Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold142
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: 1427168
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 17476 characters in sequence are not A, C, G, or T
File 8 of 8
Found at i:1259812 original size:13 final size:13
Alignment explanation
Indices: 1259796--1259820 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1259786 ATATATAAAA
1259796 TATAAATATATAT
1 TATAAATATATAT
1259809 TATAAATATATA
1 TATAAATATATA
1259821 AATTTATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATAAATATATAT
Found at i:1261311 original size:23 final size:23
Alignment explanation
Indices: 1261285--1261329 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1261275 AATTTAAAAA
1261285 ATAAA-AAATTATAAATTAATTAG
1 ATAAATAAATT-TAAATTAATTAG
* *
1261308 ATAAATATATTTAAATTCATTA
1 ATAAATAAATTTAAATTAATTA
1261330 ATTTCATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
ATAAATAAATTTAAATTAATTAG
Found at i:1273809 original size:198 final size:195
Alignment explanation
Indices: 1273536--1273913 Score: 641
Period size: 198 Copynumber: 1.9 Consensus size: 195
1273526 AAGGGTTTAG
* *
1273536 AGTTAAAGAAAGGAAAAATTGCAAACTTTTCCCATAAAATTTTCTTGTGATGACTTTGCAAATTA
1 AGTTAAAGAAAGGAAAAATTGCAAACTTTTCCCATAAAATTTTCTTGTCATGACTTAGCAAATTA
*
1273601 TAGGAGCAACCACTCCAATTTTCTTGTGGTAAGGGTTTAAAAAAAATAATGTTATACTCAATTTC
66 TAGGAGCAACCACTCCAATTTTCTTGGGGTAAGGGTTT--AAAAAATAATGTTATACTCAATTTC
* *
1273666 TTCAAAAGAAATTTTTAGGTTCAAAATAATCCAAAGAAACCTATTATAGTTTGGTAACCAAGAAA
129 TTCAAAAGAAA-TTTTAGGTTCAAAATAATCCAAAGAAACCCATTATAATTTGGTAACCAAGAAA
1273731 ATA
193 ATA
1273734 AGTTAAAGAAAGGAAAAAATTGCAAACTTTTCCCATAAAA-TTTCTTGTCATGACTTAGCAAATT
1 AGTTAAAGAAAGG-AAAAATTGCAAACTTTTCCCATAAAATTTTCTTGTCATGACTTAGCAAATT
**
1273798 ATAGGAGCAACCACTCCAATTTTCTTGGGGTAAGGGTTTAAAAGTTAATGTTATACTCAATTTCT
65 ATAGGAGCAACCACTCCAATTTTCTTGGGGTAAGGGTTTAAAAAATAATGTTATACTCAATTTCT
*
1273863 TCAAAAGAAATTTTAGGTTTAAAATAATCCAAAGAAACCCATTATAATTTG
130 TCAAAAGAAATTTTAGGTTCAAAATAATCCAAAGAAACCCATTATAATTTG
1273914 ATGTGTAATA
Statistics
Matches: 171, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
195 38 0.22
196 34 0.20
198 73 0.43
199 26 0.15
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (195 bp):
AGTTAAAGAAAGGAAAAATTGCAAACTTTTCCCATAAAATTTTCTTGTCATGACTTAGCAAATTA
TAGGAGCAACCACTCCAATTTTCTTGGGGTAAGGGTTTAAAAAATAATGTTATACTCAATTTCTT
CAAAAGAAATTTTAGGTTCAAAATAATCCAAAGAAACCCATTATAATTTGGTAACCAAGAAAATA
Found at i:1276062 original size:12 final size:12
Alignment explanation
Indices: 1276041--1276097 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
1276031 TGGCAGTTGG
*
1276041 AAATAAATAAAT
1 AAATATATAAAT
1276053 AAATATATAAAT
1 AAATATATAAAT
* * *
1276065 AATTTTATATAT
1 AAATATATAAAT
* *
1276077 ATATATATATAT
1 AAATATATAAAT
*
1276089 ATATATATA
1 AAATATATA
1276098 TTATGCAGAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AAATATATAAAT
Found at i:1276075 original size:2 final size:2
Alignment explanation
Indices: 1276070--1276098 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1276060 TAAATAATTT
1276070 TA 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 TA T
1276099 TATGCAGATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1277104 original size:13 final size:13
Alignment explanation
Indices: 1277086--1277126 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1277076 ATTTAATAAT
1277086 TTATATATTTATA
1 TTATATATTTATA
1277099 TTATAT-TTTATA
1 TTATATATTTATA
*
1277111 TT-TTTATTTTATA
1 TTATATA-TTTATA
1277124 TTA
1 TTA
1277127 ATTATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
11 2 0.08
12 8 0.33
13 14 0.58
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATATATTTATA
Found at i:1277110 original size:20 final size:20
Alignment explanation
Indices: 1277085--1277125 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1277075 GATTTAATAA
1277085 TTTATATATTTATATTATAT
1 TTTATATATTTATATTATAT
* *
1277105 TTTATATTTTTATTTTATAT
1 TTTATATATTTATATTATAT
1277125 T
1 T
1277126 AATTATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATATATTTATATTATAT
Found at i:1277196 original size:24 final size:25
Alignment explanation
Indices: 1277161--1277249 Score: 80
Period size: 24 Copynumber: 3.6 Consensus size: 25
1277151 AAATTTTTTT
1277161 ATTTTTTT-AA-AAAATAATATATA
1 ATTTTTTTAAATAAAATAATATATA
*
1277184 ATTTTTTTAAA-AAAATAA-ATAGTT
1 ATTTTTTTAAATAAAATAATATA-TA
* *
1277208 ATTTTTTCAAATAAAA-AGATAAATA
1 ATTTTTTTAAATAAAATA-ATATATA
*
1277233 GTTTCTTTTAAATAAAA
1 ATTT-TTTTAAATAAAA
1277250 GAATTAAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
23 11 0.20
24 21 0.39
25 9 0.17
26 13 0.24
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (25 bp):
ATTTTTTTAAATAAAATAATATATA
Found at i:1277212 original size:21 final size:23
Alignment explanation
Indices: 1277165--1277212 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
1277155 TTTTTTATTT
*
1277165 TTTTAAAAAATAATATATAATT-
1 TTTTAAAAAATAATAAATAATTA
* *
1277187 TTTTTAAAAA-AATAAATAGTTA
1 TTTTAAAAAATAATAAATAATTA
1277209 TTTT
1 TTTT
1277213 TTCAAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTTAAAAAATAATAAATAATTA
Found at i:1277222 original size:28 final size:26
Alignment explanation
Indices: 1277191--1277259 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 26
1277181 ATAATTTTTT
*
1277191 TAAAAAAATAAATAGTTATTTTTTCAAA
1 TAAAAAAATAAATAGTT-TCTTTT-AAA
*
1277219 TAAAAAGATAAATAGTTTCTTTTAAA
1 TAAAAAAATAAATAGTTTCTTTTAAA
*
1277245 TAAAAGAATTAAATA
1 TAAAA-AAATAAATA
1277260 ATTAATTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 8 0.22
27 12 0.33
28 16 0.44
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (26 bp):
TAAAAAAATAAATAGTTTCTTTTAAA
Found at i:1277494 original size:23 final size:21
Alignment explanation
Indices: 1277442--1277483 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
1277432 AAAAAAATTA
1277442 ATATT-TATATTAAATATATC
1 ATATTATATATTAAATATATC
1277462 ATATTAATATATATAAATATAT
1 ATATT-ATATAT-TAAATATAT
1277484 TTTTATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
22 5 0.26
23 9 0.47
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATTATATATTAAATATATC
Found at i:1277898 original size:22 final size:22
Alignment explanation
Indices: 1277867--1277923 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
1277857 ATATAAATAA
*
1277867 AAATTTTTAAAT-TTAATCAGTT
1 AAATTATTAAATATTAAT-AGTT
* *
1277889 AAATTATTAATTATTAATATTT
1 AAATTATTAAATATTAATAGTT
1277911 AAATTA--AAATATT
1 AAATTATTAAATATT
1277924 TTTTAATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.20
22 19 0.63
23 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
AAATTATTAAATATTAATAGTT
Found at i:1277923 original size:27 final size:28
Alignment explanation
Indices: 1277887--1277942 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
1277877 ATTTAATCAG
* *
1277887 TTAAATTATTAATTATTAATA-TTTAAA
1 TTAAAATATTAATTAATAATATTTTAAA
**
1277914 TTAAAATATTTTTTAATAATATTTTAAA
1 TTAAAATATTAATTAATAATATTTTAAA
1277942 T
1 T
1277943 AATAAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTAAAATATTAATTAATAATATTTTAAA
Found at i:1279530 original size:17 final size:17
Alignment explanation
Indices: 1279499--1279574 Score: 57
Period size: 17 Copynumber: 4.4 Consensus size: 17
1279489 TAAACACGAT
*
1279499 ATATTTAAATATAATTA
1 ATATTTTAATATAATTA
*
1279516 ATATTTTAATTTAA-TA
1 ATATTTTAATATAATTA
*
1279532 TATATTATAAT-TACATTTA
1 -ATATTTTAATATA-A-TTA
* * *
1279551 AAATTTTTATATATTTA
1 ATATTTTAATATAATTA
1279568 ATATTTT
1 ATATTTT
1279575 TTATATTTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
16 4 0.09
17 31 0.67
18 7 0.15
19 4 0.09
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTTTAATATAATTA
Found at i:1279552 original size:45 final size:45
Alignment explanation
Indices: 1279501--1279592 Score: 107
Period size: 45 Copynumber: 2.0 Consensus size: 45
1279491 AACACGATAT
*
1279501 ATTTAAATATAATTA-ATATTTTA-ATTTAATATATATTATAATTAC
1 ATTTAAA-ATAATTATATATTTAATATTTAATATAT-TTATAATTAC
** **
1279546 ATTTAAAATTTTTATATATTTAATATTTTTTATATTTATAATTAC
1 ATTTAAAATAATTATATATTTAATATTTAATATATTTATAATTAC
1279591 AT
1 AT
1279593 AACTCATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
44 5 0.12
45 26 0.65
46 9 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.55
Consensus pattern (45 bp):
ATTTAAAATAATTATATATTTAATATTTAATATATTTATAATTAC
Found at i:1279579 original size:16 final size:17
Alignment explanation
Indices: 1279546--1279588 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
1279536 TTATAATTAC
1279546 ATTTAAAATTTTTATAT
1 ATTTAAAATTTTTATAT
*
1279563 ATTTAATATTTTT-TAT
1 ATTTAAAATTTTTATAT
*
1279579 ATTTATAATT
1 ATTTAAAATT
1279589 ACATAACTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTAAAATTTTTATAT
Found at i:1282685 original size:166 final size:168
Alignment explanation
Indices: 1282409--1282744 Score: 595
Period size: 166 Copynumber: 2.0 Consensus size: 168
1282399 CATTCATAAG
* * *
1282409 CATTCAGAAAGAAAAGAAGTACTTGAACGTCTAAGAGCGAAGAACTTTCTTTATTAGAGTGTTTT
1 CATTCAGAAAGAAAAGAAGTACTTGAACATCTAAGAGCGAAGAACTTTCATTATTAGAATGTTTT
*
1282474 AAAATTTAATAATCAAGACAGAGCAACATGCTAGAGTTTTAGGAGATTAACATGATAGGTTTATG
66 AAAATTTAATAATCAAGACAGAGCAACATGCTAGAGTTTTAGGAGATTAACATAATAGGTTTATG
* *
1282539 AAACATCAAAATTACGCCGAGGTGGTACCATGGCCCCT
131 AAACATCAAAATTACGCCAAGGTGGTACCATGCCCCCT
1282577 CATTCAGAAAGAAAAGAAGTACTTGAACATCTAAGAGCGAAGAACTTT-ATTATT-GAATGTTTT
1 CATTCAGAAAGAAAAGAAGTACTTGAACATCTAAGAGCGAAGAACTTTCATTATTAGAATGTTTT
1282640 AAAATTTAATAATCAAGACAGAGCAACATGCTAGAGTTTTAGGAGATTAACATAATAGGTTTATG
66 AAAATTTAATAATCAAGACAGAGCAACATGCTAGAGTTTTAGGAGATTAACATAATAGGTTTATG
*
1282705 AAACATCAAAATTATGCCAAGGTGGTACCATGCCCCCT
131 AAACATCAAAATTACGCCAAGGTGGTACCATGCCCCCT
1282743 CA
1 CA
1282745 CTACTCAAGA
Statistics
Matches: 161, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
166 109 0.68
167 5 0.03
168 47 0.29
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (168 bp):
CATTCAGAAAGAAAAGAAGTACTTGAACATCTAAGAGCGAAGAACTTTCATTATTAGAATGTTTT
AAAATTTAATAATCAAGACAGAGCAACATGCTAGAGTTTTAGGAGATTAACATAATAGGTTTATG
AAACATCAAAATTACGCCAAGGTGGTACCATGCCCCCT
Found at i:1294876 original size:2 final size:2
Alignment explanation
Indices: 1294869--1294929 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1294859 CAAACTCACA
1294869 AG AG AG 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
1294911 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
1294930 AGCGGCTACA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1306525 original size:27 final size:29
Alignment explanation
Indices: 1306481--1306536 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
1306471 AATGTATCAC
*
1306481 TAAATAAATATATGATAAAT-TTATGATTT
1 TAAATAAATATATCATAAATATTAT-ATTT
1306510 TAAA-AAATA-ATCATAAATATTATATTT
1 TAAATAAATATATCATAAATATTATATTT
1306537 ATATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 12 0.48
28 9 0.36
29 4 0.16
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (29 bp):
TAAATAAATATATCATAAATATTATATTT
Found at i:1307974 original size:26 final size:26
Alignment explanation
Indices: 1307874--1307969 Score: 122
Period size: 26 Copynumber: 3.7 Consensus size: 26
1307864 TAAAATTTTT
* *
1307874 AATAAAATTAAACTTTAGTAATCTCA
1 AATAAAATTAAATTTTATTAATCTCA
*
1307900 GATAAAATTAAATTTTATTAATCTCA
1 AATAAAATTAAATTTTATTAATCTCA
* * *
1307926 AATCAAGTTAAAGTTTATTAAT-TCTA
1 AATAAAATTAAATTTTATTAATCTC-A
1307952 AATAAAATTAAATTTTAT
1 AATAAAATTAAATTTTAT
1307970 CAATTTTATC
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
25 2 0.03
26 57 0.97
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (26 bp):
AATAAAATTAAATTTTATTAATCTCA
Found at i:1308082 original size:17 final size:18
Alignment explanation
Indices: 1308041--1308086 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
1308031 TTCTCTAAAT
1308041 TTATAAAAATTTTAAATAA
1 TTAT-AAAATTTTAAATAA
1308060 --ACTAAAATTTTAAA-AA
1 TTA-TAAAATTTTAAATAA
1308076 TTATAAAATTT
1 TTATAAAATTT
1308087 AAGATACCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
16 2 0.08
17 20 0.83
18 2 0.08
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TTATAAAATTTTAAATAA
Found at i:1308978 original size:14 final size:14
Alignment explanation
Indices: 1308961--1308993 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1308951 TAAACGTATG
1308961 ATATTATTTTTATT
1 ATATTATTTTTATT
1308975 ATATTATTTTTATT
1 ATATTATTTTTATT
1308989 -TATTA
1 ATATTA
1308994 AATATTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATATTATTTTTATT
Found at i:1311883 original size:2 final size:2
Alignment explanation
Indices: 1311878--1311910 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1311868 TTAAAAAAAT
1311878 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1311911 CTGACTACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1318344 original size:35 final size:35
Alignment explanation
Indices: 1318304--1318411 Score: 88
Period size: 35 Copynumber: 3.2 Consensus size: 35
1318294 GAATGATTGG
1318304 TGAGATGTCTTCATCAATGACTTAAATGATGAGAT
1 TGAGATGTCTTCATCAATGACTTAAATGATGAGAT
* *
1318339 TGAGATATGTTC--C--T-ACTTATAATGATG-G-T
1 TGAGATGTCTTCATCAATGACTTA-AATGATGAGAT
* *
1318368 TCGGGAGATGTCTTCATTAAGGA-TTAAATGATGAGAT
1 T---GAGATGTCTTCATCAATGACTTAAATGATGAGAT
1318405 TGAGATG
1 TGAGATG
1318412 ATTTTCAATG
Statistics
Matches: 56, Mismatches: 6, Indels: 23
0.66 0.07 0.27
Matches are distributed among these distances:
29 2 0.04
30 6 0.11
31 8 0.14
32 9 0.16
33 1 0.02
34 6 0.11
35 17 0.30
36 4 0.07
37 3 0.05
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.35
Consensus pattern (35 bp):
TGAGATGTCTTCATCAATGACTTAAATGATGAGAT
Found at i:1318670 original size:7 final size:7
Alignment explanation
Indices: 1318653--1318681 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1318643 TCGAATCGAA
1318653 TTAAA-T
1 TTAAATT
1318659 TTAAATT
1 TTAAATT
1318666 TTAAATT
1 TTAAATT
1318673 TTAAATT
1 TTAAATT
1318680 TT
1 TT
1318682 TTCGAATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.23
7 17 0.77
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTAAATT
Found at i:1320505 original size:26 final size:27
Alignment explanation
Indices: 1320484--1320542 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
1320474 ATAATTATTT
*
1320484 TAAA-ATTTTATAAAATAAAATTATAA
1 TAAATATTATATAAAATAAAATTATAA
1320510 TAAATTATTATATAAAATAAATATT-TAA
1 TAAA-TATTATATAAAATAAA-ATTATAA
1320538 TAAAT
1 TAAAT
1320543 TAAATAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.14
27 1 0.03
28 21 0.72
29 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
TAAATATTATATAAAATAAAATTATAA
Found at i:1320540 original size:16 final size:18
Alignment explanation
Indices: 1320508--1320555 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 18
1320498 ATAAAATTAT
1320508 AATAAAT-TATTATATAA
1 AATAAATATATTATATAA
1320525 AATAAATAT-TTA-ATAA
1 AATAAATATATTATATAA
*
1320541 ATTAAATA-ATTATAT
1 AATAAATATATTATAT
1320556 CACTATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 14 0.52
17 12 0.44
18 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATAAATATATTATATAA
Found at i:1320553 original size:46 final size:46
Alignment explanation
Indices: 1320486--1320593 Score: 111
Period size: 46 Copynumber: 2.4 Consensus size: 46
1320476 AATTATTTTA
*
1320486 AAATTT-T-ATAAAAT-AA-AATTATAATAAAT-TATTATATAAAAT
1 AAATTTATAATAAAATAAATAATTAT-ATAAATATAATATATAAAAT
* * * *
1320528 AAATATT-TAATAAATTAAATAATTATATCACTATAATATATTAAAT
1 AAAT-TTATAATAAAATAAATAATTATATAAATATAATATATAAAAT
1320574 AAATTTATAATAAAATAAAT
1 AAATTTATAATAAAATAAAT
1320594 TTTTAACCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
42 4 0.07
43 3 0.06
44 6 0.11
45 8 0.15
46 33 0.61
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (46 bp):
AAATTTATAATAAAATAAATAATTATATAAATATAATATATAAAAT
Found at i:1324515 original size:18 final size:19
Alignment explanation
Indices: 1324468--1324517 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
1324458 GATTTAATTT
* *
1324468 TATTTGAATTATTTTTTAA
1 TATTTAAATTATATTTTAA
* *
1324487 TAATAAAATTATATTTT-A
1 TATTTAAATTATATTTTAA
1324505 TATTTAAATTATA
1 TATTTAAATTATA
1324518 AATATATAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TATTTAAATTATATTTTAA
Found at i:1324673 original size:13 final size:13
Alignment explanation
Indices: 1324649--1324686 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
1324639 CATGAATAGT
1324649 TTAAATTTAAAATA
1 TTAAA-TTAAAATA
*
1324663 TTAAATTAAAATT
1 TTAAATTAAAATA
1324676 TTAAATTAAAA
1 TTAAATTAAAA
1324687 CTTTATAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 18 0.78
14 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TTAAATTAAAATA
Found at i:1324691 original size:13 final size:12
Alignment explanation
Indices: 1324648--1324691 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 12
1324638 TCATGAATAG
1324648 TTTAAATTTAAAA
1 TTTAAA-TTAAAA
1324661 TATTAAATTAAAA
1 T-TTAAATTAAAA
1324674 TTTTAAATTAAAA
1 -TTTAAATTAAAA
1324687 CTTTA
1 -TTTA
1324692 TAGATCGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 22 0.79
14 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (12 bp):
TTTAAATTAAAA
Found at i:1326484 original size:11 final size:12
Alignment explanation
Indices: 1326452--1326509 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 12
1326442 TTAAATATTA
*
1326452 AATATATAACTAT
1 AATA-ATAAATAT
1326465 AATAATAAAT-T
1 AATAATAAATAT
*
1326476 AATATTAAATAT
1 AATAATAAATAT
* *
1326488 AATAA-ATATTT
1 AATAATAAATAT
1326499 AATAA-AAATAT
1 AATAATAAATAT
1326510 TTACTAATCA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 23 0.62
12 10 0.27
13 4 0.11
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (12 bp):
AATAATAAATAT
Found at i:1326502 original size:31 final size:31
Alignment explanation
Indices: 1326430--1326504 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
1326420 GATTATATTA
* *
1326430 ATAATAAAAAATTTAAATATTAAATATATAACT
1 ATAATAATAAA-TT-AATATTAAATATATAAAT
1326463 ATAATAATAAATTAATATTAAATATAATAAAT
1 ATAATAATAAATTAATATTAAATAT-ATAAAT
*
1326495 AT-TTAATAAA
1 ATAATAATAAA
1326505 AATATTTACT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 19 0.50
32 9 0.24
33 10 0.26
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (31 bp):
ATAATAATAAATTAATATTAAATATATAAAT
Found at i:1330123 original size:21 final size:22
Alignment explanation
Indices: 1330099--1330145 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
1330089 AAAGTAATAA
*
1330099 ATTTATTTAAGAGTTAAAA-TT
1 ATTTATTTAAAAGTTAAAATTT
*
1330120 ATTTATTTAAAATTTAAAATTT
1 ATTTATTTAAAAGTTAAAATTT
1330142 ATTT
1 ATTT
1330146 TATATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
ATTTATTTAAAAGTTAAAATTT
Found at i:1330143 original size:18 final size:18
Alignment explanation
Indices: 1330097--1330156 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
1330087 AGAAAGTAAT
* *
1330097 AAATTTATTTAAGAGTTAA
1 AAATTTATTTAA-AATTTA
1330116 AATTATTTATTTAAAATTTA
1 AA--ATTTATTTAAAATTTA
* *
1330136 AAATTTATTTTATATTTA
1 AAATTTATTTAAAATTTA
1330154 AAA
1 AAA
1330157 AAATTTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 17 0.49
19 2 0.06
20 6 0.17
21 10 0.29
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
AAATTTATTTAAAATTTA
Found at i:1331078 original size:34 final size:34
Alignment explanation
Indices: 1331030--1331120 Score: 80
Period size: 34 Copynumber: 2.7 Consensus size: 34
1331020 TAAAATTTTA
* * *
1331030 TATTAATATTTTAAAATAAATATGTAATATAAA-T
1 TATTAAAATATTAAAATAAATAT-AAATATAAATT
* **
1331064 TATTAAAATATTAAATTTTATATAAATATAAATT
1 TATTAAAATATTAAAATAAATATAAATATAAATT
* *
1331098 TATT-AAATA-TGAAGTAAATATAA
1 TATTAAAATATTAAAATAAATATAA
1331121 TACGAATATA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
32 10 0.22
33 13 0.28
34 23 0.50
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (34 bp):
TATTAAAATATTAAAATAAATATAAATATAAATT
Found at i:1331090 original size:27 final size:24
Alignment explanation
Indices: 1331020--1331090 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 24
1331010 AAAAATTAAT
1331020 TAAAATTTTATATTAATATTTTAAAA
1 TAAAATTTTATA-TAA-ATTTTAAAA
* *
1331046 TAAATATGTAATATAAATTATTAAAA
1 TAAA-ATTTTATATAAATT-TTAAAA
1331072 TATTAAATTTTATATAAAT
1 TA--AAATTTTATATAAAT
1331091 ATAAATTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
25 3 0.08
26 15 0.41
27 17 0.46
28 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (24 bp):
TAAAATTTTATATAAATTTTAAAA
Found at i:1331106 original size:15 final size:15
Alignment explanation
Indices: 1331055--1331107 Score: 63
Period size: 15 Copynumber: 3.3 Consensus size: 15
1331045 ATAAATATGT
1331055 AATATAAA-TTATTAA
1 AATATAAATTTATT-A
1331070 AATATTAAATTTTATATA
1 AATA-TAAA-TTTAT-TA
1331088 AATATAAATTTATTA
1 AATATAAATTTATTA
1331103 AATAT
1 AATAT
1331108 GAAGTAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 11 0.32
16 9 0.26
17 4 0.12
18 9 0.26
19 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATAAATTTATTA
Found at i:1331912 original size:19 final size:19
Alignment explanation
Indices: 1331888--1331925 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1331878 GTTGATTCAC
1331888 TTTATTACTAATGCTAGAA
1 TTTATTACTAATGCTAGAA
1331907 TTTATTACTAATGCTAGAA
1 TTTATTACTAATGCTAGAA
1331926 GTTTTACTGT
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:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (19 bp):
TTTATTACTAATGCTAGAA
Found at i:1334161 original size:72 final size:72
Alignment explanation
Indices: 1332831--1334129 Score: 2141
Period size: 72 Copynumber: 18.0 Consensus size: 72
1332821 TTGCAACATC
* * **
1332831 ACTGGTCCTATCCCGTATTCTCT-AGGTAATTTAACTAATTTGAAATCTTTGTATTTATCCCATA
1 ACTGGTCCTATCCCGTCTTCTCTGA-GTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATA
1332895 ACCAAATT
65 ACCAAATT
* * * * * *
1332903 ACTGGTCGTATCCCGTCTTTTTTGAGTAATTTAACCCATTTGAAATCTTTGTACTTATCCTATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1332968 CCAAATT
66 CCAAATT
*
1332975 ACTGGTCCTATCCCGTTTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1333040 CCAAATT
66 CCAAATT
** * *
1333047 ACTGGTTTTATCCCGTCTTCTCTGAGTAATTTAACCAATTTAAAATCTTTGTATCTATCCCATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1333112 CCAAATT
66 CCAAATT
* * *
1333119 ATTGGTCCTATCCCATCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTATACCTATCCCATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1333184 CCAAATT
66 CCAAATT
* *
1333191 ACTGGTCATATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTATCTATCCCATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1333256 CCAAATT
66 CCAAATT
*
1333263 ATTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1333328 CCAAATT
66 CCAAATT
** * *
1333335 ACTGGTTTTATCCCATCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTATCTATCCCATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1333400 CCAAATT
66 CCAAATT
* *
1333407 ATTGGTCCTATTCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1333472 CCAAATT
66 CCAAATT
* *
1333479 ACTGGTCATATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTATCTATCCCATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1333544 CCAAATT
66 CCAAATT
*
1333551 ATTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
*
1333616 CCCAATT
66 CCAAATT
* *
1333623 ACTGGTCATATCCCGTCTTCTCTAAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
*
1333688 TCAAATT
66 CCAAATT
*
1333695 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTAAAATCTTTGTACCTATCCCATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1333760 CCAAATT
66 CCAAATT
1333767 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
*
1333832 CTAAATT
66 CCAAATT
* * *
1333839 ACTGGTCCTATCCCGTTTTCTTTGAGTAATTTAATCAATTTGAAATCTTTGTACCTATCCCATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1333904 CCAAATT
66 CCAAATT
* * *
1333911 ACTGGTCTTATCCCGTCTTATCTGAGTAATTTAACCAATTTGAAATTTTTGTACCTATCCCATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1333976 CCAAATT
66 CCAAATT
*
1333983 ACTGGTCCTATCCCGTCTTCTCTGAGTAGTTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
*
1334048 CTAAATT
66 CCAAATT
* * * **
1334055 ACTGGTCCTATCCCGTCTTCTCTGGGTAATTTAACCAATTTAAAATCTTTGGACCTATCTTATAA
1 ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
1334120 CCAAATT
66 CCAAATT
1334127 ACT
1 ACT
1334130 AATTCTGTCC
Statistics
Matches: 1139, Mismatches: 87, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
72 1138 1.00
73 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.38
Consensus pattern (72 bp):
ACTGGTCCTATCCCGTCTTCTCTGAGTAATTTAACCAATTTGAAATCTTTGTACCTATCCCATAA
CCAAATT
Found at i:1339880 original size:19 final size:19
Alignment explanation
Indices: 1339856--1339892 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1339846 TAAATTATAC
1339856 TATGGT-GGATGGCTATCTT
1 TATGGTAGG-TGGCTATCTT
1339875 TATGGTAGGTGGCTATCT
1 TATGGTAGGTGGCTATCT
1339893 CTAGTCAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.16, C:0.11, G:0.32, T:0.41
Consensus pattern (19 bp):
TATGGTAGGTGGCTATCTT
Found at i:1339970 original size:28 final size:28
Alignment explanation
Indices: 1339912--1339972 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1339902 AAATACCACA
* *
1339912 TTTGTATTTGTCAAATATGATGGTTTCT
1 TTTGTATTTATCAAATATGATAGTTTCT
*
1339940 TTTGTATTTATCAAATATGGTAGTTAT-T
1 TTTGTATTTATCAAATATGATAGTT-TCT
1339968 TTTGT
1 TTTGT
1339973 TTGTAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.23, C:0.05, G:0.16, T:0.56
Consensus pattern (28 bp):
TTTGTATTTATCAAATATGATAGTTTCT
Found at i:1339997 original size:24 final size:24
Alignment explanation
Indices: 1339969--1340014 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1339959 GTAGTTATTT
1339969 TTGTTTGTAAAAAATGGTGGCTTG
1 TTGTTTGTAAAAAATGGTGGCTTG
* * *
1339993 TTGTTTGTCAACATTGGTGGCT
1 TTGTTTGTAAAAAATGGTGGCT
1340015 AATTTTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.20, C:0.09, G:0.28, T:0.43
Consensus pattern (24 bp):
TTGTTTGTAAAAAATGGTGGCTTG
Found at i:1343692 original size:29 final size:29
Alignment explanation
Indices: 1343630--1343699 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
1343620 AGAGTTAAAT
* ***
1343630 TATTTATTAAAATTTAAATATTTATTTAA
1 TATTTATAAAAATTTAAATAAAAATTTAA
1343659 TATTTATAAAAATTTAAATAAAAATATTAA
1 TATTTATAAAAATTTAAATAAAAAT-TTAA
1343689 -ATTTA-AAAAAT
1 TATTTATAAAAAT
1343700 AATTTTAGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 6 0.17
29 26 0.72
30 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TATTTATAAAAATTTAAATAAAAATTTAA
Found at i:1343724 original size:21 final size:21
Alignment explanation
Indices: 1343693--1343744 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1343683 TATTAAATTT
*
1343693 AAAAAA-T-AATTTTAGTAAA
1 AAAAAATTAAATTTGAGTAAA
*
1343712 AAAAAATTAAATTTGATTAAA
1 AAAAAATTAAATTTGAGTAAA
1343733 AAATAAATTAAA
1 AAA-AAATTAAA
1343745 CATTAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 6 0.21
20 1 0.04
21 13 0.46
22 8 0.29
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAAAATTAAATTTGAGTAAA
Found at i:1343806 original size:25 final size:24
Alignment explanation
Indices: 1343778--1343825 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1343768 CTAGTCAGTC
1343778 TTAA-TTTATTATTATATAATATAAA
1 TTAATTTTA-TATTATAT-ATATAAA
*
1343803 TTAATTTTATATTTTATATATAA
1 TTAATTTTATATTATATATATAA
1343826 TGTAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 11 0.52
26 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTAATTTTATATTATATATATAAA
Found at i:1343959 original size:15 final size:14
Alignment explanation
Indices: 1343941--1343985 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
1343931 TAAAGATTAA
1343941 ATTTTAAAAATATAT
1 ATTTTAAAAA-ATAT
1343956 ATTTTTAAAAAATAT
1 A-TTTTAAAAAATAT
*
1343971 ATTATAAAAAA-AT
1 ATTTTAAAAAATAT
1343984 AT
1 AT
1343986 AGACGAGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 4 0.14
14 9 0.32
15 6 0.21
16 9 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATTTTAAAAAATAT
Found at i:1343986 original size:15 final size:15
Alignment explanation
Indices: 1343945--1343986 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1343935 GATTAAATTT
* *
1343945 TAAAAATATATATTT
1 TAAAAAAATATATTA
*
1343960 TTAAAAAATATATTA
1 TAAAAAAATATATTA
1343975 TAAAAAAATATA
1 TAAAAAAATATA
1343987 GACGAGCTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAAAAATATATTA
Found at i:1345364 original size:143 final size:142
Alignment explanation
Indices: 1345073--1345425 Score: 336
Period size: 143 Copynumber: 2.5 Consensus size: 142
1345063 TACTCTGAGT
* * *
1345073 AATTTAACCAATTTGAAACAGTTGGACCGAT-TCCGTAACCAAATTACTAGTCTTATCCATTTTA
1 AATTTAA-CAATTTGAAACAGTTGGACCTATCT-CATAACCAAATTACTA-TCCTATCCATTTTA
* * ** ** ** *
1345137 CTTTACTTAATTTAATTAATCTGAATTGGTTAAACCAATCTTATAACTAAATTACTAATTCTGTC
63 CTCTACTTAATTCAACCAATCTGAATTAATTAAACCAATCTTATAACTAAATTACTAAGCCTATC
**
1345202 CATTCTAATTTGGGT
128 CATTCTAATTTGGAC
* *
1345217 AATTTAATCAATTTGAAACAGTTGGATCTATCTCATAACCAAATTACTGATCCTATCTATTTT-C
1 AATTTAA-CAATTTGAAACAGTTGGACCTATCTCATAACCAAATTACT-ATCCTATCCATTTTAC
** * * *
1345281 TCTACTTAATTCAACCAATCTGAATTAATTGGACCTATCTTGTAA-TCAAATTTCTAAGCCTATC
64 TCTACTTAATTCAACCAATCTGAATTAATTAAACCAATCTTATAACT-AAATTACTAAGCCTATC
* *
1345345 CATTTTATTTTGGAC
128 CATTCTAATTTGGAC
* * * * * *
1345360 AATTTAACGAGTCT-AGAACAGTTGGGCCTATCTTATAACCAAATTACTAATCCTACCCTTTTTA
1 AATTTAAC-AATTTGA-AACAGTTGGACCTATCTCATAACCAAATTACT-ATCCTATCCATTTTA
1345424 CT
63 CT
1345426 TTATGTGATT
Statistics
Matches: 170, Mismatches: 33, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
142 3 0.02
143 110 0.65
144 55 0.32
145 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (142 bp):
AATTTAACAATTTGAAACAGTTGGACCTATCTCATAACCAAATTACTATCCTATCCATTTTACTC
TACTTAATTCAACCAATCTGAATTAATTAAACCAATCTTATAACTAAATTACTAAGCCTATCCAT
TCTAATTTGGAC
Found at i:1345912 original size:45 final size:45
Alignment explanation
Indices: 1345852--1345941 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
1345842 ATTGTTATTT
1345852 AATTTATCAAATTTGAACATTTTACACCTTGATTTAAATTTTTTA
1 AATTTATCAAATTTGAACATTTTACACCTTGATTTAAATTTTTTA
* *
1345897 AATTTATCAGATTTGAACATTTTACACCTTGATTTAAGTTTTTTA
1 AATTTATCAAATTTGAACATTTTACACCTTGATTTAAATTTTTTA
1345942 TCTAGTTACA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (45 bp):
AATTTATCAAATTTGAACATTTTACACCTTGATTTAAATTTTTTA
Found at i:1346970 original size:206 final size:204
Alignment explanation
Indices: 1345938--1346968 Score: 1325
Period size: 204 Copynumber: 5.0 Consensus size: 204
1345928 ATTTAAGTTT
* ** * *
1345938 TTTATCTAGTTACATCTTACTAAAAACAAGCTCAAATACTTGATCCCTTTATCTCTATTTAATTT
1 TTTATCTAGTTACATCTTAGTAAAAACAAGCTCAAAGGCTTGATCCCTTCAT-TCTATCTAATTT
* * * * **
1346003 ATCCAATTTGAACATTTTGTATCTTGATTTAAATTTTTTTCAAGTCCAACCCCTCGCGAAATTGG
65 ATCCAATTTGAACATTTTGCACCTTGATTCAAATTTTTTTCAAGTCCAATCCCTCATGAAATTGG
* * *
1346068 AAACTTGAAGAATTTGTTTGAATTGAATCTCGAAAACAACAAGCTCGAAGGCATAATCTCTCTAT
130 AAACTTGAAGAATTTGTCTGAATTGAATCTCGAGAACAACAAGCTCGAAGGCATAATCCCTCTAT
*
1346133 TACTATTTAA
195 CACTATTTAA
* * * * * *
1346143 TTTATCTAGGTACATCTTAGT-AAAACAAGCTCAAAGGCTTAATTCCTTCATCGCTATTTACTTT
1 TTTATCTAGTTACATCTTAGTAAAAACAAGCTCAAAGGCTTGATCCCTTCAT-TCTATCTAATTT
* * * *
1346207 ATCCAATTTGAACATTTTGCATCTTGATTCAAATTTTTTTCAAGTCTAATTCTTCATGAAATTGG
65 ATCCAATTTGAACATTTTGCACCTTGATTCAAATTTTTTTCAAGTCCAATCCCTCATGAAATTGG
* * *
1346272 AAA-TCTAAAGAATTTGTCTGAATTGAATCTCGAGAATAACAAGCTCGAAGGCATGATCCCTCTA
130 AAACT-TGAAGAATTTGTCTGAATTGAATCTCGAGAACAACAAGCTCGAAGGCATAATCCCTCTA
1346336 TCACTATTTAA
194 TCACTATTTAA
* * ** *
1346347 TTTATCTAATTACATCTTAAT-AAAACAAGCTCAAAGGCTTGATCTTTTCATCACTATCTAATTT
1 TTTATCTAGTTACATCTTAGTAAAAACAAGCTCAAAGGCTTGATCCCTTCAT-TCTATCTAATTT
* * *
1346411 ATCCAATTAGAACATTTTGAACCTTGATTCAAATTTTTTCCAAGTCCAATCCCTCATGAAATTGG
65 ATCCAATTTGAACATTTTGCACCTTGATTCAAATTTTTTTCAAGTCCAATCCCTCATGAAATTGG
* * * * **
1346476 AAACCTGGAGAATTTGTCT-AGATTGAATCTCAAGAACAACAAGCTCGAAGGTATAATCTTTCTA
130 AAACTTGAAGAATTTGTCTGA-ATTGAATCTCGAGAACAACAAGCTCGAAGGCATAATCCCTCTA
1346540 TCACTATTTAA
194 TCACTATTTAA
* * * * *
1346551 TTTATCGAATTATATCTTAGTAAAAACAAGTTCAAAGGCTTGATCTCTTCATCTCTATCTAATTT
1 TTTATCTAGTTACATCTTAGTAAAAACAAGCTCAAAGGCTTGATCCCTTCAT-TCTATCTAATTT
* *
1346616 ATCCAATTTGAACATTTTGCACCTTGATTCAAATTTTTTATC-GGTCCAATCCCTTATGAAATTT
65 ATCCAATTTGAACATTTTGCACCTTGATTCAAATTTTTT-TCAAGTCCAATCCCTCATGAAA-TT
* * * * * * * *
1346680 AGAAACCTGAAGAATTTGTTTGAATTGAATCTCGAGAATAACAAACTCAAAGGCATGATTCCTCT
128 GGAAACTTGAAGAATTTGTCTGAATTGAATCTCGAGAACAACAAGCTCGAAGGCATAATCCCTCT
1346745 ATCACTATTTAA
193 ATCACTATTTAA
*
1346757 TTTATCCAGTTACATCTTAGTAAAAACAAGCTCAAAGGCTTGATCCCTTCATTGCTATCTAATTT
1 TTTATCTAGTTACATCTTAGTAAAAACAAGCTCAAAGGCTTGATCCCTTCATT-CTATCTAATTT
* * * *
1346822 ATTCAATTTGAATATTTTGCACCTTGATTCAAATTTTTTTGCAGGTCCAATCCCTCATCAAATTG
65 ATCCAATTTGAACATTTTGCACCTTGATTCAAATTTTTTT-CAAGTCCAATCCCTCATGAAATTG
* * * * *
1346887 GCAACTTAAAGAATTTGTCTGAATTGAATCTCGGGAGCAACAAGCTCAAAGGCATAATCCCTCTA
129 GAAACTTGAAGAATTTGTCTGAATTGAATCTCGAGAACAACAAGCTCGAAGGCATAATCCCTCTA
*
1346952 TCAGTATTTAA
194 TCACTATTTAA
1346963 TTTATC
1 TTTATC
1346969 CAATTTGAGA
Statistics
Matches: 722, Mismatches: 94, Indels: 19
0.86 0.11 0.02
Matches are distributed among these distances:
203 2 0.00
204 352 0.49
205 115 0.16
206 235 0.33
207 18 0.02
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (204 bp):
TTTATCTAGTTACATCTTAGTAAAAACAAGCTCAAAGGCTTGATCCCTTCATTCTATCTAATTTA
TCCAATTTGAACATTTTGCACCTTGATTCAAATTTTTTTCAAGTCCAATCCCTCATGAAATTGGA
AACTTGAAGAATTTGTCTGAATTGAATCTCGAGAACAACAAGCTCGAAGGCATAATCCCTCTATC
ACTATTTAA
Found at i:1347111 original size:144 final size:143
Alignment explanation
Indices: 1346770--1347157 Score: 374
Period size: 144 Copynumber: 2.7 Consensus size: 143
1346760 ATCCAGTTAC
* * *
1346770 ATCTTAGTAAAAACAAGCTCAAAGGCTTGATCCCTTCATTGCTATCTAATTTATTCAATTTGA-A
1 ATCTTAGTAACAACAAGCTCAAAGGCTTGATCCCTTCATCG-TTTCTAATTTATTCAATTTGAGA
* * * ** *
1346834 TATTTTGCACCTTGATTCAAATTTTTTTGC-AGGTCCAATCCCTCATCAAATTGGCAACTTAAAG
65 TA-TTTGTACCTTGATTCAAA-TCTTTTACAAGGTCCAATCCCTCATCAAATTGAAAACCTAAAG
*
1346898 AATTTGTCTGAATTGA
128 AATTGGTCTGAATTGA
** * * * * *
1346914 ATCTCGGGAGCAACAAGCTCAAAGGCATAATCCC-TCTATCAGTATT-TAATTTATCCAATTTGA
1 ATCTTAGTAACAACAAGCTCAAAGGCTTGATCCCTTC-ATC-GT-TTCTAATTTATTCAATTTGA
* ** *
1346977 GATATTTGTACCTTGATTCAAATCATTTACAAGGTCCAATCTTTCATGAAATTGAAAACCTAAAG
63 GATATTTGTACCTTGATTCAAATCTTTTACAAGGTCCAATCCCTCATCAAATTGAAAACCTAAA-
*
1347042 GAATTGGT-TGCATTGA
127 GAATTGGTCTGAATTGA
* * *
1347058 ATCTTAGTAACAATAAGCTCAAAGGCTTGATCCCTTCATCGTTGTCCAGTTTATTCAGA-TTGAG
1 ATCTTAGTAACAACAAGCTCAAAGGCTTGATCCCTTCATCGTT-TCTAATTTATTCA-ATTTGAG
* * * * * *
1347122 CTCTTTATACCTTGGTTCAAATGTTTTAGAAGGTCC
64 ATATTTGTACCTTGATTCAAATCTTTTACAAGGTCC
1347158 CATACCAAAA
Statistics
Matches: 195, Mismatches: 39, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
142 1 0.01
143 10 0.05
144 169 0.87
145 15 0.08
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (143 bp):
ATCTTAGTAACAACAAGCTCAAAGGCTTGATCCCTTCATCGTTTCTAATTTATTCAATTTGAGAT
ATTTGTACCTTGATTCAAATCTTTTACAAGGTCCAATCCCTCATCAAATTGAAAACCTAAAGAAT
TGGTCTGAATTGA
Found at i:1351880 original size:72 final size:72
Alignment explanation
Indices: 1351646--1351983 Score: 270
Period size: 72 Copynumber: 4.7 Consensus size: 72
1351636 GAATTGCAGC
* * * * * * **
1351646 ATTATTGGTCCTATCCCATCTTCACC-GGGTAATTTAACCAATTTAAAACAGTTGAACCTATCTT
1 ATTATTGGTCCCATCCCTTCTAC-CCTGAGTAATTTAACTAATTTAAAACAGTTGGACCTATCCA
*
1351710 ACAATCAA
65 ATAATCAA
** * *
1351718 ATTATTGGTCATATCCCTTCTATCCTTG-GTAATTTAACTAATTTGAAAA-AGTTGGACTTATCC
1 ATTATTGGTCCCATCCCTTCTA-CCCTGAGTAATTTAACTAATTT-AAAACAGTTGGACCTATCC
*
1351781 AATAACCAA
64 AATAATCAA
* * * *
1351790 ATTATTGGCCCCATCCCTTTTACCCCGAGTAATTTAATTAATTTAAAACAGTTGGACCTATCCAA
1 ATTATTGGTCCCATCCCTTCTACCCTGAGTAATTTAACTAATTTAAAACAGTTGGACCTATCCAA
1351855 TAATCAA
66 TAATCAA
* * * * * ** ** * * ** *
1351862 ATTACTGGTCCGATCCCTTCTAACCTGAGCAATTTAACCAAGCTAAAACTCTTGAACTTGGCCTA
1 ATTATTGGTCCCATCCCTTCTACCCTGAGTAATTTAACTAATTTAAAACAGTTGGACCTATCCAA
*
1351927 TAACCAA
66 TAATCAA
* * * * *
1351934 ATTGA-TGGTTCTATCCCTTCTACCCTGGGTAATTTAACCAATTTGAAACA
1 ATT-ATTGGTCCCATCCCTTCTACCCTGAGTAATTTAACTAATTTAAAACA
1351984 AATGAACCTC
Statistics
Matches: 212, Mismatches: 48, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
71 7 0.03
72 198 0.93
73 7 0.03
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.33
Consensus pattern (72 bp):
ATTATTGGTCCCATCCCTTCTACCCTGAGTAATTTAACTAATTTAAAACAGTTGGACCTATCCAA
TAATCAA
Found at i:1351930 original size:144 final size:144
Alignment explanation
Indices: 1351674--1351992 Score: 329
Period size: 144 Copynumber: 2.2 Consensus size: 144
1351664 TCTTCACCGG
** * *
1351674 GTAATTTAACCAATTTAAAACAGTTGAACCTATCTTACAATCAAATTATTGGTCATATCCCTTCT
1 GTAATTTAACCAATTTAAAACAGTTGAACCTATCCAACAATCAAATTACTGGTCAGATCCCTTCT
* * * ** * * *
1351739 ATCCTTGGTAATTTAACTAATTTGAAAAAGTTGGACTTATCCAATAACCAAATTATTGGCCCCAT
66 AACCTTGGCAATTTAACCAAGCTGAAAAACTTGAACTTAGCCAATAACCAAATTATTGGCCCCAT
1351804 CCCTTTTACCCCGA
131 CCCTTTTACCCCGA
** * * *
1351818 GTAATTTAATTAATTTAAAACAGTTGGACCTATCCAATAATCAAATTACTGGTCCGATCCCTTCT
1 GTAATTTAACCAATTTAAAACAGTTGAACCTATCCAACAATCAAATTACTGGTCAGATCCCTTCT
* * * **
1351883 AACC-TGAGCAATTTAACCAAGCT-AAAACTCTTGAACTTGGCCTATAACCAAATTGA-TGGTTC
66 AACCTTG-GCAATTTAACCAAGCTGAAAA-ACTTGAACTTAGCCAATAACCAAATT-ATTGGCCC
* * * *
1351945 TATCCCTTCTACCCTGG
128 CATCCCTTTTACCCCGA
* **
1351962 GTAATTTAACCAATTTGAAACAAATGAACCT
1 GTAATTTAACCAATTTAAAACAGTTGAACCT
1351993 CAGCCATAAC
Statistics
Matches: 140, Mismatches: 32, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
143 6 0.04
144 133 0.95
145 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (144 bp):
GTAATTTAACCAATTTAAAACAGTTGAACCTATCCAACAATCAAATTACTGGTCAGATCCCTTCT
AACCTTGGCAATTTAACCAAGCTGAAAAACTTGAACTTAGCCAATAACCAAATTATTGGCCCCAT
CCCTTTTACCCCGA
Found at i:1357210 original size:2 final size:2
Alignment explanation
Indices: 1357192--1357231 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1357182 TACATGTCCC
* *
1357192 TA TA AA TA TA AA 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 TA TA TA
1357232 GCTTTTGGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1358028 original size:34 final size:34
Alignment explanation
Indices: 1357990--1358062 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
1357980 CTTGCTTACT
* * *
1357990 TAACACATCACCTAATACACCTAATATGTTCACC
1 TAACACACCACCTAACACACCTAATATGCTCACC
* *
1358024 TAACATACCACCTAACACATCTAATATGCTCACC
1 TAACACACCACCTAACACACCTAATATGCTCACC
1358058 TAACA
1 TAACA
1358063 TACATAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.40, C:0.33, G:0.03, T:0.25
Consensus pattern (34 bp):
TAACACACCACCTAACACACCTAATATGCTCACC
Found at i:1358063 original size:34 final size:34
Alignment explanation
Indices: 1357998--1358065 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
1357988 CTTAACACAT
* *
1357998 CACCTAATACACCTAATATGTTCACCTAACATAC
1 CACCTAACACACCTAATATGCTCACCTAACATAC
*
1358032 CACCTAACACATCTAATATGCTCACCTAACATAC
1 CACCTAACACACCTAATATGCTCACCTAACATAC
1358066 ATAATATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.38, C:0.34, G:0.03, T:0.25
Consensus pattern (34 bp):
CACCTAACACACCTAATATGCTCACCTAACATAC
Found at i:1358070 original size:22 final size:21
Alignment explanation
Indices: 1358023--1358087 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
1358013 ATATGTTCAC
* *
1358023 CTAACATAC-CACCTAACACA
1 CTAATATACTCACCTAACATA
*
1358043 TCTAATATGCTCACCTAACATA
1 -CTAATATACTCACCTAACATA
* *
1358065 CATAATATATTTACCTAACATA
1 C-TAATATACTCACCTAACATA
1358087 C
1 C
1358088 CACCTAACAC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 8 0.22
22 28 0.78
ACGTcount: A:0.42, C:0.29, G:0.02, T:0.28
Consensus pattern (21 bp):
CTAATATACTCACCTAACATA
Found at i:1362557 original size:18 final size:18
Alignment explanation
Indices: 1362534--1362569 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1362524 TTAATACATC
1362534 ACCTAATACACTTAATAT
1 ACCTAATACACTTAATAT
1362552 ACCTAATACACTTAATAT
1 ACCTAATACACTTAATAT
1362570 GTTCACTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (18 bp):
ACCTAATACACTTAATAT
Found at i:1362597 original size:34 final size:34
Alignment explanation
Indices: 1362548--1362636 Score: 117
Period size: 34 Copynumber: 2.6 Consensus size: 34
1362538 AATACACTTA
*
1362548 ATAT-ACCTAATACACTTAATATGTTCACTTAAC
1 ATATCACCTAATACACTTAATATATTCACTTAAC
* * *
1362581 ATATCACCTAACACACTTAATATATTTACTTAAT
1 ATATCACCTAATACACTTAATATATTCACTTAAC
* *
1362615 ATATCACTTAATATACTTAATA
1 ATATCACCTAATACACTTAATA
1362637 AAAATATTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 4 0.08
34 44 0.92
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (34 bp):
ATATCACCTAATACACTTAATATATTCACTTAAC
Found at i:1362613 original size:13 final size:12
Alignment explanation
Indices: 1362594--1362629 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1362584 TCACCTAACA
1362594 CACTTAATATATT
1 CACTTAATATA-T
*
1362607 TACTTAATATAT
1 CACTTAATATAT
1362619 CACTTAATATA
1 CACTTAATATA
1362630 CTTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (12 bp):
CACTTAATATAT
Found at i:1362643 original size:25 final size:25
Alignment explanation
Indices: 1362594--1362643 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1362584 TCACCTAACA
* * * *
1362594 CACTTAATATATTTACTTAATATAT
1 CACTTAATATACTTAATAAAAATAT
1362619 CACTTAATATACTTAATAAAAATAT
1 CACTTAATATACTTAATAAAAATAT
1362644 TAATAAAAAT
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:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (25 bp):
CACTTAATATACTTAATAAAAATAT
Found at i:1362646 original size:12 final size:12
Alignment explanation
Indices: 1362631--1362655 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1362621 CTTAATATAC
1362631 TTAATAAAAATA
1 TTAATAAAAATA
1362643 TTAATAAAAATA
1 TTAATAAAAATA
1362655 T
1 T
1362656 ATAAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTAATAAAAATA
Found at i:1364599 original size:21 final size:21
Alignment explanation
Indices: 1364573--1364641 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
1364563 GATATAAATA
1364573 TTTAAAAATGATTGATTTATT
1 TTTAAAAATGATTGATTTATT
**
1364594 TTT-AAAATGAATCAAATTT-TT
1 TTTAAAAATG-AT-TGATTTATT
1364615 TTTAAGAAA-GATTGA--TATT
1 TTTAA-AAATGATTGATTTATT
1364634 TTTAAAAA
1 TTTAAAAA
1364642 GAATAAATCC
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
18 4 0.10
19 7 0.18
20 7 0.18
21 12 0.31
22 6 0.15
23 3 0.08
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.46
Consensus pattern (21 bp):
TTTAAAAATGATTGATTTATT
Found at i:1364634 original size:40 final size:40
Alignment explanation
Indices: 1364573--1364649 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
1364563 GATATAAATA
*
1364573 TTTAAAAATGATTGATTTATTTTTAAAATGAATCAAATTTTT
1 TTTAAAAATGATTGA-TTATTTTTAAAAAGAAT-AAATTTTT
1364615 TTTAAGAAA-GATTGA-TATTTTTAAAAAGAATAAAT
1 TTTAA-AAATGATTGATTATTTTTAAAAAGAATAAAT
1364650 CCTTTCAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
39 4 0.12
40 15 0.45
42 11 0.33
43 3 0.09
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.44
Consensus pattern (40 bp):
TTTAAAAATGATTGATTATTTTTAAAAAGAATAAATTTTT
Found at i:1365979 original size:2 final size:2
Alignment explanation
Indices: 1365972--1366013 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1365962 AAAGACTTAA
*
1365972 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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
1366014 TTGCCAGACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1367327 original size:27 final size:27
Alignment explanation
Indices: 1367289--1367340 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1367279 GTCAAGACTT
*
1367289 TATGGGCTCCCCTGCTAGAAGCAGAGG
1 TATGGGCTCCCCTACTAGAAGCAGAGG
1367316 TATGGGCTCCCCTACTAGAAGCAGA
1 TATGGGCTCCCCTACTAGAAGCAGA
1367341 TGTTTTAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.19
Consensus pattern (27 bp):
TATGGGCTCCCCTACTAGAAGCAGAGG
Found at i:1367443 original size:12 final size:12
Alignment explanation
Indices: 1367426--1367450 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1367416 CAGCGCGTAT
1367426 ATAAAAAAAAAA
1 ATAAAAAAAAAA
1367438 ATAAAAAAAAAA
1 ATAAAAAAAAAA
1367450 A
1 A
1367451 AATTGGTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (12 bp):
ATAAAAAAAAAA
Found at i:1368441 original size:3 final size:3
Alignment explanation
Indices: 1368435--1368461 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1368425 TGTCAATGCT
1368435 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1368462 TTGTGCTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:1371761 original size:31 final size:31
Alignment explanation
Indices: 1371719--1371777 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1371709 GTTCAGAATA
*
1371719 AAAAACTACTATTCTT-ATCCGGTGGCACGGT
1 AAAAACCACTATTCTTAAT-CGGTGGCACGGT
1371750 AAAAACCACTATTCTTAATCGGTGGCAC
1 AAAAACCACTATTCTTAATCGGTGGCAC
1371778 AGTTTGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (31 bp):
AAAAACCACTATTCTTAATCGGTGGCACGGT
Found at i:1372636 original size:14 final size:15
Alignment explanation
Indices: 1372617--1372645 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1372607 TTGCGACTAT
1372617 AAAATA-ATTTATTA
1 AAAATATATTTATTA
1372631 AAAATATATTTATTA
1 AAAATATATTTATTA
1372646 TGTCATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATATATTTATTA
Found at i:1375775 original size:18 final size:18
Alignment explanation
Indices: 1375754--1375804 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
1375744 AAATATTAAG
* *
1375754 TTAAAAAAGTAACTTTGC
1 TTAAAAAAGTAAATTTGA
*
1375772 TTAAAAAAATTAAATTTGA
1 TT-AAAAAAGTAAATTTGA
1375791 TTAAAAAA-TAAATT
1 TTAAAAAAGTAAATT
1375805 ACGCTTTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 6 0.21
18 8 0.28
19 15 0.52
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (18 bp):
TTAAAAAAGTAAATTTGA
Found at i:1376027 original size:27 final size:27
Alignment explanation
Indices: 1375978--1376032 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1375968 TAATAAAGAT
* * * *
1375978 TAAATTTTAAAATATATTTTAAAAAAA
1 TAAATTATAAAAAATAATATAAAAAAA
*
1376005 TAAATTATAAAAAATAATATAAATAAA
1 TAAATTATAAAAAATAATATAAAAAAA
1376032 T
1 T
1376033 TTAAATAGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
TAAATTATAAAAAATAATATAAAAAAA
Found at i:1376608 original size:33 final size:34
Alignment explanation
Indices: 1376563--1376626 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
1376553 TTAAAAATAA
*
1376563 ATATATAATATAAATTATTAAAATATTAAATTTT
1 ATATATAATATAAATTATTAAAATATGAAATTTT
* *
1376597 ATATA-AATATAAATTTTTTAAATATGAAAT
1 ATATATAATATAAATTATTAAAATATGAAAT
1376627 AAATATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 22 0.81
34 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (34 bp):
ATATATAATATAAATTATTAAAATATGAAATTTT
Found at i:1376611 original size:17 final size:16
Alignment explanation
Indices: 1376564--1376626 Score: 67
Period size: 16 Copynumber: 3.8 Consensus size: 16
1376554 TAAAAATAAA
*
1376564 TATATAATATAAATTAT
1 TATA-AATATAAATTTT
1376581 TA-AAATATTAAATTTT
1 TATAAATA-TAAATTTT
1376597 ATATAAATATAAATTTT
1 -TATAAATATAAATTTT
1376614 T-TAAATATGAAAT
1 TATAAATAT-AAAT
1376627 AAATATAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
15 11 0.27
16 13 0.32
17 12 0.29
18 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
TATAAATATAAATTTT
Found at i:1377538 original size:23 final size:25
Alignment explanation
Indices: 1377503--1377548 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1377493 AATAAAAATT
1377503 AGCCATCAA-TTTTGACAAACAACA
1 AGCCATCAATTTTTGACAAACAACA
1377527 AGCCAT-AATTTTTGACAAACAA
1 AGCCATCAATTTTTGACAAACAA
1377549 AAAGGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.24
Consensus pattern (25 bp):
AGCCATCAATTTTTGACAAACAACA
Found at i:1377572 original size:27 final size:27
Alignment explanation
Indices: 1377534--1377601 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
1377524 ACAAGCCATA
1377534 ATTTTTGACAAACAAAAAGGAACCACC
1 ATTTTTGACAAACAAAAAGGAACCACC
* * *
1377561 ATTTTTGACAAATACAAAGTAACCACC
1 ATTTTTGACAAACAAAAAGGAACCACC
*
1377588 ATTGTTGACAAACA
1 ATTTTTGACAAACA
1377602 CATGGTGGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.24
Consensus pattern (27 bp):
ATTTTTGACAAACAAAAAGGAACCACC
Found at i:1377620 original size:24 final size:25
Alignment explanation
Indices: 1377589--1377646 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
1377579 GTAACCACCA
*
1377589 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
1377613 TTGTTGACAAACACAAAGGGTGGCTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
1377639 TTGTTGAC
1 TTGTTGAC
1377647 TAGCCACCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 14 0.45
26 17 0.55
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:1382134 original size:23 final size:25
Alignment explanation
Indices: 1382099--1382144 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1382089 AATAAAAATT
1382099 AGCCATCAA-TTTTGACAAACAACA
1 AGCCATCAATTTTTGACAAACAACA
1382123 AGCCAT-AATTTTTGACAAACAA
1 AGCCATCAATTTTTGACAAACAA
1382145 AAAGGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.24
Consensus pattern (25 bp):
AGCCATCAATTTTTGACAAACAACA
Found at i:1382168 original size:27 final size:27
Alignment explanation
Indices: 1382130--1382197 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
1382120 ACAAGCCATA
1382130 ATTTTTGACAAACAAAAAGGAACCACC
1 ATTTTTGACAAACAAAAAGGAACCACC
* * *
1382157 ATTTTTGACAAATACAAAGTAACCACC
1 ATTTTTGACAAACAAAAAGGAACCACC
*
1382184 ATTGTTGACAAACA
1 ATTTTTGACAAACA
1382198 CATGGTGGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.24
Consensus pattern (27 bp):
ATTTTTGACAAACAAAAAGGAACCACC
Found at i:1382216 original size:24 final size:25
Alignment explanation
Indices: 1382185--1382242 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
1382175 GTAACCACCA
*
1382185 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
1382209 TTGTTGACAAACACAAAGGGTGGCTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
1382235 TTGTTGAC
1 TTGTTGAC
1382243 TAGCCACCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 14 0.45
26 17 0.55
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:1382277 original size:2 final size:2
Alignment explanation
Indices: 1382270--1382306 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1382260 CTTCTCTAAT
*
1382270 TA TA TA TA TA CA 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 TA TA TA TA TA T
1382307 TTGCTCAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1383317 original size:45 final size:43
Alignment explanation
Indices: 1383268--1383358 Score: 112
Period size: 45 Copynumber: 2.1 Consensus size: 43
1383258 ATCATAGAAT
* *
1383268 AAAAATATACTAA-TTTAATTTAATTAATAAAAATTAAAAAAGTAA
1 AAAAATATA-AAACTTTAATTAAATTAATAAAAA-TAAAAAA-TAA
* *
1383313 AAAAATATAAAACTTTGATTAAATTGATAAAAATAAAAAATAA
1 AAAAATATAAAACTTTAATTAAATTAATAAAAATAAAAAATAA
1383356 AAA
1 AAA
1383359 TTAATTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 6 0.15
44 9 0.22
45 26 0.63
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (43 bp):
AAAAATATAAAACTTTAATTAAATTAATAAAAATAAAAAATAA
Found at i:1383957 original size:13 final size:13
Alignment explanation
Indices: 1383878--1384007 Score: 54
Period size: 13 Copynumber: 10.1 Consensus size: 13
1383868 TACTTGATTT
* *
1383878 TTTTATTTAAATT
1 TTTTATATAAATA
1383891 TTTTAT-TAAATA
1 TTTTATATAAATA
* *
1383903 TGATTATATTAATA
1 T-TTTATATAAATA
** *
1383917 TGATATGTAAA-A
1 TTTTATATAAATA
* *
1383929 ATTAAT-TAAA-A
1 TTTTATATAAATA
1383940 TTTTATATAAATA
1 TTTTATATAAATA
*
1383953 TTTTAAAATAAATA
1 TTTT-ATATAAATA
* *
1383967 TATAATATAAATTA
1 TTTTATATAAA-TA
** *
1383981 TTAAAATATTAA-A
1 TT-TTATATAAATA
1383994 TTTTATATAAATA
1 TTTTATATAAATA
1384007 T
1 T
1384008 AAATTTTTTA
Statistics
Matches: 86, Mismatches: 23, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
11 9 0.10
12 19 0.22
13 32 0.37
14 19 0.22
15 7 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
TTTTATATAAATA
Found at i:1384001 original size:27 final size:26
Alignment explanation
Indices: 1383935--1384008 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 26
1383925 AAAAATTAAT
*
1383935 TAAAATTTTATATAAATATTTTAAAA
1 TAAAATTTTATATAAATATATTAAAA
* *
1383961 TAAATATATAATATAAAT-TATTAAAA
1 TAAA-ATTTTATATAAATATATTAAAA
1383987 TATTAAATTTTATATAAATATA
1 TA--AAATTTTATATAAATATA
1384009 AATTTTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 13 0.33
27 22 0.56
28 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TAAAATTTTATATAAATATATTAAAA
Found at i:1384005 original size:18 final size:18
Alignment explanation
Indices: 1383937--1384022 Score: 67
Period size: 17 Copynumber: 4.9 Consensus size: 18
1383927 AAATTAATTA
1383937 AAATTTTATATAAATATTTT
1 AAATTTTATATAAATA--TT
* **
1383957 AAAATAAATATATAATA-T
1 AAATTTTATATA-AATATT
*
1383975 AAATTAT-TA-AAATATT
1 AAATTTTATATAAATATT
1383991 AAATTTTATATAAATA-T
1 AAATTTTATATAAATATT
1384008 AAATTTT-T-TAAATAT
1 AAATTTTATATAAATAT
1384023 GAAGTAAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
15 10 0.18
16 9 0.16
17 12 0.22
18 11 0.20
20 9 0.16
21 4 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATTTTATATAAATATT
Found at i:1384034 original size:32 final size:33
Alignment explanation
Indices: 1383955--1384035 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 33
1383945 TATAAATATT
*
1383955 TTAAAATAAATATATAATATAAATTATTAAAATA
1 TTAAAGTAAATATA-AATATAAATTATTAAAATA
* ** * *
1383989 TTAAATTTTATATAAATATAAATTTTTTAAATA
1 TTAAAGTAAATATAAATATAAATTATTAAAATA
*
1384022 -TGAAGTAAATATAA
1 TTAAAGTAAATATAA
1384036 TATGAATATA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 10 0.26
33 17 0.45
34 11 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (33 bp):
TTAAAGTAAATATAAATATAAATTATTAAAATA
Found at i:1386268 original size:72 final size:72
Alignment explanation
Indices: 1385720--1386229 Score: 750
Period size: 72 Copynumber: 7.1 Consensus size: 72
1385710 AAGTTGCAAC
* * * * *
1385720 ATTACTGGTCCTATCCCATATTCTCTTGGTAATTTAACCAATTTAAAATATTTGGACCTATCCTA
1 ATTACTGGTCCTATCCCGTCTTCTCTGGGTAATTTAACCAATTTGAAATATTTGTACCTATCCTA
*
1385785 TAACCCA
66 TAACCAA
* * * *
1385792 ATTACTGATCCTATCCCGTCTTTTCTGGGTAATTTAACCAATTTGAAATATTTGGATCTATCCTA
1 ATTACTGGTCCTATCCCGTCTTCTCTGGGTAATTTAACCAATTTGAAATATTTGTACCTATCCTA
*
1385857 TAATCAA
66 TAACCAA
* *
1385864 ATTGCTGGTCCTATCCCGTCTTCTCTGGGTAATTTAACCAATTTGAAATCTTTGTACCTATCCTA
1 ATTACTGGTCCTATCCCGTCTTCTCTGGGTAATTTAACCAATTTGAAATATTTGTACCTATCCTA
1385929 TAACCAA
66 TAACCAA
* * * * *
1385936 ATTACTGGTCCTATCCCCTCCTCTCTGGGTAATTTAACCAATTTAAAATCTTTGTACTTATCCTA
1 ATTACTGGTCCTATCCCGTCTTCTCTGGGTAATTTAACCAATTTGAAATATTTGTACCTATCCTA
1386001 TAACCAA
66 TAACCAA
* * * *
1386008 ATTACTGGTCTTATCCCGTCTTCTCTGGGTAATTTAATCAATTTGAAATCTTTGTACCTATCTTA
1 ATTACTGGTCCTATCCCGTCTTCTCTGGGTAATTTAACCAATTTGAAATATTTGTACCTATCCTA
1386073 TAACCAA
66 TAACCAA
** * * *
1386080 ATTGTTGGTCCTATCCCGTCTTCTCTGGGTAATTTAACCAATTTGAAATTTTTGTATCTATCTTA
1 ATTACTGGTCCTATCCCGTCTTCTCTGGGTAATTTAACCAATTTGAAATATTTGTACCTATCCTA
1386145 TAACCAA
66 TAACCAA
* * *
1386152 ATTACTGGTCCTATCCCATCTTCTCTGAGTAATTTAACCAATTTGAAATATTTGGACCTATCCTA
1 ATTACTGGTCCTATCCCGTCTTCTCTGGGTAATTTAACCAATTTGAAATATTTGTACCTATCCTA
1386217 TAACCAA
66 TAACCAA
1386224 ATTACT
1 ATTACT
1386230 AATTCTGTCC
Statistics
Matches: 396, Mismatches: 42, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 396 1.00
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.39
Consensus pattern (72 bp):
ATTACTGGTCCTATCCCGTCTTCTCTGGGTAATTTAACCAATTTGAAATATTTGTACCTATCCTA
TAACCAA
Found at i:1386302 original size:216 final size:214
Alignment explanation
Indices: 1385720--1386304 Score: 789
Period size: 216 Copynumber: 2.7 Consensus size: 214
1385710 AAGTTGCAAC
*
1385720 ATTACTGGTCCTATCCCATATTCTCTTGGTAATTTAACCAATTTAAAATATTTGGACCTATCCTA
1 ATTACTGGTCCTATCCCATCTTCTC-TGGTAATTTAACCAATTTAAAATATTTGGACCTATCCTA
* * * *
1385785 TAACCCAATTACTGATCCTATCCCGTCTTTTCTGGGTAATTTAACCAATTTGAAATATTTGGATC
65 TAACCAAATTACT-ATTCTATCCCGTCTTTTCTGGGTAATTTAACTAATTTGAAACATTTGGATC
*
1385850 TATCCTATAATCAAATTGCTGGTCCTATCCCGTCTTCTCTGGGTAATTTAACCAATTTGAAATCT
129 TATCCTATAATCAAATTGTTGGTCCTATCCCGTCTTCTCTGGGTAATTTAACCAATTTGAAATCT
1385915 TTGTACCTATCCTATAACCAA
194 TTGTACCTATCCTATAACCAA
* * * * *
1385936 ATTACTGGTCCTATCCCCTCCTCTCTGGGTAATTTAACCAATTTAAAATCTTTGTACTTATCCTA
1 ATTACTGGTCCTATCCCATCTTCTCT-GGTAATTTAACCAATTTAAAATATTTGGACCTATCCTA
** * *
1386001 TAACCAAATTACTGGTCTTATCCCGTCTTCTCTGGGTAATTTAA-TCAATTTGAAATC-TTTGTA
65 TAACCAAATTACTATTC-TATCCCGTCTTTTCTGGGTAATTTAACT-AATTTGAAA-CATTTGGA
* * *
1386064 CCTATCTTATAACCAAATTGTTGGTCCTATCCCGTCTTCTCTGGGTAATTTAACCAATTTGAAAT
127 TCTATCCTATAATCAAATTGTTGGTCCTATCCCGTCTTCTCTGGGTAATTTAACCAATTTGAAAT
* * *
1386129 TTTTGTATCTATCTTATAACCAA
192 CTTTGTACCTATCCTATAACCAA
*
1386152 ATTACTGGTCCTATCCCATCTTCTCTGAGTAATTTAACCAATTTGAAATATTTGGACCTATCCTA
1 ATTACTGGTCCTATCCCATCTTCTCTG-GTAATTTAACCAATTTAAAATATTTGGACCTATCCTA
* * * * * *
1386217 TAACCAAATTACTAATTCTGT-CCATTTTGTTTTGGGTAATTTAACTAATTTGGAACAGTTGGAT
65 TAACCAAATTACT-ATTCTATCCCGTCTT-TTCTGGGTAATTTAACTAATTTGAAACATTTGGAT
* * *
1386281 TTATCCCATAATCAGATTGTTGGT
128 CTATCCTATAATCAAATTGTTGGT
1386305 GCTGTCCATT
Statistics
Matches: 317, Mismatches: 43, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
215 9 0.03
216 305 0.96
217 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (214 bp):
ATTACTGGTCCTATCCCATCTTCTCTGGTAATTTAACCAATTTAAAATATTTGGACCTATCCTAT
AACCAAATTACTATTCTATCCCGTCTTTTCTGGGTAATTTAACTAATTTGAAACATTTGGATCTA
TCCTATAATCAAATTGTTGGTCCTATCCCGTCTTCTCTGGGTAATTTAACCAATTTGAAATCTTT
GTACCTATCCTATAACCAA
Found at i:1390926 original size:14 final size:15
Alignment explanation
Indices: 1390907--1390938 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1390897 AACATTTTCC
1390907 ATTAATATAAAAA-A
1 ATTAATATAAAAATA
1390921 ATTAATATAAAAATA
1 ATTAATATAAAAATA
1390936 ATT
1 ATT
1390939 TTTTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATTAATATAAAAATA
Found at i:1392134 original size:18 final size:20
Alignment explanation
Indices: 1392113--1392155 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1392103 ATATTAAGTT
*
1392113 AAAAAAA-TAAATTTAA-TA
1 AAAAAAATTAAATTCAATTA
1392131 AAAAAAATTAAATTCAATTA
1 AAAAAAATTAAATTCAATTA
1392151 AAAAA
1 AAAAA
1392156 TAGACCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
19 8 0.36
20 7 0.32
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAAATTAAATTCAATTA
Found at i:1392368 original size:15 final size:14
Alignment explanation
Indices: 1392348--1392407 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
1392338 ATAAAAAATT
1392348 ATTAAATTAATAAAA
1 ATTAAATT-ATAAAA
*
1392363 ATTAAATTTTAAAA
1 ATTAAATTATAAAA
* *
1392377 ATATATATTTTTAAAA
1 AT-TA-AATTATAAAA
*
1392393 AGTAAATTATAAAA
1 ATTAAATTATAAAA
1392407 A
1 A
1392408 ATAATATAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
14 16 0.42
15 12 0.32
16 10 0.26
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
ATTAAATTATAAAA
Found at i:1392998 original size:24 final size:26
Alignment explanation
Indices: 1392971--1393030 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 26
1392961 AATTTGATAT
1392971 AATATAAATAT-ATA-AATATT-TTAA
1 AATATAAATATAATATAA-ATTATTAA
1392995 AATATAAATATAATATAAATTATTAA
1 AATATAAATATAATATAAATTATTAA
1393021 AATATCAAAT
1 AATAT-AAAT
1393031 TTTATATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 11 0.34
25 6 0.19
26 11 0.34
27 4 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
AATATAAATATAATATAAATTATTAA
Found at i:1393030 original size:27 final size:27
Alignment explanation
Indices: 1392980--1393064 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
1392970 TAATATAAAT
*
1392980 ATATAAATATTTTAAAATAT-AAATATA
1 ATATAAAT-TATTAAAATATCAAATATA
* *
1393007 ATATAAATTATTAAAATATCAAATTTT
1 ATATAAATTATTAAAATATCAAATATA
* *
1393034 ATATTAA-TA-TAAAATTTCTAAATA-A
1 ATATAAATTATTAAAATATC-AAATATA
1393059 ATATAA
1 ATATAA
1393065 TAAAAATACA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
25 13 0.27
26 16 0.33
27 19 0.40
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
ATATAAATTATTAAAATATCAAATATA
Found at i:1393063 original size:19 final size:18
Alignment explanation
Indices: 1393020--1393064 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1393010 TAAATTATTA
* *
1393020 AAATATCAAATTTTATAT
1 AAATATAAAATTTTAAAT
*
1393038 TAATATAAAATTTCTAAAT
1 AAATATAAAATTT-TAAAT
1393057 AAATATAA
1 AAATATAA
1393065 TAAAAATACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATAAAATTTTAAAT
Found at i:1396583 original size:34 final size:33
Alignment explanation
Indices: 1396535--1396755 Score: 257
Period size: 34 Copynumber: 6.5 Consensus size: 33
1396525 TGGTAAAAAC
*
1396535 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
1396568 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
1396602 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
1396636 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
1396670 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
* *
1396704 CACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
1396738 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1396756 TCTCCCACTT
Statistics
Matches: 160, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 22 0.14
34 132 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:1396651 original size:68 final size:67
Alignment explanation
Indices: 1396537--1396755 Score: 287
Period size: 68 Copynumber: 3.2 Consensus size: 67
1396527 GTAAAAACCA
* * *
1396537 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
1396602 CAC
65 CAC
* * * *
1396605 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
1396670 CTC
65 CAC
* * * * *
1396673 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
1396738 CA-
65 CAC
1396740 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1396756 TCTCCCACTT
Statistics
Matches: 131, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 17 0.13
68 113 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:1396679 original size:102 final size:101
Alignment explanation
Indices: 1396535--1396755 Score: 361
Period size: 102 Copynumber: 2.2 Consensus size: 101
1396525 TGGTAAAAAC
* *
1396535 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
*
1396600 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
** * * *
1396636 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
1396701 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
1396738 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1396756 TCTCCCACTT
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 93 0.85
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
Found at i:1400848 original size:19 final size:19
Alignment explanation
Indices: 1400821--1400883 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1400811 TCACGTGTAC
* *
1400821 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
1400840 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
1400859 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
1400878 AGTACC
1 AGTACC
1400884 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:1401235 original size:34 final size:33
Alignment explanation
Indices: 1401187--1401405 Score: 253
Period size: 34 Copynumber: 6.5 Consensus size: 33
1401177 TGGTAAAAAC
*
1401187 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
1401220 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
1401254 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
1401288 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
1401322 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
* *
1401356 CACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
1401390 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1401406 GAAAATGTTT
Statistics
Matches: 158, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 20 0.13
34 132 0.84
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:1401303 original size:68 final size:67
Alignment explanation
Indices: 1401189--1401405 Score: 283
Period size: 68 Copynumber: 3.2 Consensus size: 67
1401179 GTAAAAACCA
* * *
1401189 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
1401254 CAC
65 CAC
* * * *
1401257 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
1401322 CTC
65 CAC
* * * * *
1401325 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
1401390 CA-
65 CAC
1401392 CCATTTAATCAACA
1 CCATTTAATCAACA
1401406 GAAAATGTTT
Statistics
Matches: 129, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 15 0.12
68 113 0.88
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:1401331 original size:102 final size:101
Alignment explanation
Indices: 1401187--1401405 Score: 357
Period size: 102 Copynumber: 2.2 Consensus size: 101
1401177 TGGTAAAAAC
* *
1401187 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
*
1401252 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
** * * *
1401288 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
1401353 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
1401390 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1401406 GAAAATGTTT
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 14 0.13
102 93 0.87
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
Found at i:1402423 original size:25 final size:26
Alignment explanation
Indices: 1402360--1402434 Score: 116
Period size: 27 Copynumber: 2.9 Consensus size: 26
1402350 TAAAAGTTAC
*
1402360 TCTTTTTGTTTATAAAAAATGATGGT
1 TCTTTTTGTTTATAAAAAATGGTGGT
*
1402386 TCCTTTTTGTTTATATAAAATGGTGGT
1 T-CTTTTTGTTTATAAAAAATGGTGGT
1402413 T-TTTTTGTTTATAAAAAATGGT
1 TCTTTTTGTTTATAAAAAATGGT
1402435 AGCTTATTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 20 0.44
26 1 0.02
27 24 0.53
ACGTcount: A:0.28, C:0.04, G:0.16, T:0.52
Consensus pattern (26 bp):
TCTTTTTGTTTATAAAAAATGGTGGT
Found at i:1405449 original size:27 final size:26
Alignment explanation
Indices: 1405410--1405502 Score: 82
Period size: 27 Copynumber: 3.6 Consensus size: 26
1405400 AAAGTCACCT
* * *
1405410 TTTTTGTTCGTCAAAAATTGTGGTTCC
1 TTTTTATTTGTCAAAAATAGTGGTT-C
*
1405437 TTTTTATTTGTCAAAAATAGTGATTC
1 TTTTTATTTGTCAAAAATAGTGGTTC
* * * *
1405463 TTTTTGTTTATGAAAAATGGTGG--C
1 TTTTTATTTGTCAAAAATAGTGGTTC
*
1405487 TTGTTATTTGTCAAAA
1 TTTTTATTTGTCAAAA
1405503 TTGGTAGCTA
Statistics
Matches: 53, Mismatches: 13, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
24 13 0.25
26 19 0.36
27 21 0.40
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.48
Consensus pattern (26 bp):
TTTTTATTTGTCAAAAATAGTGGTTC
Found at i:1405478 original size:26 final size:27
Alignment explanation
Indices: 1405420--1405480 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
1405410 TTTTTGTTCG
* * *
1405420 TCAAAAATTGTGGTTCCTTTTTATTTG
1 TCAAAAATAGTGATTCCTTTTTATTTA
*
1405447 TCAAAAATAGTGATT-CTTTTTGTTTA
1 TCAAAAATAGTGATTCCTTTTTATTTA
*
1405473 TGAAAAAT
1 TCAAAAAT
1405481 GGTGGCTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 16 0.55
27 13 0.45
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (27 bp):
TCAAAAATAGTGATTCCTTTTTATTTA
Found at i:1405735 original size:19 final size:20
Alignment explanation
Indices: 1405713--1405750 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1405703 TTATTAAATC
1405713 TTTAGT-GTTTTATTTTTTT
1 TTTAGTAGTTTTATTTTTTT
* *
1405732 TTTATTATTTTTATTTTTT
1 TTTAGTAGTTTTATTTTTT
1405751 AATAACTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTAGTAGTTTTATTTTTTT
Found at i:1406176 original size:12 final size:12
Alignment explanation
Indices: 1406161--1406185 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1406151 TCTAATTTCT
1406161 TTTATATATATA
1 TTTATATATATA
1406173 TTTATATATATA
1 TTTATATATATA
1406185 T
1 T
1406186 ATCCAATCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTATATATATA
Found at i:1408690 original size:72 final size:71
Alignment explanation
Indices: 1408567--1408722 Score: 215
Period size: 72 Copynumber: 2.2 Consensus size: 71
1408557 TTCTAAATGG
* * * *
1408567 ATCCATCCCCCCTGAGATTGGAAATATGAAGAATCTAAGATATTTATATCTTTATTCCAATCGCA
1 ATCCATCCCTCCTGAAATTGGAAATATGAAGAATCTAAGATATTTAGATCTTGATTCCAATCGCA
1408632 TTTCCA
66 TTTCCA
* *
1408638 ATTCCATCCCTTCTGAAATTGGAAATATGAAGAATCTAAGA-ATTTTAGATCTTGGTTCCAATCG
1 A-TCCATCCCTCCTGAAATTGGAAATATGAAGAATCTAAGATA-TTTAGATCTTGATTCCAATCG
*
1408702 CCTTTCCA
64 CATTTCCA
1408710 ATCGCATCCCTCC
1 ATC-CATCCCTCC
1408723 ATCTCTATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
71 4 0.05
72 70 0.95
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (71 bp):
ATCCATCCCTCCTGAAATTGGAAATATGAAGAATCTAAGATATTTAGATCTTGATTCCAATCGCA
TTTCCA
Found at i:1416425 original size:16 final size:17
Alignment explanation
Indices: 1416404--1416480 Score: 97
Period size: 16 Copynumber: 4.6 Consensus size: 17
1416394 ACATATCATA
1416404 AATATAAT-TAAAATAT
1 AATATAATATAAAATAT
1416420 AATATAATATAAAA-AT
1 AATATAATATAAAATAT
*
1416436 AATATAATATTAAAT-T
1 AATATAATATAAAATAT
*
1416452 TATATAAATATAAAATAT
1 AATAT-AATATAAAATAT
1416470 AATTATAATAT
1 AA-TATAATAT
1416481 TATAAAATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
16 28 0.54
17 14 0.27
18 7 0.13
19 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATATAATATAAAATAT
Found at i:1416430 original size:21 final size:21
Alignment explanation
Indices: 1416396--1416491 Score: 60
Period size: 21 Copynumber: 4.7 Consensus size: 21
1416386 GACATAAAAC
*
1416396 ATATCATA-AATATAATTAAA
1 ATATAATATAATATAATTAAA
*
1416416 ATATAATATAATATAA-AAATA
1 ATATAATATAATATAATTAA-A
* *
1416437 ATATAATAT--TA-AATTTAT
1 ATATAATATAATATAATTAAA
*
1416455 ATA-AATATAAAATATAATTATA
1 ATATAATAT--AATATAATTAAA
* *
1416477 ATATTATAAAATATA
1 ATATAATATAATATA
1416492 TAAATATGAT
Statistics
Matches: 57, Mismatches: 10, Indels: 17
0.68 0.12 0.20
Matches are distributed among these distances:
17 5 0.09
18 5 0.09
19 3 0.05
20 9 0.16
21 25 0.44
22 7 0.12
23 3 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATAATATAATATAATTAAA
Found at i:1416620 original size:2 final size:2
Alignment explanation
Indices: 1416613--1416639 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1416603 GTTTGTGCTG
1416613 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
1416640 GTAGAAAAAT
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:1420691 original size:15 final size:16
Alignment explanation
Indices: 1420671--1420719 Score: 66
Period size: 15 Copynumber: 3.2 Consensus size: 16
1420661 ATAAAGAAAT
*
1420671 AAAAATTTGAA-TTAA
1 AAAAATTTAAATTTAA
1420686 AAAAA-TTAAATTTAA
1 AAAAATTTAAATTTAA
*
1420701 AATAATTTAAATTTAA
1 AAAAATTTAAATTTAA
1420717 AAA
1 AAA
1420720 GTTTCGAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 4 0.14
15 13 0.45
16 12 0.41
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
AAAAATTTAAATTTAA
Found at i:1420712 original size:16 final size:15
Alignment explanation
Indices: 1420682--1420719 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
1420672 AAAATTTGAA
1420682 TTAAAAAAATTAAAT
1 TTAAAAAAATTAAAT
*
1420697 TTAAAATAATTTAAAT
1 TTAAAA-AAATTAAAT
1420713 TTAAAAA
1 TTAAAAA
1420720 GTTTCGAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAAAAAAATTAAAT
Done.