Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 9 of 310
Found at i:2177019 original size:58 final size:58
Alignment explanation
Indices: 2176929--2177045 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 58
2176919 TGTCTTAAAC
* * *
2176929 GAGCGTCGTGGTAGTGCTTCGTTGCTTCCTTGTATAGGCGTGAATTTTCATATGCATT
1 GAGCGTCGTGGTAGCGCTTCATTGCTTCCTTGTAAAGGCGTGAATTTTCATATGCATT
*
2176987 GAGCGTCGTGGTGGCGCTTCATTGCTTCCTTGTAAAGGCGTGAATTTTCATATGCATT
1 GAGCGTCGTGGTAGCGCTTCATTGCTTCCTTGTAAAGGCGTGAATTTTCATATGCATT
2177045 G
1 G
2177046 GTTCACCATT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.16, C:0.18, G:0.28, T:0.38
Consensus pattern (58 bp):
GAGCGTCGTGGTAGCGCTTCATTGCTTCCTTGTAAAGGCGTGAATTTTCATATGCATT
Found at i:2200824 original size:28 final size:28
Alignment explanation
Indices: 2200751--2200825 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 28
2200741 TATATATATG
*
2200751 TGGCACTTAGTGTGCGAAATATTGAGAA
1 TGGCACTTAGTGTGCGAGATATTGAGAA
* * *
2200779 TGGAACTTGGTGTGCGAGATATTGAGTA
1 TGGCACTTAGTGTGCGAGATATTGAGAA
2200807 TGGCACTTAGTGTGCGAGA
1 TGGCACTTAGTGTGCGAGA
2200826 CATCGAAGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.27, C:0.11, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTTAGTGTGCGAGATATTGAGAA
Found at i:2201719 original size:245 final size:245
Alignment explanation
Indices: 2201289--2201766 Score: 956
Period size: 245 Copynumber: 2.0 Consensus size: 245
2201279 CCCTCGTTCT
2201289 GATTTGGGAAAATCATTAAAAATTGTACAGAAATAATTGTGGGTTATAATTTATATGCTTAAAAT
1 GATTTGGGAAAATCATTAAAAATTGTACAGAAATAATTGTGGGTTATAATTTATATGCTTAAAAT
2201354 AATTAATTAGTTTATTTTTTTAAAAAATAAATGGAAACATCATTTGAATCCCGTATGAGGAGATA
66 AATTAATTAGTTTATTTTTTTAAAAAATAAATGGAAACATCATTTGAATCCCGTATGAGGAGATA
2201419 ATAAATTTTTAGTAAAGAAAGGTCGAAGCTGTCAAACAGCAGAATATGGGTAACTTTGAAAAATA
131 ATAAATTTTTAGTAAAGAAAGGTCGAAGCTGTCAAACAGCAGAATATGGGTAACTTTGAAAAATA
2201484 AATTGTACTTATTGGCTAATCCATAAATTCTTAAAATTAAAAATTGTACA
196 AATTGTACTTATTGGCTAATCCATAAATTCTTAAAATTAAAAATTGTACA
2201534 GATTTGGGAAAATCATTAAAAATTGTACAGAAATAATTGTGGGTTATAATTTATATGCTTAAAAT
1 GATTTGGGAAAATCATTAAAAATTGTACAGAAATAATTGTGGGTTATAATTTATATGCTTAAAAT
2201599 AATTAATTAGTTTATTTTTTTAAAAAATAAATGGAAACATCATTTGAATCCCGTATGAGGAGATA
66 AATTAATTAGTTTATTTTTTTAAAAAATAAATGGAAACATCATTTGAATCCCGTATGAGGAGATA
2201664 ATAAATTTTTAGTAAAGAAAGGTCGAAGCTGTCAAACAGCAGAATATGGGTAACTTTGAAAAATA
131 ATAAATTTTTAGTAAAGAAAGGTCGAAGCTGTCAAACAGCAGAATATGGGTAACTTTGAAAAATA
2201729 AATTGTACTTATTGGCTAATCCATAAATTCTTAAAATT
196 AATTGTACTTATTGGCTAATCCATAAATTCTTAAAATT
2201767 TTATGGTAGA
Statistics
Matches: 233, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
245 233 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (245 bp):
GATTTGGGAAAATCATTAAAAATTGTACAGAAATAATTGTGGGTTATAATTTATATGCTTAAAAT
AATTAATTAGTTTATTTTTTTAAAAAATAAATGGAAACATCATTTGAATCCCGTATGAGGAGATA
ATAAATTTTTAGTAAAGAAAGGTCGAAGCTGTCAAACAGCAGAATATGGGTAACTTTGAAAAATA
AATTGTACTTATTGGCTAATCCATAAATTCTTAAAATTAAAAATTGTACA
Found at i:2204231 original size:74 final size:74
Alignment explanation
Indices: 2204142--2204289 Score: 260
Period size: 74 Copynumber: 2.0 Consensus size: 74
2204132 CATTAATTTA
* *
2204142 TTAAACAATCACTTAGTTTTAACAACAAATTTAAGTAAAAAGGTGATAAATTGTATAAGAAAAAT
1 TTAAACAATCACTTAGTTTTAACAACAAATTTAAGTAAAAAGGTGAGAAATTGCATAAGAAAAAT
2204207 CCTATATAT
66 CCTATATAT
* *
2204216 TTAAACAATTACTTAGTTTTAACAACAAATTTAAGTAAAAAGGTGAGAAATTGCATAGGAAAAAT
1 TTAAACAATCACTTAGTTTTAACAACAAATTTAAGTAAAAAGGTGAGAAATTGCATAAGAAAAAT
2204281 CCTATATAT
66 CCTATATAT
2204290 ATTTTAGTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (74 bp):
TTAAACAATCACTTAGTTTTAACAACAAATTTAAGTAAAAAGGTGAGAAATTGCATAAGAAAAAT
CCTATATAT
Found at i:2205609 original size:22 final size:22
Alignment explanation
Indices: 2205562--2205643 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
2205552 TAGCTCATTG
* *
2205562 GAGCTTACCGTTCCACCTTGATA
1 GAGCTTACCGTT-CAGCTCGATA
*
2205585 GAGCTTACTGTTCAGCTCGATA
1 GAGCTTACCGTTCAGCTCGATA
* *
2205607 GAGTTTACCGTTTCAGCTCAATA
1 GAGCTTACCG-TTCAGCTCGATA
* *
2205630 AAGCTTACTGTTCA
1 GAGCTTACCGTTCA
2205644 TTAGCTCAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 20 0.41
23 29 0.59
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (22 bp):
GAGCTTACCGTTCAGCTCGATA
Found at i:2215484 original size:20 final size:19
Alignment explanation
Indices: 2215439--2215476 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2215429 GAGTGAAAGG
2215439 AACGAG-AAATGGGCCAAA
1 AACGAGAAAATGGGCCAAA
*
2215457 AACGGAGAAAATGGGTCAAA
1 AAC-GAGAAAATGGGCCAAA
2215477 GTACGAGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 3 0.18
20 11 0.65
ACGTcount: A:0.50, C:0.13, G:0.29, T:0.08
Consensus pattern (19 bp):
AACGAGAAAATGGGCCAAA
Found at i:2223730 original size:43 final size:43
Alignment explanation
Indices: 2223683--2223837 Score: 172
Period size: 43 Copynumber: 3.7 Consensus size: 43
2223673 TGTGTTCTCA
* *
2223683 TGTAAGACCACGTCTGGAACGTTGGCATCGATATGTGATTACG
1 TGTAAGACCATGTCTGGGACGTTGGCATCGATATGTGATTACG
* * * *
2223726 TGTAAGACCATGTCTGGGACATCGGCATCG-TATTTAATT-CG
1 TGTAAGACCATGTCTGGGACGTTGGCATCGATATGTGATTACG
* * * **
2223767 TGTAAGACCTTGTCTGGGACAG-TGGTATCGATATGAGATTATA
1 TGTAAGACCATGTCTGGGAC-GTTGGCATCGATATGTGATTACG
*
2223810 TGTAAGACCATGTCTGGGATGTTGGCAT
1 TGTAAGACCATGTCTGGGACGTTGGCAT
2223838 TGTACGATAT
Statistics
Matches: 90, Mismatches: 18, Indels: 8
0.78 0.16 0.07
Matches are distributed among these distances:
41 27 0.30
42 14 0.16
43 49 0.54
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACGTTGGCATCGATATGTGATTACG
Found at i:2240804 original size:14 final size:14
Alignment explanation
Indices: 2240785--2240815 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2240775 AAGAGAGAAT
2240785 GATGATGGATGAGG
1 GATGATGGATGAGG
*
2240799 GATGATTGATGAGG
1 GATGATGGATGAGG
2240813 GAT
1 GAT
2240816 CAAACGAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.45, T:0.26
Consensus pattern (14 bp):
GATGATGGATGAGG
Found at i:2241372 original size:87 final size:87
Alignment explanation
Indices: 2241273--2241441 Score: 320
Period size: 87 Copynumber: 1.9 Consensus size: 87
2241263 TTATATTTTA
*
2241273 TTATTTAATTTAATCATGCGTGACCCATTTTATGTCTTAAAAATATAATATGTTCAAATAAATAT
1 TTATTTAATTTAATCATGCATGACCCATTTTATGTCTTAAAAATATAATATGTTCAAATAAATAT
*
2241338 AAAATAAGTCATTTTATCCATG
66 AAAATAAGCCATTTTATCCATG
2241360 TTATTTAATTTAATCATGCATGACCCATTTTATGTCTTAAAAATATAATATGTTCAAATAAATAT
1 TTATTTAATTTAATCATGCATGACCCATTTTATGTCTTAAAAATATAATATGTTCAAATAAATAT
2241425 AAAATAAGCCATTTTAT
66 AAAATAAGCCATTTTAT
2241442 GCATAAAAAC
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.41
Consensus pattern (87 bp):
TTATTTAATTTAATCATGCATGACCCATTTTATGTCTTAAAAATATAATATGTTCAAATAAATAT
AAAATAAGCCATTTTATCCATG
Found at i:2243773 original size:31 final size:31
Alignment explanation
Indices: 2243735--2243798 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
2243725 TTCATCAAAA
2243735 AGGCCAACATGCAACGCTGAAAAGTAGTAGG
1 AGGCCAACATGCAACGCTGAAAAGTAGTAGG
*
2243766 AGGCCAACATGCAACGCTGAAAATTAGTAGG
1 AGGCCAACATGCAACGCTGAAAAGTAGTAGG
2243797 AG
1 AG
2243799 CATTACATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (31 bp):
AGGCCAACATGCAACGCTGAAAAGTAGTAGG
Found at i:2250038 original size:31 final size:31
Alignment explanation
Indices: 2250002--2250080 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
2249992 TTTAATGGTT
2250002 ACTAGGCTGAAGCCTTTTCATAAATCATATC
1 ACTAGGCTGAAGCCTTTTCATAAATCATATC
*
2250033 ACTAGGCCGAAGCCTTTTCATAAATCATATC
1 ACTAGGCTGAAGCCTTTTCATAAATCATATC
* *
2250064 ATTGGGCTGAAGCCTTT
1 ACTAGGCTGAAGCCTTT
2250081 ACTGTAAACG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (31 bp):
ACTAGGCTGAAGCCTTTTCATAAATCATATC
Found at i:2250404 original size:26 final size:26
Alignment explanation
Indices: 2250286--2250423 Score: 185
Period size: 26 Copynumber: 5.3 Consensus size: 26
2250276 CTGGAGGCCT
2250286 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
**
2250310 AGCCCTTTTCGGTAAACTGGGGCA-A
1 AGCCCTTTTCAATAAACTGGGGCATA
2250335 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
2250361 AGCCCTTTTTTCGGTAAACTGGGGCATA
1 AGCCC--TTTTCAATAAACTGGGGCATA
2250389 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
2250415 AGCCCTTTT
1 AGCCCTTTT
2250424 GCACTTCCTC
Statistics
Matches: 101, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.05
24 5 0.05
25 33 0.33
26 34 0.34
28 24 0.24
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:2250406 original size:54 final size:53
Alignment explanation
Indices: 2250286--2250423 Score: 223
Period size: 54 Copynumber: 2.7 Consensus size: 53
2250276 CTGGAGGCCT
2250286 AGCCTCTTTT-AAT-AACTGGGGCA-AAGCCC--TTTTCGGTAAACTGGGGCAA
1 AGCC-CTTTTCAATAAACTGGGGCATAAGCCCTTTTTTCGGTAAACTGGGGCAA
2250335 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTTTCGGTAAACTGGGGCA-A
2250389 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT
2250424 GCACTTCCTC
Statistics
Matches: 83, Mismatches: 0, Indels: 7
0.92 0.00 0.08
Matches are distributed among these distances:
48 5 0.06
49 7 0.08
50 10 0.12
51 6 0.07
53 19 0.23
54 36 0.43
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (53 bp):
AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTTTCGGTAAACTGGGGCAA
Found at i:2251322 original size:27 final size:27
Alignment explanation
Indices: 2251227--2251313 Score: 131
Period size: 27 Copynumber: 3.2 Consensus size: 27
2251217 CATTCGTCAT
* *
2251227 TTTACCATACAGGGG-TATTACGGTCAC
1 TTTACCCTACAGGGGCT-TTACGGTCTC
2251254 TTTACCCTACAGGGGCTTTACGGTCTC
1 TTTACCCTACAGGGGCTTTACGGTCTC
*
2251281 TTTACCCTACAGGGGCTTTACGGTCTT
1 TTTACCCTACAGGGGCTTTACGGTCTC
2251308 TTTACC
1 TTTACC
2251314 TAATAGGGGT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 55 0.98
28 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.34
Consensus pattern (27 bp):
TTTACCCTACAGGGGCTTTACGGTCTC
Found at i:2251436 original size:29 final size:28
Alignment explanation
Indices: 2251367--2251465 Score: 85
Period size: 28 Copynumber: 3.5 Consensus size: 28
2251357 GTAAATCTAC
*
2251367 AAACCAAGGGTATTTCAATAATTTTGTT
1 AAACCAAGGGTATTTCAATAATTTTGTG
* *
2251395 AAACCAATGGTATTTCCATAATTTT-TAG
1 AAACCAAGGGTATTTCAATAATTTTGT-G
* ** *
2251423 AAAGTCAAGGGTATTTCTGTAACTTTGT-
1 AAA-CCAAGGGTATTTCAATAATTTTGTG
* *
2251451 AAATCAGGGGTATTT
1 AAACCAAGGGTATTT
2251466 TGGTAATTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
27 12 0.20
28 29 0.49
29 17 0.29
30 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38
Consensus pattern (28 bp):
AAACCAAGGGTATTTCAATAATTTTGTG
Found at i:2251544 original size:81 final size:81
Alignment explanation
Indices: 2251456--2251800 Score: 622
Period size: 81 Copynumber: 4.3 Consensus size: 81
2251446 TTTGTAAATC
2251456 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTT
2251521 GGTAATTTTACAAACT
66 GGTAATTTTACAAACT
2251537 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTT
2251602 GGTAATTTTACAAACT
66 GGTAATTTTACAAACT
2251618 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTT
2251683 GGTAATTTTACAAACT
66 GGTAATTTTACAAACT
* *
2251699 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAAG-GGTATTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACC-AGTGGTATTT
* * *
2251763 TAGCAATTTTACAGACT
65 TGGTAATTTTACAAACT
2251780 A-GGGTATTTTGGTAATTTTAC
1 AGGGGTATTTTGGTAATTTTAC
2251801 TGATCGAGAG
Statistics
Matches: 258, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
80 20 0.08
81 236 0.91
82 2 0.01
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTT
GGTAATTTTACAAACT
Found at i:2251840 original size:27 final size:27
Alignment explanation
Indices: 2251458--2251866 Score: 391
Period size: 27 Copynumber: 15.2 Consensus size: 27
2251448 TGTAAATCAG
*
2251458 GGGTATTTTGGTAATTTTACAAATTGA
1 GGGTATTTTGGTAATTTTACAAATCGA
** * *
2251485 GGGTATTTCAGTAATTTCACAAA-CCA
1 GGGTATTTTGGTAATTTTACAAATCGA
*
2251511 GTGGTATTTTGGTAATTTTACAAA-CTA
1 G-GGTATTTTGGTAATTTTACAAATCGA
*
2251538 GGGGTATTTTGGTAATTTTACAAATTGA
1 -GGGTATTTTGGTAATTTTACAAATCGA
** * *
2251566 GGGTATTTCAGTAATTTCACAAA-CCA
1 GGGTATTTTGGTAATTTTACAAATCGA
*
2251592 GTGGTATTTTGGTAATTTTACAAA-CTA
1 G-GGTATTTTGGTAATTTTACAAATCGA
*
2251619 GGGGTATTTTGGTAATTTTACAAATTGA
1 -GGGTATTTTGGTAATTTTACAAATCGA
** * *
2251647 GGGTATTTCAGTAATTTCACAAA-CCA
1 GGGTATTTTGGTAATTTTACAAATCGA
*
2251673 GTGGTATTTTGGTAATTTTACAAA-CTA
1 G-GGTATTTTGGTAATTTTACAAATCGA
*
2251700 GGGGTATTTTGGTAATTTTACAAATTGA
1 -GGGTATTTTGGTAATTTTACAAATCGA
* * *
2251728 GGGTATTTCGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAATCGA
* * * *
2251755 GGGTATTTTAGCAATTTTACAGA-CTA
1 GGGTATTTTGGTAATTTTACAAATCGA
**
2251781 GGGTATTTTGGTAATTTTACTGATCGA
1 GGGTATTTTGGTAATTTTACAAATCGA
* ** *
2251808 GAGTATTTTGGTAATTTTGTAAACCGA
1 GGGTATTTTGGTAATTTTACAAATCGA
* * **
2251835 TGGTATTTTAGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTACAAATCGA
2251862 GGGTA
1 GGGTA
2251867 AAACAGTAAT
Statistics
Matches: 315, Mismatches: 57, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
26 28 0.09
27 281 0.89
28 6 0.02
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATCGA
Found at i:2251874 original size:27 final size:27
Alignment explanation
Indices: 2251844--2251974 Score: 190
Period size: 27 Copynumber: 4.9 Consensus size: 27
2251834 ATGGTATTTT
* *
2251844 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
* *
2251871 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
* *
2251898 AATAATTCTATAAATTGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
* *
2251925 GGTAATTCTATAAATCAAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
2251952 AGTAATTCTATAAATCGAGGGTA
1 AGTAATTCTATAAATCGAGGGTA
2251975 CTTTGGTAAT
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 92 1.00
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (27 bp):
AGTAATTCTATAAATCGAGGGTAAAAC
Found at i:2252011 original size:81 final size:81
Alignment explanation
Indices: 2251836--2252012 Score: 183
Period size: 81 Copynumber: 2.2 Consensus size: 81
2251826 GTAAACCGAT
* * * * *
2251836 GGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAAT
1 GGTATTTCAGTAATTCTATAAATCAAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAACAAT
*
2251901 AATTCTATAAATTGAG
66 AATTCTACAAATTGAG
*** * * ******
2251917 GGTAAAACGGTAATTCTATAAATCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTACTTTGGT
1 GGTATTTCAGTAATTCTATAAATCAAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAACAAT
* *
2251982 AATTTTACAATTTGAG
66 AATTCTACAAATTGAG
2251998 GGTATTTCAGTAATT
1 GGTATTTCAGTAATT
2252013 TGGTAAACTA
Statistics
Matches: 73, Mismatches: 23, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.34
Consensus pattern (81 bp):
GGTATTTCAGTAATTCTATAAATCAAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAACAAT
AATTCTACAAATTGAG
Found at i:2254517 original size:28 final size:27
Alignment explanation
Indices: 2254454--2254578 Score: 187
Period size: 28 Copynumber: 4.6 Consensus size: 27
2254444 ATATTAAGTC
* *
2254454 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
2254481 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
2254509 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
2254537 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
2254564 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
2254579 GCACAATTTA
Statistics
Matches: 93, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
27 39 0.42
28 54 0.58
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:2254599 original size:56 final size:56
Alignment explanation
Indices: 2254454--2254578 Score: 173
Period size: 55 Copynumber: 2.3 Consensus size: 56
2254444 ATATTAAGTC
* * * *
2254454 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCTACATAATCAAACT
* * *
2254509 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTC-AATT
1 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCTACATAATCAAACT
2254564 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
2254579 GCACAATTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
55 38 0.59
56 26 0.41
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (56 bp):
CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCTACATAATCAAACT
Found at i:2258616 original size:39 final size:39
Alignment explanation
Indices: 2258526--2258689 Score: 154
Period size: 40 Copynumber: 4.1 Consensus size: 39
2258516 CGGAATTTAA
** *
2258526 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGG-CTTAGC
*
2258566 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGCTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGC
* * *
2258605 CCGGGAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGT
1 CC-GGATATAGTAACTCGCACAAATGCCTTCGG-GCTTAGC
* * * *
2258645 CCGGATATGGTCACTTAGCACAAA-GCCTTCAGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTC-GGGCTTAGC
2258685 CCGGA
1 CCGGA
2258690 CACATTCAAA
Statistics
Matches: 104, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
39 36 0.35
40 58 0.56
41 10 0.10
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (39 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGC
Found at i:2261354 original size:47 final size:47
Alignment explanation
Indices: 2261244--2261369 Score: 139
Period size: 47 Copynumber: 2.7 Consensus size: 47
2261234 ATGGATGTAT
* * ** *
2261244 GCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCACATTATGAGA
1 GCTAGTGTAAAACATGTCTGGGACATGGCATCAGCCACAAGATGAAA
* * *
2261290 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAG-CATTAAGATGAAA
1 GCTAGTGTAA-AACATGTCTGGGACATGGCATCAGCCA-CAAGATGAAA
*
2261338 GCTAGTGTAAAACATGTTTGGGACATGGCATC
1 GCTAGTGTAAAACATGTCTGGGACATGGCATC
2261370 GGCTTGACAT
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
46 9 0.14
47 36 0.55
48 21 0.32
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (47 bp):
GCTAGTGTAAAACATGTCTGGGACATGGCATCAGCCACAAGATGAAA
Found at i:2268591 original size:23 final size:23
Alignment explanation
Indices: 2268563--2268608 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2268553 GATTTAAAAG
2268563 TATGATTTTTCTTACGAATTTAA
1 TATGATTTTTCTTACGAATTTAA
2268586 TATGATTTTTCTTACGAATTTAA
1 TATGATTTTTCTTACGAATTTAA
2268609 ATTTATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (23 bp):
TATGATTTTTCTTACGAATTTAA
Found at i:2268924 original size:22 final size:20
Alignment explanation
Indices: 2268884--2268932 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
2268874 TGATTTAATC
*
2268884 TTTTTTTTTAGATACATCAAA
1 TTTTTTTTTAGAGACATC-AA
2268905 TATTTTTTTTATGAGA-ATCAA
1 T-TTTTTTTTA-GAGACATCAA
2268926 TTTTTTT
1 TTTTTTT
2268933 CTAATAATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.24
21 4 0.16
22 12 0.48
23 3 0.12
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (20 bp):
TTTTTTTTTAGAGACATCAA
Found at i:2279618 original size:2 final size:2
Alignment explanation
Indices: 2279613--2279639 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2279603 TTTATGAACT
2279613 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 T
2279640 TGAATTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2280513 original size:11 final size:11
Alignment explanation
Indices: 2280481--2280515 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2280471 TAGACCATGA
* *
2280481 AACATTTTAAC
1 AACAATTTAAT
2280492 AACAATTTAAT
1 AACAATTTAAT
2280503 AACAATTTAAT
1 AACAATTTAAT
2280514 AA
1 AA
2280516 GAGTAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (11 bp):
AACAATTTAAT
Found at i:2285835 original size:18 final size:19
Alignment explanation
Indices: 2285812--2285849 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2285802 GGAAGCAAGC
*
2285812 AATGATTGAAGA-AATCAG
1 AATGATTGAAAAGAATCAG
2285830 AATGATTGAAAAGAATCAG
1 AATGATTGAAAAGAATCAG
2285849 A
1 A
2285850 CCTGGAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGATTGAAAAGAATCAG
Found at i:2298448 original size:42 final size:42
Alignment explanation
Indices: 2298400--2298563 Score: 197
Period size: 42 Copynumber: 3.9 Consensus size: 42
2298390 TTAGGGTTAC
*
2298400 TGAGACTACGTGTAAGACCATATCTGGGATATGACATCAGTA
1 TGAGACTACGTGTAAGACCATATCTGGGATATGGCATCAGTA
* *
2298442 TGAGACTACGTGTAAGACCATATCTAGGATATGGCATCAATA
1 TGAGACTACGTGTAAGACCATATCTGGGATATGGCATCAGTA
* * *
2298484 TGAGACTTCGTGTAAGACTATAGT-TGGGCTATTGGCATC-GATA
1 TGAGACTACGTGTAAGACCATA-TCTGGGATA-TGGCATCAG-TA
* * * *
2298527 CGAGATTACATGTAATACCATATCTGGGATATGGCAT
1 TGAGACTACGTGTAAGACCATATCTGGGATATGGCAT
2298564 TGGTATAGTA
Statistics
Matches: 103, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
42 71 0.69
43 32 0.31
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (42 bp):
TGAGACTACGTGTAAGACCATATCTGGGATATGGCATCAGTA
Found at i:2298557 original size:85 final size:84
Alignment explanation
Indices: 2298400--2298563 Score: 206
Period size: 85 Copynumber: 1.9 Consensus size: 84
2298390 TTAGGGTTAC
* *
2298400 TGAGACTACGTGTAAGACCATATCTGGGATATGACATCAGTATGAGACTACGTGTAAGACCATAT
1 TGAGACTACGTGTAAGACCATATCTGGGATATGACATCAGTACGAGACTACATGTAAGACCATAT
2298465 CTAGGATATGGCATCAATA
66 CTAGGATATGGCATCAATA
* * * * * *
2298484 TGAGACTTCGTGTAAGACTATAGT-TGGGCTATTGGCATC-GATACGAGATTACATGTAATACCA
1 TGAGACTACGTGTAAGACCATA-TCTGGGATA-TGACATCAG-TACGAGACTACATGTAAGACCA
*
2298547 TATCTGGGATATGGCAT
63 TATCTAGGATATGGCAT
2298564 TGGTATAGTA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
84 27 0.40
85 41 0.60
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (84 bp):
TGAGACTACGTGTAAGACCATATCTGGGATATGACATCAGTACGAGACTACATGTAAGACCATAT
CTAGGATATGGCATCAATA
Found at i:2298760 original size:15 final size:15
Alignment explanation
Indices: 2298740--2298780 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
2298730 ACCCTTGGTA
2298740 AGGTTATGATTGAGT
1 AGGTTATGATTGAGT
2298755 AGGTTATGATTGAGT
1 AGGTTATGATTGAGT
* *
2298770 AAGTAATGATT
1 AGGTTATGATT
2298781 ATAAGATCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (15 bp):
AGGTTATGATTGAGT
Found at i:2327490 original size:20 final size:21
Alignment explanation
Indices: 2327452--2327500 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
2327442 TGAGCTAGAT
*
2327452 CGAGCTGAATTCTAGCTCAAA
1 CGAGCTGAATTCGAGCTCAAA
*
2327473 CGAGCTGAA-TCGAGCTCAAG
1 CGAGCTGAATTCGAGCTCAAA
*
2327493 TGAGCTGA
1 CGAGCTGA
2327501 TGGGAGCTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
CGAGCTGAATTCGAGCTCAAA
Found at i:2338417 original size:41 final size:43
Alignment explanation
Indices: 2338346--2338475 Score: 138
Period size: 43 Copynumber: 3.0 Consensus size: 43
2338336 GTCTTACATG
* * * *
2338346 TTATCACATATCGATGCCATTGACCCAGACAGGGTCTTACACAAA
1 TTATCAC-TA-CGATGCCAATGTCCTAGACATGGTCTTACACAAA
* **
2338391 TTAT-A-TACGATGCCAATGTTCTAGACATGGTCTTACACATT
1 TTATCACTACGATGCCAATGTCCTAGACATGGTCTTACACAAA
* * *
2338432 TTCTCACTTCGATGCCAATGTCCTAGACATGATCTTACACAAA
1 TTATCACTACGATGCCAATGTCCTAGACATGGTCTTACACAAA
2338475 T
1 T
2338476 CACACATCGA
Statistics
Matches: 70, Mismatches: 13, Indels: 6
0.79 0.15 0.07
Matches are distributed among these distances:
41 30 0.43
42 3 0.04
43 32 0.46
44 1 0.01
45 4 0.06
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (43 bp):
TTATCACTACGATGCCAATGTCCTAGACATGGTCTTACACAAA
Found at i:2342154 original size:22 final size:22
Alignment explanation
Indices: 2342128--2342171 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2342118 GAAAATAATC
2342128 AAAATTAATCAAAATTAATTAT
1 AAAATTAATCAAAATTAATTAT
* *
2342150 AAAATTAATTAAAATTCATTAT
1 AAAATTAATCAAAATTAATTAT
2342172 GTTAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATTAATCAAAATTAATTAT
Found at i:2342170 original size:10 final size:10
Alignment explanation
Indices: 2342119--2342170 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
2342109 AAATCTGTCG
*
2342119 AAAA-TAATC
1 AAAATTAATT
*
2342128 AAAATTAATC
1 AAAATTAATT
2342138 AAAATTAATTAT
1 AAAATTAA-T-T
2342150 AAAATTAATT
1 AAAATTAATT
*
2342160 AAAATTCATT
1 AAAATTAATT
2342170 A
1 A
2342171 TGTTAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 4 0.11
10 24 0.63
11 2 0.05
12 8 0.21
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAATTAATT
Found at i:2345013 original size:5 final size:5
Alignment explanation
Indices: 2345003--2345033 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
2344993 GTAAATATAT
2345003 TATTA TATTA TATTA TATTA TTATTA TATTA
1 TATTA TATTA TATTA TATTA -TATTA TATTA
2345034 AAATATGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:2347295 original size:15 final size:17
Alignment explanation
Indices: 2347277--2347309 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2347267 AGCATAATTT
2347277 ACCAAA-TCA-ATTCAC
1 ACCAAACTCACATTCAC
2347292 ACCAAACTCACATTCAC
1 ACCAAACTCACATTCAC
2347309 A
1 A
2347310 AGTTTCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.18
Consensus pattern (17 bp):
ACCAAACTCACATTCAC
Found at i:2347956 original size:13 final size:13
Alignment explanation
Indices: 2347938--2347966 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2347928 ACCATCTCGA
2347938 ATAATAATGTCGG
1 ATAATAATGTCGG
2347951 ATAATAATGTCGG
1 ATAATAATGTCGG
2347964 ATA
1 ATA
2347967 CTCGAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (13 bp):
ATAATAATGTCGG
Found at i:2348105 original size:41 final size:41
Alignment explanation
Indices: 2348060--2348160 Score: 193
Period size: 41 Copynumber: 2.5 Consensus size: 41
2348050 ATCGACGGGC
*
2348060 CTGCTCACACAAGCTGTCAGTTAAGATGTAGCTACGCGGTG
1 CTGCTCACACAAGCTGTCAGTCAAGATGTAGCTACGCGGTG
2348101 CTGCTCACACAAGCTGTCAGTCAAGATGTAGCTACGCGGTG
1 CTGCTCACACAAGCTGTCAGTCAAGATGTAGCTACGCGGTG
2348142 CTGCTCACACAAGCTGTCA
1 CTGCTCACACAAGCTGTCA
2348161 AGTATTCACA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.23
Consensus pattern (41 bp):
CTGCTCACACAAGCTGTCAGTCAAGATGTAGCTACGCGGTG
Found at i:2351675 original size:12 final size:13
Alignment explanation
Indices: 2351647--2351673 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2351637 TTTTATTATT
2351647 AATTAAAAGAAAA
1 AATTAAAAGAAAA
2351660 AATTAAAAGAAAA
1 AATTAAAAGAAAA
2351673 A
1 A
2351674 TTGCTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (13 bp):
AATTAAAAGAAAA
Found at i:2353631 original size:15 final size:16
Alignment explanation
Indices: 2353611--2353644 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
2353601 AAACCTGTAA
2353611 AAATTAAAT-TAAAAT
1 AAATTAAATATAAAAT
2353626 AAATTAAATACTAAAAT
1 AAATTAAATA-TAAAAT
2353643 AA
1 AA
2353645 CCAAACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATTAAATATAAAAT
Found at i:2355263 original size:20 final size:20
Alignment explanation
Indices: 2355238--2355287 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2355228 AGGGACTAAA
* *
2355238 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
2355258 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
2355278 ATGAATAAAT
1 ATGAA-AAAT
2355288 GTGCTGGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:2360263 original size:87 final size:87
Alignment explanation
Indices: 2360169--2360340 Score: 263
Period size: 87 Copynumber: 2.0 Consensus size: 87
2360159 TGTAGACGTG
* * * *
2360169 CGTGTGGCATGGTCGTGTGTGCAAGTTAGAGAGTTACACAGGGTCAAACACGACCTCTAGTACGG
1 CGTGTGGCAGGGCCGTGTGTGCAAGTCAGAGAGTTACACAGGGTCAAACACGACCTCTAGCACGG
* *
2360234 GTGTGTCCTAGGGTCACACGGA
66 GCGTGTCCCAGGGTCACACGGA
* *
2360256 CGTGTGGCAGGGCCGTGTGTGCAAGTCAGAGAGTTACATAGGGTCGAACACGACCTCTAGCACGG
1 CGTGTGGCAGGGCCGTGTGTGCAAGTCAGAGAGTTACACAGGGTCAAACACGACCTCTAGCACGG
*
2360321 GCGTGTCCCAGGGTTACACG
66 GCGTGTCCCAGGGTCACACG
2360341 AGCGTGTCCC
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 76 1.00
ACGTcount: A:0.22, C:0.23, G:0.34, T:0.21
Consensus pattern (87 bp):
CGTGTGGCAGGGCCGTGTGTGCAAGTCAGAGAGTTACACAGGGTCAAACACGACCTCTAGCACGG
GCGTGTCCCAGGGTCACACGGA
Found at i:2367068 original size:32 final size:33
Alignment explanation
Indices: 2367023--2367086 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
2367013 ACGAAGTCAC
*
2367023 CAGATATAGATA-TTGTGGCTAAGCCACCAGAA
1 CAGATATAGATATTTGTGGCGAAGCCACCAGAA
*
2367055 CAGATATATATATTTGTGGCGAAGCCACCAGA
1 CAGATATAGATATTTGTGGCGAAGCCACCAGA
2367087 TTGCAGCAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 11 0.38
33 18 0.62
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (33 bp):
CAGATATAGATATTTGTGGCGAAGCCACCAGAA
Found at i:2367112 original size:73 final size:67
Alignment explanation
Indices: 2367030--2367172 Score: 187
Period size: 67 Copynumber: 2.0 Consensus size: 67
2367020 CACCAGATAT
* *
2367030 AGATATTGTGGCTAAGCCACCAGAACAGATATATATATTTGTGGCGAAGCCACCAGATTGCAGCA
1 AGATATTGTGACGAAGCCACCAGAACAG----ATATA--TGTGGCGAAGCCACCAGATTGCAGCA
2367095 AGGCTGCC
60 AGGCTGCC
* * *
2367103 AGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTG
1 AGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCAAGGCTG
2367168 CC
66 CC
2367170 AGA
1 AGA
2367173 ATGCTTCCTC
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
67 35 0.54
69 5 0.08
73 25 0.38
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (67 bp):
AGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCAAGGCTG
CC
Found at i:2367150 original size:27 final size:26
Alignment explanation
Indices: 2367102--2367153 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
2367092 GCAAGGCTGC
*
2367102 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
2367128 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
2367154 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:2382577 original size:101 final size:101
Alignment explanation
Indices: 2382402--2382867 Score: 880
Period size: 101 Copynumber: 4.6 Consensus size: 101
2382392 ACAAAAATTT
2382402 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTATGGCTAGGCCACCAAAC
1 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTATGGCTAGGCCACCAAAC
2382467 AGATATATATGAATATGTGGCGAAGCGACCAGATTG
66 AGATATATATGAATATGTGGCGAAGCGACCAGATTG
2382503 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTATGGCTAGGCCACCAAAC
1 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTATGGCTAGGCCACCAAAC
2382568 AGATATATATGAATATGTGGCGAAGCGACCAGATTG
66 AGATATATATGAATATGTGGCGAAGCGACCAGATTG
2382604 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTATGGCTAGGCCACCAAAC
1 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTATGGCTAGGCCACCAAAC
2382669 AGATATATATGAATATGTGGCGAAGCGACCAGATTG
66 AGATATATATGAATATGTGGCGAAGCGACCAGATTG
2382705 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTATGGCTAGGCCACCAAAC
1 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTATGGCTAGGCCACCAAAC
2382770 AGATATATATGAATATGTGGCGAAGCGACCAGATTG
66 AGATATATATGAATATGTGGCGAAGCGACCAGATTG
* * * *
2382806 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCATA-ACATATATATGTGGCGAGGCCACCA
1 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATAT-TATGGCTAGGCCACCA
2382868 GATTGCAGCG
Statistics
Matches: 360, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
100 7 0.02
101 353 0.98
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (101 bp):
CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTATGGCTAGGCCACCAAAC
AGATATATATGAATATGTGGCGAAGCGACCAGATTG
Found at i:2390931 original size:45 final size:45
Alignment explanation
Indices: 2390880--2391034 Score: 178
Period size: 45 Copynumber: 3.5 Consensus size: 45
2390870 AGGATTTCCA
*
2390880 ATATATGT-GTTCTCGTGTAAGACCACGTCTGGGACATTGGCATCG
1 ATATATGTGGTT-TCGTGTAAGACCACGTCTAGGACATTGGCATCG
* * * *
2390925 ATATATGTGGTTACATGTAAGACCACATCTAGGACGTTGGCATCG
1 ATATATGTGGTTTCGTGTAAGACCACGTCTAGGACATTGGCATCG
* *
2390970 ATATATGTGGTTAT-GTGTAAGACCATGTCTAGGACATCGGCATCG
1 ATATATGTGGTT-TCGTGTAAGACCACGTCTAGGACATTGGCATCG
*
2391015 -TAT-T-T-GATTCGTGTAAGACC
1 ATATATGTGGTTTCGTGTAAGACC
2391035 CTATCTGGGA
Statistics
Matches: 95, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
40 1 0.01
41 12 0.13
42 1 0.01
43 1 0.01
44 3 0.03
45 74 0.78
46 3 0.03
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (45 bp):
ATATATGTGGTTTCGTGTAAGACCACGTCTAGGACATTGGCATCG
Found at i:2395169 original size:40 final size:40
Alignment explanation
Indices: 2395071--2395333 Score: 309
Period size: 40 Copynumber: 6.6 Consensus size: 40
2395061 TCCTCGTTCA
* * * ** *
2395071 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
2395110 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
2395150 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
2395190 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
2395230 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
2395270 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
2395310 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
2395334 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.19
40 154 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:2403121 original size:40 final size:40
Alignment explanation
Indices: 2403021--2403232 Score: 250
Period size: 40 Copynumber: 5.3 Consensus size: 40
2403011 GCTCCTCGTT
* * * * *
2403021 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
* ** *
2403061 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
*
2403100 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
* * * *
2403140 CAAAGGCCTTCGGGGCTTAACTCGTAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCG-GATTTAGTATCTCGCA
*
2403180 CAAATGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTATCTCGCA
2403220 CAAATGCCTTCGG
1 CAAATGCCTTCGG
2403233 ATCTTAGTCC
Statistics
Matches: 152, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.22
40 114 0.75
41 4 0.03
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
Found at i:2407242 original size:36 final size:38
Alignment explanation
Indices: 2407174--2407249 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
2407164 TTCACACGGG
2407174 AATAAAAACTAATATATAGTACAAATTAACTCCTTCAA
1 AATAAAAACTAATATATAGTACAAATTAACTCCTTCAA
*
2407212 AATACAAACTAATATATAGTACAAA-T-ACTCCTTCAA
1 AATAAAAACTAATATATAGTACAAATTAACTCCTTCAA
2407248 AA
1 AA
2407250 CAATAAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
36 12 0.32
37 1 0.03
38 24 0.65
ACGTcount: A:0.53, C:0.17, G:0.03, T:0.28
Consensus pattern (38 bp):
AATAAAAACTAATATATAGTACAAATTAACTCCTTCAA
Found at i:2407372 original size:26 final size:26
Alignment explanation
Indices: 2407343--2407392 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2407333 TTTTGGACAT
* *
2407343 ATTCATAACTAAATATTTGATTTTGG
1 ATTCATAACCAAATATGTGATTTTGG
*
2407369 ATTCATAACCATATATGTGATTTT
1 ATTCATAACCAAATATGTGATTTT
2407393 AGACAACTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (26 bp):
ATTCATAACCAAATATGTGATTTTGG
Found at i:2410519 original size:30 final size:31
Alignment explanation
Indices: 2410483--2410542 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
2410473 CAATGGAAAG
*
2410483 GATGAAAATGTTATCGATT-AAAAGGTTATT
1 GATGAAAAGGTTATCGATTAAAAAGGTTATT
*
2410513 GATGAAAAGGTTATTGATTAAAAAGGTTAT
1 GATGAAAAGGTTATCGATTAAAAAGGTTAT
2410543 ACAAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.35
Consensus pattern (31 bp):
GATGAAAAGGTTATCGATTAAAAAGGTTATT
Found at i:2410538 original size:16 final size:15
Alignment explanation
Indices: 2410487--2410542 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
2410477 GGAAAGGATG
* *
2410487 AAAATGTTATCGATT
1 AAAAGGTTATTGATT
*
2410502 AAAAGGTTATTGATG
1 AAAAGGTTATTGATT
2410517 AAAAGGTTATTGATT
1 AAAAGGTTATTGATT
2410532 AAAAAGGTTAT
1 -AAAAGGTTAT
2410543 ACAAATAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
15 26 0.72
16 10 0.28
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.36
Consensus pattern (15 bp):
AAAAGGTTATTGATT
Found at i:2410963 original size:15 final size:15
Alignment explanation
Indices: 2410923--2410964 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
2410913 ACTCCATTCC
* *
2410923 CTTTAATCATGGTAA
1 CTTTAGTCATTGTAA
2410938 CTTTAGTCATTGTAA
1 CTTTAGTCATTGTAA
2410953 CTTTAGTCATTG
1 CTTTAGTCATTG
2410965 CTTGAGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.45
Consensus pattern (15 bp):
CTTTAGTCATTGTAA
Found at i:2412517 original size:27 final size:27
Alignment explanation
Indices: 2412487--2412559 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 27
2412477 TGTCTTGAAT
2412487 TTGTTAGATATTGATTATGTTTCAAGC
1 TTGTTAGATATTGATTATGTTTCAAGC
*
2412514 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTG-----ATTATGTTTCAAGC
*
2412546 TTGTTGGATATTGA
1 TTGTTAGATATTGA
2412560 AATGATTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 14 0.36
32 25 0.64
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTCAAGC
Found at i:2412539 original size:32 final size:32
Alignment explanation
Indices: 2412500--2412560 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
2412490 TTAGATATTG
2412500 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
* *
2412532 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTCAAGCTTGTTAGATATTGAA
2412561 ATGATTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (32 bp):
ATTATGTTTCAAGCTTGTTAGATATTGAATTT
Found at i:2414000 original size:14 final size:15
Alignment explanation
Indices: 2413981--2414018 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
2413971 CTAGAAAAGT
2413981 AAATTATTTTTC-AA
1 AAATTATTTTTCGAA
2413995 AAATTATTTTTCGAA
1 AAATTATTTTTCGAA
2414010 AAA-TATTTT
1 AAATTATTTT
2414019 ATTGGCAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (15 bp):
AAATTATTTTTCGAA
Found at i:2414194 original size:52 final size:52
Alignment explanation
Indices: 2414120--2414224 Score: 140
Period size: 52 Copynumber: 2.0 Consensus size: 52
2414110 AGGTGTAAAA
* * * *
2414120 ACATAATGCATGAAATGCAACAAAAG-TTGGGCCTGTTTTTGCCCCTATGTGT
1 ACATAACGCATGAAATACAACAAAAGCTT-AGCCTGTTTCTGCCCCTATGTGT
**
2414172 ACATAACGCATGAAATACAACAAAAGCTTAGCCTGTTTCTGTTCCTATGTGT
1 ACATAACGCATGAAATACAACAAAAGCTTAGCCTGTTTCTGCCCCTATGTGT
2414224 A
1 A
2414225 GGCCTATAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
52 44 0.96
53 2 0.04
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (52 bp):
ACATAACGCATGAAATACAACAAAAGCTTAGCCTGTTTCTGCCCCTATGTGT
Found at i:2416498 original size:64 final size:66
Alignment explanation
Indices: 2416425--2416557 Score: 225
Period size: 64 Copynumber: 2.0 Consensus size: 66
2416415 AGTGGCAGCA
2416425 AATTATAATAATAAAGGAATTGTATGTATATATAATA-T-TGATGATATAGTTTGGAATTGTTAT
1 AATTATAATAATAAAGGAATTGTATGTATATATAATATTATGATGATATAGTTTGGAATTGTTAT
2416488 G
66 G
**
2416489 AATTATAATAATAGTGGAATTGTATGTATATATAATATTGATGATGATATAGTTTGGAATTGTTA
1 AATTATAATAATAAAGGAATTGTATGTATATATAATATT-ATGATGATATAGTTTGGAATTGTTA
2416554 TG
65 TG
2416556 AA
1 AA
2416558 CTATCTTCAT
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
64 35 0.55
65 1 0.02
67 28 0.44
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (66 bp):
AATTATAATAATAAAGGAATTGTATGTATATATAATATTATGATGATATAGTTTGGAATTGTTAT
G
Found at i:2417823 original size:17 final size:16
Alignment explanation
Indices: 2417771--2417875 Score: 68
Period size: 17 Copynumber: 6.2 Consensus size: 16
2417761 ACACAATTTC
*
2417771 TTTAAAA-ACGAGAAT
1 TTTAAAACACGAAAAT
*
2417786 TTTAGAAACATGAAAATT
1 TTTA-AAACACGAAAA-T
*
2417804 TTTAAAACACGACAACT
1 TTTAAAACACGA-AAAT
* *
2417821 TTTGAAGCACGAGAAATT
1 TTTAAAACACGA-AAA-T
* *
2417839 TATTCAAAACACAAAAAA
1 T-TT-AAAACACGAAAAT
*
2417857 TTTAAAACACGAACAT
1 TTTAAAACACGAAAAT
2417873 TTT
1 TTT
2417876 TTGAAACAAT
Statistics
Matches: 68, Mismatches: 15, Indels: 13
0.71 0.16 0.14
Matches are distributed among these distances:
15 4 0.06
16 16 0.24
17 27 0.40
18 10 0.15
19 5 0.07
20 6 0.09
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.28
Consensus pattern (16 bp):
TTTAAAACACGAAAAT
Found at i:2417948 original size:34 final size:35
Alignment explanation
Indices: 2417910--2418109 Score: 120
Period size: 35 Copynumber: 5.7 Consensus size: 35
2417900 TTAAACAAGA
*
2417910 AAAATTTTTAAAACACGAGAATTTTAGAG-ACACG
1 AAAATTTTTAAAACACGAAAATTTTAGAGAACACG
* *
2417944 AAAATTCTTAAAACACGAAAATTTTTGAGAACACG
1 AAAATTTTTAAAACACGAAAATTTTAGAGAACACG
* * * ** * *
2417979 ACAATTTTGAAATACGCGAATTTTTTTGAAAAC-CTG
1 AAAATTTTTAAA-ACACGAAAATTTTAGAGAACAC-G
*** * * * * *
2418015 ATTTTTTTTGAAGCGCGAAAATTCGT-GA-AACATG
1 AAAATTTTTAAAACACGAAAATT-TTAGAGAACACG
* * * *
2418049 AGAATTGTTGAAAACACGAAAATTTTTGAAAACACG
1 AAAATT-TTTAAAACACGAAAATTTTAGAGAACACG
* *
2418085 AAAATTTTTGAAACATGAAAATTTT
1 AAAATTTTTAAAACACGAAAATTTT
2418110 TTGAAAACAC
Statistics
Matches: 125, Mismatches: 33, Indels: 15
0.72 0.19 0.09
Matches are distributed among these distances:
34 34 0.27
35 56 0.45
36 35 0.28
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (35 bp):
AAAATTTTTAAAACACGAAAATTTTAGAGAACACG
Found at i:2418110 original size:88 final size:88
Alignment explanation
Indices: 2417942--2418114 Score: 197
Period size: 88 Copynumber: 2.0 Consensus size: 88
2417932 TTTAGAGACA
* * * * * **
2417942 CGAAAATTCTTAAAACACGAAAATTTTTGAGAACACGACAATTTTGAAATACGCGAATTTTTTTG
1 CGAAAATTCGTAAAACACGAAAATTGTTGAAAACACGAAAATTTTGAAATACACGAAAATTTTTG
* **
2418007 AAAACCTGATTTTTTTTGAAGCG
66 AAAACATGAAATTTTTTGAAGCG
* * *
2418030 CGAAAATTCGTGAAACATGAGAATTGTTGAAAACACGAAAATTTTTGAAA-ACACGAAAATTTTT
1 CGAAAATTCGTAAAACACGAAAATTGTTGAAAACACGAAAA-TTTTGAAATACACGAAAATTTTT
2418094 G-AAACATGAAAATTTTTTGAA
65 GAAAACATG-AAATTTTTTGAA
2418115 AACACAAATT
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
87 6 0.09
88 56 0.80
89 8 0.11
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.32
Consensus pattern (88 bp):
CGAAAATTCGTAAAACACGAAAATTGTTGAAAACACGAAAATTTTGAAATACACGAAAATTTTTG
AAAACATGAAATTTTTTGAAGCG
Found at i:2418128 original size:17 final size:18
Alignment explanation
Indices: 2417910--2418182 Score: 161
Period size: 18 Copynumber: 15.5 Consensus size: 18
2417900 TTAAACAAGA
2417910 AAAATTTTT-AAAACACG
1 AAAATTTTTGAAAACACG
* * *
2417927 AGAATTTTAG-AGACACG
1 AAAATTTTTGAAAACACG
*
2417944 AAAATTCTT-AAAACACG
1 AAAATTTTTGAAAACACG
*
2417961 AAAATTTTTGAGAACACG
1 AAAATTTTTGAAAACACG
* *
2417979 ACAA-TTTTGAAATACGCG
1 AAAATTTTTGAAA-ACACG
**
2417997 AATTTTTTTGAAAAC-CTG
1 AAAATTTTTGAAAACAC-G
*** * *
2418015 ATTTTTTTTG-AAGCGCG
1 AAAATTTTTGAAAACACG
** *
2418032 AAAATTCGTG-AAACATG
1 AAAATTTTTGAAAACACG
* *
2418049 AGAATTGTTGAAAACACG
1 AAAATTTTTGAAAACACG
2418067 AAAATTTTTGAAAACACG
1 AAAATTTTTGAAAACACG
*
2418085 AAAATTTTTG-AAACATG
1 AAAATTTTTGAAAACACG
2418102 AAAATTTTTTGAAAACAC-
1 AAAA-TTTTTGAAAACACG
* *** * *
2418120 AAATTTTTTTTTGATCATG
1 AAA-ATTTTTGAAAACACG
** **
2418139 GGAATTTTTGAAAACGTG
1 AAAATTTTTGAAAACACG
2418157 AAAATTTTTG-AAACACG
1 AAAATTTTTGAAAACACG
*
2418174 AAAGTTTTT
1 AAAATTTTT
2418183 TTTTNNNNNN
Statistics
Matches: 192, Mismatches: 52, Indels: 24
0.72 0.19 0.09
Matches are distributed among these distances:
17 84 0.44
18 94 0.49
19 14 0.07
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (18 bp):
AAAATTTTTGAAAACACG
Found at i:2418458 original size:10 final size:10
Alignment explanation
Indices: 2418443--2418476 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
2418433 ATTGAACCCC
2418443 TTTTTTCTTG
1 TTTTTTCTTG
2418453 TTTTTTCTTG
1 TTTTTTCTTG
2418463 TTTTTTCTT-
1 TTTTTTCTTG
2418472 TTTTT
1 TTTTT
2418477 CTCCTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 5 0.21
10 19 0.79
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (10 bp):
TTTTTTCTTG
Found at i:2418783 original size:12 final size:12
Alignment explanation
Indices: 2418766--2418840 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
2418756 ACTGTTAAAA
2418766 TTTTTTTT-TTC
1 TTTTTTTTCTTC
2418777 TTTTTTTTCTTC
1 TTTTTTTTCTTC
*
2418789 TTTCTTCTTC-TC
1 TTT-TTTTTCTTC
*
2418801 TCTTTCTTTCTTC
1 T-TTTTTTTCTTC
* *
2418814 TTCTTCTTCTTCC
1 TTTTTTTTCTT-C
* *
2418827 TTCTTCTTCTTC
1 TTTTTTTTCTTC
2418839 TT
1 TT
2418841 CAAAACCGAG
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
11 8 0.15
12 23 0.43
13 22 0.42
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTTTTCTTC
Found at i:2418789 original size:3 final size:3
Alignment explanation
Indices: 2418783--2418841 Score: 73
Period size: 3 Copynumber: 18.0 Consensus size: 3
2418773 TTTCTTTTTT
2418783 TTC TTC TTTC TTC TTC TCTC TTTC TTTC TTC TTC TTC TTC TTCC TTC
1 TTC TTC -TTC TTC TTC T-TC -TTC -TTC TTC TTC TTC TTC TT-C TTC
2418830 TTC TTC TTC TTC
1 TTC TTC TTC TTC
2418842 AAAACCGAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
3 37 0.71
4 14 0.27
5 1 0.02
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:2418794 original size:16 final size:16
Alignment explanation
Indices: 2418773--2418840 Score: 91
Period size: 16 Copynumber: 4.1 Consensus size: 16
2418763 AAATTTTTTT
* *
2418773 TTTCTTTTTTTTCTTC
1 TTTCTTCTTCTTCTTC
2418789 TTTCTTCTTCTCTCTTTC
1 TTTCTTCTTCT-TC-TTC
2418807 TTTCTTCTTCTTCTTC
1 TTTCTTCTTCTTCTTC
*
2418823 TTCCTTCTTCTTCTTC
1 TTTCTTCTTCTTCTTC
2418839 TT
1 TT
2418841 CAAAACCGAG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
16 29 0.62
17 4 0.09
18 14 0.30
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCTTCTTCTTCTTC
Found at i:2418821 original size:34 final size:33
Alignment explanation
Indices: 2418773--2418837 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
2418763 AAATTTTTTT
* * *
2418773 TTTCTTTTTTTTCTTCTTTCTTCTTCTCTCTTTC
1 TTTCTTCTTCTTCTTCTTCCTTCTTCT-TCTTTC
2418807 TTTCTTCTTCTTCTTCTTCCTTCTTCTTCTT
1 TTTCTTCTTCTTCTTCTTCCTTCTTCTTCTT
2418838 CTTCAAAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 4 0.14
34 24 0.86
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (33 bp):
TTTCTTCTTCTTCTTCTTCCTTCTTCTTCTTTC
Found at i:2419248 original size:30 final size:29
Alignment explanation
Indices: 2419208--2419309 Score: 132
Period size: 30 Copynumber: 3.4 Consensus size: 29
2419198 AATTAGGATT
2419208 AAAATGAAATTTAATAAAAGTTTAGGGGTC
1 AAAATGAAATTTAA-AAAAGTTTAGGGGTC
* * *
2419238 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAA-AAAGTTTAGGGGTC
*
2419268 AAAATGAAATTTAGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTA-AAAAAGTTTAGGGGTC
*
2419298 AAAATGCAATTT
1 AAAATGAAATTT
2419310 TTATTTTTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 1 0.02
30 60 0.97
31 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (29 bp):
AAAATGAAATTTAAAAAAGTTTAGGGGTC
Found at i:2419332 original size:14 final size:15
Alignment explanation
Indices: 2419308--2419340 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2419298 AAAATGCAAT
2419308 TTTTATTTTTTAAAA
1 TTTTATTTTTTAAAA
*
2419323 TTTT-TTTTTTGAAA
1 TTTTATTTTTTAAAA
2419337 TTTT
1 TTTT
2419341 GAAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
TTTTATTTTTTAAAA
Found at i:2419714 original size:54 final size:55
Alignment explanation
Indices: 2419582--2419748 Score: 266
Period size: 54 Copynumber: 3.1 Consensus size: 55
2419572 CACGTGAGCC
* *
2419582 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AA
* * *
2419637 AAGGCTCAACTCACCTTTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
2419691 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
2419746 AAG
1 AAG
2419749 TAGAAATTGA
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
54 51 0.50
55 41 0.40
56 10 0.10
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
Found at i:2419746 original size:14 final size:14
Alignment explanation
Indices: 2419727--2419761 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2419717 GAGTTGATTT
2419727 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
**
2419741 TTGAAAAGTAGAAA
1 TTGAAAAACAGAAA
2419755 TTGAAAA
1 TTGAAAA
2419762 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:2420042 original size:15 final size:16
Alignment explanation
Indices: 2420009--2420042 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2419999 TTGATTTTTG
* *
2420009 AAAAGCATAGATTGAA
1 AAAAACATAAATTGAA
2420025 AAAAACATAAATTGAA
1 AAAAACATAAATTGAA
2420041 AA
1 AA
2420043 TACCTCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAAACATAAATTGAA
Found at i:2420084 original size:91 final size:86
Alignment explanation
Indices: 2419849--2420103 Score: 295
Period size: 91 Copynumber: 2.9 Consensus size: 86
2419839 AACAGAAATT
* *
2419849 AAAAACAAAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAAAA-TTGAAAATACCTCAGC-TGTGGCC-GAGGCTCAACTCACCTCTTGCAATATGAG
*
2419914 TTGA--TTTGAAAAGTAGAATTAG
63 TTGATTTTTGAAAAGTAGAATTAA
* * * * *
2419936 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCTTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACA-AAATTGAAAATACCTCAGCTGTGGC--CGAGGCTCAACTCACCTCTTGCAATATGAG
2419999 TTGATTTTTGAAAAGCATAG-ATTGAA
63 TTGATTTTTGAAAAG--TAGAATT-AA
2420025 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTTGCAATATGAG
1 AAAAACA-AAATTGAAAATACCTCAGC-TGTG-GCCGAGGCTCAACTCACCTCTTGCAATATGAG
2420090 TTGATTTTTGAAAA
63 TTGATTTTTGAAAA
2420104 ACAAAAATTA
Statistics
Matches: 142, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
84 2 0.01
85 32 0.23
87 29 0.20
88 6 0.04
89 28 0.20
91 43 0.30
93 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (86 bp):
AAAAACAAAATTGAAAATACCTCAGCTGTGGCCGAGGCTCAACTCACCTCTTGCAATATGAGTTG
ATTTTTGAAAAGTAGAATTAA
Found at i:2420399 original size:195 final size:193
Alignment explanation
Indices: 2420061--2420678 Score: 1094
Period size: 193 Copynumber: 3.2 Consensus size: 193
2420051 CATGTGAGCC
* *
2420061 GAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCATCTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACT
*
2420126 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
65 CACCTCTCGCAACATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
* *
2420191 AACTCATTTCTCGCAATATGAGTTGATTTTTTTTTTAAAAATTTAAAAATACCTCAACATGTCTT
130 AACTCACTTCTCGCAATATGAGTTGA-TTTTTTTTTAAAAATTTAAAAATACCTCAACGTGTCTT
*
2420256 GATGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GA-GGCTCAACTCATCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACT
* *
2420321 CACCTCTCGTAACATGAGTCAATTTAAAACATAAACTAAACATACCTCGGCGTGCCCCGAGGCTC
65 CACCTCTCGCAACATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
* *
2420386 AACTCACTTCTCGCAATATGAGTTGATTTTTCTTAAAAAATTTAAAAATACCTCAACGTGTCTT
130 AACTCACTTCTCGCAATATGAGTTGATTTTTTTTTAAAAATTTAAAAATACCTCAACGTGTCTT
* *
2420450 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGTCTTAACTC
1 GAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
2420515 ACCTCTCGCAACATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAACATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
2420580 ACTCACTTCTCGCAATATGAGTTGATTTTTTTTT-AAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTTTAAAAATTTAAAAATACCTCAACGTGTCTT
2420642 GAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTT
1 GAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTT
2420679 CCTTGGAAAG
Statistics
Matches: 406, Mismatches: 16, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
192 64 0.16
193 157 0.39
194 37 0.09
195 120 0.30
196 28 0.07
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.31
Consensus pattern (193 bp):
GAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCGCAACATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
ACTCACTTCTCGCAATATGAGTTGATTTTTTTTTAAAAATTTAAAAATACCTCAACGTGTCTT
Found at i:2433683 original size:3 final size:3
Alignment explanation
Indices: 2433677--2433735 Score: 73
Period size: 3 Copynumber: 18.0 Consensus size: 3
2433667 TTCTTTTTTT
2433677 TTC TTC TTTC TTC TTC TCTC TTTC TTTC TTC TTC TTC TTC TTCC TTC
1 TTC TTC -TTC TTC TTC T-TC -TTC -TTC TTC TTC TTC TTC TT-C TTC
2433724 TTC TTC TTC TTC
1 TTC TTC TTC TTC
2433736 AAAACCGAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
3 37 0.71
4 14 0.27
5 1 0.02
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:2433692 original size:10 final size:10
Alignment explanation
Indices: 2433667--2433735 Score: 74
Period size: 10 Copynumber: 7.3 Consensus size: 10
2433657 NAAATTTTTT
* *
2433667 TTCTTTTTTT
1 TTCTTCTTTC
2433677 TTCTTCTTTC
1 TTCTTCTTTC
*
2433687 TTCTTCTCTC
1 TTCTTCTTTC
2433697 -T-TTCTTTC
1 TTCTTCTTTC
2433705 TTCTTC-TTC
1 TTCTTCTTTC
*
2433714 TTCTTCCTTC
1 TTCTTCTTTC
2433724 TTCTTC-TTC
1 TTCTTCTTTC
2433733 TTC
1 TTC
2433736 AAAACCGAGC
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
8 6 0.12
9 17 0.33
10 29 0.56
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TTCTTCTTTC
Found at i:2433723 original size:13 final size:13
Alignment explanation
Indices: 2433677--2433732 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
2433667 TTCTTTTTTT
*
2433677 TTCTTCTTTCTTC
1 TTCTTCCTTCTTC
*
2433690 TTCTCTCTTTC-T-
1 TTCT-TCCTTCTTC
2433702 TTCTT-CTTCTTC
1 TTCTTCCTTCTTC
2433714 TTCTTCCTTCTTC
1 TTCTTCCTTCTTC
2433727 TTCTTC
1 TTCTTC
2433733 TTCAAAACCG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
10 3 0.08
11 2 0.05
12 9 0.24
13 18 0.47
14 6 0.16
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (13 bp):
TTCTTCCTTCTTC
Found at i:2433859 original size:18 final size:18
Alignment explanation
Indices: 2433836--2433878 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2433826 TCTCTCCCCT
* *
2433836 TTTTTTTATTTTTGAAGC
1 TTTTTTTATCTTTGAAAC
*
2433854 TTTTTTTCTCTTTGAAAC
1 TTTTTTTATCTTTGAAAC
2433872 TTTTTTT
1 TTTTTTT
2433879 TTGGAGATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.09, G:0.07, T:0.70
Consensus pattern (18 bp):
TTTTTTTATCTTTGAAAC
Found at i:2434126 original size:29 final size:30
Alignment explanation
Indices: 2434093--2434209 Score: 96
Period size: 30 Copynumber: 3.9 Consensus size: 30
2434083 TGTAATTTTT
*
2434093 AGAAAATTT-AGGATTAAAATGAAATTTAA
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * *
2434122 TGAAAGTTTAAGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTAAGGGT-TAAAATGAAATTTAA
* * *
2434152 AGAAAGTTTAAGGGTCAAAACGAAATTT-A
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * * *
2434181 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTAAGGGTTAAAATGAAATTT
2434210 TTATTTTTTT
Statistics
Matches: 71, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
29 12 0.17
30 58 0.82
31 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.29
Consensus pattern (30 bp):
AGAAAATTTAAGGGTTAAAATGAAATTTAA
Found at i:2434177 original size:30 final size:30
Alignment explanation
Indices: 2434108--2434209 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
2434098 ATTTAGGATT
*
2434108 AAAATGAAATTTAATGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
2434138 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* * *
2434168 AAAACGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAAGGGTC
*
2434198 AAAATGCAATTT
1 AAAATGAAATTT
2434210 TTATTTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 2 0.03
30 59 0.97
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.28
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAAGGGTC
Found at i:2434231 original size:15 final size:16
Alignment explanation
Indices: 2434205--2434241 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2434195 GTCAAAATGC
*
2434205 AATTTTTATTTTTTTA
1 AATTTTTATTTTTTGA
2434221 AATTTTT-TTTTTTGA
1 AATTTTTATTTTTTGA
2434236 AATTTT
1 AATTTT
2434242 GAAAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
AATTTTTATTTTTTGA
Found at i:2438967 original size:31 final size:31
Alignment explanation
Indices: 2438932--2439025 Score: 179
Period size: 31 Copynumber: 3.0 Consensus size: 31
2438922 GAGATGGAAA
2438932 AAAGTTGAAGAATGGAAGAAAAAGAAGGCTT
1 AAAGTTGAAGAATGGAAGAAAAAGAAGGCTT
2438963 AAAGTTGAAGAATGGAAGAAAAAGAAGGCTT
1 AAAGTTGAAGAATGGAAGAAAAAGAAGGCTT
*
2438994 AAAGTTGAAGAACGGAAGAAAAAGAAGGCTT
1 AAAGTTGAAGAATGGAAGAAAAAGAAGGCTT
2439025 A
1 A
2439026 CCTGGATGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.52, C:0.04, G:0.29, T:0.15
Consensus pattern (31 bp):
AAAGTTGAAGAATGGAAGAAAAAGAAGGCTT
Found at i:2441949 original size:25 final size:25
Alignment explanation
Indices: 2441898--2441949 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
2441888 AGCTAAATAT
* *
2441898 AACTTTGAATGAATTGCATAATAAA
1 AACTGTGAATGAATTGCATAAAAAA
*
2441923 AACTGTGAATGAA-TGTATAAAACAA
1 AACTGTGAATGAATTGCATAAAA-AA
2441948 AA
1 AA
2441950 TAGATTGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.52, C:0.08, G:0.13, T:0.27
Consensus pattern (25 bp):
AACTGTGAATGAATTGCATAAAAAA
Found at i:2444634 original size:21 final size:21
Alignment explanation
Indices: 2444608--2444648 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2444598 ATCTGCTCAA
* *
2444608 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2444629 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2444649 TTGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2450332 original size:24 final size:23
Alignment explanation
Indices: 2450304--2450348 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
2450294 TATAAAATTG
*
2450304 AATATATATTATTTATTTCATAAA
1 AATATATATT-TTAATTTCATAAA
2450328 AATATATATTTTAATTTCATA
1 AATATATATTTTAATTTCATA
2450349 TTTAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATATATTTTAATTTCATAAA
Found at i:2451044 original size:40 final size:41
Alignment explanation
Indices: 2450995--2451074 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 41
2450985 AAAATATTTG
* * *
2450995 TATTAAAAAATACTAC-CATAAATATAATAAATATTTTATTA
1 TATTAAAAAAAAC-ACAAATAAATATAATAAAAATTTTATTA
*
2451036 TATT-AAAAAAACACAAATAAATATAGTAAAAATTTTATT
1 TATTAAAAAAAACACAAATAAATATAATAAAAATTTTATT
2451075 TTACTAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
39 2 0.06
40 28 0.82
41 4 0.12
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.36
Consensus pattern (41 bp):
TATTAAAAAAAACACAAATAAATATAATAAAAATTTTATTA
Found at i:2451507 original size:17 final size:19
Alignment explanation
Indices: 2451477--2451511 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2451467 GTAGTTTTCT
2451477 AAATTATAGAAAAATATAA
1 AAATTATAGAAAAATATAA
2451496 AAATTA-AG-AAAATATA
1 AAATTATAGAAAAATATA
2451512 CATAGAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (19 bp):
AAATTATAGAAAAATATAA
Found at i:2452025 original size:15 final size:16
Alignment explanation
Indices: 2451997--2452026 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2451987 TTTAAATAAA
2451997 TTTATTTCTTAATTTT
1 TTTATTTCTTAATTTT
2452013 TTTATTT-TTAATTT
1 TTTATTTCTTAATTT
2452027 CTTTCTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTATTTCTTAATTTT
Found at i:2452335 original size:18 final size:18
Alignment explanation
Indices: 2452309--2452355 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 18
2452299 TTATATATTC
*
2452309 TTTAGAAATATTTTGAAT
1 TTTAAAAATATTTTGAAT
2452327 TTTAAAAATTATTTTGAAT
1 TTTAAAAA-TATTTTGAAT
2452346 TCTTAAAAAT
1 T-TTAAAAAT
2452356 TATATTGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.27
19 12 0.46
20 7 0.27
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (18 bp):
TTTAAAAATATTTTGAAT
Found at i:2452353 original size:20 final size:19
Alignment explanation
Indices: 2452317--2452367 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
2452307 TCTTTAGAAA
2452317 TATTTTGAATTTTAAAAAT
1 TATTTTGAATTTTAAAAAT
2452336 TATTTTGAATTCTTAAAAAT
1 TATTTTGAATT-TTAAAAAT
*
2452356 TATATTG-ATTTT
1 TATTTTGAATTTT
2452368 TTTTTGTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 2 0.07
19 14 0.47
20 14 0.47
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (19 bp):
TATTTTGAATTTTAAAAAT
Found at i:2467760 original size:28 final size:28
Alignment explanation
Indices: 2467697--2467760 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
2467687 AATAATTTAA
*
2467697 AAAATTTAATTAATTATCAAAATAACCC
1 AAAATTTAATTAAATATCAAAATAACCC
*** * *
2467725 ATTTTTTAATTAAATATGAAAATAACCT
1 AAAATTTAATTAAATATCAAAATAACCC
2467753 AAAATTTA
1 AAAATTTA
2467761 CAATAAAAAT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.38
Consensus pattern (28 bp):
AAAATTTAATTAAATATCAAAATAACCC
Found at i:2469594 original size:40 final size:40
Alignment explanation
Indices: 2469491--2469706 Score: 314
Period size: 40 Copynumber: 5.5 Consensus size: 40
2469481 GGATGATAAT
* *
2469491 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TC
*
2469531 CGGGCTAAG-CCCGAAGGCATTTGTGTGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
2469570 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
*
2469610 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* *
2469650 CGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATC
* *
2469690 C-GGCTAAATTCCGAAGG
1 CGGGCTAAGTCCCGAAGG
2469707 TACTTGGTTT
Statistics
Matches: 163, Mismatches: 10, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
39 50 0.31
40 113 0.69
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:2472231 original size:22 final size:21
Alignment explanation
Indices: 2472205--2472269 Score: 89
Period size: 20 Copynumber: 3.1 Consensus size: 21
2472195 TTGGCTCAGA
2472205 AATATTATTAAAAAATATATTT
1 AATATT-TTAAAAAATATATTT
2472227 AATA-TTTAAAAAATAATATTT
1 AATATTTTAAAAAAT-ATATTT
*
2472248 AAAATTTTAAAAAATA-ATTT
1 AATATTTTAAAAAATATATTT
2472268 AA
1 AA
2472270 AAATAATATT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
20 15 0.38
21 11 0.28
22 14 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATATTTTAAAAAATATATTT
Found at i:2472237 original size:20 final size:21
Alignment explanation
Indices: 2472212--2472343 Score: 90
Period size: 22 Copynumber: 5.9 Consensus size: 21
2472202 AGAAATATTA
*
2472212 TTAAAAAATATATTTAATA-T
1 TTAAAAAATATATTTAAAATT
2472232 TTAAAAAATAATATTTAAAATT
1 TTAAAAAAT-ATATTTAAAATT
2472254 TTAAAAAATA-ATTTAAAAATAAT
1 TTAAAAAATATATTT-AAAAT--T
* * ***
2472277 ATT-TAAAATTTAGAAAAAATAGT
1 -TTAAAAAATATATTTAAAAT--T
2472300 TTCAAAAATATATATTTAAAATT
1 TT-AAAAA-ATATATTTAAAATT
2472323 TTAAAAATATATATTATAAAA
1 TTAAAAA-ATATATT-TAAAA
2472344 CATTTCAAAT
Statistics
Matches: 89, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
20 13 0.15
21 15 0.17
22 25 0.28
23 21 0.24
24 6 0.07
25 9 0.10
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
TTAAAAAATATATTTAAAATT
Found at i:2472245 original size:14 final size:14
Alignment explanation
Indices: 2472226--2472284 Score: 55
Period size: 14 Copynumber: 4.9 Consensus size: 14
2472216 AAAATATATT
2472226 TAATATTTAAAAAA
1 TAATATTTAAAAAA
2472240 TAATATTT----AA
1 TAATATTTAAAAAA
2472250 -AAT-TTTAAAAAA
1 TAATATTTAAAAAA
2472262 T-A-ATTT-AAAAA
1 TAATATTTAAAAAA
2472273 TAATATTTAAAA
1 TAATATTTAAAA
2472285 TTTAGAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 18
0.67 0.00 0.33
Matches are distributed among these distances:
8 3 0.08
9 3 0.08
10 2 0.06
11 6 0.17
12 7 0.19
13 4 0.11
14 11 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATATTTAAAAAA
Found at i:2472268 original size:34 final size:34
Alignment explanation
Indices: 2472230--2472343 Score: 149
Period size: 33 Copynumber: 3.2 Consensus size: 34
2472220 TATATTTAAT
2472230 ATTTAAAAAATAATATTTAAAATTTTAAAAAATA
1 ATTTAAAAAATAATATTTAAAATTTTAAAAAATA
*
2472264 ATTT-AAAAATAATATTTAAAATTTAGAAAAAATA
1 ATTTAAAAAATAATATTTAAAATTT-TAAAAAATA
* *
2472298 GTTTCAAAAATATATATTTAAAATTTTAAAAATATA
1 ATTTAAAAAATA-ATATTTAAAATTTTAAAAA-ATA
2472334 TATTATAAAA
1 -ATT-TAAAA
2472344 CATTTCAAAT
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
33 20 0.29
34 15 0.22
35 12 0.17
36 16 0.23
37 2 0.03
38 4 0.06
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (34 bp):
ATTTAAAAAATAATATTTAAAATTTTAAAAAATA
Found at i:2472329 original size:22 final size:22
Alignment explanation
Indices: 2472212--2472369 Score: 96
Period size: 21 Copynumber: 7.1 Consensus size: 22
2472202 AGAAATATTA
*
2472212 TTAAAAA-ATATATTTAATATT
1 TTAAAAATATATATTTAAAATT
*
2472233 TAAAAAATA-ATATTTAAAATT
1 TTAAAAATATATATTTAAAATT
2472254 TTAAAAA-ATA-ATTTAAAAATAAT
1 TTAAAAATATATATTT-AAAAT--T
* ***
2472277 ATTTAAAAT-T-TAGAAAAAATAGT
1 -TTAAAAATATATATTTAAAAT--T
2472300 TTCAAAAATATATATTTAAAATT
1 TT-AAAAATATATATTTAAAATT
*
2472323 TTAAAAATATATATTATAAAACAT
1 TTAAAAATATATATT-TAAAA-TT
* * *
2472347 TT-CAAATATACATTTCAAATT
1 TTAAAAATATATATTTAAAATT
2472368 TT
1 TT
2472370 TTAAAATTAA
Statistics
Matches: 107, Mismatches: 17, Indels: 26
0.71 0.11 0.17
Matches are distributed among these distances:
20 5 0.05
21 32 0.30
22 20 0.19
23 31 0.29
24 12 0.11
25 7 0.07
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (22 bp):
TTAAAAATATATATTTAAAATT
Found at i:2472353 original size:23 final size:22
Alignment explanation
Indices: 2472212--2472361 Score: 73
Period size: 22 Copynumber: 6.7 Consensus size: 22
2472202 AGAAATATTA
*
2472212 TTAAAAA-ATATATTT-AATAT
1 TTAAAAATATATATTTAAAAAT
*
2472232 TTAAAAA-ATAATATTTAAAATT
1 TTAAAAATAT-ATATTTAAAAAT
2472254 TTAAAAA-ATA-ATTTAAAAATAAT
1 TTAAAAATATATATTT--AAA-AAT
* ***
2472277 ATTTAAAAT-T-TAGAAAAAATAGT
1 -TTAAAAATATATATTTAAAA-A-T
*
2472300 TTCAAAAATATATATTTAAAATT
1 TT-AAAAATATATATTTAAAAAT
2472323 TTAAAAATATATATTATAAAACAT
1 TTAAAAATATATATT-TAAAA-AT
* *
2472347 TT-CAAATATACATTT
1 TTAAAAATATATATTT
2472362 CAAATTTTTT
Statistics
Matches: 100, Mismatches: 15, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
20 13 0.13
21 8 0.08
22 35 0.35
23 26 0.26
24 12 0.12
25 6 0.06
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (22 bp):
TTAAAAATATATATTTAAAAAT
Found at i:2472399 original size:14 final size:15
Alignment explanation
Indices: 2472382--2472413 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
2472372 AAAATTAATA
2472382 AAAATAAATAAA-AT
1 AAAATAAATAAAGAT
2472396 AAAATAAATAAAGAT
1 AAAATAAATAAAGAT
2472411 AAA
1 AAA
2472414 GACAAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (15 bp):
AAAATAAATAAAGAT
Found at i:2472457 original size:39 final size:42
Alignment explanation
Indices: 2472414--2472491 Score: 99
Period size: 39 Copynumber: 1.9 Consensus size: 42
2472404 TAAAGATAAA
** *
2472414 GACAAAACTTAAAAAAGT-AATAA-AA-AAAAGAAACAATAT
1 GACAAAACAAAAAAAAGTAAATAATAATAAAAAAAACAATAT
*
2472453 GACAAAAGAAAAAAAAGTAAATAATAATAAAAAAAACAA
1 GACAAAACAAAAAAAAGTAAATAATAATAAAAAAAACAA
2472492 AGTAAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 15 0.47
40 5 0.16
41 2 0.06
42 10 0.31
ACGTcount: A:0.73, C:0.06, G:0.08, T:0.13
Consensus pattern (42 bp):
GACAAAACAAAAAAAAGTAAATAATAATAAAAAAAACAATAT
Found at i:2472475 original size:24 final size:24
Alignment explanation
Indices: 2472435--2472497 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 24
2472425 AAAAAGTAAT
*
2472435 AAAAAAAAG-AAACAATATGACAAAA
1 AAAAAAAAGTAAATAATA--ACAAAA
*
2472460 GAAAAAAAAGTAAATAATAATAAAA
1 -AAAAAAAAGTAAATAATAACAAAA
*
2472485 AAAACAAAGTAAA
1 AAAAAAAAGTAAA
2472498 AAAAGTAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 12 0.36
25 5 0.15
26 9 0.27
27 7 0.21
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (24 bp):
AAAAAAAAGTAAATAATAACAAAA
Found at i:2472486 original size:27 final size:26
Alignment explanation
Indices: 2472435--2472487 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
2472425 AAAAAGTAAT
*
2472435 AAAAAAAAGAAACAATATGACAAAAG
1 AAAAAAAAGAAACAATATGAAAAAAG
* *
2472461 AAAAAAAAGTAAATAATAATAAAAAAA
1 AAAAAAAAG-AAACAAT-ATGAAAAAA
2472488 ACAAAGTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 9 0.41
27 6 0.27
28 7 0.32
ACGTcount: A:0.77, C:0.04, G:0.08, T:0.11
Consensus pattern (26 bp):
AAAAAAAAGAAACAATATGAAAAAAG
Found at i:2480387 original size:22 final size:24
Alignment explanation
Indices: 2480333--2480387 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 24
2480323 TATATAACTG
2480333 ATAATAT-TA-AAATATATACATA
1 ATAATATATATAAATATATACATA
* *
2480355 ATATTATATATAAAT-TATTCAT-
1 ATAATATATATAAATATATACATA
2480377 ATAATATATAT
1 ATAATATATAT
2480388 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 16 0.57
23 8 0.29
24 4 0.14
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATATATATAAATATATACATA
Found at i:2481826 original size:74 final size:74
Alignment explanation
Indices: 2481551--2482195 Score: 798
Period size: 74 Copynumber: 8.7 Consensus size: 74
2481541 CTCAACTCAT
* * *
2481551 TCAGCGTGTCCTGAGGCTCAATTCACCTCTCGCAATATGAGTTGA--TTTTTGAAACATACAAAA
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-AT---AGA
*
2481614 AATTGACAA-TACC
62 AATT-AAAATTACC
* ** ** * * * * *
2481627 TAAGTATGTCTTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGACAACACAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
*
2481692 GAAATTACC
66 AAAATTACC
**
2481701 TCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAATAGAAA
1 TCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAA
2481764 TTGAAAA-TACC
64 TT-AAAATTACC
** ** ** *
2481775 TCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
*
2481840 GAAATTACC
66 AAAATTACC
** * * * *
2481849 TCAGCGTGTCCTAAGGCTCAATTCATCTTTCGCAATATGAGTTGATTTTTTTAAAAATAGAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
2481914 AAAATTACC
66 AAAATTACC
* *
2481923 TCAGCGTGTCCCGAGGCTCAATTCATCTCTCGCAATATGAGTTGATTTTTTTTGAAAATAGAAAT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAATAGAAAT
2481988 TAAAATTACC
65 TAAAATTACC
*
2481998 TCAGCGTGTCCCGAGGCTCACCTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
2482063 AAAATTACC
66 AAAATTACC
*
2482072 TCAGCGTGTCCCGAGGCTCACCTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
2482137 AAAATTACC
66 AAAATTACC
* * ** * *
2482146 TCAGCGTGTCCCGAGGCTTAACCCATTTCTCGCAATATAAGTTGAATTTT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
2482196 GAAAACGGAA
Statistics
Matches: 500, Mismatches: 59, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
72 34 0.07
73 5 0.01
74 308 0.62
75 73 0.15
76 71 0.14
77 1 0.00
78 8 0.02
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (74 bp):
TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
AAAATTACC
Found at i:2482041 original size:223 final size:222
Alignment explanation
Indices: 2481551--2482195 Score: 834
Period size: 223 Copynumber: 2.9 Consensus size: 222
2481541 CTCAACTCAT
* *
2481551 TCAGCGTGTCCTGAGGCTCAATTCACCTCTCGCAATATGAGTTGA--TTTTTGAAACATACAAAA
1 TCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AA-A-AC-AGA
* ** * * *
2481614 AATTGACAA-TACCTAAGTATGTCTTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTT
62 AATTGA-AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
* * * * ** *
2481678 TGACAACACAAATTGAAATTACCTCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATGA
126 TGAAAATAGAAATTAAAATTACCTCAGC--GTGTCCCGAGGCTCAACTCATCTCTCGCAATATGA
2481743 GTTGA--TTTTTGAAAATAGAAATTGAAAATACC
189 GTTGATTTTTTTGAAAATAGAAATTGAAAATACC
** * **
2481775 TCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATT
1 TCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATT
* * * * *
2481840 GAAATTACCTCAGCGTGTCCTAAGGCTCAATTCATCTTTCGCAATATGAGTTGATTTTTTTAAAA
66 GAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
*
2481905 ATAGAAATTAAAATTACCTCAGCGTGTCCCGAGGCTCAATTCATCTCTCGCAATATGAGTTGATT
131 ATAGAAATTAAAATTACCTCAGCGTGTCCCGAGGCTCAACTCATCTCTCGCAATATGAGTTGA-T
2481970 TTTTTTGAAAATAGAAATT-AAAATTACC
195 TTTTTTGAAAATAGAAATTGAAAA-TACC
* * *
2481998 TCAGCGTGTCCCGAGGCTCACCTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
1 TCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATT
* * *
2482063 AAAATTACCTCAGCGTGTCCCGAGGCTCACCTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
66 GAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
* * * * *
2482128 ATAGAAATTAAAATTACCTCAGCGTGTCCCGAGGCTTAACCCATTTCTCGCAATATAAGTTGAAT
131 ATAGAAATTAAAATTACCTCAGCGTGTCCCGAGGCTCAACTCATCTCTCGCAATATGAGTTGATT
2482193 TTT
196 TTT
2482196 GAAAACGGAA
Statistics
Matches: 366, Mismatches: 48, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
220 36 0.10
221 2 0.01
222 84 0.23
223 196 0.54
224 40 0.11
225 2 0.01
226 6 0.02
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (222 bp):
TCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATT
GAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
ATAGAAATTAAAATTACCTCAGCGTGTCCCGAGGCTCAACTCATCTCTCGCAATATGAGTTGATT
TTTTTGAAAATAGAAATTGAAAATACC
Found at i:2483150 original size:35 final size:35
Alignment explanation
Indices: 2483111--2483183 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
2483101 GATTCGACAA
*
2483111 CTCTTTCTCATCCATCTCGGTAAGGATCAAAGCTC
1 CTCTTTCCCATCCATCTCGGTAAGGATCAAAGCTC
*
2483146 CTCTTTCCCATCCATCTTGGTAAGGATCAAAGCTC
1 CTCTTTCCCATCCATCTCGGTAAGGATCAAAGCTC
2483181 CTC
1 CTC
2483184 CTGAGAATGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.32
Consensus pattern (35 bp):
CTCTTTCCCATCCATCTCGGTAAGGATCAAAGCTC
Found at i:2494647 original size:22 final size:24
Alignment explanation
Indices: 2494593--2494647 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 24
2494583 TATATAACTG
2494593 ATAATAT-TA-AAATATATACATA
1 ATAATATATATAAATATATACATA
* *
2494615 ATATTATATATAAAT-TATTCAT-
1 ATAATATATATAAATATATACATA
2494637 ATAATATATAT
1 ATAATATATAT
2494648 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 16 0.57
23 8 0.29
24 4 0.14
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATATATATAAATATATACATA
Found at i:2495033 original size:35 final size:35
Alignment explanation
Indices: 2494987--2495055 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
2494977 GGGTGTGTGA
2494987 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
*
2495022 TGGTGCTGGTGGCAGGCAGCATGGGAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
2495056 AGAGGCAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.19, C:0.12, G:0.52, T:0.17
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
Found at i:2496503 original size:3 final size:3
Alignment explanation
Indices: 2496497--2496540 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2496487 AATAATAATA
2496497 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
2496541 TAAGAAGTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:2496958 original size:23 final size:23
Alignment explanation
Indices: 2496916--2496959 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2496906 TAAATATTAT
*
2496916 TTTATTAATATTTTGCTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
2496939 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
2496960 AAAATGGTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:2500279 original size:17 final size:17
Alignment explanation
Indices: 2500257--2500291 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2500247 TGCACATGTG
2500257 ATTAATTTGTCTCATAA
1 ATTAATTTGTCTCATAA
2500274 ATTAATTTGTCTCATAA
1 ATTAATTTGTCTCATAA
2500291 A
1 A
2500292 GTTCCTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (17 bp):
ATTAATTTGTCTCATAA
Found at i:2502126 original size:28 final size:28
Alignment explanation
Indices: 2502091--2502146 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2502081 TTTATGTAAC
*
2502091 AACTTAGCTTTACTCAAGAGAGGTATGT
1 AACTTAGCTTTACTCAAGAGAAGTATGT
**
2502119 AACTTAGCTTTGTTCAAGAGAAGTATGT
1 AACTTAGCTTTACTCAAGAGAAGTATGT
2502147 CTTGTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.34
Consensus pattern (28 bp):
AACTTAGCTTTACTCAAGAGAAGTATGT
Found at i:2505373 original size:42 final size:40
Alignment explanation
Indices: 2505245--2505372 Score: 129
Period size: 40 Copynumber: 3.1 Consensus size: 40
2505235 GCTTTTTGGC
2505245 ATTTTTGTGAATCTTTTTT-AAGCTTCA-TTATAAGTCTTAT
1 ATTTTTGTGAATCTTTTTTAAAGCTT-AGTTATAA-TCTTAT
* ** *
2505285 ATATTTGTGAAT-TCTTTTTATCG-TTAGTTATAAATTTTAT
1 ATTTTTGTGAATCT-TTTTTAAAGCTTAGTTAT-AATCTTAT
*
2505325 CATTTTTGTAAATCTTTTTTAAAGCTTAGTTATATATCTTAT
1 -ATTTTTGTGAATCTTTTTTAAAGCTTAGTTATA-ATCTTAT
2505367 ATTTTT
1 ATTTTT
2505373 TTGTGAAATT
Statistics
Matches: 71, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
39 2 0.03
40 27 0.38
41 27 0.38
42 15 0.21
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.57
Consensus pattern (40 bp):
ATTTTTGTGAATCTTTTTTAAAGCTTAGTTATAATCTTAT
Found at i:2505394 original size:82 final size:80
Alignment explanation
Indices: 2505244--2505415 Score: 188
Period size: 82 Copynumber: 2.1 Consensus size: 80
2505234 AGCTTTTTGG
* * * *
2505244 CATTTTTGTGAATCTTTTTTAAGCTTCATTATAAGTCTTATATATTTGTGAATTCTTTTTATCGT
1 CATTTTTGTAAATCTTTTTTAAGCTTCATTATAAGTCTTATATATTTGTGAA-TATTTGTATCAT
* *
2505309 TAGTTATAAATTTTAT
65 TAGTTACAAATCTTAT
*
2505325 CATTTTTGTAAATCTTTTTTAAAGCTT-AGTTATATA-TCTTATATTTTTTTGTGAA-ATTTGTA
1 CATTTTTGTAAATCTTTTTT-AAGCTTCA-TTATA-AGTCTTATA--TATTTGTGAATATTTGTA
*
2505387 TTATTAGTTACAAATCTTAT
61 TCATTAGTTACAAATCTTAT
*
2505407 AATTTTTGT
1 CATTTTTGT
2505416 TTCACTTTTG
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
81 20 0.26
82 47 0.61
83 1 0.01
84 9 0.12
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.56
Consensus pattern (80 bp):
CATTTTTGTAAATCTTTTTTAAGCTTCATTATAAGTCTTATATATTTGTGAATATTTGTATCATT
AGTTACAAATCTTAT
Found at i:2507504 original size:19 final size:19
Alignment explanation
Indices: 2507480--2507517 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2507470 AAATTATTTT
*
2507480 TAGAATTTGATAAA-ATTAA
1 TAGAATATG-TAAATATTAA
2507499 TAGAATATGTAAATATTAA
1 TAGAATATGTAAATATTAA
2507518 GTGTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (19 bp):
TAGAATATGTAAATATTAA
Found at i:2509387 original size:43 final size:43
Alignment explanation
Indices: 2509326--2509535 Score: 251
Period size: 43 Copynumber: 4.9 Consensus size: 43
2509316 GCGTTTTTCA
* *
2509326 TAAAGCGCCACTAAAGGTCATGTTCTTTAGCGGTGTTTATGGG
1 TAAAGCGCCACTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGG
* **
2509369 TAAAGTGCCACTAAAGGTCATGTTCTTTAGCGTTGTTTGTGGG
1 TAAAGCGCCACTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGG
* * * * *
2509412 TAAAGTGCCACTAAAGGTTAGGATCTTTAGCGGCGTTTGT-GA
1 TAAAGCGCCACTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGG
* * * *
2509454 TAAAAGCACCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTCGG
1 T-AAAGCGCCACTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGG
* * *
2509498 TGAAGCGCCACTAAAGATCATGTTCTTTAGCAGCGTTT
1 TAAAGCGCCACTAAAGGTCATGTTCTTTAGCGGCGTTT
2509536 TTTACATAAA
Statistics
Matches: 144, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
42 2 0.01
43 140 0.97
44 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
TAAAGCGCCACTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGG
Found at i:2514290 original size:12 final size:12
Alignment explanation
Indices: 2514275--2514299 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2514265 TCCGGCTCCA
2514275 CCACCTCCACCT
1 CCACCTCCACCT
2514287 CCACCTCCACCT
1 CCACCTCCACCT
2514299 C
1 C
2514300 ATGGACTAGG
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:0.16, C:0.68, G:0.00, T:0.16
Consensus pattern (12 bp):
CCACCTCCACCT
Found at i:2517556 original size:172 final size:172
Alignment explanation
Indices: 2517253--2517670 Score: 529
Period size: 172 Copynumber: 2.4 Consensus size: 172
2517243 AAAGCCCTAA
* *
2517253 AACTTTTAAATAGTTTAGTGACCAACTTGTAA-TGTTTTTGAAATTGAGTGACCAAGGCATAAAC
1 AACTTTTAAATAGTTTAGTGACCAACTTGTAACT-TTTTTGAAATTGAGTGACCAAAGTATAAAC
* * * * * **
2517317 TTACTAATAGTTGAGTGACCTTGGTTGTAGTTTGCCCTATGATGAAGAGTAAATTAACGGTCACA
65 TTACTAATAGTTAAGTGACCCTAGCTGTAGTTTACCCTATGATGAAGAGTAAATTAACGACCACA
*
2517382 TCAAACATCCATTAGCAATTTAATGA-CCAATAACTTAAATGAC
130 TCAAACATCCATTAGCAACTTAAT-ACCCAATAACTTAAATGAC
* * *
2517425 AACTTTTAAATAGTTTAATGACCAACTTGTAACTTTTTTGAAATTGAGTAATCAAAGTATAAACT
1 AACTTTTAAATAGTTTAGTGACCAACTTGTAACTTTTTTGAAATTGAGTGACCAAAGTATAAACT
* *** * *
2517490 TACTAATAGTTAAGTGACCCTAGCTGTAGTTTACTCTATGATGAATTTTGAATTAATGACCACAT
66 TACTAATAGTTAAGTGACCCTAGCTGTAGTTTACCCTATGATGAAGAGTAAATTAACGACCACAT
* * * *
2517555 CATACATCCATTAGCAACTTAATACCCAATAAGTTAGATGAT
131 CAAACATCCATTAGCAACTTAATACCCAATAACTTAAATGAC
* ** * * *
2517597 AACTTTCAAATAGTTTAGTGATTAATTTGTAAC-TTTTTAAAATT-AGTGACCAAAATATAAACT
1 AACTTTTAAATAGTTTAGTGACCAACTTGTAACTTTTTTGAAATTGAGTGACCAAAGTATAAACT
2517660 TACTAATAGTT
66 TACTAATAGTT
2517671 GGTGACCTTG
Statistics
Matches: 212, Mismatches: 32, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
170 27 0.13
171 11 0.05
172 173 0.82
173 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (172 bp):
AACTTTTAAATAGTTTAGTGACCAACTTGTAACTTTTTTGAAATTGAGTGACCAAAGTATAAACT
TACTAATAGTTAAGTGACCCTAGCTGTAGTTTACCCTATGATGAAGAGTAAATTAACGACCACAT
CAAACATCCATTAGCAACTTAATACCCAATAACTTAAATGAC
Done.