Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2916.1
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: 181813
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 6729 characters in sequence are not A, C, G, or T
Found at i:13904 original size:39 final size:39
Alignment explanation
Indices: 13858--14048 Score: 337
Period size: 39 Copynumber: 4.9 Consensus size: 39
13848 AAGCAAGACA
*
13858 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
13897 TTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
13936 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
13975 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
14014 TTGGAAATGTATCCGAGCTAAAGTCCCGCAGGCTT
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTT
14049 TGTTCTGGTA
Statistics
Matches: 145, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 145 1.00
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:22907 original size:14 final size:14
Alignment explanation
Indices: 22880--22963 Score: 62
Period size: 14 Copynumber: 5.8 Consensus size: 14
22870 CATGATATAC
22880 ATAAAATA-AATAA
1 ATAAAATATAATAA
22893 ATAAAATATAATAA
1 ATAAAATATAATAA
**
22907 ATATTATATAATAAA
1 ATAAAATATAAT-AA
** *
22922 ATGTAATATAAATAT
1 ATAAAATAT-AATAA
*
22937 ATAAGAAATATAATAG
1 AT-A-AAATATAATAA
*
22953 ATATAATATAA
1 ATAAAATATAA
22964 AATAACATGT
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
13 8 0.14
14 22 0.39
15 13 0.23
16 9 0.16
17 5 0.09
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (14 bp):
ATAAAATATAATAA
Found at i:22961 original size:5 final size:5
Alignment explanation
Indices: 22874--22968 Score: 60
Period size: 5 Copynumber: 20.2 Consensus size: 5
22864 GCGATACATG
* * * *
22874 ATATA CATAAA ATA-A ATA-A ATAAA ATATA ATA-A ATATT ATATA ATAAA
1 ATATA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * * *
22922 ATGTA ATATA A-AT- ATATA AGA-A ATATA ATA-G ATATA ATATA AAATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
22968 A
1 A
22969 CATGTAAAAC
Statistics
Matches: 70, Mismatches: 13, Indels: 13
0.73 0.14 0.14
Matches are distributed among these distances:
3 1 0.01
4 22 0.31
5 43 0.61
6 4 0.06
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (5 bp):
ATATA
Found at i:24962 original size:83 final size:83
Alignment explanation
Indices: 24863--25071 Score: 321
Period size: 83 Copynumber: 2.5 Consensus size: 83
24853 TTGATTTGTT
** * *
24863 TTCCTTGTAAGTACAAGGATACTAAATCATCTTGAGTCTGTTTGAGAACATCTGAGAGTCAAATC
1 TTCCTTGTAAACACAAGAATACCAAATCATCTTGAGTCTGTTTGAGAACATCTGAGAGTCAAATC
24928 TGCTATGTCCTCAATTTG
66 TGCTATGTCCTCAATTTG
* * *
24946 TTCCTTGTAAACACAAGAATGCCAAACCATCTTGAGTCTGTTTGAGAACATCTGAGAGTCTAATC
1 TTCCTTGTAAACACAAGAATACCAAATCATCTTGAGTCTGTTTGAGAACATCTGAGAGTCAAATC
*
25011 TGCTATGTCCTCGATTTG
66 TGCTATGTCCTCAATTTG
*
25029 TTTCTTGTAAACACAAGAATACCAAATCATCTTG-GATCTGTTT
1 TTCCTTGTAAACACAAGAATACCAAATCATCTTGAG-TCTGTTT
25072 CAGTATAAAC
Statistics
Matches: 114, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
82 1 0.01
83 113 0.99
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (83 bp):
TTCCTTGTAAACACAAGAATACCAAATCATCTTGAGTCTGTTTGAGAACATCTGAGAGTCAAATC
TGCTATGTCCTCAATTTG
Found at i:25199 original size:119 final size:119
Alignment explanation
Indices: 24988--25934 Score: 1579
Period size: 119 Copynumber: 8.0 Consensus size: 119
24978 TGAGTCTGTT
* *
24988 TGAGAACATCTGAGAGTCTAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCA
1 TGAGAACATCTGAGAGTCAAATCTACTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCA
*
25053 AATCATCTTGGATCTGTTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATC
66 AATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATC
* * *
25107 TGAGAACACCTGAGAATCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCA
1 TGAGAACATCTGAGAGTCAAATCTACTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCA
* *
25172 AATCATCTTGGATCTGTTTCATTATAAACATCTGAAGGTTAGATCTGCTATATC
66 AATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATC
* * * *
25226 TGAGAACACCCGAGAATCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCA
1 TGAGAACATCTGAGAGTCAAATCTACTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCA
* * *
25291 AATCATCTTGGATCTGCTTCAGTCTAAATATCTGAAGGTTAGATCTACTATATC
66 AATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATC
* * *
25345 TGAGAACGTCTGAGAGCCAAATCTACTATGTCCTCGATTTGTTTCTTATAAACACAAGAATACCA
1 TGAGAACATCTGAGAGTCAAATCTACTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCA
* *
25410 AATCATCTTGGATCTACTTCAGTATAAACATTTGAAGGTTAGATCTGCTATATC
66 AATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATC
* * * *
25464 TGAGAACATCTGAGAGTCAAATATACTATGTCCTCGATTTGTTTATTATAGACACAAGAATACCA
1 TGAGAACATCTGAGAGTCAAATCTACTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCA
* *
25529 AATCATCTTGGATCTGCTTCAGTCTAAACGTCTGAAGGTTAGATCTGCTATATC
66 AATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATC
* * *
25583 TGAGAACATCTGAGAGCCAAATCTACTATGTCCTCGATTTTTTTCTTATAAACACAAGAATACCA
1 TGAGAACATCTGAGAGTCAAATCTACTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCA
*
25648 AATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTTCTATATC
66 AATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATC
*
25702 TGAGAACATTTGAGAGTCAAATCTACTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCA
1 TGAGAACATCTGAGAGTCAAATCTACTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCA
* *
25767 AATCTTCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTTCTATATC
66 AATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATC
*
25821 TGAGAACATCTGAGAGTCAAATCTACTATGTCCTCGATTTGTTTCTTGTAAATACAAGAATACCA
1 TGAGAACATCTGAGAGTCAAATCTACTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCA
*
25886 AATCATCTTGGATCTGCTTCAGTATAAACATCTAAAGGTTAGATCTGCT
66 AATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCT
25935 GTACTGCGGC
Statistics
Matches: 779, Mismatches: 49, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
119 779 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Consensus pattern (119 bp):
TGAGAACATCTGAGAGTCAAATCTACTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCA
AATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATC
Found at i:30885 original size:32 final size:32
Alignment explanation
Indices: 30849--30913 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
30839 TGTATGCATT
30849 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
30881 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
30913 T
1 T
30914 GGTAAGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:39043 original size:14 final size:16
Alignment explanation
Indices: 39011--39044 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
39001 AGCTCATGTG
39011 GCTGCTATTGAACCAA
1 GCTGCTATTGAACCAA
39027 GCTGCT-TTGAA-CAA
1 GCTGCTATTGAACCAA
39041 GCTG
1 GCTG
39045 AAGCTCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 5 0.28
16 6 0.33
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (16 bp):
GCTGCTATTGAACCAA
Found at i:42197 original size:18 final size:18
Alignment explanation
Indices: 42174--42233 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
42164 ACTGAGGATC
42174 TCCAAGGTTTCGAAGAAA
1 TCCAAGGTTTCGAAGAAA
* *
42192 TCCAAGGTCTCTG-GGAAA
1 TCCAAGGTTTC-GAAGAAA
42210 TCCAAGGTTTC-AGAGAAA
1 TCCAAGGTTTCGA-AGAAA
42228 TCCAAG
1 TCCAAG
42234 TCGAACATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 34 0.97
19 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (18 bp):
TCCAAGGTTTCGAAGAAA
Found at i:50617 original size:14 final size:16
Alignment explanation
Indices: 50585--50618 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
50575 AGCTCATGTG
50585 GCTGCTATTGAACCAA
1 GCTGCTATTGAACCAA
50601 GCTGCT-TTGAA-CAA
1 GCTGCTATTGAACCAA
50615 GCTG
1 GCTG
50619 AAGCTCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 5 0.28
16 6 0.33
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (16 bp):
GCTGCTATTGAACCAA
Found at i:53771 original size:18 final size:18
Alignment explanation
Indices: 53748--53807 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
53738 ACTGAGGATC
53748 TCCAAGGTTTCGAAGAAA
1 TCCAAGGTTTCGAAGAAA
* *
53766 TCCAAGGTCTCTG-GGAAA
1 TCCAAGGTTTC-GAAGAAA
53784 TCCAAGGTTTC-AGAGAAA
1 TCCAAGGTTTCGA-AGAAA
53802 TCCAAG
1 TCCAAG
53808 TCGAACATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 34 0.97
19 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (18 bp):
TCCAAGGTTTCGAAGAAA
Found at i:63446 original size:40 final size:40
Alignment explanation
Indices: 63391--63472 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
63381 ATCAACCAGA
63391 CTACATAAAACTAAAAAAGATATAGACAAAAAGATGCTTC
1 CTACATAAAACTAAAAAAGATATAGACAAAAAGATGCTTC
63431 CTACATAAAACTAAAAAAGATATAGACAAAAAGATGCTTC
1 CTACATAAAACTAAAAAAGATATAGACAAAAAGATGCTTC
63471 CT
1 CT
63473 CTATAGCCCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.54, C:0.16, G:0.10, T:0.21
Consensus pattern (40 bp):
CTACATAAAACTAAAAAAGATATAGACAAAAAGATGCTTC
Found at i:66454 original size:21 final size:21
Alignment explanation
Indices: 66428--66496 Score: 65
Period size: 17 Copynumber: 3.3 Consensus size: 21
66418 CTCTTTACCT
66428 ATTAAAAAATATATTAAATAA
1 ATTAAAAAATATATTAAATAA
66449 ATT--AAAAT-T-TTAAATAA
1 ATTAAAAAATATATTAAATAA
* *
66466 ATTTTTAAAAAATATATTGAATAT
1 A---TTAAAAAATATATTAAATAA
66490 ATTAAAA
1 ATTAAAA
66497 TTTTAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
17 9 0.23
18 1 0.03
19 5 0.13
20 2 0.05
21 9 0.23
22 5 0.13
23 1 0.03
24 7 0.18
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (21 bp):
ATTAAAAAATATATTAAATAA
Found at i:66548 original size:18 final size:18
Alignment explanation
Indices: 66520--66556 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
66510 TATACTTAAC
66520 ATTTTTTAAAATAT-TTA
1 ATTTTTTAAAATATATTA
66537 ATTTTTTAAAAATATATTA
1 ATTTTTT-AAAATATATTA
66556 A
1 A
66557 ATATATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 7 0.39
19 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTTTAAAATATATTA
Found at i:66608 original size:19 final size:18
Alignment explanation
Indices: 66515--66614 Score: 66
Period size: 19 Copynumber: 5.5 Consensus size: 18
66505 TTAGTTATAC
66515 TTAACATTTTTTAAAATAT
1 TTAA-ATTTTTTAAAATAT
66534 TT-AATTTTTTAAAAATAT
1 TTAAATTTTTT-AAAATAT
* *
66552 ATTAAATATATTAAAAT-T
1 -TTAAATTTTTTAAAATAT
* *
66570 TTAAAATTTGTT---ATAC
1 TT-AAATTTTTTAAAATAT
*
66586 TTAACATTTTTTAATATAT
1 TTAA-ATTTTTTAAAATAT
66605 TTAAAATTTT
1 TT-AAATTTT
66615 AATAGATTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
15 4 0.06
16 8 0.12
17 9 0.14
18 16 0.25
19 19 0.30
20 8 0.12
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (18 bp):
TTAAATTTTTTAAAATAT
Found at i:66615 original size:71 final size:71
Alignment explanation
Indices: 66463--66616 Score: 254
Period size: 71 Copynumber: 2.2 Consensus size: 71
66453 AAATTTTAAA
*
66463 TAAATTTTTAAAAAATATATTGAATATATTAAAATTTTAAAATTAGTTATACTTAACATTTTTTA
1 TAAATTTTT-AAAAATATATTAAATATATTAAAATTTTAAAATTAGTTATACTTAACATTTTTTA
66528 AAATATT
65 AAATATT
* *
66535 TAATTTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTTGTTATACTTAACATTTTTTAA
1 TAAATTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTAGTTATACTTAACATTTTTTAA
*
66600 TATATT
66 AATATT
*
66606 TAAAATTTTAA
1 TAAATTTTTAA
66617 TAGATTTAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
71 68 0.89
72 8 0.11
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (71 bp):
TAAATTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTAGTTATACTTAACATTTTTTAA
AATATT
Found at i:66616 original size:17 final size:18
Alignment explanation
Indices: 66594--66663 Score: 58
Period size: 17 Copynumber: 4.0 Consensus size: 18
66584 ACTTAACATT
66594 TTTTAA-TATATTTAAAA
1 TTTTAACTATATTTAAAA
* *
66611 TTTTAA-TAGATTTAATTTA
1 TTTTAACTATATTTAA--AA
* *
66630 TTTTAAGT-TTTTTAAAA
1 TTTTAACTATATTTAAAA
66647 TTTTAACTATA-TTAAAA
1 TTTTAACTATATTTAAAA
66664 AAATATTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
17 28 0.67
18 1 0.02
19 12 0.29
20 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTTAACTATATTTAAAA
Found at i:66772 original size:20 final size:20
Alignment explanation
Indices: 66739--66777 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
66729 ACTTTTAAAA
66739 TTAATTATACTTAACATTTTC
1 TTAATTATACTTAA-ATTTTC
*
66760 TTAA-TATATTTAAATTTT
1 TTAATTATACTTAAATTTT
66778 TAAAAAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATTATACTTAAATTTTC
Found at i:69909 original size:3 final size:3
Alignment explanation
Indices: 69901--69926 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
69891 ATTACATCCA
69901 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
69927 AACATGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:74225 original size:73 final size:73
Alignment explanation
Indices: 74143--74547 Score: 801
Period size: 73 Copynumber: 5.5 Consensus size: 73
74133 ACAACTTGAC
74143 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
74208 CACTAACA
66 CACTAACA
74216 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
74281 CACTAACA
66 CACTAACA
74289 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
74354 CACTAACA
66 CACTAACA
74362 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
74427 CACTAACA
66 CACTAACA
74435 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
74500 CACTAACA
66 CACTAACA
*
74508 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
74548 AATAATAATA
Statistics
Matches: 331, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 331 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:74556 original size:3 final size:3
Alignment explanation
Indices: 74548--74573 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
74538 ATTACATCCA
74548 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
74574 AACATGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:75351 original size:16 final size:16
Alignment explanation
Indices: 75327--75358 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
75317 AAACATGAAG
75327 TTCAAATACATATATA
1 TTCAAATACATATATA
*
75343 TTCATATACATATATA
1 TTCAAATACATATATA
75359 ATAAGGGGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
TTCAAATACATATATA
Found at i:76080 original size:16 final size:17
Alignment explanation
Indices: 76057--76091 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
76047 GGTTGAACCA
76057 ATTTTTT-TAATATTTTT
1 ATTTTTTATAA-ATTTTT
76074 ATTTTTTATAAATTTTT
1 ATTTTTTATAAATTTTT
76091 A
1 A
76092 ATGATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTATAAATTTTT
Found at i:79636 original size:91 final size:87
Alignment explanation
Indices: 79491--79672 Score: 206
Period size: 91 Copynumber: 2.0 Consensus size: 87
79481 TAAACTCCTC
* * *
79491 TTTTTTTTCATTCATTTGGGTACTTAAACTTTCAAAATACATTAAAAAGGCCCTCAAACCTTTTT
1 TTTTTTTTCACTCAATTGGGTACTTAAACTTTCAAAATACATTAAAAAGACCCTCAAA-C-TTTT
*
79556 TAAAAAAAAGCAATTAAGCCCCTGCT
64 CAAAAAAAA-CAATTAAGCCCCTG-T
* ** *
79582 TTTTTTTTCACTCAATTGGTTACTTGAAA-TTTCAAAATGTA-TCAAAAGCACCCTCAAACTTTT
1 TTTTTTTTCACTCAATTGGGTACTT-AAACTTTCAAAATACATTAAAAAG-ACCCTCAAACTTTT
* *
79645 CAAGAAAAATAATTAAGCCCCTGT
64 CAAAAAAAACAATTAAGCCCCTGT
79669 TTTT
1 TTTT
79673 ATGAAAAAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
87 5 0.06
88 13 0.16
89 11 0.14
90 7 0.09
91 40 0.51
92 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (87 bp):
TTTTTTTTCACTCAATTGGGTACTTAAACTTTCAAAATACATTAAAAAGACCCTCAAACTTTTCA
AAAAAAACAATTAAGCCCCTGT
Found at i:79817 original size:19 final size:18
Alignment explanation
Indices: 79768--79856 Score: 56
Period size: 18 Copynumber: 4.8 Consensus size: 18
79758 AAAAATTAGA
*
79768 AAAAAATCGT-AAATTTAT
1 AAAAAATCATAAAATTT-T
* **
79786 TAAAAATTTTAAAATTTT
1 AAAAAATCATAAAATTTT
*
79804 ATAAAAATCATAAAAAATTT
1 A-AAAAATCAT-AAAATTTT
* *
79824 AAAATAT-ATAGAAATATT
1 AAAAAATCATA-AAATTTT
*
79842 AAAAAATTATAAAAT
1 AAAAAATCATAAAAT
79857 ATATAAATTC
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
17 1 0.02
18 25 0.45
19 21 0.38
20 8 0.15
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (18 bp):
AAAAAATCATAAAATTTT
Found at i:79858 original size:26 final size:27
Alignment explanation
Indices: 79783--79861 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 27
79773 ATCGTAAATT
* * *
79783 TATTAAAAATTTTAAAATTTTATAAAAA
1 TATTAAAAAATTTAAAA-TATATAGAAA
79811 TCA-TAAAAAATTTAAAATATATAGAAA
1 T-ATTAAAAAATTTAAAATATATAGAAA
79838 TATTAAAAAATTATAAAATATATA
1 TATTAAAAAATT-TAAAATATATA
79862 AATTCGTAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
26 1 0.02
27 18 0.40
28 25 0.56
29 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (27 bp):
TATTAAAAAATTTAAAATATATAGAAA
Found at i:79861 original size:9 final size:9
Alignment explanation
Indices: 79803--79863 Score: 54
Period size: 9 Copynumber: 6.7 Consensus size: 9
79793 TTTAAAATTT
79803 TATAAAA-A
1 TATAAAATA
*
79811 TCATAAAAAA
1 T-ATAAAATA
*
79821 TTTAAAATA
1 TATAAAATA
79830 TATAGAAATA
1 TATA-AAATA
*
79840 T-TAAAAAA
1 TATAAAATA
79848 TTATAAAATA
1 -TATAAAATA
79858 TATAAA
1 TATAAA
79864 TTCGTAAGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
8 5 0.12
9 24 0.56
10 14 0.33
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
TATAAAATA
Found at i:79863 original size:19 final size:19
Alignment explanation
Indices: 79787--79863 Score: 70
Period size: 19 Copynumber: 4.1 Consensus size: 19
79777 TAAATTTATT
*
79787 AAAAATTTTAAAAT-TTTA
1 AAAAATTATAAAATATTTA
* *
79805 TAAAAATCATAAAAAATTTA
1 -AAAAATTATAAAATATTTA
*
79825 AAATA-TATAGAAATA-TTA
1 AAAAATTATA-AAATATTTA
*
79843 AAAAATTATAAAATATATA
1 AAAAATTATAAAATATTTA
79862 AA
1 AA
79864 TTCGTAAGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
18 15 0.33
19 27 0.59
20 4 0.09
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (19 bp):
AAAAATTATAAAATATTTA
Found at i:79875 original size:28 final size:28
Alignment explanation
Indices: 79823--79901 Score: 72
Period size: 28 Copynumber: 2.8 Consensus size: 28
79813 ATAAAAAATT
*
79823 TAAAATATATAGAAATATTAAAAAATTA
1 TAAAATATATAGAAATAGTAAAAAATTA
* *
79851 TAAAATATATA-AATTCGTAAGAAAATTA
1 TAAAATATATAGAAATAGTAA-AAAATTA
* *
79879 TTCAAAATGTAAAGAAATA-TAAA
1 -T-AAAATATATAGAAATAGTAAA
79902 TTTCGTAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
27 6 0.15
28 18 0.45
29 2 0.05
30 11 0.28
31 3 0.08
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (28 bp):
TAAAATATATAGAAATAGTAAAAAATTA
Found at i:80135 original size:17 final size:17
Alignment explanation
Indices: 80100--80132 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
80090 TGTTAAAAGG
80100 ATTTTTTGATGCATTTT
1 ATTTTTTGATGCATTTT
*
80117 ATTTTTTTATG-ATTTT
1 ATTTTTTGATGCATTTT
80133 TATAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.18, C:0.03, G:0.09, T:0.70
Consensus pattern (17 bp):
ATTTTTTGATGCATTTT
Found at i:102717 original size:19 final size:19
Alignment explanation
Indices: 102678--102717 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
102668 TAAATTTTAA
* *
102678 TTTAATTGTAAGTTATATT
1 TTTAATTATAAGATATATT
102697 TTTAATTATAAGATAT-TT
1 TTTAATTATAAGATATATT
102715 TTT
1 TTT
102718 GTTTTCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTAATTATAAGATATATT
Found at i:109622 original size:11 final size:12
Alignment explanation
Indices: 109600--109629 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
109590 TTACAATTAC
109600 AATATAATTATA
1 AATATAATTATA
109612 AATATAA-TATA
1 AATATAATTATA
109623 AATATAA
1 AATATAA
109630 AAATATGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AATATAATTATA
Found at i:110604 original size:5 final size:5
Alignment explanation
Indices: 110589--110632 Score: 81
Period size: 5 Copynumber: 9.0 Consensus size: 5
110579 TTCACCTTTT
110589 TCTTC -CTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC
1 TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC
110633 CTTTCACCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 34 0.89
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (5 bp):
TCTTC
Found at i:117208 original size:16 final size:16
Alignment explanation
Indices: 117187--117218 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
117177 ATGCTTCAGT
117187 ATACTATAGCCCCTCC
1 ATACTATAGCCCCTCC
117203 ATACTATAGCCCCTCC
1 ATACTATAGCCCCTCC
117219 CAAACCCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.44, G:0.06, T:0.25
Consensus pattern (16 bp):
ATACTATAGCCCCTCC
Found at i:123044 original size:14 final size:14
Alignment explanation
Indices: 123025--123074 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
123015 GAGTTGATTT
* *
123025 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
123039 TTGAAAAAACAGAAA
1 TTG-AAAAACAGAAA
*
123054 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
123068 TT-AAAAA
1 TTGAAAAA
123075 GACCTCAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:123184 original size:78 final size:77
Alignment explanation
Indices: 123054--123339 Score: 343
Period size: 78 Copynumber: 3.8 Consensus size: 77
123044 AAAACAGAAA
* *
123054 TTGA-AAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCC-GAGACTCAACTCACCTCTCACAAT
1 TTGACAAA-CAGAAATTGAAAAGACCTCAGCATGTGAGCCAAAG-CTCAACTCACCTCTCACAAT
123117 ATGAGTTGATTTTT
64 ATGAGTTGATTTTT
* * * *
123131 TTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAAGCTCAACTCACCTCTCGCAATA
1 TTGACAAACAGAAATTG-AAAAGACCTCAGCATGTGAGCCAAAGCTCAACTCACCTCTCACAATA
*
123196 TGAGTT-A-ATTT
65 TGAGTTGATTTTT
** ** * * *
123207 TTGACAAACAGAAATTGAAATTACCTCAGC--GTGTCCCGAGGCTCAACTCACCTTTCGA-AATA
1 TTGACAAACAGAAATTGAAAAGACCTCAGCATGTGAGCCAAAGCTCAACTCACCTCTC-ACAATA
123269 TGAGTTGATTTTT
65 TGAGTTGATTTTT
* *
123282 TTGAAAAACAGAAATTGAAAAGACCTCAGCATGTGAGCCAAGGCTCAACTCACCTCTC
1 TTGACAAACAGAAATTGAAAAGACCTCAGCATGTGAGCCAAAGCTCAACTCACCTCTC
123340 GCAAAAGTAG
Statistics
Matches: 178, Mismatches: 23, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
73 30 0.17
74 1 0.01
75 42 0.24
76 20 0.11
77 35 0.20
78 48 0.27
79 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (77 bp):
TTGACAAACAGAAATTGAAAAGACCTCAGCATGTGAGCCAAAGCTCAACTCACCTCTCACAATAT
GAGTTGATTTTT
Found at i:123434 original size:14 final size:14
Alignment explanation
Indices: 123415--123464 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
123405 GAGTTGATTT
* *
123415 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
123429 TTGAAAAAACAGAAA
1 TTG-AAAAACAGAAA
*
123444 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
123458 TT-AAAAA
1 TTGAAAAA
123465 GACCTCAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:123574 original size:78 final size:76
Alignment explanation
Indices: 123444--123694 Score: 289
Period size: 78 Copynumber: 3.3 Consensus size: 76
123434 AAAACAGAAA
* * * *
123444 TTGA-AAAGCAGAAATT-AAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAAT
1 TTGACAAA-CAGAAATTGAAAAATACCTCAGCGTGT-AGCCAAG-CTCAACTCACCTCTCGCAAT
123507 ATGAGTTGATTTTT
63 ATGAGTTGATTTTT
123521 TTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAAGCTCAACTCACCTCTCGCAATA
1 TTGACAAACAGAAATTGAAAAATACCTCAGCGTGT-AGCC-AAGCTCAACTCACCTCTCGCAATA
*
123586 TGAGTT-A-ATTT
64 TGAGTTGATTTTT
* * * *
123597 TTGACAAACAGAAATTG-AAATTACCTCAGCGTGT-CCCGAGGCTCAACTCACCTTTCGCAATAT
1 TTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAGCC-AAGCTCAACTCACCTCTCGCAATAT
123660 GAGTTGATTTTT
65 GAGTTGATTTTT
* * *
123672 TTGAAAAAATATAAATTGAAAAA
1 TTG-ACAAACAGAAATTGAAAAA
123695 ACAGAAATTG
Statistics
Matches: 151, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
73 30 0.20
74 1 0.01
75 22 0.15
76 31 0.21
77 16 0.11
78 49 0.32
79 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (76 bp):
TTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAGCCAAGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTT
Found at i:123614 original size:390 final size:391
Alignment explanation
Indices: 122895--123693 Score: 1537
Period size: 390 Copynumber: 2.0 Consensus size: 391
122885 ACTAGACATT
* *
122895 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAAAAGTAG
1 AAAAACAGAAATTGAAAAGACCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAAAAGTAG
122960 ATTTTGAAAATACCTCGACATGTGAACCCAAGGCTCAACTCACATCTCGCAATATGAGTTGATTT
66 ATTTTGAAAATACCTCGACATGTGAACCCAAGGCTCAACTCACATCTCGCAATATGAGTTGATTT
123025 TTGAAAAATATAAATTGAAAAAACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGA
131 TTGAAAAATATAAATTGAAAAAACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGA
123090 GCCGAGACTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAAATA
196 GCCGAGACTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAAATA
123155 CCTCAGCGTGTAAGCCAAAGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGACAAACAGAA
261 CCTCAGCGTGTAAGCCAAAGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGACAAACAGAA
123220 ATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGAAATATGAGTTGATTTTTTTG
326 ATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGAAATATGAGTTGATTTTTTTG
123285 -
391 A
*
123285 AAAAACAGAAATTGAAAAGACCTCAGCATGTGAGCCAAGGCTCAACTCACCTCTCGCAAAAGTAG
1 AAAAACAGAAATTGAAAAGACCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAAAAGTAG
123350 ATTTTGAAAATACCTCGACATGTGAACCCAAGGCTCAACTCACATCTCGCAATATGAGTTGATTT
66 ATTTTGAAAATACCTCGACATGTGAACCCAAGGCTCAACTCACATCTCGCAATATGAGTTGATTT
123415 TTGAAAAATATAAATTGAAAAAACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGA
131 TTGAAAAATATAAATTGAAAAAACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGA
123480 GCCGAGACTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAAATA
196 GCCGAGACTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAAATA
123545 CCTCAGCGTGTAAGCCAAAGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGACAAACAGAA
261 CCTCAGCGTGTAAGCCAAAGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGACAAACAGAA
*
123610 ATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTG
326 ATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGAAATATGAGTTGATTTTTTTG
123675 A
391 A
* *
123676 AAAAATATAAATTGAAAA
1 AAAAACAGAAATTGAAAA
123694 AACAGAAATT
Statistics
Matches: 402, Mismatches: 6, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
390 386 0.96
391 16 0.04
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.25
Consensus pattern (391 bp):
AAAAACAGAAATTGAAAAGACCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAAAAGTAG
ATTTTGAAAATACCTCGACATGTGAACCCAAGGCTCAACTCACATCTCGCAATATGAGTTGATTT
TTGAAAAATATAAATTGAAAAAACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGA
GCCGAGACTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAAATA
CCTCAGCGTGTAAGCCAAAGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGACAAACAGAA
ATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGAAATATGAGTTGATTTTTTTG
A
Found at i:123692 original size:15 final size:15
Alignment explanation
Indices: 123672--123722 Score: 61
Period size: 14 Copynumber: 3.5 Consensus size: 15
123662 GTTGATTTTT
* *
123672 TTGAAAAAATATAAA
1 TTGAAAAAACAGAAA
123687 TTGAAAAAACAGAAA
1 TTGAAAAAACAGAAA
*
123702 TTG-AAAAGCAGAAA
1 TTGAAAAAACAGAAA
123716 TT-AAAAA
1 TTGAAAAA
123723 GACCTCAGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 16 0.50
15 16 0.50
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.20
Consensus pattern (15 bp):
TTGAAAAAACAGAAA
Found at i:123770 original size:180 final size:183
Alignment explanation
Indices: 123521--123876 Score: 503
Period size: 180 Copynumber: 2.0 Consensus size: 183
123511 GTTGATTTTT
* * *
123521 TTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAAGCTCAACTCACCTCTCGCAATA
1 TTGACAAACAGAAATTGAAAAAGACCTCAGCATGTAAGCCAAAGCTCAACTCACCTCTCACAATA
* * *
123586 TGAGTT-A-ATTTTTGACAAACAGAAATTG-AAATTACCTCAGCGTGT-CCCGAGGCTCAACTCA
66 TGAGTTGATATTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTACCCAAAGCTCAACTCA
*
123647 CCTTTCGCAATATGAGTTGATTTTTTTGAAAAAATAT-AAATTGAAAAAACAGAAA
131 CCTCTCGCAATATGAGTTGA-TTTTTTG-AAAAAT-TGAAATTGAAAAAACAGAAA
* *
123702 TTGA-AAAGCAGAAATT-AAAAAGACCTCAGCATGTGAGCC-GAGACTCAACTCACCTCTCACAA
1 TTGACAAA-CAGAAATTGAAAAAGACCTCAGCATGTAAGCCAAAG-CTCAACTCACCTCTCACAA
* *
123764 TATGAGTTGATTTTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAAGCTCAAC
64 TATGAGTTGATATTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGT-ACCCAAAGCTCAAC
123829 TCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATTGAAATTGAAAA
128 TCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATTGAAATTGAAAA
123877 CACCTCAGCA
Statistics
Matches: 156, Mismatches: 11, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
179 2 0.01
180 49 0.31
181 13 0.08
182 21 0.13
183 32 0.21
184 7 0.04
185 32 0.21
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.26
Consensus pattern (183 bp):
TTGACAAACAGAAATTGAAAAAGACCTCAGCATGTAAGCCAAAGCTCAACTCACCTCTCACAATA
TGAGTTGATATTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTACCCAAAGCTCAACTCA
CCTCTCGCAATATGAGTTGATTTTTTGAAAAATTGAAATTGAAAAAACAGAAA
Found at i:123832 original size:78 final size:75
Alignment explanation
Indices: 123702--123943 Score: 289
Period size: 78 Copynumber: 3.2 Consensus size: 75
123692 AAAACAGAAA
* * * *
123702 TTGAAAAGCAGAAATT-AAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATA
1 TTGAAAAACAGAAATTGAAAAACACCTCAGCATGT-AGCCAAG-CTCAACTCACCTCTCGCAATA
123766 TGAGTTGATTTTT
64 TGAGTTGA-TTTT
* * *
123779 TTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAAGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTGAAAAACACCTCAGCATGT-AGCC-AAGCTCAACTCACCTCTCGCAATA
123844 TGAGTTGATTTT
64 TGAGTTGATTTT
** * *
123856 TTGAAAAATTGAAATTG-AAAACACCTCAGCATGT-G--AGGCTCAACACACCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAAAACACCTCAGCATGTAGCCAAGCTCAACTCACCTCTCGCAATATG
123917 AGTTGA-TTT
66 AGTTGATTTT
*
123926 TTGAAAAACATAAATTGA
1 TTGAAAAACAGAAATTGA
123944 GCAGAAATTG
Statistics
Matches: 145, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
70 17 0.12
71 30 0.21
74 1 0.01
76 15 0.10
77 32 0.22
78 48 0.33
79 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (75 bp):
TTGAAAAACAGAAATTGAAAAACACCTCAGCATGTAGCCAAGCTCAACTCACCTCTCGCAATATG
AGTTGATTTT
Found at i:123834 original size:258 final size:253
Alignment explanation
Indices: 123380--123943 Score: 968
Period size: 258 Copynumber: 2.2 Consensus size: 253
123370 TGTGAACCCA
*
123380 AGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAACAGAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAACAGAAAT
123445 TGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATATG
66 TGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATATG
123510 AGTTGATTTTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAAGCTCAACTCAC
131 AGTTGATTTTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAAGCTCAACTCAC
* ** *
123575 CTCTCGCAATATGAGTT-AATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCG
196 CTCTCGCAATATGAGTTGAATTTTTGAAAAACAGAAATTGAAAACACCTCAGCATGT---G
*
123635 AGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAAAATATAAATTGAAAAAACAGA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTG-AAAAATATAAATTGAAAAAACAGA
123700 AATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAAT
63 AATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAAT
123765 ATGAGTTGATTTTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAAGCTCAACT
128 ATGAGTTGATTTTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAAGCTCAACT
* **
123830 CACCTCTCGCAATATGAGTTGATTTTTTGAAAAATTGAAATTGAAAACACCTCAGCATGTG
193 CACCTCTCGCAATATGAGTTGAATTTTTGAAAAACAGAAATTGAAAACACCTCAGCATGTG
* *
123891 AGGCTCAACACACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGA
123944 GCAGAAATTG
Statistics
Matches: 293, Mismatches: 12, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
253 14 0.05
254 6 0.02
255 30 0.10
256 31 0.11
257 6 0.02
258 174 0.59
259 32 0.11
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (253 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAACAGAAAT
TGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATATG
AGTTGATTTTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAAGCTCAACTCAC
CTCTCGCAATATGAGTTGAATTTTTGAAAAACAGAAATTGAAAACACCTCAGCATGTG
Found at i:123897 original size:71 final size:71
Alignment explanation
Indices: 123712--124086 Score: 274
Period size: 71 Copynumber: 4.9 Consensus size: 71
123702 TTGAAAAGCA
* * *
123712 GAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCACAATATGAGTTGATTT
1 GAAATTGAAAATACCTCAGCATGTGA---G-G-CTCAACTCACCTCTCGCAATATGAGTTGA-TT
* **
123777 TTTTGACAAACA
60 TTTTGAAAAATT
* *
123789 GAAATTGAAAAATACCTCAGCGTGTAAGCCAAAGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 GAAATTG-AAAATACCTCAGCATGT--G---AGGCTCAACTCACCTCTCGCAATATGAGTTGATT
123854 TTTTGAAAAATT
60 TTTTGAAAAATT
* *
123866 GAAATTGAAAACACCTCAGCATGTGAGGCTCAACACACCTCTCGCAATATGAGTTGA-TTTTTGA
1 GAAATTGAAAATACCTCAGCATGTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-
123930 AAAACATAAATT
65 ---A-A-AAATT
** * *
123942 GAGCAGAAATTGAAAATACCTCAACGGGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGA
1 -----GAAATTGAAAATACCTC-A-GCAT-GTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
**
124007 TTTTTTG-ATGA-T
58 TTTTTTGAAAAATT
* * *
124019 -AAATTGAAAATACCTCAATGTGACT-TGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTT
1 GAAATTGAAAATACCTC-A-G-CA-TGTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
124082 TTGAA
62 TTGAA
124087 TTAAAACAGA
Statistics
Matches: 251, Mismatches: 23, Indels: 53
0.77 0.07 0.16
Matches are distributed among these distances:
70 6 0.02
71 89 0.35
72 2 0.01
73 1 0.00
74 2 0.01
75 1 0.00
76 20 0.08
77 25 0.10
78 44 0.18
79 2 0.01
80 1 0.00
81 16 0.06
82 1 0.00
83 3 0.01
84 32 0.13
85 6 0.02
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (71 bp):
GAAATTGAAAATACCTCAGCATGTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGA
AAAATT
Found at i:124010 original size:155 final size:158
Alignment explanation
Indices: 123824--124191 Score: 448
Period size: 155 Copynumber: 2.3 Consensus size: 158
123814 AAGCCAAAGC
123824 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATTGAAATTGAAAACACCTC-A-G-C
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAA-T-AAATTGAAAACACCTCAATGTC
* * *
123886 A-TGTGAGGCTCAACACACCTCTCGCAATATGAGTTGA-TTTTTG-A-AAAACATAAATTG-AGC
64 ACT-TGAGGCTCAACACACCTCTCACAATATGAGTTGATTTTTTGAATAAAACAGAAATTGAAAC
* * *
123946 AGAAATTGAAAATACCTCAACGGGTCTTGAGGT
128 AGAAATGGAAAACACCTC-A-GCGTCTTGAGGT
** * *
123979 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-ATGATAAATTGAAAATACCTCAATGTGAC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAAATTGAAAACACCTCAATGTCAC
* * *
124043 TTGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAATTAAAACAGAAATTGAAAATA
66 TTGAGGCTCAACACACCTCTCACAATATGAGTTGATTTTTTGAA-TAAAACAGAAATTG-AAACA
124108 GAAATGGAAAACACCTCAGCGTCTTGAGGT
129 GAAATGGAAAACACCTCAGCGTCTTGAGGT
* *
124138 TCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAACACATAAATTAAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-A-ATAAATTGAAAA
124192 AAAAGAAATT
Statistics
Matches: 182, Mismatches: 17, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
152 15 0.08
153 2 0.01
154 3 0.02
155 67 0.37
156 7 0.04
157 1 0.01
159 50 0.27
160 8 0.04
161 18 0.10
163 11 0.06
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (158 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAAATTGAAAACACCTCAATGTCAC
TTGAGGCTCAACACACCTCTCACAATATGAGTTGATTTTTTGAATAAAACAGAAATTGAAACAGA
AATGGAAAACACCTCAGCGTCTTGAGGT
Found at i:124327 original size:75 final size:73
Alignment explanation
Indices: 124242--124518 Score: 301
Period size: 77 Copynumber: 3.7 Consensus size: 73
124232 TGGCCTGAGA
*
124242 CTCAACTCACCTCTCGCAATATGAGTTGATTCTTTTAAAAAGCAAAAATTGAAAATACCTCAGCG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAA-CAAAAATTGAAAATACCTCAGCG
124307 TGCCCCT-AGG
65 TG--CCTAAGG
* * *
124317 CTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGATAAAA-ATAGAATTTGAAAATATCTCA
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT-A-AAAACA-A-AAATTGAAAATACCTCA
* *
124381 ACGTGTCCTGAGG
62 GCGTG-CCTAAGG
* * * * *
124394 CTCAACTCACCTCTCGTAATATGAGTTGA-TTTTTGACAAACAAAAATTGAAATTACCTCAGCAT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAAAAATTGAAAATACCTCAGCGT
*
124458 -CTTAAGG
66 GCCTAAGG
* ** * *
124465 CTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAACATAAATTAAAAA
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAAAAATTGAAAA
124519 AACGAAAATT
Statistics
Matches: 170, Mismatches: 25, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
71 32 0.19
72 18 0.11
73 16 0.09
74 4 0.02
75 37 0.22
76 10 0.06
77 53 0.31
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.32
Consensus pattern (73 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAAAAATTGAAAATACCTCAGCGT
GCCTAAGG
Found at i:124406 original size:77 final size:77
Alignment explanation
Indices: 124201--124500 Score: 294
Period size: 77 Copynumber: 4.0 Consensus size: 77
124191 AAAAAGAAAT
* * ** * *
124201 TAAAAATAGAATTTGAAAGGACCTCGACGTGTGGCCTGAGACTCAACTCACCTCTCGCAATATGA
1 TAAAAACAGAAATTGAAAATACCTCAACGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGA
*
124266 GTTGATTCTTTT-A
64 GTTGATTTTTTTGA
* * * * *
124279 -AAAAGCAAAAATTGAAAATACCTCAGCGTGCCCCT-AGGCTCAACTCACCTCTCACAATATGAG
1 TAAAAACAGAAATTGAAAATACCTCAACGTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAG
124342 TTGATTTTTTTGA
65 TTGATTTTTTTGA
* * * *
124355 TAAAAATAGAATTTGAAAATATCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGTAATATGAGT
1 TAAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
124420 TGA--TTTTTG-
66 TGATTTTTTTGA
* * * ** * * *
124429 -ACAAACAAAAATTGAAATTACCTC-A-GCATCTTAAGGCTCAACTCACTTCTCGCAATATGAGT
1 TAAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
124491 TGATTTTTTT
66 TGATTTTTTT
124501 TGAAACATAA
Statistics
Matches: 183, Mismatches: 33, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
71 34 0.19
72 1 0.01
73 23 0.13
75 42 0.23
76 7 0.04
77 76 0.42
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (77 bp):
TAAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTTGA
Found at i:124472 original size:416 final size:416
Alignment explanation
Indices: 123823--124578 Score: 962
Period size: 416 Copynumber: 1.8 Consensus size: 416
123813 TAAGCCAAAG
***
123823 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATTGAAATTGAAAACACCTCAGCAT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAAAAATTGAAAACACCTCAGCAT
*
123888 GTGAGGCTCAACACACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAGCAGAAATT
66 GTGAGGCTCAACACACCTCTCACAATATGAGTTGATTTTTGAAAAACATAAATT--G-AGAAATT
* * **
123953 GAAAATACCTCAACGGGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATGA
128 GAAAATACCTCAACGGGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAACA
* * * *
124018 TAAATTGAAAATACCTCAATGTGACTTGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTT
193 AAAATTGAAAATACCTCAATGTCACTTAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTT
* * * *
124083 TGAATTAAAACAGAAATTGAAAATA-G-AAATGGAAAACACCTCAGC-GTCTTGAGGTTCAACTC
258 T---TTAAAACAGAAATTAAAAAAACGAAAATGGAAAACACCTCAGCGGTCCTGAGGCTCAACTC
124145 ACCTCTCGCAATATGAGCTGATTTTTTTGAAACACATAAATTAAAAAAAAAGAAATTAAAAATAG
320 ACCTCTCGCAATATGAGCTGATTTTTTTGAAACACATAAATTAAAAAAAAAGAAATTAAAAATAG
124210 AATTTGAAAGGACCTCGACGTGTGGCCTGAGA
385 AATTTGAAAGGACCTCGACGTGTGGCCTGAGA
*
124242 CTCAACTCACCTCTCGCAATATGAGTTGATTCTTTT-AAAAAGCAAAAATTGAAAATACCTCAGC
1 CTCAACTCACCTCTCGCAATATGAGTTGATT-TTTTGAAAAA-CAAAAATTGAAAACACCTCAGC
* * *** *
124306 GTGCCCCT-AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGATA-A-AAA-T-AGAA
64 ATG----TGAGGCTCAACACACCTCTCACAATATGAGTTGATTTTTGAAAAACATAAATTGAGAA
* * * *
124366 TTTGAAAATATCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTGA-TTTTTGA
125 ATTGAAAATACCTCAACGGGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-
* * *
124430 CAAACAAAAATTGAAATTACCTC-A-G-CATCTTAAGGCTCAACTCACTTCTCGCAATATGAGTT
189 --AACAAAAATTGAAAATACCTCAATGTCA-CTTAAGGCTCAACTCACCTCTCACAATATGAGTT
* * * *
124492 GATTTTTTTTGAAACATAAATTAAAAAAACGAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTC
251 GATTTTTTTTAAAACAGAAATTAAAAAAACGAAAATGGAAAACACCTCAGCG-GTCCTGAGGCTC
124557 AACTCACCTCTCGCAATATGAG
315 AACTCACCTCTCGCAATATGAG
124579 TTGAAATTAA
Statistics
Matches: 289, Mismatches: 34, Indels: 30
0.82 0.10 0.08
Matches are distributed among these distances:
413 17 0.06
414 1 0.00
415 24 0.08
416 94 0.33
417 33 0.11
418 17 0.06
419 36 0.12
420 25 0.09
421 3 0.01
422 1 0.00
423 37 0.13
424 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (416 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAAAAATTGAAAACACCTCAGCAT
GTGAGGCTCAACACACCTCTCACAATATGAGTTGATTTTTGAAAAACATAAATTGAGAAATTGAA
AATACCTCAACGGGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAACAAAA
ATTGAAAATACCTCAATGTCACTTAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTT
AAAACAGAAATTAAAAAAACGAAAATGGAAAACACCTCAGCGGTCCTGAGGCTCAACTCACCTCT
CGCAATATGAGCTGATTTTTTTGAAACACATAAATTAAAAAAAAAGAAATTAAAAATAGAATTTG
AAAGGACCTCGACGTGTGGCCTGAGA
Found at i:124627 original size:72 final size:73
Alignment explanation
Indices: 124509--124650 Score: 232
Period size: 72 Copynumber: 2.0 Consensus size: 73
124499 TTTGAAACAT
* * *
124509 AAATTAAAAAAACGAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
1 AAATTAAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAAT
124574 ATGAGTTG
66 ATGAGTTG
* *
124582 AAATT-AAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAAT
1 AAATTAAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAAT
124646 ATGAG
66 ATGAG
124651 CTGATTTTGA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
72 59 0.92
73 5 0.08
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (73 bp):
AAATTAAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAAT
ATGAGTTG
Found at i:124677 original size:160 final size:157
Alignment explanation
Indices: 124191--124664 Score: 445
Period size: 160 Copynumber: 3.0 Consensus size: 157
124181 TAAATTAAAA
* * * ** * *
124191 AAAAAGAAATTAAAAATA-G-AATTTGAAAGGACCTCGACGTGTGGCCTGAGACTCAACTCACCT
1 AAAAATAAATTAAAAAAACGAAAATTGAAAATACCTCAACGTGT--CCTGAGGCTCAACTCACCT
** * * *
124254 CTCGCAATATGAGTTGATTCTTTTAAAAAGCAAAAATTGAAAATACCTCAGCGTGCCCCTAGGCT
64 CTCGCAATATGAGTTGA-TAATTGAAAAA-CAAAAATTGAAAATACCTCAGCAT--CCCAAGGCT
* *
124319 CAACTCACCTCTCACAATATGAGTTGATTTTT-
125 CAACTCACCTCTCGCAATATGAGCTGATTTTTG
** * * *
124351 -----TTGA-TAAAAATA-G-AATTTGAAAATATCTCAACGTGTCCTGAGGCTCAACTCACCTCT
1 AAAAATAAATTAAAAAAACGAAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCT
* ** * * **
124408 CGTAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAGCATCTTAAGGCTCAACTC
66 CGCAATATGAGTTGATAATTGAAAAACAAAAATTGAAAATACCTCAGCATCCCAAGGCTCAACTC
* *
124473 ACTTCTCGCAATATGAGTTGATTTTTTTTG
131 ACCTCTCGCAATATGAGCTGA---TTTTTG
* *
124503 AAACATAAATTAAAAAAACGAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
1 AAAAATAAATTAAAAAAACGAAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCT
* *
124568 CGCAATATGAGTTGA-AATT-AAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAA
66 CGCAATATGAGTTGATAATTGAAAA-ACAAAAATTGAAAATACCTCAGCAT--CCCAAGGCTCAA
*
124631 CTCACCTCTTGCAATATGAGCTGA-TTTTG
128 CTCACCTCTCGCAATATGAGCTGATTTTTG
124660 AAAAA
1 AAAAA
124665 GTAGAAATTA
Statistics
Matches: 261, Mismatches: 38, Indels: 33
0.79 0.11 0.10
Matches are distributed among these distances:
148 31 0.12
150 22 0.08
151 13 0.05
152 34 0.13
154 28 0.11
155 1 0.00
157 11 0.04
158 10 0.04
159 26 0.10
160 55 0.21
161 30 0.11
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (157 bp):
AAAAATAAATTAAAAAAACGAAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCT
CGCAATATGAGTTGATAATTGAAAAACAAAAATTGAAAATACCTCAGCATCCCAAGGCTCAACTC
ACCTCTCGCAATATGAGCTGATTTTTG
Found at i:125111 original size:75 final size:74
Alignment explanation
Indices: 124821--125218 Score: 521
Period size: 75 Copynumber: 5.3 Consensus size: 74
124811 TGAACTCACC
* * * ***
124821 TCTCGCAATATGAGTTGATTTTTTTAAAAAACAGAAATTGAAAATACCTCAGCATGTGAACCGAG
1 TCTCGCAATATGAGTTGATTTTTTT-TAAAACAGAAATTGAAATTACCTCAGCGTGT-CTTC-AG
**
124886 GCTCAACTCACC
63 GCTCAACTCATT
* * * *
124898 TCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAG
1 TCTCGCAATATGAGTTGA--TTTTTTTT-AAAACAGAAATTGAAATTACCTCAGCGTGTCTTCAG
124963 GCTCAACTCATT
63 GCTCAACTCATT
* * *
124975 TCTCGCAATATAAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTCAGGCT
1 TCTCGCAATATGAGTTGATTTTTTTTAAAACAGAAATTGAAATTACCTCAGCGTGTCTTCAGGCT
125038 CAACTCATT
66 CAACTCATT
*
125047 TCTCGCAATATGAGTTGATTTTTTTTAACAACAAAAATTGAAATTACCTCAGCGTGTCTTCAGGC
1 TCTCGCAATATGAGTTGATTTTTTTTAA-AACAGAAATTGAAATTACCTCAGCGTGTCTTCAGGC
125112 TCAACTCATT
65 TCAACTCATT
* *
125122 TCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGC
1 TCTCGCAATATGAGTTGATTTTTTTTAA-AACAGAAATTGAAATTACCTCAGCGTGTCTTCAGGC
**
125187 TCAACTCACC
65 TCAACTCATT
*
125197 TCTAGCAATATGAGTTGATTTT
1 TCTCGCAATATGAGTTGATTTT
125219 GAAAAACAAA
Statistics
Matches: 290, Mismatches: 25, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
72 62 0.21
73 4 0.01
74 6 0.02
75 136 0.47
77 47 0.16
79 35 0.12
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Consensus pattern (74 bp):
TCTCGCAATATGAGTTGATTTTTTTTAAAACAGAAATTGAAATTACCTCAGCGTGTCTTCAGGCT
CAACTCATT
Found at i:125227 original size:147 final size:147
Alignment explanation
Indices: 124821--125236 Score: 520
Period size: 147 Copynumber: 2.8 Consensus size: 147
124811 TGAACTCACC
* *
124821 TCTCGCAATATGAGTTGATTTTTTTAAAAAACAGAAATTGAAAATACCTCAGCATGTGAACC-GA
1 TCTCGCAATATGAGTTGATTTTTTT-AAAAACAGAAATTGAAATTACCTCAGC--GTG-TCCTGA
* *
124885 GGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTG-AAAACAGAAATTGAAAATACCT
62 GGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTGAAAAACAAAAATTGAAAATACCT
*
124949 CAACGTGTCTTGAGGCTCAACTCATT
122 CAACGTGTCTTCAGGCTCAACTCATT
* * * * *
124975 TCTCGCAATATAAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTCAGGCT
1 TCTCGCAATATGAGTTGATTTTTTTAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCT
** * * * *
125038 CAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAACAAAAATTGAAATTACCTCAGCGTG
66 CAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAAAAATTGAAAATACCTCAACGTG
125103 TCTTCAGGCTCAACTCATT
129 TCTTCAGGCTCAACTCATT
*
125122 TCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGC
1 TCTCGCAATATGAGTTGA-TTTTTTTAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGC
*
125187 TCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAAATT-AAAA
65 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTGAAAA
125237 GGCTTATCTT
Statistics
Matches: 229, Mismatches: 28, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
146 10 0.04
147 76 0.33
148 1 0.00
149 32 0.14
150 64 0.28
151 25 0.11
152 4 0.02
154 17 0.07
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (147 bp):
TCTCGCAATATGAGTTGATTTTTTTAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCT
CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTGAAAATACCTCAACGTGTC
TTCAGGCTCAACTCATT
Found at i:125381 original size:70 final size:70
Alignment explanation
Indices: 125244--125410 Score: 187
Period size: 70 Copynumber: 2.4 Consensus size: 70
125234 AAAGGCTTAT
* * * * * **
125244 CTTACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGG
1 CTTACTTCTCGCAATATGAGTTGATTTTAAAACAAAAAATAAAAATACCTCAACGTGCCCCGAGG
125308 CTCAA
66 CTCAA
* **
125313 CTTACTTCTCGCAATATGAGTTGATTTTGAAAA-AAAAAATAAAAATACCTCAACGTGTCTTGAG
1 CTTACTTCTCGCAATATGAGTTGATTTT-AAAACAAAAAATAAAAATACCTCAACGTGCCCCGAG
125377 GCTCAA
65 GCTCAA
* *
125383 CTCA-TCTCTGGCAATATGAGTTGATTTT
1 CTTACT-TCTCGCAATATGAGTTGATTTT
125411 CCTTGGAAAG
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
69 20 0.24
70 59 0.71
71 4 0.05
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (70 bp):
CTTACTTCTCGCAATATGAGTTGATTTTAAAACAAAAAATAAAAATACCTCAACGTGCCCCGAGG
CTCAA
Found at i:146507 original size:30 final size:29
Alignment explanation
Indices: 146473--146530 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
146463 GTTTATAATT
*
146473 TTTTTAAATGACTAAATCAAAATTTTATCC
1 TTTTTAAATGACAAAAT-AAAATTTTATCC
* * *
146503 TTTTTTAATGTCAAAATATAATTTTATC
1 TTTTTAAATGACAAAATAAAATTTTATC
146531 TATACTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTTTAAATGACAAAATAAAATTTTATCC
Found at i:153842 original size:11 final size:11
Alignment explanation
Indices: 153818--153863 Score: 55
Period size: 10 Copynumber: 4.5 Consensus size: 11
153808 ATTCTAGTTA
153818 TATTAAATAAAT
1 TATTAAA-AAAT
153830 TATTAAAAAAT
1 TATTAAAAAAT
153841 TA-TAAAAAAT
1 TATTAAAAAAT
153851 TA--AAAAAA-
1 TATTAAAAAAT
153859 TATTA
1 TATTA
153864 GTTTAACCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 2 0.06
9 6 0.19
10 11 0.34
11 6 0.19
12 7 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TATTAAAAAAT
Found at i:164533 original size:6 final size:7
Alignment explanation
Indices: 164519--164544 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
164509 TATTATTTTT
164519 AAATAAA
1 AAATAAA
164526 AAATAAA
1 AAATAAA
164533 AAATAAA
1 AAATAAA
164540 AAATA
1 AAATA
164545 TAATCTAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAATAAA
Found at i:164738 original size:15 final size:13
Alignment explanation
Indices: 164722--164746 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
164712 AACATCCATA
164722 TATAAATTTTAAG
1 TATAAATTTTAAG
164735 TATAAATTTTAA
1 TATAAATTTTAA
164747 AAGGATCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TATAAATTTTAAG
Found at i:166522 original size:16 final size:17
Alignment explanation
Indices: 166501--166534 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
166491 GCTTTCATAG
166501 AAAGGAAAAA-AAAGAA
1 AAAGGAAAAACAAAGAA
166517 AAAGGAAAAACAAAGAA
1 AAAGGAAAAACAAAGAA
166534 A
1 A
166535 CATCCGCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAGGAAAAACAAAGAA
Found at i:171223 original size:65 final size:65
Alignment explanation
Indices: 171119--171296 Score: 347
Period size: 65 Copynumber: 2.7 Consensus size: 65
171109 GCTTCCAGCA
*
171119 CCCAAAATATCTAATCTTGAGGAGTCCCGGGACCTGCATATCGCCGCACTACCGAGAGTTGTTTG
1 CCCAATATATCTAATCTTGAGGAGTCCCGGGACCTGCATATCGCCGCACTACCGAGAGTTGTTTG
171184 CCCAATATATCTAATCTTGAGGAGTCCCGGGACCTGCATATCGCCGCACTACCGAGAGTTGTTTG
1 CCCAATATATCTAATCTTGAGGAGTCCCGGGACCTGCATATCGCCGCACTACCGAGAGTTGTTTG
171249 CCCAATATATCTAATCTTGAGGAGTCCCGGGACCTGCATATCGCCGCA
1 CCCAATATATCTAATCTTGAGGAGTCCCGGGACCTGCATATCGCCGCA
171297 ATATGAATCA
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 112 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (65 bp):
CCCAATATATCTAATCTTGAGGAGTCCCGGGACCTGCATATCGCCGCACTACCGAGAGTTGTTTG
Found at i:179537 original size:18 final size:18
Alignment explanation
Indices: 179509--179563 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
179499 GTAAATATAC
*
179509 CGTATATGTGAATAGTGT
1 CGTATACGTGAATAGTGT
*
179527 TGTATACGTGAATAGTGT
1 CGTATACGTGAATAGTGT
179545 CGTATACGTGAATAGTGT
1 CGTATACGTGAATAGTGT
179563 C
1 C
179564 ATAAATGGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.36
Consensus pattern (18 bp):
CGTATACGTGAATAGTGT
Found at i:179556 original size:36 final size:35
Alignment explanation
Indices: 179492--179562 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 35
179482 TGAACAGTAC
*
179492 TGTATACGTAAATATACCGTATATGTGAATAGTGT
1 TGTATACGTAAATATACCGTATACGTGAATAGTGT
* **
179527 TGTATACGTGAATAGTGTCGTATACGTGAATAGTGT
1 TGTATACGTAAATA-TACCGTATACGTGAATAGTGT
179563 CATAAATGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 13 0.42
36 18 0.58
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37
Consensus pattern (35 bp):
TGTATACGTAAATATACCGTATACGTGAATAGTGT
Found at i:180550 original size:33 final size:33
Alignment explanation
Indices: 180513--180582 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
180503 AATCAATCAT
180513 CAATGCTAAGATAAGTTTGCATCAACTGACCAA
1 CAATGCTAAGATAAGTTTGCATCAACTGACCAA
180546 CAATGCTAAGATAAGTTTGCATCAACTGACCAA
1 CAATGCTAAGATAAGTTTGCATCAACTGACCAA
180579 CAAT
1 CAAT
180583 AATTACAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (33 bp):
CAATGCTAAGATAAGTTTGCATCAACTGACCAA
Done.