Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007084.1 Hibiscus syriacus cultivar Beakdansim tig00018483_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: 192361
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:4158 original size:30 final size:30
Alignment explanation
Indices: 4100--4157 Score: 93
Period size: 28 Copynumber: 2.0 Consensus size: 30
4090 ATAAATATTA
4100 AATAAATCAAAGAGGAAAAAAAGAAAAAAT
1 AATAAATCAAAGAGGAAAAAAAGAAAAAAT
4130 AATAAATC-AA-AGGAAAAAAAGTAAAAAA
1 AATAAATCAAAGAGGAAAAAAAG-AAAAAA
4158 AGGAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 11 0.41
29 8 0.30
30 8 0.30
ACGTcount: A:0.74, C:0.03, G:0.12, T:0.10
Consensus pattern (30 bp):
AATAAATCAAAGAGGAAAAAAAGAAAAAAT
Found at i:4159 original size:18 final size:18
Alignment explanation
Indices: 4115--4168 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
4105 ATCAAAGAGG
4115 AAAAAAA-GAAAAAATAAT
1 AAAAAAAGGAAAAAA-AAT
* *
4133 AAATCAAAGGAAAAAAAGT
1 AAA-AAAAGGAAAAAAAAT
4152 AAAAAAAGGAAAAAAAA
1 AAAAAAAGGAAAAAAAA
4169 AAGTAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 15 0.50
19 8 0.27
20 7 0.23
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (18 bp):
AAAAAAAGGAAAAAAAAT
Found at i:4177 original size:30 final size:30
Alignment explanation
Indices: 4138--4197 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
4128 ATAATAAATC
4138 AAAGGAAAAAAAGTAAA-AAAAGGAAAAAAA
1 AAAGGAAAAAAAGTAAAGAAAA-GAAAAAAA
* * *
4168 AAAGTAAAAAAATTAAAGAGAAGAAAAAAA
1 AAAGGAAAAAAAGTAAAGAAAAGAAAAAAA
4198 CAAAATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (30 bp):
AAAGGAAAAAAAGTAAAGAAAAGAAAAAAA
Found at i:4179 original size:9 final size:9
Alignment explanation
Indices: 4138--4167 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
4128 ATAATAAATC
4138 AAAGGAAAA
1 AAAGGAAAA
*
4147 AAAGTAAAA
1 AAAGGAAAA
4156 AAAGGAAAA
1 AAAGGAAAA
4165 AAA
1 AAA
4168 AAAGTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (9 bp):
AAAGGAAAA
Found at i:4212 original size:29 final size:29
Alignment explanation
Indices: 4173--4242 Score: 67
Period size: 29 Copynumber: 2.5 Consensus size: 29
4163 AAAAAAAAGT
*
4173 AAAAA-AA-TTAAAGAGAAGAA-AA-AAA
1 AAAAATAAGTTAAAGAAAAGAATAATAAA
* *
4198 CAAAATATAATTTAATGAAAAGAATAATAAA
1 -AAAA-ATAAGTTAAAGAAAAGAATAATAAA
4229 AAAAATAAGTTAAA
1 AAAAATAAGTTAAA
4243 TATTGGAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
26 4 0.11
27 1 0.03
28 2 0.06
29 19 0.54
30 6 0.17
31 3 0.09
ACGTcount: A:0.71, C:0.01, G:0.09, T:0.19
Consensus pattern (29 bp):
AAAAATAAGTTAAAGAAAAGAATAATAAA
Found at i:5580 original size:28 final size:29
Alignment explanation
Indices: 5544--5624 Score: 87
Period size: 31 Copynumber: 2.8 Consensus size: 29
5534 AATTATATGA
5544 TAAA-TATATATATATTTCAAAAAA-ATT
1 TAAACTATATATATATTTCAAAAAAGATT
*
5571 TAAACTATATAT-TATATTCAAAAAAGTTT
1 TAAACTATATATATAT-TTCAAAAAAGATT
**
5600 TCAAAACTATATATAGCTTTCAAAA
1 T--AAACTATATATATATTTCAAAA
5625 TGTTTTGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
27 7 0.16
28 16 0.36
29 3 0.07
31 18 0.40
32 1 0.02
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (29 bp):
TAAACTATATATATATTTCAAAAAAGATT
Found at i:5624 original size:29 final size:29
Alignment explanation
Indices: 5591--5653 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
5581 ATTATATTCA
*
5591 AAAAAGTTTTCAAAACTATATAT-AGCTTTC
1 AAAATGTTTT-AAAA-TATATATAAGCTTTC
* *
5621 AAAATGTTTTGAAATATATATAAGTTTTC
1 AAAATGTTTTAAAATATATATAAGCTTTC
5650 AAAA
1 AAAA
5654 AAAAATGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 7 0.24
29 13 0.45
30 9 0.31
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (29 bp):
AAAATGTTTTAAAATATATATAAGCTTTC
Found at i:5712 original size:37 final size:38
Alignment explanation
Indices: 5654--5980 Score: 331
Period size: 37 Copynumber: 8.9 Consensus size: 38
5644 GTTTTCAAAA
*
5654 AAAAATGTTTTTAAAACTATATATTATATAAT-TTTTC
1 AAAAATGTTTTAAAAACTATATATTATATAATATTTTC
* * *
5691 AAAAATGTTTTCAAAATTATATATTATAT-ATTTTTTC
1 AAAAATGTTTTAAAAACTATATATTATATAATATTTTC
* *
5728 AAAAATGTTTTCAAAACTATATATTATATAAT-TTTTA
1 AAAAATGTTTTAAAAACTATATATTATATAATATTTTC
* * * *
5765 AAAAATATTTTTAAAACTATATATTATAT-TTATCTTC
1 AAAAATGTTTTAAAAACTATATATTATATAATATTTTC
* *
5802 --AAATGTTTTAAAAACTATATAATATAT-ATATATTC
1 AAAAATGTTTTAAAAACTATATATTATATAATATTTTC
* *
5837 -AAAATATTTTAAAAACTATATATTATAT-TTATTTTC
1 AAAAATGTTTTAAAAACTATATATTATATAATATTTTC
* *
5873 -AAAATGTTTTAAAAATTATATAATATATAAATATTTTC
1 AAAAATGTTTTAAAAACTATATATTATAT-AATATTTTC
* * * * *
5911 AAATATATTTT-CAAATTCATATATTATAT-ATACTTTC
1 AAAAATGTTTTAAAAACT-ATATATTATATAATATTTTC
*
5948 AAAAAT-TATTTACAAACTATATA-TATATAATAT
1 AAAAATGT-TTTAAAAACTATATATTATATAATAT
5981 ATATAAAATA
Statistics
Matches: 249, Mismatches: 30, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
35 30 0.12
36 65 0.26
37 117 0.47
38 19 0.08
39 18 0.07
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.47
Consensus pattern (38 bp):
AAAAATGTTTTAAAAACTATATATTATATAATATTTTC
Found at i:5750 original size:74 final size:75
Alignment explanation
Indices: 5654--5980 Score: 388
Period size: 74 Copynumber: 4.5 Consensus size: 75
5644 GTTTTCAAAA
* * * *
5654 AAAAATGTTTTTAAAACTATATATTATATAAT-TTTTCAAAAATGTTTTCAAAATTATATATTAT
1 AAAAATGTTTTAAAAACTATATAATATATAATATTTTCAAAAATATTTTCAAAACTATATATTAT
5718 ATATT-TTTTC
66 AT-TTATTTTC
* * * *
5728 AAAAATGTTTTCAAAACTATATATTATATAAT-TTTTAAAAAATATTTTTAAAACTATATATTAT
1 AAAAATGTTTTAAAAACTATATAATATATAATATTTTCAAAAATATTTTCAAAACTATATATTAT
*
5792 ATTTATCTTC
66 ATTTATTTTC
* *
5802 --AAATGTTTTAAAAACTATATAATATAT-ATATATTC-AAAATATTTTAAAAACTATATATTAT
1 AAAAATGTTTTAAAAACTATATAATATATAATATTTTCAAAAATATTTTCAAAACTATATATTAT
5863 ATTTATTTTC
66 ATTTATTTTC
* * *
5873 -AAAATGTTTTAAAAATTATATAATATATAAATATTTTCAAATATATTTTC-AAATTCATATATT
1 AAAAATGTTTTAAAAACTATATAATATAT-AATATTTTCAAAAATATTTTCAAAACT-ATATATT
* *
5936 ATATATACTTTC
64 ATATTTATTTTC
*
5948 AAAAAT-TATTTACAAACTATAT-ATATATAATAT
1 AAAAATGT-TTTAAAAACTATATAATATATAATAT
5981 ATATAAAATA
Statistics
Matches: 223, Mismatches: 21, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
71 36 0.16
72 54 0.24
73 2 0.01
74 81 0.36
75 33 0.15
76 17 0.08
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.47
Consensus pattern (75 bp):
AAAAATGTTTTAAAAACTATATAATATATAATATTTTCAAAAATATTTTCAAAACTATATATTAT
ATTTATTTTC
Found at i:9181 original size:94 final size:92
Alignment explanation
Indices: 9002--9276 Score: 282
Period size: 94 Copynumber: 2.9 Consensus size: 92
8992 GAGGACCTGG
* * * * *
9002 CAGTTTGGATCCGATATTACTAATTATCATGTACATTAACCATCGATAGGTTCAGATTCGATATA
1 CAGTTTAGATACGATATCACTAATTATCATGTACATTAACCATCGATCGGTTTAGA-TCGATATA
* * **
9067 TCTAATTATCATGTACATTAATTAC-TGAC
65 T-TGATTATCATGGACATTAACCACAT-AC
* ** * *
9096 CGGTTTAGATTTGATATCACTAATTATCATGTACATTAACCACCGACCGGTTTAGATCGGATATC
1 CAGTTTAGATACGATATCACTAATTATCATGTACATTAACCATCGATCGGTTTAGATC-GATAT-
* *
9161 ATTGATTATCATGGATATTAACCACATAT
64 ATTGATTATCATGGACATTAACCACATAC
* ** * *
9190 TAGTTTAGATACGATATCACTAATTATCATGTACATTAACCATTTATCGGTTTGGATTTGATATT
1 CAGTTTAGATACGATATCACTAATTATCATGTACATTAACCATCGATCGGTTTAGA-TCGATA-T
*
9255 ATTGATTATCATGTACATTAAC
64 ATTGATTATCATGGACATTAAC
9277 TCTCGACCGG
Statistics
Matches: 149, Mismatches: 27, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
93 2 0.01
94 142 0.95
95 5 0.03
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.38
Consensus pattern (92 bp):
CAGTTTAGATACGATATCACTAATTATCATGTACATTAACCATCGATCGGTTTAGATCGATATAT
TGATTATCATGGACATTAACCACATAC
Found at i:9288 original size:47 final size:47
Alignment explanation
Indices: 9004--9417 Score: 253
Period size: 47 Copynumber: 9.1 Consensus size: 47
8994 GGACCTGGCA
* * * **
9004 GTTTGGATCCGATATTACTAATTATCATGTACATTAACCATCGATAG
1 GTTTAGATTCGATATCACTAATTATCATGTACATTAACCATCGACCG
* **
9051 GTTCAGATTCGATAT-ATCTAATTATCATGTACATTAATTA-CTGACCG
1 GTTTAGATTCGATATCA-CTAATTATCATGTACATTAACCATC-GACCG
* *
9098 GTTTAGATTTGATATCACTAATTATCATGTACATTAACCACCGACCG
1 GTTTAGATTCGATATCACTAATTATCATGTACATTAACCATCGACCG
* * * * * ***
9145 GTTTAGA-TCGGATATCATTGATTATCATGGATATTAACCA-CATATTA
1 GTTTAGATTC-GATATCACTAATTATCATGTACATTAACCATC-GACCG
* ** *
9192 GTTTAGATACGATATCACTAATTATCATGTACATTAACCATTTATCG
1 GTTTAGATTCGATATCACTAATTATCATGTACATTAACCATCGACCG
* * * * *
9239 GTTTGGATTTGATATTATTGATTATCATGTACATTAACTC-TCGACC-
1 GTTTAGATTCGATATCACTAATTATCATGTACATTAAC-CATCGACCG
* **
9285 -----G----G-T-TCACTAATTATCATGTACATTAAACATTTACCG
1 GTTTAGATTCGATATCACTAATTATCATGTACATTAACCATCGACCG
* * *
9321 ATTCT-GATCT-GATACT-ACTGATTATCATGTACATTAACCA-CTAACCG
1 GTT-TAGAT-TCGATA-TCACTAATTATCATGTACATTAACCATC-GACCG
* *
9368 GTTCA-ATTCCGATATCAC-AATTTATCATGTACATAAACCATCGACCG
1 GTTTAGATT-CGATATCACTAA-TTATCATGTACATTAACCATCGACCG
9415 GTT
1 GTT
9418 CGGATTTGAT
Statistics
Matches: 285, Mismatches: 52, Indels: 60
0.72 0.13 0.15
Matches are distributed among these distances:
34 1 0.00
35 24 0.08
36 1 0.00
37 1 0.00
41 2 0.01
45 2 0.01
46 9 0.03
47 239 0.84
48 6 0.02
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (47 bp):
GTTTAGATTCGATATCACTAATTATCATGTACATTAACCATCGACCG
Found at i:9302 original size:82 final size:82
Alignment explanation
Indices: 9206--9358 Score: 236
Period size: 82 Copynumber: 1.9 Consensus size: 82
9196 AGATACGATA
* * * * * *
9206 TCACTAATTATCATGTACATTAACCATTTATCGGTT-TGGATTTGATATTATTGATTATCATGTA
1 TCACTAATTATCATGTACATTAAACATTTACCGATTCT-GATCTGATACTACTGATTATCATGTA
9270 CATTAACTCTCGACCGGT
65 CATTAACTCTCGACCGGT
9288 TCACTAATTATCATGTACATTAAACATTTACCGATTCTGATCTGATACTACTGATTATCATGTAC
1 TCACTAATTATCATGTACATTAAACATTTACCGATTCTGATCTGATACTACTGATTATCATGTAC
9353 ATTAAC
66 ATTAAC
9359 CACTAACCGG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
82 63 0.98
83 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (82 bp):
TCACTAATTATCATGTACATTAAACATTTACCGATTCTGATCTGATACTACTGATTATCATGTAC
ATTAACTCTCGACCGGT
Found at i:9440 original size:47 final size:45
Alignment explanation
Indices: 9294--9442 Score: 104
Period size: 47 Copynumber: 3.2 Consensus size: 45
9284 CGGTTCACTA
** * * *
9294 ATTATCATGTACATTAAA-CATTTACCGATTCTGATCTGATACTACTG
1 ATTATCATGTACA-TAAACCATCAACCGGTTC-GATTTGATATTA-TG
* * * * **
9341 ATTATCATGTACATTAACCA-CTAACCGGTTCAATTCCGATATCACA
1 ATTATCATGTACATAAACCATC-AACCGGTTCGATT-TGATATTATG
*
9387 ATTTATCATGTACATAAACCATCGACCGGTTCGGATTTGATATTATTG
1 A-TTATCATGTACATAAACCATCAACCGGTTC-GATTTGATATTA-TG
9435 ATTATCAT
1 ATTATCAT
9443 ATATATTAAC
Statistics
Matches: 77, Mismatches: 18, Indels: 14
0.71 0.17 0.13
Matches are distributed among these distances:
46 6 0.08
47 66 0.86
48 5 0.06
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.36
Consensus pattern (45 bp):
ATTATCATGTACATAAACCATCAACCGGTTCGATTTGATATTATG
Found at i:16181 original size:15 final size:15
Alignment explanation
Indices: 16161--16209 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
16151 GGGGTGATTT
16161 GGAGGAAGAAGAGGA
1 GGAGGAAGAAGAGGA
*
16176 GGAGGAGGAAGAGGA
1 GGAGGAAGAAGAGGA
*
16191 GGAGGAAGAAGAAGA
1 GGAGGAAGAAGAGGA
16206 GGAG
1 GGAG
16210 ATTGAGGAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (15 bp):
GGAGGAAGAAGAGGA
Found at i:16222 original size:15 final size:13
Alignment explanation
Indices: 16174--16224 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
16164 GGAAGAAGAG
16174 GAGGAGGAGGA-A
1 GAGGAGGAGGAGA
16186 GAGGAGGAGGA-A
1 GAGGAGGAGGAGA
* *
16198 GAAGAAGAGGAGA
1 GAGGAGGAGGAGA
16211 TTGAGGAGGAGGAG
1 --GAGGAGGAGGAG
16225 TTAGAGGATG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 21 0.66
13 1 0.03
15 10 0.31
ACGTcount: A:0.41, C:0.00, G:0.55, T:0.04
Consensus pattern (13 bp):
GAGGAGGAGGAGA
Found at i:16231 original size:15 final size:15
Alignment explanation
Indices: 16170--16232 Score: 53
Period size: 15 Copynumber: 4.4 Consensus size: 15
16160 TGGAGGAAGA
**
16170 AGAGGAGGAGGAGGA
1 AGAGGAGGAGGAGTT
16185 AGAGGAGGAGGA---
1 AGAGGAGGAGGAGTT
* *
16197 AGAAGAAGAGGAGATT
1 AGAGGAGGAGGAG-TT
16213 -GAGGAGGAGGAGTT
1 AGAGGAGGAGGAGTT
16227 AGAGGA
1 AGAGGA
16233 TGGAATCCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
12 10 0.26
14 2 0.05
15 27 0.69
ACGTcount: A:0.41, C:0.00, G:0.52, T:0.06
Consensus pattern (15 bp):
AGAGGAGGAGGAGTT
Found at i:17417 original size:6 final size:6
Alignment explanation
Indices: 17351--17414 Score: 92
Period size: 6 Copynumber: 10.7 Consensus size: 6
17341 AAAAATGTCG
* * *
17351 TAATAA TAATAA TAATAA TAATGA TAATGA TAATGA TAATGA TAATGA
1 TAATGA TAATGA TAATGA TAATGA TAATGA TAATGA TAATGA TAATGA
*
17399 TAATGA TAATAA TAAT
1 TAATGA TAATGA TAAT
17415 AATGCTTCAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.34
Consensus pattern (6 bp):
TAATGA
Found at i:18799 original size:25 final size:25
Alignment explanation
Indices: 18750--18799 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
18740 CATCTTCGTT
* * * *
18750 TACATCTTTATTAACATTGCTGACA
1 TACATCTTTAATAAAATGGCAGACA
18775 TACATCTTTAATAAAATGGCAGACA
1 TACATCTTTAATAAAATGGCAGACA
18800 ATAAGATCGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (25 bp):
TACATCTTTAATAAAATGGCAGACA
Found at i:19706 original size:28 final size:30
Alignment explanation
Indices: 19668--19731 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
19658 AGGACAGAAG
* *
19668 TATAAATAACAG-AAAA-AGAGTGCATAAA
1 TATAAACAACAGAAAAATAAAGTGCATAAA
*
19696 TGTAAACAACAGAAAAATAAAGTGCATAAA
1 TATAAACAACAGAAAAATAAAGTGCATAAA
19726 TATAAA
1 TATAAA
19732 TGACAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 10 0.33
29 4 0.13
30 16 0.53
ACGTcount: A:0.61, C:0.08, G:0.12, T:0.19
Consensus pattern (30 bp):
TATAAACAACAGAAAAATAAAGTGCATAAA
Found at i:19739 original size:28 final size:28
Alignment explanation
Indices: 19668--19746 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 28
19658 AGGACAGAAG
*
19668 TATAAATAACAGAAAA-AGAGTGCATAAA
1 TATAAATAACA-AAAATAAAGTGCATAAA
* *
19696 TGTAAACAACAGAAAAATAAAGTGCATAAA
1 TATAAATAAC--AAAAATAAAGTGCATAAA
*
19726 TATAAATGACAAAAATTAAAG
1 TATAAATAACAAAAA-TAAAG
19747 AATAGAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
28 13 0.32
29 9 0.22
30 19 0.46
ACGTcount: A:0.61, C:0.08, G:0.13, T:0.19
Consensus pattern (28 bp):
TATAAATAACAAAAATAAAGTGCATAAA
Found at i:19805 original size:31 final size:34
Alignment explanation
Indices: 19738--19811 Score: 102
Period size: 31 Copynumber: 2.3 Consensus size: 34
19728 TAAATGACAA
*
19738 AAAT-TAAAGAATAGAAATAAATAAATAAGGCAT
1 AAATGTAAATAATAGAAATAAATAAATAAGGCAT
*
19771 AAATGTAAATAATGGAAA-AAATAAAT-A-GCAT
1 AAATGTAAATAATAGAAATAAATAAATAAGGCAT
19802 AAATGTAAAT
1 AAATGTAAAT
19812 CGAATAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 14 0.37
32 1 0.03
33 12 0.32
34 11 0.29
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.23
Consensus pattern (34 bp):
AAATGTAAATAATAGAAATAAATAAATAAGGCAT
Found at i:19972 original size:15 final size:15
Alignment explanation
Indices: 19954--19992 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
19944 AAGCAAAAAA
19954 TTAGTAAGTTAGGA-G
1 TTAGTAA-TTAGGATG
*
19969 TTAGTAATTAGTATG
1 TTAGTAATTAGGATG
19984 TTAGTAATT
1 TTAGTAATT
19993 TAGAGGCTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (15 bp):
TTAGTAATTAGGATG
Found at i:24627 original size:19 final size:19
Alignment explanation
Indices: 24603--24642 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
24593 TCATCCGACT
24603 ATTAATATGTTTCAAACTC
1 ATTAATATGTTTCAAACTC
24622 ATTAATATGTTTCAAACTC
1 ATTAATATGTTTCAAACTC
24641 AT
1 AT
24643 CATTTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (19 bp):
ATTAATATGTTTCAAACTC
Found at i:27254 original size:66 final size:66
Alignment explanation
Indices: 27125--27256 Score: 165
Period size: 66 Copynumber: 2.0 Consensus size: 66
27115 CAGATCTCCG
* * ** * *
27125 GTTTCATCAACAAATTCACCATTTTATTCTTTTTCTTGTTCCTCAGTCAAAATCTTGGATTGCTT
1 GTTTCATCAACAAATTCACCATCTCATTCTTTACCTTGTTCCTCAATCAAAACCTTGGATTGCTT
27190 C
66 C
* * * **
27191 GTTTCATCAACAGATTCACCATCTCCTTCTTTACCTTGTTCCTCAATCATAACCTTGTTTTGCTT
1 GTTTCATCAACAAATTCACCATCTCATTCTTTACCTTGTTCCTCAATCAAAACCTTGGATTGCTT
27256 C
66 C
27257 AAAAACTGGG
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.21, C:0.27, G:0.08, T:0.44
Consensus pattern (66 bp):
GTTTCATCAACAAATTCACCATCTCATTCTTTACCTTGTTCCTCAATCAAAACCTTGGATTGCTT
C
Found at i:31430 original size:21 final size:24
Alignment explanation
Indices: 31380--31432 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 24
31370 TTTCAAACTC
*
31380 AACTCGAACTCAAAAATAATATTGA
1 AACTC-AACTCAAAAATAATATTCA
31405 AACTCAACTC-AAAA-AA-ATTCA
1 AACTCAACTCAAAAATAATATTCA
31426 AACTCAA
1 AACTCAA
31433 AAATAAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 11 0.41
22 2 0.07
23 4 0.15
24 5 0.19
25 5 0.19
ACGTcount: A:0.55, C:0.21, G:0.04, T:0.21
Consensus pattern (24 bp):
AACTCAACTCAAAAATAATATTCA
Found at i:31600 original size:33 final size:33
Alignment explanation
Indices: 31540--31603 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
31530 GCTCGAGTTT
** *
31540 CAAACTCAATTAAAACTGGATTGAAGCTCAATA
1 CAAACTCAATTAAAACTAAATTCAAGCTCAATA
* *
31573 CAAACTCAATTCAAGCTAAATTCAAGCTCAA
1 CAAACTCAATTAAAACTAAATTCAAGCTCAA
31604 GAATTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.45, C:0.22, G:0.09, T:0.23
Consensus pattern (33 bp):
CAAACTCAATTAAAACTAAATTCAAGCTCAATA
Found at i:33051 original size:14 final size:14
Alignment explanation
Indices: 33032--33061 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
33022 ATGAGATAAG
*
33032 TATGATTTAGGGTT
1 TATGATTTAGAGTT
33046 TATGATTTAGAGTT
1 TATGATTTAGAGTT
33060 TA
1 TA
33062 GGGTTTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (14 bp):
TATGATTTAGAGTT
Found at i:33153 original size:11 final size:11
Alignment explanation
Indices: 33137--33199 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
33127 GTATTATAGA
33137 ATTTTTAATAT
1 ATTTTTAATAT
33148 ATTTTTAA-A-
1 ATTTTTAATAT
33157 ATTTTATAAT-T
1 ATTTT-TAATAT
*** * *
33168 ATCAATAGTGT
1 ATTTTTAATAT
33179 ATTTTTAATAT
1 ATTTTTAATAT
33190 ATTTTTAATA
1 ATTTTTAATA
33200 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:33452 original size:20 final size:19
Alignment explanation
Indices: 33429--33482 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
33419 ACTACAAGGT
33429 AAGTTTCGAAACTCTTGTCA
1 AAGTTTCGAAACTCTTGT-A
* *
33449 AAGTTTCGAAGCTTTTGTA
1 AAGTTTCGAAACTCTTGTA
* *
33468 AAATTTTGAAACTCT
1 AAGTTTCGAAACTCT
33483 AAAGCCTACT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (19 bp):
AAGTTTCGAAACTCTTGTA
Found at i:36215 original size:20 final size:20
Alignment explanation
Indices: 36190--36237 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
36180 CCAATCTGTC
*
36190 ATGTCATCCGTCATGTTAAT
1 ATGTCACCCGTCATGTTAAT
36210 ATGTCACCCGTCATGTTAAT
1 ATGTCACCCGTCATGTTAAT
36230 ATGTCACC
1 ATGTCACC
36238 ATGAATTGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGTCACCCGTCATGTTAAT
Found at i:38164 original size:15 final size:15
Alignment explanation
Indices: 38146--38187 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
38136 TAAAGGATTA
38146 AATATTAT-TAAATAT
1 AATATTATAT-AATAT
*
38161 AATATTATATAGTAT
1 AATATTATATAATAT
38176 AATATTA-ATAAT
1 AATATTATATAAT
38188 TTGGGCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.17
15 19 0.79
16 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
AATATTATATAATAT
Found at i:38313 original size:60 final size:60
Alignment explanation
Indices: 38203--38328 Score: 164
Period size: 60 Copynumber: 2.1 Consensus size: 60
38193 CAAAATTCAC
* * * ** *
38203 AAATGGTCCCTCGACTATAGGATGTTGTTTTGTTGAGTCTTTCGAATATTACAAA-TTATA
1 AAATGATCCCTCGACTATAGGACGTTGCTTTGTTGAGTCCCTCGAATATTA-AAAGTTACA
**
38263 AAATGATCCCTCGACTATAGGACGTTGCTTTGTTGAGTCCCTCGCCTATTAAAAGTTACA
1 AAATGATCCCTCGACTATAGGACGTTGCTTTGTTGAGTCCCTCGAATATTAAAAGTTACA
38323 AAATGA
1 AAATGA
38329 CCACATGACT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 3 0.05
60 54 0.95
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (60 bp):
AAATGATCCCTCGACTATAGGACGTTGCTTTGTTGAGTCCCTCGAATATTAAAAGTTACA
Found at i:38711 original size:2 final size:2
Alignment explanation
Indices: 38704--38732 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38694 TATTAGTTAC
38704 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38733 AAGCGTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40512 original size:10 final size:9
Alignment explanation
Indices: 40478--40510 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
40468 TATATTTATT
40478 AATTAATT-
1 AATTAATTA
40486 AATTAATTA
1 AATTAATTA
40495 AATTAAATTA
1 AATT-AATTA
40505 AATTAA
1 AATTAA
40511 ATATTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 6 0.26
10 9 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAATTA
Found at i:41712 original size:22 final size:22
Alignment explanation
Indices: 41670--41718 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
41660 AAATTTAAAA
* *
41670 ATTTTAAATTTTGATATTAATT
1 ATTTTAAATTTTGAAAATAATT
41692 ATTTTAAATATTT-AAAATAATT
1 ATTTTAAAT-TTTGAAAATAATT
*
41714 TTTTT
1 ATTTT
41719 TTGATGAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTTTAAATTTTGAAAATAATT
Found at i:47266 original size:25 final size:25
Alignment explanation
Indices: 47232--47280 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
47222 TAAGGGATTC
47232 TAATCTCGTTTGAATATCTAATCTT
1 TAATCTCGTTTGAATATCTAATCTT
47257 TAATCTCGTTTGAATATCTAATCT
1 TAATCTCGTTTGAATATCTAATCT
47281 GACTCGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (25 bp):
TAATCTCGTTTGAATATCTAATCTT
Found at i:48879 original size:36 final size:37
Alignment explanation
Indices: 48804--48879 Score: 102
Period size: 35 Copynumber: 2.1 Consensus size: 37
48794 TTTTTATATT
*
48804 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* *
48841 TTTAATTTT-TAAATAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
48877 TTT
1 TTT
48880 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 13 0.37
36 13 0.37
37 9 0.26
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:57698 original size:31 final size:31
Alignment explanation
Indices: 57663--57755 Score: 73
Period size: 31 Copynumber: 3.1 Consensus size: 31
57653 TGGTTGTTTT
57663 GTAACTTTTGATAGTCGATAGACTCAATAAA
1 GTAACTTTTGATAGTCGATAGACTCAATAAA
** ** * * * ***
57694 GTAACACTCCATTGTCGAAATA-TC-ATTTT
1 GTAACTTTTGATAGTCGATAGACTCAATAAA
*
57723 GTAACTTTTGATAGTCGATAGACTTAATAAA
1 GTAACTTTTGATAGTCGATAGACTCAATAAA
57754 GT
1 GT
57756 TGTACCCTAT
Statistics
Matches: 39, Mismatches: 21, Indels: 4
0.61 0.33 0.06
Matches are distributed among these distances:
29 17 0.44
30 3 0.08
31 19 0.49
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (31 bp):
GTAACTTTTGATAGTCGATAGACTCAATAAA
Found at i:59375 original size:188 final size:187
Alignment explanation
Indices: 59013--59538 Score: 571
Period size: 188 Copynumber: 2.8 Consensus size: 187
59003 GAATCTATGT
* * * * * * *
59013 TGTTTCGATTCTTCATTTTTATAGAATTATCTTGTTCGAAACTTATGTTGCAACACTTGCGTACG
1 TGTTTCGTTTCTTCATTTTTGTTGAACTATCATGTTTGAAACTTATGTTGCAACACTTGCATACG
** * *
59078 AGTCTGAGTAAACACCTAGGATCCCCGAAAACGTAAAAATGATGAATGTTAATTTTATGCAGGAC
66 AGTCCAAGTAAGCACCTAGGATCCCAGAAAA-G-AAAAATGATGAATGTTAATTTTATGCAGGAC
* * * * * *
59143 TGACCCCGTCTCATTCTTAAGTATGCAGGCTGTTTGTCAAAATGCATAAC-TT-CGAT-
129 TGACCCTGTGTCTTTCTTAAGTATGCAAGATGTTTGTCAAAATGCATAACATTCCAATC
* *
59199 TGTTTGGTTTCTTCAAATTTTTTTTTTGAACTATCATGTTTGAAACTTATGTTGCAACACTTGCA
1 TGTTTCGTTTCTTC--A--TTTTTGTTGAACTATCATGTTTGAAACTTATGTTGCAACACTTGCA
* ** *
59264 TACGAATCCAAGTAAGCACCTAGGATCCCAGACGAGAAAAACGATGAATGTTAATTTTATGCAGG
62 TACGAGTCCAAGTAAGCACCTAGGATCCCAGAAAAGAAAAATGATGAATGTTAATTTTATGCAGG
* * *
59329 ATTGACCCTGTGTCTTTCTTAGGTATGCAAGAT-TCTTGTTAAAATGCATAACTTAGATTCCAAT
127 ACTGACCCTGTGTCTTTCTTAAGTATGCAAGATGT-TTGTCAAAATGCATAAC----ATTCCAAT
59393 CC
187 -C
* * * **
59395 ATGTTTCGTTTCTTCATTTTTGTTGAATTATCGTG-TT-ACACTTATGTCACAACACTTGCATAC
1 -TGTTTCGTTTCTTCATTTTTGTTGAACTATCATGTTTGAAACTTATGTTGCAACACTTGCATAC
*
59458 GAGTCCTAGTAAGCACCTAGGATCCCAGATAATAGAAAAATGATGAATGTTAATTTTATGCACGG
65 GAGTCCAAGTAAGCACCTAGGATCCCAGA-AA-AGAAAAATGATGAATGTTAATTTTATGCA-GG
59523 -CTGACCCTGTGTCTTT
127 ACTGACCCTGTGTCTTT
59539 TCTGGAATGT
Statistics
Matches: 285, Mismatches: 38, Indels: 27
0.81 0.11 0.08
Matches are distributed among these distances:
186 12 0.04
187 1 0.00
188 71 0.25
189 1 0.00
190 68 0.24
191 50 0.18
192 2 0.01
193 61 0.21
194 5 0.02
195 1 0.00
197 13 0.05
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (187 bp):
TGTTTCGTTTCTTCATTTTTGTTGAACTATCATGTTTGAAACTTATGTTGCAACACTTGCATACG
AGTCCAAGTAAGCACCTAGGATCCCAGAAAAGAAAAATGATGAATGTTAATTTTATGCAGGACTG
ACCCTGTGTCTTTCTTAAGTATGCAAGATGTTTGTCAAAATGCATAACATTCCAATC
Found at i:67172 original size:20 final size:21
Alignment explanation
Indices: 67118--67180 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
67108 GATTCCCCTG
67118 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
67142 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
67162 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
67181 TGTACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:71025 original size:22 final size:21
Alignment explanation
Indices: 70983--71022 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
70973 GAGTTTGTTT
*
70983 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
71004 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
71023 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:78491 original size:2 final size:2
Alignment explanation
Indices: 78484--78518 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
78474 TATAACGTAT
* *
78484 TA TA TA TA CA TA TA TA CA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
78519 GACATTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:79170 original size:16 final size:16
Alignment explanation
Indices: 79145--79175 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
79135 TGAGAAAATA
79145 TTATTGATTTTATTTT
1 TTATTGATTTTATTTT
*
79161 TTATTTATTTTATTT
1 TTATTGATTTTATTT
79176 AAATTTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (16 bp):
TTATTGATTTTATTTT
Found at i:89329 original size:11 final size:11
Alignment explanation
Indices: 89315--89346 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
89305 ATTTTTATCC
89315 ATTTTTTAATT
1 ATTTTTTAATT
89326 ATTTTTTAATT
1 ATTTTTTAATT
*
89337 ATTATTTAAT
1 ATTTTTTAAT
89347 ATTATTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
ATTTTTTAATT
Found at i:89366 original size:24 final size:25
Alignment explanation
Indices: 89334--89386 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
89324 TTATTTTTTA
*
89334 ATTATTATTTAATATT-ATTAATATT
1 ATTATTATTT-ATATTAATAAATATT
*
89359 ATTA-TATTTTTATTAATAAATATT
1 ATTATTATTTATATTAATAAATATT
89383 ATTA
1 ATTA
89387 CAAACAGGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.16
24 17 0.68
25 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTATTATTTATATTAATAAATATT
Found at i:89371 original size:20 final size:19
Alignment explanation
Indices: 89326--89376 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
89316 TTTTTTAATT
89326 ATTTT-TTAATTATTATTTA
1 ATTTTATTAA-TATTATTTA
*
89345 ATATTATTAATATTATTATA
1 ATTTTATTAATATTATT-TA
*
89365 TTTTTATTAATA
1 ATTTTATTAATA
89377 AATATTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTATTAATATTATTTA
Found at i:90898 original size:21 final size:21
Alignment explanation
Indices: 90874--90937 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
90864 GCAAATTCGC
90874 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
90895 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
90915 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
90936 GT
1 GT
90938 CTACAGTTGT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:91078 original size:6 final size:6
Alignment explanation
Indices: 91067--91106 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
91057 AGACACGTAT
91067 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
91107 CGAGACGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:91625 original size:6 final size:6
Alignment explanation
Indices: 91614--91646 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
91604 TCTCGTCTCG
91614 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
91647 AATACGTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:91761 original size:22 final size:22
Alignment explanation
Indices: 91734--91849 Score: 132
Period size: 22 Copynumber: 5.4 Consensus size: 22
91724 AATTTTGAAA
91734 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
91756 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* **
91778 ATCGCAACG--AA-TTTAGAAA
1 ATCGCAACGACAACTGTAGACT
91797 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * *
91819 ATCGCAACG-CGAAATATAGACA
1 ATCGCAACGAC-AACTGTAGACT
91841 ATCGCAACG
1 ATCGCAACG
91850 CGAAATGGAA
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
19 14 0.18
20 2 0.03
21 3 0.04
22 60 0.76
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:91839 original size:63 final size:63
Alignment explanation
Indices: 91712--91849 Score: 206
Period size: 63 Copynumber: 2.2 Consensus size: 63
91702 TTTTTTTTTA
* * * *
91712 ACTATCACAACGAATTTTGAAAATCGCAACGACAACTGTAGACTATCGCAACAACAACTGTAG
1 ACTATCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTATCGCAACAACAAATATAG
*
91775 ACTATCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTATCGCAAC-GCGAAATATAG
1 ACTATCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTATCGCAACAAC-AAATATAG
*
91838 ACAATCGCAACG
1 ACTATCGCAACG
91850 CGAAATGGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 1 0.01
63 67 0.99
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (63 bp):
ACTATCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTATCGCAACAACAAATATAG
Found at i:91865 original size:20 final size:20
Alignment explanation
Indices: 91819--91913 Score: 82
Period size: 20 Copynumber: 4.6 Consensus size: 20
91809 ACTGTAGACT
*
91819 ATCGCAACGCGAAATATAGACA
1 ATCGCAACGCG-AA-ATAGAAA
*
91841 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATAGAAA
* ** ** *
91861 ATCGCAACACGATTTTCAACT
1 ATCGCAACGCGAAATAGAA-A
*
91882 ATCGCAACGTGAAATAGAAA
1 ATCGCAACGCGAAATAGAAA
91902 ATCGCAACGCGA
1 ATCGCAACGCGA
91914 TTTTCAACTA
Statistics
Matches: 56, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
20 30 0.54
21 15 0.27
22 11 0.20
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATAGAAA
Found at i:91896 original size:41 final size:41
Alignment explanation
Indices: 91841--91938 Score: 169
Period size: 41 Copynumber: 2.4 Consensus size: 41
91831 AATATAGACA
91841 ATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCAACT
* * *
91882 ATCGCAACGTGAAATAGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCAACT
91923 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
91939 CAACGCGAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCAACT
Found at i:91942 original size:21 final size:21
Alignment explanation
Indices: 91819--91942 Score: 92
Period size: 21 Copynumber: 6.0 Consensus size: 21
91809 ACTGTAGACT
**
91819 ATCGCAACGCGAAATATAGACA
1 ATCGCAACGCGAAATGCA-ACA
*
91841 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGAAATGCAACA
* ** * *
91861 ATCGCAACACGATTTTCAACT
1 ATCGCAACGCGAAATGCAACA
*
91882 ATCGCAACGTGAAATAG-AA-A
1 ATCGCAACGCGAAAT-GCAACA
** * *
91902 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACA
91923 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
91943 GCGAATTTGC
Statistics
Matches: 76, Mismatches: 22, Indels: 9
0.71 0.21 0.08
Matches are distributed among these distances:
20 29 0.38
21 31 0.41
22 16 0.21
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACA
Found at i:96122 original size:15 final size:15
Alignment explanation
Indices: 96102--96133 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
96092 GATCAATACC
96102 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
96117 TTTTGCATACATTCA
1 TTTTGCATACATGCA
96132 TT
1 TT
96134 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:99936 original size:17 final size:19
Alignment explanation
Indices: 99909--99944 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
99899 AGATGGCAAT
99909 CATTCTTTACATTT-TTTA
1 CATTCTTTACATTTATTTA
99927 CATT-TTTACATTTATTTA
1 CATTCTTTACATTTATTTA
99945 TTTCATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.25, C:0.14, G:0.00, T:0.61
Consensus pattern (19 bp):
CATTCTTTACATTTATTTA
Found at i:103490 original size:7 final size:6
Alignment explanation
Indices: 103464--103548 Score: 77
Period size: 7 Copynumber: 13.7 Consensus size: 6
103454 CTTGAAGAAA
* *
103464 AAAAAG AAAAAG -AAAAG AAAAAGG AAAAA- AAAAGAG AAGAAG AATAAG
1 AAAAAG AAAAAG AAAAAG AAAAA-G AAAAAG AAAA-AG AAAAAG AAAAAG
103512 AAAAAAG AAAAAAG AAAAAAG AAAAAAG AAAAA- AAAA
1 -AAAAAG -AAAAAG -AAAAAG -AAAAAG AAAAAG AAAA
103549 GAGGAGGTCA
Statistics
Matches: 71, Mismatches: 3, Indels: 11
0.84 0.04 0.13
Matches are distributed among these distances:
5 13 0.18
6 23 0.32
7 35 0.49
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:103493 original size:14 final size:14
Alignment explanation
Indices: 103463--103545 Score: 93
Period size: 14 Copynumber: 5.9 Consensus size: 14
103453 GCTTGAAGAA
103463 AAAAAAG-AAAAAG
1 AAAAAAGAAAAAAG
*
103476 --AAAAGAAAAAGG
1 AAAAAAGAAAAAAG
103488 AAAAAA-AAAGAGAAG
1 AAAAAAGAAA-A-AAG
103503 AAGAATAAGAAAAAAG
1 AA-AA-AAGAAAAAAG
103519 AAAAAAGAAAAAAG
1 AAAAAAGAAAAAAG
103533 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
103546 AAAGAGGAGG
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
11 5 0.08
12 5 0.08
13 3 0.05
14 28 0.47
15 6 0.10
16 7 0.12
17 3 0.05
18 3 0.05
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (14 bp):
AAAAAAGAAAAAAG
Found at i:104475 original size:114 final size:114
Alignment explanation
Indices: 104270--104494 Score: 378
Period size: 114 Copynumber: 2.0 Consensus size: 114
104260 TGCCACGTTA
*
104270 TCATGGTAGAAATAAGGAGGCCCAATAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGGCCCAATAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* * *
104335 TTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTGC
66 TTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGC
* *
104384 TCATAGTAGAAATAAGGAGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGGCCCAATAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* *
104449 TTCGGTAGGAACTCCAGAACCAATCATTAGAATTGAAAGATGAATT
66 TTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATT
104495 GCATGACCGT
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (114 bp):
TCATAGTAGAAATAAGGAGGCCCAATAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
TTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGC
Found at i:105301 original size:20 final size:20
Alignment explanation
Indices: 105237--105302 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
105227 TTCCAGAGAA
105237 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* * **
105257 CG-TC-TAAAGAAGGAAGAAGA
1 AGTTCATAATG-A-GAAGAACT
105277 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
105297 TGTTCA
1 AGTTCA
105303 ACTTTTTGCT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
18 4 0.12
19 3 0.09
20 19 0.58
21 3 0.09
22 4 0.12
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.23
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:105373 original size:101 final size:107
Alignment explanation
Indices: 105236--105526 Score: 382
Period size: 101 Copynumber: 2.7 Consensus size: 107
105226 TTTCCAGAGA
* *
105236 AAGTTCATAATGAGAAGAACTCGTCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
105301 CAACTTTTTGCTTGAATT-CA-TC-A-GCATTTCCAG-GTC-G
66 CAACCTTTTGCTTGAATTCCATTCGATGCATTACC-GTGTCAG
* *
105338 -AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACCTATT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * *
105402 CAACCTTTTGCTCGAATTCACCATTCGATGGATTAGCGTTGTCAG
66 CAACCTTTTGCTTGAATT--CCATTCGATGCATTACCG-TGTCAG
* *
105447 AAGGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGT
1 AA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
105511 TCAACCTTTTGCTTGA
65 TCAACCTTTTGCTTGA
105527 CTCTATCACA
Statistics
Matches: 164, Mismatches: 14, Indels: 14
0.85 0.07 0.07
Matches are distributed among these distances:
101 76 0.46
104 2 0.01
105 2 0.01
106 2 0.01
107 5 0.03
108 3 0.02
109 1 0.01
110 46 0.28
111 27 0.16
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (107 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTTTGCTTGAATTCCATTCGATGCATTACCGTGTCAG
Found at i:105751 original size:236 final size:234
Alignment explanation
Indices: 105325--105758 Score: 699
Period size: 236 Copynumber: 1.8 Consensus size: 234
105315 AATTCATCAG
* * *
105325 CATTTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAATTCATAATGA
* * * *
105390 GAAGAACCTATTCAACCTTTTGCTCGAATTCACCATTCGATGGATTAGCGTTGTCAGAAGGTTCA
66 GAAGAACCTAGTCAACCTTTTGCTCGAATTCACCATTCGATGGATCAACGTTGTCAGAAAGTTCA
105455 TAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
131 TAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
105520 TGCTTGACTCTATCACATAAGAAGATAGATCAGCATTAA
196 TGCTTGACTCTATCACATAAGAAGATAGATCAGCATTAA
*
105559 CATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAATTCATAATGA
1 CATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAATTCATAATGA
** * * * * *
105624 GAAGAATTTGGTCAAACCTTTTGTTTGAATTCATCATTCGATGGATCAAC-TTTTCCAGAGAAGT
66 GAAGAACCTAGTC-AACCTTTTGCTCGAATTCACCATTCGATGGATCAACGTTGT-CAGA-AAGT
105688 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACC
128 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACC
105753 TTTTGC
193 TTTTGC
105759 ATAAGGAGAT
Statistics
Matches: 182, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
234 73 0.40
235 35 0.19
236 74 0.41
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (234 bp):
CATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAATTCATAATGA
GAAGAACCTAGTCAACCTTTTGCTCGAATTCACCATTCGATGGATCAACGTTGTCAGAAAGTTCA
TAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
TGCTTGACTCTATCACATAAGAAGATAGATCAGCATTAA
Found at i:106077 original size:3 final size:3
Alignment explanation
Indices: 106071--106140 Score: 67
Period size: 3 Copynumber: 24.0 Consensus size: 3
106061 ATCCATTTTT
* *
106071 TTA TTA TTA TT- TT- TTA TTTA ATA TTA TTA ATA TTA TT- TTA TTTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
106115 TTA TTA TTA TTA TTA -TA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
106141 ATAAATATTA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 8 0.14
3 42 0.75
4 6 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:106084 original size:14 final size:14
Alignment explanation
Indices: 106065--106122 Score: 57
Period size: 13 Copynumber: 4.2 Consensus size: 14
106055 ATTTTTATCC
106065 ATTTTTTTATTATT
1 ATTTTTTTATTATT
*
106079 A-TTTTTTATT-TA
1 ATTTTTTTATTATT
* * *
106091 ATATTATTAATATT
1 ATTTTTTTATTATT
106105 ATTTTATTTATTATT
1 ATTTT-TTTATTATT
106120 ATT
1 ATT
106123 ATTATTATAT
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
12 2 0.06
13 15 0.45
14 6 0.18
15 10 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTTTTTATTATT
Found at i:106114 original size:24 final size:24
Alignment explanation
Indices: 106071--106153 Score: 96
Period size: 24 Copynumber: 3.4 Consensus size: 24
106061 ATCCATTTTT
106071 TTATTATTATT-TTTTATTTAATA
1 TTATTATTATTATTTTATTTAATA
* *
106094 TTATTAATATTATTTTATTTATTA
1 TTATTATTATTATTTTATTTAATA
*
106118 TTATTATTATTATATTTTTATTAATAA
1 TTATTATTATTAT-TTTAT-TTAAT-A
*
106145 ATATTATTA
1 TTATTATTA
106154 CAAACATGCC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
23 10 0.20
24 23 0.46
25 4 0.08
26 4 0.08
27 9 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATTATTATTATTTTATTTAATA
Found at i:106139 original size:41 final size:40
Alignment explanation
Indices: 106065--106143 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
106055 ATTTTTATCC
*
106065 ATTTTTTTATTATTATTTTTTATTTAATATTATTAATATT
1 ATTTTTTTATTATTATTTATTATTTAATATTATTAATATT
* *
106105 ATTTTATTTATTATTA-TTATTATTATATTTTTATTAATA
1 ATTTT-TTTATTATTATTTATTATT-TAATATTATTAATA
106144 AATATTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 12 0.35
41 22 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (40 bp):
ATTTTTTTATTATTATTTATTATTTAATATTATTAATATT
Found at i:106151 original size:21 final size:21
Alignment explanation
Indices: 106092--106143 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
106082 TTTTATTTAA
*
106092 TATTATTAATATTATTTTATT
1 TATTATTAATATTATTATATT
*
106113 TATTATTATTATTATTATATT
1 TATTATTAATATTATTATATT
106134 T-TTATTAATA
1 TATTATTAATA
106144 AATATTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTATTAATATTATTATATT
Found at i:109140 original size:19 final size:19
Alignment explanation
Indices: 109099--109156 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
109089 ACGTTTTTAT
109099 ATTTAATAATATTTATT-A
1 ATTTAATAATATTTATTAA
*
109117 A--TAATAAT-TTTTTTAA
1 ATTTAATAATATTTATTAA
109133 TATTTAATAATATTTATTAA
1 -ATTTAATAATATTTATTAA
109153 ATTT
1 ATTT
109157 TAAAATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
15 5 0.15
16 8 0.24
17 1 0.03
18 1 0.03
19 11 0.33
20 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTAATAATATTTATTAA
Found at i:109142 original size:22 final size:21
Alignment explanation
Indices: 109114--109174 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
109104 ATAATATTTA
*
109114 TTAATAATAATTTTTTTAATAT
1 TTAATAATAATTTTTTAAAT-T
*
109136 TTAATAAT-ATTTATTAAATT
1 TTAATAATAATTTTTTAAATT
109156 TTAA-AATTAATTTTTTAAA
1 TTAATAA-TAATTTTTTAAA
109175 AATATTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 2 0.06
20 6 0.18
21 18 0.53
22 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAATAATAATTTTTTAAATT
Found at i:109816 original size:11 final size:10
Alignment explanation
Indices: 109769--109832 Score: 58
Period size: 10 Copynumber: 6.1 Consensus size: 10
109759 CTTTACATTA
109769 TATTTTTATT
1 TATTTTTATT
* *
109779 GAATTTTATT
1 TATTTTTATT
*
109789 CATTTTTAATT
1 TATTTTT-ATT
109800 CT-TTTTTATT
1 -TATTTTTATT
109810 GTATTTTTATT
1 -TATTTTTATT
109821 TATTTTATATT
1 TATTTT-TATT
109832 T
1 T
109833 TTTATAATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
10 23 0.52
11 21 0.48
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (10 bp):
TATTTTTATT
Found at i:109826 original size:21 final size:20
Alignment explanation
Indices: 109769--109832 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
109759 CTTTACATTA
* *
109769 TATTTTTATTGAATTTTATT
1 TATTTTTATTTATTTTTATT
*
109789 CATTTTTAATTCT-TTTTTATT
1 TATTTTT-ATT-TATTTTTATT
109810 GTATTTTTATTTATTTTATATT
1 -TATTTTTATTTATTTT-TATT
109832 T
1 T
109833 TTTATAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
20 7 0.20
21 18 0.51
22 10 0.29
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (20 bp):
TATTTTTATTTATTTTTATT
Found at i:109827 original size:31 final size:31
Alignment explanation
Indices: 109771--109835 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
109761 TTACATTATA
109771 TTTTTATTGAATTTTATTCATTTTTA-ATTCT
1 TTTTTATTGAATTTTATTCATTTTTATATT-T
* *
109802 TTTTTATTGTATTTTTATTTA-TTTTATATTT
1 TTTTTATTG-AATTTTATTCATTTTTATATTT
109833 TTT
1 TTT
109836 ATAATTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 18 0.60
32 12 0.40
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (31 bp):
TTTTTATTGAATTTTATTCATTTTTATATTT
Found at i:110261 original size:22 final size:20
Alignment explanation
Indices: 110221--110261 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
110211 TAATATATTT
*
110221 CTAAATAAAAAAAATTAAAG
1 CTAAACAAAAAAAATTAAAG
110241 CTAAACAAAAAGATAATTAAA
1 CTAAACAAAAA-A-AATTAAA
110262 ATCGAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (20 bp):
CTAAACAAAAAAAATTAAAG
Found at i:111517 original size:2 final size:2
Alignment explanation
Indices: 111504--111561 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
111494 ACATTTATGC
*
111504 AG AG AC AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
111546 AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG
111562 TTGGTGACAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:111854 original size:21 final size:21
Alignment explanation
Indices: 111828--111905 Score: 113
Period size: 21 Copynumber: 3.7 Consensus size: 21
111818 GTTTCCAGAT
*
111828 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
111849 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
111870 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
111891 TCGCAATGCGAACTT
1 TCGCAATGCGAACTT
111906 GGTAATGCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
20 1 0.02
21 48 0.96
22 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:111958 original size:21 final size:21
Alignment explanation
Indices: 111911--111986 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
111901 AACTTGGTAA
111911 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCCAAGTTCGCAT
* * *
111932 TACGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCAT
* *
111953 TGCGATTTATTCCAAATTCG--T
1 TGCGA--TAGTCCAAGTTCGCAT
111974 TGCGATAGTCCAA
1 TGCGATAGTCCAA
111987 AATCGCAACG
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 7 0.16
21 28 0.62
23 10 0.22
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (21 bp):
TGCGATAGTCCAAGTTCGCAT
Found at i:112087 original size:6 final size:6
Alignment explanation
Indices: 112076--112100 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
112066 GACACGAATT
112076 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
112101 GACGAGACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:112744 original size:23 final size:20
Alignment explanation
Indices: 112693--112779 Score: 61
Period size: 21 Copynumber: 4.2 Consensus size: 20
112683 TACCGTCGTT
* *
112693 GCGATTTTGGACTATCGCAA
1 GCGAATTTGGAATATCGCAA
*
112713 -CGAACTTGGAATAAATCGCAA
1 GCGAATTTGGAAT--ATCGCAA
*
112734 CGCGAATTTGGACTATCGCAA
1 -GCGAATTTGGAATATCGCAA
* *
112755 TGCGAATATGTAA-ATCGCAA
1 -GCGAATTTGGAATATCGCAA
112775 TGCGA
1 -GCGA
112780 TAGTCGAAGT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
19 9 0.17
20 12 0.22
21 23 0.43
23 10 0.19
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (20 bp):
GCGAATTTGGAATATCGCAA
Found at i:112751 original size:21 final size:20
Alignment explanation
Indices: 112693--112761 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 20
112683 TACCGTCGTT
*
112693 GCGATTTTGGACTATCGCAA
1 GCGAATTTGGACTATCGCAA
* *
112713 -CGAACTTGGAATAAATCGCAA
1 GCGAATTTGGACT--ATCGCAA
112734 CGCGAATTTGGACTATCGCAA
1 -GCGAATTTGGACTATCGCAA
112755 TGCGAAT
1 -GCGAAT
112762 ATGTAAATCG
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
19 9 0.23
21 20 0.51
23 10 0.26
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (20 bp):
GCGAATTTGGACTATCGCAA
Found at i:112773 original size:20 final size:20
Alignment explanation
Indices: 112724--112779 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
112714 GAACTTGGAA
* *
112724 TAAATCGCAACGCGAATTTG
1 TAAATCGCAATGCGAATATG
* *
112744 GACTATCGCAATGCGAATATG
1 TA-AATCGCAATGCGAATATG
112765 TAAATCGCAATGCGA
1 TAAATCGCAATGCGA
112780 TAGTCGAAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (20 bp):
TAAATCGCAATGCGAATATG
Found at i:113923 original size:2 final size:2
Alignment explanation
Indices: 113916--113949 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
113906 ACCTTTCATT
113916 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
113950 AAGATAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:114607 original size:78 final size:79
Alignment explanation
Indices: 114468--114626 Score: 223
Period size: 78 Copynumber: 2.0 Consensus size: 79
114458 ATAAAAAAAT
* *
114468 AATATTTTAAGTAACGTCTAATATTAATATTTTTTGTAAAAAAAATAATATTTTAAGTAGCGTTT
1 AATATTTTAAGTAACGTCTAATATTAACATTTTATGTAAAAAAAATAATATTTTAAGTAGCGTTT
*
114533 TATCAAAAATATTA
66 TACCAAAAATATTA
* * * *
114547 AATATTTTAGGTAGCGTTTAATATTAACATTTTCAT-T-AAAAAAATATTATTTTAAGTAGCGTT
1 AATATTTTAAGTAACGTCTAATATTAACATTTT-ATGTAAAAAAAATAATATTTTAAGTAGCGTT
*
114610 TTACCAGAAATATTA
65 TTACCAAAAATATTA
114625 AA
1 AA
114627 AAAATATTAA
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
78 40 0.56
79 30 0.42
80 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (79 bp):
AATATTTTAAGTAACGTCTAATATTAACATTTTATGTAAAAAAAATAATATTTTAAGTAGCGTTT
TACCAAAAATATTA
Found at i:118320 original size:3 final size:3
Alignment explanation
Indices: 118308--118391 Score: 134
Period size: 3 Copynumber: 28.3 Consensus size: 3
118298 TCCTACTATC
118308 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
118355 ATT ATT ATT ATT ATT ATT ATT ATC ATC ATC ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
118392 ATACAATATA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 2 0.03
3 76 0.97
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:118451 original size:22 final size:22
Alignment explanation
Indices: 118423--118466 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
118413 TCTGTAAGCT
*
118423 TGTACAAGACCCAAGGTCCAAA
1 TGTACAAGACCCAAGGCCCAAA
118445 TGTACAAGACCCAAGGCCCAAA
1 TGTACAAGACCCAAGGCCCAAA
118467 AAATTTGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.30, G:0.18, T:0.11
Consensus pattern (22 bp):
TGTACAAGACCCAAGGCCCAAA
Found at i:119354 original size:20 final size:20
Alignment explanation
Indices: 119307--119354 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
119297 AATGTCATTT
*
119307 GTGTATCCGTACACTGAGGA
1 GTGTATCGGTACACTGAGGA
119327 GTGTATCGGTACACTGAGGA
1 GTGTATCGGTACACTGAGGA
119347 GTGTATCG
1 GTGTATCG
119355 ATACCCTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (20 bp):
GTGTATCGGTACACTGAGGA
Found at i:119382 original size:75 final size:75
Alignment explanation
Indices: 119251--119413 Score: 272
Period size: 75 Copynumber: 2.2 Consensus size: 75
119241 AGATGTTCAA
119251 AGTGTATCGATACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGTCATTTGTGTATCCG
1 AGTGTATCGATACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGTCATTTGTGTATCCG
119316 TACACTGAGG
66 TACACTGAGG
* * * *
119326 AGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAGTGTTATTTGTGTATCGG
1 AGTGTATCGATACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGTCATTTGTGTATCCG
*
119391 TACACTGGGG
66 TACACTGAGG
*
119401 AGTATATCGATAC
1 AGTGTATCGATAC
119414 CCCCAAGTAT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 81 1.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (75 bp):
AGTGTATCGATACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGTCATTTGTGTATCCG
TACACTGAGG
Found at i:123337 original size:64 final size:64
Alignment explanation
Indices: 123251--123412 Score: 211
Period size: 64 Copynumber: 2.5 Consensus size: 64
123241 CGGTGCACCA
*
123251 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
123315 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
123380 AGAGTGCATCGGTGCATGGAATGCA-TCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
123413 CAATTAATTC
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
63 2 0.02
64 43 0.51
65 39 0.46
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:123385 original size:19 final size:19
Alignment explanation
Indices: 123361--123410 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
123351 GAAAATATTC
123361 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
123380 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
123399 A-A-TGCATCGATG
1 AGAGTGCATCGATG
123411 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.31
18 1 0.03
19 19 0.66
ACGTcount: A:0.26, C:0.16, G:0.36, T:0.22
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:130825 original size:64 final size:64
Alignment explanation
Indices: 130739--130901 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
130729 CAGTGCACCA
*
130739 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
130803 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
130868 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
130902 CAATTAATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 39 0.46
65 46 0.54
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:130873 original size:19 final size:19
Alignment explanation
Indices: 130849--130899 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
130839 GAAAATATTC
130849 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
130868 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
130887 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
130900 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:130941 original size:65 final size:65
Alignment explanation
Indices: 130743--130950 Score: 207
Period size: 65 Copynumber: 3.2 Consensus size: 65
130733 GCACCAAGTG
* * ** *
130743 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTT
1 TGCATCGGTGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-T
130806 G-
64 GA
* * *
130807 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
130870 A
65 A
* *
130871 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGA
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGA
130933 CTGA
62 CTGA
130937 TGCATCGGTGCATG
1 TGCATCGGTGCATG
130951 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 10, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
62 3 0.02
63 8 0.06
64 51 0.41
65 60 0.48
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (65 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA
Found at i:132693 original size:2 final size:2
Alignment explanation
Indices: 132686--132723 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
132676 TGCATATCTA
132686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
132724 TGACGTGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:133756 original size:2 final size:2
Alignment explanation
Indices: 133749--133800 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
133739 ATCTAACATG
133749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
133791 AT AT AT AT AT
1 AT AT AT AT AT
133801 GAATTGACGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:134304 original size:21 final size:21
Alignment explanation
Indices: 134278--134317 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
134268 AATATTTTAT
*
134278 TTTTAAATTATAA-AAATAATA
1 TTTT-AATAATAATAAATAATA
134299 TTTTAATAATAATAAATAA
1 TTTTAATAATAATAAATAA
134318 AGTACTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTTAATAATAATAAATAATA
Found at i:138599 original size:18 final size:18
Alignment explanation
Indices: 138565--138604 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
138555 ATTTGATATG
*
138565 TTTTTCATTTCATTTTTA
1 TTTTTCATTTAATTTTTA
138583 TTTTT-ATTTAATATTTTA
1 TTTTTCATTTAAT-TTTTA
138601 TTTT
1 TTTT
138605 AAGATGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTCATTTAATTTTTA
Found at i:142192 original size:2 final size:2
Alignment explanation
Indices: 142185--142217 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
142175 ACATGTCGTG
142185 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
142218 CGACCATCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:143261 original size:32 final size:32
Alignment explanation
Indices: 143188--143272 Score: 111
Period size: 31 Copynumber: 2.7 Consensus size: 32
143178 AGAGTCGAGG
* *
143188 GTTACCTATGT-CTTTCGAGACATATGGATAGT
1 GTTACCTATGTCCTTT-GGGACATATGGACAGT
*
143220 -TTACCTATGTCCTTTGGGATATATGGACAGT
1 GTTACCTATGTCCTTTGGGACATATGGACAGT
*
143251 GTTACCTATGTCCTTCGGGACA
1 GTTACCTATGTCCTTTGGGACA
143273 AATGCATAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
31 23 0.50
32 23 0.50
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (32 bp):
GTTACCTATGTCCTTTGGGACATATGGACAGT
Found at i:143440 original size:2 final size:2
Alignment explanation
Indices: 143433--143476 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
143423 AATGTATGTA
143433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
143475 AT
1 AT
143477 GATGTGTGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:146866 original size:37 final size:39
Alignment explanation
Indices: 146788--146867 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 39
146778 AACAAGTTGA
* *
146788 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAATATTTATATATTTTCTTTAAAAAATTGAAAATCAT
*
146827 AAAAT-TTATATATATTTT-TTTACAAAATTGAAAAT-AT
1 AAAATATT-TATATATTTTCTTTAAAAAATTGAAAATCAT
146864 AAAA
1 AAAA
146868 AGATTTAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 6 0.16
38 16 0.43
39 15 0.41
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (39 bp):
AAAATATTTATATATTTTCTTTAAAAAATTGAAAATCAT
Found at i:148278 original size:16 final size:16
Alignment explanation
Indices: 148257--148289 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
148247 TAATAAATAG
148257 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
148273 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
148289 A
1 A
148290 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:148370 original size:10 final size:10
Alignment explanation
Indices: 148355--148429 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
148345 CATTTAATAA
148355 ATAAACGAAC
1 ATAAACGAAC
148365 ATAAACGAAC
1 ATAAACGAAC
148375 ----ACGAAC
1 ATAAACGAAC
148381 ATAAACGAAC
1 ATAAACGAAC
** *
148391 ACGAAC-ATAA
1 ATAAACGA-AC
148401 ATGAACACGAAC
1 AT-AA-ACGAAC
148413 ATAAACGAAC
1 ATAAACGAAC
148423 ATAAACG
1 ATAAACG
148430 TTAGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:148380 original size:16 final size:16
Alignment explanation
Indices: 148359--148423 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
148349 TAATAAATAA
148359 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
148375 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
148391 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
148407 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
148423 A
1 A
148424 TAAACGTTAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:149196 original size:14 final size:14
Alignment explanation
Indices: 149179--149224 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
149169 AATGAACATA
*
149179 AACGAACATAATCG
1 AACGAACATAAACG
149193 AACGAACATAAACG
1 AACGAACATAAACG
*
149207 AACGAACATAACCG
1 AACGAACATAAACG
149221 AACG
1 AACG
149225 TTCACGAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.52, C:0.24, G:0.15, T:0.09
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:149199 original size:24 final size:24
Alignment explanation
Indices: 149159--149209 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
149149 GATTGGGTTA
*
149159 AACATAAATGAATGAACATAAACG
1 AACATAAATGAACGAACATAAACG
149183 AACAT-AATCGAACGAACATAAACG
1 AACATAAAT-GAACGAACATAAACG
149207 AAC
1 AAC
149210 GAACATAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.57, C:0.18, G:0.12, T:0.14
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:149670 original size:15 final size:15
Alignment explanation
Indices: 149650--149679 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
149640 TTCCAATTCG
149650 AATAAAATCCCTAAA
1 AATAAAATCCCTAAA
149665 AATAAAATCCCTAAA
1 AATAAAATCCCTAAA
149680 TCTCATTTAC
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:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (15 bp):
AATAAAATCCCTAAA
Found at i:151520 original size:18 final size:19
Alignment explanation
Indices: 151497--151539 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
151487 CAGTAATCCT
151497 ATTCC-CTGGCAATCTTAC
1 ATTCCACTGGCAATCTTAC
*
151515 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGCAATCTTAC
151535 ATTCC
1 ATTCC
151540 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.23, C:0.33, G:0.09, T:0.35
Consensus pattern (19 bp):
ATTCCACTGGCAATCTTAC
Found at i:151530 original size:20 final size:20
Alignment explanation
Indices: 151502--151539 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
151492 ATCCTATTCC
151502 CTGGCAATCTTACATTCCCA
1 CTGGCAATCTTACATTCCCA
*
151522 CTGGTAATCTTACATTCC
1 CTGGCAATCTTACATTCC
151540 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.32, G:0.11, T:0.34
Consensus pattern (20 bp):
CTGGCAATCTTACATTCCCA
Found at i:154627 original size:27 final size:24
Alignment explanation
Indices: 154596--154650 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
154586 GTTAGATTAT
*
154596 ATTTGAATTTAGTATAAAAAATATATG
1 ATTTG-ATTTA-TATAAAAAA-ATATA
*
154623 ATTTGATTTATTTAAAAAAATATA
1 ATTTGATTTATATAAAAAAATATA
154647 ATTT
1 ATTT
154651 TATCTTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 8 0.31
25 8 0.31
26 5 0.19
27 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (24 bp):
ATTTGATTTATATAAAAAAATATA
Found at i:158646 original size:2 final size:2
Alignment explanation
Indices: 158639--158666 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
158629 ACTAAACACC
158639 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
158667 GAAGAAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:159190 original size:19 final size:19
Alignment explanation
Indices: 159166--159203 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
159156 CATATACTCA
159166 CCATGCAGACGAGCCATAC
1 CCATGCAGACGAGCCATAC
159185 CCATGCAGACGAGCCATAC
1 CCATGCAGACGAGCCATAC
159204 AAGCCATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.37, G:0.21, T:0.11
Consensus pattern (19 bp):
CCATGCAGACGAGCCATAC
Found at i:159262 original size:32 final size:32
Alignment explanation
Indices: 159218--159288 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
159208 CATATACTCA
* *
159218 CCATGCAGACGAGCCAGCCAACGGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
*
159250 CCATGCAAACGAGCCAGCCAATAGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
159282 CCATGCA
1 CCATGCA
159289 GTCTGGGCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.31, C:0.31, G:0.30, T:0.08
Consensus pattern (32 bp):
CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
Found at i:159320 original size:29 final size:29
Alignment explanation
Indices: 159276--159370 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
159266 GCCAATAGAG
* **
159276 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
159305 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
159334 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
159363 AGGTCGCC
1 AGGTCGCC
159371 CCGGCGGCCT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:159463 original size:49 final size:49
Alignment explanation
Indices: 159391--159505 Score: 177
Period size: 49 Copynumber: 2.4 Consensus size: 49
159381 CCCGAGACCA
159391 TGCATG-C-ACATGCA-GCCAAATAACTTCACGTGCTCCTGCT-CCCGC
1 TGCATGCCTACATGCATGCCAAATAACTTCACGTGCTCCTGCTCCCCGC
*
159436 TGCATGCCTGCATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCCGC
1 TGCATGCCTACATGCATGCCAA-ATAACTTCACGTGCTCCTGCTCCCCGC
159486 TGCATGCCTACA-GCATGCCA
1 TGCATGCCTACATGCATGCCA
159506 TGTGATCCTA
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
45 6 0.10
46 1 0.02
47 6 0.10
48 5 0.08
49 29 0.46
50 16 0.25
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (49 bp):
TGCATGCCTACATGCATGCCAAATAACTTCACGTGCTCCTGCTCCCCGC
Found at i:159738 original size:16 final size:18
Alignment explanation
Indices: 159717--159755 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
159707 GGAGATAAGG
*
159717 TAAATTTGTTTA-TATT-
1 TAAATTAGTTTATTATTA
159733 TAAATTAGTTTATTATTA
1 TAAATTAGTTTATTATTA
159751 TAAAT
1 TAAAT
159756 GTTAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAAATTAGTTTATTATTA
Found at i:160205 original size:28 final size:28
Alignment explanation
Indices: 160174--160227 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
160164 ATAATCTAAT
*
160174 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
160202 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
160228 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:160234 original size:28 final size:28
Alignment explanation
Indices: 160170--160234 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
160160 TTATATAATC
*
160170 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
160198 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
160226 TAATTTATA
1 TAATATATA
160235 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:160237 original size:21 final size:21
Alignment explanation
Indices: 160204--160252 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
160194 TTAATATAAT
160204 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
160225 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
160246 ATTAACT
1 A-TAACT
160253 AAATTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:160904 original size:30 final size:30
Alignment explanation
Indices: 160864--160973 Score: 175
Period size: 30 Copynumber: 3.7 Consensus size: 30
160854 TTTGGCGAGC
*
160864 TGGGCGTGCATGGAGGTCGTTGGCCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGACGTGCA
* *
160894 TGGCCGTGCATGGAGGTCGTTGGACGTGCC
1 TGGGCGTGCATGGAGGTCGTTGGACGTGCA
* *
160924 TGGGCATGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGACGTGCA
160954 TGGGCGTGCATGGAGGTCGT
1 TGGGCGTGCATGGAGGTCGT
160974 GGGGTAGGTC
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.11, C:0.19, G:0.46, T:0.24
Consensus pattern (30 bp):
TGGGCGTGCATGGAGGTCGTTGGACGTGCA
Found at i:161021 original size:29 final size:29
Alignment explanation
Indices: 160980--161091 Score: 206
Period size: 29 Copynumber: 3.9 Consensus size: 29
160970 TCGTGGGGTA
*
160980 GGTCGCAGGGCGTGCATGGCGACCTGGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
161009 GGTCGCCGGGCGTGCATGGCGACCTGGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
*
161038 GGTCGCCGGGCGTGCATGGCGACCTTGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
161067 GGTCGCCGGGCGTGCATGGCGACCT
1 GGTCGCCGGGCGTGCATGGCGACCT
161092 ACCCCCGGTA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.08, C:0.28, G:0.44, T:0.21
Consensus pattern (29 bp):
GGTCGCCGGGCGTGCATGGCGACCTGGTT
Found at i:168821 original size:42 final size:44
Alignment explanation
Indices: 168771--168865 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
168761 TTGTGCTTCA
*
168771 TGCATCGATACACC-T-AACAGTGCATCGATGCAT-CCTTGAATG
1 TGCATCGATACACCATGAA-AGTGCACCGATGCATGCCTTGAATG
* *
168813 TGTATCGATACACCATGAAGGTGCACCGATGCATGCCTTGAATG
1 TGCATCGATACACCATGAAAGTGCACCGATGCATGCCTTGAATG
168857 TGCATCGAT
1 TGCATCGAT
168866 GCACAAGGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 13 0.28
43 14 0.30
44 19 0.41
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.26
Consensus pattern (44 bp):
TGCATCGATACACCATGAAAGTGCACCGATGCATGCCTTGAATG
Done.