Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 63 of 161
Found at i:19746354 original size:14 final size:14
Alignment explanation
Indices: 19746337--19746448 Score: 64
Period size: 14 Copynumber: 7.4 Consensus size: 14
19746327 CCCCATCATT
19746337 TAAACCATAAACCC
1 TAAACCATAAACCC
*
19746351 TAAACCATAATCCC
1 TAAACCATAAACCC
* *
19746365 TAAACTCATAATCCA
1 TAAAC-CATAAACCC
*
19746380 TAAACCTTAAAATGGTAGCACC
1 TAAACC--ATAA----A-C-CC
*
19746402 TAAA-CATTAAACTC
1 TAAACCA-TAAACCC
*
19746416 TAAACCATATACCC
1 TAAACCATAAACCC
*
19746430 TAAACCAAAAACCC
1 TAAACCATAAACCC
19746444 TAAAC
1 TAAAC
19746449 TATAGTGATA
Statistics
Matches: 76, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
14 46 0.61
15 16 0.21
16 4 0.05
19 1 0.01
20 2 0.03
21 2 0.03
22 5 0.07
ACGTcount: A:0.47, C:0.29, G:0.03, T:0.21
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:19746376 original size:15 final size:14
Alignment explanation
Indices: 19746337--19746385 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
19746327 CCCCATCATT
*
19746337 TAAACCATAAACCC
1 TAAACCATAATCCC
19746351 TAAACCATAATCCC
1 TAAACCATAATCCC
*
19746365 TAAACTCATAATCCA
1 TAAAC-CATAATCCC
19746380 TAAACC
1 TAAACC
19746386 TTAAAATGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 19 0.59
15 13 0.41
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:19746675 original size:41 final size:41
Alignment explanation
Indices: 19746618--19747017 Score: 592
Period size: 41 Copynumber: 9.9 Consensus size: 41
19746608 TAAATCCCTA
* *
19746618 AGCATTAGCGGCGCTTTATCAAAAACGCCACTAAAGACCCG
1 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
*
19746659 AGCATTAGCTGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
1 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
19746700 AGCATTAGCGGCG---T-TCAAAAACGCCGCTAAAGACCCG
1 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
* *
19746737 AGCATTAGCGGTGCTTTCTCAAAAACGCCGCTAAAGACCAG
1 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
* *
19746778 AGCATTAGTGGCGCTTTCTCAAAAACGCCGCTAAAGACCAG
1 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
* * *
19746819 AGCATTAGCGGCGCTTCCCCAAAAACGCCGCTAAAGACCCT
1 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
* * *
19746860 AGCTTTAGCGGCGCTTTATCAAAAACGCCGTTAAAGACCCG
1 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
** * * *
19746901 AGCATTAGTAGCGCTTTCTCAAAAATGCCGTTAAAGACCAG
1 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
19746942 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
1 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
* *
19746983 AGCATTAGCGGCGCTTTCTAAAAAACGCCACTAAA
1 AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAA
19747018 TCTTTGAAAG
Statistics
Matches: 323, Mismatches: 32, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
37 35 0.11
38 1 0.00
40 1 0.00
41 286 0.89
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.19
Consensus pattern (41 bp):
AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGACCCG
Found at i:19747151 original size:40 final size:40
Alignment explanation
Indices: 19747075--19747190 Score: 137
Period size: 40 Copynumber: 3.0 Consensus size: 40
19747065 GCGCTTTCTG
* *
19747075 AAAAA-CGCCGCTAATGCT-TATATTTAGCGGCTTTTTCC
1 AAAAAGCGCCGCTAATGCTCGATATTTAGCGGCGTTTTCC
** * * *
19747113 ATGAAGCGCCACTAATGCTCGATCTTTAGTGGCGTTTTCC
1 AAAAAGCGCCGCTAATGCTCGATATTTAGCGGCGTTTTCC
* *
19747153 AAAAAGTGCCGCTAATGCTCGATTTTTAGCGGCGTTTT
1 AAAAAGCGCCGCTAATGCTCGATATTTAGCGGCGTTTT
19747191 TTATCCAAAC
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
38 3 0.05
39 12 0.19
40 48 0.76
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (40 bp):
AAAAAGCGCCGCTAATGCTCGATATTTAGCGGCGTTTTCC
Found at i:19754090 original size:12 final size:11
Alignment explanation
Indices: 19754073--19754110 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
19754063 TTATGTTATT
19754073 AAAAAAAATTG
1 AAAAAAAATTG
19754084 AAAAAAAATT-
1 AAAAAAAATTG
* *
19754094 TAAAAAAATTT
1 AAAAAAAATTG
19754105 AAAAAA
1 AAAAAA
19754111 TTTCCATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:19754113 original size:9 final size:10
Alignment explanation
Indices: 19754074--19754110 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
19754064 TATGTTATTA
*
19754074 AAAAAAATTGA
1 AAAAAAATT-T
19754085 AAAAAAATTT
1 AAAAAAATTT
19754095 AAAAAAATTT
1 AAAAAAATTT
19754105 AAAAAA
1 AAAAAA
19754111 TTTCCATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (10 bp):
AAAAAAATTT
Found at i:19754455 original size:16 final size:16
Alignment explanation
Indices: 19754430--19754476 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
19754420 CACCCCTTGA
*
19754430 ATATTTGTTTATTATT
1 ATATTAGTTTATTATT
19754446 ATATTAG-TT-TTATT
1 ATATTAGTTTATTATT
*
19754460 ATATATATTTTATTATT
1 ATAT-TAGTTTATTATT
19754477 GTTACTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 9 0.35
15 4 0.15
16 8 0.31
17 5 0.19
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (16 bp):
ATATTAGTTTATTATT
Found at i:19754459 original size:17 final size:15
Alignment explanation
Indices: 19754437--19754476 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 15
19754427 TGAATATTTG
19754437 TTTATTATTATATTAGT
1 TTTATTATTATA-TA-T
19754454 TTTATTA-TATATAT
1 TTTATTATTATATAT
19754468 TTTATTATT
1 TTTATTATT
19754477 GTTACTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 8 0.36
15 3 0.14
16 4 0.18
17 7 0.32
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTATTATTATATAT
Found at i:19755242 original size:6 final size:6
Alignment explanation
Indices: 19755231--19755258 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
19755221 TTGTTTATTT
19755231 ATTTTA ATTTTA ATTTTA ATTTTA ATTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTT
19755259 CATTTTTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTTA
Found at i:19755265 original size:18 final size:18
Alignment explanation
Indices: 19755231--19755266 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19755221 TTGTTTATTT
*
19755231 ATTTTAATTTTAATTTTA
1 ATTTTAATTTCAATTTTA
*
19755249 ATTTTAATTTCATTTTTA
1 ATTTTAATTTCAATTTTA
19755267 GTTGTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTAATTTCAATTTTA
Found at i:19761914 original size:84 final size:84
Alignment explanation
Indices: 19761804--19762041 Score: 449
Period size: 84 Copynumber: 2.8 Consensus size: 84
19761794 AAGGATCCCA
*
19761804 GTGGAATGAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCC
1 GTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCC
19761869 TTTCACAATCAAGGATACG
66 TTTCACAATCAAGGATACG
* *
19761888 GTGGATTCATCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCC
1 GTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCC
19761953 TTTCACAATCAAGGATACG
66 TTTCACAATCAAGGATACG
19761972 GTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCC
1 GTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCC
19762037 TTTCA
66 TTTCA
19762042 TTCATAGAAT
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 149 1.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (84 bp):
GTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCC
TTTCACAATCAAGGATACG
Found at i:19761921 original size:42 final size:40
Alignment explanation
Indices: 19761806--19762038 Score: 295
Period size: 41 Copynumber: 5.6 Consensus size: 40
19761796 GGATCCCAGT
* *
19761806 GGAATGAGCACTTAGCAACCACCTTATAATCAATGATACGG
1 GGAATCAGCACATAGCAACC-CCTTATAATCAATGATACGG
* *
19761847 GGAATCAGCACATAGCAACCCCTTTCACAATCAAGGATACGG
1 GGAATCAGCACATAGCAACCCC-TT-ATAATCAATGATACGG
* * *
19761889 TGGATTCATCACTTAGCAACCACCTTATAATCAATGATACGG
1 -GGAATCAGCACATAGCAACC-CCTTATAATCAATGATACGG
* *
19761931 GGAATCAGCACATAGCAACCCCTTTCACAATCAAGGATACGG
1 GGAATCAGCACATAGCAACCCC-TT-ATAATCAATGATACGG
*
19761973 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGG
1 -GGAATCAGCACATAGCAACC-CCTTATAATCAATGATACGG
19762015 GGAATCAGCACATAGCAACCCCTT
1 GGAATCAGCACATAGCAACCCCTT
19762039 TCATTCATAG
Statistics
Matches: 166, Mismatches: 18, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
40 8 0.05
41 58 0.35
42 56 0.34
43 40 0.24
44 4 0.02
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (40 bp):
GGAATCAGCACATAGCAACCCCTTATAATCAATGATACGG
Found at i:19764225 original size:27 final size:27
Alignment explanation
Indices: 19764179--19764242 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
19764169 GGAGGCTTGC
19764179 AGATTGTCCATCTGTAAGAATGTTGGT
1 AGATTGTCCATCTGTAAGAATGTTGGT
* * *
19764206 AGATTGTCTATGTGTGAGAATGTTGGT
1 AGATTGTCCATCTGTAAGAATGTTGGT
* *
19764233 GGACTGTCCA
1 AGATTGTCCA
19764243 AGTGAGAACA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.36
Consensus pattern (27 bp):
AGATTGTCCATCTGTAAGAATGTTGGT
Found at i:19764540 original size:41 final size:41
Alignment explanation
Indices: 19764480--19764715 Score: 332
Period size: 41 Copynumber: 5.8 Consensus size: 41
19764470 CTGACCTTTC
* *
19764480 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCTGCTAATGCTT
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
* * * * *
19764521 GGGGCTTTGGCGGCATTTTTCAAAAAGTGCCGCTAATTCTCA
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCT-A
* * *
19764563 -GGGATTTAGCAGCGTTTTTGAAAAAGCGTCGCTAATGCTA
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
19764603 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
* * *
19764644 GGGGCTTTAGCGGCGTTTCTGAAAAGGCGCCACTAATGC-A
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
19764684 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCG
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCG
19764716 TTAAAAACAT
Statistics
Matches: 169, Mismatches: 24, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
40 31 0.18
41 138 0.82
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (41 bp):
GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
Found at i:19765086 original size:15 final size:15
Alignment explanation
Indices: 19765061--19765097 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
19765051 GTTACTATTT
19765061 TATGG-TTTAGGGAG
1 TATGGATTTAGGGAG
*
19765075 TATGGATTTAGGGAT
1 TATGGATTTAGGGAG
19765090 TATGGATT
1 TATGGATT
19765098 ACTGATTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (15 bp):
TATGGATTTAGGGAG
Found at i:19765177 original size:15 final size:16
Alignment explanation
Indices: 19765124--19765177 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
19765114 GGGTTGAGAT
19765124 TTAAG-GTT-TAGGGG
1 TTAAGAGTTATAGGGG
*
19765138 TTAGGAGTT-TAGGGG
1 TTAAGAGTTATAGGGG
19765153 TT-AGACGTTAT-GGGG
1 TTAAGA-GTTATAGGGG
19765168 TTAAGAGTTA
1 TTAAGAGTTA
19765178 GGGATTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 6 0.18
15 24 0.71
16 4 0.12
ACGTcount: A:0.24, C:0.02, G:0.39, T:0.35
Consensus pattern (16 bp):
TTAAGAGTTATAGGGG
Found at i:19765514 original size:21 final size:20
Alignment explanation
Indices: 19765453--19765519 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
19765443 GGGATTTAAG
*
19765453 GATTAGGGGTTAGGGGTTTAT
1 GATTAGGGTTTA-GGGTTTAT
* * * *
19765474 GATTTATGTTTTATGTTTTAT
1 GA-TTAGGGTTTAGGGTTTAT
19765495 GATTCAGGGTTTAGGGTTTA-
1 GATT-AGGGTTTAGGGTTTAT
19765515 GATTA
1 GATTA
19765520 ATTAGGGTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
19 1 0.03
20 6 0.17
21 21 0.60
22 7 0.20
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.48
Consensus pattern (20 bp):
GATTAGGGTTTAGGGTTTAT
Found at i:19768792 original size:27 final size:27
Alignment explanation
Indices: 19768762--19768817 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
19768752 AATTTCGAGG
*
19768762 TTTACAATTTT-TAATTTTTATTAATTA
1 TTTAC-ATTTTCTAACTTTTATTAATTA
* *
19768789 TTTACGTTTTCTCACTTTTATTAATTA
1 TTTACATTTTCTAACTTTTATTAATTA
19768816 TT
1 TT
19768818 ATTATTTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTACATTTTCTAACTTTTATTAATTA
Found at i:19770025 original size:43 final size:43
Alignment explanation
Indices: 19769965--19770055 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
19769955 CTTTGAGTTC
* * *
19769965 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
* *
19770007 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATTTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
19770050 ATTACC
1 ATTACC
19770056 TTGCAATGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
Found at i:19770519 original size:43 final size:43
Alignment explanation
Indices: 19770406--19770533 Score: 136
Period size: 43 Copynumber: 3.0 Consensus size: 43
19770396 TTTAAATGTT
* * * *
19770406 ATGTT-TTTAGCGGCCTTT-TTACGAGAAGCGTCGCTAAAGGT-
1 ATGTTCTTTAGCGGCGTTTGTGAC-AAAAGCGCCGCTAAAGGTC
* * * *
19770447 TTGTTCTATAGCAGCGTTTGTGATAAAAAGCGCCGCTAAAGGTC
1 ATGTTCTTTAGCGGCGTTTGTGA-CAAAAGCGCCGCTAAAGGTC
*
19770491 ATGTTCTTTAGCGGCGTTTGTGACAAAAGCGCCACTAAAGGTC
1 ATGTTCTTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTC
19770534 GTTTGTGATA
Statistics
Matches: 70, Mismatches: 13, Indels: 6
0.79 0.15 0.07
Matches are distributed among these distances:
41 4 0.06
42 10 0.14
43 36 0.51
44 20 0.29
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
ATGTTCTTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTC
Found at i:19770546 original size:28 final size:28
Alignment explanation
Indices: 19770505--19770561 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
19770495 TCTTTAGCGG
19770505 CGTTTGTGACAAAAGCGCCACTAAAGGT
1 CGTTTGTGACAAAAGCGCCACTAAAGGT
* * **
19770533 CGTTTGTGATAAAAGTGCCGTTAAAGGT
1 CGTTTGTGACAAAAGCGCCACTAAAGGT
19770561 C
1 C
19770562 ATGATTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (28 bp):
CGTTTGTGACAAAAGCGCCACTAAAGGT
Found at i:19770579 original size:71 final size:72
Alignment explanation
Indices: 19770461--19770604 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
19770451 TCTATAGCAG
*
19770461 CGTTTGTGATAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGACAAAAGCGCCAC
1 CGTTTGTGATAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCAGCGTTTGTGACAAAAGCGCCAC
19770526 TAAAGGT
66 TAAAGGT
* * * *
19770533 CGTTTGTGAT-AAAAGTGCCGTTAAAGGTCATGATT-TTTAGCAGCGTTTGTGATAAAAGCGCCT
1 CGTTTGTGATAAAAAGCGCCGCTAAAGGTCATG-TTCTTTAGCAGCGTTTGTGACAAAAGCGCCA
19770596 CTAAAGGT
65 CTAAAGGT
19770604 C
1 C
19770605 ATGGTATTTA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (72 bp):
CGTTTGTGATAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCAGCGTTTGTGACAAAAGCGCCAC
TAAAGGT
Found at i:19770615 original size:43 final size:43
Alignment explanation
Indices: 19770533--19770615 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
19770523 CACTAAAGGT
* *
19770533 CGTTTGTGATAAAAGTGCCGTTAAAGGTCATGATTTTTAGCAG
1 CGTTTGTGATAAAAGCGCCGTTAAAGGTCATGATATTTAGCAG
*
19770576 CGTTTGTGATAAAAGCGCC-TCTAAAGGTCATGGTATTTAG
1 CGTTTGTGATAAAAGCGCCGT-TAAAGGTCATGATATTTAG
19770616 TGGCATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (43 bp):
CGTTTGTGATAAAAGCGCCGTTAAAGGTCATGATATTTAGCAG
Found at i:19770748 original size:22 final size:22
Alignment explanation
Indices: 19770718--19770760 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
19770708 AGTGGCGCTT
* *
19770718 AAAAGCGCCGCTAAAGACCTAA
1 AAAAACGCCGCTAAAAACCTAA
19770740 AAAAACGCCGCTAAAAACCTA
1 AAAAACGCCGCTAAAAACCTA
19770761 TTTTGTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.28, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAAACGCCGCTAAAAACCTAA
Found at i:19774228 original size:41 final size:41
Alignment explanation
Indices: 19774163--19774478 Score: 499
Period size: 41 Copynumber: 7.7 Consensus size: 41
19774153 CCTTTCAAGG
** *
19774163 CTTTAGCGGCGTTTTTACAAAAGCGCCGCTAATGCTCAGGT
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGT
*
19774204 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGT
*
19774245 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGT
* *
19774286 CTTTAGCGGCGTTTTTGGAGAAGCGCTGCTAATGCTCAGGG
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGT
* *
19774327 CTTTAGCGGCGTTTTTGGAGAAGTGCCGCTAATGCTCAGTT
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGT
19774368 CTTTAGCGGCGTTTTCTGG-GAAGCGCCGCTAATGCTCAGGT
1 CTTTAGCGGCGTTTT-TGGAGAAGCGCCGCTAATGCTCAGGT
* *
19774409 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGT
* *
19774450 CTTTAGCAGCGTTTTTGGAAAAGCGCCGC
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGC
19774479 AAAAACATTT
Statistics
Matches: 257, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
40 3 0.01
41 251 0.98
42 3 0.01
ACGTcount: A:0.17, C:0.22, G:0.30, T:0.31
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGT
Found at i:19775026 original size:7 final size:7
Alignment explanation
Indices: 19775012--19775043 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
19775002 GAGGTTAGTA
19775012 GTTAGGG
1 GTTAGGG
*
19775019 GTTTGGG
1 GTTAGGG
19775026 GTTAGGG
1 GTTAGGG
19775033 GTTAGGG
1 GTTAGGG
19775040 GTTA
1 GTTA
19775044 AGAGTTAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.53, T:0.34
Consensus pattern (7 bp):
GTTAGGG
Found at i:19775050 original size:21 final size:21
Alignment explanation
Indices: 19775012--19775051 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19775002 GAGGTTAGTA
** *
19775012 GTTAGGGGTTTGGGGTTAGGG
1 GTTAGGGGTTAAGAGTTAGGG
19775033 GTTAGGGGTTAAGAGTTAG
1 GTTAGGGGTTAAGAGTTAG
19775052 TGATTTAAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (21 bp):
GTTAGGGGTTAAGAGTTAGGG
Found at i:19775678 original size:27 final size:27
Alignment explanation
Indices: 19775646--19775699 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
19775636 TTACATGTTG
19775646 AAATTAATTAAGGGAATGTAAACAAGA
1 AAATTAATTAAGGGAATGTAAACAAGA
19775673 AAATTAATTAAGGGAATGTAAACAAGA
1 AAATTAATTAAGGGAATGTAAACAAGA
19775700 GAAAAGAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.19, T:0.22
Consensus pattern (27 bp):
AAATTAATTAAGGGAATGTAAACAAGA
Found at i:19780530 original size:24 final size:23
Alignment explanation
Indices: 19780502--19780549 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
19780492 AATTTAAAAA
19780502 ATAAAACATAATATAATATTT-ATT
1 ATAAAA-ATAA-ATAATATTTGATT
*
19780526 ATAAAAATAAATATTATTTGATT
1 ATAAAAATAAATAATATTTGATT
19780549 A
1 A
19780550 AAATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
ATAAAAATAAATAATATTTGATT
Found at i:19780648 original size:42 final size:43
Alignment explanation
Indices: 19780602--19780710 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 43
19780592 CTAGAATCGT
* *
19780602 CGCTAAAGG-ATTGTTCTTTAGCGGCGTTTGTGAGAAAAGCGC
1 CGCTAAAGGTAGTGGTCTTTAGCGGCGTTTGTGAGAAAAGCGC
* *
19780644 CGCTAAAGGTAGTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGT
1 CGCTAAAGGTAGTGGTCTTTAGCGGCGTTTGTGAGAAAAGCGC
* *
19780687 TGCTAAAGGTCA-CGGTCTTTAGCG
1 CGCTAAAGGT-AGTGGTCTTTAGCG
19780711 AGTGAAAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
42 9 0.15
43 49 0.83
44 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (43 bp):
CGCTAAAGGTAGTGGTCTTTAGCGGCGTTTGTGAGAAAAGCGC
Found at i:19780800 original size:44 final size:42
Alignment explanation
Indices: 19780720--19780802 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 42
19780710 GAGTGAAAAA
* *
19780720 ACGATCTTTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACC
1 ACGACCTTTAGCAGCGCTTTTCCAAAAACGCCGCTAAAGACC
* * *
19780762 ACGACCTTTAGCAGCGTTTATTTCAAGAAACGCTGCTAAAG
1 ACGACCTTTAGCAGCGCTT-TTCCAA-AAACGCCGCTAAAG
19780803 TTAGCGACAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 16 0.47
43 5 0.15
44 13 0.38
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (42 bp):
ACGACCTTTAGCAGCGCTTTTCCAAAAACGCCGCTAAAGACC
Found at i:19782952 original size:79 final size:81
Alignment explanation
Indices: 19782816--19782998 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 81
19782806 TTGAATGATG
* * *
19782816 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
19782880 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
19782895 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
19782957 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
19782975 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
19782999 TGAACGAGTA
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.65
80 30 0.34
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:19783014 original size:40 final size:40
Alignment explanation
Indices: 19782817--19783000 Score: 198
Period size: 40 Copynumber: 4.6 Consensus size: 40
19782807 TGAATGATGT
* * * *
19782817 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
19782857 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
19782897 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
19782935 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
19782976 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
19783001 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
39 34 0.28
40 78 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:19783022 original size:79 final size:79
Alignment explanation
Indices: 19782869--19783033 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
19782859 GGACTAAGAT
* * **
19782869 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
19782934 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
19782948 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
19783011 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
19783027 CCGAAGG
1 CCGAAGG
19783034 TACGTGATTC
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 24 0.33
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:19793480 original size:33 final size:33
Alignment explanation
Indices: 19793443--19793510 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
19793433 TGTTTTGACT
*
19793443 TTTTGGTTAGTATCCTTTTTGGGCTTAACAAAA
1 TTTTGGTTAGTATCCTTTTTGGACTTAACAAAA
19793476 TTTTGGTTAGTATCCTTTTTGGACTTAACAAAA
1 TTTTGGTTAGTATCCTTTTTGGACTTAACAAAA
19793509 TT
1 TT
19793511 ATATTTTGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (33 bp):
TTTTGGTTAGTATCCTTTTTGGACTTAACAAAA
Found at i:19796755 original size:18 final size:17
Alignment explanation
Indices: 19796727--19796761 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19796717 ATTATTAAGA
*
19796727 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
19796744 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
19796762 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:19796899 original size:18 final size:17
Alignment explanation
Indices: 19796871--19796905 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19796861 ATTATTAAGA
*
19796871 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
19796888 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
19796906 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:19797116 original size:44 final size:45
Alignment explanation
Indices: 19797067--19797161 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
19797057 TTACACCTCT
* *
19797067 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
19797111 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
19797156 ATTACA
1 ATTACA
19797162 CCTTTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:19797161 original size:16 final size:16
Alignment explanation
Indices: 19797142--19797193 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
19797132 GATTTGCTAT
* *
19797142 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
*
19797158 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
19797174 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
19797190 TACA
1 TACA
19797194 GCGAACCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:19798070 original size:6 final size:6
Alignment explanation
Indices: 19798059--19798090 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
19798049 CTGCAGGAGC
19798059 CATTGG CATTGG CATTGG CATTGG CATTGG CA
1 CATTGG CATTGG CATTGG CATTGG CATTGG CA
19798091 CCCCCAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (6 bp):
CATTGG
Found at i:19801207 original size:18 final size:18
Alignment explanation
Indices: 19801156--19801211 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
19801146 TATATTTAAA
*
19801156 ATAAATTTTA-ATAAGAAA
1 ATAAATTTTATATAA-AAT
** *
19801174 AT-AATTAAATACAAAAT
1 ATAAATTTTATATAAAAT
19801191 ATAAATTTTATATAAAAT
1 ATAAATTTTATATAAAAT
19801209 ATA
1 ATA
19801212 TTATAAGAGT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
17 9 0.31
18 20 0.69
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
ATAAATTTTATATAAAAT
Found at i:19805296 original size:4 final size:4
Alignment explanation
Indices: 19805289--19805344 Score: 60
Period size: 4 Copynumber: 13.2 Consensus size: 4
19805279 AGATTAATAC
19805289 TAAA TAAAA TAAA TTTAAA TAAA TAAA TAAA TAAA TAAA TAAA -AAA CTAAA
1 TAAA T-AAA TAAA --TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA -TAAA
*
19805340 AAAA T
1 TAAA T
19805345 GAAACAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
3 3 0.07
4 31 0.69
5 7 0.16
6 4 0.09
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:19807156 original size:30 final size:30
Alignment explanation
Indices: 19807122--19807182 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
19807112 CACGGGCTGG
* * *
19807122 CACATGGGTGTGTGTCCAGCCCGTGTGGCT
1 CACATAGGTGTGTGCCCAACCCGTGTGGCT
19807152 CACATAGGTGTGTGCCCAACCCGTGTGGCT
1 CACATAGGTGTGTGCCCAACCCGTGTGGCT
19807182 C
1 C
19807183 CTAAAATCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.13, C:0.30, G:0.33, T:0.25
Consensus pattern (30 bp):
CACATAGGTGTGTGCCCAACCCGTGTGGCT
Found at i:19808989 original size:5 final size:6
Alignment explanation
Indices: 19808975--19809056 Score: 60
Period size: 6 Copynumber: 13.5 Consensus size: 6
19808965 GAAATTTAAG
* * * *
19808975 AAAATA AAAATAA AACAACTA AAAACA AAAATA AAAGTA AACATA AAAAGA
1 AAAATA AAAAT-A AA-AA-TA AAAATA AAAATA AAAATA AAAATA AAAATA
* * *
19809026 AAAAGA AAACTA AAAA-G AAAA-A AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAA
19809057 TCAATGATCC
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
5 8 0.13
6 41 0.68
7 5 0.08
8 5 0.08
9 1 0.02
ACGTcount: A:0.79, C:0.06, G:0.05, T:0.10
Consensus pattern (6 bp):
AAAATA
Found at i:19815112 original size:30 final size:30
Alignment explanation
Indices: 19815078--19815138 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
19815068 CACGGGCTAG
** * * *
19815078 CACATGGGTGTGTGTCCAGCCCGTGTGGCT
1 CACATGGGCATGTGGCCAACCCATGTGGCT
19815108 CACATGGGCATGTGGCCAACCCATGTGGCT
1 CACATGGGCATGTGGCCAACCCATGTGGCT
19815138 C
1 C
19815139 TTGAAATCTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.15, C:0.30, G:0.33, T:0.23
Consensus pattern (30 bp):
CACATGGGCATGTGGCCAACCCATGTGGCT
Found at i:19817266 original size:15 final size:14
Alignment explanation
Indices: 19817232--19817271 Score: 71
Period size: 14 Copynumber: 2.8 Consensus size: 14
19817222 CTTTCAAGGA
19817232 ATTTTGTGGGTTCTT
1 ATTTT-TGGGTTCTT
19817247 ATTTTTGGGTTCTT
1 ATTTTTGGGTTCTT
19817261 ATTTTTGGGTT
1 ATTTTTGGGTT
19817272 TCGAGGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.07, C:0.05, G:0.25, T:0.62
Consensus pattern (14 bp):
ATTTTTGGGTTCTT
Found at i:19822153 original size:15 final size:15
Alignment explanation
Indices: 19822133--19822163 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
19822123 GTTATGTAAG
19822133 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
19822148 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
19822163 T
1 T
19822164 ATGTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:19823149 original size:22 final size:22
Alignment explanation
Indices: 19823121--19823163 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
19823111 ACAAGTATTT
**
19823121 TTTTTAAATTTCAAATATAATA
1 TTTTTAAAAATCAAATATAATA
19823143 TTTTTAAAAATCAAATATAAT
1 TTTTTAAAAATCAAATATAAT
19823164 CACAAGCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTTTAAAAATCAAATATAATA
Found at i:19837387 original size:46 final size:46
Alignment explanation
Indices: 19837336--19837429 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
19837326 ATAGTGTGGT
* *
19837336 GTTCATCATATACCAAGGTTTCTATCATCCTTAATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATCCTTAATAGTGAGTCGAG
* *
19837382 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGAGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATCCTTAATAGTGAGTCGAG
19837428 GT
1 GT
19837430 CTTTTAAACC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATCCTTAATAGTGAGTCGAG
Found at i:19844895 original size:25 final size:25
Alignment explanation
Indices: 19844834--19844910 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
19844824 AAGATAACAA
** *
19844834 GCCACAAAGGC-TTCCAGAAAGAGGTA
1 GCCACAAAGGCTTTCCAG--AGAATTC
*
19844860 GCCACATAGGCTTTCCAGAGAATTC
1 GCCACAAAGGCTTTCCAGAGAATTC
**
19844885 GCCACAAAGGCTTTTTAGAGAATTC
1 GCCACAAAGGCTTTCCAGAGAATTC
19844910 G
1 G
19844911 TGTTTATTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
25 27 0.63
26 10 0.23
27 6 0.14
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.21
Consensus pattern (25 bp):
GCCACAAAGGCTTTCCAGAGAATTC
Found at i:19846160 original size:109 final size:111
Alignment explanation
Indices: 19845982--19846274 Score: 434
Period size: 111 Copynumber: 2.7 Consensus size: 111
19845972 TCTGGCTATA
* * * ** * *
19845982 TGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGTA-CATTCCTCAAATTTCCAAACGCAA
1 TGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
*
19846044 AACATTGCCTTATTTT-GAA-ATTTTTAAAAGGATATTTAGCCATT
66 AACATTGCCTTATTTTAGAATATTTTTAAAAGGATATTAAGCCATT
*
19846088 TGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
1 TGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
*
19846153 AACATTGCCTTATTTTAGAATTTTTTTAAAAGGATATTAAGCCATT
66 AACATTGCCTTATTTTAGAATATTTTTAAAAGGATATTAAGCCATT
*
19846199 TGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCCAAACGCT
1 TGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTT-CCAAACGCA
*
19846264 AAATATTGCCT
65 AAACATTGCCT
19846275 CAATTAGAAA
Statistics
Matches: 168, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
106 10 0.06
108 24 0.14
109 36 0.21
110 3 0.02
111 77 0.46
112 18 0.11
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (111 bp):
TGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAA
AACATTGCCTTATTTTAGAATATTTTTAAAAGGATATTAAGCCATT
Found at i:19846353 original size:21 final size:18
Alignment explanation
Indices: 19846321--19846360 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
19846311 ATTTATATGC
19846321 ATAATGGAATAATAAACATG
1 ATAATGGAATAA-AAA-ATG
19846341 ATAATGTGAATAAAAAATG
1 ATAATG-GAATAAAAAATG
19846360 A
1 A
19846361 ACAAAAACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.57, C:0.03, G:0.15, T:0.25
Consensus pattern (18 bp):
ATAATGGAATAAAAAATG
Found at i:19846681 original size:3 final size:3
Alignment explanation
Indices: 19846673--19846703 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
19846663 ATATAAAAGC
*
19846673 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
19846704 TGAAATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19848210 original size:50 final size:50
Alignment explanation
Indices: 19848143--19848248 Score: 140
Period size: 50 Copynumber: 2.1 Consensus size: 50
19848133 CTATCATCTC
* * ** *
19848143 CAATCTGTTTAACTGCAATGTCGAGGAAGTAAGATTCACCGTCATAGCTT
1 CAATCTATTTAACTGCAATGTCAAGGAAACAAAATTCACCGTCATAGCTT
* **
19848193 CAATCTATTTAATTGCAATGTCAAGGAAACAAAATTCACCGTTGTAGCTT
1 CAATCTATTTAACTGCAATGTCAAGGAAACAAAATTCACCGTCATAGCTT
19848243 CAATCT
1 CAATCT
19848249 GTTCCGCTGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (50 bp):
CAATCTATTTAACTGCAATGTCAAGGAAACAAAATTCACCGTCATAGCTT
Found at i:19848280 original size:50 final size:49
Alignment explanation
Indices: 19848226--19848598 Score: 209
Period size: 50 Copynumber: 7.5 Consensus size: 49
19848216 AGGAAACAAA
* * * * *
19848226 ATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCACCACCTGGAAAGTAAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCGCCTGGAAA-TGAG
* * * ** * *
19848276 ATTCACC-TTAGTAGCTTCAATATTTTGAATTGCAAT-G-TTGGAGAAGTGAG
1 ATTCGCCGTT-GTAGCTTCAATCTGTTCCACTGC-ATCGCCTGGA-AA-TGAG
* * * *
19848326 ATTCGCCATCGTAGCTTCAATCTGTTCCACTGCATCACTCGGGAAATGAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCGC-CTGGAAATGAG
* * ** * * *
19848376 ATTTGCCGTTGT-GACTTCAATCTTTTGAATTGCAAT-GTCGGGAAAGTGAG
1 ATTCGCCGTTGTAG-CTTCAATCTGTTCCACTGC-ATCGCCTGGAAA-TGAG
* * * *
19848426 ATTCGCCGTCGTAGCTTCAATTTGTTCCGCTGCATCGCCTAGGAAATAAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCGCCT-GGAAATGAG
* * * * ** * *
19848476 ATTCGCCATTGTGGCTTCGATCTTTTAAACTGCAAT-GTCGGGAAAATGAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGC-ATCGCCTGG-AAATGAG
* * * *
19848526 ATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATTGCCTAGGAAATAAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCGCCT-GGAAATGAG
* * *
19848576 ATTCACCGTTGTGGCTTCGATCT
1 ATTCGCCGTTGTAGCTTCAATCT
19848599 TTTTAAACTA
Statistics
Matches: 239, Mismatches: 67, Indels: 34
0.70 0.20 0.10
Matches are distributed among these distances:
49 22 0.09
50 198 0.83
51 16 0.07
52 3 0.01
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (49 bp):
ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCGCCTGGAAATGAG
Found at i:19848340 original size:100 final size:98
Alignment explanation
Indices: 19848226--19848799 Score: 598
Period size: 100 Copynumber: 5.8 Consensus size: 98
19848216 AGGAAACAAA
* * * *
19848226 ATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCACCACCTGGAAAGTAAGATTCACC-TTAGTAG
1 ATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCACCTGGAAA-TAAGATTCACCGTT-GTGG
* *
19848290 CTTCAATATTTTGAATTGCAATGTTGGAGAAGTGAG
64 CTTCGATATTTTGAATTGCAATGTCGG-GAAGTGAG
* * * * ** *
19848326 ATTCGCCATCGTAGCTTCAATCTGTTCCACTGCATCACTCGGGAAATGAGATTTGCCGTTGTGAC
1 ATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCAC-CTGGAAATAAGATTCACCGTTGTGGC
* *
19848391 TTCAATCTTTTGAATTGCAATGTCGGGAAAGTGAG
65 TTCGATATTTTGAATTGCAATGTCGGG-AAGTGAG
* * * *
19848426 ATTCGCCGTCGTAGCTTCAATTTGTTCCGCTGCATCGCCTAGGAAATAAGATTCGCCATTGTGGC
1 ATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCACCT-GGAAATAAGATTCACCGTTGTGGC
* * * *
19848491 TTCGATCTTTTAAACTGCAATGTCGGGAAAATGAG
65 TTCGATATTTTGAATTGCAATGTCGGG-AAGTGAG
**
19848526 ATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATTGCCTAGGAAATAAGATTCACCGTTGTGGC
1 ATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCACCT-GGAAATAAGATTCACCGTTGTGGC
* * * * **
19848591 TTCGATCTTTTTAAACTACAATGTCTTAGAAGTGAG
65 TTCGAT-ATTTTGAATTGCAATGTC-GGGAAGTGAG
* * * **
19848627 ATTCACCGTCGTAGCTCCAATTTGTTCCGCTGCATCGTCTGGGAGAA-AA-ATTCACCGTTGTGG
1 ATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCACCT-GGA-AATAAGATTCACCGTTGTGG
**
19848690 CTTCGATATTTTGAATTGCAATGTCGGGGAAGCAAG
64 CTTCGATATTTTGAATTGCAATGTC-GGGAAGTGAG
* * * * * *
19848726 ATTCGCTGTTGTAGCTTCAATTTGTTCCACTGCATCACCTAGAAGTAAGATTCACC-TTGTGGCT
1 ATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCACCTGGAAATAAGATTCACCGTTGTGGCT
*
19848790 TCGATCTTTT
66 TCGATATTTT
19848800 AAACTATTCC
Statistics
Matches: 405, Mismatches: 60, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
97 1 0.00
98 21 0.05
99 62 0.15
100 248 0.61
101 70 0.17
102 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (98 bp):
ATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCACCTGGAAATAAGATTCACCGTTGTGGCT
TCGATATTTTGAATTGCAATGTCGGGAAGTGAG
Found at i:19848934 original size:46 final size:46
Alignment explanation
Indices: 19848882--19850492 Score: 2097
Period size: 46 Copynumber: 35.2 Consensus size: 46
19848872 AAGATTCACC
*** * * *
19848882 ATCTTCGATCTCCTCCGCTGCTGGATACAAGAAGATAATATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* *
19848928 ACCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAATATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
19848974 ATCTTCGATCTCCTCTGCTGCCAAATATAGGAAGACAAGATCTGCC
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
*
19849020 ATCTTTGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* *
19849066 ATCTTCGATCTCCTCCACAGCCAAATACAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * * * *
19849112 ATCTTCGATCTCTTTCGCTGCCAAATACAGTAAGATAAGATCGGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * * *
19849158 ATCTTCGATCTCCTTCACTACCAAATACAGGAAGATAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * * *
19849204 ATTTTCGATCTCCTCCGCTGCCAAATACAAGAAGATAAGATCTGCC
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
19849250 ATCTTCGATCTCTTCCGCTGCCAAATACAGGAAGATAAGATCTACT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
19849296 ATCTTCGATCTCCTTCGCTACCAAATACAGCAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* *
19849342 ATCTTCGATCTCTTCCGCTGCCAAATACAGGAAAACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* *
19849388 ATCTTCGATCTCCTCCACTGCCCAAATACAGGAAGACAAGATCTACT
1 ATCTTCGATCTCCTCCGCTG-CCAAATACAGGAAGACAAGATCTGCT
* * *
19849435 ATCTTTGATCTACTCCGCTGCCAAATACAGGAAGACAAGATTTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * ** *
19849481 ATCTTTGATCTACTCTACTGCCAAATACAGGAAGATAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
*
19849527 ATCTTCGATCTACT-C-C-G-C---T--AGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
19849564 ATCTTCGATCTCTTCCACTGCCCAAATACAGTAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTG-CCAAATACAGGAAGACAAGATCTGCT
*
19849611 ATCTTCGATCTCCTCAGCTGCCAAATACAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
19849657 ATCTTTGATCTACTCCGCTGCCAAATACAGGAAGATAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* *
19849703 ATCTTCTATCTCCTCCGCTGCCAAATACAGGAACACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
19849749 ATCTTTGATCTACTCCGCTGCCAAATACAGGAAGATAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
19849795 ATCTTCGATCTACTCTGCTGCCAAATATAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
19849841 ATCTTCGATCTCCTCCCCTACCCAAATACAAGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCT-GCCAAATACAGGAAGACAAGATCTGCT
* *
19849888 ATCTTCGATCTTCTCCGCTGCCAAATGCAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
*
19849934 ATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * * * * * * *
19849980 ATATTTGATTTACTCCGTTGCTAAATACAAGAAGATAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
19850026 ATCTTCGATCTACTCCGCTGCCAAATACAGGAAGATAAGATCTGCC
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
19850072 ATCTTCGATCTCCTCTGCTGCTAAAGACAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * * * * * * *
19850118 ATATTTGATTTACTCCGTTGCTAAATACAAGAAGATAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* **
19850164 ATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACTGGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* *
19850210 ATCTTTGATCTCCTCCGCTGCCAAATATAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * * * * * * *
19850256 ATATTTGATTTACTCCGTTGCTAAATACAAGAAGATAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
19850302 ATCTTCGATCTACTCCGCTGCCAAATACAGGAAGATAAGATCTGCC
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
19850348 ATCTTCGATCTCCTCTGCTGCTAAATACAGGAAGACAAGATCTGAT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* ** **
19850394 ATCTTCGATCTTCTCTACTGCCAAATACAGGAAGACTGGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* *
19850440 ATCTTTGATCTCCTCCGCTGCCAAATATAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
19850486 ATCTTCG
1 ATCTTCG
19850493 TTGATCTGTT
Statistics
Matches: 1364, Mismatches: 189, Indels: 24
0.86 0.12 0.02
Matches are distributed among these distances:
37 29 0.02
38 1 0.00
39 2 0.00
40 1 0.00
42 2 0.00
43 1 0.00
44 1 0.00
45 1 0.00
46 1210 0.89
47 116 0.09
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (46 bp):
ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
Found at i:19851722 original size:9 final size:9
Alignment explanation
Indices: 19851708--19851761 Score: 55
Period size: 9 Copynumber: 6.6 Consensus size: 9
19851698 CCATTTTTAC
19851708 TTTTTCATT
1 TTTTTCATT
19851717 TTTTTCA--
1 TTTTTCATT
19851724 TTTTTCA-T
1 TTTTTCATT
19851732 TTTTT--TT
1 TTTTTCATT
**
19851739 TCATTCATT
1 TTTTTCATT
19851748 TTTTTCATT
1 TTTTTCATT
19851757 TTTTT
1 TTTTT
19851762 TGTTTGACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 11 0.30
8 5 0.14
9 21 0.57
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTCATT
Found at i:19851727 original size:15 final size:15
Alignment explanation
Indices: 19851709--19851758 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
19851699 CATTTTTACT
19851709 TTTTCATTTTTTTCA
1 TTTTCATTTTTTTCA
19851724 TTTTTCATTTTTTT--
1 -TTTTCATTTTTTTCA
19851738 TTCATTCATTTTTTTCA
1 TT--TTCATTTTTTTCA
19851755 TTTT
1 TTTT
19851759 TTTTGTTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.07
15 13 0.43
16 13 0.43
17 2 0.07
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCATTTTTTTCA
Found at i:19851749 original size:13 final size:11
Alignment explanation
Indices: 19851724--19851762 Score: 60
Period size: 11 Copynumber: 3.4 Consensus size: 11
19851714 ATTTTTTTCA
19851724 TTTTTCATTTT
1 TTTTTCATTTT
19851735 TTTTTCATTCATT
1 TTTTTCATT--TT
19851748 TTTTTCATTTT
1 TTTTTCATTTT
19851759 TTTT
1 TTTT
19851763 GTTTGACTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 15 0.58
13 11 0.42
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTCATTTT
Found at i:19852583 original size:19 final size:18
Alignment explanation
Indices: 19852556--19852607 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 18
19852546 CGCCTTGACC
19852556 TCTCATTTTTCTTTTCTTTT
1 TCTC-TTTTT-TTTTCTTTT
19852576 TCTCTTTTTTTTTTCTTTT
1 TCTC-TTTTTTTTTCTTTT
19852595 TCTCTTTTTTTTT
1 TCTCTTTTTTTTT
19852608 GATTTTTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 9 0.29
19 13 0.42
20 9 0.29
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (18 bp):
TCTCTTTTTTTTTCTTTT
Found at i:19852607 original size:13 final size:13
Alignment explanation
Indices: 19852561--19852602 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
19852551 TGACCTCTCA
19852561 TTTT-TCTTTTCT
1 TTTTCTCTTTTCT
*
19852573 TTTTCTCTTTTTT
1 TTTTCTCTTTTCT
19852586 TTTTCT-TTTTCT
1 TTTTCTCTTTTCT
19852598 CTTTT
1 -TTTT
19852603 TTTTTGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 9 0.35
13 17 0.65
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTCTTTTCT
Found at i:19852613 original size:8 final size:8
Alignment explanation
Indices: 19852602--19852639 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
19852592 TTTTCTCTTT
19852602 TTTTTTGA
1 TTTTTTGA
19852610 TTTTTTG-
1 TTTTTTGA
19852617 TTTGTTTGA
1 TTT-TTTGA
19852626 TTTTTTGA
1 TTTTTTGA
19852634 TTTTTT
1 TTTTTT
19852640 TACTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 3 0.11
8 22 0.79
9 3 0.11
ACGTcount: A:0.08, C:0.00, G:0.13, T:0.79
Consensus pattern (8 bp):
TTTTTTGA
Found at i:19852613 original size:19 final size:19
Alignment explanation
Indices: 19852572--19852614 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
19852562 TTTTCTTTTC
**
19852572 TTTTTCTCTTTTTTTTTTC
1 TTTTTCTCTTTTTTTTTGA
19852591 TTTTTCTCTTTTTTTTTGA
1 TTTTTCTCTTTTTTTTTGA
19852610 TTTTT
1 TTTTT
19852615 TGTTTGTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (19 bp):
TTTTTCTCTTTTTTTTTGA
Found at i:19852649 original size:12 final size:11
Alignment explanation
Indices: 19852561--19852660 Score: 51
Period size: 11 Copynumber: 9.2 Consensus size: 11
19852551 TGACCTCTCA
* *
19852561 TTTTTCTTTTC
1 TTTTTATTTTT
* *
19852572 TTTTTCTCTTT
1 TTTTTATTTTT
*
19852583 TTTTT-TTCTT
1 TTTTTATTTTT
* *
19852593 TTTCTCTTTTT
1 TTTTTATTTTT
*
19852604 TTTTGATTTTT
1 TTTTTATTTTT
* * **
19852615 TGTTTGTTTGA
1 TTTTTATTTTT
**
19852626 TTTTT-TGATT
1 TTTTTATTTTT
19852636 TTTTTACTTTTT
1 TTTTTA-TTTTT
19852648 TTTTTATTTTT
1 TTTTTATTTTT
19852659 TT
1 TT
19852661 ATTTTTCTTT
Statistics
Matches: 65, Mismatches: 21, Indels: 6
0.71 0.23 0.07
Matches are distributed among these distances:
10 13 0.20
11 43 0.66
12 9 0.14
ACGTcount: A:0.05, C:0.08, G:0.05, T:0.82
Consensus pattern (11 bp):
TTTTTATTTTT
Found at i:19855388 original size:10 final size:9
Alignment explanation
Indices: 19855364--19855396 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
19855354 TTTCTTACAA
19855364 TATTTTTTT
1 TATTTTTTT
19855373 TATTTTTTT
1 TATTTTTTT
*
19855382 T-GTTTTTT
1 TATTTTTTT
19855390 TATTTTT
1 TATTTTT
19855397 GGTTGCCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (9 bp):
TATTTTTTT
Found at i:19859385 original size:3 final size:3
Alignment explanation
Indices: 19859377--19859416 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
19859367 ATATAAAAGC
*
19859377 AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
19859417 TGAAATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19861540 original size:42 final size:42
Alignment explanation
Indices: 19861486--19861585 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
19861476 GCTCTCGGTA
*
19861486 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
* *
19861528 TCGCACACTTAGTGCCCATTATTCAACATCGTCATTTTAGTT
1 TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
19861570 TCGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
19861586 GTTCATATAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
Found at i:19872846 original size:3 final size:3
Alignment explanation
Indices: 19872838--19872919 Score: 55
Period size: 3 Copynumber: 27.3 Consensus size: 3
19872828 TATGCGTAGG
* *
19872838 ATA ATA ATA ATA TATC AT- ATA ATA ATA ATA A-A CTA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
19872882 CAGTA ATA GA-A ATA ATA TTA ACA ATA TTA ATA A-A ATA A
1 -A-TA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
19872920 ACTAAAAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
2 6 0.10
3 49 0.79
4 5 0.08
5 2 0.03
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:19874351 original size:43 final size:43
Alignment explanation
Indices: 19874245--19874603 Score: 285
Period size: 43 Copynumber: 8.6 Consensus size: 43
19874235 CCTCAGTCTG
* * * *
19874245 CTCCACTGCAACTTCAAGGAGATAAGA-CT-TGATGTGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTAATCTA
* * ** *
19874286 CT-CTCTGCAACCTCAGAAAGATAAGATCTGTGATTTAATCCA
1 CTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTAATCTA
* * *
19874328 CTCCACTGCAACTTCAGGGAGATAGGAT-TG-GTTCTTCAGTCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATCTGTGAT-TT-AATCTA
* * *
19874371 CTCCACTGCAACTTCAGGGAGATAAGA-CT-TGATATGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTAATCTA
* * * * * *
19874412 CT-CTCTACAACCTCAGAGAGATAAGATCTGTGACTTAATCCA
1 CTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTAATCTA
* * * *
19874454 CTCCACTACAACTTCAGGGAGATAGGAT-TG-GTTCTTCAGTCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATCTGTGAT-TT-AATCTA
* * * * *
19874497 CTCCACTACAACTTCAGGGAGATAAGA-CT-TGATGTGATTTT
1 CTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTAATCTA
* * * *
19874538 CT-CTCTGCAACCTCAGAGAGATAAGATCTGTGATTTAATCCA
1 CTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTAATCTA
19874580 CTCCACTGCAACTTCAGGGAGATA
1 CTCCACTGCAACTTCAGGGAGATA
19874604 GGATTGGTTC
Statistics
Matches: 242, Mismatches: 59, Indels: 32
0.73 0.18 0.10
Matches are distributed among these distances:
40 59 0.24
41 20 0.08
42 38 0.16
43 125 0.52
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTAATCTA
Found at i:19874409 original size:126 final size:126
Alignment explanation
Indices: 19874107--19874616 Score: 768
Period size: 126 Copynumber: 4.0 Consensus size: 126
19874097 GGAATTAATG
* * * * * * *
19874107 CTTCAATCCACTCCACTGTAACTTTAAGGAGATAGGACTTGATGGGATCTGTTCTCTGCAACCTC
1 CTTCAGTCTACTCCACTGCAACTTCAAGGAGATAAGACTTGATGTGATCTGCTCTCTGCAACCTC
* * * * * *
19874172 AGAAAGATAAGATCTATGGTTTTAATCCGCTCCACTGCGACCTCAGGGAGATAGGATTTGGGT
66 AGAAAGATAAGATCTGT-GATTTAATCCACTCCACTGCAACTTCAGGGAGATAGGA-TTGGTT
* *
19874235 CCTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGATGTGATCTGCTCTCTGCAACCTC
1 CTTCAGTCTACTCCACTGCAACTTCAAGGAGATAAGACTTGATGTGATCTGCTCTCTGCAACCTC
19874300 AGAAAGATAAGATCTGTGATTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTT
66 AGAAAGATAAGATCTGTGATTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTT
* * *
19874361 CTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTGATATGATCTGCTCTCTACAACCTC
1 CTTCAGTCTACTCCACTGCAACTTCAAGGAGATAAGACTTGATGTGATCTGCTCTCTGCAACCTC
* * *
19874426 AGAGAGATAAGATCTGTGACTTAATCCACTCCACTACAACTTCAGGGAGATAGGATTGGTT
66 AGAAAGATAAGATCTGTGATTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTT
* * * *
19874487 CTTCAGTCTACTCCACTACAACTTCAGGGAGATAAGACTTGATGTGATTTTCTCTCTGCAACCTC
1 CTTCAGTCTACTCCACTGCAACTTCAAGGAGATAAGACTTGATGTGATCTGCTCTCTGCAACCTC
*
19874552 AGAGAGATAAGATCTGTGATTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTT
66 AGAAAGATAAGATCTGTGATTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTT
19874613 CTTC
1 CTTC
19874617 GGTTTGTTCT
Statistics
Matches: 352, Mismatches: 30, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
126 246 0.70
127 34 0.10
128 72 0.20
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (126 bp):
CTTCAGTCTACTCCACTGCAACTTCAAGGAGATAAGACTTGATGTGATCTGCTCTCTGCAACCTC
AGAAAGATAAGATCTGTGATTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTT
Found at i:19879323 original size:25 final size:25
Alignment explanation
Indices: 19879290--19879354 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 25
19879280 ATTATGAAAT
*
19879290 GAATAAAAGAATGATGTA-GAAAAAA
1 GAATAAAAGAATAAT-TACGAAAAAA
19879315 GAATAAAAGAATAATTACTCGAAAAAA
1 GAATAAAAGAATAATTA--CGAAAAAA
19879342 GAATAAAAGAATA
1 GAATAAAAGAATA
19879355 CTGGCTCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
24 2 0.06
25 14 0.39
27 20 0.56
ACGTcount: A:0.65, C:0.03, G:0.15, T:0.17
Consensus pattern (25 bp):
GAATAAAAGAATAATTACGAAAAAA
Found at i:19879366 original size:27 final size:27
Alignment explanation
Indices: 19879309--19879366 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
19879299 AATGATGTAG
* *
19879309 AAAAAAGAATAAAAGAATAATTACTCG
1 AAAAAAGAATAAAAGAATAATGACTCA
* *
19879336 AAAAAAGAATAAAAGAATACTGGCTCA
1 AAAAAAGAATAAAAGAATAATGACTCA
19879363 AAAA
1 AAAA
19879367 TGCATACGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.64, C:0.09, G:0.12, T:0.16
Consensus pattern (27 bp):
AAAAAAGAATAAAAGAATAATGACTCA
Found at i:19890699 original size:3 final size:3
Alignment explanation
Indices: 19890691--19890728 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
19890681 TATCACATAA
19890691 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
19890729 ATATATATAT
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19891163 original size:15 final size:15
Alignment explanation
Indices: 19891143--19891177 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
19891133 TAGATTTAGG
19891143 ATCAAGTTC-AATCGA
1 ATCAAG-TCGAATCGA
19891158 ATCAAGTCGAATCGA
1 ATCAAGTCGAATCGA
19891173 ATCAA
1 ATCAA
19891178 TTGAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (15 bp):
ATCAAGTCGAATCGA
Found at i:19891589 original size:20 final size:20
Alignment explanation
Indices: 19891552--19891614 Score: 78
Period size: 19 Copynumber: 3.3 Consensus size: 20
19891542 TAAAATTTGA
* *
19891552 AATTTTTATAAA-TATTTTG
1 AATTTTTAAAAATTATTTTT
*
19891571 AA-TTTTAAAATTTATTTTT
1 AATTTTTAAAAATTATTTTT
19891590 AATTTTTAAAAATTA-TTTT
1 AATTTTTAAAAATTATTTTT
19891609 AATTTT
1 AATTTT
19891615 CTTGTAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 7 0.18
19 20 0.53
20 11 0.29
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTT
Found at i:19891958 original size:26 final size:26
Alignment explanation
Indices: 19891903--19891969 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 26
19891893 GAATTATAAA
* * *
19891903 TTTTTACTTATTAATTTGGGTTTGGG
1 TTTTTATTTTTTAATTTGGGTATGGG
19891929 -TTTTATTTTTTATATTTGGG-ATGGG
1 TTTTTATTTTTTA-ATTTGGGTATGGG
19891954 TTTTTAGTTTATTTAA
1 TTTTTA-TTT-TTTAA
19891970 AAAAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 14 0.41
26 12 0.35
27 4 0.12
28 4 0.12
ACGTcount: A:0.18, C:0.01, G:0.19, T:0.61
Consensus pattern (26 bp):
TTTTTATTTTTTAATTTGGGTATGGG
Found at i:19892229 original size:16 final size:16
Alignment explanation
Indices: 19892208--19892256 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
19892198 CGTTTGGTTC
19892208 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
19892224 GCTGTAATGAAATAGAA
1 GCTGTAATGGAATAG-A
*
19892241 AC-GTAATGGAATAGA
1 GCTGTAATGGAATAGA
19892256 G
1 G
19892257 GCGTAATAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 1 0.04
16 25 0.89
17 2 0.07
ACGTcount: A:0.43, C:0.06, G:0.29, T:0.22
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:19892261 original size:16 final size:15
Alignment explanation
Indices: 19892211--19892263 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
19892201 TTGGTTCGCT
19892211 GTAATGGAATAGAGC
1 GTAATGGAATAGAGC
* *
19892226 TGTAATGAAATAGAAAC
1 -GTAATGGAATAG-AGC
19892243 GTAATGGAATAGAGGC
1 GTAATGGAATAGA-GC
19892259 GTAAT
1 GTAAT
19892264 AGGTAATCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 28 0.90
17 2 0.06
ACGTcount: A:0.43, C:0.06, G:0.28, T:0.23
Consensus pattern (15 bp):
GTAATGGAATAGAGC
Found at i:19892298 original size:46 final size:44
Alignment explanation
Indices: 19892245--19892338 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
19892235 ATAGAAACGT
* *
19892245 AATGGAATAGAGGCGTAATAGGTAATCCTTTTGTTTGGTTGAATGA
1 AATGGAATAAAGGCGTAATA-GT-ATCCTTGTGTTTGGTTGAATGA
* *
19892291 AATGGAATAAAGGCGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAAAGGCGTAATAGTATCCTTGTGTTTGGTTGAATGA
19892335 AATG
1 AATG
19892339 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 23 0.52
45 2 0.05
46 19 0.43
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (44 bp):
AATGGAATAAAGGCGTAATAGTATCCTTGTGTTTGGTTGAATGA
Found at i:19892460 original size:21 final size:22
Alignment explanation
Indices: 19892445--19892489 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
19892435 TAATAAGATT
19892445 TTTAAT-ATAAATAATAAATAA
1 TTTAATCATAAATAATAAATAA
*
19892466 TTTAATCATATATAATAAATAA
1 TTTAATCATAAATAATAAATAA
19892488 TT
1 TT
19892490 ATTATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAATCATAAATAATAAATAA
Found at i:19892528 original size:28 final size:29
Alignment explanation
Indices: 19892451--19892653 Score: 97
Period size: 28 Copynumber: 6.9 Consensus size: 29
19892441 GATTTTTAAT
* *
19892451 ATAAATAATAAATAATTTAATCAT-ATATA
1 ATAAATAATATATAATTTAAT-ATAATTTA
* *
19892480 ATAAATAAT-TATTATTAAATATAATTTA
1 ATAAATAATATATAATTTAATATAATTTA
*
19892508 ATAAA-AATATATAATTTAATAAAATTCTTA
1 ATAAATAATATATAATTTAATATAA-T-TTA
*
19892538 AT-ATTAA-ATAT--TCTT-ATATGAATTTA
1 ATAAATAATATATAAT-TTAATAT-AATTTA
*
19892564 CTAAAATCATAATATATAATACTATAAAATATAATTT-
1 --ATAA--ATAATATATAAT--T-T--AATATAATTTA
* *
19892601 A-AAATAAT-TATTATTAAATATAATTTA
1 ATAAATAATATATAATTTAATATAATTTA
* *
19892628 ATAAA-AATATATAATTTGATAAAATT
1 ATAAATAATATATAATTTAATATAATT
19892654 CTTAGTATTA
Statistics
Matches: 134, Mismatches: 17, Indels: 47
0.68 0.09 0.24
Matches are distributed among these distances:
26 13 0.10
27 14 0.10
28 50 0.37
29 17 0.13
30 7 0.05
31 8 0.06
32 9 0.07
34 3 0.02
35 3 0.02
36 1 0.01
38 5 0.04
39 4 0.03
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (29 bp):
ATAAATAATATATAATTTAATATAATTTA
Found at i:19892583 original size:61 final size:60
Alignment explanation
Indices: 19892513--19892713 Score: 212
Period size: 61 Copynumber: 3.3 Consensus size: 60
19892503 ATTTAATAAA
19892513 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTT-ATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
* * * * * * ** * *
19892574 AATATATAATACTATAAAA-T-ATAAT-TTAAAATAATTATTAT-TAAATATAATTTAATAAA
1 AATATATAAT-TTATAAAATTCTTAATATT-AAAT-ATTCTTATATGAATTTACTAAAATCAT
*
19892633 AATATATAATTTGATAAAATTCTTAGTATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTT-ATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
*
19892694 AATATATAATACTATAAAAT
1 AATATATAAT-TTATAAAAT
19892714 ATAATTTAAA
Statistics
Matches: 109, Mismatches: 22, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
58 3 0.03
59 35 0.32
60 16 0.15
61 51 0.47
62 4 0.04
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (60 bp):
AATATATAATTTATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
Found at i:19892665 original size:120 final size:120
Alignment explanation
Indices: 19892482--19892747 Score: 514
Period size: 120 Copynumber: 2.2 Consensus size: 120
19892472 CATATATAAT
19892482 AAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAAT
1 AAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAAT
19892547 ATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTA
66 ATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTA
* *
19892602 AAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTGATAAAATTCTTAGTATTAAAT
1 AAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAAT
19892667 ATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTA
66 ATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTA
19892722 AAATAATTATTATTAAATATAATTTA
1 AAATAATTATTATTAAATATAATTTA
19892748 TAATCTACTT
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 144 1.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (120 bp):
AAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAAT
ATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTA
Found at i:19894981 original size:51 final size:50
Alignment explanation
Indices: 19894898--19895002 Score: 149
Period size: 51 Copynumber: 2.1 Consensus size: 50
19894888 ATGCTGGTTT
* *
19894898 TGATACCCTATCTTGATACGTGCAACAAATGGACACTTAAATATACAA-AAA
1 TGATACCCTATCTTGATACATACAACAAATGGACACTT-AATATA-AACAAA
* *
19894949 TGATACCCTATCTTGATACATACATCACATGGACACTTAATATAAACAAA
1 TGATACCCTATCTTGATACATACAACAAATGGACACTTAATATAAACAAA
19894999 TGAT
1 TGAT
19895003 TTATAGCTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
49 2 0.04
50 13 0.27
51 34 0.69
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (50 bp):
TGATACCCTATCTTGATACATACAACAAATGGACACTTAATATAAACAAA
Found at i:19895655 original size:227 final size:227
Alignment explanation
Indices: 19895260--19895711 Score: 832
Period size: 227 Copynumber: 2.0 Consensus size: 227
19895250 TAGCCGATTG
* *
19895260 GATCCTTTGCTGTCTATTCTGAAAAGAGATACTCTAAAGTTACCCCCCATAACTCAGTGTGAAGA
1 GATCCTTTGCTATCTATTCTGAAAAGAGATACTCTAAAGTTACCCCCCAAAACTCAGTGTGAAGA
* * *
19895325 TGATTGAGTAGCCGTACACTAACAGCTATAGGAGGCTACTATGGGTGGTGGGGGCCAATCCCAAG
66 TGATTGAGTAGCCGTACACTAACAGCTATAAGAGGCTACTATAGGTGGTGGGAGCCAATCCCAAG
*
19895390 GGGAAGAAGGGCTGAGACATTATAACTAATGAAACAAAGAAAAACATGGATGATGGAGGATCTAA
131 GGGAAGAAGGGCCGAGACATTATAACTAATGAAACAAAGAAAAACATGGATGATGGAGGATCTAA
19895455 CCACCTTCGGCCCTATTTGTCAAGAATCGATA
196 CCACCTTCGGCCCTATTTGTCAAGAATCGATA
*
19895487 GATCCTTTGCTATCTGTTCTGAAAAGAGATACTCTAAAGTTACCCCCCAAAACTCAGTGTGAAGA
1 GATCCTTTGCTATCTATTCTGAAAAGAGATACTCTAAAGTTACCCCCCAAAACTCAGTGTGAAGA
*
19895552 TGATTGAGTAGCCGTTCACTAACAGCTATAAGAGGCTACTATAGGTGGTGGGAGCCAATCCCAAG
66 TGATTGAGTAGCCGTACACTAACAGCTATAAGAGGCTACTATAGGTGGTGGGAGCCAATCCCAAG
19895617 GGGAAGAAGGGCCGAGACATTATAACTAATGAAACAAAGAAAAACATGGATGATGGAGGATCTAA
131 GGGAAGAAGGGCCGAGACATTATAACTAATGAAACAAAGAAAAACATGGATGATGGAGGATCTAA
19895682 CCACCTTCGGCCCTATTTGTCAAGAATCGA
196 CCACCTTCGGCCCTATTTGTCAAGAATCGA
19895712 CAATGCTGGA
Statistics
Matches: 217, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
227 217 1.00
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (227 bp):
GATCCTTTGCTATCTATTCTGAAAAGAGATACTCTAAAGTTACCCCCCAAAACTCAGTGTGAAGA
TGATTGAGTAGCCGTACACTAACAGCTATAAGAGGCTACTATAGGTGGTGGGAGCCAATCCCAAG
GGGAAGAAGGGCCGAGACATTATAACTAATGAAACAAAGAAAAACATGGATGATGGAGGATCTAA
CCACCTTCGGCCCTATTTGTCAAGAATCGATA
Found at i:19907371 original size:20 final size:21
Alignment explanation
Indices: 19907334--19907372 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19907324 GGAACTAAAA
*
19907334 TAAAAAAATATAATATTAGAT
1 TAAAAAAATATAAAATTAGAT
*
19907355 TAAAATAATA-AAAATTAG
1 TAAAAAAATATAAAATTAG
19907373 GCATAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (21 bp):
TAAAAAAATATAAAATTAGAT
Found at i:19907949 original size:25 final size:26
Alignment explanation
Indices: 19907908--19907966 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
19907898 TACATTAATT
* *
19907908 AGAGTTTAAGTGTGAAATTAAAAA-A
1 AGAGTTTAAGAGTGAAACTAAAAACA
19907933 AGAGTTTAAGAAG-GAAACTAAAAACA
1 AGAGTTTAAG-AGTGAAACTAAAAACA
19907959 A-AGTTTAA
1 AGAGTTTAA
19907967 CTGGGAGAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 27 0.90
26 3 0.10
ACGTcount: A:0.54, C:0.03, G:0.19, T:0.24
Consensus pattern (26 bp):
AGAGTTTAAGAGTGAAACTAAAAACA
Found at i:19909895 original size:25 final size:25
Alignment explanation
Indices: 19909867--19909923 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
19909857 CATTGATCAG
*
19909867 AGTTTAAGTGTGAAACTAAAAACAA
1 AGTTTAAGTGAGAAACTAAAAACAA
*
19909892 AGTTTGAGTGAGAAACTAAAAACAA
1 AGTTTAAGTGAGAAACTAAAAACAA
19909917 AGTTTAA
1 AGTTTAA
19909924 TTGGGAGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.25
Consensus pattern (25 bp):
AGTTTAAGTGAGAAACTAAAAACAA
Found at i:19910092 original size:13 final size:13
Alignment explanation
Indices: 19910071--19910101 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
19910061 GATAATTAAC
*
19910071 AGAACTATAAAAA
1 AGAATTATAAAAA
19910084 AGAATTATAAAAA
1 AGAATTATAAAAA
19910097 AGAAT
1 AGAAT
19910102 AAGACGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.10, T:0.19
Consensus pattern (13 bp):
AGAATTATAAAAA
Found at i:19912683 original size:25 final size:25
Alignment explanation
Indices: 19912655--19912708 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
19912645 ACAGCTTGGG
**
19912655 AGAGAATACTGATTTATAGCTCGTA
1 AGAGAATACCAATTTATAGCTCGTA
* *
19912680 AGAGCATACCAATTTATATCTCGTA
1 AGAGAATACCAATTTATAGCTCGTA
19912705 AGAG
1 AGAG
19912709 CATATCGATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (25 bp):
AGAGAATACCAATTTATAGCTCGTA
Found at i:19912727 original size:25 final size:25
Alignment explanation
Indices: 19912672--19912727 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
19912662 ACTGATTTAT
* *
19912672 AGCTCGTAAGAGCATACCAATTTAT
1 AGCTCGTAAGAGCATACCAATCTAC
* * *
19912697 ATCTCGTAAGAGCATATCGATCTAC
1 AGCTCGTAAGAGCATACCAATCTAC
19912722 AGCTCG
1 AGCTCG
19912728 AATAAGTATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (25 bp):
AGCTCGTAAGAGCATACCAATCTAC
Found at i:19915419 original size:18 final size:18
Alignment explanation
Indices: 19915398--19915432 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19915388 GAAAATTGGG
*
19915398 AAAATGAAAAAAAAAAGA
1 AAAAAGAAAAAAAAAAGA
*
19915416 AAAAAGATAAAAAAAAG
1 AAAAAGAAAAAAAAAAG
19915433 GGATATTGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (18 bp):
AAAAAGAAAAAAAAAAGA
Found at i:19916588 original size:30 final size:28
Alignment explanation
Indices: 19916552--19916628 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 28
19916542 AACCCCCTTT
* *
19916552 AGGCGAACCTTTGTATGTGCGAACCTCTAC
1 AGGCGAACCCTTGTATGTG-AAACC-CTAC
* *
19916582 AGGCGAAACCCCTTGCATGTGAAACCCTAT
1 AGGCG-AA-CCCTTGTATGTGAAACCCTAC
19916612 AGGCGAACCCTTGTATG
1 AGGCGAACCCTTGTATG
19916629 CGGCCCCCTA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 9 0.22
29 2 0.05
30 13 0.32
31 6 0.15
32 10 0.25
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.23
Consensus pattern (28 bp):
AGGCGAACCCTTGTATGTGAAACCCTAC
Found at i:19919205 original size:14 final size:14
Alignment explanation
Indices: 19919186--19919212 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19919176 TATTATAATA
19919186 AATTAAAGAAAAAT
1 AATTAAAGAAAAAT
19919200 AATTAAAGAAAAA
1 AATTAAAGAAAAA
19919213 AAGAAGAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (14 bp):
AATTAAAGAAAAAT
Found at i:19920473 original size:27 final size:27
Alignment explanation
Indices: 19920435--19920500 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
19920425 ATGATTATGT
19920435 GAAATGATTATA-AGAATTGGTTATATA
1 GAAATGATTATATAGAA-TGGTTATATA
19920462 GAAATAGA-TATATAGAATGGTTATAT-
1 GAAAT-GATTATATAGAATGGTTATATA
19920488 G-AATCGATTATAT
1 GAAAT-GATTATAT
19920501 GGAAATAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
25 5 0.14
26 6 0.17
27 18 0.51
28 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.36
Consensus pattern (27 bp):
GAAATGATTATATAGAATGGTTATATA
Found at i:19920498 original size:13 final size:13
Alignment explanation
Indices: 19920417--19920539 Score: 92
Period size: 13 Copynumber: 9.4 Consensus size: 13
19920407 TTGAAATCGC
19920417 TATATGAAATGAT
1 TATATGAAATGAT
*
19920430 TATGTGAAATGAT
1 TATATGAAATGAT
* * *
19920443 TATAAGAATTGGT
1 TATATGAAATGAT
19920456 TATATAGAAATAGA-
1 TATAT-GAAAT-GAT
*
19920470 TATAT-AGAATGGT
1 TATATGA-AATGAT
19920483 TATATG-AATCGAT
1 TATATGAAAT-GAT
*
19920496 TATATGGAAATAAT
1 TATAT-GAAATGAT
* *
19920510 TATATTAAGTG-T
1 TATATGAAATGAT
*
19920522 TATATGAAATGTT
1 TATATGAAATGAT
19920535 TATAT
1 TATAT
19920540 TCATAAATAT
Statistics
Matches: 85, Mismatches: 16, Indels: 18
0.71 0.13 0.15
Matches are distributed among these distances:
12 15 0.18
13 49 0.58
14 17 0.20
15 4 0.05
ACGTcount: A:0.42, C:0.01, G:0.17, T:0.40
Consensus pattern (13 bp):
TATATGAAATGAT
Found at i:19933501 original size:22 final size:22
Alignment explanation
Indices: 19933470--19933512 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
19933460 TGGGGGTAGA
*
19933470 CTCTAAATCAATATCTGATATG
1 CTCTAAATCAATACCTGATATG
* *
19933492 CTCTACATCAGTACCTGATAT
1 CTCTAAATCAATACCTGATAT
19933513 ACTTTGTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (22 bp):
CTCTAAATCAATACCTGATATG
Found at i:19950687 original size:25 final size:25
Alignment explanation
Indices: 19950659--19950728 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
19950649 CAGGCCCATT
*
19950659 TTCACAGCTTGTGTGAGCATTCTGA
1 TTCACAGCTTGTGTGAGCATTCTAA
**
19950684 TTCACAGCTCATGTGAGCATTCTAA
1 TTCACAGCTTGTGTGAGCATTCTAA
*
19950709 TTCACCGCTTGTGTGAGCAT
1 TTCACAGCTTGTGTGAGCAT
19950729 ACATGTACAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (25 bp):
TTCACAGCTTGTGTGAGCATTCTAA
Found at i:19957016 original size:14 final size:16
Alignment explanation
Indices: 19956993--19957024 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19956983 GTCTGTTTGA
19956993 TTTCCAGTAAAAT-AT
1 TTTCCAGTAAAATGAT
19957008 TTTCC-GTAAAATGAT
1 TTTCCAGTAAAATGAT
19957023 TT
1 TT
19957025 CTGGAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.44
Consensus pattern (16 bp):
TTTCCAGTAAAATGAT
Found at i:19957047 original size:20 final size:20
Alignment explanation
Indices: 19957022--19957061 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19957012 CGTAAAATGA
*
19957022 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
19957042 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
19957062 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:19957051 original size:34 final size:35
Alignment explanation
Indices: 19957007--19957073 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
19956997 CAGTAAAATA
*
19957007 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
19957041 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
19957074 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:19957077 original size:14 final size:15
Alignment explanation
Indices: 19957001--19957077 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
19956991 GATTTCCAGT
* *
19957001 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
19957015 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
19957029 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
19957049 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
19957064 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
19957078 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:19958155 original size:40 final size:40
Alignment explanation
Indices: 19958100--19958197 Score: 133
Period size: 40 Copynumber: 2.5 Consensus size: 40
19958090 AGGTTCTGTT
* * *
19958100 TCTAGCAGGTTTATTGTCACTGAAATTTTCAAATTTAATG
1 TCTAGCAGGCTTATTGCCACTGAAATTTTCAAACTTAATG
* *
19958140 TCTAGCAGGCTTATTGCCAGTGAAATTTTCAGACTTAATG
1 TCTAGCAGGCTTATTGCCACTGAAATTTTCAAACTTAATG
* *
19958180 TCTAGTAGGCTTAATGCC
1 TCTAGCAGGCTTATTGCC
19958198 GGTGTCCTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (40 bp):
TCTAGCAGGCTTATTGCCACTGAAATTTTCAAACTTAATG
Found at i:19959174 original size:52 final size:52
Alignment explanation
Indices: 19959093--19959196 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
19959083 AGTTAATGAG
*
19959093 GAAGTAGGAATGAGTGTTTTATCTTAAACTATTTGATCTTAGATGAACAAGT
1 GAAGTAGGAATGAGTGTTTTATCTCAAACTATTTGATCTTAGATGAACAAGT
19959145 GAAGTAGGAATGAGTGTTTTATCTCAAACTATTTGATCTTAGATGAACAAGT
1 GAAGTAGGAATGAGTGTTTTATCTCAAACTATTTGATCTTAGATGAACAAGT
19959197 TGAATCTGTG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.36
Consensus pattern (52 bp):
GAAGTAGGAATGAGTGTTTTATCTCAAACTATTTGATCTTAGATGAACAAGT
Found at i:19961280 original size:27 final size:27
Alignment explanation
Indices: 19961223--19961302 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
19961213 AATTGAACTA
*
19961223 ATCATTCAT-CCTTCATGGGATAATA-T
1 ATCATTCATCCCTT-AAGGGATAATATT
*
19961249 GTCATTCATCCCTTAAGGGATAATATT
1 ATCATTCATCCCTTAAGGGATAATATT
* *
19961276 ATCA-TCTATCCCTTGATGGATAATATT
1 ATCATTC-ATCCCTTAAGGGATAATATT
19961303 TCACATTTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
26 20 0.43
27 26 0.57
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (27 bp):
ATCATTCATCCCTTAAGGGATAATATT
Found at i:19962636 original size:26 final size:26
Alignment explanation
Indices: 19962585--19962637 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
19962575 CATTAGGGTG
*
19962585 TAGCAGGCTTTGTACCGGTGTATATT
1 TAGCAGGCTTTGTACCGATGTATATT
* * *
19962611 TAGCAGGCTTTGTGCTGATGTTTATT
1 TAGCAGGCTTTGTACCGATGTATATT
19962637 T
1 T
19962638 TGTAGGCATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.26, T:0.43
Consensus pattern (26 bp):
TAGCAGGCTTTGTACCGATGTATATT
Found at i:19963650 original size:12 final size:12
Alignment explanation
Indices: 19963633--19963657 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19963623 GGTGTTCAGT
19963633 CGGTTAACCGAC
1 CGGTTAACCGAC
19963645 CGGTTAACCGAC
1 CGGTTAACCGAC
19963657 C
1 C
19963658 CGAAATTTGT
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:19963832 original size:9 final size:9
Alignment explanation
Indices: 19963818--19963871 Score: 72
Period size: 9 Copynumber: 5.6 Consensus size: 9
19963808 TTTGGTTAAA
19963818 AATTACCCG
1 AATTACCCG
19963827 AATTACCCG
1 AATTACCCG
19963836 AATTACCCG
1 AATTACCCG
19963845 AAAATTACCCG
1 --AATTACCCG
19963856 AAAATTACCCG
1 --AATTACCCG
19963867 AATTA
1 AATTA
19963872 AATCACTACA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
9 23 0.53
11 20 0.47
ACGTcount: A:0.41, C:0.28, G:0.09, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:19963852 original size:11 final size:11
Alignment explanation
Indices: 19963816--19963868 Score: 78
Period size: 11 Copynumber: 5.2 Consensus size: 11
19963806 TTTTTGGTTA
19963816 AAAATTACCCG
1 AAAATTACCCG
19963827 --AATTACCCG
1 AAAATTACCCG
19963836 --AATTACCCG
1 AAAATTACCCG
19963845 AAAATTACCCG
1 AAAATTACCCG
19963856 AAAATTACCCG
1 AAAATTACCCG
19963867 AA
1 AA
19963869 TTAAATCACT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
9 18 0.45
11 22 0.55
ACGTcount: A:0.43, C:0.28, G:0.09, T:0.19
Consensus pattern (11 bp):
AAAATTACCCG
Found at i:19963937 original size:17 final size:17
Alignment explanation
Indices: 19963915--19964012 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 17
19963905 TTTAAATTGC
19963915 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
19963932 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
19963952 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
** * *
19963969 TACATAAGTCTTGAATTAAC
1 TACATAA-T-TAAAAAT-AT
*
19963989 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
19964006 TACATAA
1 TACATAA
19964013 GTCTTGAATT
Statistics
Matches: 56, Mismatches: 19, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
17 23 0.41
18 8 0.14
19 9 0.16
20 16 0.29
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:19964018 original size:37 final size:38
Alignment explanation
Indices: 19963876--19964033 Score: 227
Period size: 37 Copynumber: 4.3 Consensus size: 38
19963866 GAATTAAATC
* * *
19963876 ACTACATAATTAAAAGCATTACATAAATCTTTAAATT-
1 ACTACATAATTAAAAACATTACATAAGTCTTTGAATTA
* * *
19963913 GCTACATAATTAAAAATATTACATAAGTCTTTGAA-TC
1 ACTACATAATTAAAAACATTACATAAGTCTTTGAATTA
19963950 ACTACATAATTAAAAACATTACATAAGTC-TTGAATTA
1 ACTACATAATTAAAAACATTACATAAGTCTTTGAATTA
19963987 ACTACATAATTAAAAACATTACATAAGTC-TTGAATTA
1 ACTACATAATTAAAAACATTACATAAGTCTTTGAATTA
19964024 AC-ACATAATT
1 ACTACATAATT
19964034 GACATGTAAG
Statistics
Matches: 111, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
36 14 0.13
37 97 0.87
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (38 bp):
ACTACATAATTAAAAACATTACATAAGTCTTTGAATTA
Found at i:19968045 original size:6 final size:6
Alignment explanation
Indices: 19968034--19968070 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
19968024 TGTGAGTGAC
* *
19968034 AGAGTG AGAGTG AGAGTG AGAGTG AAAGTG AAAGTG A
1 AGAGTG AGAGTG AGAGTG AGAGTG AGAGTG AGAGTG A
19968071 AATTGTGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.43, T:0.16
Consensus pattern (6 bp):
AGAGTG
Found at i:19968080 original size:8 final size:8
Alignment explanation
Indices: 19968067--19968098 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
19968057 GAAAGTGAAA
19968067 GTGAAATT
1 GTGAAATT
19968075 GTGAAATT
1 GTGAAATT
19968083 GTGAAATT
1 GTGAAATT
19968091 GTGAAATT
1 GTGAAATT
19968099 AGGGAGGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (8 bp):
GTGAAATT
Found at i:19968271 original size:16 final size:16
Alignment explanation
Indices: 19968250--19968289 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
19968240 GGTGTTGTGA
19968250 AAATTGGGCTGGAATT
1 AAATTGGGCTGGAATT
**
19968266 AAATTGGGCTGGGTTT
1 AAATTGGGCTGGAATT
19968282 AAATTGGG
1 AAATTGGG
19968290 AGGGAATAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.05, G:0.35, T:0.33
Consensus pattern (16 bp):
AAATTGGGCTGGAATT
Found at i:19972670 original size:12 final size:12
Alignment explanation
Indices: 19972653--19972677 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19972643 GGTGTTCATT
19972653 CGGTTAACCGAC
1 CGGTTAACCGAC
19972665 CGGTTAACCGAC
1 CGGTTAACCGAC
19972677 C
1 C
19972678 CGAAATTACT
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:19972851 original size:9 final size:9
Alignment explanation
Indices: 19972837--19972906 Score: 122
Period size: 9 Copynumber: 7.8 Consensus size: 9
19972827 TTTGGTTAAA
19972837 AATTACCCG
1 AATTACCCG
19972846 AATTACCCG
1 AATTACCCG
19972855 AATTACCCG
1 AATTACCCG
19972864 AATTACCCG
1 AATTACCCG
19972873 AATTACCCG
1 AATTACCCG
*
19972882 AATTAACCG
1 AATTACCCG
*
19972891 AATTAACCG
1 AATTACCCG
19972900 AATTACC
1 AATTACC
19972907 GAAAAATACC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 59 1.00
ACGTcount: A:0.37, C:0.30, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:19980057 original size:3 final size:3
Alignment explanation
Indices: 19980049--19980073 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19980039 AGTTATCACT
19980049 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
19980074 AAAATTTATT
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:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:19981451 original size:9 final size:9
Alignment explanation
Indices: 19981437--19981473 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
19981427 TATAGTTTGA
19981437 TATTCGAAT
1 TATTCGAAT
19981446 TATTCGAAT
1 TATTCGAAT
*
19981455 TATTCGAGT
1 TATTCGAAT
19981464 TATTCGAAT
1 TATTCGAAT
19981473 T
1 T
19981474 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:19981733 original size:16 final size:16
Alignment explanation
Indices: 19981704--19981739 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
19981694 ATCTAAATAA
19981704 TCAA-ATTCAATCTAT
1 TCAATATTCAATCTAT
*
19981719 TCAATATTCATTCTAT
1 TCAATATTCAATCTAT
19981735 TCAAT
1 TCAAT
19981740 TCAGTCCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.44
Consensus pattern (16 bp):
TCAATATTCAATCTAT
Done.