Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009604.1 Hibiscus syriacus cultivar Beakdansim tig00116984_pilon, whole genome shotgun sequence
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: 3548142
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 17
Found at i:1214266 original size:26 final size:26
Alignment explanation
Indices: 1214205--1214279 Score: 104
Period size: 26 Copynumber: 3.0 Consensus size: 26
1214195 ATTTTACATA
1214205 TATTAACTTAA--AAATATATTTTA-
1 TATTAACTTAATTAAATATATTTTAT
1214228 TATTAACTT-ATTAAATATATTTTAT
1 TATTAACTTAATTAAATATATTTTAT
* *
1214253 TATTAACTTAATTAAAAATATATTAT
1 TATTAACTTAATTAAATATATTTTAT
1214279 T
1 T
1214280 TTTATTTTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.02
23 9 0.20
24 12 0.26
25 9 0.20
26 15 0.33
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
TATTAACTTAATTAAATATATTTTAT
Found at i:1214478 original size:30 final size:31
Alignment explanation
Indices: 1214442--1214508 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
1214432 ATAAAAACAC
* *
1214442 ATCTTAATTAAAT-TAAACGAAAGTGATCAT
1 ATCTTAATTAAATAAAAACGAAAATGATCAT
*
1214472 ATCTTAATTAAATAAAAATGAAAATGATCAT
1 ATCTTAATTAAATAAAAACGAAAATGATCAT
1214503 ATCTTA
1 ATCTTA
1214509 TGTTTTTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 13 0.39
31 20 0.61
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.34
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACGAAAATGATCAT
Found at i:1221087 original size:54 final size:54
Alignment explanation
Indices: 1221023--1221538 Score: 693
Period size: 54 Copynumber: 9.6 Consensus size: 54
1221013 GATTACCAAA
** *
1221023 TAGGCACTAAGTGTGCATTTCACTTAATTCATCCTAGGTTGATGAATAACCGTT
1 TAGGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTT
*
1221077 TAGGCACTAAGTGTGCATTTCACGAAATTCATCCTAGGT-GATGAATAACCGTT
1 TAGGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTT
*
1221130 TCA-GCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACTGTT
1 T-AGGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTT
* ** * * * ***
1221184 TCGGCACTGGGTGTGCATTTCACGAAATTCACCCTATGTGGATGAATAGTTGTT
1 TAGGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTT
* *
1221238 TCGGCACTAAATGTGCATTTCACGGAATTCATCC-AGGTGGATGAATAACCGTT
1 TAGGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTT
* * * *
1221291 TCGGCACTAAGTGTGCATTTCACAGAATTCATCCTAGATGGATGAATAA-CTTCT
1 TAGGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGT-T
* *
1221345 TCGGCACTAAGTGTGCATTTCACGGAATTCATCATAGGTGGATGAATAACCGTT
1 TAGGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTT
*
1221399 TCA-GCACTAAGTGTGCATTTCACAGAATTCATCCTAGGTGGATGAATAACCGTT
1 T-AGGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTT
* * * *
1221453 TCGGCACTAAGTGTGGATTTCATGGAATTCATCCTATGTGGATGAATAACCGTT
1 TAGGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTT
**
1221507 TCA-GCACTAAGTGTGCATTTCACATAATTCAT
1 T-AGGCACTAAGTGTGCATTTCACGGAATTCAT
1221539 AATTTTTTAT
Statistics
Matches: 411, Mismatches: 42, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
53 99 0.24
54 310 0.75
55 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (54 bp):
TAGGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTT
Found at i:1221300 original size:161 final size:162
Alignment explanation
Indices: 1221025--1221538 Score: 757
Period size: 161 Copynumber: 3.2 Consensus size: 162
1221015 TTACCAAATA
** * *
1221025 GGCACTAAGTGTGCATTTCACTTAATTCATCCTAGGTTGATGAATAACCGTTTAGGCACTAAGTG
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAAGTG
* *
1221090 TGCATTTCACGAAATTCATCCTAGGT-GATGAATAACCGTTTCAGCACTAAGTGTGCATTTCACG
66 TGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACG
1221154 GAATTCATCCTAGGTGGATGAATAACTGTTTC
131 GAATTCATCCTAGGTGGATGAATAACTGTTTC
** * * *** *
1221186 GGCACTGGGTGTGCATTTCACGAAATTCACCCTATGTGGATGAATAGTTGTTTCGGCACTAAATG
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAAGTG
*
1221251 TGCATTTCACGGAATTCATCC-AGGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACA
66 TGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACG
*
1221315 GAATTCATCCTAGATGGATGAATAACT-TCTTC
131 GAATTCATCCTAGGTGGATGAATAACTGT-TTC
* * *
1221347 GGCACTAAGTGTGCATTTCACGGAATTCATCATAGGTGGATGAATAACCGTTTCAGCACTAAGTG
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAAGTG
* * *
1221412 TGCATTTCACAGAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAAGTGTGGATTTCATG
66 TGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACG
* *
1221477 GAATTCATCCTATGTGGATGAATAACCGTTTC
131 GAATTCATCCTAGGTGGATGAATAACTGTTTC
*
1221509 AGCACTAAGTGTGCATTTCAC-ATAATTCAT
1 GGCACTAAGTGTGCATTTCACGA-AATTCAT
1221539 AATTTTTTAT
Statistics
Matches: 312, Mismatches: 36, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
160 5 0.02
161 212 0.68
162 94 0.30
163 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (162 bp):
GGCACTAAGTGTGCATTTCACGAAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAAGTG
TGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACG
GAATTCATCCTAGGTGGATGAATAACTGTTTC
Found at i:1227579 original size:20 final size:19
Alignment explanation
Indices: 1227535--1227583 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
1227525 TGATTCAATC
*
1227535 GGTATCGATACCGAAGGGG
1 GGTATCGATACCGAAGGGA
1227554 GAGTATCGATACCGAAGGGAA
1 G-GTATCGATACCGAAGGG-A
1227575 GGTATCGAT
1 GGTATCGAT
1227584 TCCATTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.31, C:0.14, G:0.37, T:0.18
Consensus pattern (19 bp):
GGTATCGATACCGAAGGGA
Found at i:1227655 original size:22 final size:22
Alignment explanation
Indices: 1227629--1227671 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1227619 ACCACAGCAC
1227629 AGTATC-AGTACCATAGTATGGT
1 AGTATCGA-TACCATAGTATGGT
*
1227651 AGTATCGATACCATGGTATGG
1 AGTATCGATACCATAGTATGG
1227672 GTATCAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (22 bp):
AGTATCGATACCATAGTATGGT
Found at i:1228097 original size:54 final size:54
Alignment explanation
Indices: 1228008--1228340 Score: 481
Period size: 54 Copynumber: 6.2 Consensus size: 54
1227998 ACCAAATAGG
* *
1228008 CACTAACTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAATCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTTTCGA
* *
1228062 CATTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAAACC-TTTCGT
1 CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAAT-AACCGTTTCGA
* * *
1228116 CACTAAGTGTGAATTTCACGGAATTCATCCTAGGTGGATGAATAATCATTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTTTCGA
* *
1228170 AACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAAT-ACCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTTTCGA
* * ** *
1228223 CACTAAGTTTGCATTTCACGGAATTTATCCTAGGTGGATGAATAACTATTTCAA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTTTCGA
* * * *
1228277 CACTGATTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAACCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTTTCGA
1228331 CACTAAGTGT
1 CACTAAGTGT
1228341 AATACTCCAA
Statistics
Matches: 245, Mismatches: 31, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
53 50 0.20
54 192 0.78
55 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (54 bp):
CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTTTCGA
Found at i:1228295 original size:161 final size:162
Alignment explanation
Indices: 1228009--1228340 Score: 488
Period size: 161 Copynumber: 2.1 Consensus size: 162
1227999 CCAAATAGGC
* * *
1228009 ACTAACTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAATCGTTTCGACATTAAGTGTGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTTTCGACACTAAGTGTGC
* **
1228074 ATTTCACGGAATTCATCCTAGGTGGATGAATAAACCTTTCGTCACTAAGTGTGAATTTCACGGAA
66 ATTTCACGGAATTCATCCTAGGTGGATGAATAAACATTTCAACACTAAGTGTGAATTTCACGGAA
*
1228139 TTCATCCTAGGTGGATGAATAATCATTTCGAA
131 TTCATCCTAGGTGGATGAATAACCATTTCGAA
* *
1228171 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAAT-ACCGTTTCGACACTAAGTTTGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTTTCGACACTAAGTGTGC
* * * *
1228235 ATTTCACGGAATTTATCCTAGGTGGATGAAT-AACTATTTCAACACTGATTGTGCATTTCACGGA
66 ATTTCACGGAATTCATCCTAGGTGGATGAATAAAC-ATTTCAACACTAAGTGTGAATTTCACGGA
* * * *
1228299 ATTCATTCTATGTGGATGAATAACCGTTTCGAC
130 ATTCATCCTAGGTGGATGAATAACCATTTCGAA
1228332 ACTAAGTGT
1 ACTAAGTGT
1228341 AATACTCCAA
Statistics
Matches: 152, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
160 3 0.02
161 109 0.72
162 40 0.26
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (162 bp):
ACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTTTCGACACTAAGTGTGC
ATTTCACGGAATTCATCCTAGGTGGATGAATAAACATTTCAACACTAAGTGTGAATTTCACGGAA
TTCATCCTAGGTGGATGAATAACCATTTCGAA
Found at i:1229289 original size:20 final size:21
Alignment explanation
Indices: 1229236--1229289 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
1229226 TACCGGAAGG
1229236 GGGTATCAATACCATAGTATA
1 GGGTATCAATACCATAGTATA
* * *
1229257 GTAGTATCGATACCATGGTA-A
1 G-GGTATCAATACCATAGTATA
1229278 GGGTATCAATAC
1 GGGTATCAATAC
1229290 TAAAGAACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 9 0.33
21 3 0.11
22 15 0.56
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (21 bp):
GGGTATCAATACCATAGTATA
Found at i:1229863 original size:79 final size:79
Alignment explanation
Indices: 1229743--1229896 Score: 245
Period size: 79 Copynumber: 1.9 Consensus size: 79
1229733 CATTATTAGC
* * * *
1229743 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATAAAAGGATGTCATAGTTGAAATGCTTTTG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATAAAAGGATGCCATAGCTGAAATGCATATG
1229808 GGTGCATTATCAAT
66 GGTGCATTATCAAT
* * *
1229822 ATAAAAGAATAATGCATATGGGTGCATTATTTGTATGAAAGGATGCCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATAAAAGGATGCCATAGCTGAAATGCATATG
1229887 GGTGCATTAT
66 GGTGCATTAT
1229897 TGGCATGAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 68 1.00
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATAAAAGGATGCCATAGCTGAAATGCATATG
GGTGCATTATCAAT
Found at i:1229896 original size:45 final size:43
Alignment explanation
Indices: 1229832--1230584 Score: 527
Period size: 45 Copynumber: 18.5 Consensus size: 43
1229822 ATAAAAGAAT
* *
1229832 AATGCATATGGGTGCATTATTTGTATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-AG-TGA
1229877 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-AG-TGA
*
1229922 AATGCATATGGGTGCATTATTAGCAT-AAA--A-G--AA-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAGTGA
* * * * *
1229956 AATGCATATAGGTGTATTATTGTCATGAATGGATGTCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-AG-TGA
**
1230001 AATGCATATGGGTGCATTATCAGCAT-AAA--A-G--AA-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAGTGA
*
1230035 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-AG-TGA
** * *
1230080 AATGCATATGGGTGCATTA-T--CAACATA-GAAG--AA-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAGTGA
1230114 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGATGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-AG-TGA
***
1230159 AATGCATATGGGTGCATTATCAACAT-AAA--A-G--AA-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAGTGA
* *
1230193 AATGCATATGGGTACATTATTGGCATGAAAGAATGCCATAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-AG-TGA
***
1230238 AATGCATATGGGTGCATTATCAACAT-AAA--A-G--AA-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAGTGA
* *
1230272 AATGCATATGGGTGCATTATTGGAATGGAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-AG-TGA
*
1230317 AATGCATATGGGTGCATT-TTCAGCAT-AAA--A-G--AA-T--
1 AATGCATATGGGTGCATTATT-GGCATGAAAGGATGCCAAGTGA
* **
1230351 AATGCATATGGGTGCATGATTGGCATGAAATAATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-AG-TGA
*
1230396 AATGCATATGGGTGCATTATTGGCATGAAATGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-AG-TGA
* ***
1230441 AATGCATATGGGTGAATTATCAACAT-AAA--A-G--AA-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAGTGA
*
1230475 AATGCATATGGGTGCATTATTGGCATGACAGGATGCCAACGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAA-G-TGA
*
1230520 AATGCATATGGGTGCATTATTGGCATGACAGGATGCCAATGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAA-G-TGA
1230565 AATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
1230585 AAACCTAAAA
Statistics
Matches: 572, Mismatches: 57, Indels: 158
0.73 0.07 0.20
Matches are distributed among these distances:
34 152 0.27
35 18 0.03
36 7 0.01
37 10 0.02
38 16 0.03
39 7 0.01
40 8 0.01
41 15 0.03
42 10 0.02
43 7 0.01
44 19 0.03
45 303 0.53
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (43 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAGTGA
Found at i:1229975 original size:124 final size:123
Alignment explanation
Indices: 1229753--1230257 Score: 479
Period size: 124 Copynumber: 4.2 Consensus size: 123
1229743 ATAAAAGAAT
* * * *
1229753 AATGCATATGGGTGCATTATTGGCATAAAAGGATGTCATAGTTGAAATGCTTTTGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAG-TGAAATGCATATGGGTGCATTAT
* *
1229818 CAATATAAAAGAATAATGCATATGGGTGCATTATTTGTATGAAAGGATGCCATAGCTGA
65 CAACATAAAAGAATAATGCATATAGGTGCATTATTTGTATGAAAGGATGCCATAGCTGA
1229877 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAG-TGAAATGCATATGGGTGCATTAT
* * * * *
1229942 TAGCATAAAAGAATAATGCATATAGGTGTATTA-TTGTCATGAATGGATGTCATAGCTGA
65 CAACATAAAAGAATAATGCATATAGGTGCATTATTTGT-ATGAAAGGATGCCATAGCTGA
** *
1230001 AATGCATATGGGTGCATTATCAGCAT-AAA--A-G--A-A-T--AATGCATATGGGTGCATTATT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTGAAATGCATATGGGTGCATTATC
** * * * ** ** * ** **
1230056 GGCATGAAAGGAT-GT-CATAGCTGAAATGCA-TA--TGGGTG-CATTAT-CAACATAGAAGAA
66 AACATAAAAGAATAATGCATA--T-AGGTGCATTATTTGTATGAAAGGATGC--CATAGCTG-A
1230113 TAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGATGAAATGCATATGGGTGCATTA
1 -AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAG-TGAAATGCATATGGGTGCATTA
* * * * * *
1230178 TCAACATAAAAGAATAATGCATATGGGTACATTATTGGCATGAAAGAATGCCATAGTTGA
64 TCAACATAAAAGAATAATGCATATAGGTGCATTATTTGTATGAAAGGATGCCATAGCTGA
1230238 AATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
1230258 CAACATAAAA
Statistics
Matches: 305, Mismatches: 50, Indels: 52
0.75 0.12 0.13
Matches are distributed among these distances:
110 2 0.01
111 12 0.04
112 4 0.01
113 58 0.19
114 7 0.02
115 1 0.00
116 1 0.00
117 2 0.01
118 1 0.00
119 1 0.00
120 2 0.01
121 1 0.00
122 1 0.00
123 10 0.03
124 183 0.60
125 2 0.01
126 13 0.04
127 3 0.01
128 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (123 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTGAAATGCATATGGGTGCATTATC
AACATAAAAGAATAATGCATATAGGTGCATTATTTGTATGAAAGGATGCCATAGCTGA
Found at i:1230008 original size:79 final size:79
Alignment explanation
Indices: 1229877--1230415 Score: 889
Period size: 79 Copynumber: 6.8 Consensus size: 79
1229867 CCATAGCTGA
1229877 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
*
1229942 TAGCATAAAAGAAT
66 CAGCATAAAAGAAT
* * * * *
1229956 AATGCATATAGGTGTATTATTGTCATGAATGGATGTCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
1230021 CAGCATAAAAGAAT
66 CAGCATAAAAGAAT
*
1230035 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
* *
1230100 CAACATAGAAGAAT
66 CAGCATAAAAGAAT
*
1230114 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGATGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
*
1230179 CAACATAAAAGAAT
66 CAGCATAAAAGAAT
* * *
1230193 AATGCATATGGGTACATTATTGGCATGAAAGAATGCCATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
*
1230258 CAACATAAAAGAAT
66 CAGCATAAAAGAAT
* * *
1230272 AATGCATATGGGTGCATTATTGGAATGGAAGGATGCCATAGCTGAAATGCATATGGGTGCATTTT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
1230337 CAGCATAAAAGAAT
66 CAGCATAAAAGAAT
* **
1230351 AATGCATATGGGTGCATGATTGGCATGAAATAATGCCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
1230416 TGGCATGAAA
Statistics
Matches: 429, Mismatches: 31, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 429 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (79 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
CAGCATAAAAGAAT
Found at i:1230079 original size:203 final size:203
Alignment explanation
Indices: 1229730--1230099 Score: 623
Period size: 203 Copynumber: 1.8 Consensus size: 203
1229720 GGAATTGTGT
* *
1229730 GTGCATTATTAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATAAAAGGATGTCATAGT
1 GTGCATTATTAGCATAAAAGAATAATGCATATAGGTGCATTATTGGCATAAAAGGATGTCATAGC
* * * * *
1229795 TGAAATGCTTTTGGGTGCATTATCAATATAAAAGAATAATGCATATGGGTGCATTATTTGTATGA
66 TGAAATGCATATGGGTGCATTATCAACATAAAAGAATAATGCATATGGGTGCATTATTGGCATGA
1229860 AAGGATGCCATAGCTGAAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAAT
131 AAGGATGCCATAGCTGAAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAAT
1229925 GCATATGG
196 GCATATGG
* * * *
1229933 GTGCATTATTAGCATAAAAGAATAATGCATATAGGTGTATTATTGTCATGAATGGATGTCATAGC
1 GTGCATTATTAGCATAAAAGAATAATGCATATAGGTGCATTATTGGCATAAAAGGATGTCATAGC
*
1229998 TGAAATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGA
66 TGAAATGCATATGGGTGCATTATCAACATAAAAGAATAATGCATATGGGTGCATTATTGGCATGA
*
1230063 AAGGATGTCATAGCTGAAATGCATATGGGTGCATTAT
131 AAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
1230100 CAACATAGAA
Statistics
Matches: 154, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
203 154 1.00
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (203 bp):
GTGCATTATTAGCATAAAAGAATAATGCATATAGGTGCATTATTGGCATAAAAGGATGTCATAGC
TGAAATGCATATGGGTGCATTATCAACATAAAAGAATAATGCATATGGGTGCATTATTGGCATGA
AAGGATGCCATAGCTGAAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAAT
GCATATGG
Found at i:1230197 original size:34 final size:34
Alignment explanation
Indices: 1230159--1230291 Score: 131
Period size: 34 Copynumber: 3.6 Consensus size: 34
1230149 CCATAGATGA
1230159 AATGCATATGGGTGCATTATCAACATAAAAGAAT
1 AATGCATATGGGTGCATTATCAACATAAAAGAAT
* ***
1230193 AATGCATATGGGTACATTATTGGCATGAAAGAATGCCATAGTT
1 AATGCATATGGGTGCATTATCAACAT--AA-AA-G--A-A--T
1230236 GAAATGCATATGGGTGCATTATCAACATAAAAGAAT
1 --AATGCATATGGGTGCATTATCAACATAAAAGAAT
1230272 AATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
1230292 TGGAATGGAA
Statistics
Matches: 80, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
34 42 0.52
36 3 0.04
37 2 0.03
38 2 0.03
39 1 0.01
40 1 0.01
41 2 0.03
42 2 0.03
43 3 0.04
45 22 0.28
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCAACATAAAAGAAT
Found at i:1230416 original size:124 final size:124
Alignment explanation
Indices: 1230272--1230598 Score: 480
Period size: 124 Copynumber: 2.6 Consensus size: 124
1230262 ATAAAAGAAT
* *
1230272 AATGCATATGGGTGCATTATTGGAATGGAAGGATGCCATAGCTGAAATGCATATGGGTGCATTTT
1 AATGCATATGGGTGCATTATTGGCATGGAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
* *
1230337 CAGCATAAAAGAATAATGCATATGGGTGCATGATTGGCATGAAATAATGCCATA-GCTGA
66 CAACATAAAAGAATAATGCATATGGGTGCATGATTGGCATGAAAGAATGCCA-ACGCTGA
* * *
1230396 AATGCATATGGGTGCATTATTGGCATGAAATGATGCCATAGCTGAAATGCATATGGGTGAATTAT
1 AATGCATATGGGTGCATTATTGGCATGGAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
* * * *
1230461 CAACATAAAAGAATAATGCATATGGGTGCATTATTGGCATGACAGGATGCCAACGTTGA
66 CAACATAAAAGAATAATGCATATGGGTGCATGATTGGCATGAAAGAATGCCAACGCTGA
*
1230520 AATGCATATGGGTGCATTATTGGCAT-GACAGGATGCCA-ATGTTGAAATGCATATGGGTGCATT
1 AATGCATATGGGTGCATTATTGGCATGGA-AGGATGCCATA-GCTGAAATGCATATGGGTGCATT
* *
1230583 ATAAACCTAAAAGAAT
64 ATCAACATAAAAGAAT
1230599 GCTATAATTG
Statistics
Matches: 183, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
123 3 0.02
124 180 0.98
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.28
Consensus pattern (124 bp):
AATGCATATGGGTGCATTATTGGCATGGAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
CAACATAAAAGAATAATGCATATGGGTGCATGATTGGCATGAAAGAATGCCAACGCTGA
Found at i:1230934 original size:29 final size:29
Alignment explanation
Indices: 1230892--1230952 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
1230882 TATGCCAGTT
* * *
1230892 AGATGAACGGTTAAATACTGTTGAGTAAA
1 AGATGAAAGGTTAAACACTATTGAGTAAA
1230921 AGATGAAAGGTTAAACACTATTGAGTAAA
1 AGATGAAAGGTTAAACACTATTGAGTAAA
1230950 AGA
1 AGA
1230953 ATAATGGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.46, C:0.07, G:0.23, T:0.25
Consensus pattern (29 bp):
AGATGAAAGGTTAAACACTATTGAGTAAA
Found at i:1232019 original size:54 final size:54
Alignment explanation
Indices: 1231873--1232113 Score: 321
Period size: 54 Copynumber: 4.5 Consensus size: 54
1231863 TATGGGTTTT
* *
1231873 ACACTAAGTGTGTATTTCACGGAATTCATCCTAGGTGGATGAATAATCGTTTCG
1 ACACTAAGTGTGTATTTCACAGAATTCATCCTAGGTGGATGAATAACCGTTTCG
* *
1231927 GCAC-AAGTGTGATATTTCAC-GAA---ATCCTAGGTGAATGAATAACCGTTTCG
1 ACACTAAGTGTG-TATTTCACAGAATTCATCCTAGGTGGATGAATAACCGTTTCG
* *
1231977 ACACTAAGTGTGTATTTCACAGAATTCATCCTAGGTGGATGAATAATCATTTCG
1 ACACTAAGTGTGTATTTCACAGAATTCATCCTAGGTGGATGAATAACCGTTTCG
* * *
1232031 ACACTAACTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCG
1 ACACTAAGTGTGTATTTCACAGAATTCATCCTAGGTGGATGAATAACCGTTTCG
* * * *
1232085 GCAATAAGTGTGCATTTCACGGAATTCAT
1 ACACTAAGTGTGTATTTCACAGAATTCAT
1232114 AATTTGTTTA
Statistics
Matches: 165, Mismatches: 16, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
50 36 0.22
51 10 0.06
53 10 0.06
54 109 0.66
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (54 bp):
ACACTAAGTGTGTATTTCACAGAATTCATCCTAGGTGGATGAATAACCGTTTCG
Found at i:1232144 original size:108 final size:108
Alignment explanation
Indices: 1231877--1232144 Score: 242
Period size: 108 Copynumber: 2.5 Consensus size: 108
1231867 GGTTTTACAC
* * ** * * * * * * *
1231877 TAAGTGTGTATTTCACGGAATTCATCCTAGGTGGATGAATAATCGTTTCGGCAC-AAGTGTGATA
1 TAAGTGTGCATTTCACAGAATTCATAATAGGTGGATAAATAAACATATCGACACTAACTGTG-CA
*
1231941 TTTCAC-GAA---ATCCTAGGTGAATGAATAACCGTTTCGACAC
65 TTTCACAGAATTCATCCTAGGTGAATGAATAACCGTTTCGACAA
* ** * * *
1231981 TAAGTGTGTATTTCACAGAATTCATCCTAGGTGGATGAATAATCATTTCGACACTAACTGTGCAT
1 TAAGTGTGCATTTCACAGAATTCATAATAGGTGGATAAATAAACATATCGACACTAACTGTGCAT
* * *
1232046 TTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGGCAA
66 TTCACAGAATTCATCCTAGGTGAATGAATAACCGTTTCGACAA
* ** **
1232089 TAAGTGTGCATTTCACGGAATTCATAATTTGTTTATAAATAAACATAT-GAGCACTA
1 TAAGTGTGCATTTCACAGAATTCATAATAGGTGGATAAATAAACATATCGA-CACTA
1232145 CGGGTGCATT
Statistics
Matches: 138, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
104 58 0.42
105 9 0.07
107 2 0.01
108 69 0.50
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (108 bp):
TAAGTGTGCATTTCACAGAATTCATAATAGGTGGATAAATAAACATATCGACACTAACTGTGCAT
TTCACAGAATTCATCCTAGGTGAATGAATAACCGTTTCGACAA
Found at i:1234292 original size:12 final size:13
Alignment explanation
Indices: 1234275--1234303 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1234265 TTTAATTGTG
1234275 AAAATTAAAA-TT
1 AAAATTAAAATTT
1234287 AAAATTAAAATTT
1 AAAATTAAAATTT
1234300 AAAA
1 AAAA
1234304 CATTCGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:1234551 original size:5 final size:5
Alignment explanation
Indices: 1234541--1234599 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
1234531 AGAATAGATA
* * *
1234541 AAAAT AAAAT AAAAT -AAAT AAAA- AAACGAA AAAAT GAAAT AAAAT GAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA--AT AAAAT AAAAT AAAAT AAAAT
*
1234591 AAATT AAAA
1 AAAAT AAAA
1234600 ATTAATTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
4 7 0.16
5 32 0.74
6 1 0.02
7 3 0.07
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1234601 original size:11 final size:11
Alignment explanation
Indices: 1234587--1234617 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1234577 AAATAAAATG
*
1234587 AAATAAATTAA
1 AAATTAATTAA
1234598 AAATTAATTAA
1 AAATTAATTAA
1234609 AAATTAATT
1 AAATTAATT
1234618 TTGAAAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATTAATTAA
Found at i:1234741 original size:12 final size:11
Alignment explanation
Indices: 1234714--1234740 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1234704 TAAAAAAGGG
1234714 AAAAATAATTA
1 AAAAATAATTA
1234725 AAAAATAATTA
1 AAAAATAATTA
1234736 AAAAA
1 AAAAA
1234741 ACTTAGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAAATAATTA
Found at i:1236768 original size:29 final size:30
Alignment explanation
Indices: 1236718--1236790 Score: 112
Period size: 29 Copynumber: 2.4 Consensus size: 30
1236708 GTCGAACTCG
*
1236718 AAGGTTTTGTGTTTCAAAAGAAACATTTTCA
1 AAGGTTTT-TGTTTCAAAAGAAACAATTTCA
*
1236749 AAGGTTTTT-TTTCAAGAGAAACAATTTCA
1 AAGGTTTTTGTTTCAAAAGAAACAATTTCA
1236778 AAGGTTTTTGTTT
1 AAGGTTTTTGTTT
1236791 TGTGTTTCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
29 27 0.69
30 4 0.10
31 8 0.21
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.42
Consensus pattern (30 bp):
AAGGTTTTTGTTTCAAAAGAAACAATTTCA
Found at i:1236868 original size:68 final size:67
Alignment explanation
Indices: 1236792--1236970 Score: 202
Period size: 73 Copynumber: 2.6 Consensus size: 67
1236782 TTTTTGTTTT
* * * *
1236792 GTGTTTCAAGAGAAATTGTCTCAAGGGAGGCAAAATTTTTGTTTCAAGAGAAACATGT-TCAAAG
1 GTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-CTTTGTTTCAAGAGAAAC-TGTCTCAAAG
1236856 ATTG
64 ATTG
*
1236860 GTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 GTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTC-A-A-A
1236925 GACAAAATT-
63 G-----ATTG
1236934 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 GTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1236971 AGTTCCAAAA
Statistics
Matches: 97, Mismatches: 5, Indels: 13
0.84 0.04 0.11
Matches are distributed among these distances:
66 3 0.03
67 18 0.19
68 33 0.34
69 1 0.01
70 2 0.02
73 37 0.38
75 3 0.03
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (67 bp):
GTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAAGAT
TG
Found at i:1236948 original size:36 final size:37
Alignment explanation
Indices: 1236861--1236970 Score: 204
Period size: 36 Copynumber: 3.0 Consensus size: 37
1236851 CAAAGATTGG
1236861 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
*
1236898 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1236934 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1236971 AGTTCCAAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
36 35 0.50
37 35 0.50
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
Found at i:1236988 original size:88 final size:88
Alignment explanation
Indices: 1236896--1237070 Score: 253
Period size: 88 Copynumber: 2.0 Consensus size: 88
1236886 GAGACAAAAC
* *
1236896 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGA-CAAAATTTGTTTCAAGAGAAACTGTCTCAAGAG
1 TTTGTTACAAGGGAAACTGTCTCAAGAGAGACCAAAATTT-TTTCAAGAGAAACTGTCTCAAGAA
*
1236960 AGACAAAACTTAGTTCCAAAAGAT
65 AGACAAAAATTAGTTCCAAAAGAT
* * * *
1236984 TTTGTTACAAGGGAAATTTTCTCAAGAGAGACCAAAATTTTTTCATGGGAAACTGTCTCAAGAAA
1 TTTGTTACAAGGGAAACTGTCTCAAGAGAGACCAAAATTTTTTCAAGAGAAACTGTCTCAAGAAA
* *
1237049 GACAAAAATTTGTTTCAAAAGA
66 GACAAAAATTAGTTCCAAAAGA
1237071 AACTGTTTCA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 69 0.90
89 8 0.10
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (88 bp):
TTTGTTACAAGGGAAACTGTCTCAAGAGAGACCAAAATTTTTTCAAGAGAAACTGTCTCAAGAAA
GACAAAAATTAGTTCCAAAAGAT
Found at i:1237010 original size:125 final size:125
Alignment explanation
Indices: 1236878--1237107 Score: 367
Period size: 125 Copynumber: 1.8 Consensus size: 125
1236868 AGAGAAACTG
*
1236878 TCTCAAGAGAGA-CAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAATTTGTTTCA
1 TCTCAAGAGAGACCAAAA-TTT-TTTCAAGGGAAACTGTCTCAAGAAAGACAAAAATTTGTTTCA
*
1236941 AGAGAAACTGTCTCAAGAGAGACAAAACTTAGT-TCCAAAAGATTTTGTTACAAGGGAAATTT
64 AAAGAAACTGTCTCAAGAGAGACAAAACTTA-TATCCAAAAGATTTTGTTACAAGGGAAATTT
*
1237003 TCTCAAGAGAGACCAAAATTTTTTCATGGGAAACTGTCTCAAGAAAGACAAAAATTTGTTTCAAA
1 TCTCAAGAGAGACCAAAATTTTTTCAAGGGAAACTGTCTCAAGAAAGACAAAAATTTGTTTCAAA
* *
1237068 AGAAACTGTTTCAAGAGAGAGAAAACTTATATCCAAAAGA
66 AGAAACTGTCTCAAGAGAGACAAAACTTATATCCAAAAGA
1237108 AATTGTCTCA
Statistics
Matches: 97, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
124 27 0.28
125 65 0.67
126 5 0.05
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (125 bp):
TCTCAAGAGAGACCAAAATTTTTTCAAGGGAAACTGTCTCAAGAAAGACAAAAATTTGTTTCAAA
AGAAACTGTCTCAAGAGAGACAAAACTTATATCCAAAAGATTTTGTTACAAGGGAAATTT
Found at i:1237074 original size:37 final size:37
Alignment explanation
Indices: 1236984--1237517 Score: 394
Period size: 36 Copynumber: 15.2 Consensus size: 37
1236974 TCCAAAAGAT
* * * *
1236984 TTTGTTACAAGGGAAATTTTCTCAAGAGAGACCAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
* *
1237021 TTT-TTTCATGGGAAACTGTCTCAAGAAAGACAAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
** * * *
1237057 TTTGTTTCAAAAGAAACTGTTTCAAGAGAGAGAAAAC
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
* * ** * *
1237094 TTAT-ATCCAAAAGAAATTGTCTCAAGAGAGACAAAAC
1 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
* * ** * *
1237131 TTAGTTCCAAAAGAAACTGTCTCAAGGGAGAC-GAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
** *
1237167 TTTGTTTCAAGGGAAA------C-A-A-ATTCAAAGAT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA-AA
* *
1237196 TTTGTTTCAAGGGAAACCGTCTCAAGAAAGA-AAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
*
1237232 TTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
* *
1237269 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC--AAC
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
* ** *
1237303 TTTGTTTTAAAAGAAACTGTCTCAAGAGTA-AC-GAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAG-AGACAAAAA
** *
1237339 TTTGTTTCAA-GGAAA-------AA-AGATTCAAAGAT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA-AA
* * *
1237368 TTTGTTTCAAGGGAAACTATCTCAAGAGATAC-CAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
* *
1237404 TTTGTTTCAAGGGAAACTGTCTCAAGATAGAC-CAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
1237440 TTTGTTTCAAGGGAAACTGTCTC-A-AGAGAC-AAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
** *
1237474 TTTGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAAC
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
1237511 TTTGTTT
1 TTTGTTT
1237518 TGAGTAAATT
Statistics
Matches: 405, Mismatches: 59, Indels: 66
0.76 0.11 0.12
Matches are distributed among these distances:
26 1 0.00
27 5 0.01
28 4 0.01
29 29 0.07
30 6 0.01
34 31 0.08
35 34 0.08
36 180 0.44
37 108 0.27
38 7 0.02
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (37 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
Found at i:1237339 original size:172 final size:173
Alignment explanation
Indices: 1236793--1237517 Score: 715
Period size: 172 Copynumber: 4.2 Consensus size: 173
1236783 TTTTGTTTTG
* * * * * *
1236793 TGTTTCAAGAGAAATTGTCTCAAG-GGAGGCAAAATTTTTGTTTCAAGAGAAACATG-TTCAAAG
1 TGTTTCAAAAGAAACTGTCTCAAGAGGAGACGAAA--TTTGTTTCAAG-GAAAAAAGATTCAAAG
* * * *
1236856 ATTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAA
63 ATT-TTGTTTCAAGGGAAACTGTCTCAAGAAAGA-AAAAATTTGTTTCAAGGGAAACTGTCTCAA
*
1236921 GAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
126 GAGAGACAAAAATTGTTTCAAGAGAAACTGTCTCAAGAGAGAC--AACTT
* * *** * * *
1236971 AGTTCCAAAAGATTTTGT-T-ACA-A-G-G--GAAATTT-TCTCAA-G---AGAGA-CCAAA-A-
1 TGTTTCAAAAGAAACTGTCTCA-AGAGGAGACGAAATTTGTTTCAAGGAAAAAAGATTCAAAGAT
* ** *
1237021 TTT-TTTCATGGGAAACTGTCTCAAGAAAGACAAAAATTTGTTTCAAAAGAAACTGTTTCAAGAG
65 TTTGTTTCAAGGGAAACTGTCTCAAGAAAGA-AAAAATTTGTTTCAAGGGAAACTGTCTCAAGAG
* * * * * *
1237085 AGAGAAAACTTATATCCAAAAGAAATTGTCTCAAGAGAGACAAAACTT
129 AGACAAAAATTGT-TTCAAGAGAAACTGTCTCAAGAGAGAC--AACTT
* * *
1237133 AGTTCCAAAAGAAACTGTCTCAAG-GGAGACGAAATTTGTTTCAAGGGAAACAA-ATTCAAAGAT
1 TGTTTCAAAAGAAACTGTCTCAAGAGGAGACGAAATTTGTTTCAA-GGAAAAAAGATTCAAAGAT
* *
1237196 TTTGTTTCAAGGGAAACCGTCTCAAGAAAGAAAAAATTTGTTTCAAGGGAAACCGTCTCAAGAGA
65 TTTGTTTCAAGGGAAACTGTCTCAAGAAAGAAAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1237261 GACAAAAATTGTTTCAAGAGAAACTGTCTCAAGAGAGACAACTT
130 GACAAAAATTGTTTCAAGAGAAACTGTCTCAAGAGAGACAACTT
* *
1237305 TGTTTTAAAAGAAACTGTCTCAAGAGTA-ACGAAATTTGTTTCAAGGAAAAAAGATTCAAAGATT
1 TGTTTCAAAAGAAACTGTCTCAAGAGGAGACGAAATTTGTTTCAAGGAAAAAAGATTCAAAGATT
* * * ** *
1237369 TTGTTTCAAGGGAAACTATCTCAAGAGATACCAAATTTGTTTCAAGGGAAACTGTCTCAAGATAG
66 TTGTTTCAAGGGAAACTGTCTCAAGAAAGAAAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAG
* * * * *
1237434 ACCAAATTTGTTTCAAGGGAAACTGTCTCAAGAGACA-AAATT
131 ACAAAAATTGTTTCAAGAGAAACTGTCTCAAGAGAGACAACTT
*
1237476 TGTTTCAAGAA-AAACTGTCTCAAGA-GAGACAAAACTTTGTTT
1 TGTTTCAA-AAGAAACTGTCTCAAGAGGAGACGAAA-TTTGTTT
1237518 TGAGTAAATT
Statistics
Matches: 456, Mismatches: 65, Indels: 58
0.79 0.11 0.10
Matches are distributed among these distances:
161 64 0.14
162 47 0.10
163 3 0.01
164 3 0.01
165 6 0.01
167 7 0.02
168 6 0.01
170 7 0.02
171 40 0.09
172 153 0.34
173 10 0.02
174 25 0.05
175 43 0.09
176 27 0.06
177 2 0.00
178 13 0.03
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (173 bp):
TGTTTCAAAAGAAACTGTCTCAAGAGGAGACGAAATTTGTTTCAAGGAAAAAAGATTCAAAGATT
TTGTTTCAAGGGAAACTGTCTCAAGAAAGAAAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAG
ACAAAAATTGTTTCAAGAGAAACTGTCTCAAGAGAGACAACTT
Found at i:1237372 original size:136 final size:134
Alignment explanation
Indices: 1237232--1237489 Score: 374
Period size: 136 Copynumber: 1.9 Consensus size: 134
1237222 AAAGAAAAAA
*
1237232 TTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAAATTGTTTCAAGAGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACCATCTCAAGAGAGACAAAAATTGTTTCAAGAGAAACTGTCTCAAGAGA
* * *
1237297 GA-CAACTTTGTTTTAAAAGAAACTGTCTCAAGAGTAACGAAATTTGTTTCAAGGAAAAAAGATT
66 GACCAAATTTGTTTCAAAAGAAACTGTCTCAAGAG--ACAAAATTTGTTTCAA-GAAAAAAGATT
1237361 CAAAGAT
128 CAAAGAT
* * * * * *
1237368 TTTGTTTCAAGGGAAACTATCTCAAGAGATACCAAATTTGTTTCAAGGGAAACTGTCTCAAGATA
1 TTTGTTTCAAGGGAAACCATCTCAAGAGAGACAAAAATTGTTTCAAGAGAAACTGTCTCAAGAGA
**
1237433 GACCAAATTTGTTTCAAGGGAAACTGTCTCAAGAGACAAAATTTGTTTCAAGAAAAA
66 GACCAAATTTGTTTCAAAAGAAACTGTCTCAAGAGACAAAATTTGTTTCAAGAAAAA
1237490 CTGTCTCAAG
Statistics
Matches: 109, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
134 6 0.06
135 15 0.14
136 60 0.55
137 28 0.26
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (134 bp):
TTTGTTTCAAGGGAAACCATCTCAAGAGAGACAAAAATTGTTTCAAGAGAAACTGTCTCAAGAGA
GACCAAATTTGTTTCAAAAGAAACTGTCTCAAGAGACAAAATTTGTTTCAAGAAAAAAGATTCAA
AGAT
Found at i:1237441 original size:101 final size:100
Alignment explanation
Indices: 1237269--1237451 Score: 269
Period size: 101 Copynumber: 1.8 Consensus size: 100
1237259 GAGACAAAAA
* * *
1237269 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAACTTTGTTTTAAAAGAAACTGTCTCAAGAGTAA
1 TTGTTTCAAGAGAAACTATCTCAAGAGAGACAAATTTGTTTCAAAAGAAACTGTCTCAAGAGTAA
*
1237334 CGAAATTTGTTTCAAGGAAAAAAGATTCAAAGATT
66 CCAAATTTGTTTCAAGGAAAAAAGATTCAAAGATT
* * **
1237369 TTGTTTCAAGGGAAACTATCTCAAGAGATACCAAATTTGTTTCAAGGGAAACTGTCTCAAGA-TA
1 TTGTTTCAAGAGAAACTATCTCAAGAGAGA-CAAATTTGTTTCAAAAGAAACTGTCTCAAGAGTA
1237433 GACCAAATTTGTTTCAAGG
65 -ACCAAATTTGTTTCAAGG
1237452 GAAACTGTCT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
100 29 0.40
101 44 0.60
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (100 bp):
TTGTTTCAAGAGAAACTATCTCAAGAGAGACAAATTTGTTTCAAAAGAAACTGTCTCAAGAGTAA
CCAAATTTGTTTCAAGGAAAAAAGATTCAAAGATT
Found at i:1239311 original size:18 final size:18
Alignment explanation
Indices: 1239263--1239352 Score: 80
Period size: 18 Copynumber: 5.0 Consensus size: 18
1239253 ATGCGTCTTG
1239263 TTTTC-TTTTTTCTTTATT
1 TTTTCTTTTTTTCTTT-TT
1239281 TTTCCTCTATTTTTTCTTTTT
1 TTT--TCT-TTTTTTCTTTTT
1239302 TTTTCTTTTTTTC---TT
1 TTTTCTTTTTTTCTTTTT
* *
1239317 TTTGCTTTTTTTCTTTGT
1 TTTTCTTTTTTTCTTTTT
* *
1239335 TTTTCTTCTTCTCTTTTT
1 TTTTCTTTTTTTCTTTTT
1239353 GTTATTGATT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
15 14 0.24
18 25 0.42
19 3 0.05
20 2 0.03
21 5 0.08
22 10 0.17
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTTTTCTTTTT
Found at i:1239327 original size:33 final size:33
Alignment explanation
Indices: 1239290--1239353 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1239280 TTTTCCTCTA
* * *
1239290 TTTTTTCTTTTTTTTTCTTTTTTTCTTTTTGCT
1 TTTTTTCTTTGTTTTTCTTCTTCTCTTTTTGCT
1239323 TTTTTTCTTTGTTTTTCTTCTTCTCTTTTTG
1 TTTTTTCTTTGTTTTTCTTCTTCTCTTTTTG
1239354 TTATTGATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (33 bp):
TTTTTTCTTTGTTTTTCTTCTTCTCTTTTTGCT
Found at i:1239328 original size:10 final size:9
Alignment explanation
Indices: 1239268--1239341 Score: 57
Period size: 9 Copynumber: 8.0 Consensus size: 9
1239258 TCTTGTTTTC
1239268 TTTTTTCTT
1 TTTTTTCTT
1239277 TATTTTTCCTCT
1 T-TTTTT-CT-T
1239289 ATTTTTTCTT
1 -TTTTTTCTT
1239299 TTTTTT-TCT
1 TTTTTTCT-T
1239308 TTTTTTC--
1 TTTTTTCTT
*
1239315 TTTTTGC-T
1 TTTTTTCTT
1239323 TTTTTTCTT
1 TTTTTTCTT
1239332 TGTTTTTCTT
1 T-TTTTTCTT
1239342 CTTCTCTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
7 6 0.11
8 7 0.13
9 16 0.30
10 14 0.26
11 4 0.07
12 6 0.11
13 1 0.02
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.81
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:1242239 original size:6 final size:6
Alignment explanation
Indices: 1242228--1242255 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1242218 TTTAATTTTG
1242228 AAAATT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAA
1242256 ACATTCGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:1242406 original size:14 final size:13
Alignment explanation
Indices: 1242389--1242439 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
1242379 ATCAAAAGGA
1242389 AAAAGGAAAAAAAT
1 AAAA-GAAAAAAAT
1242403 AAAA-ATAAAAAAT
1 AAAAGA-AAAAAAT
*
1242416 CAAAGGAAAAAAAAT
1 -AAAAG-AAAAAAAT
1242431 AAAAGAAAA
1 AAAAGAAAA
1242440 TAAAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
12 1 0.03
13 11 0.35
14 11 0.35
15 7 0.23
16 1 0.03
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.08
Consensus pattern (13 bp):
AAAAGAAAAAAAT
Found at i:1242427 original size:35 final size:32
Alignment explanation
Indices: 1242359--1242447 Score: 99
Period size: 32 Copynumber: 2.7 Consensus size: 32
1242349 TGAAAAACAT
* * *
1242359 AAAATAAAAAATAATAATAAATCAAAAGGAAA
1 AAAAAAAAAAAAAATAAAAAATCAAAAGGAAA
1242391 AAGGAAAAAAATAAAAATAAAAAATC-AAAGGAAA
1 AA--AAAAAAA-AAAAATAAAAAATCAAAAGGAAA
*
1242425 AAAAATAAAAGAAAATAAAAAAT
1 AAAAA-AAAAAAAAATAAAAAAT
1242448 ATCAAATAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
32 17 0.35
33 4 0.08
34 16 0.33
35 12 0.24
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.12
Consensus pattern (32 bp):
AAAAAAAAAAAAAATAAAAAATCAAAAGGAAA
Found at i:1242435 original size:15 final size:14
Alignment explanation
Indices: 1242389--1242444 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
1242379 ATCAAAAGGA
*
1242389 AAAAGGAAAAAAAT
1 AAAAGAAAAAAAAT
*
1242403 AAAA-ATAAAAAAT
1 AAAAGAAAAAAAAT
*
1242416 CAAAGGAAAAAAAAT
1 -AAAAGAAAAAAAAT
1242431 AAAAGAAAATAAAA
1 AAAAGAAAA-AAAA
1242445 AATATCAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
13 7 0.21
14 15 0.44
15 12 0.35
ACGTcount: A:0.80, C:0.02, G:0.09, T:0.09
Consensus pattern (14 bp):
AAAAGAAAAAAAAT
Found at i:1242521 original size:41 final size:40
Alignment explanation
Indices: 1242476--1242568 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 40
1242466 AAAACGTAAA
* *
1242476 AAAATAAAAAAAAGGAAAGGAAAAAAGGTAAA-ACAAT-AGAT
1 AAAATAAAAAAAA--AAAGGAAAAAAGG-AAACAAAATGAAAT
**
1242517 AAAATAAAATAAAAAAATTAAAAAAGGAAACAAAATGAAAT
1 AAAATAAAA-AAAAAAAGGAAAAAAGGAAACAAAATGAAAT
1242558 AAAATAAAAAA
1 AAAATAAAAAA
1242569 TAATTTTGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
39 3 0.07
40 17 0.38
41 21 0.47
42 4 0.09
ACGTcount: A:0.75, C:0.02, G:0.11, T:0.12
Consensus pattern (40 bp):
AAAATAAAAAAAAAAAGGAAAAAAGGAAACAAAATGAAAT
Found at i:1242695 original size:11 final size:12
Alignment explanation
Indices: 1242671--1242698 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1242661 TAAAAAAGGG
1242671 AAAATAATTAAA
1 AAAATAATTAAA
1242683 AAAATAATTAAA
1 AAAATAATTAAA
1242695 AAAA
1 AAAA
1242699 CTTAGAGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAATAATTAAA
Found at i:1246427 original size:51 final size:51
Alignment explanation
Indices: 1246334--1246435 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 51
1246324 GAAGGCGCAA
* **
1246334 CCCATGCACCACACCTTACGCTGATCTGGTGTTACGTGGGGTAAGACGCGG
1 CCCATGCACCACACCTTACGCTGATCTGGCGACACGTGGGGTAAGACGCGG
* *
1246385 CCCATGCACCGCACCTTACGCTGATCTGGCGACACGCT-GGGTAAGGCGCGG
1 CCCATGCACCACACCTTACGCTGATCTGGCGACACG-TGGGGTAAGACGCGG
1246436 TGCATGGGCC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
51 44 0.98
52 1 0.02
ACGTcount: A:0.19, C:0.32, G:0.30, T:0.19
Consensus pattern (51 bp):
CCCATGCACCACACCTTACGCTGATCTGGCGACACGTGGGGTAAGACGCGG
Found at i:1249006 original size:34 final size:38
Alignment explanation
Indices: 1248982--1249067 Score: 110
Period size: 38 Copynumber: 2.3 Consensus size: 38
1248972 TTTATTTTGT
1248982 TAATTTTTGT-TTA-TTACCATTTAATATCAGTTATTG
1 TAATTTTTGTATTATTTACCATTTAATATCAGTTATTG
*
1249018 TAATTTTTTTATTATTTACCATTTAATA-C--TTATTG
1 TAATTTTTGTATTATTTACCATTTAATATCAGTTATTG
1249053 TAAGTTTGTTGTATT
1 TAA-TTT-TTGTATT
1249068 TAAAATTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
35 9 0.20
36 12 0.27
37 10 0.23
38 13 0.30
ACGTcount: A:0.27, C:0.07, G:0.08, T:0.58
Consensus pattern (38 bp):
TAATTTTTGTATTATTTACCATTTAATATCAGTTATTG
Found at i:1253391 original size:2 final size:2
Alignment explanation
Indices: 1253384--1253413 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1253374 GTATACATAC
1253384 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1253414 GTTTGCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1253472 original size:23 final size:25
Alignment explanation
Indices: 1253426--1253486 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
1253416 TTGCAAATGG
1253426 ATTTTGAAAATGTATATAATATATA
1 ATTTTGAAAATGTATATAATATATA
1253451 ATTTTGAAAATGTATATAATATATA
1 ATTTTGAAAATGTATATAATATATA
* *
1253476 GTTTTTAAAAT
1 ATTTTGAAAAT
1253487 TATTTTGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (25 bp):
ATTTTGAAAATGTATATAATATATA
Found at i:1253553 original size:38 final size:37
Alignment explanation
Indices: 1253452--1253639 Score: 154
Period size: 38 Copynumber: 5.1 Consensus size: 37
1253442 TAATATATAA
* * *
1253452 TTTTGAAAATGTATATAATATATA-GTTTTTAAAA-TT
1 TTTTG-AAATATATATATTATATAGGTTTTTAAAACAT
*
1253488 ATTTTGAAAACATTTATATATTATATAGGTTTTTAAAACAT
1 -TTTTG--AA-ATATATATATTATATAGGTTTTTAAAACAT
* *
1253529 TTTTGAATATATATATATTATATAGTTTTTTAAAACGT
1 TTTTGAA-ATATATATATTATATAGGTTTTTAAAACAT
** * *
1253567 TTTTGAAATACGTATAATATATAGTTTTTTAAAA-A-
1 TTTTGAAATATATATATTATATAGGTTTTTAAAACAT
** *
1253602 AATTGAAA-CTATATATTATAT-GGATTTTTAAAACAT
1 TTTTGAAATATATATATTATATAGG-TTTTTAAAACAT
1253638 TT
1 TT
1253640 ATTTATTATT
Statistics
Matches: 124, Mismatches: 20, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
33 1 0.01
34 18 0.15
35 7 0.06
37 29 0.23
38 39 0.31
39 14 0.11
40 15 0.12
41 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (37 bp):
TTTTGAAATATATATATTATATAGGTTTTTAAAACAT
Found at i:1253671 original size:5 final size:5
Alignment explanation
Indices: 1253637--1253681 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
1253627 TTTTAAAACA
*
1253637 TTTA- TTTAT TATTAT TATTAT TTTAC TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT T-TTAT T-TTAT TTTAT TTTAT TTTAT TTTAT TTTA
1253682 GGGTCTAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
4 4 0.11
5 22 0.59
6 11 0.30
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:1253859 original size:15 final size:16
Alignment explanation
Indices: 1253824--1253859 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1253814 GCCAGCCAAA
1253824 GATCCCGGGACTGACC
1 GATCCCGGGACTGACC
*
1253840 CATCCCGGGA-TGACC
1 GATCCCGGGACTGACC
1253855 GATCC
1 GATCC
1253860 ACCACGAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.19, C:0.39, G:0.28, T:0.14
Consensus pattern (16 bp):
GATCCCGGGACTGACC
Found at i:1254817 original size:2 final size:2
Alignment explanation
Indices: 1254810--1254834 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1254800 TATTTAAATT
1254810 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 T
1254835 TCTTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1254893 original size:12 final size:11
Alignment explanation
Indices: 1254873--1254991 Score: 59
Period size: 12 Copynumber: 10.5 Consensus size: 11
1254863 TTTTCAGTTT
1254873 TTATTTTATTA
1 TTATTTTATTA
1254884 TTAGTTTTATTA
1 TTA-TTTTATTA
* *
1254896 TTATTTTTTCTC
1 TTATTTTAT-TA
**
1254908 TTATTTCCTT-
1 TTATTTTATTA
* *
1254918 TAAATTTATTA
1 TTATTTTATTA
1254929 TTTTATTTTATT-
1 --TTATTTTATTA
*
1254941 TT-TTTCTTTTA
1 TTATTT-TATTA
1254952 TTCATTTT-TTGA
1 TT-ATTTTATT-A
*
1254964 TT-TATTATTA
1 TTATTTTATTA
1254974 TTATTATTATTA
1 TTATT-TTATTA
1254986 TTATTT
1 TTATTT
1254992 ATCTAACATT
Statistics
Matches: 82, Mismatches: 13, Indels: 26
0.68 0.11 0.21
Matches are distributed among these distances:
9 3 0.04
10 17 0.21
11 17 0.21
12 34 0.41
13 11 0.13
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:1254973 original size:3 final size:3
Alignment explanation
Indices: 1254965--1254990 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1254955 ATTTTTTGAT
1254965 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1254991 TATCTAACAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1257563 original size:95 final size:95
Alignment explanation
Indices: 1257387--1257631 Score: 332
Period size: 95 Copynumber: 2.5 Consensus size: 95
1257377 ATATTATAAT
* * * *
1257387 ATTATATATATACAATAAAGCTTGAGTTATCCCTTTAAAGCAATTGGTTAAACGCCTTGACTTTA
1 ATTATA-ATATACAATAAAGTTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTTGACTTTA
*
1257452 TGGATAAGATTTAGCTAGCCTAATAAAGGTG
65 TGGATAAGATTCAGCTAGCCTAATAAAGGTG
*
1257483 ATTATAATATACAATAAAGTTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACG-CTCTGGCTTTA
1 ATTATAATATACAATAAAGTTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCT-TGACTTTA
* *
1257547 TGGATAATATTCAGCTAGCCTGATAAAGGTG
65 TGGATAAGATTCAGCTAGCCTAATAAAGGTG
* *
1257578 ATTATAATATA-TATACAATGATATTAAGTTGTCCCTCTAGAGCAATTGGTTAAA
1 ATTATAATATACAATA-AA-G-T-TTGAGTTGTCCCTCTAGAGCAATTGGTTAAA
1257632 TACCCTAGAT
Statistics
Matches: 134, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
94 5 0.04
95 91 0.68
96 7 0.05
97 1 0.01
98 30 0.22
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (95 bp):
ATTATAATATACAATAAAGTTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTTGACTTTAT
GGATAAGATTCAGCTAGCCTAATAAAGGTG
Found at i:1259092 original size:239 final size:239
Alignment explanation
Indices: 1258634--1259456 Score: 1132
Period size: 239 Copynumber: 3.5 Consensus size: 239
1258624 CCAACTCAAA
* * * **
1258634 GAAAC-ATACAATACTTGGATTTCAACTTCACGATGAAGGATATTCAAGTCAAGGCTCGACTTTT
1 GAAACAATACAA-GCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCA
* *
1258698 CAAAGAAGGGTCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCAACTCTAGATTGGA
65 CAATGAAGGGTCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCAACTTTAGA-TGGA
*
1258763 TTTAAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACGGAGAAGGGGCTTCCCAGT
129 TTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACGGAGAAGGGGCTTCCCAGT
* ** *
1258828 TTCATTCAGAGCCAATTTTAACTTCACGGAAAAAGATATTGGACTC
194 TTCATTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTC
*
1258874 GAAACAATACAAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTCAACTTCAC
1 GAAACAATACAAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCAC
*
1258939 AATGAATGGG-CCATCAACGATTTCAACTTCACGACGAAGGATATCGTGCCAACTTTAGATGGAT
66 AATGAA-GGGTCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCAACTTTAGATGGAT
** * *
1259003 TTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAAATTCACGGCGAAGGGGCTTCCCAGTT
130 TTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACGGAGAAGGGGCTTCCCAGTT
* *
1259068 TCATTCAGAGCTAATTTCAACTTCACGGCGAAGGTTATTGGACTC
195 TCATTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTC
*
1259113 AAAACAATACAAGCTT-GATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCAC
1 GAAACAATACAAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCAC
* * * * **
1259177 AACGAAGGGGCCATCTACGATTTCAACTTCACGACGAAGGATATC-T---AA-TTCA-A---AGC
66 AATGAAGGGTCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCAACTTTAGATGGATT
** * * *
1259233 TCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCTTGAAGAAGGGGTTTCCCATTTT
131 TCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACGGAGAAGGGGCTTCCCAGTTT
*
1259298 CATTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTAGACTC
196 CATTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTC
* * * * * *
1259342 GAAACAATACAAGCTTGGATTTTAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTTAT
1 GAAACAATACAAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCAC
* * * *
1259407 AATGAAAGGGTCC-GCCACGATTTCAACTTCATGACGAATGATATTGTGCC
66 AATG-AAGGGTCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCC
1259457 CACAAGCAGC
Statistics
Matches: 521, Mismatches: 53, Indels: 24
0.87 0.09 0.04
Matches are distributed among these distances:
229 113 0.22
230 72 0.14
231 8 0.02
232 1 0.00
233 3 0.01
234 2 0.00
237 4 0.01
238 86 0.17
239 119 0.23
240 104 0.20
241 9 0.02
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (239 bp):
GAAACAATACAAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCAC
AATGAAGGGTCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCAACTTTAGATGGATT
TCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACGGAGAAGGGGCTTCCCAGTTT
CATTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTC
Found at i:1259176 original size:34 final size:34
Alignment explanation
Indices: 1259133--1259274 Score: 123
Period size: 34 Copynumber: 4.2 Consensus size: 34
1259123 AAGCTTGATT
* *
1259133 TCAACTTCACGACGAAGGATATTCAAGTCAAGGC
1 TCAACTTCACGACGAAGGATATTCAATTCAAAGC
* ** * * **
1259167 TCAACTTCACAACGAAGG---GGCCA-TCTACGATT
1 TCAACTTCACGACGAAGGATATTCAATTC-A-AAGC
1259199 TCAACTTCACGACGAAGGATA-TCTAATTCAAAGC
1 TCAACTTCACGACGAAGGATATTC-AATTCAAAGC
* *
1259233 TCAACTTCACGATGAAGGATATCCAATTCAAAGC
1 TCAACTTCACGACGAAGGATATTCAATTCAAAGC
1259267 TCAACTTC
1 TCAACTTC
1259275 TTGAAGAAGG
Statistics
Matches: 84, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
30 2 0.02
31 3 0.04
32 17 0.20
34 57 0.68
35 3 0.04
36 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.23
Consensus pattern (34 bp):
TCAACTTCACGACGAAGGATATTCAATTCAAAGC
Found at i:1259284 original size:34 final size:34
Alignment explanation
Indices: 1259199--1259284 Score: 127
Period size: 34 Copynumber: 2.5 Consensus size: 34
1259189 ATCTACGATT
* *
1259199 TCAACTTCACGACGAAGGATATCTAATTCAAAGC
1 TCAACTTCACGAAGAAGGATATCCAATTCAAAGC
*
1259233 TCAACTTCACGATGAAGGATATCCAATTCAAAGC
1 TCAACTTCACGAAGAAGGATATCCAATTCAAAGC
**
1259267 TCAACTTCTTGAAGAAGG
1 TCAACTTCACGAAGAAGG
1259285 GGTTTCCCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.24
Consensus pattern (34 bp):
TCAACTTCACGAAGAAGGATATCCAATTCAAAGC
Found at i:1259653 original size:84 final size:84
Alignment explanation
Indices: 1259536--1260326 Score: 922
Period size: 84 Copynumber: 9.4 Consensus size: 84
1259526 TCAAGGAAAT
* * *
1259536 AAGGGTTATTTTCTAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTG
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTG
* *
1259601 TAGAATAACTCAAGGCTAG
66 CAGCATAACTCAAGGCTAG
* * * **
1259620 AAGGGTTATTTGCCAATAAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAAAGTGCATCATTT
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGA-CACATCATTT
* * * *
1259684 GCAGCACAACTTAAGTCGAG
65 GCAGCATAACTCAAGGCTAG
* * * * * * *
1259704 AAGGGCTATCTACCAACCAAAGACCTTGGAGTTTGACTACGCTTAGCTCCAAGGCACATCATTTG
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTG
*
1259769 CAGCATAACTCAAGGATAG
66 CAGCATAACTCAAGGCTAG
* * * *
1259788 AAGAGTTATCTGCCAACAAAAGACCTTCGAGTTTGACTATGCTCAGCTCCAAGGCACATCATTTG
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTG
* *
1259853 TAGCATAACTTAAGGCTAG
66 CAGCATAACTCAAGGCTAG
* * *
1259872 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTTAGCTCAAAGACATATCATTTG
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTG
* * ** * *
1259937 GAGTATAACAAAAGTCAAG
66 CAGCATAACTCAAGGCTAG
* * *
1259956 AAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTG
1260021 CAGCATAACTCAAGGCTAG
66 CAGCATAACTCAAGGCTAG
* * * * *
1260040 AAGGGTTATCTGCCAACAAAAGACCTTCAAGTTCGATTACACTCATCTCAAAGACACATCATTTG
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTG
* * * *
1260105 CAGCATAGCTTAAGTCGAG
66 CAGCATAACTCAAGGCTAG
* * * ** *
1260124 AAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGATTATACTCAGCTCAAAAGA-ACATCATTT
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC-CAAGACACATCATTT
* * * *
1260188 GCAGCATAGCTTAAGTCGAG
65 GCAGCATAACTCAAGGCTAG
* * * * * * * *
1260208 AAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATAATTTA
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTG
1260273 CAGCATAACTCAAGGCTAG
66 CAGCATAACTCAAGGCTAG
* *
1260292 AAGGGTTATCTGTCATC-AAAGACCTTCGAGTTCGA
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGA
1260327 TTACATTTAA
Statistics
Matches: 609, Mismatches: 94, Indels: 9
0.86 0.13 0.01
Matches are distributed among these distances:
83 26 0.04
84 575 0.94
85 8 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (84 bp):
AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTG
CAGCATAACTCAAGGCTAG
Found at i:1259974 original size:252 final size:251
Alignment explanation
Indices: 1259536--1260326 Score: 1091
Period size: 252 Copynumber: 3.1 Consensus size: 251
1259526 TCAAGGAAAT
* * *
1259536 AAGGGTTATTTTCTAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTG
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTG
* * * *
1259601 TAGAATAACTCAAGGCTAGAAGGGTTATTTGCCAATAAAAGACCTTCGAGTTCGACTACGCTCAG
66 TAGCATAACTTAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
* *
1259666 CTCAAA-AGTGCATCATTTGCAGCACAACTTAAGTCGAGAAGGGCTATCTACCAACCAAAGACCT
131 CTCAAAGAAT--ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTACCAACCAAAGACCT
* * * *
1259730 TGGAGTTTGACTACGCTTAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGATAG
194 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAG
* * * *
1259788 AAGAGTTATCTGCCAACAAAAGACCTTCGAGTTTGACTATGCTCAGCTCCAAGGCACATCATTTG
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTG
*
1259853 TAGCATAACTTAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTTAG
66 TAGCATAACTTAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
* * ** * *
1259918 CTCAAAGACATATCATTTGGAGTATAACAAAAGTCAAGAAGGGCTATCTGCCAACCAAAGACCTT
131 CTCAAAGA-ATATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTACCAACCAAAGACCTT
1259983 CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAG
195 CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAG
* * * * *
1260040 AAGGGTTATCTGCCAACAAAAGACCTTCAAGTTCGATTACACTCATCTCAAAGACACATCATTTG
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTG
* * * * * * * **
1260105 CAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGATTATACTCAG
66 TAGCATAACTTAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
* * * *
1260170 CTCAAAAGAACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTT
131 CTC-AAAGAATATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTACCAACCAAAGACCTT
* * * * *
1260235 CGAGTTCGATTACACTCAGCTCAAAGGCACATAATTTACAGCATAACTCAAGGCTAG
195 CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAG
* *
1260292 AAGGGTTATCTGTCATC-AAAGACCTTCGAGTTCGA
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGA
1260327 TTACATTTAA
Statistics
Matches: 476, Mismatches: 60, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
251 17 0.04
252 452 0.95
253 6 0.01
254 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (251 bp):
AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTG
TAGCATAACTTAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
CTCAAAGAATATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTACCAACCAAAGACCTTC
GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAG
Found at i:1260387 original size:85 final size:83
Alignment explanation
Indices: 1259770--1260419 Score: 302
Period size: 84 Copynumber: 7.7 Consensus size: 83
1259760 CATCATTTGC
* * * * * * * *** *
1259770 AGCATAACTCAAGGATAGAAGAGTTATCTGCCAACAAAAGACCTTCGAGTTTGACTATGCTCAGC
1 AGCATAACTCAAGGAAAGAAGGGATATCTGTCAGC-AAAGACCTTCGAGTTCGATTACATTCAAC
* * * **
1259835 TCCAAGGCACATCATTTGT
65 TCAAAGGCAAATAATTTAA
* ** * * * * * *
1259854 AGCATAACTTAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTT-AG
1 AGCATAACTCAAGGAAAGAAGGGATATCTGTCAGC-AAAGACCTTCGAGTTCGATTAC-ATTCAA
* * * **
1259918 CTCAAAGACATATCATTTGG
64 CTCAAAGGCAAATAATTTAA
* ** ** * * * * ** *
1259938 AGTATAACAAAAGTCAAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
1 AGCATAACTCAAGGAAAGAAGGGATATCTGTC-AGCAAAGACCTTCGAGTTCGATTACATTCAAC
* * * **
1260003 TCCAAGGCACATCATTTGC
65 TCAAAGGCAAATAATTTAA
** * * * * * *
1260022 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCAAGTTCGATTACACTCATC
1 AGCATAACTCAAGGAAAGAAGGGATATCTGTCAGC-AAAGACCTTCGAGTTCGATTACATTCAAC
* * * **
1260087 TCAAAGACACATCATTTGC
65 TCAAAGGCAAATAATTTAA
* * *** * * * * * *
1260106 AGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGATTATACTCAGC
1 AGCATAACTCAAGGAAAGAAGGGATATCTGTC-AGCAAAGACCTTCGAGTTCGATTACATTCAAC
* * **
1260171 TCAAAAG-AACATCATTTGC
65 TCAAAGGCAA-ATAATTTAA
* * *** * * * *
1260190 AGCATAGCTTAAGTCGAGAAGGGTTATCT-TCCAACCAAAGACCTTCGAGTTCGATTACACTCAG
1 AGCATAACTCAAGGAAAGAAGGGATATCTGT-C-AGCAAAGACCTTCGAGTTCGATTACATTCAA
* *
1260254 CTCAAAGGCACATAATTTAC
64 CTCAAAGGCAAATAATTTAA
** * * *
1260274 AGCATAACTCAAGGCTAGAAGGGTTATCTGTCATCAAAGACCTTCGAGTTCGATTACATTTAACT
1 AGCATAACTCAAGGAAAGAAGGGATATCTGTCAGCAAAGACCTTCGAGTTCGATTACATTCAACT
*
1260339 CAGAGGCAAATCAAATTTAA
66 CAAAGGCAAAT--AATTTAA
* * *
1260359 AGCATAGCTCAAGGAAAGAAGGGATATCTGTCAGCAAA-A-TTATCGAGTTCGATTTCATTCA
1 AGCATAACTCAAGGAAAGAAGGGATATCTGTCAGCAAAGACCT-TCGAGTTCGATTACATTCA
1260420 GCTCGATGAC
Statistics
Matches: 479, Mismatches: 75, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
83 43 0.09
84 390 0.81
85 46 0.10
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (83 bp):
AGCATAACTCAAGGAAAGAAGGGATATCTGTCAGCAAAGACCTTCGAGTTCGATTACATTCAACT
CAAAGGCAAATAATTTAA
Found at i:1260972 original size:4 final size:4
Alignment explanation
Indices: 1260965--1260998 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
1260955 ATATACATAT
*
1260965 CTAC CTAC CTAC CTAC CGAC CTAC CTAC CTAC CT
1 CTAC CTAC CTAC CTAC CTAC CTAC CTAC CTAC CT
1260999 TATAGTTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.24, C:0.50, G:0.03, T:0.24
Consensus pattern (4 bp):
CTAC
Found at i:1261076 original size:73 final size:72
Alignment explanation
Indices: 1261016--1261271 Score: 293
Period size: 76 Copynumber: 3.5 Consensus size: 72
1261006 TGCAAACGGT
* * *
1261016 TTTTGAAAATTTATATAATATATAATTTTAAAAACATTTTGAAAATGTATATAATATATAGTTTT
1 TTTTGAAAATTTATATAATATATAGTTTTTAAAACATTTTGAAAATATATATAATATATAG-TTT
*
1261081 TAAAACAC
65 TAAAACAA
*
1261089 TTTTGAAAA-CTATATAATATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGTTT
1 TTTTGAAAATTTATATAATATATAGTTTTTAAAACATTTT-GAAAATATATATAATATATAG-TT
1261153 TTAAAATC-A
64 TTAAAA-CAA
* * *
1261162 TTTTGAAAATATTTATATATTATATAGTTTTTAAAACATTTTTGAAAAAATATATATTATATAGT
1 TTTTG-AAA-ATTTATATAATATATAGTTTTTAAAACA-TTTTGAAAATATATATAATATATAG-
**
1261227 TTTTTAAAACGT
62 -TTTTAAAACAA
***
1261239 TTTTG-AAATACGTATAATATATAGTTTTTAAAA
1 TTTTGAAAATTTATATAATATATAGTTTTTAAAA
1261272 AATAAATTTT
Statistics
Matches: 161, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
72 27 0.17
73 43 0.27
74 26 0.16
75 3 0.02
76 44 0.27
77 18 0.11
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (72 bp):
TTTTGAAAATTTATATAATATATAGTTTTTAAAACATTTTGAAAATATATATAATATATAGTTTT
AAAACAA
Found at i:1261093 original size:37 final size:36
Alignment explanation
Indices: 1261016--1261271 Score: 327
Period size: 36 Copynumber: 6.9 Consensus size: 36
1261006 TGCAAACGGT
* * *
1261016 TTTTGAAAATTTATATAATATATAATTTTAAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAACA
*
1261052 TTTTGAAAATGTATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAACA
*
1261088 CTTTTGAAAA-CTATATAATATATAGTTTTTAAAACA
1 -TTTTGAAAATATATATAATATATAGTTTTTAAAACA
1261124 TTTTAGAAAATATATATAATATATAGTTTTTAAAATCA
1 TTTT-GAAAATATATATAATATATAGTTTTTAAAA-CA
*
1261162 TTTTGAAAATATTTATATATTATATAGTTTTTAAAACA
1 TTTTGAAAATA--TATATAATATATAGTTTTTAAAACA
* * *
1261200 TTTTTGAAAAAATATATATTATATAGTTTTTTAAAACGT
1 -TTTTGAAAATATATATAATATATAG-TTTTTAAAAC-A
**
1261239 TTTTG-AAATACGTATAATATATAGTTTTTAAAA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAA
1261272 AATAAATTTT
Statistics
Matches: 199, Mismatches: 12, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
35 4 0.02
36 72 0.36
37 68 0.34
38 23 0.12
39 32 0.16
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAACA
Found at i:1261304 original size:38 final size:34
Alignment explanation
Indices: 1261027--1261315 Score: 188
Period size: 37 Copynumber: 7.8 Consensus size: 34
1261017 TTTGAAAATT
* *
1261027 TATATAATATATA-ATTTTAAAAACA-TTTTGAAAA
1 TATATATTATATAGTTTTTAAAAA-ATTTTTG-AAA
* * *
1261061 TGTATATAATATATAGTTTTTAAAACACTTTTGAAAA
1 --TATATATTATATAGTTTTTAAAAAATTTTTG-AAA
* * *
1261098 CTATATAATATATAGTTTTTAAAACATTTTAGAAAA
1 -TATATATTATATAGTTTTTAAAAAATTTTTG-AAA
*
1261134 TATATATAATATATAGTTTTTAAAATCA-TTTTGAAAATA
1 TATATAT--TATATAGTTTTTAAAA-AATTTTTG--AA-A
*
1261173 TTTATATATTATATAGTTTTTAAAACATTTTTGAAAAAA
1 --TATATATTATATAGTTTTTAAAAAATTTTTG---AAA
**
1261212 TATATATTATATAGTTTTTTAAAACGTTTTTGAAA
1 TATATATTATATAG-TTTTTAAAAAATTTTTGAAA
*
1261247 TACGTATAATATATAGTTTTTAAAAAATAAATTTTGAAA
1 TA--TATATTATATAGTTTTTAAAAAAT---TTTTGAAA
* *
1261286 CTATATATTATATGGTTTTTTAAAATATTT
1 -TATATATTATATAG-TTTTTAAAAAATTT
1261316 ATTTTATTTA
Statistics
Matches: 220, Mismatches: 14, Indels: 38
0.81 0.05 0.14
Matches are distributed among these distances:
35 11 0.05
36 59 0.27
37 62 0.28
38 33 0.15
39 42 0.19
40 6 0.03
41 7 0.03
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (34 bp):
TATATATTATATAGTTTTTAAAAAATTTTTGAAA
Found at i:1261361 original size:18 final size:17
Alignment explanation
Indices: 1261313--1261361 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
1261303 TTTTAAAATA
* *
1261313 TTTATTTTATTTATTAT
1 TTTATTTTATTTTTTAC
1261330 TATTATTTTATTTTTTAAC
1 T-TTATTTTATTTTTT-AC
1261349 TTTATTTTATTTT
1 TTTATTTTATTTT
1261362 ATTTTTAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 1 0.04
18 25 0.89
19 2 0.07
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTTATTTTTTAC
Found at i:1261528 original size:16 final size:15
Alignment explanation
Indices: 1261507--1261536 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1261497 ACGGCAGAAG
1261507 ATCCCGGGACTGACCC
1 ATCCCGGGA-TGACCC
1261523 ATCCCGGGATGACC
1 ATCCCGGGATGACC
1261537 GGTCCACCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13
Consensus pattern (15 bp):
ATCCCGGGATGACCC
Found at i:1262493 original size:2 final size:2
Alignment explanation
Indices: 1262486--1262512 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1262476 ACACTAGCAT
1262486 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
1262513 TCTTTTTTAT
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:1264046 original size:12 final size:12
Alignment explanation
Indices: 1264031--1264058 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1264021 GAATTGAGTG
1264031 CTCAATTAGTTT
1 CTCAATTAGTTT
1264043 CTCAATTAGTTT
1 CTCAATTAGTTT
1264055 CTCA
1 CTCA
1264059 GTGCTGCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.46
Consensus pattern (12 bp):
CTCAATTAGTTT
Found at i:1270949 original size:31 final size:32
Alignment explanation
Indices: 1270914--1270974 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
1270904 TGATTTTGAA
1270914 AAAATTGAAAGTTTAGGTACTAAAA-CATATC
1 AAAATTGAAAGTTTAGGTACTAAAAGCATATC
*
1270945 AAAATTGATAGTTTAGGTACTAAAAGCATA
1 AAAATTGAAAGTTTAGGTACTAAAAGCATA
1270975 ATTCACCCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.30
Consensus pattern (32 bp):
AAAATTGAAAGTTTAGGTACTAAAAGCATATC
Found at i:1279191 original size:14 final size:15
Alignment explanation
Indices: 1279162--1279191 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1279152 ATAATGAATA
1279162 ATATTTTAACAAATC
1 ATATTTTAACAAATC
1279177 ATATTTTAA-AAATC
1 ATATTTTAACAAATC
1279191 A
1 A
1279192 ATTAGTGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATTTTAACAAATC
Found at i:1280668 original size:21 final size:22
Alignment explanation
Indices: 1280635--1280687 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1280625 ATTCTGACTA
1280635 TCGCATTGCGATTTTCC-AAAT
1 TCGCATTGCGATTTTCCTAAAT
* *
1280656 TCGCGTTGTGATTTTCCTAAA-
1 TCGCATTGCGATTTTCCTAAAT
*
1280677 TCGCAATGCGA
1 TCGCATTGCGA
1280688 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCTAAAT
Found at i:1280698 original size:20 final size:20
Alignment explanation
Indices: 1280673--1280729 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
1280663 GTGATTTTCC
1280673 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
1280693 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
*
1280713 TAAATCGCAACGCGAAT
1 TAAATCGCAATGCGAAT
1280730 CTGACTATCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (20 bp):
TAAATCGCAATGCGAATACG
Found at i:1280953 original size:22 final size:22
Alignment explanation
Indices: 1280925--1280990 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
1280915 GGCGACATCC
**
1280925 GTCCCCATCTTTGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
1280947 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
** *
1280969 GTCTTCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
1280991 TTCACGGTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1281350 original size:19 final size:19
Alignment explanation
Indices: 1281326--1281429 Score: 83
Period size: 20 Copynumber: 5.6 Consensus size: 19
1281316 GCGATTATGT
1281326 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1281345 CGTTGCGA--TTC--TT-G
1 CGTTGCGATTTTCATTTCG
** *
1281359 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTC-ATTTCG
**
1281379 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
* *
1281398 TGTTTCGATTTTCATTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1281418 TGTTGCGATTTT
1 CGTTGCGATTTT
1281430 AAGTTTCAGA
Statistics
Matches: 71, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
14 9 0.13
15 2 0.03
16 2 0.03
17 3 0.04
19 25 0.35
20 30 0.42
ACGTcount: A:0.13, C:0.18, G:0.23, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1281436 original size:20 final size:20
Alignment explanation
Indices: 1281393--1281436 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1281383 GCGATAGTCA
* * *
1281393 TTTCGTGTTTCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
1281413 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1281433 TTTC
1 TTTC
1281437 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.14, G:0.18, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:1283165 original size:20 final size:20
Alignment explanation
Indices: 1283152--1283337 Score: 92
Period size: 20 Copynumber: 9.9 Consensus size: 20
1283142 TATCGTAATG
1283152 CGAAAATGACTATCGCAACA
1 CGAAAATGACTATCGCAACA
1283172 CGAAAATGACTATCGC-A-A
1 CGAAAATGACTATCGCAACA
* **
1283190 CG-AGA-GA--ATCGCAATG
1 CGAAAATGACTATCGCAACA
** *
1283206 CG-AAATGAAAATCACAACA
1 CGAAAATGACTATCGCAACA
* **
1283225 --ACAA--A--ATCGCAATG
1 CGAAAATGACTATCGCAACA
**
1283239 CGAAAATGACTATCGCAATG
1 CGAAAATGACTATCGCAACA
* **
1283259 CAAAAATGACTATCGCAATG
1 CGAAAATGACTATCGCAACA
* **
1283279 CGAGAATGACTATCGCAATG
1 CGAAAATGACTATCGCAACA
**
1283299 CGAAAATGACTATCGCAATG
1 CGAAAATGACTATCGCAACA
**
1283319 CGAATTTGACTATCGCAAC
1 CGAAAATGACTATCGCAAC
1283338 GAAAGAATCG
Statistics
Matches: 136, Mismatches: 18, Indels: 24
0.76 0.10 0.13
Matches are distributed among these distances:
14 11 0.08
15 1 0.01
16 10 0.07
17 4 0.03
18 6 0.04
19 7 0.05
20 97 0.71
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
CGAAAATGACTATCGCAACA
Found at i:1283287 original size:40 final size:39
Alignment explanation
Indices: 1283230--1283336 Score: 169
Period size: 40 Copynumber: 2.7 Consensus size: 39
1283220 CAACAACAAA
1283230 ATCGCAATGCGAAAATGACTATCGCAATGCAAAAATGACT
1 ATCGCAATGCG-AAATGACTATCGCAATGCAAAAATGACT
*
1283270 ATCGCAATGCGAGAATGACTATCGCAATGCGAAAATGACT
1 ATCGCAATGCGA-AATGACTATCGCAATGCAAAAATGACT
*
1283310 ATCGCAATGCGAATTTGACTATCGCAA
1 ATCGCAATGCGAA-ATGACTATCGCAA
1283337 CGAAAGAATC
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
39 2 0.03
40 61 0.97
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (39 bp):
ATCGCAATGCGAAATGACTATCGCAATGCAAAAATGACT
Found at i:1283329 original size:60 final size:54
Alignment explanation
Indices: 1283140--1283374 Score: 182
Period size: 60 Copynumber: 4.3 Consensus size: 54
1283130 AGAATAGTTT
* *
1283140 ACTATCGTAATGCGAAAATGACTATCGCAACACGAAAATGACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATGACTATCGC-A-ACG-AAA-GA--ATCGCAATGCGAAAATG
** * *
1283196 A--ATCGCAATGCG-AAATGAAAATCACAAC-AACAAAATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAACGAA-AGAATCGCAATGCGAAAATG
*
1283247 ACTATCGCAATGCAAAAATGACTATCGCAATGCGAGAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAA--CGA-AA-GA--ATCGCAATGCGAAAATG
**
1283307 ACTATCGCAATGCGAATTTGACTATCGCAACGAAAGAATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCGAAAATG
** *
1283360 AAAATCGCATTGCGA
1 ACTATCGCAATGCGA
1283375 TTCTCTCGTT
Statistics
Matches: 147, Mismatches: 17, Indels: 33
0.75 0.09 0.17
Matches are distributed among these distances:
47 7 0.05
49 5 0.03
50 3 0.02
51 4 0.03
52 1 0.01
53 37 0.25
54 33 0.22
56 4 0.03
57 4 0.03
58 5 0.03
60 44 0.30
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.18
Consensus pattern (54 bp):
ACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCGAAAATG
Found at i:1283479 original size:20 final size:20
Alignment explanation
Indices: 1283381--1283469 Score: 133
Period size: 20 Copynumber: 4.5 Consensus size: 20
1283371 GCGATTCTCT
**
1283381 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
* **
1283401 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1283421 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1283441 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1283461 CGTTGCGAT
1 CGTTGCGAT
1283470 TTTAAGTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1284000 original size:21 final size:20
Alignment explanation
Indices: 1283909--1284013 Score: 68
Period size: 21 Copynumber: 5.0 Consensus size: 20
1283899 GACTCACCTG
1283909 TCATCGTTCAAGAGG-CCTCC
1 TCATCGTTCAAGAGGCCCT-C
* *
1283929 CCTATCGTTCAAGAGGCTCCTA
1 TC-ATCGTTCAAGAGGC-CCTC
** *
1283951 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAG-GCCCTC
* * *
1283972 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCC-CTC
*
1283993 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGG-CCCTC
1284014 CCAACATTCT
Statistics
Matches: 62, Mismatches: 17, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
20 3 0.05
21 52 0.84
22 4 0.06
23 3 0.05
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCTC
Found at i:1284006 original size:42 final size:42
Alignment explanation
Indices: 1283905--1284016 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
1283895 GCCCGACTCA
* * *
1283905 CCTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCT
1 CCTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCT
* **
1283947 CCTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGC-
1 CCTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCT
*
1283988 CACTGTCATCGTTGAAGAGGT-CCCTCCCA
1 C-CTGTCATCGTTCAAGA-GTCCCCTCCCA
1284017 ACATTCTAGA
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
41 3 0.05
42 52 0.91
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCT
Found at i:1285413 original size:14 final size:14
Alignment explanation
Indices: 1285394--1285429 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1285384 ATTGTTTAAT
1285394 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1285408 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1285422 TGATTTGT
1 TGATTTGT
1285430 TTAATTAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1285601 original size:20 final size:20
Alignment explanation
Indices: 1285576--1285638 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
1285566 AGAATCGCAA
1285576 TGCGATAGTCAATTCCGCGT
1 TGCGATAGTCAATTCCGCGT
* *
1285596 TGCGATAGTCATTTCCGTGT
1 TGCGATAGTCAATTCCGCGT
1285616 TGCGATAGTCATATT-CGCGT
1 TGCGATAGTCA-ATTCCGCGT
1285636 TGC
1 TGC
1285639 TAATAAGTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 36 0.95
21 2 0.05
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
TGCGATAGTCAATTCCGCGT
Found at i:1288077 original size:24 final size:24
Alignment explanation
Indices: 1288043--1288096 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1288033 CTGAAAAATC
1288043 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1288067 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1288091 ATCAAA
1 ATCAAA
1288097 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1288110 original size:24 final size:24
Alignment explanation
Indices: 1288043--1288110 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1288033 CTGAAAAATC
* * *
1288043 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1288067 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1288091 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1288111 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1288963 original size:20 final size:20
Alignment explanation
Indices: 1288938--1288984 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1288928 AAATTCAGTA
*
1288938 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
1288958 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
1288978 TTGCGAT
1 TTGCGAT
1288985 TTACGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:1288994 original size:20 final size:20
Alignment explanation
Indices: 1288971--1289027 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
1288961 CGATAGTCAG
*
1288971 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1288991 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1289011 ATTCGCATTGCGATTTA
1 ATTCGCATTGCGATTTA
1289028 GGAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1291274 original size:12 final size:12
Alignment explanation
Indices: 1291255--1291286 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1291245 ACATATCACT
1291255 TCATTATTCTTA
1 TCATTATTCTTA
*
1291267 TTATTATTCTTA
1 TCATTATTCTTA
1291279 TCATTATT
1 TCATTATT
1291287 AGCATGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (12 bp):
TCATTATTCTTA
Found at i:1295587 original size:12 final size:12
Alignment explanation
Indices: 1295568--1295599 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1295558 ACATATCATT
1295568 TCATTATTCTTA
1 TCATTATTCTTA
*
1295580 TTATTATTCTTA
1 TCATTATTCTTA
1295592 TCATTATT
1 TCATTATT
1295600 AGCATGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (12 bp):
TCATTATTCTTA
Found at i:1299948 original size:14 final size:14
Alignment explanation
Indices: 1299931--1299965 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1299921 TATGTCCTGT
1299931 TTGACTCAGATGAG
1 TTGACTCAGATGAG
* *
1299945 TTGACTCTGCTGAG
1 TTGACTCAGATGAG
1299959 TTGACTC
1 TTGACTC
1299966 GGATCAAATC
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:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (14 bp):
TTGACTCAGATGAG
Found at i:1302895 original size:14 final size:14
Alignment explanation
Indices: 1302876--1302902 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1302866 TCCTCACAGT
1302876 CGACTATCATTTAG
1 CGACTATCATTTAG
1302890 CGACTATCATTTA
1 CGACTATCATTTA
1302903 TGTTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (14 bp):
CGACTATCATTTAG
Found at i:1303023 original size:29 final size:29
Alignment explanation
Indices: 1302985--1303051 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
1302975 AATGATTCAG
* **
1302985 AGTGATTAAAAGGAGTAAATCAAAAGTTT
1 AGTGAGTAAAAGGAAAAAATCAAAAGTTT
**
1303014 AGTGAGTAAATTGAAAAAATCAAAAGTTT
1 AGTGAGTAAAAGGAAAAAATCAAAAGTTT
1303043 AGTGAGTAA
1 AGTGAGTAA
1303052 GGTCAGTGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.21, T:0.27
Consensus pattern (29 bp):
AGTGAGTAAAAGGAAAAAATCAAAAGTTT
Found at i:1304969 original size:30 final size:30
Alignment explanation
Indices: 1304929--1304988 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1304919 CTTCGGTAAT
1304929 ATGGGCGGAATGGGCGGCATGGGTGACATG
1 ATGGGCGGAATGGGCGGCATGGGTGACATG
* *
1304959 ATGGGTGGAATGGGCGGCATGGGTGGCATG
1 ATGGGCGGAATGGGCGGCATGGGTGACATG
1304989 GATGAGTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.18, C:0.12, G:0.52, T:0.18
Consensus pattern (30 bp):
ATGGGCGGAATGGGCGGCATGGGTGACATG
Found at i:1306024 original size:2 final size:2
Alignment explanation
Indices: 1306017--1306056 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1306007 ATTTATCCTC
* *
1306017 AT AT AT AT AT AT AT AT AT AT AT AT AT TT A- AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1306057 CAAAACAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1306281 original size:22 final size:22
Alignment explanation
Indices: 1306254--1306297 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1306244 TGATGGTGTC
1306254 CCCCTTGGTCAGACATCGTGCT
1 CCCCTTGGTCAGACATCGTGCT
1306276 CCCCTTGGTCAGACATCGTGCT
1 CCCCTTGGTCAGACATCGTGCT
1306298 GCTGGGACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.36, G:0.23, T:0.27
Consensus pattern (22 bp):
CCCCTTGGTCAGACATCGTGCT
Found at i:1314422 original size:15 final size:15
Alignment explanation
Indices: 1314398--1314431 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1314388 CTTTTTTCTC
1314398 AAAT-TTGCATACGA
1 AAATGTTGCATACGA
1314412 AAATGTTGCATACGA
1 AAATGTTGCATACGA
1314427 AAATG
1 AAATG
1314432 GTGAACGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (15 bp):
AAATGTTGCATACGA
Found at i:1315754 original size:64 final size:64
Alignment explanation
Indices: 1315686--1315842 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 64
1315676 TTGAAGGTGT
** * *
1315686 ATCGATGCATTGGTAATGCATCGATGCA-CTCTTTTAA-AATAGAAACATCGAATGCA-ATTAGT
1 ATCGATGCATAAGTAATGCATCGATGCATC-CCTATAATAATA-AAACATCGAATGCATATTA-T
1315748 GC
63 GC
* * *
1315750 ATCGATGCATAAGTCATGCATCGATGCATCCCTATAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAATGCATCGATGCATCCCTATAATAATAAAACATCGAATGCATATTATGC
* * *
1315814 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAATGCATCGATGCAT
1315843 ACCTTCATTA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
64 71 0.90
65 8 0.10
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAATGCATCGATGCATCCCTATAATAATAAAACATCGAATGCATATTATGC
Found at i:1316802 original size:65 final size:64
Alignment explanation
Indices: 1316675--1316836 Score: 236
Period size: 65 Copynumber: 2.5 Consensus size: 64
1316665 TTGTTTAAGG
* * * *
1316675 TGCATCGATGCACATGCAGTGCATCGATGCATGAATTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCAATTTAAATAGAAAACATCGAATAGGATTTA
*
1316739 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGTAGTGCATCGATGCAT--CAATTTAAATAGAAAACATCGAATAGGATTT
1316803 A
64 A
*
1316804 TGCATCGATGCATGGAGTAGTGCATCGATGCAT
1 TGCATCGATGCAT-AAGTAGTGCATCGATGCAT
1316837 ACCTTCATTA
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
64 29 0.33
65 41 0.46
66 19 0.21
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAAGTAGTGCATCGATGCATCAATTTAAATAGAAAACATCGAATAGGATTTA
Found at i:1317351 original size:18 final size:18
Alignment explanation
Indices: 1317328--1317362 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1317318 CTAGGAGATT
1317328 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1317346 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1317363 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1318425 original size:147 final size:146
Alignment explanation
Indices: 1318254--1318564 Score: 502
Period size: 147 Copynumber: 2.1 Consensus size: 146
1318244 GAGTCGAGGG
* * *
1318254 TCTACGCGGTCCTTCAGG-ATATATATATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATA
1 TCTACGCGGTCCTTCGGGAATATATATATTCTGTAGAACATGTGTGAAGTCT--TGAAACACATA
1318318 -TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
64 CT-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1318382 TATGGCACTACGGTGCAAT
128 TATGGCACTACGGTGCAAT
* *
1318401 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACATAC
1 TCTACGCGGTCCTTCGGGA-ATATATATATTCTGTAGAACATGTGTGAAGTCTTGAAACACATAC
*
1318466 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATA
65 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA
1318531 TGGCACTACGGTGCAAT
130 TGGCACTACGGTGCAAT
1318548 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1318565 TGCAATTATA
Statistics
Matches: 154, Mismatches: 6, Indels: 8
0.92 0.04 0.05
Matches are distributed among these distances:
146 1 0.01
147 121 0.79
148 1 0.01
149 31 0.20
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (146 bp):
TCTACGCGGTCCTTCGGGAATATATATATTCTGTAGAACATGTGTGAAGTCTTGAAACACATACT
TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATAT
GGCACTACGGTGCAAT
Found at i:1318565 original size:23 final size:23
Alignment explanation
Indices: 1318532--1318576 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1318522 ATTATTATAT
*
1318532 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
1318555 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
1318577 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1321956 original size:64 final size:65
Alignment explanation
Indices: 1321867--1321990 Score: 223
Period size: 64 Copynumber: 1.9 Consensus size: 65
1321857 ATGCATGAAT
1321867 TTAAATAGAAAACATCGAATAGGATTATGCATCGATGCAT-AAGTAGTGCATCGATGCATCCCCA
1 TTAAATAGAAAACATCGAATAGGATTATGCATCGATGCATGAAGTAGTGCATCGATGCATCCCCA
**
1321931 TTAAATAGAAAACATCGAATAGGATTATGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TTAAATAGAAAACATCGAATAGGATTATGCATCGATGCATGAAGTAGTGCATCGATGCAT
1321991 ACCTTCATTA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 40 0.70
65 17 0.30
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (65 bp):
TTAAATAGAAAACATCGAATAGGATTATGCATCGATGCATGAAGTAGTGCATCGATGCATCCCCA
Found at i:1323363 original size:34 final size:34
Alignment explanation
Indices: 1323320--1323436 Score: 122
Period size: 34 Copynumber: 3.6 Consensus size: 34
1323310 TTCGTCCTAC
1323320 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
1323354 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1323389 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
1323418 TATGATTTAAACTCCTAAA
1 TAGGATTCAAACTCCTAAA
1323437 GATATGATCC
Statistics
Matches: 67, Mismatches: 6, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
27 6 0.09
29 4 0.06
30 13 0.19
34 32 0.48
35 4 0.06
37 8 0.12
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:1323758 original size:19 final size:20
Alignment explanation
Indices: 1323706--1323758 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1323696 TTTTTTTTTC
1323706 ATGTAATATTTTTTTACATTT
1 ATGT-ATATTTTTTTACATTT
*
1323727 ATGTATTTCTTTTTTAC-TTT
1 ATGTATAT-TTTTTTACATTT
*
1323747 A-GTATATATTTT
1 ATGTATATTTTTT
1323759 ATTTTTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 4 0.14
19 5 0.18
20 7 0.25
21 12 0.43
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.64
Consensus pattern (20 bp):
ATGTATATTTTTTTACATTT
Found at i:1323851 original size:6 final size:6
Alignment explanation
Indices: 1323842--1323948 Score: 62
Period size: 6 Copynumber: 17.5 Consensus size: 6
1323832 ATATTTACTT
* *
1323842 TTTTTA TTTTTA TTTATATA TATATTA TTTTTA CTTTTTA TTATTA -TTTTA
1 TTTTTA TTTTTA TTT-T-TA T-TTTTA TTTTTA -TTTTTA TTTTTA TTTTTA
* * *
1323893 TTTATT- TGTTTA TTTCTATA TTTTT- TTTTT- TCTTT- TTCTTA TTTTTA
1 TTT-TTA TTTTTA TTT-T-TA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
*
1323940 TATTTA TTT
1 TTTTTA TTT
1323949 ACTTACTATT
Statistics
Matches: 79, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
5 18 0.23
6 37 0.47
7 14 0.18
8 9 0.11
9 1 0.01
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTTTA
Found at i:1323857 original size:35 final size:39
Alignment explanation
Indices: 1323817--1323897 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 39
1323807 TTAATTTATA
1323817 TATTTATATATATA-TATATTTACTTTTT-TTA-T-TTT
1 TATTTATATATATATTATATTTACTTTTTATTATTATTT
*
1323852 TATTTATATATATATTATTTTTACTTTTTATTATTATTT
1 TATTTATATATATATTATATTTACTTTTTATTATTATTT
1323891 TATTTAT
1 TATTTAT
1323898 TTGTTTATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
35 14 0.34
36 13 0.32
37 3 0.07
38 1 0.02
39 10 0.24
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.69
Consensus pattern (39 bp):
TATTTATATATATATTATATTTACTTTTTATTATTATTT
Found at i:1323894 original size:27 final size:28
Alignment explanation
Indices: 1323805--1323899 Score: 79
Period size: 31 Copynumber: 3.3 Consensus size: 28
1323795 TTATCAGTTT
* * * *
1323805 TATTAATTTATATATTTATATATATATA
1 TATTTATTTTTATTTTTATTTATATATA
1323833 TATTTACTTTTTTTATTTTTATTTATATATA
1 TATTTA---TTTTTATTTTTATTTATATATA
*
1323864 TA-TTATTTTTACTTTTTA-TTAT-TATTT
1 TATTTATTTTTA-TTTTTATTTATATA-TA
1323891 TATTTATTT
1 TATTTATTT
1323900 GTTTATTTCT
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
26 2 0.04
27 13 0.23
28 17 0.30
30 3 0.05
31 21 0.38
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (28 bp):
TATTTATTTTTATTTTTATTTATATATA
Found at i:1323898 original size:4 final size:4
Alignment explanation
Indices: 1323803--1323949 Score: 54
Period size: 4 Copynumber: 37.0 Consensus size: 4
1323793 TTTTATCAGT
* * * * * *
1323803 TTTA TTAA TTTA TATA TTTA TATA TATA TATA TTTA CTTTT TTTA -TT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA
* * * *
1323850 TTTA TTTA TATA TATA TTATT TTTA CTT- TTTA -TTA -TTA TTTTA TTTA
1 TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA
* * * * * * *
1323897 TTTG TTTA TTTC TATA TTTT TTTT TTTC TTTT TCTTA TTT- TTATA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TT-TA TTTA
1323946 TTTA
1 TTTA
1323950 CTTACTATTT
Statistics
Matches: 109, Mismatches: 24, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
3 14 0.13
4 81 0.74
5 14 0.13
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:1323998 original size:21 final size:21
Alignment explanation
Indices: 1323972--1324016 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1323962 CTTTGTTTTC
1323972 TTTGTTTTCTCTTTATTTTAA
1 TTTGTTTTCTCTTTATTTTAA
1323993 TTTGTTTTCTCTTTATTTTAA
1 TTTGTTTTCTCTTTATTTTAA
1324014 TTT
1 TTT
1324017 AATTAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.73
Consensus pattern (21 bp):
TTTGTTTTCTCTTTATTTTAA
Found at i:1324053 original size:15 final size:15
Alignment explanation
Indices: 1324035--1324064 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1324025 AATTTATTTC
1324035 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
1324050 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
1324065 ACATGGTTTT
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:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:1327874 original size:16 final size:16
Alignment explanation
Indices: 1327848--1327881 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1327838 AGATCCAATC
1327848 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
1327863 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
1327880 AA
1 AA
1327882 AAAACAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:1327920 original size:8 final size:7
Alignment explanation
Indices: 1327854--1327920 Score: 55
Period size: 8 Copynumber: 8.9 Consensus size: 7
1327844 AATCAAGAAC
1327854 AAAAAAG
1 AAAAAAG
1327861 AAAAGAAG
1 AAAA-AAG
1327869 CAAAAAAG
1 -AAAAAAG
1327877 CAAAAAA-
1 -AAAAAAG
*
1327884 AACAAAG
1 AAAAAAG
1327891 AAAAAGAG
1 AAAAA-AG
*
1327899 AAACAAG
1 AAAAAAG
1327906 AACAAAAGG
1 AA-AAAA-G
1327915 AAAAAA
1 AAAAAA
1327921 TAGCAAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
6 5 0.10
7 12 0.24
8 26 0.52
9 7 0.14
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1328602 original size:22 final size:22
Alignment explanation
Indices: 1328577--1328647 Score: 124
Period size: 22 Copynumber: 3.2 Consensus size: 22
1328567 CCATCAATCT
*
1328577 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
1328599 TTTGAGCATCAAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
*
1328621 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGTCAAACC
1328643 TTTGA
1 TTTGA
1328648 CCAAACACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (22 bp):
TTTGAGCATCAAATGTCAAACC
Found at i:1329603 original size:100 final size:99
Alignment explanation
Indices: 1329428--1329695 Score: 373
Period size: 100 Copynumber: 2.7 Consensus size: 99
1329418 AAGGATATCC
*
1329428 AATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACAT-AACATTGAAAACATTTCCCTTGAAATA
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AACATAAACATTGAAAACATTTCCCTTGAAATA
1329492 AATTGT-CTCTCTTGAGAATAGTTTCCCTTGAAACAA
65 AATTGTCCTCTCTTGAG-ATAGTTTCCCTTGAAAC-A
*
1329528 AATTTTGTCTCCCTTGAGACAATTTCTCTTGAACATAAACATTGAAAACATTTCCCTTGAAATGA
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAACATAAACATTGAAAACATTTCCCTTGAAAT-A
*
1329593 ATTTTGT-CTCTCTTGAGATAGTTTCCCTTGAAACA
65 A-ATTGTCCTCTCTTGAGATAGTTTCCCTTGAAACA
* * * * *
1329628 AATTTTGTCTCCTTTAAGACAGTTTCTATTGAA-ACTAAACTTTGAAAACAGTTTCCCTTGAAAC
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAACA-TAAACATTGAAAACA-TTTCCCTTGAAAT
1329692 AAAT
64 AAAT
1329696 CTTTGAATAT
Statistics
Matches: 153, Mismatches: 10, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
99 7 0.05
100 101 0.66
101 31 0.20
102 14 0.09
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.37
Consensus pattern (99 bp):
AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAACATAAACATTGAAAACATTTCCCTTGAAATAA
ATTGTCCTCTCTTGAGATAGTTTCCCTTGAAACA
Found at i:1329652 original size:36 final size:36
Alignment explanation
Indices: 1329578--1329671 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 36
1329568 ATTGAAAACA
** * *
1329578 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAG
1329614 TTTCCCTTGAAACAAATTTTGTCTC-CTTTAAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTC-TTAAGACAG
** *
1329650 TTTCTATTGAAACTAAACTTTG
1 TTTCCCTTGAAAC-AAATTTTG
1329672 AAAACAGTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
35 1 0.02
36 41 0.84
37 7 0.14
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.43
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAG
Found at i:1329680 original size:29 final size:29
Alignment explanation
Indices: 1329646--1329702 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1329636 CTCCTTTAAG
*
1329646 ACAGTTTCTATTGAAACTAAA-CTTTGAAA
1 ACAGTTTCCATTGAAAC-AAATCTTTGAAA
*
1329675 ACAGTTTCCCTTGAAACAAATCTTTGAA
1 ACAGTTTCCATTGAAACAAATCTTTGAA
1329703 TATGTTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.33
Consensus pattern (29 bp):
ACAGTTTCCATTGAAACAAATCTTTGAAA
Found at i:1329792 original size:36 final size:36
Alignment explanation
Indices: 1329716--1329828 Score: 156
Period size: 36 Copynumber: 3.1 Consensus size: 36
1329706 GTTTTACATT
* *
1329716 AAACAAATTTCGTCTCTCTTGAGATAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
1329752 AAACAAATTTTGTCTATCTTAAGACATGTTT-TCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCTCTTG
*
1329788 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
1329824 AAACA
1 AAACA
1329829 TCAATCCTTG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
35 4 0.06
36 58 0.88
37 4 0.06
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:1329933 original size:32 final size:32
Alignment explanation
Indices: 1329870--1329982 Score: 149
Period size: 32 Copynumber: 3.5 Consensus size: 32
1329860 CCTTGATACA
1329870 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACAC---AA-AAACCTTTGAAATT
*
1329906 GTTTCTCTTGAAACACAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAACCTTTGAAATT
*
1329938 GTTTCTCTTGAAACAC--AAACCTTTGAGATT
1 GTTTCTCTTGAAACACAAAAACCTTTGAAATT
*
1329968 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
1329983 AATTTTTGTC
Statistics
Matches: 73, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
30 26 0.36
32 29 0.40
33 2 0.03
36 16 0.22
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (32 bp):
GTTTCTCTTGAAACACAAAAACCTTTGAAATT
Found at i:1330011 original size:68 final size:66
Alignment explanation
Indices: 1329938--1330130 Score: 208
Period size: 69 Copynumber: 2.8 Consensus size: 66
1329928 CTTTGAAAAT
*
1329938 GTTTCTCTTGAAACACAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTTGTCTCCCTTGAGA
1 GTTTCTCTTGAAACACAAATCTTTGAGATTGTTTCCCTTGAAACAAA-TTTTGTCTCCCTTGAGA
*
1330003 CAT
65 C-C
* * * * *
1330006 TTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCTTTAAAACAAAATTTTGTCTCCCTTGAG
1 GTTTCTCTTGAAACAC-AAATCTTTGAGATTGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAG
*
1330071 GCC
64 ACC
* * * *
1330074 GTTTCTCATG-AACAACATATATCTTTAAGATCGTTTCCCTTGAAACGAATTTTGTCT
1 GTTTCTCTTGAAAC-ACA-A-ATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCT
1330131 TTTTTAAGAC
Statistics
Matches: 103, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
67 4 0.04
68 36 0.35
69 60 0.58
70 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (66 bp):
GTTTCTCTTGAAACACAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGAC
C
Found at i:1330882 original size:104 final size:104
Alignment explanation
Indices: 1330685--1330874 Score: 321
Period size: 104 Copynumber: 1.8 Consensus size: 104
1330675 GATTTCAAAC
* *
1330685 TCCACGATGGAGGATATCGTGCCACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGC
1 TCCACGACGGAGGATATCATGCCACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGC
1330750 TGGTTGTCAACGAACAATTTCCAATTTCAAAGCTGATTT
66 TGGTTGTCAACGAACAATTTCCAATTTCAAAGCTGATTT
* *
1330789 TCCACGACGGAGGATATCATGCTAC-CTATGACAACACAAGTTCAACTTCACAACGAAGGGACGG
1 TCCACGACGGAGGATATCATGCCACTC-AAGACAACACAAGTTCAACTTCACAACGAAGGGACGG
1330853 CTGGTTGTCAAC-AACAATTTCC
65 CTGGTTGTCAACGAACAATTTCC
1330875 CAGTTTCAGG
Statistics
Matches: 81, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
103 11 0.14
104 70 0.86
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (104 bp):
TCCACGACGGAGGATATCATGCCACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGC
TGGTTGTCAACGAACAATTTCCAATTTCAAAGCTGATTT
Found at i:1330931 original size:104 final size:102
Alignment explanation
Indices: 1330711--1331107 Score: 327
Period size: 104 Copynumber: 4.0 Consensus size: 102
1330701 TCGTGCCACT
1330711 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAATTTCCAATT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTCC-ATT
** * *
1330776 TCAAAGCTGATTT----TCCAC-GACGGAGGATATCATGCTACC
64 TC-AAGCCAATTTCAACTTCACAG-CGGAGGATAT--TG-GACC
* *
1330815 TATGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAGTT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTT-CCA-TT
*
1330880 TCAGGGCCAATTTCAACTTCACAGCGGAGGAT-TTGGACC
64 TCA-AGCCAATTTCAACTTCACAGCGGAGGATATTGGACC
* * * **
1330919 CAAGACAGCACAAGCTCAACTTCACAGCGAATGGG-CGGCTGACTGTC-AC-A-AA----CA---
1 CAAGACAACACAAGTTCAACTTCACAACGAA-GGGACGGCTGGTTGTCAACAACAATTTCCATTT
* * * *
1330973 -AAGCCAATCTCAACTTCACAACGAAGGATATTGGACT
65 CAAGCCAATTTCAACTTCACAGCGGAGGATATTGGACC
* * * *
1331010 CGAGACAACACAAATTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACATTTTCGGA---
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTC-CATTT
*
1331072 -GAGCCAATTTCAACTTCAC-GACGGAGGATATTGGAC
65 CAAGCCAATTTCAACTTCACAG-CGGAGGATATTGGAC
1331108 TTGGAACAAT
Statistics
Matches: 241, Mismatches: 32, Indels: 45
0.76 0.10 0.14
Matches are distributed among these distances:
90 27 0.11
91 43 0.18
92 2 0.01
93 1 0.00
94 1 0.00
96 2 0.01
99 32 0.13
101 2 0.01
102 1 0.00
103 12 0.05
104 99 0.41
105 5 0.02
107 1 0.00
108 12 0.05
109 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (102 bp):
CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCATTTC
AAGCCAATTTCAACTTCACAGCGGAGGATATTGGACC
Found at i:1331057 original size:91 final size:90
Alignment explanation
Indices: 1330885--1331050 Score: 226
Period size: 91 Copynumber: 1.8 Consensus size: 90
1330875 CAGTTTCAGG
* * * * * *
1330885 GCCAATTTCAACTTCACAGCGGAGGATTTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAA
1 GCCAATCTCAACTTCACAACGAAGGATTTGGACCCAAGACAACACAAACTCAACTTCACAACGAA
1330950 TGGGCGGCTGACTGTCACAAACAAA
66 TGGGCGGCTGACTGTCACAAACAAA
* * *
1330975 GCCAATCTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAATTCAACTTCACAACGA
1 GCCAATCTCAACTTCACAACGAAGGAT-TTGGACCCAAGACAACACAAACTCAACTTCACAACGA
1331040 A-GGGACGGCTG
65 ATGGG-CGGCTG
1331051 GTTGTCAACA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
90 27 0.42
91 38 0.58
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (90 bp):
GCCAATCTCAACTTCACAACGAAGGATTTGGACCCAAGACAACACAAACTCAACTTCACAACGAA
TGGGCGGCTGACTGTCACAAACAAA
Done.