Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 6 of 444
Found at i:1815249 original size:33 final size:33
Alignment explanation
Indices: 1815178--1815260 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
1815168 CCACATCTGC
* *
1815178 ACTCTACTCCTCCCGGCTCATATCCACCATCAT
1 ACTCTACTCCTCCCGGCCCATATCCACCACCAT
* * * *
1815211 ACTCTACTCCTCCTGGCCCATATCCAGCGCCGT
1 ACTCTACTCCTCCCGGCCCATATCCACCACCAT
* *
1815244 TCTCTACTCCACCCGGC
1 ACTCTACTCCTCCCGGC
1815261 TCGAGTTCAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.17, C:0.47, G:0.11, T:0.25
Consensus pattern (33 bp):
ACTCTACTCCTCCCGGCCCATATCCACCACCAT
Found at i:1819251 original size:27 final size:27
Alignment explanation
Indices: 1819213--1819276 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
1819203 CTGCAGGGGA
1819213 GTCGCGCCTCTGCAGCAGGAGCGACTG
1 GTCGCGCCTCTGCAGCAGGAGCGACTG
1819240 GTCGCGCCTCTGCAGCAGGAGCGACTG
1 GTCGCGCCTCTGCAGCAGGAGCGACTG
1819267 GTCGCGCCTC
1 GTCGCGCCTC
1819277 CGGGTCTGGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.12, C:0.36, G:0.36, T:0.16
Consensus pattern (27 bp):
GTCGCGCCTCTGCAGCAGGAGCGACTG
Found at i:1819374 original size:26 final size:27
Alignment explanation
Indices: 1819334--1819392 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 27
1819324 AAAAATTATT
1819334 AAAATATAATAAAATAATAATATTTAAA
1 AAAATATAATAAAATAATAATA-TTAAA
* *
1819362 AAAATA-AAT-AAATTATATTATTAAA
1 AAAATATAATAAAATAATAATATTAAA
1819387 AAAATA
1 AAAATA
1819393 GGTCGCGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 11 0.38
26 9 0.31
27 3 0.10
28 6 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
AAAATATAATAAAATAATAATATTAAA
Found at i:1826095 original size:30 final size:30
Alignment explanation
Indices: 1826040--1826170 Score: 180
Period size: 30 Copynumber: 4.5 Consensus size: 30
1826030 ATAGTGAATC
*
1826040 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
1826069 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
1826099 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AACT
* * *
1826127 CGCACACTTAGTGCTGTATAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAACT
1826157 CGCACACTTAGTGC
1 CGCACACTTAGTGC
1826171 CAATCTTGTC
Statistics
Matches: 93, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.25
29 19 0.20
30 48 0.52
31 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAACT
Found at i:1826147 original size:58 final size:58
Alignment explanation
Indices: 1826039--1826170 Score: 185
Period size: 58 Copynumber: 2.3 Consensus size: 58
1826029 TATAGTGAAT
* * * *
1826039 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGC
1 CCGCACACTTAGTGCTATATA-TATCAACTCGCACACTTAGTGCTATATAATTTTAAAC
* *
1826098 TCGCACACTTAGTGCTATATA-ATCAAACTCGCACACTTAGTGCTGTATAATTTTAAAC
1 CCGCACACTTAGTGCTATATATATC-AACTCGCACACTTAGTGCTATATAATTTTAAAC
1826156 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
1826171 CAATCTTGTC
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 43 0.66
59 20 0.31
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (58 bp):
CCGCACACTTAGTGCTATATATATCAACTCGCACACTTAGTGCTATATAATTTTAAAC
Found at i:1838251 original size:39 final size:38
Alignment explanation
Indices: 1838083--1838251 Score: 194
Period size: 39 Copynumber: 4.3 Consensus size: 38
1838073 TATTTTATGT
* * * *
1838083 GGATGAAGATCAGTTTGATGAGATGAGCAAAGATGTATC
1 GGATGAAGATCA-ATTGATGAGACGAGCAATGATGCATC
* * *
1838122 GGGTGAAGGTCAGATTGATGAGACGAGCAATGATGAATC
1 GGATGAAGATCA-ATTGATGAGACGAGCAATGATGCATC
* * *
1838161 AGATGAAGATCAGATTGATGAGACGAGCAGTGAGGCATC
1 GGATGAAGATCA-ATTGATGAGACGAGCAATGATGCATC
* *
1838200 GGATGAAGATCAATTTGATAAGACGAGCAGTGATGCATC
1 GGATGAAGATCAA-TTGATGAGACGAGCAATGATGCATC
1838239 GGATGAAGATCAA
1 GGATGAAGATCAA
1838252 GAAAAGTTCA
Statistics
Matches: 114, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
38 1 0.01
39 113 0.99
ACGTcount: A:0.36, C:0.11, G:0.32, T:0.21
Consensus pattern (38 bp):
GGATGAAGATCAATTGATGAGACGAGCAATGATGCATC
Found at i:1841853 original size:142 final size:142
Alignment explanation
Indices: 1841343--1842746 Score: 1716
Period size: 139 Copynumber: 9.9 Consensus size: 142
1841333 AAAAATGTGA
* *
1841343 TTGTTGTCATTGATGATGTTAATGACCCAGATTAGATAGATTGTATGAGTGTTAAATATTTTAGT
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
* *
1841408 GATGGAAGTAGAATTATTTTAACATCTCAAAATAGATAAAGATGGGTTAACTA-GGTAAAGGACT
66 GATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAAC-AGGGTAAAGGACT
1841472 TTCTT-AGGTCTT
130 TTCTTCAGGTCTT
* * *
1841484 TTGTTGTCATTGATGATGTTAATGGCCCATATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
* * * *
1841549 GATGGAAGTAGAATCATTGTAACATCT-AGAGATAGACAAAGATGGGTTAACAAGG-AAAAGAGC
66 GATGGAAGTAGAATCATTGTAACATCTCA-AAATAGATAAAGATGGGTTAACAGGGTAAAGGA-C
1841612 TTTCTTCAGGTC--
129 TTTCTTCAGGTCTT
*
1841624 -TGTTGTCCTTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
*
1841688 GATGGAAGTAGAATCATTATAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACTT
66 GATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACTT
*
1841753 TCTTCAAGTCTT
131 TCTTCAGGTCTT
* * * *
1841765 TTGTTGTCATTGATGATGTTAATGACCCAGATTAGATAGATTGTATGGGTATTTAATATTTTGGT
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
* * * * * *
1841830 GATGGAAGTAG-ATCCATTGTAACATCTCGAGATAGACAAAGATGGGTTAACAAGGAAAATGACT
66 GATGGAAGTAGAAT-CATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACT
* *
1841894 TCCTTTAGGTC--
130 TTCTTCAGGTCTT
* * * *
1841905 -TGTTGTCCTTGATGATATTAATGACCCAAATTGGATAGATTGTATGGGTATTAAATATTTTAGT
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
1841969 GATGGGTTGAAGAATCTTATTAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAA
66 GA-----TG--G------A--AGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAA
* *
1842034 TAAGGTAAAGGACTTTCTTCAGGTCTT
116 CAGGGTAAAGGACTTTCTTCAGGTCTT
* * *
1842061 TTGTTGTCATTGATGATGTTAATAACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTGGT
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
* * * * * * *
1842126 GATGGAAGTCGAATCATTGTAACATCTCGAGATAGACAAAGACGGGTTAACAGGGAAAAGGATTT
66 GATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACTT
1842191 TCTTCAGG-C--
131 TCTTCAGGTCTT
* * * * *
1842200 CTGTTGTCCTTAATGATATTAATGACCTAGATTAGATAGATTGTATGGGTGTTAAATATTCTT-C
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATT-TTAG
* * * *
1842264 TGATGGAAGTAGAATCATTGTAACATCTC-AAATAGATAATGTTTGGTTAATAGGGTAAACGG-C
65 TGATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAA-GGAC
1842327 TTTCTTCAGGTCTT
129 TTTCTTCAGGTCTT
*
1842341 TTGTTGTCATTGATGATATTAATGACTCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
* * * *
1842406 GATGGAAGTAGAGTCATTATAAAATCTCAAAATAGATAAAGATGGGTTAACAAGGTAAAGGACTT
66 GATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACTT
*
1842471 TCTTCTGGTCTT
131 TCTTCAGGTCTT
* *
1842483 TTGTTGTCATTGATGATGTTAATGACCCAGATT-GAATAGATTGTATGGGTGTTAAATATGTTAA
1 TTGTTGTCATTGATGATATTAATGACCCAGATTAG-ATAGATTGTATGGGTGTTAAATAT-TTTA
* * * * * *
1842547 GTGATAGAATTAGAATCATTGTAACATCTCTAGATAGACAAAGAT--G-----AGGGAAAAGGAC
64 GTGATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGAC
1842605 TTT-TTGCAGG-C--
129 TTTCTT-CAGGTCTT
* * * * * *
1842616 CTGTTGTCCTTAATAATATTAATGACTCTA-ATTAGATAGATTTTATGGGTGTTAAATATTTTAG
1 TTGTTGTCATTGATGATATTAATGAC-CCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAG
* *
1842680 AGATGGAAGTAGAATCATTGTAACTTCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACT
65 TGATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACT
1842745 TT
130 TT
1842747 GCTTAATCTT
Statistics
Matches: 1089, Mismatches: 125, Indels: 100
0.83 0.10 0.08
Matches are distributed among these distances:
132 41 0.04
133 47 0.04
134 4 0.00
135 3 0.00
136 16 0.01
138 32 0.03
139 280 0.26
140 17 0.02
141 204 0.19
142 278 0.26
143 40 0.04
144 3 0.00
146 1 0.00
150 1 0.00
152 3 0.00
154 58 0.05
155 2 0.00
157 59 0.05
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.35
Consensus pattern (142 bp):
TTGTTGTCATTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
GATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACTT
TCTTCAGGTCTT
Found at i:1844139 original size:75 final size:75
Alignment explanation
Indices: 1844048--1844187 Score: 226
Period size: 75 Copynumber: 1.9 Consensus size: 75
1844038 CTCAAACTGA
* *
1844048 CACATGCCTTAACTTCATCACTTATCTACTCAAAGCTGTGAAAGAGGCAATGATGAAGGTCTTCT
1 CACATGCCTTAACTTCATCACTCATCTACTCAAAGCTGTGAAAGAGGCAATGACGAAGGTCTTCT
1844113 TCTTCTTCTT
66 TCTTCTTCTT
* * * *
1844123 CACATGCTTTAACTTCATCACTCATCTACTCAAAGCTTTGAAAGAGGTAATGACGAATGTCTTCT
1 CACATGCCTTAACTTCATCACTCATCTACTCAAAGCTGTGAAAGAGGCAATGACGAAGGTCTTCT
1844188 CCCATGATGA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 59 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (75 bp):
CACATGCCTTAACTTCATCACTCATCTACTCAAAGCTGTGAAAGAGGCAATGACGAAGGTCTTCT
TCTTCTTCTT
Found at i:1848013 original size:98 final size:99
Alignment explanation
Indices: 1847900--1848097 Score: 335
Period size: 99 Copynumber: 2.0 Consensus size: 99
1847890 TTCTAGAAAT
* * * * *
1847900 AGATGCAAGATG-TTTTGAAATGATTGATTTAGGTTTGATGACTTATTTTCTTAGCTTTGAAGTG
1 AGATGCAAGATGTTTTTAAAATAACTGATTTAGGTTTGATGACTTATTTTCTTAGCATGGAAGTG
1847964 AATCAGATTGAACATGGCATCCTCATAAGCCAAC
66 AATCAGATTGAACATGGCATCCTCATAAGCCAAC
*
1847998 AGATGTAAGATGTTTTTAAAATAACTGATTTAGGTTTGATGACTTATTTTCTTAGCATGGAAGTG
1 AGATGCAAGATGTTTTTAAAATAACTGATTTAGGTTTGATGACTTATTTTCTTAGCATGGAAGTG
1848063 AATCAGATTGAACATGGCATCCTCATAAGCCAAC
66 AATCAGATTGAACATGGCATCCTCATAAGCCAAC
1848097 A
1 A
1848098 AGCTTTTGCA
Statistics
Matches: 93, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 11 0.12
99 82 0.88
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (99 bp):
AGATGCAAGATGTTTTTAAAATAACTGATTTAGGTTTGATGACTTATTTTCTTAGCATGGAAGTG
AATCAGATTGAACATGGCATCCTCATAAGCCAAC
Found at i:1849398 original size:168 final size:167
Alignment explanation
Indices: 1849121--1849456 Score: 654
Period size: 168 Copynumber: 2.0 Consensus size: 167
1849111 AATGTAATGA
1849121 AGCTATTTATGCAAATTGTATTGCTACTAATTATAGTAATGAGAGTTGTCAATTTTTCTCTCAAC
1 AGCTATTTATGCAAATTGTATTGCTACTAATTATAGTAATGAGAGTTGTCAATTTTTCTCTCAAC
*
1849186 CGATTTGTTTTTGCTTCTGTTTTTCATCTTTTAAACACAAATTTTCTTTGTTTTGATCTTTGGAT
66 CGATTTGTTTTTGCTTCTGTTTTTCATCTTTCAAACACAAATTTTCTTTGTTTTGATCTTTGGAT
1849251 GCTGATATAACTCAACAAACTGTCATGCTCTAGTCCG
131 GCTGATATAACTCAACAAACTGTCATGCTCTAGTCCG
1849288 AGCTATTTATGCAAATTGTATTGCTACTAATTATAGTAATGAGAGTTGTCAATTTTTTCTCTCAA
1 AGCTATTTATGCAAATTGTATTGCTACTAATTATAGTAATGAGAGTTGTCAA-TTTTTCTCTCAA
1849353 CCGATTTGTTTTTGCTTCTGTTTTTCATCTTTCAAACACAAATTTTCTTTGTTTTGATCTTTGGA
65 CCGATTTGTTTTTGCTTCTGTTTTTCATCTTTCAAACACAAATTTTCTTTGTTTTGATCTTTGGA
1849418 TGCTGATATAACTCAACAAACTGTCATGCTCTAGTCCG
130 TGCTGATATAACTCAACAAACTGTCATGCTCTAGTCCG
1849456 A
1 A
1849457 AGCTTCAAGC
Statistics
Matches: 167, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
167 52 0.31
168 115 0.69
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (167 bp):
AGCTATTTATGCAAATTGTATTGCTACTAATTATAGTAATGAGAGTTGTCAATTTTTCTCTCAAC
CGATTTGTTTTTGCTTCTGTTTTTCATCTTTCAAACACAAATTTTCTTTGTTTTGATCTTTGGAT
GCTGATATAACTCAACAAACTGTCATGCTCTAGTCCG
Found at i:1855265 original size:15 final size:15
Alignment explanation
Indices: 1855241--1855291 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
1855231 ATAAATTAAA
*
1855241 TTTAACATTTAATAT
1 TTTAACATTTAATTT
*
1855256 TTTAATATTTAATTT
1 TTTAACATTTAATTT
*
1855271 TTTAACACTTAATTT
1 TTTAACATTTAATTT
1855286 TTTAAC
1 TTTAAC
1855292 TTATCATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAACATTTAATTT
Found at i:1857567 original size:28 final size:29
Alignment explanation
Indices: 1857525--1857579 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
1857515 ATATTTATAA
1857525 ATTTTTAAAAATTAAA-T-TAATTTTTAT
1 ATTTTTAAAAATTAAAGTGTAATTTTTAT
*
1857552 ATTTTTAAGAGATTAAAGTGTAATTTTT
1 ATTTTTAA-AAATTAAAGTGTAATTTTT
1857580 TTTATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 7 0.29
29 1 0.04
30 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (29 bp):
ATTTTTAAAAATTAAAGTGTAATTTTTAT
Found at i:1862166 original size:189 final size:189
Alignment explanation
Indices: 1861834--1862352 Score: 650
Period size: 189 Copynumber: 2.7 Consensus size: 189
1861824 GTTGGAATCA
* * * *
1861834 CTTCATGATCTGGATCTTAGTCATTGCCCAATAGCCGAATTCCCAAAAATCCCAAGAAGCTTGAC
1 CTTCGTGATCTGAATCTTAGTCATTGCCCAATAGCCGAATTCCCAGAAATCCCAAGAAGCTTAAC
* * * * *
1861899 AGAATTAAACTTATCTGAAACTCAAATTGAAGATGTGTGCTTGTCTAGCGACACTCCAAGCAATC
66 AGAATTAAACTTATCTGGAACTCAAATTGAAGAAGTGTCCTTGTCTATCGACTCTCCAAGCAATC
* * **
1861964 TTCAGAAGTTAGATATGAGTGGCTCAAGGGTGAAA-AATGTATCCATCAAGATGGATTCC
131 TTCAGAAGTTAGATATGAGGGGCTCAAGAGT-AAAGAATGTATCCATCAAGATGGAAGCC
* * *
1862023 CTTCGTGATCTGAATCTTAGTCATTGCCCAATAGTCAAATTTCCC-GAAATCCCAAGAACCTTAA
1 CTTCGTGATCTGAATCTTAGTCATTGCCCAATAGCCGAA-TTCCCAGAAATCCCAAGAAGCTTAA
* * * * ** *
1862087 CAAAATTGAACTTATCTGGAACTCAAATTGAAGAGGTGTCCTTGTCTCTCGACTCTGTAGGCAAT
65 CAGAATTAAACTTATCTGGAACTCAAATTGAAGAAGTGTCCTTGTCTATCGACTCTCCAAGCAAT
*
1862152 CTTCA-AACGTTAGATATGAGGGGCTCAAGAGTAAAGAATGTATCGATCAAGATGGAAGCC
130 CTTCAGAA-GTTAGATATGAGGGGCTCAAGAGTAAAGAATGTATCCATCAAGATGGAAGCC
* * *
1862212 CTCCGTGATCTGAATCTTAGTCATTGCCCAATAACCGAATTCCCAGAAATCCCAAGAAGCTTAAG
1 CTTCGTGATCTGAATCTTAGTCATTGCCCAATAGCCGAATTCCCAGAAATCCCAAGAAGCTTAAC
* * * * * * **
1862277 AGAATTAAATTTATCTGGGACTCAAATT-AAGGAAGTGACCTTGTCTTTAGACTCTCTAAATAAT
66 AGAATTAAACTTATCTGGAACTCAAATTGAA-GAAGTGTCCTTGTCTATCGACTCTCCAAGCAAT
*
1862341 CTTCAGATGTTA
130 CTTCAGAAGTTA
1862353 AAGATGAGCT
Statistics
Matches: 282, Mismatches: 42, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
188 12 0.04
189 264 0.94
190 6 0.02
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (189 bp):
CTTCGTGATCTGAATCTTAGTCATTGCCCAATAGCCGAATTCCCAGAAATCCCAAGAAGCTTAAC
AGAATTAAACTTATCTGGAACTCAAATTGAAGAAGTGTCCTTGTCTATCGACTCTCCAAGCAATC
TTCAGAAGTTAGATATGAGGGGCTCAAGAGTAAAGAATGTATCCATCAAGATGGAAGCC
Found at i:1864641 original size:15 final size:15
Alignment explanation
Indices: 1864621--1864650 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1864611 ATAATAATAT
1864621 TAAATATATACATAC
1 TAAATATATACATAC
*
1864636 TAAATATATATATAC
1 TAAATATATACATAC
1864651 ATAGTATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATACATAC
Found at i:1865562 original size:3 final size:3
Alignment explanation
Indices: 1865554--1865608 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
1865544 AAGGATACTG
1865554 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1865602 ATA ATA A
1 ATA ATA A
1865609 GCAAAGTGAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1866081 original size:33 final size:33
Alignment explanation
Indices: 1866042--1866111 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
1866032 AAAGTATATA
1866042 TATATTAGAAATAATAATTATATATAAAAAAGG
1 TATATTAGAAATAATAATTATATATAAAAAAGG
1866075 TATATTAGAAATAATAATTATATATAAAAAAGG
1 TATATTAGAAATAATAATTATATATAAAAAAGG
1866108 TATA
1 TATA
1866112 GTACATGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (33 bp):
TATATTAGAAATAATAATTATATATAAAAAAGG
Found at i:1869245 original size:23 final size:23
Alignment explanation
Indices: 1869192--1869284 Score: 123
Period size: 23 Copynumber: 3.8 Consensus size: 23
1869182 CACTTTGTGC
1869192 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GG-----AT
1869221 TATTCTGGTGTGTTTTGGAGGAT
1 TATTCTGGTGTGTTTTGGAGGAT
1869244 TATTCTGGTGTGTTTTGGAGGAT
1 TATTCTGGTGTGTTTTGGAGGAT
*
1869267 TATACTGGTGTGTTTTGG
1 TATTCTGGTGTGTTTTGG
1869285 TTGGACATTT
Statistics
Matches: 63, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
23 42 0.67
28 2 0.03
29 19 0.30
ACGTcount: A:0.14, C:0.04, G:0.32, T:0.49
Consensus pattern (23 bp):
TATTCTGGTGTGTTTTGGAGGAT
Found at i:1869505 original size:23 final size:23
Alignment explanation
Indices: 1869475--1869562 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 23
1869465 GCTTTACTGA
* *
1869475 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTTGTGTGTCGTATT
*
1869498 TCAGGCACCTTGTGTGTCGCA--
1 TCAGGCACCTTGTGTGTCGTATT
* *
1869519 GCAGGCACCTCGTGTGTC--ATT
1 TCAGGCACCTTGTGTGTCGTATT
*
1869540 TCAGGCA-CTTTTGTGTCGTATT
1 TCAGGCACCTTGTGTGTCGTATT
1869562 T
1 T
1869563 TGATCAGGTA
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
19 1 0.02
20 8 0.15
21 22 0.42
22 4 0.08
23 18 0.34
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTTGTGTGTCGTATT
Found at i:1872849 original size:28 final size:27
Alignment explanation
Indices: 1872817--1872869 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
1872807 TTGAAATCTA
1872817 AAAAGGA-AAGGGACTAAATTTCTAAAAT
1 AAAAGGACAAGGG-CTAAA-TTCTAAAAT
*
1872845 AAAAGGACATGGGCTAAATTCTAAA
1 AAAAGGACAAGGGCTAAATTCTAAA
1872870 TTTGTGTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.30
28 12 0.52
29 4 0.17
ACGTcount: A:0.51, C:0.09, G:0.19, T:0.21
Consensus pattern (27 bp):
AAAAGGACAAGGGCTAAATTCTAAAAT
Found at i:1874019 original size:21 final size:21
Alignment explanation
Indices: 1873995--1874036 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1873985 TTTGGGCTGT
*
1873995 ATAAAAATGAAATTAAA-AATA
1 ATAAAAAT-AAATCAAATAATA
1874016 ATAAAAATAAATCAAATAATA
1 ATAAAAATAAATCAAATAATA
1874037 TTGCTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (21 bp):
ATAAAAATAAATCAAATAATA
Found at i:1881260 original size:44 final size:44
Alignment explanation
Indices: 1881207--1881293 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
1881197 TTTCACTGTG
1881207 AATGAGCATTGTCTTAGGATACATAACATGAGATTTTCACAATT
1 AATGAGCATTGTCTTAGGATACATAACATGAGATTTTCACAATT
*
1881251 AATGAGCATTGTCTTAGGATATATAACATGAGATTTTCACAAT
1 AATGAGCATTGTCTTAGGATACATAACATGAGATTTTCACAAT
1881294 GATTTATTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (44 bp):
AATGAGCATTGTCTTAGGATACATAACATGAGATTTTCACAATT
Found at i:1882542 original size:189 final size:187
Alignment explanation
Indices: 1882214--1882757 Score: 645
Period size: 189 Copynumber: 2.9 Consensus size: 187
1882204 ATTTCAAAGT
* * *
1882214 TGGAATCACTTCGTGATATGGATCTTAGTCATTGTCCAATGGTCGAATTCCCAGAAATTCCC-AG
1 TGGAATCCCTTCGTGATATGAATCTTAGTCATTGCCCAAT-GTCGAATTCCCAGAAA-TCCCAAG
* * * * * *
1882278 AAGCTT-GACAGATTTAAACTTATCTGAAACTCAAATTGAAGAGGTGTGCTTGTCTCTTGCCACT
64 AAGCTTAG-CAGAATTAAACTTATCTGGAACTCAAATTGAAGAGGTGTACTTGTCTCTAGACTCT
* *
1882342 CCAAGTAATCTTCAGAGCTTAAATATGAGTGGCTCAAGGG-ACAAAA-TTGTATCGATCAAGA
128 CTAAATAATCTTCAGAGCTTAAATATGAGT-GCTCAAGGGTA-AAAAGTT-TATCGATCAAGA
* *
1882403 TGGAATCCCTTCGTGATCTGAATCTTAGTCATTGCCCAATAGTCAAATTTCCC-GAAATCCCAAG
1 TGGAATCCCTTCGTGATATGAATCTTAGTCATTGCCCAAT-GTCGAA-TTCCCAGAAATCCCAAG
* * * *
1882467 AAGCTTAGCAAAATTAAACTTATCCGGAACTCAAATTGAAGAGGTGTACTTGTCTCTCGACTCTT
64 AAGCTTAGCAGAATTAAACTTATCTGGAACTCAAATTGAAGAGGTGTACTTGTCTCTAGACTCTC
** *
1882532 TATTTAATCTTCAGA-CGTTAGATATGAGTTGCTCAAGGGTAAAAAGTTTATCGATCAAGA
129 TAAATAATCTTCAGAGC-TTAAATATGAG-TGCTCAAGGGTAAAAAGTTTATCGATCAAGA
*
1882592 TGGAATCCCTTTGTGATATGAATCTTAGTCATTGCCCAATGATCGAATTCCCAGAAATCCCAAGA
1 TGGAATCCCTTCGTGATATGAATCTTAGTCATTGCCCAATG-TCGAATTCCCAGAAATCCCAAGA
* * * * * * *
1882657 AGCTTAAG-AGAATTAAATTTATCTGGGACTCAAATTAAAGAAGCGAACTTGTCTTTAGACTCTC
65 AGCTT-AGCAGAATTAAACTTATCTGGAACTCAAATTGAAGAGGTGTACTTGTCTCTAGACTCTC
*
1882721 TAAATAATCTTCAGAAG-TTAAAGATGAGCTGCTCAAG
129 TAAATAATCTTCAG-AGCTTAAATATGAG-TGCTCAAG
1882758 TATTCAAAAG
Statistics
Matches: 305, Mismatches: 38, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
188 11 0.04
189 281 0.92
190 13 0.04
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (187 bp):
TGGAATCCCTTCGTGATATGAATCTTAGTCATTGCCCAATGTCGAATTCCCAGAAATCCCAAGAA
GCTTAGCAGAATTAAACTTATCTGGAACTCAAATTGAAGAGGTGTACTTGTCTCTAGACTCTCTA
AATAATCTTCAGAGCTTAAATATGAGTGCTCAAGGGTAAAAAGTTTATCGATCAAGA
Found at i:1885666 original size:21 final size:21
Alignment explanation
Indices: 1885640--1885680 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1885630 AGACAAGCGA
* *
1885640 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1885661 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1885681 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1890223 original size:25 final size:25
Alignment explanation
Indices: 1890195--1890273 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 25
1890185 AATTGTTCAT
1890195 AATAAATACAAATTTATTTACACAA
1 AATAAATACAAATTTATTTACACAA
* *
1890220 AATAATATA-ATAA-TT-GTT---CAT
1 AATAA-ATACA-AATTTATTTACACAA
*
1890241 AATAAATACAAATTTATTTACATAA
1 AATAAATACAAATTTATTTACACAA
1890266 AATAAATA
1 AATAAATA
1890274 AACATATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 16
0.66 0.08 0.26
Matches are distributed among these distances:
20 5 0.12
21 10 0.24
22 2 0.05
24 2 0.05
25 17 0.41
26 5 0.12
ACGTcount: A:0.56, C:0.08, G:0.01, T:0.35
Consensus pattern (25 bp):
AATAAATACAAATTTATTTACACAA
Found at i:1890246 original size:46 final size:46
Alignment explanation
Indices: 1890179--1890274 Score: 176
Period size: 46 Copynumber: 2.1 Consensus size: 46
1890169 GTGCAACAAT
1890179 TATAATAATTGTTCATAATAAATACAAATTTATTTACACAAAATAA
1 TATAATAATTGTTCATAATAAATACAAATTTATTTACACAAAATAA
*
1890225 TATAATAATTGTTCATAATAAATACAAATTTATTTACATAAAATAA
1 TATAATAATTGTTCATAATAAATACAAATTTATTTACACAAAATAA
1890271 -ATAA
1 TATAA
1890275 ACATATTTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 4 0.08
46 45 0.92
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (46 bp):
TATAATAATTGTTCATAATAAATACAAATTTATTTACACAAAATAA
Found at i:1894634 original size:21 final size:21
Alignment explanation
Indices: 1894608--1894648 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1894598 ATCTGCTCAA
* *
1894608 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1894629 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1894649 TCGCTCGTCT
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:1905208 original size:19 final size:19
Alignment explanation
Indices: 1905184--1905221 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1905174 AGGTAGGGTA
*
1905184 TGTGTACTTCAGAATTCAG
1 TGTGTACCTCAGAATTCAG
1905203 TGTGTACCTCAGAATTCAG
1 TGTGTACCTCAGAATTCAG
1905222 AGCTCATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (19 bp):
TGTGTACCTCAGAATTCAG
Found at i:1907017 original size:35 final size:35
Alignment explanation
Indices: 1906990--1907155 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
1906980 CATGGCAAAG
*
1906990 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
1907025 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
1907060 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
1907100 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
1907135 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
1907156 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:1907109 original size:75 final size:75
Alignment explanation
Indices: 1906990--1907160 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
1906980 CATGGCAAAG
** *
1906990 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
1907049 CCATACTGAGC
65 CCATACCGAGC
1907060 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
1907125 CATACCGAGT
66 CATACCGAGC
**
1907135 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
1907161 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:1914500 original size:35 final size:35
Alignment explanation
Indices: 1914473--1914638 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
1914463 CATGGCAAAG
*
1914473 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
1914508 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
1914543 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
1914583 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
1914618 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
1914639 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:1914592 original size:75 final size:75
Alignment explanation
Indices: 1914473--1914643 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
1914463 CATGGCAAAG
** *
1914473 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
1914532 CCATACTGAGC
65 CCATACCGAGC
1914543 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
1914608 CATACCGAGT
66 CATACCGAGC
**
1914618 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
1914644 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:1921925 original size:25 final size:27
Alignment explanation
Indices: 1921877--1921927 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
1921867 AAAATACTTT
**
1921877 AAATTTATTTATATATTTTTAAAATTA
1 AAATTTATTTATATATTTACAAAATTA
1921904 AAATTTA-TT-TATATTTACAAAATT
1 AAATTTATTTATATATTTACAAAATT
1921928 TTTATTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 13 0.59
26 2 0.09
27 7 0.32
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
AAATTTATTTATATATTTACAAAATTA
Found at i:1926098 original size:189 final size:189
Alignment explanation
Indices: 1925767--1926132 Score: 527
Period size: 189 Copynumber: 1.9 Consensus size: 189
1925757 GTCTTAGTGC
* * * ** * ** *
1925767 TCTGACTCTTGGTGATTGCCCATTAGTTGAATTTCCAGAAATCCCAAGAAGCTTAAGAGTATTGA
1 TCTGAATCTTAGTGATTGCCCAATAGTCAAATTTCCAGAAATCCCAAGAAACTTAAGAAAATTAA
*
1925832 ACTTACCTGGAACTCAAATTGAAGAGGTGTACCTGTCTCTCGACTCTCAAAGTAATCTTCGGACC
66 ACTTACCTGGAACTCAAATTGAAGAGGTGTACCTGTCTCTCGACTCTCAAAGTAATCTTCAGACC
1925897 TTAAATATGAGTGGCTCAAGAGTAAAAAATGCATCCATCAAGATGGAATCCCTTCGTGA
131 TTAAATATGAGTGGCTCAAGAGTAAAAAATGCATCCATCAAGATGGAATCCCTTCGTGA
* * *
1925956 TCTGAATCTTAGTGATTGCCCAATCGTCAAATTTCCCGAAATCCCAAGAAACTTGAGAAAATTAA
1 TCTGAATCTTAGTGATTGCCCAATAGTCAAATTTCCAGAAATCCCAAGAAACTTAAGAAAATTAA
* * *
1926021 ACTTATCTGGAACTCAAATTGAAGAGGTGT-CCTTGTCTCTCGACTCTCTAGGTAATCTTCAGAC
66 ACTTACCTGGAACTCAAATTGAAGAGGTGTACC-TGTCTCTCGACTCTCAAAGTAATCTTCAGAC
* * * * *
1926085 CTTAAATATGAGTGGTTCAAGGGTAAAAAGTGTATCGATCAAGATGGA
130 CTTAAATATGAGTGGCTCAAGAGTAAAAAATGCATCCATCAAGATGGA
1926133 TTTGTTAAGC
Statistics
Matches: 155, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
188 2 0.01
189 153 0.99
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (189 bp):
TCTGAATCTTAGTGATTGCCCAATAGTCAAATTTCCAGAAATCCCAAGAAACTTAAGAAAATTAA
ACTTACCTGGAACTCAAATTGAAGAGGTGTACCTGTCTCTCGACTCTCAAAGTAATCTTCAGACC
TTAAATATGAGTGGCTCAAGAGTAAAAAATGCATCCATCAAGATGGAATCCCTTCGTGA
Found at i:1932886 original size:12 final size:12
Alignment explanation
Indices: 1932871--1932897 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1932861 TTTGTTACTT
1932871 GTTTTGCTAGTC
1 GTTTTGCTAGTC
1932883 GTTTTGCTAGTC
1 GTTTTGCTAGTC
1932895 GTT
1 GTT
1932898 GAGTTCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.15, G:0.26, T:0.52
Consensus pattern (12 bp):
GTTTTGCTAGTC
Found at i:1933915 original size:29 final size:28
Alignment explanation
Indices: 1933863--1933923 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
1933853 TTATATAAAA
* * *
1933863 ATATGTGTGTGTATGCCATGTGATATAGG
1 ATATATGTGTGTATGACATATGAT-TAGG
* *
1933892 ATATATGTGTGTATGATATATGATTATG
1 ATATATGTGTGTATGACATATGATTAGG
1933920 ATAT
1 ATAT
1933924 GCATGTGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.30, C:0.03, G:0.25, T:0.43
Consensus pattern (28 bp):
ATATATGTGTGTATGACATATGATTAGG
Found at i:1934159 original size:5 final size:5
Alignment explanation
Indices: 1934149--1934175 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1934139 GAGGTAGAAC
1934149 ATGAT ATGAT ATGAT ATGAT ATGAT AT
1 ATGAT ATGAT ATGAT ATGAT ATGAT AT
1934176 TGGAACCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (5 bp):
ATGAT
Found at i:1934747 original size:20 final size:20
Alignment explanation
Indices: 1934724--1934775 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1934714 TAAGATATGC
* *
1934724 TATGTTATGATTTGATGT-AA
1 TATGATATGATATGAT-TCAA
*
1934744 TATGATATGCTATGATTCAA
1 TATGATATGATATGATTCAA
1934764 TATGATATGATA
1 TATGATATGATA
1934776 CGTTAAGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (20 bp):
TATGATATGATATGATTCAA
Found at i:1938896 original size:61 final size:61
Alignment explanation
Indices: 1938801--1938925 Score: 250
Period size: 61 Copynumber: 2.0 Consensus size: 61
1938791 TAAATTGGTT
1938801 TTTGTTGTTAGGGGATTAATCTAATTCAAGGAATAAAGTTAGACATATCTCAAATTGATAA
1 TTTGTTGTTAGGGGATTAATCTAATTCAAGGAATAAAGTTAGACATATCTCAAATTGATAA
1938862 TTTGTTGTTAGGGGATTAATCTAATTCAAGGAATAAAGTTAGACATATCTCAAATTGATAA
1 TTTGTTGTTAGGGGATTAATCTAATTCAAGGAATAAAGTTAGACATATCTCAAATTGATAA
1938923 TTT
1 TTT
1938926 ACGGTTACAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.38
Consensus pattern (61 bp):
TTTGTTGTTAGGGGATTAATCTAATTCAAGGAATAAAGTTAGACATATCTCAAATTGATAA
Found at i:1940227 original size:189 final size:189
Alignment explanation
Indices: 1939830--1940309 Score: 563
Period size: 189 Copynumber: 2.5 Consensus size: 189
1939820 TCTTAGTGGT
* * * * * * *
1939830 CTGACTCTTAGTCATTGCCCATTAGTTGAATTTCCGGAAATCCCAAGAAGCTTAAGAGTATTGAA
1 CTGAATCTCAGTCATTGCCCAATAGTCGAATTTCCCGAAATCCCAAGAAGCTTAAGAGAATTAAA
* *
1939895 CTTACCTGGAACTCATATTGAAGAGGTGTACC-TGTCTCTCGACTCCCCAAGTAATCTTCAGACC
66 CTTATCTGGAACTCAAATTGAAGAGGTGT-CCTTGTCTCTCGACTCCCCAAGTAATCTTCAGACC
* *
1939959 TTAAATATGAGTGGCTCAAAGGTAAAAAATGCATCCATCAAGATGGAATCCCTTCGTGAT
130 TTAAATATGAGTGGCTCAAAGGTAAAAAATGCATCCATCAAGATGGAATCCCTTCATGAC
* * * * * *
1940019 CTGAATCTTAGTGATTGCCCAATAGTCAAATTTCCCGAAATCCCAAGAAACTTGAGAAAATTAAA
1 CTGAATCTCAGTCATTGCCCAATAGTCGAATTTCCCGAAATCCCAAGAAGCTTAAGAGAATTAAA
* * *
1940084 CTTATCTGGAACTCAAATTGAAGAGGTGTCCTTGTCTCTCGACTCTCTAGGTAATCTTCAGACCT
66 CTTATCTGGAACTCAAATTGAAGAGGTGTCCTTGTCTCTCGACTCCCCAAGTAATCTTCAGACCT
* * * * *
1940149 TAAATATGAGTGGCTCAAGGGTAAAAAGTGTATCGATCAAGATGGATTCCCTTCAT-AGC
131 TAAATATGAGTGGCTCAAAGGTAAAAAATGCATCCATCAAGATGGAATCCCTTCATGA-C
** * * *
1940208 CT-AGATCTCAGTCATTGCCCAACGGTCGAA-TTCCCAGAAATTCCAGGAAGTTTAAGAGAATTA
1 CTGA-ATCTCAGTCATTGCCCAATAGTCGAATTTCCC-GAAATCCCAAGAAGCTTAAGAGAATTA
* * * * * * *
1940271 TATTTATCTGGGACTCAAATTAAACAAGCGTCCTTGTCT
64 AACTTATCTGGAACTCAAATTGAAGAGGTGTCCTTGTCT
1940310 TTAAACTCTC
Statistics
Matches: 246, Mismatches: 41, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
188 9 0.04
189 237 0.96
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (189 bp):
CTGAATCTCAGTCATTGCCCAATAGTCGAATTTCCCGAAATCCCAAGAAGCTTAAGAGAATTAAA
CTTATCTGGAACTCAAATTGAAGAGGTGTCCTTGTCTCTCGACTCCCCAAGTAATCTTCAGACCT
TAAATATGAGTGGCTCAAAGGTAAAAAATGCATCCATCAAGATGGAATCCCTTCATGAC
Found at i:1944059 original size:22 final size:21
Alignment explanation
Indices: 1944002--1944060 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 21
1943992 ATGCCACATC
1944002 AGTATTTTTATCCTGAATTTTA
1 AGTA-TTTTATCCTGAATTTTA
1944024 AG-ATTTTATCCTGAATTTT-
1 AGTATTTTATCCTGAATTTTA
1944043 AGTATTTTAAATCCTGAA
1 AGTATTTT--ATCCTGAA
1944061 ATTCAGGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.06
20 21 0.62
21 1 0.03
22 10 0.29
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (21 bp):
AGTATTTTATCCTGAATTTTA
Found at i:1945589 original size:5 final size:5
Alignment explanation
Indices: 1945579--1945668 Score: 60
Period size: 5 Copynumber: 18.2 Consensus size: 5
1945569 GAGGTAGAAC
* * *
1945579 ATGAT ATGAT ATGAT ATGAT ATGAT A--ATT AAGAT ATGCT ATGTT ATGAT
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGA-T ATGAT ATGAT ATGAT ATGAT
* * * * * *
1945628 TTGAT GTAAT ATGAT ATGCT ATTAT -TCAAT ATGAT ATGAT A
1 ATGAT ATGAT ATGAT ATGAT ATGAT AT-GAT ATGAT ATGAT A
1945669 CTTAAGGTAA
Statistics
Matches: 66, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
3 1 0.02
4 3 0.05
5 60 0.91
6 2 0.03
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (5 bp):
ATGAT
Found at i:1949476 original size:3 final size:3
Alignment explanation
Indices: 1949468--1949510 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1949458 TTGGATAAAT
1949468 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1949511 CCAGCCCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1954749 original size:16 final size:17
Alignment explanation
Indices: 1954719--1954752 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1954709 AGAAAAATTA
*
1954719 TTAAAATATTTTTATAT
1 TTAAAATATTATTATAT
1954736 TTAAAATA-TATTATAT
1 TTAAAATATTATTATAT
1954752 T
1 T
1954753 ATTAGATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAAATATTATTATAT
Found at i:1954755 original size:19 final size:18
Alignment explanation
Indices: 1954715--1954755 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
1954705 AATTAGAAAA
*
1954715 ATTA-TTAAAATATTTTT
1 ATTATTTAAAATATTTAT
1954732 A-TATTTAAAATATATTAT
1 ATTATTTAAAATAT-TTAT
1954750 ATTATT
1 ATTATT
1954756 AGATGTTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 2 0.10
17 10 0.50
18 4 0.20
19 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATTTAAAATATTTAT
Found at i:1964304 original size:21 final size:20
Alignment explanation
Indices: 1964262--1964321 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
1964252 AGCTTATTTA
* * *
1964262 TATTTTAATTATTCCTATTT
1 TATTTTAATTAATCTTAATT
1964282 TAGTTTTAATTAATCTTAATT
1 TA-TTTTAATTAATCTTAATT
* *
1964303 TA-CTTAATTAAGCTTAATT
1 TATTTTAATTAATCTTAATT
1964322 GTTAATTTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 15 0.44
20 2 0.06
21 17 0.50
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (20 bp):
TATTTTAATTAATCTTAATT
Found at i:1978833 original size:10 final size:10
Alignment explanation
Indices: 1978819--1978857 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
1978809 AAAAAGTGAT
1978819 AAAAAAAGTAC
1 AAAAAAA-TAC
1978830 AAAAAAATAC
1 AAAAAAATAC
1978840 AAAAAAAATA-
1 -AAAAAAATAC
1978850 AAAAAAAT
1 AAAAAAAT
1978858 TCTGTGGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 8 0.30
10 3 0.11
11 16 0.59
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAATAC
Found at i:1978833 original size:11 final size:11
Alignment explanation
Indices: 1978807--1978856 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 11
1978797 TTTCCCACAA
*
1978807 AAAAAAAGTGAT
1 AAAAAAAGT-AC
1978819 AAAAAAAGTAC
1 AAAAAAAGTAC
1978830 AAAAAAA-TAC
1 AAAAAAAGTAC
*
1978840 AAAAAAAATA-
1 AAAAAAAGTAC
1978850 AAAAAAA
1 AAAAAAA
1978857 TTCTGTGGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
10 17 0.47
11 10 0.28
12 9 0.25
ACGTcount: A:0.80, C:0.04, G:0.06, T:0.10
Consensus pattern (11 bp):
AAAAAAAGTAC
Found at i:1979002 original size:8 final size:8
Alignment explanation
Indices: 1978989--1979016 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1978979 GCTTCGCAGT
1978989 TTTTCGGG
1 TTTTCGGG
1978997 TTTTCGGG
1 TTTTCGGG
1979005 TTTTCGGG
1 TTTTCGGG
1979013 TTTT
1 TTTT
1979017 AACAATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.32, T:0.57
Consensus pattern (8 bp):
TTTTCGGG
Found at i:1980420 original size:44 final size:45
Alignment explanation
Indices: 1980330--1980458 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
1980320 GACAGAACGA
*
1980330 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
1980376 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
1980420 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
1980459 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:1992306 original size:3 final size:3
Alignment explanation
Indices: 1992298--1992322 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1992288 CGATCATTTA
1992298 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
1992323 TCATTTGGTT
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:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:1993904 original size:11 final size:11
Alignment explanation
Indices: 1993888--1993913 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1993878 TGAAGGTCCT
1993888 TTACTTCGAGA
1 TTACTTCGAGA
1993899 TTACTTCGAGA
1 TTACTTCGAGA
1993910 TTAC
1 TTAC
1993914 AAGTGGATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (11 bp):
TTACTTCGAGA
Found at i:1994575 original size:9 final size:9
Alignment explanation
Indices: 1994537--1994634 Score: 74
Period size: 9 Copynumber: 10.6 Consensus size: 9
1994527 CACTATAAAA
1994537 TTTTATAAT
1 TTTTATAAT
*
1994546 TTTT-TTAT
1 TTTTATAAT
*
1994554 TTCTAT-AT
1 TTTTATAAT
1994562 ATTTTATAATT
1 -TTTTATAA-T
*
1994573 TTTTACAAT
1 TTTTATAAT
*
1994582 TTTTATAAAA
1 TTTTAT-AAT
*
1994592 TTTTATGAT
1 TTTTATAAT
*
1994601 TTTTATGAT
1 TTTTATAAT
*
1994610 TTTTCTAAT
1 TTTTATAAT
1994619 TTTTAATAAAT
1 TTTT-AT-AAT
1994630 TTTTA
1 TTTTA
1994635 ACATTTAAAC
Statistics
Matches: 71, Mismatches: 11, Indels: 13
0.75 0.12 0.14
Matches are distributed among these distances:
8 8 0.11
9 37 0.52
10 18 0.25
11 8 0.11
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:1994587 original size:19 final size:19
Alignment explanation
Indices: 1994563--1994634 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
1994553 TTTCTATATA
*
1994563 TTTTATAATTTTTTACAAT
1 TTTTATAAATTTTTACAAT
* **
1994582 TTTTATAAAATTTTATGAT
1 TTTTATAAATTTTTACAAT
*
1994601 TTTTAT-GATTTTT-CTAAT
1 TTTTATAAATTTTTAC-AAT
1994619 TTTTAATAAATTTTTA
1 TTTT-ATAAATTTTTA
1994635 ACATTTAAAC
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
18 11 0.28
19 23 0.57
20 6 0.15
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTATAAATTTTTACAAT
Found at i:1994588 original size:26 final size:26
Alignment explanation
Indices: 1994536--1994604 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 26
1994526 ACACTATAAA
*
1994536 ATTTTATAATTTTTTTATTTCTATAT
1 ATTTTATAATTTTTTAATTTCTATAT
* *
1994562 ATTTTATAATTTTTTACAATTTTTATAAA
1 ATTTTATAATTTTTT--AATTTCTAT-AT
*
1994591 ATTTTATGATTTTT
1 ATTTTATAATTTTT
1994605 ATGATTTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 15 0.42
28 7 0.19
29 14 0.39
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (26 bp):
ATTTTATAATTTTTTAATTTCTATAT
Found at i:1994826 original size:91 final size:88
Alignment explanation
Indices: 1994729--1994931 Score: 219
Period size: 90 Copynumber: 2.2 Consensus size: 88
1994719 AAAGCATGGG
* * * *
1994729 TTTAATTTTATTTTTTTGAAAGAAGTTCGAATGTCTTTTTTATACCTTTTGAAAGTTTAAGTACC
1 TTTAATTTT-TTTTTTTGAAA-AAGTTCGAAGGTCTTTTTGATACATTTTGAAAGCTTAAGTACC
*
1994794 CAATTGAGTGTAAAAAGATGTAAGA-A
64 CAATTGAGTGTAAAAA-A-ATAAGAGA
* * * * ***
1994820 TTTAATTGCTTTTTTTTGAAAAGGTTTGAGGGTCTTTTTGATACATTTTGAAAGCTTAAGTGTTC
1 TTTAATT-TTTTTTTTTGAAAAAGTTCGAAGGTCTTTTTGATACATTTTGAAAGCTTAAGTACCC
* *
1994885 AATTTAGTGTAAAAAAATAAGAGG
65 AATTGAGTGTAAAAAAATAAGAGA
1994909 TTTAATTTTTTTTTTTTGAAAAA
1 TTTAA-TTTTTTTTTTTGAAAAA
1994932 ATTGAAAGTG
Statistics
Matches: 93, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
88 5 0.05
89 19 0.20
90 50 0.54
91 18 0.19
92 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (88 bp):
TTTAATTTTTTTTTTTGAAAAAGTTCGAAGGTCTTTTTGATACATTTTGAAAGCTTAAGTACCCA
ATTGAGTGTAAAAAAATAAGAGA
Found at i:1996863 original size:34 final size:34
Alignment explanation
Indices: 1996820--1996889 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
1996810 TGTCTTGGAA
1996820 TTCAATTTTAAGCAATCAAATGATAGTTAGAGAT
1 TTCAATTTTAAGCAATCAAATGATAGTTAGAGAT
1996854 TTCAATTTTAAGCAATCAAATGATAGTTAGAGAT
1 TTCAATTTTAAGCAATCAAATGATAGTTAGAGAT
1996888 TT
1 TT
1996890 TAGAATGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (34 bp):
TTCAATTTTAAGCAATCAAATGATAGTTAGAGAT
Found at i:1999153 original size:18 final size:17
Alignment explanation
Indices: 1999113--1999151 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1999103 CCTAAAGGTG
*
1999113 ATTTTATCTTCTTTATT
1 ATTTTATCTTATTTATT
1999130 ATTTTACTCTTATTT-TT
1 ATTTTA-TCTTATTTATT
1999147 ATTTT
1 ATTTT
1999152 TATTTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTATCTTATTTATT
Found at i:1999219 original size:11 final size:12
Alignment explanation
Indices: 1999197--1999247 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
1999187 TATATACATC
1999197 ATAATAAAAAAT
1 ATAATAAAAAAT
1999209 ATAATAAAAATAT
1 ATAATAAAAA-AT
*
1999222 ATATACAAAACAAAT
1 ATA-A-TAAA-AAAT
1999237 ATAA-AAAAAAT
1 ATAATAAAAAAT
1999248 TACCTTTTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
11 4 0.12
12 13 0.38
13 5 0.15
14 2 0.06
15 8 0.24
16 2 0.06
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAATAAAAAAT
Found at i:1999690 original size:11 final size:11
Alignment explanation
Indices: 1999672--1999701 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1999662 GTGTATATTG
1999672 TATATATTATA
1 TATATATTATA
*
1999683 TTTATATTATA
1 TATATATTATA
1999694 TATATATT
1 TATATATT
1999702 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:2001358 original size:21 final size:20
Alignment explanation
Indices: 2001334--2001374 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
2001324 CAATTTTGGG
2001334 CCACCCCAAAACCCAACTAAC
1 CCACCCCAAAACCCAA-TAAC
2001355 CCACCCCAAAACCCAATAAC
1 CCACCCCAAAACCCAATAAC
2001375 TAAACCTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.44, C:0.51, G:0.00, T:0.05
Consensus pattern (20 bp):
CCACCCCAAAACCCAATAAC
Found at i:2002572 original size:3 final size:3
Alignment explanation
Indices: 2002564--2002597 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2002554 CCACTTTTTA
*
2002564 TAT TAT TAT TAT TAT TAT TA- TAT TAT TTT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2002598 CTATGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2015765 original size:35 final size:35
Alignment explanation
Indices: 2015721--2015887 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
2015711 TCCTCATTGA
** *
2015721 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
2015756 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
2015796 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
2015831 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
2015866 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
2015888 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:2015804 original size:75 final size:73
Alignment explanation
Indices: 2015716--2015887 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
2015706 GGTTTTCCTC
** * * **
2015716 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
2015780 TCAGTATGG
65 TCAGTATGG
*
2015789 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
2015854 CTCAGTATGG
64 CTCAGTATGG
2015864 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
2015888 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:2020623 original size:32 final size:32
Alignment explanation
Indices: 2020583--2020645 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
2020573 TGTAGACCAG
2020583 GATCATTAAAGCATACAC-GAATCATCAAAAA
1 GATCATTAAAGCATACACAGAATCATCAAAAA
2020614 GATCAATTAAAGCATACACAGAATCATCAAAA
1 GATC-ATTAAAGCATACACAGAATCATCAAAA
2020646 GATAGAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 4 0.13
32 14 0.47
33 12 0.40
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (32 bp):
GATCATTAAAGCATACACAGAATCATCAAAAA
Found at i:2026565 original size:3 final size:3
Alignment explanation
Indices: 2026559--2026584 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2026549 ATAAAGTATG
2026559 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
2026585 TCTACAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2026639 original size:14 final size:15
Alignment explanation
Indices: 2026614--2026642 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2026604 TTAGGAAACG
2026614 TACATAAAAAATATA
1 TACATAAAAAATATA
2026629 TACAT-AAAAATATA
1 TACATAAAAAATATA
2026643 CAACAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (15 bp):
TACATAAAAAATATA
Found at i:2026681 original size:2 final size:2
Alignment explanation
Indices: 2026674--2026707 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2026664 ATATGTACAA
* *
2026674 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2026708 GTACATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2026852 original size:32 final size:31
Alignment explanation
Indices: 2026793--2026852 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
2026783 ACACAATATG
* *
2026793 GTATTTAAAATATATATATATATATATAATA
1 GTATTTAAAATATATACATATAAATATAATA
2026824 GTATTTAAGAATATATACATA-AGAATATA
1 GTATTTAA-AATATATACATATA-AATATA
2026853 TAACTAATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 9 0.36
32 16 0.64
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.40
Consensus pattern (31 bp):
GTATTTAAAATATATACATATAAATATAATA
Found at i:2027401 original size:16 final size:17
Alignment explanation
Indices: 2027377--2027444 Score: 54
Period size: 18 Copynumber: 4.1 Consensus size: 17
2027367 GTGGCTAGGG
2027377 TTTTT-TTA-GTTTTTT
1 TTTTTGTTAGGTTTTTT
2027392 TTTTTGTTAGGTTTTTCT
1 TTTTTGTTAGGTTTTT-T
* * *
2027410 TTATTCTT--CTTTTTT
1 TTTTTGTTAGGTTTTTT
*
2027425 TTTTGGGTTAGGTTTTTT
1 TTTT-TGTTAGGTTTTTT
2027443 TT
1 TT
2027445 GGGGGGACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
15 9 0.22
16 10 0.25
17 6 0.15
18 15 0.38
ACGTcount: A:0.06, C:0.04, G:0.13, T:0.76
Consensus pattern (17 bp):
TTTTTGTTAGGTTTTTT
Found at i:2029826 original size:7 final size:8
Alignment explanation
Indices: 2029804--2029828 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2029794 TAATTCATTT
2029804 TTTAAAAA
1 TTTAAAAA
2029812 TTTAAAAA
1 TTTAAAAA
2029820 TTTAAAAA
1 TTTAAAAA
2029828 T
1 T
2029829 ATTATAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TTTAAAAA
Found at i:2030743 original size:21 final size:20
Alignment explanation
Indices: 2030710--2030748 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2030700 TTTAGTGGTA
*
2030710 TCAAGTTGTGAACCACTAAGT
1 TCAAGTTGAGAA-CACTAAGT
*
2030731 TCAATTTGAGAACACTAA
1 TCAAGTTGAGAACACTAA
2030749 ATTGCTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (20 bp):
TCAAGTTGAGAACACTAAGT
Found at i:2034534 original size:70 final size:71
Alignment explanation
Indices: 2034409--2034549 Score: 248
Period size: 70 Copynumber: 2.0 Consensus size: 71
2034399 TATAGGAATT
2034409 TGGTTAAATCAAATCACACCACTCCTGGGGCCGAATTTTCATGGAAGTTCCACAAAATTTGCACA
1 TGGTTAAATCAAATCACACCACTCCTGGGGCCGAATTTTCATGGAAGTTCCACAAAATTTGCACA
2034474 TCACAA
66 TCACAA
* * *
2034480 TGGTTAAATCAAATCAGACCACTCCT-GGGCCGAATTTTCATGGAAGTTCTACAAAATTTGTACA
1 TGGTTAAATCAAATCACACCACTCCTGGGGCCGAATTTTCATGGAAGTTCCACAAAATTTGCACA
2034544 TCACAA
66 TCACAA
2034550 CCATACATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
70 42 0.63
71 25 0.37
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (71 bp):
TGGTTAAATCAAATCACACCACTCCTGGGGCCGAATTTTCATGGAAGTTCCACAAAATTTGCACA
TCACAA
Found at i:2037348 original size:21 final size:20
Alignment explanation
Indices: 2037315--2037353 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2037305 TTTAGTGGTA
*
2037315 TCAAGTTGTGAACCACTAAGT
1 TCAAGTTGAGAA-CACTAAGT
*
2037336 TCAATTTGAGAACACTAA
1 TCAAGTTGAGAACACTAA
2037354 ATTGATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (20 bp):
TCAAGTTGAGAACACTAAGT
Found at i:2039703 original size:12 final size:12
Alignment explanation
Indices: 2039686--2039710 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2039676 GATAATTTAA
2039686 AAAAAAGAAAAG
1 AAAAAAGAAAAG
2039698 AAAAAAGAAAAG
1 AAAAAAGAAAAG
2039710 A
1 A
2039711 CAATTGCATC
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:2040152 original size:27 final size:27
Alignment explanation
Indices: 2040114--2040168 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2040104 TGTCATGGAT
2040114 GAAAGGTTGAGAACAGCAGCTCGTACA
1 GAAAGGTTGAGAACAGCAGCTCGTACA
2040141 GAAAGGTTGAGAACAGCAGCTCGTACA
1 GAAAGGTTGAGAACAGCAGCTCGTACA
2040168 G
1 G
2040169 GAAATGTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.31, T:0.15
Consensus pattern (27 bp):
GAAAGGTTGAGAACAGCAGCTCGTACA
Found at i:2042893 original size:17 final size:17
Alignment explanation
Indices: 2042871--2042903 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2042861 ACCAACTCAA
2042871 TTGGTTAACTAACATAG
1 TTGGTTAACTAACATAG
*
2042888 TTGGTTAACTATCATA
1 TTGGTTAACTAACATA
2042904 AAGCCATGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (17 bp):
TTGGTTAACTAACATAG
Found at i:2055854 original size:21 final size:19
Alignment explanation
Indices: 2055795--2055862 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
2055785 AAAGTATGGC
2055795 AATATGAAAAATGAAATGAA
1 AATATGAAAAATGAAATG-A
* *
2055815 AAAACTGAAAAATG-TATGA
1 AATA-TGAAAAATGAAATGA
*
2055834 TAATATGAAAAAATGAGATGA
1 -AATATG-AAAAATGAAATGA
2055855 AA-ATGAAA
1 AATATGAAA
2055863 CCCCTACCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
18 3 0.08
19 6 0.15
20 18 0.45
21 13 0.32
ACGTcount: A:0.62, C:0.01, G:0.16, T:0.21
Consensus pattern (19 bp):
AATATGAAAAATGAAATGA
Found at i:2060153 original size:4 final size:4
Alignment explanation
Indices: 2060144--2060177 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
2060134 CTCGCTTACT
2060144 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
2060178 ACCAAAACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:2065595 original size:13 final size:15
Alignment explanation
Indices: 2065564--2065593 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2065554 TTAGGAAACG
2065564 TACATAAAAAATATA
1 TACATAAAAAATATA
2065579 TACATAAAAAATATA
1 TACATAAAAAATATA
2065594 CAACAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (15 bp):
TACATAAAAAATATA
Found at i:2065638 original size:18 final size:18
Alignment explanation
Indices: 2065615--2065671 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
2065605 TAAAATAATG
*
2065615 ATATGTACAAATATATAT
1 ATATGTACAAATATATAC
* *
2065633 ATATGTATATATATATAC
1 ATATGTACAAATATATAC
*
2065651 ATATGTACATAAAATATAC
1 ATATGTACA-AATATATAC
2065670 AT
1 AT
2065672 TAATATAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 23 0.72
19 9 0.28
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (18 bp):
ATATGTACAAATATATAC
Found at i:2065839 original size:38 final size:39
Alignment explanation
Indices: 2065754--2065839 Score: 104
Period size: 38 Copynumber: 2.2 Consensus size: 39
2065744 TTTAAAATAT
* *
2065754 ATATATATATATATAATAGTATTTAAGAATATATACATA
1 ATATATATATATATAATAGCATTTAAAAATATATACATA
* * *
2065793 AGAAATATATA-ACTAATGGCA-TTAAAAATATATACATA
1 ATATATATATATA-TAATAGCATTTAAAAATATATACATA
2065831 ATATATATA
1 ATATATATA
2065840 AAATACCTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
38 24 0.62
39 15 0.38
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (39 bp):
ATATATATATATATAATAGCATTTAAAAATATATACATA
Found at i:2066354 original size:31 final size:33
Alignment explanation
Indices: 2066311--2066373 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2066301 GGTGGCTAGG
2066311 TTTTTTTATC-TTTTTTT-TTGTTAGGTTTTTC
1 TTTTTTTATCTTTTTTTTCTTGTTAGGTTTTTC
*
2066342 TTTTTTCT-TCTTTTTTTTCTTTTTAGGTTTTT
1 TTTTTT-TATCTTTTTTTTCTTGTTAGGTTTTT
2066374 TTGGGTAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 8 0.29
32 8 0.29
33 12 0.43
ACGTcount: A:0.05, C:0.08, G:0.08, T:0.79
Consensus pattern (33 bp):
TTTTTTTATCTTTTTTTTCTTGTTAGGTTTTTC
Found at i:2066361 original size:9 final size:9
Alignment explanation
Indices: 2066336--2066365 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2066326 TTTTGTTAGG
2066336 TTTTTCTTT
1 TTTTTCTTT
2066345 TTTCTTCTTT
1 TTT-TTCTTT
2066355 TTTTTCTTT
1 TTTTTCTTT
2066364 TT
1 TT
2066366 AGGTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:2066384 original size:47 final size:45
Alignment explanation
Indices: 2066322--2066425 Score: 138
Period size: 47 Copynumber: 2.2 Consensus size: 45
2066312 TTTTTTATCT
* *
2066322 TTTTTTTTGTTAGGTTTTTCTTTTTTCTTCTTTTTTTTCTT-TTTAGG
1 TTTTTTTGGGTAGGTTTTTC-TTTTTCTT-TTTTTTTTCTTGTTT-GG
2066369 TTTTTTTGGGTAGGTTTTTCTTTTTCTTTTTTTTTTCTTGGGTTTGG
1 TTTTTTTGGGTAGGTTTTTCTTTTTCTTTTTTTTTTCTT--GTTTGG
2066416 TTTTTTTGGG
1 TTTTTTTGGG
2066426 GGGCTTAATG
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
45 11 0.21
46 8 0.15
47 30 0.58
48 3 0.06
ACGTcount: A:0.03, C:0.07, G:0.17, T:0.73
Consensus pattern (45 bp):
TTTTTTTGGGTAGGTTTTTCTTTTTCTTTTTTTTTTCTTGTTTGG
Found at i:2071128 original size:45 final size:45
Alignment explanation
Indices: 2071082--2071179 Score: 119
Period size: 45 Copynumber: 2.1 Consensus size: 45
2071072 TAAGCCCCCC
2071082 AAAAAACCAAACCCAAGAAAAAAAA-AGAAAAAGAAAAACTTACCCAAA
1 AAAAAACCAAA---AAGAAAAAAAAGA-AAAAAGAAAAACTTACCCAAA
* * *
2071130 AAAAAACTAAAAAGAAAAAAAAGAAAAAAGAAAAACCTA-ACAAA
1 AAAAAACCAAAAAGAAAAAAAAGAAAAAAGAAAAACTTACCCAAA
2071174 AAAAAA
1 AAAAAA
2071180 GATAAAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 10 0.22
45 25 0.54
46 1 0.02
48 10 0.22
ACGTcount: A:0.77, C:0.13, G:0.06, T:0.04
Consensus pattern (45 bp):
AAAAAACCAAAAAGAAAAAAAAGAAAAAAGAAAAACTTACCCAAA
Found at i:2071147 original size:16 final size:16
Alignment explanation
Indices: 2071128--2071164 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2071118 AACTTACCCA
*
2071128 AAAAAAAACTAAAAAG
1 AAAAAAAACAAAAAAG
*
2071144 AAAAAAAAGAAAAAAG
1 AAAAAAAACAAAAAAG
2071160 AAAAA
1 AAAAA
2071165 CCTAACAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.86, C:0.03, G:0.08, T:0.03
Consensus pattern (16 bp):
AAAAAAAACAAAAAAG
Found at i:2071164 original size:30 final size:30
Alignment explanation
Indices: 2071130--2071188 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2071120 CTTACCCAAA
2071130 AAAAAACTAA-AAAGAAAAAAAAGAAAAAAG
1 AAAAAACTAACAAA-AAAAAAAAGAAAAAAG
* * *
2071160 AAAAACCTAACAAAAAAAAAGATAAAAAA
1 AAAAAACTAACAAAAAAAAAAAGAAAAAA
2071189 ACCTAGCCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.81, C:0.07, G:0.07, T:0.05
Consensus pattern (30 bp):
AAAAAACTAACAAAAAAAAAAAGAAAAAAG
Found at i:2071186 original size:45 final size:44
Alignment explanation
Indices: 2071100--2071187 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 44
2071090 AAACCCAAGA
* * *
2071100 AAAAAAAAGAAAAAGAAAAACTTACCCAAAAAAAAACTAAAAAG
1 AAAAAAAAGAAAAAGAAAAACCTACACAAAAAAAAAATAAAAAG
2071144 AAAAAAAAGAAAAAAGAAAAACCTA-ACAAAAAAAAAGATAAAAA
1 AAAAAAAAG-AAAAAGAAAAACCTACACAAAAAAAAA-ATAAAAA
2071188 AACCTAGCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
44 19 0.49
45 20 0.51
ACGTcount: A:0.78, C:0.09, G:0.07, T:0.06
Consensus pattern (44 bp):
AAAAAAAAGAAAAAGAAAAACCTACACAAAAAAAAAATAAAAAG
Found at i:2071189 original size:15 final size:14
Alignment explanation
Indices: 2071127--2071189 Score: 54
Period size: 15 Copynumber: 4.3 Consensus size: 14
2071117 AAACTTACCC
*
2071127 AAAAAAAAACTAAA
1 AAAAAAAAAATAAA
*
2071141 AAGAAAAAAAAGAAA
1 AA-AAAAAAAATAAA
**
2071156 AAAGAAAAACCTAACA
1 AAA-AAAAAAATAA-A
*
2071172 AAAAAAAAGATAAA
1 AAAAAAAAAATAAA
2071186 AAAA
1 AAAA
2071190 CCTAGCCACC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
14 8 0.21
15 27 0.69
16 4 0.10
ACGTcount: A:0.83, C:0.06, G:0.06, T:0.05
Consensus pattern (14 bp):
AAAAAAAAAATAAA
Found at i:2071721 original size:39 final size:39
Alignment explanation
Indices: 2071649--2071723 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
2071639 TTTATATATA
* * *
2071649 TTATGTATATATTTTTTAATGCCATTAGTTATATATTTC
1 TTATGTATATATTCTTAAATACCATTAGTTATATATTTC
*
2071688 TTATGTATATATTCTTAAATACTATTA-TATATATAT
1 TTATGTATATATTCTTAAATACCATTAGT-TATATAT
2071724 ATATTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.03
39 30 0.97
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (39 bp):
TTATGTATATATTCTTAAATACCATTAGTTATATATTTC
Found at i:2073749 original size:12 final size:12
Alignment explanation
Indices: 2073729--2073764 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2073719 AGTCATTTGA
2073729 CATTCATGCATT
1 CATTCATGCATT
*
2073741 CATTTATGCATT
1 CATTCATGCATT
*
2073753 CATTCATTCATT
1 CATTCATGCATT
2073765 GCATATTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:2080598 original size:71 final size:69
Alignment explanation
Indices: 2080500--2080674 Score: 217
Period size: 71 Copynumber: 2.5 Consensus size: 69
2080490 TTTTCAAGGG
* *
2080500 AAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTT
1 AAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAAGACACGCTGAGGTATTTTTAATTTAT
2080564 GTTTT
65 GTTTT
* ** * *
2080569 CAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGTTTA
1 --AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTTAATTTA
2080634 TGTTTT
64 TGTTTT
** * *
2080640 AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
2080675 TTTAATTTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
69 30 0.33
71 59 0.65
72 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (69 bp):
AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTTAATTTATG
TTTT
Found at i:2080847 original size:126 final size:124
Alignment explanation
Indices: 2080553--2080894 Score: 453
Period size: 126 Copynumber: 2.8 Consensus size: 124
2080543 GTTGAGGTAT
* *
2080553 TTTTAATTTT--TGTTTTCAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCGGGGCACGC
1 TTTTAATTTTACT-TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC
* * * * * *
2080616 TGAGGTATTTT-TA-GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
65 TGAGGTATTTTCAATTTTTGTGTTTTAATTTAACTCATATTGCAAGAGGTGAGTTAAGCC
** *
2080674 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTACTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCT
*
2080739 GAGGTATTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCAAGAGGTGGGTTGAA-CC
66 GAGGTATTTTCAATTTTTGTGTTTTAATTT-AACTCATATTGCAAGAGGTGAGTT-AAGCC
* * *
2080799 TTTTAATTTCTACTTTTTCAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC
1 TTTTAATTT-TACTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC
* *
2080864 TGAGGTATTTTCAATTTCTGT-TTTCAATTTA
65 TGAGGTATTTTCAATTTTTGTGTTTTAATTTA
2080895 CGTTGTTCAA
Statistics
Matches: 196, Mismatches: 18, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
121 10 0.05
122 59 0.30
123 2 0.01
124 14 0.07
125 40 0.20
126 71 0.36
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (124 bp):
TTTTAATTTTACTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCT
GAGGTATTTTCAATTTTTGTGTTTTAATTTAACTCATATTGCAAGAGGTGAGTTAAGCC
Found at i:2081020 original size:140 final size:140
Alignment explanation
Indices: 2080768--2081030 Score: 490
Period size: 140 Copynumber: 1.9 Consensus size: 140
2080758 TGTTTTAATT
*
2080768 TCAACTCATATTGCAAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAGCTCATAT
1 TCAACTCATATTGCAAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAACTCATAT
* *
2080833 TGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAATTTACGT
66 TGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAATTTACGT
2080898 TGTTCAAGAA
131 TGTTCAAGAA
*
2080908 TCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAACTCATAT
1 TCAACTCATATTGCAAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAACTCATAT
2080973 TGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAA
66 TGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAA
2081031 AAAAATCAAC
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 119 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (140 bp):
TCAACTCATATTGCAAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAACTCATAT
TGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAATTTACGT
TGTTCAAGAA
Found at i:2081206 original size:74 final size:74
Alignment explanation
Indices: 2080958--2081247 Score: 438
Period size: 74 Copynumber: 3.9 Consensus size: 74
2080948 CTACTTTTTC
2080958 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
*
2081023 GTTGTCAAA
66 GTTGTAAAA
* * *
2081032 AAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTGTCAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
**
2081096 CGTATGTTTCAA
66 -GT-TG-TAAAA
* *
2081108 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
2081173 GTTGTAAAA
66 GTTGTAAAA
* *
2081182 AAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATTT
2081247 C
64 C
2081248 CGTTTTTCAA
Statistics
Matches: 194, Mismatches: 16, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
73 25 0.13
74 79 0.41
75 4 0.02
76 62 0.32
77 24 0.12
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (74 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
GTTGTAAAA
Found at i:2081256 original size:150 final size:150
Alignment explanation
Indices: 2080958--2081257 Score: 498
Period size: 150 Copynumber: 2.0 Consensus size: 150
2080948 CTACTTTTTC
2080958 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
* *
2081023 GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTATTGT
66 GTTGTAAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCGGACACGCCGAGGTATTGT
*
2081088 CAATTTTTCGTATGTTTCAA
131 CAATTTTCCGTATGTTTCAA
* *
2081108 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
2081173 GTTGTAAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGGTAT
66 GTTGTAAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTC-GG--ACACGCCGAGGTAT
*
2081238 TTTCAA-TTTCCGT-T-TTTCAA
128 TGTCAATTTTCCGTATGTTTCAA
2081258 TTTCTGCCTT
Statistics
Matches: 141, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
150 114 0.81
151 3 0.02
152 6 0.04
153 18 0.13
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (150 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
GTTGTAAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCGGACACGCCGAGGTATTGT
CAATTTTCCGTATGTTTCAA
Found at i:2081447 original size:77 final size:77
Alignment explanation
Indices: 2081251--2081785 Score: 492
Period size: 77 Copynumber: 6.7 Consensus size: 77
2081241 CAATTTCCGT
* *
2081251 TTTTCAATTTCTGCCTTTCAAAAAACAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAG
1 TTTTCAATTTCTGTCTTTC---AAA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
*
2081316 G--ACACGCTGAGGTA
62 GTCACACGCTGAGATA
* * *
2081330 ATTTCAATTTCTGT-TGT-AAAAAAATCAACTCGTATTGCGAGCA-GTGAGTTGAGCCTCAGGTC
1 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAG-AGGTGAGTTGAGCCTCAGGTC
*
2081392 ACACGCCGAGATA
65 ACACGCTGAGATA
* *
2081405 TTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTC
1 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TC
* *
2081469 ACGCGCTGAGCTA
65 ACACGCTGAGATA
* * *
2081482 TTTTAAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCA
1 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCA
* *
2081547 CACACTGAGGTATT
66 CACGCTGA-G-ATA
* * * * * *
2081561 TTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCAAGATGTGAGTTGAGCCTCAGGTCA
1 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCA
* *
2081626 CATG-TCGAGGTA
66 CACGCT-GAGATA
** * *
2081638 TTTTCAAAATCTGTTTTTCAAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGA
1 TTTTCAATTTCTGTCTTTC-AA----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* ** *
2081703 GCCT-TGGCTCACGTGCTGAGCTA
55 GCCTCAGG-TCACACGCTGAGATA
*
2081726 TTTTCAATTTCTGTTTTTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGC
1 TTTTCAATTTCTG---TCTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC
2081786 TTTTTAATTT
Statistics
Matches: 378, Mismatches: 50, Indels: 54
0.78 0.10 0.11
Matches are distributed among these distances:
73 36 0.10
74 4 0.01
75 23 0.06
76 5 0.01
77 128 0.34
78 8 0.02
79 73 0.19
80 5 0.01
81 29 0.08
87 2 0.01
88 56 0.15
89 1 0.00
90 2 0.01
91 6 0.02
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (77 bp):
TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCA
CACGCTGAGATA
Found at i:2081462 original size:245 final size:244
Alignment explanation
Indices: 2081032--2081502 Score: 650
Period size: 245 Copynumber: 1.9 Consensus size: 244
2081022 TGTTGTCAAA
* * *
2081032 AAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTATTGTCAATTTTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGACACGCTGAGGTATTGTCAATTTCTC
* * * *
2081097 GTATGTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAT
66 GTATG-TTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCCGAGATAT
* *
2081162 TTTTAATTTCTGTTGTAAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGG-TCAC
130 TTTCAATTTCTGTTGTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGCTCAC
* * *
2081226 ACGCCGAGGTATTTTCAATTTCCGTTTTTCAATTTCTGCCTTTCAAAAAAC
194 ACGCCGAGCTATTTTAAATTTCCGTCTTTCAATTTCTGCCTTTCAAAAAAC
2081277 AAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGACACGCTGAGGTAATT-TCAATTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTC-GGACACGCTGAGGT-ATTGTCAATTTC
*
2081341 T-GT-TG-TAAAAAAATCAACTCGTATTGCGAGCA-GTGAGTTGAGCCTCAGGTCACACGCCGAG
64 TCGTATGTTAAAAAAATCAACTCATATTGCGAG-AGGTGAGTTGAGCCTCAGG--ACACGCCGAG
* *
2081402 ATATTTTCAATTTCTGCCTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGG
126 ATATTTTCAATTTCTG--TTGTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGG
* * *
2081466 CTCACGCGCTGAGCTATTTTAAATTTCTGTCTTTCAA
189 CTCACACGCCGAGCTATTTTAAATTTCCGTCTTTCAA
2081503 AAAAATCAAC
Statistics
Matches: 200, Mismatches: 18, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
242 39 0.19
243 1 0.00
244 27 0.14
245 106 0.53
246 24 0.12
247 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (244 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGACACGCTGAGGTATTGTCAATTTCTC
GTATGTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCCGAGATATT
TTCAATTTCTGTTGTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCTCACAC
GCCGAGCTATTTTAAATTTCCGTCTTTCAATTTCTGCCTTTCAAAAAAC
Found at i:2081640 original size:156 final size:153
Alignment explanation
Indices: 2081277--2081785 Score: 447
Period size: 156 Copynumber: 3.2 Consensus size: 153
2081267 TTCAAAAAAC
* * *
2081277 AAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGG--ACACGCTGAGGTAATTTCAATTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTAAATTT
* * * *
2081340 CTGTTGT-AAAAAAATCAACTCGTATTGCGAGCAGTGAGTTGAGCCTCAGGTCACACGCCGAGAT
66 CTGTTTTCAAAAAAATCAACTCATATTGCGAGCAGTGAGTTGAGCCTCAGATCACACACCGAGAT
* *
2081404 ATTTTCAATTTCTGCCTTTCAAA
131 ATTTTCAATTTATACCTTTCAAA
* * *
2081427 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACGCGCTGAGCTATTTTAAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCACACGCTGAGGTATTTTAAATT
* *
2081491 TCTGTCTTTCAAAAAAATCAACTCATATTGCGAG-AGGTGAGTTGAGCTTCAGATCACACACTGA
65 TCTGT-TTTCAAAAAAATCAACTCATATTGCGAGCA-GTGAGTTGAGCCTCAGATCACACACCGA
* **
2081555 GGTATTTTTTCAATTTATATTTTTCAAA
128 -G-ATATTTTCAATTTATACCTTTCAAA
* * * *
2081583 AAAATCAACTCACATTGCAAGATGTGAGTTGAGCCTCAGGTCACATG-TCGAGGTATTTTCAAA-
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCT-GAGGTATTTT-AAAT
* * ** *
2081646 ATCTGTTTTTCAAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGC
64 TTCTG-TTTTC-AA----------AAAAATCAACTCATATTGCGAGCAGTGAGTTGAGCCTCAGA
*** * * * ***
2081711 TCACGTGCTGAGCTATTTTCAATTTCTGTTTTTTTTCAAA
117 TCACACACCGAGATATTTTCAA-TT-T-ATACCTTTCAAA
2081751 AAAATTCAACTCATATTGCGAGAGGTGAGTTGAGC
1 AAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC
2081786 TTTTTAATTT
Statistics
Matches: 292, Mismatches: 39, Indels: 37
0.79 0.11 0.10
Matches are distributed among these distances:
149 2 0.01
150 35 0.12
152 23 0.08
153 3 0.01
154 47 0.16
155 2 0.01
156 75 0.26
157 8 0.03
165 8 0.03
166 3 0.01
167 44 0.15
168 15 0.05
169 27 0.09
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (153 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTAAATTT
CTGTTTTCAAAAAAATCAACTCATATTGCGAGCAGTGAGTTGAGCCTCAGATCACACACCGAGAT
ATTTTCAATTTATACCTTTCAAA
Found at i:2081654 original size:13 final size:14
Alignment explanation
Indices: 2081638--2081673 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2081628 TGTCGAGGTA
2081638 TTTTCAAAATCTGT
1 TTTTCAAAATCTGT
*
2081652 TTTTCAAATTCTG-
1 TTTTCAAAATCTGT
2081665 TTTTCAAAA
1 TTTTCAAAA
2081674 ATCAACTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.50
Consensus pattern (14 bp):
TTTTCAAAATCTGT
Found at i:2081731 original size:88 final size:88
Alignment explanation
Indices: 2081582--2081743 Score: 220
Period size: 88 Copynumber: 1.8 Consensus size: 88
2081572 TATTTTTCAA
* *
2081582 AAAAATCAACTCACATTGCAAGATGTGAGTTGAGCCTCAGGTCACATGTCGAGGTATTTTCAAAA
1 AAAAATCAACTCACATTGCAAGAAGTGAGTTGAGCCTCAGGTCACATGTCGAGCTATTTTCAAAA
2081647 TCTGTTTTTCAAATTCTGTTTTC
66 TCTGTTTTTCAAATTCTGTTTTC
* * * *
2081670 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT-TGGCTCACGTG-CTGAGCTATTTTCAA
1 AAAAATCAACTCACATTGCAAGAAGTGAGTTGAGCCTCAGG-TCACATGTC-GAGCTATTTTCAA
**
2081733 TTTCTGTTTTT
64 AATCTGTTTTT
2081744 TTTCAAAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 3 0.05
88 61 0.95
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (88 bp):
AAAAATCAACTCACATTGCAAGAAGTGAGTTGAGCCTCAGGTCACATGTCGAGCTATTTTCAAAA
TCTGTTTTTCAAATTCTGTTTTC
Found at i:2081803 original size:30 final size:30
Alignment explanation
Indices: 2081767--2081828 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2081757 CAACTCATAT
2081767 TGCGAGAGGTGAGTTGAG-CTTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTC-TTTTAATTTC
*
2081797 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
2081827 TG
1 TG
2081829 TTTTTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (30 bp):
TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
Found at i:2081934 original size:253 final size:247
Alignment explanation
Indices: 2081420--2081995 Score: 758
Period size: 253 Copynumber: 2.3 Consensus size: 247
2081410 AATTTCTGCC
*
2081420 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTT
1 TTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTT
* *
2081485 TAAATTTCTG---TCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCA
65 TCAATTTCTGTTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCA
* *
2081547 CACACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCAAGATGTGAGT
130 CACACTGAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCACATTGCAAGAGGTGAGT
* * * * **
2081612 TGAGCCTCAGGTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAATTCTGT
194 TAAACCTCAGGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAAGT
*
2081666 TTTC-AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTT
1 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTT
*
2081730 CAATTTCTGTTTTTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTA-AT
66 CAATTTCTGTTTTTTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC--TTCAGA-
* * * * * * * *
2081794 TTCTGCGAGAGTTGAGTTGAGTCTTTT-AATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAG
127 -TC-AC-ACA-CTGAGGT-A-TCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGCAAG
*
2081857 AGGTGAGTTAAACCTCCA-GTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAGTTAAG-
186 AGGTGAGTTAAACCT-CAGGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAAGT
*
2081918 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTAAGCTATTTT
1 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTT
2081983 CAATTTCT-TTTTT
66 CAATTTCTGTTTTT
2081996 AATGTCTGTT
Statistics
Matches: 291, Mismatches: 24, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
244 66 0.23
246 4 0.01
247 12 0.04
248 30 0.10
249 1 0.00
250 3 0.01
251 2 0.01
252 10 0.03
253 138 0.47
254 7 0.02
255 13 0.04
256 5 0.02
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (247 bp):
TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTT
CAATTTCTGTTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCAC
ACACTGAGGTATCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGCAAGAGGTGAGTTA
AACCTCAGGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAAGT
Found at i:2082693 original size:36 final size:37
Alignment explanation
Indices: 2082653--2082723 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
2082643 AGCCCCCCCA
** *
2082653 AAAAAACCTAACCCAAAAA-AAAAAAGAAGAAAAATG
1 AAAAAACCTAACAAAAAAATAAAAAAGAAAAAAAATG
*
2082689 AAAAAACCTAACAAAAAAATAAAAAATAAAAAAAA
1 AAAAAACCTAACAAAAAAATAAAAAAGAAAAAAAA
2082724 CCTAGCCACC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 17 0.57
37 13 0.43
ACGTcount: A:0.77, C:0.11, G:0.04, T:0.07
Consensus pattern (37 bp):
AAAAAACCTAACAAAAAAATAAAAAAGAAAAAAAATG
Found at i:2082720 original size:34 final size:35
Alignment explanation
Indices: 2082653--2082720 Score: 95
Period size: 34 Copynumber: 1.9 Consensus size: 35
2082643 AGCCCCCCCA
2082653 AAAAAACCTAACCCAAAAAAAAAAAGAAGAAAAATG
1 AAAAAACCTAA-CCAAAAAAAAAAAGAAGAAAAATG
*
2082689 AAAAAACCTAA-CAAAAAAATAAAA-AATAAAAA
1 AAAAAACCTAACCAAAAAAA-AAAAGAAGAAAAA
2082721 AAACCTAGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 15 0.50
35 4 0.13
36 11 0.37
ACGTcount: A:0.76, C:0.12, G:0.04, T:0.07
Consensus pattern (35 bp):
AAAAAACCTAACCAAAAAAAAAAAGAAGAAAAATG
Found at i:2083002 original size:13 final size:13
Alignment explanation
Indices: 2082984--2083026 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
2082974 TTCTTTCGAA
2082984 TCTTTTTTTTCTT
1 TCTTTTTTTTCTT
* *
2082997 TCTTTTTTGT-GT
1 TCTTTTTTTTCTT
*
2083009 TATTTTTTTTCTT
1 TCTTTTTTTTCTT
2083022 TCTTT
1 TCTTT
2083027 ATATATACAT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (13 bp):
TCTTTTTTTTCTT
Found at i:2088287 original size:16 final size:15
Alignment explanation
Indices: 2088264--2088320 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
2088254 ATTGACTCCA
2088264 ATTT-AAATTTGAATT
1 ATTTCAAATTT-AATT
*
2088279 ATTTCAAATTTATTT
1 ATTTCAAATTTAATT
* * *
2088294 GATTTCGAGTTTCATT
1 -ATTTCAAATTTAATT
2088310 ATTTCAAATTT
1 ATTTCAAATTT
2088321 TGGGATTAAG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 16 0.48
16 17 0.52
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (15 bp):
ATTTCAAATTTAATT
Found at i:2091370 original size:22 final size:22
Alignment explanation
Indices: 2091340--2091387 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
2091330 ACTGCTCTTA
* *
2091340 TATTGTTGTTTTGTTACAATTT
1 TATTATTGTATTGTTACAATTT
*
2091362 TATTATTGTATTGTTACTATTT
1 TATTATTGTATTGTTACAATTT
2091384 TATT
1 TATT
2091388 GTTATTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.21, C:0.04, G:0.10, T:0.65
Consensus pattern (22 bp):
TATTATTGTATTGTTACAATTT
Found at i:2095846 original size:23 final size:23
Alignment explanation
Indices: 2095814--2095869 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
2095804 AATGCAACAA
* *
2095814 GAGACCAGCAGCAGTTCAGCATG
1 GAGACCAGCAGCAGCTCAACATG
*
2095837 GAGACTAGCAGCAGCTCAACATG
1 GAGACCAGCAGCAGCTCAACATG
* *
2095860 AAGATCAGCA
1 GAGACCAGCA
2095870 TTGGAGTTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.36, C:0.25, G:0.27, T:0.12
Consensus pattern (23 bp):
GAGACCAGCAGCAGCTCAACATG
Found at i:2097177 original size:10 final size:10
Alignment explanation
Indices: 2097158--2097189 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
2097148 TTTTAGGATT
2097158 TTAT-TTTAA
1 TTATCTTTAA
2097167 TTATCTTTAA
1 TTATCTTTAA
2097177 TTATCTTTAA
1 TTATCTTTAA
2097187 TTA
1 TTA
2097190 AATGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:2101728 original size:17 final size:17
Alignment explanation
Indices: 2101703--2101738 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2101693 GAATTATCAA
*
2101703 AAATGATTAAAAAAATT
1 AAATCATTAAAAAAATT
*
2101720 AAATCATTAAAAATATT
1 AAATCATTAAAAAAATT
2101737 AA
1 AA
2101739 TTTTCAGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (17 bp):
AAATCATTAAAAAAATT
Found at i:2107664 original size:28 final size:28
Alignment explanation
Indices: 2107629--2107685 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
2107619 CATATTATCA
2107629 TTCTTATCCAAGAGATATATCCAAAATC
1 TTCTTATCCAAGAGATATATCCAAAATC
*
2107657 TTCTTATCCAATAGATATATCCAAAATC
1 TTCTTATCCAAGAGATATATCCAAAATC
2107685 T
1 T
2107686 ACTGCAAGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (28 bp):
TTCTTATCCAAGAGATATATCCAAAATC
Found at i:2116341 original size:9 final size:9
Alignment explanation
Indices: 2116327--2116362 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
2116317 TTTTGAGTAG
2116327 CATCTGTAT
1 CATCTGTAT
*
2116336 CATCTGTAG
1 CATCTGTAT
*
2116345 CATCTATAT
1 CATCTGTAT
2116354 CATCTGTAT
1 CATCTGTAT
2116363 AACTCTCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (9 bp):
CATCTGTAT
Found at i:2116344 original size:18 final size:18
Alignment explanation
Indices: 2116323--2116361 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
2116313 TCTCTTTTGA
*
2116323 GTAGCATCTGTATCATCT
1 GTAGCATCTATATCATCT
2116341 GTAGCATCTATATCATCT
1 GTAGCATCTATATCATCT
2116359 GTA
1 GTA
2116362 TAACTCTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (18 bp):
GTAGCATCTATATCATCT
Found at i:2116454 original size:15 final size:15
Alignment explanation
Indices: 2116434--2116501 Score: 82
Period size: 15 Copynumber: 4.5 Consensus size: 15
2116424 CTTGAAATCG
* *
2116434 TCTTCTACTTCATAA
1 TCTTCTTCTTCTTAA
*
2116449 TCTTCTTCTTCTTCA
1 TCTTCTTCTTCTTAA
*
2116464 TCTTCTTCTTCTTTA
1 TCTTCTTCTTCTTAA
**
2116479 TCTTCTTCTTCTTCT
1 TCTTCTTCTTCTTAA
2116494 TCTTCTTC
1 TCTTCTTC
2116502 AGGGTAAACG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.09, C:0.31, G:0.00, T:0.60
Consensus pattern (15 bp):
TCTTCTTCTTCTTAA
Found at i:2116455 original size:18 final size:18
Alignment explanation
Indices: 2116429--2116475 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2116419 TTTACCTTGA
*
2116429 AATCGTCTTCTACTTCAT
1 AATCTTCTTCTACTTCAT
*
2116447 AATCTTCTTCTTCTTCAT
1 AATCTTCTTCTACTTCAT
**
2116465 CTTCTTCTTCT
1 AATCTTCTTCT
2116476 TTATCTTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.15, C:0.30, G:0.02, T:0.53
Consensus pattern (18 bp):
AATCTTCTTCTACTTCAT
Found at i:2116457 original size:3 final size:3
Alignment explanation
Indices: 2116449--2116501 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
2116439 TACTTCATAA
*
2116449 TCT TCT TCT TCT TCA TCT TCT TCT TCT T-T ATCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT TCT TCT
2116494 TCT TCT TC
1 TCT TCT TC
2116502 AGGGTAAACG
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 1 0.02
3 44 0.96
4 1 0.02
ACGTcount: A:0.04, C:0.32, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:2118492 original size:2 final size:2
Alignment explanation
Indices: 2118485--2118513 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2118475 CATATTAAAA
2118485 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2118514 AATACAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2125620 original size:15 final size:15
Alignment explanation
Indices: 2125600--2125628 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2125590 ATAATCCTAA
2125600 TAATTATCTTAATAT
1 TAATTATCTTAATAT
2125615 TAATTATCTTAATA
1 TAATTATCTTAATA
2125629 AAATAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTATCTTAATAT
Found at i:2127932 original size:20 final size:19
Alignment explanation
Indices: 2127901--2127943 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
2127891 GTGGCCGGAG
2127901 CTCCCCCTCCCTCTCTTCT
1 CTCCCCCTCCCTCTCTTCT
*
2127920 CTCCCCGCTCCCTCTTTTCT
1 CTCCCC-CTCCCTCTCTTCT
2127940 CTCC
1 CTCC
2127944 TTCCCCTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.00, C:0.60, G:0.02, T:0.37
Consensus pattern (19 bp):
CTCCCCCTCCCTCTCTTCT
Done.