTTTTTA
1 TTTTAATTTGATTTTTTA
*
30548883 TTTTCATTT-A-TTTTTA
1 TTTTAATTTGATTTTTTA
30548899 TTTT
1 TTTT
30548903 TTTCTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 1 0.05
18 8 0.42
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTTAATTTGATTTTTTA
Found at i:30548933 original size:21 final size:20
Alignment explanation
Indices: 30548900--30548946 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 20
30548890 TTATTTTTAT
30548900 TTTTTTCTATATTTTCATTTTCC
1 TTTTTTC-ATATTTTC--TTTCC
30548923 TTTTTTC-TATTTTCTTTCC
1 TTTTTTCATATTTTCTTTCC
30548942 TTTTT
1 TTTTT
30548947 CTTTGTTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.42
21 7 0.29
23 7 0.29
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTTCATATTTTCTTTCC
Found at i:30551387 original size:30 final size:30
Alignment explanation
Indices: 30551351--30551414 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
30551341 ATCCTCTTCA
30551351 TCATGATTTCTATGATCATTTTGAATCTCT
1 TCATGATTTCTATGATCATTTTGAATCTCT
30551381 TCATGATTTCTATGATCATTTTGAATCTCT
1 TCATGATTTCTATGATCATTTTGAATCTCT
30551411 TCAT
1 TCAT
30551415 TAGCTTATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.23, C:0.17, G:0.09, T:0.50
Consensus pattern (30 bp):
TCATGATTTCTATGATCATTTTGAATCTCT
Found at i:30552171 original size:276 final size:277
Alignment explanation
Indices: 30551675--30552234 Score: 1052
Period size: 276 Copynumber: 2.0 Consensus size: 277
30551665 TTAAATGGCC
* *
30551675 AATATAAAATCAACAATCAAAATTTCTAATTCAAATAAATTAACTATCACATAAAATAAAAAGAA
1 AATATAAAATCAACAATAAAAATTTCTAATTCAAATAAATTAACTACCACATAAAAT-AAAAGAA
30551740 TATAACAACATAATATAAGCTCTAAATTAAAGTAAAAAAATCTGTAAAGATTAAAACAATAGTAC
65 TATAACAACATAATATAAGCTCTAAATTAAAGTAAAAAAATCTGTAAAGATTAAAACAATAGTAC
30551805 CTAATTATTGAATGCTTATTGCAAACCACAAATGAGACTCACAACTTTATGAAGATAATAAAGAA
130 CTAATTATTGAATGCTTATTGCAAACCACAAATGAGACTCACAACTTTATGAAGATAATAAAGAA
*
30551870 CAGATTTCTTGTGTATTGTTTGGAGAAAAATTGAAGTTAAAGAAAAAAAGAGCAAATGAGAATGG
195 CAGATTTCTTGTGTATTGTTTGGAGAAAAATTGAAGTTAAAGAAAAAAAGAGCAAATGAGAAAGG
30551935 AAGATTTCAAAAATAGAT
260 AAGATTTCAAAAATAGAT
30551953 NAATATAAAATCAACAATAAAAATTTCTAATTCAAATAAATTAACTACCACATAAAAT-AAAG-A
1 -AATATAAAATCAACAATAAAAATTTCTAATTCAAATAAATTAACTACCACATAAAATAAAAGAA
30552016 TATAACAACATAATATAAGCTCTAAATTAAAGTAAAAAAATCTGTAAAGATTAAAACAATAGTAC
65 TATAACAACATAATATAAGCTCTAAATTAAAGTAAAAAAATCTGTAAAGATTAAAACAATAGTAC
30552081 CTAATTATTGAATGCTTATTGCAAACCACAAATGAGACTCACAACTTTATGAAGATAATAAAGAA
130 CTAATTATTGAATGCTTATTGCAAACCACAAATGAGACTCACAACTTTATGAAGATAATAAAGAA
30552146 CAGATTTCTTGTGTATTGTTTGGAGAAAAATTGAAGTTAAAGAAAAAAAGAGCAAATGAGAAAGG
195 CAGATTTCTTGTGTATTGTTTGGAGAAAAATTGAAGTTAAAGAAAAAAAGAGCAAATGAGAAAGG
30552211 AAGATTTCAAAAATAGAT
260 AAGATTTCAAAAATAGAT
*
30552229 ATTATA
1 AATATA
30552235 CATTGAAAAA
Statistics
Matches: 277, Mismatches: 4, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
275 5 0.02
276 213 0.77
277 4 0.01
279 55 0.20
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.27
Consensus pattern (277 bp):
AATATAAAATCAACAATAAAAATTTCTAATTCAAATAAATTAACTACCACATAAAATAAAAGAAT
ATAACAACATAATATAAGCTCTAAATTAAAGTAAAAAAATCTGTAAAGATTAAAACAATAGTACC
TAATTATTGAATGCTTATTGCAAACCACAAATGAGACTCACAACTTTATGAAGATAATAAAGAAC
AGATTTCTTGTGTATTGTTTGGAGAAAAATTGAAGTTAAAGAAAAAAAGAGCAAATGAGAAAGGA
AGATTTCAAAAATAGAT
Found at i:30552533 original size:12 final size:14
Alignment explanation
Indices: 30552503--30552529 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30552493 ATTTTTACTT
30552503 TTATATATTTTAAA
1 TTATATATTTTAAA
30552517 TTATATATTTTAA
1 TTATATATTTTAA
30552530 TATAATTAAT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATATATTTTAAA
Found at i:30554442 original size:21 final size:21
Alignment explanation
Indices: 30554391--30554443 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
30554381 ATCACCGTGT
* *
30554391 GACTAGTTTTTAGTCATTACGT
1 GACTAG-TTTTAGGCATTACGC
* *
30554413 GATTGGTTTTAGGCATTACGC
1 GACTAGTTTTAGGCATTACGC
30554434 GACTAGTTTT
1 GACTAGTTTT
30554444 TATATATTGC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (21 bp):
GACTAGTTTTAGGCATTACGC
Found at i:30554579 original size:22 final size:23
Alignment explanation
Indices: 30554478--30554587 Score: 125
Period size: 23 Copynumber: 4.8 Consensus size: 23
30554468 AGCAATACTT
* * *
30554478 AAGTCACACAACGCCTTACGAAC
1 AAGTCACGCAATGCCTTACTAAC
* * *
30554501 TAGTCACACAATGCTTTACTAAC
1 AAGTCACGCAATGCCTTACTAAC
30554524 AAGTCACGCAATGCCTTACTAAC
1 AAGTCACGCAATGCCTTACTAAC
30554547 AAGTCACGCAATGCC-TA-TCAAC
1 AAGTCACGCAATGCCTTACT-AAC
* *
30554569 TAGTCATGCAATGCCTTAC
1 AAGTCACGCAATGCCTTAC
30554588 CCAAAATTAG
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
21 1 0.01
22 18 0.24
23 56 0.75
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.23
Consensus pattern (23 bp):
AAGTCACGCAATGCCTTACTAAC
Found at i:30554605 original size:26 final size:25
Alignment explanation
Indices: 30554498--30554644 Score: 110
Period size: 23 Copynumber: 6.1 Consensus size: 25
30554488 ACGCCTTACG
* * *
30554498 AACTAGTCACACAATGCTTTA-C-T
1 AACTAGTCACGCAATGCCTTACCAA
* *
30554521 AACAAGTCACGCAATGCCTTA-C-T
1 AACTAGTCACGCAATGCCTTACCAA
* *
30554544 AACAAGTCACGCAATGCC-TATC--
1 AACTAGTCACGCAATGCCTTACCAA
*
30554566 AACTAGTCATGCAATGCCTTACCCAA
1 AACTAGTCACGCAATGCCTTA-CCAA
* * *
30554592 AATTAGTCACGCAATGCTTTATCAGA
1 AACTAGTCACGCAATGCCTTACCA-A
* *
30554618 AACTAGTCAAGCAATGCCTTATCAA
1 AACTAGTCACGCAATGCCTTACCAA
30554643 AA
1 AA
30554645 ATCAGTTACA
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
22 18 0.17
23 41 0.39
24 1 0.01
25 5 0.05
26 40 0.38
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (25 bp):
AACTAGTCACGCAATGCCTTACCAA
Found at i:30555754 original size:2 final size:2
Alignment explanation
Indices: 30555749--30555777 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30555739 AAAAAACAAA
30555749 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
30555778 TAATATACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30556041 original size:2 final size:2
Alignment explanation
Indices: 30556036--30556066 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30556026 AAAAAAAAAA
30556036 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
30556067 TATACACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30556231 original size:287 final size:287
Alignment explanation
Indices: 30555650--30556231 Score: 1105
Period size: 286 Copynumber: 2.0 Consensus size: 287
30555640 GGTTTGAATT
30555650 ATAATATACTCGAGTGGGATTTATGGCATGTGATAATTGTTATAGCCTATCTCAGTATACAATTC
1 ATAATATACTCGAGTGGGATTTATGGCATGTGATAATTGTTATAGCCTATCTCAGTATACAATTC
30555715 TTTTGGTCTATTACCAAAAAACAAAAAAAACAAAACACACACACACACACACACACACACACATA
66 TTTTGGTCTATTACCAAAAAACAAAAAAAACAAAACACACACACACACACACACACACACACATA
30555780 ATATACACAAAATAAATAAAAAATCTTTGACAATCTGTCACATGTAAGTGTTTGTATCTATATAA
131 ATATACACAAAATAAATAAAAAATCTTTGACAATCTGTCACATGTAAGTGTTTGTATCTATATAA
30555845 TAAGTGAATAGTTGTCATTTTATCTTTTACCAACTAAAAAATAAAATATCTCAAAAGAATGAAAT
196 TAAGTGAATAGTTGTCATTTTATCTTTTACCAACTAAAAAATAAAATATCTCAAAAGAATGAAAT
**
30555910 TAGAAAACCCTACTTTTCATTAACANT
261 TAGAAAACCCTACTTTTCATTAACAAG
30555937 ATAATATACTCGAGTGGGATTTATGGCATGTGATAATTGTTATAGCCTATCTCAGTATACAATTC
1 ATAATATACTCGAGTGGGATTTATGGCATGTGATAATTGTTATAGCCTATCTCAGTATACAATTC
30556002 TTTTGGTCTATTACCAAAAAAACAAAAAAAA-AAAACACACACACACACACACACACACACACA-
66 TTTTGGTCTATTACC-AAAAAACAAAAAAAACAAAACACACACACACACACACACACACACACAT
*
30556065 CATATACACAAAATAAATAAAAAATCTTTGACAATCTGTCACATGTAAGTGTTTGTATCTATATA
130 AATATACACAAAATAAATAAAAAATCTTTGACAATCTGTCACATGTAAGTGTTTGTATCTATATA
30556130 ATAAGTGAATAGTTGTCATTTTATCTTTTACCAACTAAAAAATAAAATATCTCAAAAGAATGAAA
195 ATAAGTGAATAGTTGTCATTTTATCTTTTACCAACTAAAAAATAAAATATCTCAAAAGAATGAAA
30556195 TTAGAAAACCCTACTTTTCATTAACAAG
260 TTAGAAAACCCTACTTTTCATTAACAAG
30556223 ATTAATATA
1 A-TAATATA
30556232 TATATATATA
Statistics
Matches: 290, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
286 156 0.54
287 119 0.41
288 15 0.05
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (287 bp):
ATAATATACTCGAGTGGGATTTATGGCATGTGATAATTGTTATAGCCTATCTCAGTATACAATTC
TTTTGGTCTATTACCAAAAAACAAAAAAAACAAAACACACACACACACACACACACACACACATA
ATATACACAAAATAAATAAAAAATCTTTGACAATCTGTCACATGTAAGTGTTTGTATCTATATAA
TAAGTGAATAGTTGTCATTTTATCTTTTACCAACTAAAAAATAAAATATCTCAAAAGAATGAAAT
TAGAAAACCCTACTTTTCATTAACAAG
Found at i:30556234 original size:2 final size:2
Alignment explanation
Indices: 30556227--30556268 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
30556217 AACAAGATTA
30556227 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30556268 A
1 A
30556269 AGGTTTACTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30559192 original size:2 final size:2
Alignment explanation
Indices: 30559185--30559231 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
30559175 GGTTAGTGGA
30559185 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30559227 AT AT A
1 AT AT A
30559232 GTAAATAAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30559769 original size:2 final size:2
Alignment explanation
Indices: 30559764--30559796 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
30559754 GGATAAAAAA
30559764 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30559797 GAGGTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30563323 original size:2 final size:2
Alignment explanation
Indices: 30563316--30563344 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30563306 ATGAAGACAT
30563316 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
30563345 AAGTTTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30565376 original size:16 final size:17
Alignment explanation
Indices: 30565354--30565410 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
30565344 ATTAATATTT
*
30565354 TTAATAAATTATTAAAA
1 TTAATAAATTATAAAAA
*
30565371 -TAATAAATAATAAAAA
1 TTAATAAATTATAAAAA
*
30565387 TTAA-AAATTA-AAAAC
1 TTAATAAATTATAAAAA
30565402 TATAATAAA
1 T-TAATAAA
30565411 GAGTATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 5 0.15
16 22 0.67
17 6 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAATAAATTATAAAAA
Found at i:30569292 original size:2 final size:2
Alignment explanation
Indices: 30569287--30569318 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30569277 TTAGTGTGTG
30569287 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30569319 GATGATTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30569592 original size:23 final size:21
Alignment explanation
Indices: 30569532--30569595 Score: 58
Period size: 24 Copynumber: 2.9 Consensus size: 21
30569522 TCAAAACAAT
*
30569532 ATAAATTACTAATAT-TTAAAA
1 ATAAATAAC-AATATATTAAAA
* *
30569553 ATAAAAAAAAATCATATTAAAA
1 ATAAATAACAAT-ATATTAAAA
30569575 ATTTAAATAACAATATATTAA
1 A--TAAATAACAATATATTAA
30569596 TATTTTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 3 0.09
21 8 0.24
22 7 0.21
23 7 0.21
24 9 0.26
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAATAACAATATATTAAAA
Found at i:30569817 original size:16 final size:18
Alignment explanation
Indices: 30569785--30569818 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
30569775 AATTTGAATA
30569785 ATAAAATTATATTTAATT
1 ATAAAATTATATTTAATT
30569803 ATAAAA-TAT-TTTAATT
1 ATAAAATTATATTTAATT
30569819 TAATCATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATAAAATTATATTTAATT
Found at i:30581949 original size:79 final size:79
Alignment explanation
Indices: 30581855--30582009 Score: 274
Period size: 79 Copynumber: 2.0 Consensus size: 79
30581845 TTATTGATAT
* *
30581855 CTTATTTGTCTCTCTTTCAGTTTTTATCTTGGAATTTTAATAATGTTGTGAGCTTCATGTGTCCT
1 CTTATCTGTCTCTCTTTCAGTTTTTATCTTGGAATTTTAATAATGTTGTGAACTTCATGTGTCCT
30581920 TTTTACTTTACTGA
66 TTTTACTTTACTGA
* *
30581934 CTTATCTGTCTCTCTTTCAGTTTTTATCTTGGAATTTTAATAATGTTGTTAACTTCTTGTGTCCT
1 CTTATCTGTCTCTCTTTCAGTTTTTATCTTGGAATTTTAATAATGTTGTGAACTTCATGTGTCCT
30581999 TTTTACTTTAC
66 TTTTACTTTAC
30582010 AAAGTGAATT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 72 1.00
ACGTcount: A:0.17, C:0.16, G:0.12, T:0.54
Consensus pattern (79 bp):
CTTATCTGTCTCTCTTTCAGTTTTTATCTTGGAATTTTAATAATGTTGTGAACTTCATGTGTCCT
TTTTACTTTACTGA
Found at i:30595568 original size:18 final size:19
Alignment explanation
Indices: 30595537--30595572 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
30595527 AAGTCAAAAA
*
30595537 TTATCTTAATAAATATTTT
1 TTATCTTAAAAAATATTTT
30595556 TTAT-TTAAAAAATATTT
1 TTATCTTAAAAAATATTT
30595573 ATATATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATCTTAAAAAATATTTT
Found at i:30597126 original size:15 final size:15
Alignment explanation
Indices: 30597106--30597148 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
30597096 CTTAAGATGG
30597106 TCAAATCAAAATAAT
1 TCAAATCAAAATAAT
* *
30597121 TCAAATTAAAAAAAT
1 TCAAATCAAAATAAT
30597136 TCAAACTCAAAAT
1 TCAAA-TCAAAAT
30597149 GACAGTGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (15 bp):
TCAAATCAAAATAAT
Found at i:30606777 original size:17 final size:17
Alignment explanation
Indices: 30606739--30606778 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
30606729 TTTTATGTAC
30606739 AGTAA-AACCTCGATAA
1 AGTAATAACCTCGATAA
* *
30606755 ATTAATAACCTCGATTA
1 AGTAATAACCTCGATAA
30606772 AGTAATA
1 AGTAATA
30606779 TTTTTTACTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (17 bp):
AGTAATAACCTCGATAA
Found at i:30607817 original size:14 final size:15
Alignment explanation
Indices: 30607795--30607828 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
30607785 GAAAAGGAAT
30607795 AATATATTAAATATA
1 AATATATTAAATATA
30607810 AATA-ATTAAATAT-
1 AATATATTAAATATA
30607823 AATATA
1 AATATA
30607829 CAAGATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 10 0.56
15 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATATTAAATATA
Found at i:30612371 original size:14 final size:14
Alignment explanation
Indices: 30612352--30612378 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30612342 TGTAAGATTA
30612352 ACACTAATAAAAAG
1 ACACTAATAAAAAG
30612366 ACACTAATAAAAA
1 ACACTAATAAAAA
30612379 TACTTTTACC
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:0.67, C:0.15, G:0.04, T:0.15
Consensus pattern (14 bp):
ACACTAATAAAAAG
Found at i:30619747 original size:25 final size:26
Alignment explanation
Indices: 30619690--30619748 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
30619680 ACATTTAACT
30619690 TATAAATAAAAAATTAAAATATTAATA
1 TATAAATAAAAAA-TAAAATATTAATA
*
30619717 -ATTAAATAATAAA-AAAATATTAATA
1 TA-TAAATAAAAAATAAAATATTAATA
30619742 TATAAAT
1 TATAAAT
30619749 TATCAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
25 17 0.59
26 2 0.07
27 10 0.34
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (26 bp):
TATAAATAAAAAATAAAATATTAATA
Found at i:30619757 original size:52 final size:52
Alignment explanation
Indices: 30619649--30619748 Score: 123
Period size: 51 Copynumber: 1.9 Consensus size: 52
30619639 TTTAAAAATT
* * * * *
30619649 AATTAAAATTATTAATATTTTAATCATAACAACATTTAACTTATAAATAAAA
1 AATTAAAATTATTAATAATTAAATAATAAAAAAATTTAACTTATAAATAAAA
30619701 AATTAAAA-TATTAATAATTAAATAATAAAAAAATATTAA-TATATAAAT
1 AATTAAAATTATTAATAATTAAATAATAAAAAAAT-TTAACT-TATAAAT
30619749 TATCAATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
51 22 0.54
52 19 0.46
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (52 bp):
AATTAAAATTATTAATAATTAAATAATAAAAAAATTTAACTTATAAATAAAA
Found at i:30619834 original size:176 final size:185
Alignment explanation
Indices: 30619604--30620068 Score: 533
Period size: 176 Copynumber: 2.5 Consensus size: 185
30619594 TCTCTCTAAT
*
30619604 TTTTAATTATATATCT-TAAAAATTTATATTTTAAATTTAAAAATTAATTAAAATTATTAATATT
1 TTTTAATTATATAT-TATAAAAA-TAATATTTTAAATTT-AAAATTAATTAAAATTATTAATATT
* *
30619668 TTAATCATAACAACATTTAACTTATAAATAA-A-AA-A-TTAAAATATTAATAATTAA-ATAATA
63 TTAATCATAATAACATTTAA-TTATAAAAAATATAATATTTAAAATATTAATAATTAATATAA-A
*
30619728 AAAAAATATTAATA-TATAAATT-ATCA-A-TTATTCATATTT-AAAATAAAAT-AAA-A
126 AAAAAATATTAATATTATAAATTAATCAGACTTATTAATATTTAAAAATAAAATAAAACA
* * *
30619781 TTTTAATTACATATTATAAAAATAATAGTTTAAATTTAAACATTAATTAAAATTATTATTATTTT
1 TTTTAATTATATATTATAAAAATAATATTTTAAATTTAAA-ATTAATTAAAATTATTAATATTTT
* *
30619846 AATCATAATAACATTTAAATATAAAAAAATTATTAATATTTTAAAATGTTAATAATTAATTATAA
65 AATCATAATAACATTTAATTAT-AAAAAA-TA-TAATA-TTTAAAATATTAATAATTAA-TATAA
* * *
30619911 ATAAAAATATTAATATTTTAAATTAATTATGACTTATTAATATTTAAAAATAAAATAAAAACTA
125 AAAAAAATATTAATATTATAAATTAATCA-GACTTATTAATATTTAAAAATAAAAT-AAAAC-A
* *
30619975 TTCTTAGTTATATATTATAAAAAATAATATTTTTAAATTTGAAAATTAATTTAAATTTATTAATA
1 TT-TTAATTATATATTAT-AAAAATAATA-TTTTAAATTT-AAAATTAA-TTAAAATTATTAATA
30620040 TTTTAATCATAATAACATTTAAATTATAA
61 TTTTAATCATAATAACATTT-AATTATAA
30620069 TTTAAATGAT
Statistics
Matches: 242, Mismatches: 18, Indels: 35
0.82 0.06 0.12
Matches are distributed among these distances:
175 6 0.02
176 59 0.24
177 19 0.08
178 1 0.00
180 2 0.01
181 1 0.00
183 18 0.07
184 14 0.06
185 11 0.05
186 3 0.01
188 1 0.00
189 11 0.05
190 10 0.04
192 3 0.01
194 3 0.01
195 13 0.05
196 10 0.04
197 14 0.06
198 38 0.16
199 5 0.02
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (185 bp):
TTTTAATTATATATTATAAAAATAATATTTTAAATTTAAAATTAATTAAAATTATTAATATTTTA
ATCATAATAACATTTAATTATAAAAAATATAATATTTAAAATATTAATAATTAATATAAAAAAAA
ATATTAATATTATAAATTAATCAGACTTATTAATATTTAAAAATAAAATAAAACA
Found at i:30620130 original size:24 final size:26
Alignment explanation
Indices: 30620080--30620131 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
30620070 TTAAATGATC
* *
30620080 AATTATTAATATTTTAAATTAATTAAA
1 AATTATTAATATTTT-AATAAAGTAAA
30620107 AATTATTAATA-TTT-ATAAAGTAAA
1 AATTATTAATATTTTAATAAAGTAAA
30620131 A
1 A
30620132 TAAAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 9 0.39
26 3 0.13
27 11 0.48
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
AATTATTAATATTTTAATAAAGTAAA
Found at i:30620256 original size:41 final size:42
Alignment explanation
Indices: 30620161--30620246 Score: 122
Period size: 40 Copynumber: 2.1 Consensus size: 42
30620151 GTAATAATAT
* *
30620161 TTAAATTATAAATAAAATATTAATATTTTAAAATATTAATGA
1 TTAAATTATAAATAAAATATTAATATTTCAAAATATCAATGA
* *
30620203 TTAAATTATAAAT-AAATATTAATA-TTCAAATTATCAATTA
1 TTAAATTATAAATAAAATATTAATATTTCAAAATATCAATGA
30620243 TTAA
1 TTAA
30620247 TGTTTTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 16 0.40
41 11 0.28
42 13 0.32
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (42 bp):
TTAAATTATAAATAAAATATTAATATTTCAAAATATCAATGA
Found at i:30620294 original size:27 final size:27
Alignment explanation
Indices: 30620238--30620294 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
30620228 TCAAATTATC
* * * *
30620238 AATTATTAATGTTTTAAATTAATTATA
1 AATTATTAATATTTAAAATAAAATATA
30620265 AATTATTAATATTTAAAAATAAAATA-A
1 AATTATTAATATTT-AAAATAAAATATA
30620292 AAT
1 AAT
30620295 AAAAATAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
AATTATTAATATTTAAAATAAAATATA
Found at i:30620953 original size:175 final size:174
Alignment explanation
Indices: 30620625--30620954 Score: 416
Period size: 175 Copynumber: 1.9 Consensus size: 174
30620615 AAAACCCTAG
* * *
30620625 TTTTCAATTTCCTTCATTTGTATTCCCTTTTCGATTTTTTTTATAAACTAGATAAATTATTATAT
1 TTTTCAATTTCCCTCATTTGTATTCCCTCTCCGATTTTTTTTATAAACTAGATAAATTATTATAT
* * * * * *
30620690 ACATTACGTGTATCACGCGCTAGAACTTCAATCCAACTCAGTGCAGCTTTAAACTCTAAAAATAG
66 ACACTACATGTATCACACGCGAGAACTTCAACCCAACTCAGTGCAACTTTAAACTCTAAAAATAG
30620755 AACTTAAGTAAGTCTATAAATCACAGGTGACGTTCCTAACCCAA
131 AACTTAAGTAAGTCTATAAATCACAGGTGACGTTCCTAACCCAA
* *
30620799 TTTTCAGTTTCCCTCCTTTGTATTCCCTCTCCGATTTTCTTTTTATAAACTAGATAAATTATTAT
1 TTTTCAATTTCCCTCATTTGTATTCCCTCTCCGA-TTT-TTTTTATAAACTAGATAAATTATTAT
* * * * **
30620864 ATACACTACATGTGTCGCAAC-CGA-AACTTGAACCCAA-TCCCGTGCAACTTTAAGTTCTAAAA
64 ATACACTACATGTATCAC-ACGCGAGAACTTCAACCCAACT-CAGTGCAACTTTAAACTCTAAAA
**
30620926 ATAGAGTTTAAGTAAGTGC-ATAAATCACA
127 ATAGAACTTAAGTAAGT-CTATAAATCACA
30620955 AGTCCACGTT
Statistics
Matches: 132, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
174 30 0.23
175 58 0.44
176 43 0.33
177 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (174 bp):
TTTTCAATTTCCCTCATTTGTATTCCCTCTCCGATTTTTTTTATAAACTAGATAAATTATTATAT
ACACTACATGTATCACACGCGAGAACTTCAACCCAACTCAGTGCAACTTTAAACTCTAAAAATAG
AACTTAAGTAAGTCTATAAATCACAGGTGACGTTCCTAACCCAA
Found at i:30621105 original size:18 final size:18
Alignment explanation
Indices: 30621082--30621126 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
30621072 TCACATTATT
30621082 GTGTTTAAACGTATAAAC
1 GTGTTTAAACGTATAAAC
* * * *
30621100 GTGTTTAATCGTGTTATC
1 GTGTTTAAACGTATAAAC
30621118 GTGTTTAAA
1 GTGTTTAAA
30621127 TATGTATACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (18 bp):
GTGTTTAAACGTATAAAC
Found at i:30621319 original size:17 final size:17
Alignment explanation
Indices: 30621287--30621319 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30621277 TTTTAATTTT
30621287 TGTTTTGTTATATTTGA
1 TGTTTTGTTATATTTGA
30621304 TGTTCTTGTTAT-TTTG
1 TGTT-TTGTTATATTTG
30621320 TTTTGTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.12, C:0.03, G:0.18, T:0.67
Consensus pattern (17 bp):
TGTTTTGTTATATTTGA
Found at i:30621347 original size:31 final size:31
Alignment explanation
Indices: 30621284--30621347 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
30621274 TAATTTTAAT
* * **
30621284 TTTTGTTTTGTTATATTTGATGTTCTTGTTA
1 TTTTGTTTTGTTATAATTGATGTTATAATTA
* *
30621315 TTTTGTTTTGTTATAATTGTTTTTATAATTA
1 TTTTGTTTTGTTATAATTGATGTTATAATTA
30621346 TT
1 TT
30621348 GATTTTAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.17, C:0.02, G:0.12, T:0.69
Consensus pattern (31 bp):
TTTTGTTTTGTTATAATTGATGTTATAATTA
Found at i:30622441 original size:2 final size:2
Alignment explanation
Indices: 30622434--30622470 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
30622424 AAATTGACTC
30622434 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30622471 ATTAAATTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:30627859 original size:31 final size:31
Alignment explanation
Indices: 30627818--30627899 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
30627808 GCCACGTTAT
*
30627818 AAGGATTAAATTGAACAAAAAT-ATATAGTAC
1 AAGGACTAAATTGAACAAAAATAATATA-TAC
* **
30627849 AAGGACTAAATTGAACAAAACTAATATATTG
1 AAGGACTAAATTGAACAAAAATAATATATAC
*
30627880 AGGGACTAAATTGAACAAAA
1 AAGGACTAAATTGAACAAAA
30627900 TTAAGATGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
31 40 0.89
32 5 0.11
ACGTcount: A:0.54, C:0.09, G:0.15, T:0.23
Consensus pattern (31 bp):
AAGGACTAAATTGAACAAAAATAATATATAC
Found at i:30627912 original size:31 final size:31
Alignment explanation
Indices: 30627851--30627931 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
30627841 TATAGTACAA
* *
30627851 GGACTAAATTGAACAAAACTAATATATTGAG
1 GGACTAAATTGAACAAAATTAAGATATTGAG
*
30627882 GGACTAAATTGAACAAAATTAAGATGTTGAG
1 GGACTAAATTGAACAAAATTAAGATATTGAG
* *
30627913 GGATTAAATTGAAAAAAAT
1 GGACTAAATTGAACAAAAT
30627932 ATTTAAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (31 bp):
GGACTAAATTGAACAAAATTAAGATATTGAG
Found at i:30628859 original size:108 final size:109
Alignment explanation
Indices: 30628695--30628901 Score: 292
Period size: 108 Copynumber: 1.9 Consensus size: 109
30628685 AGAAATTTTT
* **
30628695 AGTAAATTTAAATAAAAAGGTAAATTAGGTAAGAGTTGAATAATTGCAAAAAAATGTGTATTTGT
1 AGTAAATTTAAATAAAAAGGTAAATTAGGTAAGAGTTGAATAATTGCAAAAAAATGTGCATTTAC
** *
30628760 AAATTGTGAAAGTTGTGACTAAATCAATATATTTTTTTAATTTG
66 AAATTGTGAAAGTTGAAACTAAATCAAAATATTTTTTTAATTTG
* ** * *
30628804 AGTAAATTTAAATAAAAA-GTATATT-GGTTAAGAGTTGAATAATTTTAGAAGAATGTGCATTTA
1 AGTAAATTTAAATAAAAAGGTAAATTAGG-TAAGAGTTGAATAATTGCAAAAAAATGTGCATTTA
30628867 CAAATTGTGAAAGTTGAAACTAAATCAAAATATTT
65 CAAATTGTGAAAGTTGAAACTAAATCAAAATATTT
30628902 AATCATTTTA
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
107 2 0.02
108 66 0.77
109 18 0.21
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.36
Consensus pattern (109 bp):
AGTAAATTTAAATAAAAAGGTAAATTAGGTAAGAGTTGAATAATTGCAAAAAAATGTGCATTTAC
AAATTGTGAAAGTTGAAACTAAATCAAAATATTTTTTTAATTTG
Found at i:30638435 original size:20 final size:18
Alignment explanation
Indices: 30638406--30638462 Score: 53
Period size: 20 Copynumber: 3.0 Consensus size: 18
30638396 TATTACTTTC
30638406 ATTT-TATTTTATTTTTT
1 ATTTCTATTTTATTTTTT
* *
30638423 ATTATCATATTTTCTATTTT
1 ATT-TC-TATTTTATTTTTT
30638443 ATTTCTAATTGTTATTTTTT
1 ATTTCT-ATT-TTATTTTTT
30638463 TATACTTTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
17 3 0.10
18 2 0.06
19 5 0.16
20 21 0.68
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (18 bp):
ATTTCTATTTTATTTTTT
Found at i:30638613 original size:17 final size:19
Alignment explanation
Indices: 30638578--30638629 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
30638568 TTTTATTTTT
30638578 TTATTATACTATTTCTTA-TA
1 TTATTATA-TATTT-TTATTA
30638598 TT-TTATATATTTTTATTA
1 TTATTATATATTTTTATTA
30638616 TTATTATAT-TTTTT
1 TTATTATATATTTTT
30638630 CATAAGCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.10
18 14 0.47
19 11 0.37
20 2 0.07
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATTATATATTTTTATTA
Found at i:30645730 original size:2 final size:2
Alignment explanation
Indices: 30645723--30645774 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
30645713 ATGAATTTGA
30645723 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30645765 AT AT AT AT AT
1 AT AT AT AT AT
30645775 GTGTGTGTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30649104 original size:21 final size:21
Alignment explanation
Indices: 30649080--30649121 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
30649070 TGTTTTAATG
* *
30649080 AGAAATAAAATTTGAAGGAGA
1 AGAAAGAAAAATTGAAGGAGA
30649101 AGAAAGAAAAATTGAAGGAGA
1 AGAAAGAAAAATTGAAGGAGA
30649122 GATATTAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.14
Consensus pattern (21 bp):
AGAAAGAAAAATTGAAGGAGA
Found at i:30662938 original size:15 final size:15
Alignment explanation
Indices: 30662918--30662960 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
30662908 TTTAGTATAG
30662918 TTTAATTAATAATAT
1 TTTAATTAATAATAT
30662933 TTTAATTAATAATAT
1 TTTAATTAATAATAT
* *
30662948 TTTTATTTATAAT
1 TTTAATTAATAAT
30662961 TTAATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAATTAATAATAT
Found at i:30662965 original size:20 final size:21
Alignment explanation
Indices: 30662942--30662998 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 21
30662932 TTTTAATTAA
*
30662942 TAATATTTTTATTTATAAT-T
1 TAATATTTTTATTTAAAATAT
*
30662962 TAATATTATTATGATTAAAATAT
1 TAATATTTTTAT--TTAAAATAT
30662985 TAATATTTTTATTT
1 TAATATTTTTATTT
30662999 TTTATTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 11 0.35
21 2 0.06
22 6 0.19
23 12 0.39
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TAATATTTTTATTTAAAATAT
Found at i:30662971 original size:23 final size:21
Alignment explanation
Indices: 30662930--30662999 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 21
30662920 TAATTAATAA
30662930 TATTTTAATTAATAATATTTT
1 TATTTTAATTAATAATATTTT
*
30662951 TATTTATAATT--TAATATTAT
1 TATTT-TAATTAATAATATTTT
* * *
30662971 TATGATTAAAATATTAATATTTT
1 TAT--TTTAATTAATAATATTTT
30662994 TATTTT
1 TATTTT
30663000 TTATTTATAC
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 11 0.28
21 10 0.26
22 7 0.18
23 11 0.28
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (21 bp):
TATTTTAATTAATAATATTTT
Found at i:30663054 original size:16 final size:16
Alignment explanation
Indices: 30663029--30663063 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
30663019 ATTTAATAAA
30663029 TAAAACATTAATAGTT
1 TAAAACATTAATAGTT
* *
30663045 TAAAATATTAATATTT
1 TAAAACATTAATAGTT
30663061 TAA
1 TAA
30663064 TATTTTAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (16 bp):
TAAAACATTAATAGTT
Found at i:30663063 original size:8 final size:8
Alignment explanation
Indices: 30663036--30663129 Score: 55
Period size: 8 Copynumber: 11.4 Consensus size: 8
30663026 AAATAAAACA
*
30663036 TTAATAGT
1 TTAATATT
* *
30663044 TTAAAATA
1 TTAATATT
30663052 TTAATATT
1 TTAATATT
30663060 TTAATATT
1 TTAATATT
*
30663068 TTAATCATA
1 TTAAT-ATT
30663077 TTAATATT
1 TTAATATT
* *
30663085 AATAATGTT
1 -TTAATATT
*
30663094 TAAATCATAT
1 TTAAT-AT-T
* * *
30663104 ATAAAATA
1 TTAATATT
30663112 TTAATATT
1 TTAATATT
30663120 TTAA-ATT
1 TTAATATT
30663127 TTA
1 TTA
30663130 CAAATAATTT
Statistics
Matches: 63, Mismatches: 19, Indels: 9
0.69 0.21 0.10
Matches are distributed among these distances:
7 6 0.10
8 38 0.60
9 16 0.25
10 3 0.05
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (8 bp):
TTAATATT
Found at i:30663172 original size:18 final size:18
Alignment explanation
Indices: 30663146--30663180 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
30663136 ATTTTTTCTT
30663146 TTTTATTCTATTTTTTTCC
1 TTTTATTCT-TTTTTTTCC
30663165 TTTT-TTCTTTTTTTTC
1 TTTTATTCTTTTTTTTC
30663181 TTCTTCATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTATTCTTTTTTTTCC
Found at i:30664067 original size:10 final size:10
Alignment explanation
Indices: 30664045--30664122 Score: 56
Period size: 10 Copynumber: 7.9 Consensus size: 10
30664035 AGGAAATGAA
*
30664045 AATA-TATTA
1 AATATTATTT
30664054 AATATTATTT
1 AATATTATTT
30664064 AATA-TA-TT
1 AATATTATTT
30664072 AATATTATTT
1 AATATTATTT
* *
30664082 AACTA-TAATA
1 AA-TATTATTT
**
30664092 AATATTATAA
1 AATATTATTT
30664102 AGCATATTATTT
1 A--ATATTATTT
30664114 AATATTATT
1 AATATTATT
30664123 ATTTGAATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
8 6 0.11
9 10 0.18
10 29 0.53
11 2 0.04
12 8 0.15
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (10 bp):
AATATTATTT
Found at i:30664069 original size:19 final size:19
Alignment explanation
Indices: 30664045--30664099 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
30664035 AGGAAATGAA
30664045 AATATATTAAATATTATTT
1 AATATATTAAATATTATTT
30664064 AATATATT-AATATTATTT
1 AATATATTAAATATTATTT
*
30664082 AACTATAATAAATATTAT
1 AA-TATATTAAATATTAT
30664100 AAAGCATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 12 0.36
19 13 0.39
20 8 0.24
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
AATATATTAAATATTATTT
Found at i:30664123 original size:45 final size:45
Alignment explanation
Indices: 30664074--30664167 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
30664064 AATATATTAA
* *
30664074 TATTATTT-AACTATAATAAATATTATAAAGCATATTATTTAATAT
1 TATTATTTGAA-TATAATAAATATAATAAAGAATATTATTTAATAT
* *
30664119 TATTATTTGAATATAATAAATGTAATAAAGAATATTATTTAGTAT
1 TATTATTTGAATATAATAAATATAATAAAGAATATTATTTAATAT
30664164 TATT
1 TATT
30664168 TAAATTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 42 0.95
46 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (45 bp):
TATTATTTGAATATAATAAATATAATAAAGAATATTATTTAATAT
Found at i:30665344 original size:19 final size:19
Alignment explanation
Indices: 30665320--30665363 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
30665310 TAGCTTAAAT
30665320 AAAAATAAAAAAATATATA
1 AAAAATAAAAAAATATATA
*
30665339 AAAAAT--AATAATATATA
1 AAAAATAAAAAAATATATA
*
30665356 AATAATAA
1 AAAAATAA
30665364 CAATAACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 15 0.71
19 6 0.29
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAAATAAAAAAATATATA
Found at i:30665351 original size:17 final size:17
Alignment explanation
Indices: 30665331--30665368 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
30665321 AAAATAAAAA
*
30665331 AATATATAAAAAATAAT
1 AATATATAAAAAATAAC
*
30665348 AATATATAAATAATAAC
1 AATATATAAAAAATAAC
30665365 AATA
1 AATA
30665369 ACAATAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AATATATAAAAAATAAC
Found at i:30665438 original size:3 final size:3
Alignment explanation
Indices: 30665424--30665452 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
30665414 GAGGCTTGCA
30665424 AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
30665453 TCATGATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:30665501 original size:18 final size:18
Alignment explanation
Indices: 30665478--30665514 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
30665468 ATATATTTTT
30665478 AAAAAATA-AGAAAAATAA
1 AAAAAATATA-AAAAATAA
30665496 AAAAAATATAAAAAATAA
1 AAAAAATATAAAAAATAA
30665514 A
1 A
30665515 TAATATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.14
Consensus pattern (18 bp):
AAAAAATATAAAAAATAA
Found at i:30666685 original size:30 final size:30
Alignment explanation
Indices: 30666649--30666745 Score: 194
Period size: 30 Copynumber: 3.2 Consensus size: 30
30666639 TGAATAGTGC
30666649 GGTTTGGATTAGGACAACTGATAAGAGCAT
1 GGTTTGGATTAGGACAACTGATAAGAGCAT
30666679 GGTTTGGATTAGGACAACTGATAAGAGCAT
1 GGTTTGGATTAGGACAACTGATAAGAGCAT
30666709 GGTTTGGATTAGGACAACTGATAAGAGCAT
1 GGTTTGGATTAGGACAACTGATAAGAGCAT
30666739 GGTTTGG
1 GGTTTGG
30666746 TTTCGGATAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.31, C:0.09, G:0.32, T:0.28
Consensus pattern (30 bp):
GGTTTGGATTAGGACAACTGATAAGAGCAT
Found at i:30667762 original size:27 final size:26
Alignment explanation
Indices: 30667707--30667770 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 26
30667697 TTGATCATAA
*
30667707 TAATATATAAATTATAAATAAATTAT
1 TAATATTTAAATTATAAATAAATTAT
* *
30667733 TAATATTTTAATTATATTATAAATTAT
1 TAATATTTAAATTATA-AATAAATTAT
30667760 TAATATTTAAA
1 TAATATTTAAA
30667771 AAAGAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 14 0.42
27 19 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TAATATTTAAATTATAAATAAATTAT
Found at i:30667781 original size:27 final size:27
Alignment explanation
Indices: 30667722--30667781 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
30667712 TATAAATTAT
* ** *
30667722 AAATAAATTATTAATATTTTAATTATA
1 AAATAAATTATTAATATTTAAAAAAGA
**
30667749 TTATAAATTATTAATATTTAAAAAAGA
1 AAATAAATTATTAATATTTAAAAAAGA
30667776 AAATAA
1 AAATAA
30667782 TATAAAAATA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
AAATAAATTATTAATATTTAAAAAAGA
Found at i:30671182 original size:17 final size:18
Alignment explanation
Indices: 30671145--30671182 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
30671135 AATTATGAGA
30671145 ATTT-ATTTTTAAATATT
1 ATTTAATTTTTAAATATT
30671162 -TTTAATTTTTAAAT-TT
1 ATTTAATTTTTAAATATT
30671178 ATTTA
1 ATTTA
30671183 TTAATGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTAATTTTTAAATATT
Found at i:30672131 original size:27 final size:26
Alignment explanation
Indices: 30672083--30672161 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 26
30672073 AAAATGGAGT
** *
30672083 AAAAAATATATATATAAT-AAAATTTTA
1 AAAAAATA-ATA-ATAATGAAAAAATGA
30672110 AAAAAATAATAATAATGAAAAAATGA
1 AAAAAATAATAATAATGAAAAAATGA
* *
30672136 AAAAAAAAATGA-AATGAAAAAA-GA
1 AAAAAATAATAATAATGAAAAAATGA
30672160 AA
1 AA
30672162 GGAGAGAGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.09
25 15 0.33
26 19 0.41
27 8 0.17
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (26 bp):
AAAAAATAATAATAATGAAAAAATGA
Found at i:30706494 original size:101 final size:103
Alignment explanation
Indices: 30706317--30706510 Score: 293
Period size: 101 Copynumber: 1.9 Consensus size: 103
30706307 TTAAATACAG
* *
30706317 TTTTGAATTTTAGATTTTTTTTTCTCTTAATCTTTGCAAGAACAAAAAAAATTTTAGATTTTGAT
1 TTTTGAATTTTAGATTTTTTTTTCTCTTAATCTTTGCAAGAACAAAAAAAATTATAGATTTTGAC
* * *
30706382 ATTTTGTTGTTGGGTCTTCTGTTTTTTTCTGAATGTAA
66 ATTCTATTGTTGGATCTTCTGTTTTTTTCTGAATGTAA
* * *
30706420 TTTTGAATTTTAGA-TTTTTTTTCTTTTAATCTTTGTAAGAA-TAAAAAAATTATAGATTTTGAC
1 TTTTGAATTTTAGATTTTTTTTTCTCTTAATCTTTGCAAGAACAAAAAAAATTATAGATTTTGAC
*
30706483 ATTCTATTGTTGGATCTTCTTTTTTTTT
66 ATTCTATTGTTGGATCTTCTGTTTTTTT
30706511 AGTAGTTTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 43 0.52
102 25 0.30
103 14 0.17
ACGTcount: A:0.26, C:0.07, G:0.12, T:0.55
Consensus pattern (103 bp):
TTTTGAATTTTAGATTTTTTTTTCTCTTAATCTTTGCAAGAACAAAAAAAATTATAGATTTTGAC
ATTCTATTGTTGGATCTTCTGTTTTTTTCTGAATGTAA
Found at i:30709258 original size:21 final size:22
Alignment explanation
Indices: 30709223--30709263 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
30709213 TTATTCTTTA
*
30709223 TTTATTTGTTCCTTT-TTTTCT
1 TTTATTTATTCCTTTATTTTCT
*
30709244 TTTATTTATTGCTTTATTTT
1 TTTATTTATTCCTTTATTTT
30709264 ATTATTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.76
Consensus pattern (22 bp):
TTTATTTATTCCTTTATTTTCT
Found at i:30721880 original size:25 final size:25
Alignment explanation
Indices: 30721835--30721887 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
30721825 TTGATCAATT
* *
30721835 AAAATATTGAAAATGATAAAGATTG
1 AAAATATTGAAAATGAAAAAGAGTG
*
30721860 AAAATTTTGAAAA-GTAAAAAGAGTG
1 AAAATATTGAAAATG-AAAAAGAGTG
30721885 AAA
1 AAA
30721888 TGTGATAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.58, C:0.00, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATATTGAAAATGAAAAAGAGTG
Found at i:30722379 original size:32 final size:32
Alignment explanation
Indices: 30722312--30722408 Score: 101
Period size: 32 Copynumber: 3.0 Consensus size: 32
30722302 GTAATATTAT
30722312 AATTAAAATAAAATAT-AT-AATGTAGGAATTAAA
1 AATTAAAATAAAATATAATAAATG-A--AATTAAA
30722345 AATTAAAATAAAATATAATAAATGAAATTAAA
1 AATTAAAATAAAATATAATAAATGAAATTAAA
* * * * *
30722377 AATTTATATAACATAGAA-AAAAGAAATTAAA
1 AATTAAAATAAAATATAATAAATGAAATTAAA
30722408 A
1 A
30722409 TAAAAAATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
31 13 0.23
32 21 0.37
33 16 0.28
34 3 0.05
35 4 0.07
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.28
Consensus pattern (32 bp):
AATTAAAATAAAATATAATAAATGAAATTAAA
Found at i:30724764 original size:2 final size:2
Alignment explanation
Indices: 30724757--30724815 Score: 91
Period size: 2 Copynumber: 29.0 Consensus size: 2
30724747 GTCGCGTCGG
* *
30724757 AT AT AT AT AT AT AT AT AT AT AT AT AT NT CGT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
30724800 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
30724816 GCCCTTACCT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
2 52 0.98
3 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30731277 original size:45 final size:45
Alignment explanation
Indices: 30731226--30731330 Score: 201
Period size: 45 Copynumber: 2.3 Consensus size: 45
30731216 AAATTCAAAT
*
30731226 TTTGGCACATGCTTTTATCTGATAATTATCTGCCTCACATCTCCC
1 TTTGGCATATGCTTTTATCTGATAATTATCTGCCTCACATCTCCC
30731271 TTTGGCATATGCTTTTATCTGATAATTATCTGCCTCACATCTCCC
1 TTTGGCATATGCTTTTATCTGATAATTATCTGCCTCACATCTCCC
30731316 TTTGGCATATGCTTT
1 TTTGGCATATGCTTT
30731331 GTATAGTATA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.19, C:0.26, G:0.12, T:0.43
Consensus pattern (45 bp):
TTTGGCATATGCTTTTATCTGATAATTATCTGCCTCACATCTCCC
Found at i:30733333 original size:2 final size:2
Alignment explanation
Indices: 30733326--30733357 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30733316 ATGATTAAGA
30733326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30733358 TGATTGAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30751351 original size:27 final size:26
Alignment explanation
Indices: 30751300--30751353 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
30751290 GAAAGAAATT
* *
30751300 TCTTTTAGTAATGATTTTTATACTTA
1 TCTTGTAGTAATGATCTTTATACTTA
30751326 TCTTGTAGATAATGATCCTTTA-ACTTA
1 TCTTGTAG-TAATGAT-CTTTATACTTA
30751353 T
1 T
30751354 ATTGATGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 13 0.54
28 4 0.17
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.52
Consensus pattern (26 bp):
TCTTGTAGTAATGATCTTTATACTTA
Found at i:30753592 original size:23 final size:22
Alignment explanation
Indices: 30753549--30753592 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
30753539 AAATACAAAC
* **
30753549 ATATTTTTATTATAATTTAATA
1 ATATTTTTATTAGAAGATAATA
30753571 ATATTTTGTATTAGAAGATAAT
1 ATATTTT-TATTAGAAGATAAT
30753593 TAAACCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
ATATTTTTATTAGAAGATAATA
Found at i:30753721 original size:45 final size:45
Alignment explanation
Indices: 30753660--30753753 Score: 116
Period size: 45 Copynumber: 2.1 Consensus size: 45
30753650 ATTAAATTTA
* * * *
30753660 AATAATACTAAATAATATTCTTTGTTACATTTATTATATTCAAAT
1 AATAATACTAAATAATATGCTTTATAACATTTATTATAGTCAAAT
* * * *
30753705 AATAATATTAAGTAATATGCTTTATAATATTTATTATAGTGAAAT
1 AATAATACTAAATAATATGCTTTATAACATTTATTATAGTCAAAT
30753750 AATA
1 AATA
30753754 TTAATATATT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (45 bp):
AATAATACTAAATAATATGCTTTATAACATTTATTATAGTCAAAT
Found at i:30754684 original size:33 final size:33
Alignment explanation
Indices: 30754642--30754707 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
30754632 TTTTTTAAGC
30754642 TTTCTTAGCCTCTGATTGAATCAAACTCATCAA
1 TTTCTTAGCCTCTGATTGAATCAAACTCATCAA
30754675 TTTCTTAGCCTCTGATTGAATCAAACTCATCAA
1 TTTCTTAGCCTCTGATTGAATCAAACTCATCAA
30754708 CTCCTTGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.36
Consensus pattern (33 bp):
TTTCTTAGCCTCTGATTGAATCAAACTCATCAA
Found at i:30766494 original size:15 final size:15
Alignment explanation
Indices: 30766475--30766507 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30766465 AATTTTGAAC
30766475 AATATA-AT-TTTTA
1 AATATATATATTTTA
30766488 AATATATATATTTTA
1 AATATATATATTTTA
30766503 AATAT
1 AATAT
30766508 GAACTCAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 2 0.11
15 10 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATATATATATTTTA
Found at i:30768174 original size:30 final size:28
Alignment explanation
Indices: 30768133--30768216 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 28
30768123 CATTAATCAC
*
30768133 AAAAGTTTATTTGATTTAAAATAAAAATA
1 AAAAATTTATTT-ATTTAAAATAAAAATA
** *
30768162 TAAAAATTTATTTAAATATAATTAAAAATA
1 -AAAAATTTATTTATTTA-AAATAAAAATA
*
30768192 AAAAAATTATTTATTTTTAAAATAA
1 AAAAATTTATTTA--TTTAAAATAA
30768217 TATAACGTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
29 15 0.35
30 26 0.60
31 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (28 bp):
AAAAATTTATTTATTTAAAATAAAAATA
Found at i:30788016 original size:3 final size:3
Alignment explanation
Indices: 30788008--30788037 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
30787998 AAAATGTTGC
30788008 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30788038 CAATATGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:30788744 original size:20 final size:20
Alignment explanation
Indices: 30788719--30788761 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
30788709 CCTCTTAACA
30788719 TTTTTCTTTCGAAATTACCC
1 TTTTTCTTTCGAAATTACCC
30788739 TTTTTCTTTCGAAATTACCC
1 TTTTTCTTTCGAAATTACCC
30788759 TTT
1 TTT
30788762 ACAAAGTTGA
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:0.19, C:0.23, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTTCTTTCGAAATTACCC
Found at i:30789099 original size:54 final size:54
Alignment explanation
Indices: 30789017--30789126 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
30789007 TTCGAACATT
30789017 TTTATAGAGCTAACATTATTGTTGACATGGCATAACTTTGATATCGTGTGTTTG
1 TTTATAGAGCTAACATTATTGTTGACATGGCATAACTTTGATATCGTGTGTTTG
30789071 TTTATAGAGCTAACATTATTGTTGACATGGCATAACTTTGATATCGTGTGTTTG
1 TTTATAGAGCTAACATTATTGTTGACATGGCATAACTTTGATATCGTGTGTTTG
30789125 TT
1 TT
30789127 GAGTTTTGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (54 bp):
TTTATAGAGCTAACATTATTGTTGACATGGCATAACTTTGATATCGTGTGTTTG
Found at i:30789840 original size:18 final size:18
Alignment explanation
Indices: 30789817--30789861 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
30789807 TAGAGAGACT
*
30789817 AAATTAAAGTAA-TTCTCA
1 AAATTAAAGCAATTTCT-A
30789835 AAATTAAAGCAATTTCTA
1 AAATTAAAGCAATTTCTA
30789853 AAATTAAAG
1 AAATTAAAG
30789862 GGCTAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (18 bp):
AAATTAAAGCAATTTCTA
Found at i:30790139 original size:51 final size:51
Alignment explanation
Indices: 30790078--30790175 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
30790068 AGTAATTCGT
30790078 AAAATTAAGGGA-TCAAATTATTACAATTTTGAGTACTAAAGTGAAGATCTC
1 AAAATTAAGGGACT-AAATTATTACAATTTTGAGTACTAAAGTGAAGATCTC
* *
30790129 AAAATTAAGGGACTAAATTGTTATAATTTTGAGTACTAAAGTGAAGA
1 AAAATTAAGGGACTAAATTATTACAATTTTGAGTACTAAAGTGAAGA
30790176 AAATGCATGA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (51 bp):
AAAATTAAGGGACTAAATTATTACAATTTTGAGTACTAAAGTGAAGATCTC
Found at i:30791135 original size:18 final size:18
Alignment explanation
Indices: 30791097--30791136 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
30791087 AACTTTAATT
*
30791097 TAATTTTAAAAGCTATTA
1 TAATTTTAAAAGCTATCA
30791115 TAATTTATAAAAGCT-TCA
1 TAATTT-TAAAAGCTATCA
30791133 TAAT
1 TAAT
30791137 AACTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (18 bp):
TAATTTTAAAAGCTATCA
Found at i:30791979 original size:23 final size:22
Alignment explanation
Indices: 30791927--30791993 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
30791917 TAATTAAAAC
* * *
30791927 TTAAAATTATAATAATA-ATAA
1 TTAAAATTATATTAATATTTAT
30791948 TTAAAATTATATTAATATTTAT
1 TTAAAATTATATTAATATTTAT
* * *
30791970 TTACAAATTAAATAAATTTTTAT
1 TTA-AAATTATATTAATATTTAT
30791993 T
1 T
30791994 AATATTAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 16 0.42
22 5 0.13
23 17 0.45
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAAAATTATATTAATATTTAT
Found at i:30792875 original size:22 final size:22
Alignment explanation
Indices: 30792831--30792883 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
30792821 CAATATCATT
**
30792831 TATAATTAAATTATTAATTTTA
1 TATAATTAAATTATTAAAATTA
30792853 TATAATTAAA-TATATAAAATTA
1 TATAATTAAATTAT-TAAAATTA
30792875 T-TAAATTAA
1 TAT-AATTAA
30792884 CTAAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATAATTAAATTATTAAAATTA
Found at i:30793276 original size:73 final size:71
Alignment explanation
Indices: 30793195--30793331 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 71
30793185 AAATTAATTG
* *
30793195 AATGGAAATT-TCAATTAA-GAAAAATTGTGAAATTAATCAATTAACAAAAAATTAATTTAATTG
1 AATGGAAATTATCAATTAACAAAAAATT-TG--ATTAATCAATTAACAAAAAATTAATTGAATTG
30793258 ACAAGGAAA
63 ACAAGGAAA
30793267 AATGTGAAATTAGTCAATTAACAAAAAATTTGATTAATCAATTAACAAAAAATTAATTGAATTGA
1 AATG-GAAATTA-TCAATTAACAAAAAATTTGATTAATCAATTAACAAAAAATTAATTGAATTGA
30793332 AATTAAAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
72 4 0.07
73 38 0.64
75 10 0.17
76 7 0.12
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.31
Consensus pattern (71 bp):
AATGGAAATTATCAATTAACAAAAAATTTGATTAATCAATTAACAAAAAATTAATTGAATTGACA
AGGAAA
Found at i:30793302 original size:24 final size:24
Alignment explanation
Indices: 30793275--30793320 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
30793265 AAAATGTGAA
*
30793275 ATTAGTCAATTAACAAAAAATTTG
1 ATTAATCAATTAACAAAAAATTTG
30793299 ATTAATCAATTAACAAAAAATT
1 ATTAATCAATTAACAAAAAATT
30793321 AATTGAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (24 bp):
ATTAATCAATTAACAAAAAATTTG
Found at i:30793317 original size:49 final size:50
Alignment explanation
Indices: 30793205--30793317 Score: 133
Period size: 49 Copynumber: 2.3 Consensus size: 50
30793195 AATGGAAATT
30793205 TCAATTAAGAAAAATTGTGAAATTAATCAATTAACAAAAAATTAATTTAA
1 TCAATTAAGAAAAATTGTGAAATTAATCAATTAACAAAAAATTAATTTAA
** * * *
30793255 TTGA-CAAGGAAAAA-TGTGAAATTAGTCAATTAACAAAAAATTTGA-TTAA
1 TCAATTAA-GAAAAATTGTGAAATTAATCAATTAACAAAAAA-TTAATTTAA
*
30793304 TCAATTAACAAAAA
1 TCAATTAAGAAAAA
30793318 ATTAATTGAA
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
49 38 0.75
50 13 0.25
ACGTcount: A:0.55, C:0.07, G:0.09, T:0.29
Consensus pattern (50 bp):
TCAATTAAGAAAAATTGTGAAATTAATCAATTAACAAAAAATTAATTTAA
Found at i:30800341 original size:2 final size:2
Alignment explanation
Indices: 30800334--30800358 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30800324 TATGATTTCC
30800334 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 T
30800359 GCACACACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30818265 original size:45 final size:45
Alignment explanation
Indices: 30818216--30818611 Score: 140
Period size: 45 Copynumber: 8.8 Consensus size: 45
30818206 AAGTCAAAAC
* *
30818216 AGCAGCATGAAACCACAGGATGAAAATGTTTCTTTAGGTCACAAT
1 AGCAGCAGGAAATCACAGGATGAAAATGTTTCTTTAGGTCACAAT
* * * * * *
30818261 AGCAGCAGGAAATCA-ACTGATGGAAGTGTTTCTGT-GAGTGACAAG
1 AGCAGCAGGAAATCACA-GGATGAAAATGTTTCTTTAG-GTCACAAT
*** * ** *
30818306 AGCAGCTTCAAATCACAGGATGAAAATGATTCTTTAGACCATAAT
1 AGCAGCAGGAAATCACAGGATGAAAATGTTTCTTTAGGTCACAAT
* * * * * ** *
30818351 AGCAGCAGGAAATTA-ATTGATGGAAGTGTTTCTCT-GAGTCGGAAA
1 AGCAGCAGGAAATCACA-GGATGAAAATGTTTCTTTAG-GTCACAAT
* * * * * * **
30818396 AGTAGCCGGAAATC-CGAGGACGGAAATGTTTCTTTACGCCGTAAT
1 AGCAGCAGGAAATCAC-AGGATGAAAATGTTTCTTTAGGTCACAAT
* ** * ** * *
30818441 AGCAGCAGAAAATCACCTGAAGGGAATGTTTCTTT-GAGTCGCAAG
1 AGCAGCAGGAAATCACAGGATGAAAATGTTTCTTTAG-GTCACAAT
* * * * * *** *
30818486 AGCAGCAGGAGATCACAGGAAGGAAATGATTCCTTACACCATAAT
1 AGCAGCAGGAAATCACAGGATGAAAATGTTTCTTTAGGTCACAAT
* * * * * * ** *
30818531 AGCAGCAAGAATTCAGC-TGATGCAAGTGTTTCTTTAAGTCGGAAG
1 AGCAGCAGGAAATCA-CAGGATGAAAATGTTTCTTTAGGTCACAAT
* * *
30818576 AGCAGCAGGAAATCACAGCATGGAAACGTTTCTTTA
1 AGCAGCAGGAAATCACAGGATGAAAATGTTTCTTTA
30818612 CACCATAATA
Statistics
Matches: 245, Mismatches: 92, Indels: 28
0.67 0.25 0.08
Matches are distributed among these distances:
44 5 0.02
45 235 0.96
46 5 0.02
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (45 bp):
AGCAGCAGGAAATCACAGGATGAAAATGTTTCTTTAGGTCACAAT
Found at i:30818311 original size:90 final size:90
Alignment explanation
Indices: 30818216--30818627 Score: 425
Period size: 90 Copynumber: 4.6 Consensus size: 90
30818206 AAGTCAAAAC
* * * *** *
30818216 AGCAGCATGAAACCACAGGATGAAAATGTTTCTTTAGGTCACAATAGCAGCAGGAAATCAACTGA
1 AGCAGCAGGAAATCACAGGATGGAAATGTTTCTTTACACCATAATAGCAGCAGGAAATCAACTGA
*
30818281 TGGAAGTGTTTCTGTGAGT-GACAAG
66 TGGAAGTGTTTCTTTGAGTCG-CAAG
*** * * * * *
30818306 AGCAGCTTCAAATCACAGGATGAAAATGATTCTTTAGACCATAATAGCAGCAGGAAATTAATTGA
1 AGCAGCAGGAAATCACAGGATGGAAATGTTTCTTTACACCATAATAGCAGCAGGAAATCAACTGA
* * *
30818371 TGGAAGTGTTTCTCTGAGTCGGAAA
66 TGGAAGTGTTTCTTTGAGTCGCAAG
* * * * * * *
30818396 AGTAGCCGGAAATC-CGAGGACGGAAATGTTTCTTTACGCCGTAATAGCAGCAGAAAATCACCTG
1 AGCAGCAGGAAATCAC-AGGATGGAAATGTTTCTTTACACCATAATAGCAGCAGGAAATCAACTG
*
30818460 AAGGGAA-TGTTTCTTTGAGTCGCAAG
65 -ATGGAAGTGTTTCTTTGAGTCGCAAG
* * * * * * *
30818486 AGCAGCAGGAGATCACAGGAAGGAAATGATTCCTTACACCATAATAGCAGCAAGAATTCAGCTGA
1 AGCAGCAGGAAATCACAGGATGGAAATGTTTCTTTACACCATAATAGCAGCAGGAAATCAACTGA
* * *
30818551 TGCAAGTGTTTCTTTAAGTCGGAAG
66 TGGAAGTGTTTCTTTGAGTCGCAAG
* *
30818576 AGCAGCAGGAAATCACAGCATGGAAACGTTTCTTTACACCATAATAGCAGCA
1 AGCAGCAGGAAATCACAGGATGGAAATGTTTCTTTACACCATAATAGCAGCA
30818628 AGGGCTCACA
Statistics
Matches: 265, Mismatches: 52, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
89 5 0.02
90 253 0.95
91 7 0.03
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Consensus pattern (90 bp):
AGCAGCAGGAAATCACAGGATGGAAATGTTTCTTTACACCATAATAGCAGCAGGAAATCAACTGA
TGGAAGTGTTTCTTTGAGTCGCAAG
Found at i:30822969 original size:19 final size:19
Alignment explanation
Indices: 30822934--30822980 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
30822924 CTAACCAATG
*
30822934 ATTAAGTAAAGAGATCATAT
1 ATTAA-TAAAGAGATCAAAT
30822954 ATTAATAAATGA-ATCAAAT
1 ATTAATAAA-GAGATCAAAT
30822973 ATTCAATA
1 ATT-AATA
30822981 TGAAAGATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (19 bp):
ATTAATAAAGAGATCAAAT
Found at i:30823366 original size:15 final size:15
Alignment explanation
Indices: 30823343--30823375 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
30823333 TCATTAAAGT
*
30823343 TATATTATAATACTA
1 TATACTATAATACTA
30823358 TATACTATAATACTA
1 TATACTATAATACTA
30823373 TAT
1 TAT
30823376 TTTAGAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (15 bp):
TATACTATAATACTA
Found at i:30827100 original size:31 final size:31
Alignment explanation
Indices: 30827065--30827128 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
30827055 AACAATTAAA
* *
30827065 TGAATGTTATTTGTTATTTTATATGAAATGT
1 TGAATGTTATTTGTCATTATATATGAAATGT
*
30827096 TGAATGTTATTTGTCATTATATATTAAATGT
1 TGAATGTTATTTGTCATTATATATGAAATGT
30827127 TG
1 TG
30827129 TTGACATGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.53
Consensus pattern (31 bp):
TGAATGTTATTTGTCATTATATATGAAATGT
Found at i:30829372 original size:21 final size:20
Alignment explanation
Indices: 30829344--30829385 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
30829334 ATTTACTGAG
* *
30829344 TGAAAAATCATAATAAAATA
1 TGAAAAATAATAAAAAAATA
30829364 TGAATAAATAATAAAAAAATA
1 TGAA-AAATAATAAAAAAATA
30829385 T
1 T
30829386 TTAATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (20 bp):
TGAAAAATAATAAAAAAATA
Found at i:30830939 original size:2 final size:2
Alignment explanation
Indices: 30830927--30830957 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
30830917 CAGACACCTG
*
30830927 TA TA AA 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 T
30830958 TCTTACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:30831858 original size:3 final size:3
Alignment explanation
Indices: 30831850--30831878 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
30831840 TTGGAGTCTA
30831850 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
30831879 CTGTGACGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:30856805 original size:10 final size:10
Alignment explanation
Indices: 30856790--30856823 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
30856780 CATTAATACA
30856790 TATTTATTAT
1 TATTTATTAT
30856800 TATTTATTAT
1 TATTTATTAT
*
30856810 ATATTTATTGT
1 -TATTTATTAT
30856821 TAT
1 TAT
30856824 ATTGTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (10 bp):
TATTTATTAT
Found at i:30866604 original size:53 final size:51
Alignment explanation
Indices: 30866488--30866605 Score: 123
Period size: 53 Copynumber: 2.2 Consensus size: 51
30866478 AAATTTTTTG
* *
30866488 TTAAAAATAA-TTTAAAATTATATAATATTATAAATAATAATAATAATAAT
1 TTAAAGATAATTTTAAAATTATAAAATATTATAAATAATAATAATAATAAT
* * *
30866538 TAAAAAGAAATAATTTTAAATTTA-AAAATATTATAAATAATAGTTATAATGATAAT
1 T-TAAAG--ATAATTTTAAAATTATAAAATATTATAAATAATA---ATAATAATAAT
30866594 TTAAAGATAATT
1 TTAAAGATAATT
30866606 ATTTAAAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
50 1 0.02
51 3 0.05
53 27 0.49
54 9 0.16
55 4 0.07
56 11 0.20
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (51 bp):
TTAAAGATAATTTTAAAATTATAAAATATTATAAATAATAATAATAATAAT
Found at i:30867069 original size:20 final size:20
Alignment explanation
Indices: 30867041--30867078 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
30867031 AGGTTGAGAA
*
30867041 ATTTTAAATATTAATAATAT
1 ATTTAAAATATTAATAATAT
30867061 ATTTAAAATATTAATAAT
1 ATTTAAAATATTAATAAT
30867079 TAAATAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTAAAATATTAATAATAT
Found at i:30867175 original size:15 final size:16
Alignment explanation
Indices: 30867149--30867235 Score: 63
Period size: 16 Copynumber: 5.4 Consensus size: 16
30867139 CTTTTANTAA
30867149 TAATATATTTAAAATAT
1 TAATATA-TTAAAATAT
30867166 TAATA-ATTAATAAT-T
1 TAATATATTAA-AATAT
* *
30867181 TAA-ATATTAATATGT
1 TAATATATTAAAATAT
* * *
30867196 TATTTATAATTTAATTAT
1 TA-ATAT-ATTAAAATAT
*
30867214 TAATATATGAAAATAT
1 TAATATATTAAAATAT
30867230 TAATAT
1 TAATAT
30867236 TTTATTTATT
Statistics
Matches: 54, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
14 3 0.06
15 16 0.30
16 17 0.31
17 10 0.19
18 8 0.15
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATATATTAAAATAT
Found at i:30867188 original size:22 final size:24
Alignment explanation
Indices: 30867149--30867234 Score: 80
Period size: 22 Copynumber: 3.9 Consensus size: 24
30867139 CTTTTANTAA
30867149 TAATATATTTAAAATATTAATAAT
1 TAATATATTTAAAATATTAATAAT
30867173 TAATA-ATTT-AAATATTAAT-A-
1 TAATATATTTAAAATATTAATAAT
* * *
30867193 T-GT-TATTTATAAT-TTAATTAT
1 TAATATATTTAAAATATTAATAAT
*
30867214 TAATATA-TGAAAATATTAATA
1 TAATATATTTAAAATATTAATA
30867235 TTTTATTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
19 10 0.20
20 5 0.10
21 2 0.04
22 16 0.33
23 11 0.22
24 5 0.10
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
TAATATATTTAAAATATTAATAAT
Found at i:30867244 original size:42 final size:42
Alignment explanation
Indices: 30867154--30867244 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
30867144 ANTAATAATA
* **
30867154 TATTTAAAATATTAATAATTAATAATTTAAATATTAATATGT
1 TATTTATAATATTAATAATTAATAATGAAAATATTAATATGT
* *
30867196 TATTTATAAT-TTAATTATTAATATATGAAAATATTAATATTT
1 TATTTATAATATTAATAATTAATA-ATGAAAATATTAATATGT
30867238 TATTTAT
1 TATTTAT
30867245 TGATTTAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 12 0.28
42 31 0.72
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (42 bp):
TATTTATAATATTAATAATTAATAATGAAAATATTAATATGT
Found at i:30869653 original size:198 final size:197
Alignment explanation
Indices: 30869417--30869804 Score: 758
Period size: 198 Copynumber: 2.0 Consensus size: 197
30869407 TTATAATGAT
30869417 AGTTTAAAGATAATTATTTACAAAAAAATTTAAAATATTTTCTCTTCTCTTATTAAGCAAAATTT
1 AGTTTAAAGATAATTATTTACAAAAAAATTTAAAATATTTTCTCTTCTCTTATTAAGCAAAATTT
30869482 TTTATTTAAATAAATTTTTTTGAAAACATTTAATTTTTTAGATCTTAATATATGCTAATATTGAT
66 TTTATTTAAATAAATTTTTTTGAAAACATTTAATTTTTTAGATCTTAATATATGCTAATATTGAT
*
30869547 TTAATCATATTTTGGTAATTATATGATTCTAATAGTAAAATCAAATTCATATTGTGAAAATACAA
131 TTAATCATATTTTGGTAATTATATGATTCTAATAGTAAAATCAAATTCATATTGAGAAAATACAA
30869612 TA
196 TA
30869614 NAGTTTAAAGATAATTATTTACAAAAAAATTTAAAATATTTTCTCTTCTCTTATTAAGCAAAATT
1 -AGTTTAAAGATAATTATTTACAAAAAAATTTAAAATATTTTCTCTTCTCTTATTAAGCAAAATT
30869679 TTTTATTTAAATAAATTTTTTTGAAAACATTTAATTTTTTAGATCTTAATATATGCTAATATTGA
65 TTTTATTTAAATAAATTTTTTTGAAAACATTTAATTTTTTAGATCTTAATATATGCTAATATTGA
30869744 TTTAATCATATTTTGGTAATTATATGATTCTAATAGTAAAATCAAATTCATATTGAGAAAA
130 TTTAATCATATTTTGGTAATTATATGATTCTAATAGTAAAATCAAATTCATATTGAGAAAA
30869805 CATAATATTT
Statistics
Matches: 189, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
198 189 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (197 bp):
AGTTTAAAGATAATTATTTACAAAAAAATTTAAAATATTTTCTCTTCTCTTATTAAGCAAAATTT
TTTATTTAAATAAATTTTTTTGAAAACATTTAATTTTTTAGATCTTAATATATGCTAATATTGAT
TTAATCATATTTTGGTAATTATATGATTCTAATAGTAAAATCAAATTCATATTGAGAAAATACAA
TA
Found at i:30873085 original size:2 final size:2
Alignment explanation
Indices: 30873073--30873104 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
30873063 TATATTATTT
*
30873073 AG AG AG CG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30873105 TTCTCAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30873966 original size:20 final size:19
Alignment explanation
Indices: 30873916--30873968 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
30873906 AAAAATATAT
*
30873916 ATATATATAATAAATAATAAA
1 ATATAT-TAA-AAATAAAAAA
* *
30873937 ATAAACTAAAATATAAAAAA
1 ATATATTAAAA-ATAAAAAA
30873957 ATATATTAAAAA
1 ATATATTAAAAA
30873969 AATTTAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 3 0.12
20 19 0.73
21 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
ATATATTAAAAATAAAAAA
Found at i:30873966 original size:25 final size:23
Alignment explanation
Indices: 30873920--30873980 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
30873910 ATATATATAT
30873920 ATATAATAAATAATAAAATAAACTAAA
1 ATATAA-AAA-AATAAAATAAA--AAA
* *
30873947 ATATAAAAAAATATATTAAAAAA
1 ATATAAAAAAATAAAATAAAAAA
*
30873970 ATTTAAAAAAA
1 ATATAAAAAAA
30873981 AANNNNNNNN
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 13 0.42
25 9 0.29
26 3 0.10
27 6 0.19
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (23 bp):
ATATAAAAAAATAAAATAAAAAA
Found at i:30890431 original size:10 final size:10
Alignment explanation
Indices: 30890416--30890449 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
30890406 CATTAATACA
30890416 TATTTATTAT
1 TATTTATTAT
30890426 TATTTATTAT
1 TATTTATTAT
*
30890436 ATATTTATTGT
1 -TATTTATTAT
30890447 TAT
1 TAT
30890450 ATTGTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (10 bp):
TATTTATTAT
Found at i:30891202 original size:2 final size:2
Alignment explanation
Indices: 30891195--30891224 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30891185 AGACGAACAG
30891195 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30891225 GTGAAATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30893798 original size:14 final size:15
Alignment explanation
Indices: 30893774--30893811 Score: 60
Period size: 14 Copynumber: 2.5 Consensus size: 15
30893764 ACGATTTCCA
30893774 TTTCGTTTTCTTTTTT
1 TTTC-TTTTCTTTTTT
30893790 TTT-TTTTCTTTTTT
1 TTTCTTTTCTTTTTT
30893804 TTTCTTTT
1 TTTCTTTT
30893812 TCTAAGTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.67
15 4 0.19
16 3 0.14
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.87
Consensus pattern (15 bp):
TTTCTTTTCTTTTTT
Found at i:30893801 original size:10 final size:10
Alignment explanation
Indices: 30893774--30893812 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
30893764 ACGATTTCCA
*
30893774 TTTCGTTTTCT
1 TTTC-TTTTTT
30893785 TTT-TTTTTT
1 TTTCTTTTTT
30893794 TTTCTTTTTT
1 TTTCTTTTTT
30893804 TTTCTTTTT
1 TTTCTTTTT
30893813 CTAAGTTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 8 0.31
10 15 0.58
11 3 0.12
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:30893805 original size:16 final size:16
Alignment explanation
Indices: 30893774--30893814 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
30893764 ACGATTTCCA
*
30893774 TTTCGTTTTC-TTTTT
1 TTTCTTTTTCTTTTTT
30893789 TTT-TTTTTCTTTTTT
1 TTTCTTTTTCTTTTTT
30893804 TTTCTTTTTCT
1 TTTCTTTTTCT
30893815 AAGTTGTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 11 0.48
16 7 0.30
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.85
Consensus pattern (16 bp):
TTTCTTTTTCTTTTTT
Done.