Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 193 of 204
Found at i:56976231 original size:2 final size:2
Alignment explanation
Indices: 56976224--56976248 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56976214 ACTTATTCTC
56976224 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
56976249 AGACTTAACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56976831 original size:49 final size:49
Alignment explanation
Indices: 56976762--56976855 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 49
56976752 CTCGTTTTCT
* * * *
56976762 CGATACCATAGTCCAACTATGGTCTTACATGTAATCACTTATCACATAC
1 CGATACCATAGCCCAACTATGGTCTTACACGGAATCACATATCACATAC
* * *
56976811 CGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATATCAC
1 CGATACCATAGCCCAACTATGGTCTTACACGGAATCACATATCAC
56976856 TTATCGAAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (49 bp):
CGATACCATAGCCCAACTATGGTCTTACACGGAATCACATATCACATAC
Found at i:56977844 original size:102 final size:102
Alignment explanation
Indices: 56977668--56978000 Score: 549
Period size: 102 Copynumber: 3.3 Consensus size: 102
56977658 CCAGTGATTA
* *
56977668 GGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGTGGAATCAGCAGTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTCAAA-ATATGGTGGAATCAGCACTTAGCAACC
*
56977733 ACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTTG
65 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
* * * * *
56977771 GGGGAATCAGCACTTAGCACCCCCCTTCACATTTAAAATACGGTGGGATTAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTCAAAATATGGTGGAATCAGCACTTAGCAACCA
56977836 CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
* * *
56977873 GGGGAATCAGCACTTAGCAACCCCCTTTATATTCAAGATATGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTCAAAATATGGTGGAATCAGCACTTAGCAACCA
*
56977938 CCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
56977975 GGGGAATCAGCACTTAGCAACCCCCT
1 GGGGAATCAGCACTTAGCAACCCCCT
56978001 AATAGTTAAT
Statistics
Matches: 213, Mismatches: 17, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
102 179 0.84
103 34 0.16
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.20
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTCAAAATATGGTGGAATCAGCACTTAGCAACCA
CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:56978232 original size:101 final size:101
Alignment explanation
Indices: 56978023--56978208 Score: 261
Period size: 101 Copynumber: 1.8 Consensus size: 101
56978013 TACCCGGTTC
* *
56978023 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATTTACATCTGATACACGTAGTAGCCTAC
1 ACATAGTAGCCCGCACATAGTACTACACATGTGACCA-TTACATCCGATACACGTAGTAGCCTAC
*
56978088 ACATAGTACTACACACGTGATCGAAGCTATCCGGTTTT
65 ACATAGTACTACACACGTGATCCAAGCTATCC-GTTTT
* * *
56978126 -CATAGTAGCCCGCACATAGTACTACACATGTGACCCA-T-CATTCCGGTACACGTAGTAGCTTG
1 ACATAGTAGCCCGCACATAGTACTACACATGTGA-CCATTACA-TCCGATACACGTAGTAGCCTA
56978188 CACATAGTACTACACACGTGA
64 CACATAGTACTACACACGTGA
56978209 CCATCACTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
100 2 0.03
101 39 0.51
102 32 0.42
103 3 0.04
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (101 bp):
ACATAGTAGCCCGCACATAGTACTACACATGTGACCATTACATCCGATACACGTAGTAGCCTACA
CATAGTACTACACACGTGATCCAAGCTATCCGTTTT
Found at i:56985711 original size:20 final size:21
Alignment explanation
Indices: 56985686--56985726 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
56985676 GAAAATATAT
*
56985686 TTTCCATTCAA-TTTTCCATC
1 TTTCCAATCAAGTTTTCCATC
*
56985706 TTTCCAATCAAGTTTTTCATC
1 TTTCCAATCAAGTTTTCCATC
56985727 CCCTCAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.22, C:0.27, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTCCAATCAAGTTTTCCATC
Found at i:56986348 original size:14 final size:15
Alignment explanation
Indices: 56986322--56986352 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
56986312 TCCAGGTTCA
56986322 TCAACACATTTTTCT
1 TCAACACATTTTTCT
56986337 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
56986351 TC
1 TC
56986353 CCATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:56993951 original size:18 final size:17
Alignment explanation
Indices: 56993916--56993962 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
56993906 ATGTAGAGAT
* *
56993916 AGCTCGTAC-TTTGGTG
1 AGCTCGCACTTTTGCTG
56993932 AGCTCGCATCTTTTGCTG
1 AGCTCGCA-CTTTTGCTG
56993950 AGCTCGCACTTTT
1 AGCTCGCACTTTT
56993963 TTAGCTTGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 7 0.26
17 6 0.22
18 14 0.52
ACGTcount: A:0.13, C:0.26, G:0.23, T:0.38
Consensus pattern (17 bp):
AGCTCGCACTTTTGCTG
Found at i:57003961 original size:14 final size:15
Alignment explanation
Indices: 57003935--57003965 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
57003925 TCCAGGTTCA
57003935 TCAACACATTTTTCT
1 TCAACACATTTTTCT
57003950 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
57003964 TC
1 TC
57003966 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:57015349 original size:87 final size:87
Alignment explanation
Indices: 57015202--57015370 Score: 277
Period size: 87 Copynumber: 1.9 Consensus size: 87
57015192 TTCTCAGCAC
*
57015202 TGTTAATGCATTCATATTCTCGGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAA-CCT
1 TGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAATCC-
*
57015266 ATTAAATTGCATACTTCACGTAG
65 ACTAAATTGCATACTTCACGTAG
* * *
57015289 TGTTAATGCATTGATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAACGGCAGCCGAATCCA
1 TGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAATCCA
57015354 CTAAATTGCATACTTCA
66 CTAAATTGCATACTTCA
57015371 AGTGAAGAAC
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
87 74 0.97
88 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (87 bp):
TGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAATCCA
CTAAATTGCATACTTCACGTAG
Found at i:57016863 original size:20 final size:21
Alignment explanation
Indices: 57016838--57016878 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
57016828 GAAAATATAT
*
57016838 TTTCCATTCAA-TTTTCCATC
1 TTTCCAGTCAAGTTTTCCATC
57016858 TTTCCAGTCAAGTTTTCCATC
1 TTTCCAGTCAAGTTTTCCATC
57016879 CCCTCAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.20, C:0.29, G:0.05, T:0.46
Consensus pattern (21 bp):
TTTCCAGTCAAGTTTTCCATC
Found at i:57017055 original size:36 final size:36
Alignment explanation
Indices: 57017015--57017087 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
57017005 AATTTATATG
57017015 TATGTTTTCTTACCTTTTATTGTCGATGATCATACC
1 TATGTTTTCTTACCTTTTATTGTCGATGATCATACC
57017051 TATGTTTTCTTACCTTTTATTGTCGATGATCATACC
1 TATGTTTTCTTACCTTTTATTGTCGATGATCATACC
57017087 T
1 T
57017088 TCAATCACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (36 bp):
TATGTTTTCTTACCTTTTATTGTCGATGATCATACC
Found at i:57017531 original size:14 final size:15
Alignment explanation
Indices: 57017505--57017535 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
57017495 TCCAGGTTCA
57017505 TCAACACATTTTTCT
1 TCAACACATTTTTCT
57017520 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
57017534 TC
1 TC
57017536 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:57031253 original size:14 final size:15
Alignment explanation
Indices: 57031229--57031257 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
57031219 CAGGTTCATT
57031229 AACACATTTTTCTTC
1 AACACATTTTTCTTC
57031244 AACA-ATTTTTCTTC
1 AACACATTTTTCTTC
57031258 CCATTTCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (15 bp):
AACACATTTTTCTTC
Found at i:57039095 original size:146 final size:146
Alignment explanation
Indices: 57038892--57039166 Score: 480
Period size: 146 Copynumber: 1.9 Consensus size: 146
57038882 TTATACCTAT
*
57038892 GTTTTTGGTTAAGCGAATCCTAGACGTTTTTCGATTTTCAACTAAACGAGTTACGTGATTATCAA
1 GTTTTTGGTTAAGCGAATCCTAGACGTTTTTCGACTTTCAACTAAACGAGTTACGTGATTATCAA
57038957 GTGAA-TTTTAAAAATAAAAATAAAAATGTCACGCAAGAGAATTTAATAGAAAAATTTTAACAAA
66 GTGAATTTTTAAAAA-AAAAATAAAAATGTCACGCAAGAGAATTTAATAGAAAAATTTTAACAAA
57039021 ATTTTTCAACTAAACGA
130 ATTTTTCAACTAAACGA
* *
57039038 GTTTTTGGTTAAGCGAATCCTAGACGTTTTTTGACTTTCAACTAAACGTGTTACGTGATTATCAA
1 GTTTTTGGTTAAGCGAATCCTAGACGTTTTTCGACTTTCAACTAAACGAGTTACGTGATTATCAA
**
57039103 GTGAATTTTTTAAAAAAAATTTAAAAATGTCACGCAAGAGAATTTAATAGAAAAATTTTAACAA
66 GTGAA-TTTTTAAAAAAAAAATAAAAATGTCACGCAAGAGAATTTAATAGAAAAATTTTAACAA
57039167 GGGTAACGAT
Statistics
Matches: 122, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
146 67 0.55
147 46 0.38
148 9 0.07
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (146 bp):
GTTTTTGGTTAAGCGAATCCTAGACGTTTTTCGACTTTCAACTAAACGAGTTACGTGATTATCAA
GTGAATTTTTAAAAAAAAAATAAAAATGTCACGCAAGAGAATTTAATAGAAAAATTTTAACAAAA
TTTTTCAACTAAACGA
Found at i:57040858 original size:19 final size:18
Alignment explanation
Indices: 57040810--57040860 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
57040800 AACTAAAAAA
*
57040810 TAAAAAATTTA-AAATTT
1 TAAAAAATTTATAAAGTT
*
57040827 TATAAAATCTTATAGAAGTT
1 TAAAAAAT-TTATA-AAGTT
57040847 TAAAAAATTTATAA
1 TAAAAAATTTATAA
57040861 TTAAAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 7 0.25
18 4 0.14
19 6 0.21
20 11 0.39
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (18 bp):
TAAAAAATTTATAAAGTT
Found at i:57041790 original size:18 final size:17
Alignment explanation
Indices: 57041758--57041791 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
57041748 CTGTTTGTGT
*
57041758 TGCTTTTATATGTTATA
1 TGCTTTTAGATGTTATA
57041775 TGCTTTTAAGATGTTAT
1 TGCTTTT-AGATGTTAT
57041792 TTAAATCCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56
Consensus pattern (17 bp):
TGCTTTTAGATGTTATA
Found at i:57042833 original size:16 final size:16
Alignment explanation
Indices: 57042812--57042862 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
57042802 TTTTAATTTT
57042812 TATGTTATGTACATTC
1 TATGTTATGTACATTC
*
57042828 TATGTT-T-TATTATT-
1 TATGTTATGTA-CATTC
*
57042842 TATGTTATGTACATAC
1 TATGTTATGTACATTC
57042858 TATGT
1 TATGT
57042863 CTTATTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
14 8 0.29
15 7 0.25
16 13 0.46
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.55
Consensus pattern (16 bp):
TATGTTATGTACATTC
Found at i:57042836 original size:30 final size:29
Alignment explanation
Indices: 57042802--57042932 Score: 131
Period size: 30 Copynumber: 4.2 Consensus size: 29
57042792 CATAATTTAA
57042802 TTTTAATTTTTATGTTATGTACATTCTATG
1 TTTT-ATTTTTATGTTATGTACATTCTATG
*
57042832 TTTTATTATTTATGTTATGTACATACTATG
1 TTTTATT-TTTATGTTATGTACATTCTATG
*
57042862 TCTTATTATTTTATCAT-TTATGTTATTATT-TATG
1 --TT-TTATTTT-T-ATGTTATG-TA-CATTCTATG
*
57042896 TTTTATTATTTATGTTATCTACATTCTATG
1 TTTTATT-TTTATGTTATGTACATTCTATG
57042926 TTTTATT
1 TTTTATT
57042933 ATTTTATTTA
Statistics
Matches: 85, Mismatches: 5, Indels: 22
0.76 0.04 0.20
Matches are distributed among these distances:
29 6 0.07
30 40 0.47
31 10 0.12
32 8 0.09
33 11 0.13
34 8 0.09
35 2 0.02
ACGTcount: A:0.24, C:0.07, G:0.08, T:0.62
Consensus pattern (29 bp):
TTTTATTTTTATGTTATGTACATTCTATG
Found at i:57042887 original size:12 final size:12
Alignment explanation
Indices: 57042867--57042914 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
57042857 CTATGTCTTA
*
57042867 TTATTTTATCAT
1 TTATGTTATCAT
*
57042879 TTATGTTATTAT
1 TTATGTTATCAT
*
57042891 TTATGTTTTATTAT
1 TTATG--TTATCAT
57042905 TTATGTTATC
1 TTATGTTATC
57042915 TACATTCTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 19 0.61
14 12 0.39
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.67
Consensus pattern (12 bp):
TTATGTTATCAT
Found at i:57042899 original size:26 final size:29
Alignment explanation
Indices: 57042870--57042936 Score: 95
Period size: 26 Copynumber: 2.4 Consensus size: 29
57042860 TGTCTTATTA
*
57042870 TTTTATCATTTATGTTAT-T-ATT-TATG
1 TTTTATTATTTATGTTATCTAATTCTATG
57042896 TTTTATTATTTATGTTATCTACATTCTATG
1 TTTTATTATTTATGTTATCTA-ATTCTATG
57042926 TTTTATTATTT
1 TTTTATTATTT
57042937 TATTTAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 17 0.47
27 1 0.03
29 3 0.08
30 15 0.42
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.66
Consensus pattern (29 bp):
TTTTATTATTTATGTTATCTAATTCTATG
Found at i:57042907 original size:64 final size:67
Alignment explanation
Indices: 57042810--57042939 Score: 203
Period size: 64 Copynumber: 2.0 Consensus size: 67
57042800 AATTTTAATT
*
57042810 TTTATGTTATGTACATTCTATGTTTTATTATTTATGTTATGTACATACTATGTCTTATTATTTTA
1 TTTATGTTATGTA-ATTCTATGTTTTATTATTTATGTTATCTACATACTATGTCTTATTATTTTA
57042875 TCA
65 TCA
* *
57042878 TTTATGTTAT-T-ATT-TATGTTTTATTATTTATGTTATCTACATTCTATGTTTTATTATTTTAT
1 TTTATGTTATGTAATTCTATGTTTTATTATTTATGTTATCTACATACTATGTCTTATTATTTTAT
57042940 TTAATTTATT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
64 45 0.76
65 3 0.05
67 1 0.02
68 10 0.17
ACGTcount: A:0.24, C:0.07, G:0.08, T:0.62
Consensus pattern (67 bp):
TTTATGTTATGTAATTCTATGTTTTATTATTTATGTTATCTACATACTATGTCTTATTATTTTAT
CA
Found at i:57043312 original size:158 final size:156
Alignment explanation
Indices: 57043100--57043481 Score: 552
Period size: 158 Copynumber: 2.4 Consensus size: 156
57043090 AATAAAAATG
* * * *
57043100 AAAATAGTATATTTACTGAAAGTAATAAAATTCGAAAA-AAAAAAAATTACGAACAAAGGGTCAA
1 AAAATAGTATATTT-TTGAAAGTAATAAAATCCGAAAATAAGAAAAA-TACGAACAAAGGGCCAA
* *
57043164 AATAAAGG-TTTTTTACTAAATTTATAAAAAAAACACACAAAAATAATATATTTCAGACATTATG
64 AATAAAGGTTTTTTTA-TAAATTTAT-AAAAAAACACACAAAAATAATACATTTCAAACATTATG
57043228 TACTAAAATAATATAAAATAATAAAATACA
127 TACTAAAATAATATAAAATAATAAAATACA
* *
57043258 AAAATAGTATATCTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATATGAACAAATAGGCCAA
1 AAAATAGTATAT-TTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAACAAA-GGGCCAA
* * * * *
57043323 AATAAGGGTTTTTTTATAAATTTATATAAAAACACACTAAATTAATACATTTCAAACTTTATGTA
64 AATAAAGGTTTTTTTATAAATTTATAAAAAAACACACAAAAATAATACATTTCAAACATTATGTA
*
57043388 CTAAAATAATATAAAATAATAAAATACG
129 CTAAAATAATATAAAATAATAAAATACA
*
57043416 AAAATAGTATATTTTTTGAAAGTAATAAAATCTGAAAATAAGAAAAATACGAACAAAGGGCCAAA
1 AAAATAGTATA-TTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAACAAAGGGCCAAA
57043481 A
65 A
57043482 AATCGGGAAA
Statistics
Matches: 202, Mismatches: 17, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
157 8 0.04
158 156 0.77
159 31 0.15
160 7 0.03
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.28
Consensus pattern (156 bp):
AAAATAGTATATTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAACAAAGGGCCAAAA
TAAAGGTTTTTTTATAAATTTATAAAAAAACACACAAAAATAATACATTTCAAACATTATGTACT
AAAATAATATAAAATAATAAAATACA
Found at i:57043533 original size:27 final size:27
Alignment explanation
Indices: 57043502--57043572 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
57043492 ACATGGCACA
* * *
57043502 GGTGCCGCTTGTGGCAGTGGCATCTTT
1 GGTGCCGCCTATGGCAGTGGCACCTTT
* * * *
57043529 GGTGCTGCCTCTGCCACTGGCACCTTT
1 GGTGCCGCCTATGGCAGTGGCACCTTT
57043556 GGTGCCGCCTATGGCAG
1 GGTGCCGCCTATGGCAG
57043573 ACCCTCGACC
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.08, C:0.30, G:0.34, T:0.28
Consensus pattern (27 bp):
GGTGCCGCCTATGGCAGTGGCACCTTT
Found at i:57045702 original size:18 final size:18
Alignment explanation
Indices: 57045675--57045725 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
57045665 AGTGTTCAAA
57045675 AAGATAATCCACTCCTAC
1 AAGATAATCCACTCCTAC
* *
57045693 AAGGTAATCCATTCCTAC
1 AAGATAATCCACTCCTAC
*
57045711 AAGATAATCAACTCC
1 AAGATAATCCACTCC
57045726 ATTGATTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.39, C:0.29, G:0.08, T:0.24
Consensus pattern (18 bp):
AAGATAATCCACTCCTAC
Found at i:57051507 original size:14 final size:15
Alignment explanation
Indices: 57051483--57051511 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
57051473 CAGGTTCATT
57051483 AACACATTTTTCTTC
1 AACACATTTTTCTTC
57051498 AACA-ATTTTTCTTC
1 AACACATTTTTCTTC
57051512 GCATTTCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (15 bp):
AACACATTTTTCTTC
Found at i:57053706 original size:20 final size:18
Alignment explanation
Indices: 57053655--57053695 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
57053645 TTCTACAATG
57053655 GATAACAGCTCTGGAGAT
1 GATAACAGCTCTGGAGAT
57053673 GATAACAGCTCTGGAGAT
1 GATAACAGCTCTGGAGAT
57053691 GATAA
1 GATAA
57053696 ACTTACTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.22
Consensus pattern (18 bp):
GATAACAGCTCTGGAGAT
Found at i:57053809 original size:27 final size:25
Alignment explanation
Indices: 57053762--57053817 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 25
57053752 TAAAAATATA
57053762 ATTTTATAATCTTAATATTTAAAAT
1 ATTTTATAATCTTAATATTTAAAAT
*
57053787 ATTTTATAACTTTATAATATTTAAAAT
1 ATTTTATAA-TCT-TAATATTTAAAAT
57053814 ATTT
1 ATTT
57053818 AAAGGATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 9 0.32
26 2 0.07
27 17 0.61
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
ATTTTATAATCTTAATATTTAAAAT
Found at i:57055240 original size:129 final size:129
Alignment explanation
Indices: 57055010--57055267 Score: 453
Period size: 129 Copynumber: 2.0 Consensus size: 129
57055000 GGAGTTAAAG
* * *
57055010 ACGATTATATGATAAAAGGCATTGTCTATGGTTTTTGCTGCAGAAAATTGTTAACTTTCGGGATG
1 ACGATTATATGATAAAAGGAATTGTCTATGGTTTCTGCTGCAGAAAATTGTTAACTTTCGAGATG
* *
57055075 ACGCCATTATAAAATTTGTTTGCATGAACTAATTAATCCATAGACTTTAATTATGTACTATGTA
66 ACGCCATTATAAAATTTGTTTGCATGAACTAATTAATACATAGACTTTAACTATGTACTATGTA
* *
57055139 ACGATTGTATGATGAAAGGAATTGTCTATGGTTTCTGCTGCAGAAAATTGTTAACTTTCGAGATG
1 ACGATTATATGATAAAAGGAATTGTCTATGGTTTCTGCTGCAGAAAATTGTTAACTTTCGAGATG
57055204 ACGCCATTATAAAATTTGTTTGCATGAACTAATTAATACATAGACTTTAACTATGTACTATGTA
66 ACGCCATTATAAAATTTGTTTGCATGAACTAATTAATACATAGACTTTAACTATGTACTATGTA
57055268 GGCGTCCTAG
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 122 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.37
Consensus pattern (129 bp):
ACGATTATATGATAAAAGGAATTGTCTATGGTTTCTGCTGCAGAAAATTGTTAACTTTCGAGATG
ACGCCATTATAAAATTTGTTTGCATGAACTAATTAATACATAGACTTTAACTATGTACTATGTA
Found at i:57058336 original size:29 final size:29
Alignment explanation
Indices: 57058304--57058364 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
57058294 ACAGTCAAGC
*
57058304 CCCTAAACTTTCC-AGAAATTACATTTTTG
1 CCCTAAACTTTCCTA-AAATCACATTTTTG
* * *
57058333 CCCTATATTTTCCTAAAATCGCATTTTTG
1 CCCTAAACTTTCCTAAAATCACATTTTTG
57058362 CCC
1 CCC
57058365 CAGAAACTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.39
Consensus pattern (29 bp):
CCCTAAACTTTCCTAAAATCACATTTTTG
Found at i:57058782 original size:13 final size:12
Alignment explanation
Indices: 57058766--57058807 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
57058756 TAGCAACCAA
57058766 AAAGAAAAGGAAG
1 AAAGAAAA-GAAG
57058779 AAAGAAAAGAAG
1 AAAGAAAAGAAG
*
57058791 AGAAGAAGA-AAG
1 A-AAGAAAAGAAG
57058803 AAAGA
1 AAAGA
57058808 GAGAAGAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 4 0.15
12 9 0.33
13 14 0.52
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (12 bp):
AAAGAAAAGAAG
Found at i:57058794 original size:23 final size:23
Alignment explanation
Indices: 57058768--57058815 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
57058758 GCAACCAAAA
*
57058768 AGAA-AAGGAAGAAAGAAAAGAAG
1 AGAAGAAGAAAGAAAG-AAAGAAG
*
57058791 AGAAGAAGAAAGAAAGAGAGAAG
1 AGAAGAAGAAAGAAAGAAAGAAG
57058814 AG
1 AG
57058816 GAGAGGCCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AGAAGAAGAAAGAAAGAAAGAAG
Found at i:57058800 original size:20 final size:18
Alignment explanation
Indices: 57058775--57058814 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 18
57058765 AAAAGAAAAG
57058775 GAAGAAAGAAAAGAAGAGAA
1 GAAGAAAG-AAAG-AGAGAA
57058795 GAAGAAAGAAAGAGAGAA
1 GAAGAAAGAAAGAGAGAA
57058813 GA
1 GA
57058815 GGAGAGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.40
19 4 0.20
20 8 0.40
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
GAAGAAAGAAAGAGAGAA
Found at i:57058923 original size:10 final size:11
Alignment explanation
Indices: 57058891--57058941 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
57058881 TGACCCGAAG
57058891 AAGAAAGAAAA
1 AAGAAAGAAAA
57058902 AAGAAAGAAAA
1 AAGAAAGAAAA
*
57058913 AAGAAGGAAAA
1 AAGAAAGAAAA
*
57058924 AGGGAAAGAAAA
1 A-AGAAAGAAAA
*
57058936 TAGAAA
1 AAGAAA
57058942 TATATATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
11 26 0.76
12 8 0.24
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (11 bp):
AAGAAAGAAAA
Found at i:57059580 original size:17 final size:18
Alignment explanation
Indices: 57059558--57059600 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
57059548 TCGTTTTTAA
57059558 AAAATTTTCAT-GT-TTTC
1 AAAATTTTC-TCGTATTTC
57059575 AAAATTTTCTCGTATTTC
1 AAAATTTTCTCGTATTTC
57059593 AAAATTTT
1 AAAATTTT
57059601 TGACTTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.04
17 11 0.46
18 12 0.50
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.51
Consensus pattern (18 bp):
AAAATTTTCTCGTATTTC
Found at i:57059643 original size:16 final size:16
Alignment explanation
Indices: 57059622--57059712 Score: 74
Period size: 17 Copynumber: 5.4 Consensus size: 16
57059612 GTTTTCAAAA
57059622 AAAATTCTCGTGTTTC
1 AAAATTCTCGTGTTTC
*
57059638 AAAATTGTCGTGTTTTC
1 AAAATTCTCGTG-TTTC
* *
57059655 AAAAATCTTCGTGTTTTT
1 AAAATTC-TCGTG-TTTC
* * *
57059673 AAGAATTTTTGTGTCTC
1 AA-AATTCTCGTGTTTC
*
57059690 TAAAATTCTCGTGTTTT
1 -AAAATTCTCGTGTTTC
57059707 AAAATT
1 AAAATT
57059713 TTTTCGTGTT
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
16 17 0.29
17 21 0.36
18 17 0.29
19 3 0.05
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.47
Consensus pattern (16 bp):
AAAATTCTCGTGTTTC
Found at i:57059659 original size:18 final size:18
Alignment explanation
Indices: 57059621--57059729 Score: 75
Period size: 18 Copynumber: 6.2 Consensus size: 18
57059611 CGTTTTCAAA
57059621 AAAAATTCTCGTG-TTTC
1 AAAAATTCTCGTGTTTTC
*
57059638 -AAAATTGTCGTGTTTTC
1 AAAAATTCTCGTGTTTTC
*
57059655 AAAAA-TCTTCGTGTTTTT
1 AAAAATTC-TCGTGTTTTC
* * * *
57059673 AAGAATTTTTGTG-TCTC
1 AAAAATTCTCGTGTTTTC
*
57059690 TAAAATTCTCGTGTTTT-
1 AAAAATTCTCGTGTTTTC
* * *
57059707 AAAATTTTTTCGTGTTTCC
1 AAAA-ATTCTCGTGTTTTC
57059726 AAAA
1 AAAA
57059730 TAATAATAGT
Statistics
Matches: 68, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
16 11 0.16
17 19 0.28
18 33 0.49
19 5 0.07
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.47
Consensus pattern (18 bp):
AAAAATTCTCGTGTTTTC
Found at i:57059730 original size:35 final size:34
Alignment explanation
Indices: 57059622--57059730 Score: 114
Period size: 35 Copynumber: 3.1 Consensus size: 34
57059612 GTTTTCAAAA
* * *
57059622 AAAATTCTCGTGTTTCAAAA-TTGTCGTGTTTTC
1 AAAATTCTCGTGTTTTAAAATTTTTCGTGTTTCC
* * *
57059655 AAAAATCTTCGTGTTTTTAAGAATTTTT-GTGTCTCT
1 AAAATTC-TCGTG-TTTTAA-AATTTTTCGTGTTTCC
57059691 AAAATTCTCGTGTTTTAAAATTTTTTCGTGTTTCC
1 AAAATTCTCGTGTTTTAAAA-TTTTTCGTGTTTCC
57059726 AAAAT
1 AAAAT
57059731 AATAATAGTA
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
33 8 0.13
34 16 0.26
35 21 0.34
36 13 0.21
37 3 0.05
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.48
Consensus pattern (34 bp):
AAAATTCTCGTGTTTTAAAATTTTTCGTGTTTCC
Found at i:57063940 original size:28 final size:28
Alignment explanation
Indices: 57063908--57063962 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
57063898 AATTAATTTT
57063908 TAATAT-TTTTTGAATTTTTAAAAAATTA
1 TAATATATTTTT-AATTTTTAAAAAATTA
* *
57063936 TAATATATTTTTTATTTTTATAAAATT
1 TAATATATTTTTAATTTTTAAAAAATT
57063963 TTTAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
TAATATATTTTTAATTTTTAAAAAATTA
Found at i:57064000 original size:38 final size:38
Alignment explanation
Indices: 57063911--57064007 Score: 110
Period size: 38 Copynumber: 2.6 Consensus size: 38
57063901 TAATTTTTAA
* *
57063911 TATTTTTTG-AATTTTTAAAAAATTATAATATATTTTT
1 TATTTTTTGAAATTTTTAAAAAATTATAATATACTTTC
* *
57063948 TATTTTTATAAAATTTTTAAATAATCT-TAATA-ACTTTC
1 TATTTTT-TGAAATTTTTAAAAAAT-TATAATATACTTTC
57063986 TATTTTTTGGAAATTTTTAAAA
1 TATTTTTT-GAAATTTTTAAAA
57064008 TTAATTAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
37 8 0.16
38 23 0.46
39 18 0.36
40 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (38 bp):
TATTTTTTGAAATTTTTAAAAAATTATAATATACTTTC
Found at i:57068332 original size:15 final size:16
Alignment explanation
Indices: 57068312--57068343 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
57068302 TTTAAATATA
57068312 TAATAAAA-ATAAAAT
1 TAATAAAACATAAAAT
57068327 TAATAAAACATAAAAT
1 TAATAAAACATAAAAT
57068343 T
1 T
57068344 TTATCATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
TAATAAAACATAAAAT
Found at i:57071544 original size:13 final size:14
Alignment explanation
Indices: 57071520--57071550 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
57071510 AAACATATAT
57071520 AATAAAATTATAAA
1 AATAAAATTATAAA
57071534 AATAAAA-TATAAA
1 AATAAAATTATAAA
57071547 AATA
1 AATA
57071551 TGTATAGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAAAATTATAAA
Found at i:57071606 original size:19 final size:18
Alignment explanation
Indices: 57071578--57071614 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
57071568 GTATATATAG
57071578 AAATAAATAAAAATAAATA
1 AAATAAATAAAAA-AAATA
*
57071597 AAATATATAAAAAAAATA
1 AAATAAATAAAAAAAATA
57071615 TATGTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATAAATAAAAAAAATA
Found at i:57071762 original size:20 final size:20
Alignment explanation
Indices: 57071681--57071767 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 20
57071671 TAATGTACGT
**
57071681 ATATATATTATAAAA-ATGT
1 ATATATATTATAAAATATAA
* *
57071700 ATATATATT-TAGATTATAA
1 ATATATATTATAAAATATAA
57071719 A-ATATA-TA-AAAACTAT--
1 ATATATATTATAAAA-TATAA
*
57071735 ATAAATATTATAAAATATAA
1 ATATATATTATAAAATATAA
57071755 ATATATATGTATA
1 ATATATAT-TATA
57071768 TAAAATAAGA
Statistics
Matches: 51, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
16 1 0.02
17 7 0.14
18 16 0.31
19 16 0.31
20 7 0.14
21 4 0.08
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.40
Consensus pattern (20 bp):
ATATATATTATAAAATATAA
Found at i:57071909 original size:15 final size:15
Alignment explanation
Indices: 57071889--57071929 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
57071879 TAAATGTAAT
57071889 AATAATATATAATA-C
1 AATAATA-ATAATAGC
*
57071904 AATAATGATAATAGC
1 AATAATAATAATAGC
57071919 AATAATAATAA
1 AATAATAATAA
57071930 CAAAAACTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (15 bp):
AATAATAATAATAGC
Found at i:57081055 original size:2 final size:2
Alignment explanation
Indices: 57081050--57081080 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
57081040 TATATAGAGA
57081050 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57081081 AAGAAAAGCA
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57089305 original size:15 final size:15
Alignment explanation
Indices: 57089285--57089314 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
57089275 TTATAATAAA
57089285 AAGTAACTTCCTTTT
1 AAGTAACTTCCTTTT
57089300 AAGTAACTTCCTTTT
1 AAGTAACTTCCTTTT
57089315 CCCCTTGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (15 bp):
AAGTAACTTCCTTTT
Found at i:57090011 original size:19 final size:18
Alignment explanation
Indices: 57089987--57090025 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
57089977 TTCTAACATA
57089987 TATCTACCTAAATAAGATT
1 TATCTACCTAAATAA-ATT
57090006 TATCTACCTAAATAAATT
1 TATCTACCTAAATAAATT
57090024 TA
1 TA
57090026 AAATATATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (18 bp):
TATCTACCTAAATAAATT
Found at i:57091921 original size:6 final size:6
Alignment explanation
Indices: 57091912--57091979 Score: 136
Period size: 6 Copynumber: 11.3 Consensus size: 6
57091902 ATTATTAATA
57091912 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
57091960 TTCTTT TTCTTT TTCTTT TT
1 TTCTTT TTCTTT TTCTTT TT
57091980 GCTTAAGAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTCTTT
Found at i:57092175 original size:111 final size:111
Alignment explanation
Indices: 57091975--57092280 Score: 524
Period size: 111 Copynumber: 2.7 Consensus size: 111
57091965 TTTCTTTTTC
** *
57091975 TTTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAAAGAGACAACAGCCAAGCACCCCACCCT
1 TTTTT-CTTAAGAATATATTGAACCTTTTGACGCGAAAAGAGATGACAGCCAAGCACCCCACCCC
57092040 GGTTACTCAGCCTAACATACTCCTAATTTATTATATTTAAATATATA
65 GGTTACTCAGCCTAACATACTCCTAATTTATTATATTTAAATATATA
*
57092087 TTTTTCTTAAGAATATATTGAACTTTTTGACGCGAAAAGAGATGACAGCCAAGCACCCCACCCCG
1 TTTTTCTTAAGAATATATTGAACCTTTTGACGCGAAAAGAGATGACAGCCAAGCACCCCACCCCG
*
57092152 GTTACTCAACCTAACATACTCCTAATTTATTATATTTAAATATATA
66 GTTACTCAGCCTAACATACTCCTAATTTATTATATTTAAATATATA
*
57092198 TTTTTCTTAAGAATATATTGAACCTTTTGACGC-AAAGAGAGATGACAGTCAAGCACCCCACCCC
1 TTTTTCTTAAGAATATATTGAACCTTTTGACGCGAAA-AGAGATGACAGCCAAGCACCCCACCCC
*
57092262 GGTTACTCAGCCCAACATA
65 GGTTACTCAGCCTAACATA
57092281 TTCTTAAAAA
Statistics
Matches: 184, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
110 3 0.02
111 176 0.96
112 5 0.03
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.30
Consensus pattern (111 bp):
TTTTTCTTAAGAATATATTGAACCTTTTGACGCGAAAAGAGATGACAGCCAAGCACCCCACCCCG
GTTACTCAGCCTAACATACTCCTAATTTATTATATTTAAATATATA
Found at i:57096933 original size:6 final size:6
Alignment explanation
Indices: 57096896--57096938 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
57096886 CCAAACACAC
* *
57096896 CAGTAAA CAGTAA TCAGTAA CGGTAG CAGTAA CAGTAA CAGTA
1 CAGT-AA CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
57096939 TTCAACACAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
6 21 0.68
7 10 0.32
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (6 bp):
CAGTAA
Found at i:57096986 original size:45 final size:45
Alignment explanation
Indices: 57096916--57097022 Score: 169
Period size: 45 Copynumber: 2.4 Consensus size: 45
57096906 TAATCAGTAA
* *
57096916 CGGTAGCAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAAT
1 CGGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAAT
* * *
57096961 CTGTAACAGTAATAGTAACAGTATTCGACACACAAAGTGCCGAAT
1 CGGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAAT
57097006 CGGTAACAGTAACAGTA
1 CGGTAACAGTAACAGTA
57097023 GTCGGCACAT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.21
Consensus pattern (45 bp):
CGGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAAT
Found at i:57105151 original size:31 final size:31
Alignment explanation
Indices: 57105102--57105184 Score: 132
Period size: 31 Copynumber: 2.6 Consensus size: 31
57105092 AACTTTTTAA
57105102 TTTTTTTAATTTTAAAAATATTT-TAAAAATAC
1 TTTTTTTAATTTT-AAAATATTTCT-AAAATAC
57105134 TTTTTTTAATTTTAAAATATTTCTAAAATAC
1 TTTTTTTAATTTTAAAATATTTCTAAAATAC
57105165 TTTTTTTAATTTTTAAAATA
1 TTTTTTTAA-TTTTAAAATA
57105185 AAATTTTAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
31 25 0.51
32 24 0.49
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (31 bp):
TTTTTTTAATTTTAAAATATTTCTAAAATAC
Found at i:57112625 original size:12 final size:12
Alignment explanation
Indices: 57112608--57112633 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
57112598 AAGTGTGCCT
57112608 TCGAAAGACATC
1 TCGAAAGACATC
57112620 TCGAAAGACATC
1 TCGAAAGACATC
57112632 TC
1 TC
57112634 ATCGCATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.19
Consensus pattern (12 bp):
TCGAAAGACATC
Found at i:57123805 original size:34 final size:34
Alignment explanation
Indices: 57123759--57123826 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
57123749 AGAATATTTC
57123759 TCCTCTCCATTGAAGAAGCATGCTATATCTAGAA
1 TCCTCTCCATTGAAGAAGCATGCTATATCTAGAA
57123793 TCCTC-CCTATTGAAGAAGCATGCTATATCTAGAA
1 TCCTCTCC-ATTGAAGAAGCATGCTATATCTAGAA
57123827 ATATATTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 2 0.06
34 31 0.94
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (34 bp):
TCCTCTCCATTGAAGAAGCATGCTATATCTAGAA
Found at i:57129794 original size:15 final size:16
Alignment explanation
Indices: 57129774--57129805 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
57129764 TTTAAATATA
57129774 TAATAAAA-ATAAAAT
1 TAATAAAACATAAAAT
57129789 TAATAAAACATAAAAT
1 TAATAAAACATAAAAT
57129805 T
1 T
57129806 TTATCATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
TAATAAAACATAAAAT
Found at i:57143614 original size:3 final size:3
Alignment explanation
Indices: 57143606--57143637 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
57143596 GGTTTGTGTT
57143606 TTA TTA TTA TTA TTA TTA TTA TT- TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
57143638 CATATCTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:57144141 original size:2 final size:2
Alignment explanation
Indices: 57144134--57144172 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
57144124 AACTCGTTGT
57144134 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57144173 TACAAATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57145063 original size:22 final size:22
Alignment explanation
Indices: 57145012--57145060 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
57145002 AGTGTATTTA
*
57145012 ATTA-TTATTTAAAGATATATG
1 ATTATTTATTTAAAAATATATG
*
57145033 ATTATTTATTTAAAAATGTAT-
1 ATTATTTATTTAAAAATATATG
57145054 ATTATTT
1 ATTATTT
57145061 TATATAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (22 bp):
ATTATTTATTTAAAAATATATG
Found at i:57149929 original size:15 final size:14
Alignment explanation
Indices: 57149908--57149943 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
57149898 ATAATCCTTA
*
57149908 ATAATTATCTTAAT
1 ATAATTATCCTAAT
57149922 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
57149937 ATAATTA
1 ATAATTA
57149944 AAATAGAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:57157976 original size:10 final size:10
Alignment explanation
Indices: 57157942--57157984 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
57157932 TAAATTCCCA
57157942 AAAGATAAAT
1 AAAGATAAAT
* ** *
57157952 ACATTTAATT
1 AAAGATAAAT
57157962 AAAGATAAAT
1 AAAGATAAAT
57157972 AAAGATAAAT
1 AAAGATAAAT
57157982 AAA
1 AAA
57157985 ATTAAATCCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:57158034 original size:15 final size:14
Alignment explanation
Indices: 57158013--57158048 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
57158003 ATAATCTTTA
*
57158013 ATAATTATCTTAAT
1 ATAATTATCCTAAT
57158027 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
57158042 ATAATTA
1 ATAATTA
57158049 AAATAAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:57162918 original size:23 final size:23
Alignment explanation
Indices: 57162888--57162998 Score: 213
Period size: 23 Copynumber: 4.8 Consensus size: 23
57162878 GTTTAGTTCC
57162888 CATGCAAAGGTGGCCATGCACGA
1 CATGCAAAGGTGGCCATGCACGA
57162911 CATGCAAAGGTGGCCATGCACGA
1 CATGCAAAGGTGGCCATGCACGA
57162934 CATGCAAAGGTGGCCATGCACGA
1 CATGCAAAGGTGGCCATGCACGA
57162957 CATGCAAAGGTGGCCATGCACGA
1 CATGCAAAGGTGGCCATGCACGA
*
57162980 CATGCAAAGGTGGTCATGC
1 CATGCAAAGGTGGCCATGC
57162999 TCGAAGAAAT
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
23 87 1.00
ACGTcount: A:0.30, C:0.25, G:0.31, T:0.14
Consensus pattern (23 bp):
CATGCAAAGGTGGCCATGCACGA
Found at i:57177952 original size:14 final size:15
Alignment explanation
Indices: 57177926--57177956 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
57177916 TCCAGGTTCA
57177926 TCAACACATTTTTCT
1 TCAACACATTTTTCT
57177941 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
57177955 TC
1 TC
57177957 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:57181081 original size:17 final size:17
Alignment explanation
Indices: 57181059--57181093 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
57181049 ATTTAATTAA
57181059 ATAAATTATTAAAA-ATT
1 ATAAA-TATTAAAATATT
57181076 ATAAATATTAAAATATT
1 ATAAATATTAAAATATT
57181093 A
1 A
57181094 GATAATAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAATATTAAAATATT
Found at i:57183381 original size:17 final size:17
Alignment explanation
Indices: 57183359--57183396 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
57183349 AAATTTACAT
57183359 AAGAAGACTAGCGAAAA
1 AAGAAGACTAGCGAAAA
* *
57183376 AAGAAGATTAGCGAAAG
1 AAGAAGACTAGCGAAAA
57183393 AAGA
1 AAGA
57183397 GCTTTAGTCC
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:0.58, C:0.08, G:0.26, T:0.08
Consensus pattern (17 bp):
AAGAAGACTAGCGAAAA
Found at i:57190041 original size:3 final size:3
Alignment explanation
Indices: 57190033--57190057 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
57190023 AGGAAAGACA
57190033 GGT GGT GGT GGT GGT GGT GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT G
57190058 AGAAACTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
GGT
Found at i:57194838 original size:3 final size:3
Alignment explanation
Indices: 57194832--57194869 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
57194822 AATAAACCTC
57194832 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
57194870 CTTGTTCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:57195428 original size:2 final size:2
Alignment explanation
Indices: 57195421--57195470 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
57195411 CAACTTAGAC
57195421 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
57195463 AT AT AT AT
1 AT AT AT AT
57195471 CTATCAAACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57196442 original size:14 final size:15
Alignment explanation
Indices: 57196416--57196446 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
57196406 TCCAGGTTCA
57196416 TCAACACATTTTTCT
1 TCAACACATTTTTCT
57196431 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
57196445 TC
1 TC
57196447 CCAGTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:57201015 original size:12 final size:12
Alignment explanation
Indices: 57200998--57201022 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57200988 AAAATAGAGG
57200998 TTATTTTCAAAA
1 TTATTTTCAAAA
57201010 TTATTTTCAAAA
1 TTATTTTCAAAA
57201022 T
1 T
57201023 CGATTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATTTTCAAAA
Found at i:57202920 original size:31 final size:31
Alignment explanation
Indices: 57202882--57202942 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
57202872 TATCAAATGA
* *
57202882 TCACTAAATTATTTTAAAATTTTTATTTAAG
1 TCACTAAATTATCTGAAAATTTTTATTTAAG
57202913 TCACTAAATTATCTGAAAATTTTTATTTAA
1 TCACTAAATTATCTGAAAATTTTTATTTAA
57202943 ATTAGTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.49
Consensus pattern (31 bp):
TCACTAAATTATCTGAAAATTTTTATTTAAG
Found at i:57205979 original size:24 final size:25
Alignment explanation
Indices: 57205933--57205980 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
57205923 AAAATAATCT
* * *
57205933 AAATTAACTAGAGTTTGATTGAAAC
1 AAATAAACTAGAGTTTAACTGAAAC
57205958 AAATAAAC-AGAGTTTAACTGAAA
1 AAATAAACTAGAGTTTAACTGAAA
57205981 AATTATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (25 bp):
AAATAAACTAGAGTTTAACTGAAAC
Found at i:57215236 original size:21 final size:21
Alignment explanation
Indices: 57215206--57215246 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
57215196 TTATTCAAAT
57215206 TTTAACAGTTTATATAAAAAA
1 TTTAACAGTTTATATAAAAAA
* *
57215227 TTTAATAGTTTATATTAAAA
1 TTTAACAGTTTATATAAAAA
57215247 TAAGTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (21 bp):
TTTAACAGTTTATATAAAAAA
Found at i:57216772 original size:14 final size:15
Alignment explanation
Indices: 57216746--57216776 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
57216736 TCCAGGTTCA
57216746 TCAACACATTTTTCT
1 TCAACACATTTTTCT
57216761 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
57216775 TC
1 TC
57216777 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:57224788 original size:60 final size:61
Alignment explanation
Indices: 57224681--57224798 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 61
57224671 GATAAATTAC
** *
57224681 ATTAAATATCACTAAATTATTAATAAGTTTATATTTTGGTCATTGAATT-T-TAAAAAGTT
1 ATTAAATATCACTAAATTATTAATAAGTTTATATTTAAGTCACTGAATTATCTAAAAAGTT
* *
57224740 ATTAAATGATCACTAAATTATTTAA-AATTTTTTATTTAAGTCACTGAATTATCTAAAAA
1 ATTAAAT-ATCACTAAATTA-TTAATAAGTTTATATTTAAGTCACTGAATTATCTAAAAA
57224799 AATTTATTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
59 7 0.14
60 32 0.64
61 5 0.10
62 6 0.12
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (61 bp):
ATTAAATATCACTAAATTATTAATAAGTTTATATTTAAGTCACTGAATTATCTAAAAAGTT
Found at i:57230680 original size:87 final size:87
Alignment explanation
Indices: 57230525--57230691 Score: 282
Period size: 87 Copynumber: 1.9 Consensus size: 87
57230515 TTCAGCACTT
* *
57230525 TTAATGCATTCATATTCTCGGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAACCTATT
1 TTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAACCTACT
57230590 AAATTGCATACTTCACGTAGTG
66 AAATTGCATACTTCACGTAGTG
* *
57230612 TTAATGCATTGATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCAGCCGAATCC-AC
1 TTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAA-CCTAC
57230676 TAAATTGCATACTTCA
65 TAAATTGCATACTTCA
57230692 AGTGAAGAAC
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 73 0.97
88 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (87 bp):
TTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAACCTACT
AAATTGCATACTTCACGTAGTG
Found at i:57232388 original size:36 final size:36
Alignment explanation
Indices: 57232348--57232416 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
57232338 TATATGTATA
57232348 TTTTCTTACCTTTTATTGTCGATGATCATACCTATG
1 TTTTCTTACCTTTTATTGTCGATGATCATACCTATG
57232384 TTTTCTTACCTTTTATTGTCGATGATCATACCT
1 TTTTCTTACCTTTTATTGTCGATGATCATACCT
57232417 TCAATCACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.19, C:0.20, G:0.10, T:0.51
Consensus pattern (36 bp):
TTTTCTTACCTTTTATTGTCGATGATCATACCTATG
Found at i:57232861 original size:14 final size:15
Alignment explanation
Indices: 57232836--57232865 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
57232826 CCAGGTTCAA
57232836 CAACACATTTTTCTT
1 CAACACATTTTTCTT
57232851 CAACA-ATTTTTCTT
1 CAACACATTTTTCTT
57232865 C
1 C
57232866 CCATTTCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (15 bp):
CAACACATTTTTCTT
Found at i:57240777 original size:28 final size:30
Alignment explanation
Indices: 57240720--57240775 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
57240710 CAATTGTACG
**
57240720 ATCAAGGATTTTATATCATTTTTTATTTAT
1 ATCAAGGATTTTATATCATTTAGTATTTAT
57240750 ATCAAGGA-TTT-TATCATGTTAGTATT
1 ATCAAGGATTTTATATCAT-TTAGTATT
57240776 ATGAACACGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 6 0.26
29 9 0.39
30 8 0.35
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (30 bp):
ATCAAGGATTTTATATCATTTAGTATTTAT
Found at i:57244329 original size:14 final size:15
Alignment explanation
Indices: 57244305--57244333 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
57244295 CAGGTTCATT
57244305 AACACATTTTTCTTC
1 AACACATTTTTCTTC
57244320 AACA-ATTTTTCTTC
1 AACACATTTTTCTTC
57244334 CCATTTCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (15 bp):
AACACATTTTTCTTC
Found at i:57247971 original size:35 final size:34
Alignment explanation
Indices: 57247932--57248011 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 34
57247922 AATTTAATTT
57247932 ATATTTTATTATTTGATTCA-AATATAATCTGT-AAA
1 ATATTTTATTATTTGATT-AGAATATAAT-T-TAAAA
*
57247967 ATATTTTGA-TATTTTATTATGAATATAATTTAAAA
1 ATATTTT-ATTATTTGATTA-GAATATAATTTAAAA
57248002 ATATTTTATT
1 ATATTTTATT
57248012 GTACATTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
34 3 0.08
35 27 0.69
36 9 0.23
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (34 bp):
ATATTTTATTATTTGATTAGAATATAATTTAAAA
Found at i:57248322 original size:21 final size:21
Alignment explanation
Indices: 57248294--57248348 Score: 94
Period size: 21 Copynumber: 2.6 Consensus size: 21
57248284 ACCGCTGTTT
57248294 CTAATCTCACCGCTACAGTATC
1 CTAATCTCACCGCTACAGTA-C
57248316 C-AATCTCACCGCTACAGTAC
1 CTAATCTCACCGCTACAGTAC
57248336 CTAATCTCACCGC
1 CTAATCTCACCGC
57248349 CACCGCTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.91
22 1 0.03
ACGTcount: A:0.27, C:0.40, G:0.09, T:0.24
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAC
Found at i:57254471 original size:5 final size:5
Alignment explanation
Indices: 57254463--57254517 Score: 62
Period size: 5 Copynumber: 11.2 Consensus size: 5
57254453 TATTTAATTT
*
57254463 ATATA ATATA ATACA ATATA ATATA ATATA TTATATA ATA-A A-ATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA ATATA --ATATA ATATA ATATA ATATA
57254512 ATATA A
1 ATATA A
57254518 AACATAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.19
5 29 0.67
7 5 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:57254498 original size:17 final size:16
Alignment explanation
Indices: 57254461--57254517 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 16
57254451 TCTATTTAAT
57254461 TTATATAATATAATACA
1 TTATATAATATAATA-A
57254478 --ATATAATATAATATA
1 TTATATAATATAATA-A
*
57254493 TTATATAATAAAATAA
1 TTATATAATATAATAA
57254509 TATATATAA
1 T-TATATAA
57254518 AACATAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 14 0.40
16 2 0.06
17 19 0.54
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
TTATATAATATAATAA
Found at i:57263831 original size:19 final size:18
Alignment explanation
Indices: 57263807--57263845 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
57263797 TTCTAACATA
57263807 TATCTACCTAAATAAGATT
1 TATCTACCTAAATAA-ATT
57263826 TATCTACCTAAATAAATT
1 TATCTACCTAAATAAATT
57263844 TA
1 TA
57263846 AAATATATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (18 bp):
TATCTACCTAAATAAATT
Found at i:57265687 original size:6 final size:6
Alignment explanation
Indices: 57265678--57265739 Score: 124
Period size: 6 Copynumber: 10.3 Consensus size: 6
57265668 ACTATTAATA
57265678 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
57265726 TTCTTT TTCTTT TT
1 TTCTTT TTCTTT TT
57265740 GCTTAAGAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTCTTT
Found at i:57265935 original size:111 final size:111
Alignment explanation
Indices: 57265735--57266040 Score: 513
Period size: 111 Copynumber: 2.7 Consensus size: 111
57265725 TTTCTTTTTC
* ** *
57265735 TTTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAAAGAGACAACAGCCAAGCACCCCACCCT
1 TTTTT-CTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCC
*
57265800 GGTTACTCAGCCTAACATACTCCTAATTTATTATATTTAAATATATA
65 GGTTACTCAGCCCAACATACTCCTAATTTATTATATTTAAATATATA
* *
57265847 TTTTTCTTAAGAATATATTGAACTTTTTGACGCGAAGAGAGATGATAGCCAAGCACCCCACCCCG
1 TTTTTCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCCG
*
57265912 GTTACTCAACCCAACATACTCCTAATTTATTATATTTAAATATATA
66 GTTACTCAGCCCAACATACTCCTAATTTATTATATTTAAATATATA
* *
57265958 TTTTTCTTAAGAATATATTGAACCTTTTGACGCAAAGAGAGATGACAGTCAAGCACCCCACCCCG
1 TTTTTCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCCG
57266023 GTTACTCAGCCCAACATA
66 GTTACTCAGCCCAACATA
57266041 TTCTTAAAAA
Statistics
Matches: 181, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
111 176 0.97
112 5 0.03
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (111 bp):
TTTTTCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCCG
GTTACTCAGCCCAACATACTCCTAATTTATTATATTTAAATATATA
Found at i:57270690 original size:6 final size:6
Alignment explanation
Indices: 57270653--57270707 Score: 74
Period size: 6 Copynumber: 8.8 Consensus size: 6
57270643 CCAAACACAC
* *
57270653 CAGTAAA CAGTAA TCAGTAA CGGTAG CAGTAA CAGTAA CAGTAA CAGTAA
1 CAGT-AA CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA
57270703 CAGTA
1 CAGTA
57270708 TTCAACACAC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
6 33 0.77
7 10 0.23
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.18
Consensus pattern (6 bp):
CAGTAA
Found at i:57270738 original size:45 final size:45
Alignment explanation
Indices: 57270687--57270791 Score: 174
Period size: 45 Copynumber: 2.3 Consensus size: 45
57270677 AGCAGTAACA
* *
57270687 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCT
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCG
* *
57270732 GTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAATCG
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCG
57270777 GTAACAGTAACAGTA
1 GTAACAGTAACAGTA
57270792 GTCGGCACAT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCG
Found at i:57278504 original size:28 final size:27
Alignment explanation
Indices: 57278448--57278506 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
57278438 GGGTTTAAAA
**
57278448 TTCAAATTCAAGGTTGTAAGTTCTTAG
1 TTCAAATTCAAGGTTGTAAGTTCGGAG
*
57278475 TTCAAGATTC-AGTGTTTTAAGTTCGGAG
1 TTCAA-ATTCAAG-GTTGTAAGTTCGGAG
57278503 TTCA
1 TTCA
57278507 GGGTTCATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (27 bp):
TTCAAATTCAAGGTTGTAAGTTCGGAG
Found at i:57291954 original size:18 final size:18
Alignment explanation
Indices: 57291912--57291954 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
57291902 TTTAAAATTT
57291912 TAATAAAATATATAATAG
1 TAATAAAATATATAATAG
* *
57291930 TAGTAAAATTTAT-ATAG
1 TAATAAAATATATAATAG
57291947 TAAATAAA
1 T-AATAAA
57291955 TGGGTAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (18 bp):
TAATAAAATATATAATAG
Found at i:57316746 original size:6 final size:6
Alignment explanation
Indices: 57316735--57316760 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
57316725 TAGCAAAGAA
57316735 TTCACT TTCACT TTCACT TTCACT TT
1 TTCACT TTCACT TTCACT TTCACT TT
57316761 TTTTTTTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.54
Consensus pattern (6 bp):
TTCACT
Found at i:57322666 original size:27 final size:31
Alignment explanation
Indices: 57322627--57322690 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 31
57322617 AATATTATTA
57322627 TATTAATAATAAAT-TT-T-ATTTTTAAAAT
1 TATTAATAATAAATATTATAATTTTTAAAAT
* *
57322655 T-TTAATATTAAATATTATAATTTTTAATAT
1 TATTAATAATAAATATTATAATTTTTAAAAT
57322685 TATTAA
1 TATTAA
57322691 ACATTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 11 0.37
28 3 0.10
29 1 0.03
30 11 0.37
31 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
TATTAATAATAAATATTATAATTTTTAAAAT
Found at i:57322683 original size:15 final size:15
Alignment explanation
Indices: 57322644--57322687 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
57322634 AATAAATTTT
* *
57322644 ATTTTTAAAATTTTA
1 ATTTTTAATATTATA
* *
57322659 ATATTAAATATTATA
1 ATTTTTAATATTATA
57322674 ATTTTTAATATTAT
1 ATTTTTAATATTAT
57322688 TAAACATTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTTAATATTATA
Found at i:57322734 original size:16 final size:16
Alignment explanation
Indices: 57322715--57322750 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
57322705 TTATTTATTT
57322715 TATTAATTTAATAAAG
1 TATTAATTTAATAAAG
*
57322731 TATTAATTTAGTAAAG
1 TATTAATTTAATAAAG
57322747 TATT
1 TATT
57322751 TAATATGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (16 bp):
TATTAATTTAATAAAG
Found at i:57322769 original size:17 final size:18
Alignment explanation
Indices: 57322749--57322782 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
57322739 TAGTAAAGTA
*
57322749 TTTAAT-ATGAATTTTAT
1 TTTAATAATAAATTTTAT
57322766 TTTAATAATAAATTTTA
1 TTTAATAATAAATTTTA
57322783 AAAATAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTAATAATAAATTTTAT
Found at i:57323151 original size:14 final size:14
Alignment explanation
Indices: 57323132--57323168 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
57323122 GTTAGTAATT
57323132 AGATCTAAATTTTG
1 AGATCTAAATTTTG
57323146 AGATCTAAATTTTG
1 AGATCTAAATTTTG
*
57323160 AAATCTAAA
1 AGATCTAAA
57323169 AAGTGTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (14 bp):
AGATCTAAATTTTG
Found at i:57323196 original size:19 final size:19
Alignment explanation
Indices: 57323174--57323211 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
57323164 CTAAAAAGTG
57323174 TGACTAAATTTCCAAAATA
1 TGACTAAATTTCCAAAATA
57323193 TGACTAAATTTCCAAAATA
1 TGACTAAATTTCCAAAATA
57323212 GAAGTATAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (19 bp):
TGACTAAATTTCCAAAATA
Found at i:57323692 original size:14 final size:14
Alignment explanation
Indices: 57323673--57323706 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
57323663 AAAGTTATTC
57323673 TATTTTTTAAAAAT
1 TATTTTTTAAAAAT
*
57323687 TATTTTTTAAAAGT
1 TATTTTTTAAAAAT
57323701 TATTTT
1 TATTTT
57323707 CAATGAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
TATTTTTTAAAAAT
Found at i:57323821 original size:2 final size:2
Alignment explanation
Indices: 57323814--57323851 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
57323804 ATGCATCTTA
57323814 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
57323852 GTGTGTGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57330610 original size:54 final size:54
Alignment explanation
Indices: 57330492--57330600 Score: 193
Period size: 54 Copynumber: 2.0 Consensus size: 54
57330482 TACTATTATG
57330492 TAAATATTAAAAAATGTTAATTTTTATAAATTTTAATAAAATAAAATAAAATAA
1 TAAATATTAAAAAATGTTAATTTTTATAAATTTTAATAAAATAAAATAAAATAA
*
57330546 TAAATATTAAAAAATGTTAATTTTT-TAAAATTTTAATAAAATAAAATAATATAA
1 TAAATATTAAAAAATGTTAATTTTTAT-AAATTTTAATAAAATAAAATAAAATAA
57330600 T
1 T
57330601 GATAGTTAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
53 1 0.02
54 52 0.98
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (54 bp):
TAAATATTAAAAAATGTTAATTTTTATAAATTTTAATAAAATAAAATAAAATAA
Found at i:57337347 original size:7 final size:7
Alignment explanation
Indices: 57337330--57337363 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
57337320 GTTATAAATT
57337330 TTAAAATA
1 TTAAAA-A
57337338 TTAAAAA
1 TTAAAAA
57337345 TTAAAAA
1 TTAAAAA
*
57337352 ATAAAAA
1 TTAAAAA
57337359 TTAAA
1 TTAAA
57337364 TTTCAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Found at i:57337364 original size:36 final size:36
Alignment explanation
Indices: 57337324--57337396 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
57337314 TTAACGGTTA
*
57337324 TAAATTTTAAAATAT-TAAAAATTA-AAAAATAAAAAT
1 TAAA-TTTAAAATATATAAAAAATACAAAAA-AAAAAT
* *
57337360 TAAATTTCAAATTTATAAAAAATACAAAAAAAAAAT
1 TAAATTTAAAATATATAAAAAATACAAAAAAAAAAT
57337396 T
1 T
57337397 GTTACATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 8 0.25
36 19 0.59
37 5 0.16
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (36 bp):
TAAATTTAAAATATATAAAAAATACAAAAAAAAAAT
Found at i:57338122 original size:41 final size:41
Alignment explanation
Indices: 57338046--57338202 Score: 194
Period size: 40 Copynumber: 3.8 Consensus size: 41
57338036 ATAAATACCA
*
57338046 AAAAATTATTTTAAAAATTAAAATAAAAATTAAAAAAACTATTTT
1 AAAAA-TATTTT-AAAATT-AAA-AAAAATTAAAAAAAGTATTTT
57338091 AAAAATATTTTAAAATTAAAAAAAATT-AAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
* * * * *
57338131 AAAAAAAATTTAAAATTTAAAAAATTTAATAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
*
57338172 AAAAGTATTTTAAAATT-AAAAAAA-TAAAAAA
1 AAAAATATTTTAAAATTAAAAAAAATTAAAAAA
57338203 TAATAAAAAT
Statistics
Matches: 100, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
39 6 0.06
40 41 0.41
41 33 0.33
42 3 0.03
43 6 0.06
44 6 0.06
45 5 0.05
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.34
Consensus pattern (41 bp):
AAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
Found at i:57338136 original size:23 final size:23
Alignment explanation
Indices: 57338106--57338175 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
57338096 TATTTTAAAA
57338106 TTAAAAAAAATTAAAAAAGTATT
1 TTAAAAAAAATTAAAAAAGTATT
*
57338129 TTAAAAAAAATT--TAAA--A-T
1 TTAAAAAAAATTAAAAAAGTATT
*
57338147 TT-AAAAAATTTAATAAAAGTATT
1 TTAAAAAAAATTAA-AAAAGTATT
57338170 TTAAAA
1 TTAAAA
57338176 GTATTTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 13
0.70 0.06 0.25
Matches are distributed among these distances:
17 8 0.22
18 3 0.08
19 1 0.03
20 3 0.08
21 3 0.08
22 1 0.03
23 15 0.41
24 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (23 bp):
TTAAAAAAAATTAAAAAAGTATT
Found at i:57340685 original size:24 final size:22
Alignment explanation
Indices: 57340656--57340713 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 22
57340646 GAATTTTTAT
57340656 AATTTTTTAAAAATATAAATTTTG
1 AATTTTTTAAAAA-AT-AATTTTG
*
57340680 AATTTTTTAAAAAATTATTTTG
1 AATTTTTTAAAAAATAATTTTG
*
57340702 AATTTTTGAAAA
1 AATTTTTTAAAA
57340714 TTATTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 17 0.53
23 2 0.06
24 13 0.41
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
AATTTTTTAAAAAATAATTTTG
Found at i:57340699 original size:22 final size:22
Alignment explanation
Indices: 57340656--57340729 Score: 82
Period size: 24 Copynumber: 3.4 Consensus size: 22
57340646 GAATTTTTAT
*
57340656 AATTTTTTAAAAATATAAATTTTG
1 AATTTTTTAAAAA-AT-TATTTTG
57340680 AATTTTTTAAAAAATTATTTTG
1 AATTTTTTAAAAAATTATTTTG
*
57340702 AA-TTTTT-GAAAATTATTTT-
1 AATTTTTTAAAAAATTATTTTG
57340721 AATTATTTT
1 AATT-TTTT
57340730 TTTGTAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
19 2 0.04
20 12 0.26
21 9 0.20
22 8 0.17
23 2 0.04
24 13 0.28
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (22 bp):
AATTTTTTAAAAAATTATTTTG
Found at i:57340699 original size:56 final size:56
Alignment explanation
Indices: 57340617--57340722 Score: 137
Period size: 56 Copynumber: 1.9 Consensus size: 56
57340607 AAATATTTTA
* *
57340617 AAATTTTAACTTTTTAAATATATATTTTGGAATTTTT-ATAATT-TTTTAAAAATAT
1 AAATTTTAACTTTTTAAAAATATATTTT-GAATTTTTGAAAATTATTTTAAAAATAT
*
57340672 AAATTTTGAATTTTTTAAAAA-ATTATTTTGAATTTTTGAAAATTATTTTAA
1 AAATTTT-AACTTTTTAAAAATA-TATTTTGAATTTTTGAAAATTATTTTAA
57340723 TTATTTTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
55 16 0.36
56 22 0.50
57 6 0.14
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.54
Consensus pattern (56 bp):
AAATTTTAACTTTTTAAAAATATATTTTGAATTTTTGAAAATTATTTTAAAAATAT
Found at i:57340713 original size:20 final size:21
Alignment explanation
Indices: 57340659--57340724 Score: 73
Period size: 20 Copynumber: 3.1 Consensus size: 21
57340649 TTTTTATAAT
*
57340659 TTTTTAAAAATATAAATTTTGAA
1 TTTTTAAAAA-AT-TATTTTGAA
57340682 TTTTTTAAAAAATTATTTTGAA
1 -TTTTTAAAAAATTATTTTGAA
*
57340704 TTTTT-GAAAATTATTTT-AA
1 TTTTTAAAAAATTATTTTGAA
57340723 TT
1 TT
57340725 ATTTTTTTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 4 0.10
20 11 0.28
21 5 0.12
22 8 0.20
23 2 0.05
24 10 0.25
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTTTAAAAAATTATTTTGAA
Found at i:57342160 original size:6 final size:6
Alignment explanation
Indices: 57342151--57342192 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
57342141 GGATTTTAAT
*
57342151 TAATCC TAATCC TAATCC TAATCC TAATCC TAATCG TAATCC
1 TAATCC TAATCC TAATCC TAATCC TAATCC TAATCC TAATCC
57342193 AACTCTATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.33
Consensus pattern (6 bp):
TAATCC
Found at i:57342604 original size:46 final size:46
Alignment explanation
Indices: 57342546--57342639 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
57342536 ACATGTAAGG
57342546 ATCTGAGAAATCACCCTCATGTTCTAACTTGAATAGAGTAAGATTT
1 ATCTGAGAAATCACCCTCATGTTCTAACTTGAATAGAGTAAGATTT
57342592 ATCTGAGAAATCACCCTCATGTTCTAACTTGAATAGAGTAAGATTT
1 ATCTGAGAAATCACCCTCATGTTCTAACTTGAATAGAGTAAGATTT
57342638 AT
1 AT
57342640 GATCAAGTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (46 bp):
ATCTGAGAAATCACCCTCATGTTCTAACTTGAATAGAGTAAGATTT
Found at i:57344607 original size:20 final size:20
Alignment explanation
Indices: 57344565--57344607 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
57344555 TTTTATATAT
** * *
57344565 ATTTTTAGATTTTTTTTAGA
1 ATTTTTAGAAATTTTTAAAA
57344585 ATTTTTAGAAATTTTTAAAA
1 ATTTTTAGAAATTTTTAAAA
57344605 ATT
1 ATT
57344608 ATTTTAATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (20 bp):
ATTTTTAGAAATTTTTAAAA
Found at i:57358148 original size:21 final size:20
Alignment explanation
Indices: 57358110--57358148 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
57358100 TGTTGGGTTA
*
57358110 ATTGATATGGAATTATGTGC
1 ATTGATATGGAATGATGTGC
*
57358130 ATTGAGTATTGAATGATGT
1 ATTGA-TATGGAATGATGT
57358149 ACCTTGTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.31, C:0.03, G:0.26, T:0.41
Consensus pattern (20 bp):
ATTGATATGGAATGATGTGC
Found at i:57359694 original size:39 final size:39
Alignment explanation
Indices: 57359651--57359726 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
57359641 TATAGGTAAC
57359651 GAGTTTAACAGAGTTTCAAGTTCGGATCGAGGAACTGCT
1 GAGTTTAACAGAGTTTCAAGTTCGGATCGAGGAACTGCT
* * * *
57359690 GAGTTTAACTGAGTTTCGAGTTTGGATTGAGGAACTG
1 GAGTTTAACAGAGTTTCAAGTTCGGATCGAGGAACTG
57359727 TTTATCAGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.32
Consensus pattern (39 bp):
GAGTTTAACAGAGTTTCAAGTTCGGATCGAGGAACTGCT
Found at i:57360626 original size:132 final size:133
Alignment explanation
Indices: 57360424--57360688 Score: 496
Period size: 132 Copynumber: 2.0 Consensus size: 133
57360414 CTTTCCTTAA
* *
57360424 AGACACAAGATTAATTGGTCCACTAATTCATAAATGCTAGATTCTTTCATGCAAATCAGACATCA
1 AGACAAAAGATTAATTGGCCCACTAATTCATAAATGCTAGATTCTTTCATGCAAATCAGACATCA
*
57360489 AACAAAGGAACAAAGACCCACTCACCTTTATATATGTGTAATATATGCAGAGATTGAATATTATA
66 AACAAAGGAACAAAGACCCACTCACCTTTATATATGTGTAATATATGCAGAGATTGAATATCATA
57360554 TTT
131 TTT
57360557 AGACAAAAGATTAATTGGCCCACTAATTCAT-AATGCTAGATTCTTTCATGCAAATCAGACATCA
1 AGACAAAAGATTAATTGGCCCACTAATTCATAAATGCTAGATTCTTTCATGCAAATCAGACATCA
57360621 AACAAAGGAACAAAGACCCACTCACCTTTATATATGTGTAATATATGCAGAGATTGAATATCATA
66 AACAAAGGAACAAAGACCCACTCACCTTTATATATGTGTAATATATGCAGAGATTGAATATCATA
57360686 TTT
131 TTT
57360689 TAAAAAATAA
Statistics
Matches: 129, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
132 100 0.78
133 29 0.22
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (133 bp):
AGACAAAAGATTAATTGGCCCACTAATTCATAAATGCTAGATTCTTTCATGCAAATCAGACATCA
AACAAAGGAACAAAGACCCACTCACCTTTATATATGTGTAATATATGCAGAGATTGAATATCATA
TTT
Found at i:57365085 original size:12 final size:13
Alignment explanation
Indices: 57365059--57365083 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57365049 TCATATATAT
57365059 TTTAAAAAATAAA
1 TTTAAAAAATAAA
57365072 TTTAAAAAATAA
1 TTTAAAAAATAA
57365084 TTAATTGAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTTAAAAAATAAA
Found at i:57366553 original size:10 final size:10
Alignment explanation
Indices: 57366538--57366580 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
57366528 GTTTTTAAGT
57366538 TTATAATATA
1 TTATAATATA
57366548 TTATAATATA
1 TTATAATATA
57366558 TTAT-AT-TA
1 TTATAATATA
* *
57366566 TTTTTATATA
1 TTATAATATA
57366576 TTATA
1 TTATA
57366581 TAATTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 5 0.18
9 4 0.14
10 19 0.68
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTATAATATA
Found at i:57367699 original size:7 final size:7
Alignment explanation
Indices: 57367687--57367713 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
57367677 TTATTTCTTT
57367687 ATTTCAA
1 ATTTCAA
57367694 ATTTCAA
1 ATTTCAA
57367701 ATTTCAA
1 ATTTCAA
57367708 ATTTCA
1 ATTTCA
57367714 CTTTTCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTTCAA
Found at i:57367870 original size:6 final size:6
Alignment explanation
Indices: 57367833--57367875 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
57367823 CCAAACACAC
* *
57367833 CAGTAAA CAGTAA TCAGTAA CGGTAG CAGTAA CAGTAA CAGTA
1 CAGT-AA CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
57367876 TTCAATACAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
6 21 0.68
7 10 0.32
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (6 bp):
CAGTAA
Found at i:57369116 original size:3 final size:3
Alignment explanation
Indices: 57369101--57369144 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
57369091 AATTTCACAT
*
57369101 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
57369145 GCTTTTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Done.