Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009782.1 Corchorus capsularis cultivar CVL-1 contig09803, 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: 117801
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3539 original size:12 final size:12
Alignment explanation
Indices: 3522--3546 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3512 CTGGATTTCC
3522 TCTTCTTTTTTT
1 TCTTCTTTTTTT
3534 TCTTCTTTTTTT
1 TCTTCTTTTTTT
3546 T
1 T
3547 TTTTAAAAGG
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TCTTCTTTTTTT
Found at i:11441 original size:11 final size:11
Alignment explanation
Indices: 11425--11449 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11415 ATTCTCCTAG
11425 TCCCTTTTCTT
1 TCCCTTTTCTT
11436 TCCCTTTTCTT
1 TCCCTTTTCTT
11447 TCC
1 TCC
11450 TGGTTCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (11 bp):
TCCCTTTTCTT
Found at i:14402 original size:106 final size:105
Alignment explanation
Indices: 14222--14482 Score: 359
Period size: 106 Copynumber: 2.5 Consensus size: 105
14212 AGTTTAGGCT
* * *
14222 TAATTTCACTAAGTTTAGCCCCAAATT-AATTTTTTTTTTATTTTAAGGGTAAATTTCAAAATTA
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTATTTTAAGGGTAAATTCCAAAATTA
14286 ATAATTTATTGTTATAGGATTTTAGAAAAAAAAATACAAAAC
66 ATAA-TTATTGTTATAGGATTTTAG-AAAAAAAATACAAAAC
*
14328 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTCATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTT-ATTTTAAGGGTAAATTCCAAAATT
* * * * *
14393 AATAA-TATTGTTATAGGGTTTTAGAAATAAAATATATAAT
65 AATAATTATTGTTATAGGATTTTAGAAAAAAAATACAAAAC
**
14433 TAA-TTCACTAAGTTTAG-CCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATT-TTATTTTATTTTAAGGGT
14483 TAGAAAAATT
Statistics
Matches: 141, Mismatches: 11, Indels: 9
0.88 0.07 0.06
Matches are distributed among these distances:
103 25 0.18
104 19 0.13
105 15 0.11
106 45 0.32
107 10 0.07
108 27 0.19
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATTATTGTTATAGGATTTTAGAAAAAAAATACAAAAC
Found at i:19461 original size:26 final size:26
Alignment explanation
Indices: 19425--19499 Score: 134
Period size: 26 Copynumber: 2.9 Consensus size: 26
19415 AGTTAATGAC
19425 TTCACTTCACAAATCAGAAATTAGAA
1 TTCACTTCACAAATCAGAAATTAGAA
*
19451 TTCACTTCACAAATCAGAAATCAGAA
1 TTCACTTCACAAATCAGAAATTAGAA
19477 TTCACTTCACAAATCAG-AATTAG
1 TTCACTTCACAAATCAGAAATTAG
19500 CATAAGTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
25 5 0.11
26 42 0.89
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (26 bp):
TTCACTTCACAAATCAGAAATTAGAA
Found at i:19525 original size:89 final size:89
Alignment explanation
Indices: 19374--19543 Score: 322
Period size: 89 Copynumber: 1.9 Consensus size: 89
19364 AAGCAAATGC
* *
19374 ATCAGAATTCATAATTCACTTCACAAATCAGAATTAGCATAAGTTAATGACTTCACTTCACAAAT
1 ATCAGAAATCAGAATTCACTTCACAAATCAGAATTAGCATAAGTTAATGACTTCACTTCACAAAT
19439 CAGAAATTAGAATTCACTTCACAA
66 CAGAAATTAGAATTCACTTCACAA
19463 ATCAGAAATCAGAATTCACTTCACAAATCAGAATTAGCATAAGTTAATGACTTCACTTCACAAAT
1 ATCAGAAATCAGAATTCACTTCACAAATCAGAATTAGCATAAGTTAATGACTTCACTTCACAAAT
19528 CAGAAATTAGAATTCA
66 CAGAAATTAGAATTCA
19544 GAAACAAAGT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 79 1.00
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (89 bp):
ATCAGAAATCAGAATTCACTTCACAAATCAGAATTAGCATAAGTTAATGACTTCACTTCACAAAT
CAGAAATTAGAATTCACTTCACAA
Found at i:19550 original size:25 final size:25
Alignment explanation
Indices: 19522--19604 Score: 60
Period size: 25 Copynumber: 3.0 Consensus size: 25
19512 ACTTCACTTC
19522 ACAAATCAGAAATTAGAATTCAGAA
1 ACAAATCAGAAATTAGAATTCAGAA
*
19547 ACAAAGTTATAAGTTAGAACTTAGAATTCAGAA
1 AC-AA---ATCAG--A-AA-TTAGAATTCAGAA
*
19580 TCAAATCAG-AATTCAGAATTCAGAA
1 ACAAATCAGAAATT-AGAATTCAGAA
19605 TTCAGGATCA
Statistics
Matches: 46, Mismatches: 3, Indels: 18
0.69 0.04 0.27
Matches are distributed among these distances:
24 2 0.04
25 15 0.33
26 2 0.04
29 8 0.17
31 1 0.02
32 4 0.09
33 14 0.30
ACGTcount: A:0.51, C:0.12, G:0.13, T:0.24
Consensus pattern (25 bp):
ACAAATCAGAAATTAGAATTCAGAA
Found at i:19579 original size:7 final size:7
Alignment explanation
Indices: 19569--19609 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
19559 GTTAGAACTT
19569 AGAATTC
1 AGAATTC
19576 AGAA-TC
1 AGAATTC
19582 A-AA-TC
1 AGAATTC
19587 AGAATTC
1 AGAATTC
19594 AGAATTC
1 AGAATTC
19601 AGAATTC
1 AGAATTC
19608 AG
1 AG
19610 GATCATACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.16
6 5 0.16
7 22 0.69
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (7 bp):
AGAATTC
Found at i:23189 original size:29 final size:29
Alignment explanation
Indices: 23121--23193 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
23111 TATGTTTGGG
* *
23121 TATATATATTTTCAATAATAATATTATTA
1 TATATATATTTTTAATAATAATAATATTA
* *
23150 TTTCTGA-ATTTTTAATAATAATAATA-TA
1 TATAT-ATATTTTTAATAATAATAATATTA
23178 TATATAATATTTTTAA
1 TATAT-ATATTTTTAA
23194 AAATTATCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
28 6 0.17
29 28 0.80
30 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (29 bp):
TATATATATTTTTAATAATAATAATATTA
Found at i:23306 original size:31 final size:30
Alignment explanation
Indices: 23243--23308 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 30
23233 AACTTTATGT
*
23243 TTTCCAATTGTACCCTTAATTTTAAAATATA
1 TTTCCAATTGTACCCTT-ATTTTAAAACATA
23274 TTTCCAATTGTACCCTT-TTTTAAAAAACATA
1 TTTCCAATTGTACCCTTATTTT--AAAACATA
23305 TTTC
1 TTTC
23309 TAAATTACCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 4 0.12
31 28 0.88
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.45
Consensus pattern (30 bp):
TTTCCAATTGTACCCTTATTTTAAAACATA
Found at i:23357 original size:20 final size:19
Alignment explanation
Indices: 23332--23369 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
23322 CTAAATAATA
23332 TTTTAATTATTCCATTATTT
1 TTTTAATTATTCC-TTATTT
23352 TTTTAATTATTCCTTATT
1 TTTTAATTATTCCTTATT
23370 AAATTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTAATTATTCCTTATTT
Found at i:23362 original size:12 final size:12
Alignment explanation
Indices: 23345--23393 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
23335 TAATTATTCC
*
23345 ATTATTTTTTTA
1 ATTATTTTTTAA
23357 ATTATTCCTTATTAA
1 ATTATT--TT-TTAA
*
23372 ATTATTTTTAAA
1 ATTATTTTTTAA
23384 ATTATTTTTT
1 ATTATTTTTT
23394 TAATCATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 18 0.58
13 2 0.06
14 2 0.06
15 9 0.29
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTATTTTTTAA
Found at i:23480 original size:22 final size:22
Alignment explanation
Indices: 23447--23573 Score: 107
Period size: 22 Copynumber: 5.8 Consensus size: 22
23437 TCTCTATGTG
23447 GTTATCAAAATTTCATAAG-AT
1 GTTATCAAAATTTCATAAGTAT
* * *
23468 AGTTATTATAATTTCATGAGTAT
1 -GTTATCAAAATTTCATAAGTAT
*
23491 GTTATCAAAATTTCAT-AGTGT
1 GTTATCAAAATTTCATAAGTAT
* * * *
23512 GGTTACCAAAATTTCATATGGAA
1 -GTTATCAAAATTTCATAAGTAT
* *
23535 GTTATCAAAACTTCAT-AGTGT
1 GTTATCAAAATTTCATAAGTAT
*
23556 GGTTACCAAAATTTCATA
1 -GTTATCAAAATTTCATA
23574 GGATCAGGTT
Statistics
Matches: 81, Mismatches: 19, Indels: 9
0.74 0.17 0.08
Matches are distributed among these distances:
21 5 0.06
22 73 0.90
23 3 0.04
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGTAT
Found at i:23522 original size:66 final size:66
Alignment explanation
Indices: 23443--23574 Score: 169
Period size: 66 Copynumber: 2.0 Consensus size: 66
23433 CTTGTCTCTA
* * * * *
23443 TGTGGTTATCAAAATTTCATA-AGATAGTTATTATAATTTCATGAGTAT-GTTATCAAAATTTCA
1 TGTGGTTACCAAAATTTCATATAGA-AGTTATCAAAACTTCAT-AGTATGGTTACCAAAATTTCA
23506 TAG
64 TAG
* *
23509 TGTGGTTACCAAAATTTCATATGGAAGTTATCAAAACTTCATAGTGTGGTTACCAAAATTTCATA
1 TGTGGTTACCAAAATTTCATATAGAAGTTATCAAAACTTCATAGTATGGTTACCAAAATTTCATA
23574 G
66 G
23575 GATCAGGTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 4 0.07
66 51 0.89
67 2 0.04
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.39
Consensus pattern (66 bp):
TGTGGTTACCAAAATTTCATATAGAAGTTATCAAAACTTCATAGTATGGTTACCAAAATTTCATA
G
Found at i:23574 original size:22 final size:22
Alignment explanation
Indices: 23477--23574 Score: 112
Period size: 22 Copynumber: 4.5 Consensus size: 22
23467 TAGTTATTAT
* *
23477 AATTTCATGAGTAT-GTTATCAA
1 AATTTCAT-AGTGTGGTTACCAA
23499 AATTTCATAGTGTGGTTACCAA
1 AATTTCATAGTGTGGTTACCAA
*
23521 AATTTCATA-TG-GAAGTTATCAA
1 AATTTCATAGTGTG--GTTACCAA
*
23543 AACTTCATAGTGTGGTTACCAA
1 AATTTCATAGTGTGGTTACCAA
23565 AATTTCATAG
1 AATTTCATAG
23575 GATCAGGTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
20 1 0.02
21 6 0.09
22 55 0.85
23 2 0.03
24 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTACCAA
Found at i:23626 original size:22 final size:22
Alignment explanation
Indices: 23445--23628 Score: 101
Period size: 22 Copynumber: 8.3 Consensus size: 22
23435 TGTCTCTATG
* * *
23445 TGGTTATCAAAATTTCATAAGA
1 TGGTTATTAAAATTTCATAGGT
* *
23467 TAGTTATTATAATTTCAT-GAGT
1 TGGTTATTAAAATTTCATAG-GT
*
23489 AT-GTTATCAAAATTTCATA-GT
1 -TGGTTATTAAAATTTCATAGGT
**
23510 GTGGTTACCAAAATTTCATATGG-
1 -TGGTTATTAAAATTTCATA-GGT
** * *
23533 AAGTTATCAAAACTTCATA-GT
1 TGGTTATTAAAATTTCATAGGT
**
23554 GTGGTTACCAAAATTTCATAGGAT
1 -TGGTTATTAAAATTTCATAGG-T
* *
23578 CAGGTTATTAAAATTTCTTAGGT
1 -TGGTTATTAAAATTTCATAGGT
*
23601 TGGTTATTGAAATTTCATATGG-
1 TGGTTATTAAAATTTCATA-GGT
23623 TGGTTA
1 TGGTTA
23629 ATTATCACAA
Statistics
Matches: 126, Mismatches: 25, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
20 1 0.01
21 3 0.02
22 98 0.78
23 5 0.04
24 19 0.15
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGT
Found at i:23732 original size:22 final size:22
Alignment explanation
Indices: 23707--23763 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
23697 TGATATTGTC
*
23707 GTTAACAAAATTTCATTAGGAG
1 GTTAACAAAATTTCATGAGGAG
* *
23729 GTT-ACTAATATTTCATGGGGAG
1 GTTAAC-AAAATTTCATGAGGAG
*
23751 GTTATCAAAATTT
1 GTTAACAAAATTT
23764 TATAGTTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 2 0.07
22 25 0.89
23 1 0.04
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (22 bp):
GTTAACAAAATTTCATGAGGAG
Found at i:23852 original size:22 final size:23
Alignment explanation
Indices: 23826--23962 Score: 99
Period size: 22 Copynumber: 6.1 Consensus size: 23
23816 TTATCCAATC
*
23826 TCAAAGAG-TGATTATCGAAATT
1 TCAAAGAGATGATTATCAAAATT
23848 TCAAAGAGATCGGATTATCAAAATT
1 TCAAAGAGAT--GATTATCAAAATT
* *
23873 T-ATAG-GAAGATTATCAAAATT
1 TCAAAGAGATGATTATCAAAATT
* * *
23894 TCATAGCGTTG-TTATCAAAATT
1 TCAAAGAGATGATTATCAAAATT
* *
23916 TCAAAGCGA-GGTTATCAAAATT
1 TCAAAGAGATGATTATCAAAATT
* * *
23938 ACATA-ATATGATTAT-AAGAATT
1 TCAAAGAGATGATTATCAA-AATT
23960 TCA
1 TCA
23963 TAAAGGGGTC
Statistics
Matches: 94, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
21 18 0.19
22 55 0.59
23 5 0.05
24 3 0.03
25 13 0.14
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (23 bp):
TCAAAGAGATGATTATCAAAATT
Found at i:23981 original size:22 final size:22
Alignment explanation
Indices: 23956--24028 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
23946 TGATTATAAG
*
23956 AATTTCATAAAG-GGGTCAACAA
1 AATTTCATAAAGAGGCT-AACAA
* *
23978 AATTTTATAAAGAGGCTATCAA
1 AATTTCATAAAGAGGCTAACAA
* *
24000 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAAAGAGGCTAACAA
*
24022 ATTTTCA
1 AATTTCA
24029 AAATGTGATT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
22 41 0.93
23 3 0.07
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (22 bp):
AATTTCATAAAGAGGCTAACAA
Found at i:24262 original size:22 final size:22
Alignment explanation
Indices: 24234--24315 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
24224 CAAAATTTGT
*
24234 AGTTATCAAGATTTTATAAGCA
1 AGTTATCAAAATTTTATAAGCA
* *
24256 AGTTATCAAAATTTTATAGGGA
1 AGTTATCAAAATTTTATAAGCA
* *
24278 GGTTTATCAAAATTTTAT-AGGA
1 AG-TTATCAAAATTTTATAAGCA
24300 AGATTTATCAAAATTT
1 AG--TTATCAAAATTT
24316 CGTAGTGAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
22 24 0.46
23 28 0.54
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.39
Consensus pattern (22 bp):
AGTTATCAAAATTTTATAAGCA
Found at i:24449 original size:42 final size:42
Alignment explanation
Indices: 24377--24463 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
24367 TGATTACTAA
* * *
24377 CAATTCATATGGAGGTTTTTAAATTTTCATAACG-TGGTTAT
1 CAATTCATATGGAGGTTATCAAATTCTCATAACGTTGGTTAT
**
24418 CAATATCATATGGAGGTTATCAACA-TCTCATAGTGTTGGTTAT
1 CAAT-TCATATGGAGGTTATCAA-ATTCTCATAACGTTGGTTAT
24461 CAA
1 CAA
24464 AATTTCATTG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
41 4 0.11
42 23 0.61
43 11 0.29
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (42 bp):
CAATTCATATGGAGGTTATCAAATTCTCATAACGTTGGTTAT
Found at i:24619 original size:22 final size:22
Alignment explanation
Indices: 24157--24626 Score: 124
Period size: 22 Copynumber: 21.6 Consensus size: 22
24147 AATTTAGTTT
* *
24157 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCATAGGAAGGTTA
* *
24179 TCAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATAGGAAGGTTA
* * *
24201 ACAAAATTTCGTAATG-AGGTTA
1 TCAAAATTTCAT-AGGAAGGTTA
*
24223 TCAAAA-TT--T--GTA-GTTA
1 TCAAAATTTCATAGGAAGGTTA
* * *
24239 TCAAGATTTTATAAGCAA-GTTA
1 TCAAAATTTCAT-AGGAAGGTTA
* *
24261 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATAGGAAGG-TTA
* *
24284 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATAGGAAG-GTTA
*
24307 TCAAAATTTCGTAGTG-AGGTTA
1 TCAAAATTTCATAG-GAAGGTTA
* * * *
24329 TCACAATTTCACAGTG-TGATTA
1 TCAAAATTTCATAG-GAAGGTTA
* * *
24351 TCACAATTTCA-ATGTG-TGATTA
1 TCAAAATTTCATA-G-GAAGGTTA
*
24373 -CTAACAA-TTCATATGG-AGGTTT
1 TC-AA-AATTTCATA-GGAAGGTTA
* * * *
24395 TTAAATTTTCATAACG-TGGTTA
1 TCAAAATTTCAT-AGGAAGGTTA
*
24417 TC--AATATCATATGG-AGGTTA
1 TCAAAATTTCATA-GGAAGGTTA
* * **
24437 TCAACATCTCATAGTGTTGGTTA
1 TCAAAATTTCATAG-GAAGGTTA
*
24460 TCAAAATTTCATTGGGAA-GTTA
1 TCAAAATTTCA-TAGGAAGGTTA
* * *
24482 TCAAAATTTTATATTG-AGATCT-
1 TCAAAATTTCATA-GGAAGGT-TA
* * *
24504 TCAAAATTCCTTAGGGAGGTTAA
1 TCAAAATTTCATAGGAAGGTT-A
*
24527 T-AAAATTTCATAAGAAGGTTAA
1 TCAAAATTTCATAGGAAGGTT-A
* * **
24549 ACAAAAATT-ATAAAAAGGTTA
1 TCAAAATTTCATAGGAAGGTTA
* * * ** *
24570 TCGAAATTCCATAGTATCGTTG
1 TCAAAATTTCATAGGAAGGTTA
* *
24592 TTAAAATTTCATAGGAATGTTA
1 TCAAAATTTCATAGGAAGGTTA
24614 TCAAAATTTCATA
1 TCAAAATTTCATA
24627 ATGGGATCAT
Statistics
Matches: 335, Mismatches: 80, Indels: 66
0.70 0.17 0.14
Matches are distributed among these distances:
16 10 0.03
17 3 0.01
19 3 0.01
20 14 0.04
21 19 0.06
22 215 0.64
23 68 0.20
24 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (22 bp):
TCAAAATTTCATAGGAAGGTTA
Found at i:24698 original size:22 final size:22
Alignment explanation
Indices: 24649--24698 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
24639 AAAATAGTGT
*
24649 AATTATCATAATTTAATAGAGA
1 AATTATCATAATTTAATAGAAA
** * *
24671 GGTTATCATAATTTCATATAAA
1 AATTATCATAATTTAATAGAAA
24693 AATTAT
1 AATTAT
24699 ATTATATAAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (22 bp):
AATTATCATAATTTAATAGAAA
Found at i:28789 original size:46 final size:46
Alignment explanation
Indices: 28722--28811 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
28712 ATTGTCTTTC
*
28722 TTTTTAAATAATCTGAGAATTTGACCGACTTTGGATCATTCTAGCT
1 TTTTTAAATAATCTGAAAATTTGACCGACTTTGGATCATTCTAGCT
* *
28768 TTTTTAAATAATCTGAAAATTTGACCTACTTTGGTTCATTCTAG
1 TTTTTAAATAATCTGAAAATTTGACCGACTTTGGATCATTCTAG
28812 ACTTCTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.43
Consensus pattern (46 bp):
TTTTTAAATAATCTGAAAATTTGACCGACTTTGGATCATTCTAGCT
Found at i:29091 original size:36 final size:36
Alignment explanation
Indices: 29047--29121 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
29037 GAGGCATGAA
29047 TTTCAATATTGGAAATTTTGTCACTTGAACTTCAAT
1 TTTCAATATTGGAAATTTTGTCACTTGAACTTCAAT
* *
29083 TTTCAATATTGGATATTTTGTCCCTTGAACTTCAAT
1 TTTCAATATTGGAAATTTTGTCACTTGAACTTCAAT
29119 TTT
1 TTT
29122 GGGACGTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.48
Consensus pattern (36 bp):
TTTCAATATTGGAAATTTTGTCACTTGAACTTCAAT
Found at i:29365 original size:29 final size:29
Alignment explanation
Indices: 29290--29365 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
29280 CGTTAGGTTG
* *
29290 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
1 AGGGGACAAAACGT-CCAAAATTGAAATTC
* ** *
29320 AGGGGATAAAATATCCAAGATTGAAATTC
1 AGGGGACAAAACGTCCAAAATTGAAATTC
29349 AGGGGACAAAACGTCCA
1 AGGGGACAAAACGTCCA
29366 TAGAATACAA
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 27 0.73
30 10 0.27
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (29 bp):
AGGGGACAAAACGTCCAAAATTGAAATTC
Found at i:33327 original size:32 final size:32
Alignment explanation
Indices: 33281--33359 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
33271 CCGTTTCTGT
* *
33281 TTTTAGGCTCAAATTG-GTAAACTTTTGAAAGG
1 TTTTAAGCTCAAATTGAG-AAACTTTCGAAAGG
* *
33313 TTTTAAGCTTAAATTGAGCAACTTTCGAAAGG
1 TTTTAAGCTCAAATTGAGAAACTTTCGAAAGG
33345 -TTT-AGACTCAAATTG
1 TTTTAAG-CTCAAATTG
33360 GTGACTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 2 0.05
31 11 0.28
32 26 0.65
33 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (32 bp):
TTTTAAGCTCAAATTGAGAAACTTTCGAAAGG
Found at i:35791 original size:49 final size:51
Alignment explanation
Indices: 35735--35838 Score: 176
Period size: 52 Copynumber: 2.1 Consensus size: 51
35725 ACTAGCTTCC
35735 TGTATTC-T-GTGATATCTTCTAGTACTACACCATTGTCTTTAGACAATCT
1 TGTATTCGTGGTGATATCTTCTAGTACTACACCATTGTCTTTAGACAATCT
*
35784 TGTATTCTGTGGTGATATCTTCTAGTATTACACCATTGTCTTTAGACAATCT
1 TGTATTC-GTGGTGATATCTTCTAGTACTACACCATTGTCTTTAGACAATCT
35836 TGT
1 TGT
35839 TTCAGGCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
49 7 0.14
51 1 0.02
52 43 0.84
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.44
Consensus pattern (51 bp):
TGTATTCGTGGTGATATCTTCTAGTACTACACCATTGTCTTTAGACAATCT
Found at i:36013 original size:61 final size:61
Alignment explanation
Indices: 35879--36001 Score: 228
Period size: 61 Copynumber: 2.0 Consensus size: 61
35869 AATCCTACTC
*
35879 TAGTACTTTTAGATTCCAAAAACAATTGCAACGCGATCTAAATAAGTAAAATTGGCGATTT
1 TAGTACTTTTAGATTCCAAAAACAATTGCAACACGATCTAAATAAGTAAAATTGGCGATTT
*
35940 TAGTACTTTTAGATTCCAAAAACAATTGCAACACGATTTAAATAAGTAAAATTGGCGATTT
1 TAGTACTTTTAGATTCCAAAAACAATTGCAACACGATCTAAATAAGTAAAATTGGCGATTT
36001 T
1 T
36002 CATGATTTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (61 bp):
TAGTACTTTTAGATTCCAAAAACAATTGCAACACGATCTAAATAAGTAAAATTGGCGATTT
Found at i:36737 original size:31 final size:32
Alignment explanation
Indices: 36664--36758 Score: 111
Period size: 31 Copynumber: 3.0 Consensus size: 32
36654 AACGGGTGGG
* * *
36664 TCAGGTTGAGTTCGGGTTCGGGTTGGATTTGGG
1 TCAGGTT-AATTCGGGTTCGGGTTGAATTTGGA
* *
36697 TCAGATTAATTCGGATTCGGG-TGAATTTGGA
1 TCAGGTTAATTCGGGTTCGGGTTGAATTTGGA
* *
36728 TCAGGTTAATTCGGGTTCGAGTTCAATTTGG
1 TCAGGTTAATTCGGGTTCGGGTTGAATTTGG
36759 GTTTTGACCA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 26 0.50
32 20 0.38
33 6 0.12
ACGTcount: A:0.18, C:0.11, G:0.35, T:0.37
Consensus pattern (32 bp):
TCAGGTTAATTCGGGTTCGGGTTGAATTTGGA
Found at i:36916 original size:15 final size:15
Alignment explanation
Indices: 36898--36927 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
36888 TTTTCATAAA
36898 TTTTCAGATTCAGGT
1 TTTTCAGATTCAGGT
*
36913 TTTTCGGATTCAGGT
1 TTTTCAGATTCAGGT
36928 GGGTTCGGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.13, G:0.23, T:0.47
Consensus pattern (15 bp):
TTTTCAGATTCAGGT
Found at i:39133 original size:32 final size:32
Alignment explanation
Indices: 39097--39178 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
39087 TAAATTGATA
*
39097 GACAAAATAGCCCTTGAACTTCCACATAAA-AG
1 GACAAAATAGCCCTTGAACTTACACA-AAATAG
** * *
39129 GACAAAATAGCCCTCAAAGTTAGACAAAATAG
1 GACAAAATAGCCCTTGAACTTACACAAAATAG
*
39161 GACAAAATGGCCCTTGAA
1 GACAAAATAGCCCTTGAA
39179 GGGGCTAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 3 0.07
32 38 0.93
ACGTcount: A:0.45, C:0.22, G:0.16, T:0.17
Consensus pattern (32 bp):
GACAAAATAGCCCTTGAACTTACACAAAATAG
Found at i:39251 original size:29 final size:29
Alignment explanation
Indices: 39219--39282 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
39209 GAGGGCATAA
*
39219 TTGTCCCAATTGAAAGTTCAGGGGCCATT
1 TTGTCCCAATTGAAAGTTCAGGGACCATT
** ** *
39248 TTGTCCCTTTTGTGAGTTCCGGGACCATT
1 TTGTCCCAATTGAAAGTTCAGGGACCATT
39277 TTGTCC
1 TTGTCC
39283 ATTAAGCCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (29 bp):
TTGTCCCAATTGAAAGTTCAGGGACCATT
Found at i:43758 original size:31 final size:31
Alignment explanation
Indices: 43718--43880 Score: 128
Period size: 31 Copynumber: 5.2 Consensus size: 31
43708 ACGTGGCCTG
* * *
43718 CCACCTGGATTAAAAAGTAACATGTGGCACA
1 CCACGTGGATTAAAAAGTGACACGTGGCACA
* * *
43749 CCACGTGGATAAAAAAGTGACACGTTTGCACG
1 CCACGTGGATTAAAAAGTGACACG-TGGCACA
* *
43781 CCACGTGTATTAAAAAGTGACACGTGGCACG
1 CCACGTGGATTAAAAAGTGACACGTGGCACA
* * * * * * *
43812 TCACATGTACTAAAAAGTGATACATGGCACG
1 CCACGTGGATTAAAAAGTGACACGTGGCACA
* * ** **
43843 CCTCGTGTACCAAAAAGTGACACGTGGCATG
1 CCACGTGGATTAAAAAGTGACACGTGGCACA
43874 CCACGTG
1 CCACGTG
43881 CACTAAAGGA
Statistics
Matches: 109, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
31 82 0.75
32 27 0.25
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (31 bp):
CCACGTGGATTAAAAAGTGACACGTGGCACA
Found at i:45959 original size:2 final size:2
Alignment explanation
Indices: 45952--45983 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
45942 ACAGGCGTCC
45952 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
45984 CCTTGACTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51249 original size:33 final size:33
Alignment explanation
Indices: 51212--51283 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
51202 TATCTTATAT
51212 ATCTTACTACTATGTAACATCACAAACTCAAAA
1 ATCTTACTACTATGTAACATCACAAACTCAAAA
51245 ATCTTACTACTATGTAACATCACAAACTCAAAA
1 ATCTTACTACTATGTAACATCACAAACTCAAAA
51278 ATCTTA
1 ATCTTA
51284 ATATCAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.44, C:0.24, G:0.03, T:0.29
Consensus pattern (33 bp):
ATCTTACTACTATGTAACATCACAAACTCAAAA
Found at i:51292 original size:15 final size:15
Alignment explanation
Indices: 51272--51300 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
51262 CATCACAAAC
51272 TCAAAAATCTTAATA
1 TCAAAAATCTTAATA
51287 TCAAAAATCTTAAT
1 TCAAAAATCTTAAT
51301 TGGGAAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (15 bp):
TCAAAAATCTTAATA
Found at i:53245 original size:39 final size:39
Alignment explanation
Indices: 53201--53282 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 39
53191 CATATTTATA
* *
53201 ATTAGGGCCTAAAACTGGATTTAATTTCTTACCTTAATT
1 ATTAGGGACTAAAACTGAATTTAATTTCTTACCTTAATT
* * *
53240 ATTAGGGACTAAACCTGAATTTAATTTGTTTCCTTAATT
1 ATTAGGGACTAAAACTGAATTTAATTTCTTACCTTAATT
53279 ATTA
1 ATTA
53283 AGGAGGGTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (39 bp):
ATTAGGGACTAAAACTGAATTTAATTTCTTACCTTAATT
Found at i:53690 original size:29 final size:29
Alignment explanation
Indices: 53624--53700 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
53614 TTTTTTTTTA
* * *
53624 CCAAACCATTGTAGTTCTTAAAAATAATTT
1 CCAAATCATTGTACTT-TTAAAAATAATTC
* *
53654 CCAAATCATTGTACTTTTAGAATTAATTC
1 CCAAATCATTGTACTTTTAAAAATAATTC
* *
53683 CCATATCATTGTATTTTT
1 CCAAATCATTGTACTTTT
53701 TGCCACATCC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 26 0.65
30 14 0.35
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (29 bp):
CCAAATCATTGTACTTTTAAAAATAATTC
Found at i:63887 original size:2 final size:2
Alignment explanation
Indices: 63880--63928 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
63870 TTCTCTTTAA
* *
63880 AT AT AT AT AT AT AT AT AT CT AT AT CT AT AT A- AT -T 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
63920 AT AT AT AT A
1 AT AT AT AT A
63929 CACACATAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:64392 original size:10 final size:10
Alignment explanation
Indices: 64377--64411 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
64367 GAACATTTTG
64377 TGTGTAGTGA
1 TGTGTAGTGA
*
64387 TGTGTATTG-
1 TGTGTAGTGA
64396 TGTGTAGTGA
1 TGTGTAGTGA
64406 TGTGTA
1 TGTGTA
64412 TTAATACATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.46
Consensus pattern (10 bp):
TGTGTAGTGA
Found at i:64398 original size:19 final size:19
Alignment explanation
Indices: 64374--64413 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
64364 ATCGAACATT
64374 TTGTGTGTAGTGATGTGTA
1 TTGTGTGTAGTGATGTGTA
64393 TTGTGTGTAGTGATGTGTA
1 TTGTGTGTAGTGATGTGTA
64412 TT
1 TT
64414 AATACATGAA
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:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (19 bp):
TTGTGTGTAGTGATGTGTA
Found at i:87857 original size:15 final size:15
Alignment explanation
Indices: 87837--87866 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
87827 AGTTATCAAA
87837 TCTTTTCCTCTAATT
1 TCTTTTCCTCTAATT
*
87852 TCTTTTCTTCTAATT
1 TCTTTTCCTCTAATT
87867 CGTAATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.63
Consensus pattern (15 bp):
TCTTTTCCTCTAATT
Found at i:91611 original size:245 final size:245
Alignment explanation
Indices: 91181--91663 Score: 894
Period size: 245 Copynumber: 2.0 Consensus size: 245
91171 ATTGAAGATA
91181 ATTTGAAGATTTGAAGACCAATGAAGAATTATTTCAAGAAGTAAGAATTGGAGATTGGAGCTTTA
1 ATTTGAAGATTTGAAGACCAATGAAGAATTATTTCAAGAAGTAAGAATTGGAGATTGGAGCTTTA
*
91246 ATTGCAAAGGATTGAAGACAAACCCAGAAGAAGCTCGGAAGCTATGGAATTTTGGAAATTTTATA
66 ATTGCAAAGGATTGAAGACAAACCCAGAAGAAGCCCGGAAGCTATGGAATTTTGGAAATTTTATA
91311 TCAGATAATACTCAGCCCATATAAATCCACAATTGGAGTTAAAATCCCAATTTGTGCCGCACATA
131 TCAGATAATACTCAGCCCATATAAATCCACAATTGGAGTTAAAATCCCAATTTGTGCCGCACATA
91376 TCCAAGGAAATATCCAATTCCCACAATTTCCCGATACTAGTCCAATGAAG
196 TCCAAGGAAATATCCAATTCCCACAATTTCCCGATACTAGTCCAATGAAG
91426 ATTTGAAGATTTGAAGACCAATGAAGAATTATTTCAAGAAGTAAGAATTGGAGATTGGAGCTTTA
1 ATTTGAAGATTTGAAGACCAATGAAGAATTATTTCAAGAAGTAAGAATTGGAGATTGGAGCTTTA
* *
91491 ATTGCAAAGGATTGAAGACAAGCCCAGAAGAAGCCCGGAAGCTATGGAATTTTGGATATTTTATA
66 ATTGCAAAGGATTGAAGACAAACCCAGAAGAAGCCCGGAAGCTATGGAATTTTGGAAATTTTATA
* * *
91556 TGAGATAATACTCAGCCCATATAAGTCCACAATTGGAGTTAAAATCCCAATTTGTGCCGCACCTA
131 TCAGATAATACTCAGCCCATATAAATCCACAATTGGAGTTAAAATCCCAATTTGTGCCGCACATA
* *
91621 TCCAAGGAAATATCCAATTCTCGCAATTTCCCGATACTAGTCC
196 TCCAAGGAAATATCCAATTCCCACAATTTCCCGATACTAGTCC
91664 TAGTTGGATT
Statistics
Matches: 230, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
245 230 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (245 bp):
ATTTGAAGATTTGAAGACCAATGAAGAATTATTTCAAGAAGTAAGAATTGGAGATTGGAGCTTTA
ATTGCAAAGGATTGAAGACAAACCCAGAAGAAGCCCGGAAGCTATGGAATTTTGGAAATTTTATA
TCAGATAATACTCAGCCCATATAAATCCACAATTGGAGTTAAAATCCCAATTTGTGCCGCACATA
TCCAAGGAAATATCCAATTCCCACAATTTCCCGATACTAGTCCAATGAAG
Found at i:93125 original size:23 final size:23
Alignment explanation
Indices: 93099--93157 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
93089 TGCGTTTTTC
93099 TAAAAAAAAAAT-GTGATTTGCGA
1 TAAAAAAAAAATAG-GATTTGCGA
**
93122 TAAAAAAAATTTAGGATTTGCGA
1 TAAAAAAAAAATAGGATTTGCGA
**
93145 TTTAAAAAAAATA
1 TAAAAAAAAAATA
93158 TTTTTCTGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.54, C:0.03, G:0.14, T:0.29
Consensus pattern (23 bp):
TAAAAAAAAAATAGGATTTGCGA
Found at i:96880 original size:174 final size:174
Alignment explanation
Indices: 96590--96941 Score: 704
Period size: 174 Copynumber: 2.0 Consensus size: 174
96580 AGGAATTCTT
96590 ATTAAGGAGACACAAGATGAAGTAAACGAAGCAAACAGTTTTGGATAACTGCTTAATTTAAGAGA
1 ATTAAGGAGACACAAGATGAAGTAAACGAAGCAAACAGTTTTGGATAACTGCTTAATTTAAGAGA
96655 AGCTTTCTTAAACCTTATCTCTATTTAATTTTTCTTGCAATGCTTTGATTGATTATTGCTTTTGA
66 AGCTTTCTTAAACCTTATCTCTATTTAATTTTTCTTGCAATGCTTTGATTGATTATTGCTTTTGA
96720 TTGTTTGTTTTGCTTTTTCCTTCATTTGAATTGCATATAGGTTC
131 TTGTTTGTTTTGCTTTTTCCTTCATTTGAATTGCATATAGGTTC
96764 ATTAAGGAGACACAAGATGAAGTAAACGAAGCAAACAGTTTTGGATAACTGCTTAATTTAAGAGA
1 ATTAAGGAGACACAAGATGAAGTAAACGAAGCAAACAGTTTTGGATAACTGCTTAATTTAAGAGA
96829 AGCTTTCTTAAACCTTATCTCTATTTAATTTTTCTTGCAATGCTTTGATTGATTATTGCTTTTGA
66 AGCTTTCTTAAACCTTATCTCTATTTAATTTTTCTTGCAATGCTTTGATTGATTATTGCTTTTGA
96894 TTGTTTGTTTTGCTTTTTCCTTCATTTGAATTGCATATAGGTTC
131 TTGTTTGTTTTGCTTTTTCCTTCATTTGAATTGCATATAGGTTC
96938 ATTA
1 ATTA
96942 GGGTTTAAAT
Statistics
Matches: 178, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 178 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (174 bp):
ATTAAGGAGACACAAGATGAAGTAAACGAAGCAAACAGTTTTGGATAACTGCTTAATTTAAGAGA
AGCTTTCTTAAACCTTATCTCTATTTAATTTTTCTTGCAATGCTTTGATTGATTATTGCTTTTGA
TTGTTTGTTTTGCTTTTTCCTTCATTTGAATTGCATATAGGTTC
Found at i:102222 original size:15 final size:15
Alignment explanation
Indices: 102176--102226 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
102166 ATAAAAACAT
102176 ATATAATTTATATAATA
1 ATAT-ATTTATATAA-A
102193 ATATA-TT-T-T-AA
1 ATATATTTATATAAA
102204 ATATATTTATATAAA
1 ATATATTTATATAAA
102219 ATATATTT
1 ATATATTT
102227 TAAATTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
11 6 0.20
12 3 0.10
13 2 0.07
14 2 0.07
15 12 0.40
16 1 0.03
17 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATATTTATATAAA
Found at i:102227 original size:26 final size:27
Alignment explanation
Indices: 102176--102310 Score: 96
Period size: 27 Copynumber: 4.7 Consensus size: 27
102166 ATAAAAACAT
102176 ATATAATTTATATAATAATATATTTTAA
1 ATAT-ATTTATATAATAATATATTTTAA
102204 ATATATTTATATAA-AATATATTTTAA
1 ATATATTTATATAATAATATATTTTAA
* * * *
102230 ATTTTATTTATTTATATATAATAAAAACATATACA
1 A-TATATTTA--TATA-ATAAT--ATA-TTTTA-A
**
102265 ATATA-ACATAT-ATAATATATTTTAA
1 ATATATTTATATAATAATATATTTTAA
*
102290 ATATATATTATATAAAAATAT
1 ATATAT-TTATATAATAATAT
102311 CTATTCGGTT
Statistics
Matches: 82, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
25 6 0.07
26 16 0.20
27 23 0.28
28 10 0.12
29 9 0.11
30 1 0.01
31 6 0.07
33 3 0.04
34 6 0.07
35 2 0.02
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
ATATATTTATATAATAATATATTTTAA
Found at i:102232 original size:84 final size:87
Alignment explanation
Indices: 102131--102310 Score: 296
Period size: 84 Copynumber: 2.1 Consensus size: 87
102121 CTAAATATTT
* * * *
102131 TAAACTATATTTTAAATTTTATTTATTTATATATAATAAAAACATATATAAT-TTATATA-ATAA
1 TAAAATATATTTTAAATTTTATTTATTTATATATAATAAAAACATATACAATATAACATATATAA
102194 TATATTTTAAATATAT-TTATA
66 TATATTTTAAATATATATTATA
102215 TAAAATATATTTTAAATTTTATTTATTTATATATAATAAAAACATATACAATATAACATATATAA
1 TAAAATATATTTTAAATTTTATTTATTTATATATAATAAAAACATATACAATATAACATATATAA
102280 TATATTTTAAATATATATTATA
66 TATATTTTAAATATATATTATA
102302 TAAAA-ATAT
1 TAAAATATAT
102311 CTATTCGGTT
Statistics
Matches: 89, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
84 50 0.56
85 5 0.06
86 24 0.27
87 10 0.11
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (87 bp):
TAAAATATATTTTAAATTTTATTTATTTATATATAATAAAAACATATACAATATAACATATATAA
TATATTTTAAATATATATTATA
Found at i:103090 original size:17 final size:17
Alignment explanation
Indices: 103070--103103 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
103060 TTTTTTCCCG
103070 TCGATTATTTGTTGAAA
1 TCGATTATTTGTTGAAA
*
103087 TCGATTATTTTTTGAAA
1 TCGATTATTTGTTGAAA
103104 AATCTGTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.50
Consensus pattern (17 bp):
TCGATTATTTGTTGAAA
Found at i:103493 original size:12 final size:12
Alignment explanation
Indices: 103476--103500 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
103466 GCTTGAGGAT
103476 CTTTTTCTCATA
1 CTTTTTCTCATA
103488 CTTTTTCTCATA
1 CTTTTTCTCATA
103500 C
1 C
103501 CTATGGTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (12 bp):
CTTTTTCTCATA
Found at i:105203 original size:20 final size:21
Alignment explanation
Indices: 105178--105222 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
105168 TTAACTTTTG
*
105178 ATTTAAT-TTATAAT-TTCTTT
1 ATTTAATGTTA-AATATTCATT
105198 ATTTAATGTTAAATATTCATT
1 ATTTAATGTTAAATATTCATT
105219 ATTT
1 ATTT
105223 TGTTAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTTAATGTTAAATATTCATT
Found at i:108213 original size:16 final size:16
Alignment explanation
Indices: 108195--108269 Score: 98
Period size: 16 Copynumber: 4.8 Consensus size: 16
108185 ATTTTTGGGT
*
108195 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAATG
*
108211 ACCCGAATCC-AAATG
1 ACCCGAACCCGAAATG
108226 ACCCGAACCCGAAATG
1 ACCCGAACCCGAAATG
* *
108242 ACCCAAACCCAAAATG
1 ACCCGAACCCGAAATG
*
108258 ATCCGAACCCGA
1 ACCCGAACCCGA
108270 TCAACCCAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
15 13 0.26
16 37 0.74
ACGTcount: A:0.40, C:0.37, G:0.13, T:0.09
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Found at i:108233 original size:31 final size:32
Alignment explanation
Indices: 108195--108269 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 32
108185 ATTTTTGGGT
* * *
108195 ACCCGAACCCGAAATTACCCGAATCC-AAATG
1 ACCCGAACCCGAAATGACCCAAACCCAAAATG
108226 ACCCGAACCCGAAATGACCCAAACCCAAAATG
1 ACCCGAACCCGAAATGACCCAAACCCAAAATG
*
108258 ATCCGAACCCGA
1 ACCCGAACCCGA
108270 TCAACCCAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 23 0.59
32 16 0.41
ACGTcount: A:0.40, C:0.37, G:0.13, T:0.09
Consensus pattern (32 bp):
ACCCGAACCCGAAATGACCCAAACCCAAAATG
Found at i:109311 original size:2 final size:2
Alignment explanation
Indices: 109295--109336 Score: 52
Period size: 2 Copynumber: 21.0 Consensus size: 2
109285 GAAAGTCTAT
109295 TA TA T- TA TA TA -A TA TA TA TA TA TA TA GTA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
109337 GATCAGAGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 2 0.06
2 30 0.83
3 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:109318 original size:13 final size:13
Alignment explanation
Indices: 109295--109336 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
109285 GAAAGTCTAT
109295 TATAT-TATATAA
1 TATATATATATAA
109307 TATATATATAT-A
1 TATATATATATAA
*
109319 TAGTATATATATAG
1 TA-TATATATATAA
109333 TATA
1 TATA
109337 GATCAGAGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 8 0.31
13 16 0.62
14 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (13 bp):
TATATATATATAA
Found at i:109330 original size:11 final size:11
Alignment explanation
Indices: 109295--109336 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
109285 GAAAGTCTAT
*
109295 TATATTATATAA
1 TATAGTATAT-A
109307 TATA-TATATA
1 TATAGTATATA
109317 TATAGTATATA
1 TATAGTATATA
109328 TATAGTATA
1 TATAGTATA
109337 GATCAGAGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 5 0.17
11 20 0.69
12 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (11 bp):
TATAGTATATA
Found at i:109639 original size:16 final size:16
Alignment explanation
Indices: 109618--109648 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
109608 AATTGTAACA
109618 ACCCGAACCCGAAAAG
1 ACCCGAACCCGAAAAG
*
109634 ACCCGAACCTGAAAA
1 ACCCGAACCCGAAAA
109649 CCCGAGGTTC
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:0.45, C:0.35, G:0.16, T:0.03
Consensus pattern (16 bp):
ACCCGAACCCGAAAAG
Found at i:109729 original size:15 final size:17
Alignment explanation
Indices: 109694--109731 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
109684 GACCCGAAAC
109694 GACCC-AACCCAGAATT
1 GACCCGAACCCAGAATT
109710 GACCCGAACCCA-AA-T
1 GACCCGAACCCAGAATT
109725 GACCCGA
1 GACCCGA
109732 CATTTGATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.37, C:0.39, G:0.16, T:0.08
Consensus pattern (17 bp):
GACCCGAACCCAGAATT
Found at i:110374 original size:19 final size:20
Alignment explanation
Indices: 110356--110391 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
110346 AATTAATTAT
110356 TTTA-ATATTA-ATTTTTTA
1 TTTATATATTATATTTTTTA
110374 TTTATATATTATATTTTT
1 TTTATATATTATATTTTT
110392 ACTTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 6 0.38
20 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATATATTATATTTTTTA
Found at i:110503 original size:19 final size:19
Alignment explanation
Indices: 110479--110529 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
110469 TTATACAAGA
* * *
110479 TAATTTTTATTTATTCATT
1 TAATTTTAATTAATTAATT
110498 TAATTTTAATTAATTAATT
1 TAATTTTAATTAATTAATT
*
110517 TATTATTTAATTA
1 TAAT-TTTAATTA
110530 TAAAGCAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TAATTTTAATTAATTAATT
Found at i:111795 original size:61 final size:61
Alignment explanation
Indices: 111720--111841 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
111710 AGTCCGGTGA
* *
111720 CTCCAAACCATTTCTTTTAGGGATACAATAAAATCTCATTAGAATTAGTTAGAATAATTCT
1 CTCCAAACCATTTCTTTTAGAGATACAATAAAATCTCATTAGAATTAGTCAGAATAATTCT
111781 CTCCAAACCATTTCTTTTAGAGATACAATAAAATCTCATTAGAATTAGTCAGAATAATTCT
1 CTCCAAACCATTTCTTTTAGAGATACAATAAAATCTCATTAGAATTAGTCAGAATAATTCT
111842 TTATATGTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (61 bp):
CTCCAAACCATTTCTTTTAGAGATACAATAAAATCTCATTAGAATTAGTCAGAATAATTCT
Done.