Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013726.1 Corchorus capsularis cultivar CVL-1 contig13747, 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: 100368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:25 original size:15 final size:16
Alignment explanation
Indices: 5--34 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1 AATA
5 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
20 ATATTATAATCTAAA
1 ATATTATAATCTAAA
35 AATAATCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:1200 original size:21 final size:19
Alignment explanation
Indices: 1157--1200 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
1147 AATTTTGTTG
**
1157 TATTTTTATTTATTTTTAA
1 TATTTTTATTTATTTGCAA
1176 TATTTATTATTTAGTTTGCAA
1 TATTT-TTATTTA-TTTGCAA
1197 TATT
1 TATT
1201 ATCCTTGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 7 0.33
21 9 0.43
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (19 bp):
TATTTTTATTTATTTGCAA
Found at i:11756 original size:31 final size:31
Alignment explanation
Indices: 11721--11786 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
11711 AACTTTATGT
*
11721 TTTCCGATTGTACCCCTATT-TTTAAAACATA
1 TTTCCAATTGTA-CCCTATTCTTTAAAACATA
*
11752 TTTCCAATTGTACCCTTTTCTTTAAAACATA
1 TTTCCAATTGTACCCTATTCTTTAAAACATA
11783 TTTC
1 TTTC
11787 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.45
Consensus pattern (31 bp):
TTTCCAATTGTACCCTATTCTTTAAAACATA
Found at i:12412 original size:22 final size:22
Alignment explanation
Indices: 12384--12523 Score: 86
Period size: 22 Copynumber: 6.3 Consensus size: 22
12374 TGTCTCTATG
*
12384 TGGTTATCAAAATTTAATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
12406 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
*
12429 -GGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
12450 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * * * *
12472 TCAGGTTATTAAAATCTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
12496 TGGTTATTGAAATTTCATATGG
1 TGGTTATCAAAATTTCATAAGA
12518 TGGTTA
1 TGGTTA
12524 ATTATCACAA
Statistics
Matches: 91, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.01
22 69 0.76
23 4 0.04
24 17 0.19
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:12464 original size:44 final size:43
Alignment explanation
Indices: 12385--12471 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 43
12375 GTCTCTATGT
** *
12385 GGTTATCAAAATTTAATAAGATGGTTATTATAATTTCATGAGGA
1 GGTTATCAAAATTTAATAAGATGGTTACCAAAATTTCAT-AGGA
* *
12429 GGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCATAGGA
1 GGTTATCAAAATTTAATAAG-ATGGTTACCAAAATTTCATAGGA
12472 TCAGGTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 6 0.16
44 31 0.84
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (43 bp):
GGTTATCAAAATTTAATAAGATGGTTACCAAAATTTCATAGGA
Found at i:12659 original size:22 final size:21
Alignment explanation
Indices: 12634--12942 Score: 141
Period size: 22 Copynumber: 14.0 Consensus size: 21
12624 TTTCATGGGG
12634 AGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* *
12656 AGGTTAT-AAAAGTCTCAATTTCATA
1 AGGTTATCAAAA-TTTC-A--T-AGA
* * *
12681 AGGAGTACCAAAATTTGATAGA
1 AGG-TTATCAAAATTTCATAGA
*
12703 AGGTTATC-AAATCTCATAG-
1 AGGTTATCAAAATTTCATAGA
*
12722 AGTGATTATCGAAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
12745 GATCGGATTATCAAAATTT-ATAGAA
1 -A--GG-TTATCAAAATTTCATAG-A
*
12770 AGATTATCAAAATTTCATAG-
1 AGGTTATCAAAATTTCATAGA
* * *
12790 TGTTGTTATCAAAATTTCAAAGCG
1 AG--GTTATCAAAATTTCATAG-A
*
12814 AGGTTATCAAAATTACATA-A
1 AGGTTATCAAAATTTCATAGA
* *
12834 TGTGATTATCAGAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
* * * * *
12857 GGGGTCAACAAAATTTTATAAA
1 -AGGTTATCAAAATTTCATAGA
*
12879 GAGGTTATCAAAATTTCATAAA
1 -AGGTTATCAAAATTTCATAGA
*
12901 GAGGTTATCAAATTTTCA-A-A
1 -AGGTTATCAAAATTTCATAGA
12921 ATGTGATTA-CAAAATTTCATAG
1 A-G-G-TTATCAAAATTTCATAG
12943 TGGTATTTCT
Statistics
Matches: 222, Mismatches: 36, Indels: 57
0.70 0.11 0.18
Matches are distributed among these distances:
19 3 0.01
20 14 0.06
21 36 0.16
22 127 0.57
23 4 0.02
24 8 0.04
25 20 0.09
26 6 0.03
27 4 0.02
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:12730 original size:21 final size:23
Alignment explanation
Indices: 12689--12942 Score: 153
Period size: 22 Copynumber: 11.6 Consensus size: 23
12679 TAAGGAGTAC
* *
12689 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
12710 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
12731 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAGAGAT--GATTAT
*
12756 CAAAATTT-ATAGA-AAGATTAT
1 CAAAATTTCATAGAGATGATTAT
* *
12777 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
12799 CAAAATTTCAAAGCGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
12821 CAAAATTACATA-ATG-TGATTAT
1 CAAAATTTCATAGA-GATGATTAT
* * * * *
12843 CAGAATTTCATAGAG-GGGTCAA
1 CAAAATTTCATAGAGATGATTAT
* * *
12865 CAAAATTTTATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
12887 CAAAATTTCATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
12909 CAAATTTTCA-AAATG-TGATTA-
1 CAAAATTTCATAGA-GATGATTAT
12930 CAAAATTTCATAG
1 CAAAATTTCATAG
12943 TGGTATTTCT
Statistics
Matches: 185, Mismatches: 32, Indels: 31
0.75 0.13 0.12
Matches are distributed among these distances:
20 10 0.05
21 34 0.18
22 119 0.64
23 4 0.02
24 5 0.03
25 13 0.07
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:12843 original size:44 final size:44
Alignment explanation
Indices: 12750--12939 Score: 181
Period size: 44 Copynumber: 4.4 Consensus size: 44
12740 ATAGAGATCG
* * * *
12750 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATG-T
* *
12794 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * * * *
12837 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * *
12881 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
12925 GATTA-CAAAATTTCA
1 GATTATCAAAATTTCA
12940 TAGTGGTATT
Statistics
Matches: 115, Mismatches: 28, Indels: 7
0.77 0.19 0.05
Matches are distributed among these distances:
43 24 0.21
44 90 0.78
45 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:13054 original size:20 final size:20
Alignment explanation
Indices: 13029--13101 Score: 87
Period size: 19 Copynumber: 3.6 Consensus size: 20
13019 TTATGGAGTA
13029 ATCAAAATTTCA-AGTAGGAT
1 ATCAAAATTTCAGAG-AGGAT
13049 ATCAAAA-TTCAGAGAGGAT
1 ATCAAAATTTCAGAGAGGAT
* *
13068 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCAGA-G-AGGAT
13090 ATCAAAATTTCA
1 ATCAAAATTTCA
13102 TAGTTTAGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
19 16 0.34
20 14 0.30
21 1 0.02
22 16 0.34
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (20 bp):
ATCAAAATTTCAGAGAGGAT
Found at i:13095 original size:22 final size:22
Alignment explanation
Indices: 13029--13549 Score: 165
Period size: 22 Copynumber: 24.0 Consensus size: 22
13019 TTATGGAGTA
* *
13029 ATCAAAATTTCA-A-GTAGGAT
1 ATCAAAATTTCATATGAAGGTT
* *
13049 ATCAAAA-TTCAGA-G-AGGAT
1 ATCAAAATTTCATATGAAGGTT
13068 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
**
13090 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * * * *
13112 TTCAAAATCTCACAAGAGGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
13134 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
* * * *
13156 ATCAAAATTGCATAGGGAGATT
1 ATCAAAATTTCATATGAAGGTT
*
13178 AACAAAATTTCATAATG-AGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
** * *
13200 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
*
13222 ATCAAAA--T--T-TGTA-GTT
1 ATCAAAATTTCATATGAAGGTT
* * *
13238 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATATGAAGGTT
* * **
13260 ATCAAAATTTTATAGGGTGGTTT
1 ATCAAAATTTCATATGAAGG-TT
* * *
13283 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATATGAAG-GTT
*
13306 ATCAAAATTTCATA-GCGAGGTT
1 ATCAAAATTTCATATG-AAGGTT
*
13328 ATCACAATTTCATAGTGTAA--TT
1 ATCAAAATTTCATA-TG-AAGGTT
* ** *
13350 ATCAAAATTTCAGA-GTCTGATT
1 ATCAAAATTTCATATG-AAGGTT
*
13372 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATATGAAGGTT
* * ** * *
13394 TTTAATTTTTCATAACG-TGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
* * *
13416 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * **
13438 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGAAGGTT
13461 ATCAAAATTTCAT-TGGGAA-GTT
1 ATCAAAATTTCATAT--GAAGGTT
13483 ATCAAAATTTCATATTG-AGGTCT
1 ATCAAAATTTCATA-TGAAGGT-T
* * * *
13506 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
13527 AACCAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
13549 A
1 A
13550 AAAAAGAAAT
Statistics
Matches: 374, Mismatches: 88, Indels: 76
0.70 0.16 0.14
Matches are distributed among these distances:
16 9 0.02
17 2 0.01
18 2 0.01
19 16 0.04
20 18 0.05
21 15 0.04
22 242 0.65
23 67 0.18
24 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:13484 original size:45 final size:45
Alignment explanation
Indices: 13411--13496 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
13401 TTTCATAACG
* * *
13411 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
13456 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
13497 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:13632 original size:44 final size:44
Alignment explanation
Indices: 13029--13630 Score: 266
Period size: 44 Copynumber: 13.8 Consensus size: 44
13019 TTATGGAGTA
* * * *
13029 ATCAAAATTTCA-A-GTAGGATATCAAAA-TTCAGAG-A-GGAT
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTATGGTT
* * *
13068 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTT
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTATGGTT
* * * * * *
13112 TTCAAAATCTCACAAGAGGGTTATCAAAATTTCATAGTAT-GTAG
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTATGGT-T
* * * * *
13156 ATCAAAATTGCATAGGGAGATTAACAAAATTTCATAATGA-GGTT
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGT-ATGGTT
** *
13200 ATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-GTA--GTT
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTATGGTT
* * * * **
13238 ATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGTGGTTT
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTATGG-TT
* * *
13283 ATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGA-GGTT
1 ATCAAAATTTCATAGGAAG-GTTATCAAAATTTCATAG-TATGGTT
* * * *
13328 ATCACAATTTCATAGTGTAA--TTATCAAAATTTCAGAGTCTGATT
1 ATCAAAATTTCATAG-G-AAGGTTATCAAAATTTCATAGTATGGTT
* * ** ***
13372 A-CTAACAA-TTCATATGG-AGGTTTTTAATTTTTCATAACGTGGTT
1 ATC-AA-AATTTCATA-GGAAGGTTATCAAAATTTCATAGTATGGTT
* * * * *
13416 ATCAATATATCATATGG-AGGTTATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-GGAAGGTTATCAAAATTTCATAGT-ATGGTT
* *
13461 ATCAAAATTTCATTGGGAA-GTTATCAAAATTTCATATTGA-GGTCT
1 ATCAAAATTTCA-TAGGAAGGTTATCAAAATTTCATAGT-ATGGT-T
* * * * * *
13506 -TCAAAATTCCTTAGGGAGGTTAACCAAATTTCATAAG-AAGGTT
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT-AGTATGGTT
** * * * * * * *
13549 AAAAAAGAAATTT-ATA-AAATGATTCTCGAAATTCCATAATATCGTT
1 --ATCA-AAATTTCATAGGAA-GGTTATCAAAATTTCATAGTATGGTT
*
13595 ATTAAAATTTCATAGGAAGGTTATCAAAATTTCATA
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
13631 ATGAGATCAT
Statistics
Matches: 415, Mismatches: 106, Indels: 79
0.69 0.18 0.13
Matches are distributed among these distances:
38 26 0.06
39 15 0.04
40 2 0.00
41 14 0.03
42 8 0.02
43 18 0.04
44 205 0.49
45 79 0.19
46 40 0.10
47 8 0.02
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (44 bp):
ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTATGGTT
Found at i:14889 original size:15 final size:16
Alignment explanation
Indices: 14864--14893 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
14854 AATAATTATT
14864 TTTAGATTATAATATA
1 TTTAGATTATAATATA
14880 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
14894 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:15957 original size:332 final size:330
Alignment explanation
Indices: 15245--17757 Score: 1751
Period size: 332 Copynumber: 7.5 Consensus size: 330
15235 AAACTTCACA
* * * * * * *
15245 TCATCTAATCAAATCTCTA-CAACATTGGATTTAAGAGTTTGTTATTACGAGTATCTGAATCTTG
1 TCATCTAATCAAATCTC-AGCCACATTGGATTTAAAAATTTGTTTTTACAAGCATCTAAATCTTG
* * * * *
15309 TTTCGATTTAATTAAAAATTAATTTAGAAAAACTAAGAAATACGATATTAAAAGCGTAAAAAGCC
65 TTTCGATTTAATTAGAAATTAATTCAGAAAAA-TATGAAAAACGATATTAAAAGCG-GAAAAGCC
* *
15374 CTCCAAT-TTTTTCGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGAAGA
128 CTTCAATCTTTTT-GGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGAA-A
* * * * * * *
15437 A-ATCTTTTGTGTCAATTTTTTGCAAAATTTAAGCTGAAATCGTTACTAACAAATCATCACGGTT
191 ATATCTTTTGGGTCAATTTTTTACAAAATTTTAGCCGAAATCG-T-GTAA-TAATCATCACAGTT
* * ** * ** * * * *
15501 TTTGGCTAAAAA-CG-CATTACGGAGACCCGAATCAATTTTGCATGATTTCCGACTCCGAGACTA
253 TTTGGCTAAAAAGCGTC-TT--GGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTC
*
15564 CTTGAAATATCCATAT
315 CTTGAAATATCTATAT
* * * ** * * *
15580 TCATCTAATAAAATCTCA-CCAACCTTAGATTTAAGGATTTGTTTTTACAAGTATCTGAATTTTG
1 TCATCTAATCAAATCTCAGCC-ACATTGGATTTAAAAATTTGTTTTTACAAGCATCTAAATCTTG
* * * * *
15644 TTTTGATTTAATTAGAGATTAATT-TGGAAAATAGGAAAAACGATATTAGAAA-CGGAAAAAGCC
65 TTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTA-AAAGCGG-AAAAGCC
15707 CTTCAATCTTTTTGGCATTGAGA-TATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGAAAA
128 CTTCAATCTTTTTGGCATTGA-ATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGAAAA
* * *
15771 TATCTTTTGGGTCAATTTTTTTTACAAACTTTTAGCCGAAATCATGTAATAATCATCACAATTTT
192 TATCTTTTGGGTCAA--TTTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACAGTTTT
* *
15836 TGGATAAAAAGCGTCTTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGA
255 TGGCTAAAAAGCGTCTTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
*
15901 GATATCTATAT
320 AATATCTATAT
15912 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACAAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACAAGCATCTAAATCTTGT
* * * * * *
15977 TTCAATTTAATTGGAAATTAATACAGAAAAATATGAAAAACGATATGAAAATCGTGAAAAGTCCT
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCG-GAAAAGCCCT
* ** * * *
16042 CCAATCTTTTTTCCATTAAATTATATATATATATATATGAGTATTTTATCCAAAAATTGAGGAAA
130 TCAATCTTTTTGGCATTGAATTATATAT-T-T-TTTATGAGTATTTTAGCCAAAAATTGA-GAAA
** * ** * * * * * * **
16107 A-AT-TTTTCAAGTC-TTTTTTTTTAAAATTTTTGCCAAAATCTTATACTAACCATCATGGTTTT
191 ATATCTTTT-GGGTCAATTTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACAGTTTT
* * * * * * *
16169 TTGCTAAAAAGTAAAAACG-CATTTAGGGGCACCAGCTTAGTTTTGCATGATTTTTTGCGCTAAC
255 TGGCTAAAAAG------CGTC--TT-GGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAG
*
16233 ACTCCTTGAAATAACTATAT
311 ACTCCTTGAAATATCTATAT
* * ** * * *
16253 TCATCTAATAAAATCAT-AGCTACATTACATTT-AATATTT-TTTTTACAAGCATCTGAATCATG
1 TCATCTAATCAAATC-TCAGCCACATTGGATTTAAAAATTTGTTTTTACAAGCATCTAAATCTTG
* * * * *
16315 TTTCGATTTAATTAGAAATTAATACAAAAAGAATATGAATAACAATATTAAAAGCGTCAAAAGCC
65 TTTCGATTTAATTAGAAATTAATTCAGAAA-AATATGAAAAACGATATTAAAAGCG-GAAAAGCC
** * * * * *
16380 CTTCAATCTTTTTGGTGTTGAATTGT-TATTTTTTCTGAGTATTAT-GACTAAAAATTGAGGAAA
128 CTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAG-CCAAAAATTGAGAAAA
* * * *
16443 TATCTTTCGGGTCAA-TTTTTGCAAAATTTTAACCAAAATCGTGTAATAATCATCACAGTTTTTT
192 TATCTTTTGGGTCAATTTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACAG--TTTT
* * * * * * * * *
16507 TGGCTAAAAACACGTTTTGGGGCCCC-ACTTCAGTTTCGAATAATTTTTGACGCTAAG-CTACTT
255 TGGCTAAAAA-GCGTCTTGGGGCCCCGGC-TCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT
* * *
16570 TATATATCCATAT
318 GAAATATCTATAT
* * * * *
16583 TCATCTAATCAAATCTCAACCACATTGCATTTAAAGATTTGTTTTTACGAGCATCTAAATCTTAT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACAAGCATCTAAATCTTGT
* * * * * *
16648 TTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAATGAAATGAAAAGCATGAAAAGTCCT
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGC-GGAAAAGCCCT
* * * * * * *
16713 CCAATCTTTTTGACGTTAAATTTTATATATTTCATGAGTATTTTAGCCAAAAAATTGAGACAAA-
130 TCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCC-AAAAATTGAGA-AAAT
** * * * * *
16777 AAATTTT-GGTC-ATTTTTTTCAAAATTTTAGGCGAAATCGTGTACTAACCATCACGGGTTTTTT
193 ATCTTTTGGGTCAATTTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCAC-AG---TTT
** * * * * * * ***
16840 TTTTCTAAAAACACGT-TTCGGGTCTCGGCTCAGTTTTGTATGATTTTTAGCGTTGAGACTCCTT
254 TTGGCTAAAAA-GCGTCTTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT
*
16904 GAAATATATATATATATATATATATATAT
318 G--------------A-A-ATATCTATAT
* * *
16933 TCATCTAATCAAATCTCAGCCACATTGAATTTAAAGATTTTGTTTTTACGAGCATCTAAATCTTG
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAA-AATTTGTTTTTACAAGCATCTAAATCTTG
* * * ***
16998 TTTTGATTTAA-CACGAAATTAATTCAGAAAAATATGAAAACCGATATTAAAAGCGTGAAAATTT
65 TTTCGATTTAATTA-GAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCG-GAAAAGCC
* ** * *
17062 C-TCTAATATTTTTGG-AGTTGAATTATATAAATTTTATGAGTATCTTAGACAAAAATTGAAGAA
128 CTTC-AATCTTTTTGGCA-TTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTG-AGAA
* * * * * * *
17125 AACTAT-TTCT-GGTCAA-TTTTTGCAAAATATTAGTCGAAATCGCGTACGTTAGTCGGAATCAC
190 AA-TATCTTTTGGGTCAATTTTTTACAAAATTTTAGCCGAAATCGTGTA--ATAATC---ATCAC
* * * * * * * * *
17187 GGTTTTTTGCTAAAAACGCGT-TCTGGGGCCCCAGTTCAATGTTGCATTATTTTTTGCGCCGAGA
249 AGTTTTTGGCTAAAAA-GCGTCT-TGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGA
* * *
17251 CTCCTTCAATTATCTATCT
312 CTCCTTGAAATATCTATAT
* * * * * * ** *** * *
17270 TAAGCTAACCAAATCTCATCCATAATGGATTTAAGGATTTG-TAAAACAAGTATCTAAATCATGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACAAGCATCTAAATCTTGT
* * * *
17334 TTCGATTTAATTATAAATTAATTCAGAAAATAATAGGAAAAACGATATTGGAAA-CATGAAAAGC
66 TTCGATTTAATTAGAAATTAATTCAG-AAA-AATATGAAAAACGATATT-AAAAGC-GGAAAAGC
* * * * * * * * * *
17398 GCTTCAATCTTATTGTCGTTGAATTATATAATTTTTATGAGTATTGTGGCTAAAAAATGAGGAAA
127 CCTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGAAAA
* * * * * *
17463 TAACTTTCGAGTCAA-TTTTTACAAAATTCTAGCCGAAAGCGTGTAATAATCATCACAGTTGTTG
192 TATCTTTTGGGTCAATTTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACAGTTTTTG
** * ** * * *
17527 GCTAAAAA-CG-CGTTCCGGCACACGAAT-ATGTTTTGCACGATTTTTGGCGTCAAGACTCTTTG
257 GCTAAAAAGCGTC-TTGGGGC-CCCGGCTCA-GTTTTGCATGATTTTTGGCGCCAAGACTCCTTG
* *
17589 AGATATCCATAT
319 AAATATCTATAT
* * * * * *
17601 TCATCTAACCAAATCTCAGCTACCTCGGATTTAAGAATTTGTTTTTA-AGAGCATCTGAATCTTG
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACA-AGCATCTAAATCTTG
* * * *
17665 TTTCGATTTAATTAAAAATTAATTCAGAAAAATATGAAAAACAATATTAAAAGTGTGAAAAG-TC
65 TTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCG-GAAAAGCCC
*
17729 TTACAATCTTTTTGGCATTAAATTATATA
129 TT-CAATCTTTTTGGCATTGAATTATATA
17758 CTCCCTCCGT
Statistics
Matches: 1714, Mismatches: 361, Indels: 211
0.75 0.16 0.09
Matches are distributed among these distances:
329 7 0.00
330 92 0.05
331 153 0.09
332 284 0.17
333 212 0.12
334 98 0.06
335 128 0.07
336 126 0.07
337 137 0.08
338 21 0.01
339 54 0.03
340 55 0.03
341 76 0.04
342 1 0.00
348 1 0.00
350 54 0.03
351 150 0.09
352 20 0.01
353 38 0.02
355 2 0.00
356 5 0.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (330 bp):
TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACAAGCATCTAAATCTTGT
TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGGAAAAGCCCTT
CAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGAAAATATC
TTTTGGGTCAATTTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCATCACAGTTTTTGGCTA
AAAAGCGTCTTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATC
TATAT
Found at i:16625 original size:671 final size:669
Alignment explanation
Indices: 15564--16839 Score: 1599
Period size: 671 Copynumber: 1.9 Consensus size: 669
15554 TCCGAGACTA
* * *
15564 CTTGAAATATCCATATTCATCTAATAAAATCTCACCAACCTTAGATTTAAGGATTTGTTTTTACA
1 CTTGAAATAACCATATTCATCTAATAAAATCTCACCAACATTACATTTAAGGATTTGTTTTTACA
* ** * * **** *
15629 AGTATCTGAATTTTGTTTTGATTTAATTAGAGATTAATTTGGAAAATAGGAAAAACGATATTAGA
66 AGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATCAAAAAAATAGGAAAAACAATATTAGA
*
15694 AACGGAAAAAGCCCTTCAATCTTTTTGGCATTGAGATATATATTTTTTATGAGTATTTTAGCCAA
131 AACGGAAAAAGCCCTTCAATCTTTTTGGCATTGAGATATATATTTTTTATGAGTATTTGAGCCAA
* * * *
15759 AAATTGAGAAAATATCTTTTGGGTCAATTTTTTTTACAAACTTTTAGCCGAAATCATGTAATAAT
196 AAATTGAGAAAATATCTTTCGGGTCAA--TTTTTTACAAAATTTTAACCAAAATCATGTAATAAT
* * * * * **
15824 CATCACAATTTTTGGATAAAAAGCGTCTTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGCC
259 CATCACAATTTTTGGATAAAAAACGTCTTGGGGCCCCGACTCAGTTTCGAATAATTTTTGACGCC
* * * *
15889 AAGACTCCTTGAGATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGT
324 AAGACTACTTGAGATATCCATATTCATCTAATCAAATCTCAACCACATTGCATTTAAAAATTTGT
* * *
15954 TTTTACAAGCATCTAAATCTTGTTTCAATTTAATTGGAAATTAATACAGAAAAATATGAAAAACG
389 TTTTACAAGCATCTAAATCTTATTTCAATTTAATTAGAAATTAATACAAAAAAATATGAAAAACG
* * * **
16019 ATATGAAAATCGTGAAAAGTCCTCCAATCTTTTTTCCATTAAATTATATATATATATAT-ATGAG
454 AAATGAAAAGCATGAAAAGTCCTCCAATCTTTTTGACATTAAATT-T-TATATAT-T-TCATGAG
* * * * * *
16083 TATTTTATCC-AAAAATTGAG-GAAAAATTTTTCAAGTCTTTTTTTTTAAAATTTTTGCCAAAAT
515 TATTTTAGCCAAAAAATTGAGACAAAAAATTTT--AGTCATTTTTTTCAAAATTTTAGCCAAAAT
* *
16146 CTTATACTAACCATCA-TGGTTTTTTGCTAAAAAGTAAAAACGCATTTAGGGGCACCAGCTTAGT
578 CGTATACTAACCATCACGGGTTTTTTGCTAAAAAGTAAAAACGCATTTAGGGGCACCAGCTTAGT
16210 TTTGCATGATTTTTTGCGCTAACACTC
643 TTTGCATGATTTTTTGCGCTAACACTC
* * * *
16237 CTTGAAATAACTATATTCATCTAATAAAATCAT-AGCTACATTACATTTAA-TATTT-TTTTTAC
1 CTTGAAATAACCATATTCATCTAATAAAATC-TCACCAACATTACATTTAAGGATTTGTTTTTAC
* *
16299 AAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATACAAAAAGAATATGAATAACAATATT
65 AAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAAT-CAAAAA-AATAGGAAAAACAATATT
** ** * *
16364 A-AAAGCGTCAAAAGCCCTTCAATCTTTTTGGTGTTGA-AT-TGTTATTTTTTCTGAGTATTATG
128 AGAAA-CGGAAAAAGCCCTTCAATCTTTTTGGCATTGAGATAT-ATATTTTTTATGAGTATT-TG
* * * *
16426 A-CTAAAAATTGAGGAAATATCTTTCGGGTCAA-TTTTTGCAAAATTTTAACCAAAATCGTGTAA
190 AGCCAAAAATTGAGAAAATATCTTTCGGGTCAATTTTTTACAAAATTTTAACCAAAATCATGTAA
* * *
16489 TAATCATCACAGTTTTTTTGGCTAAAAACACGTTTTGGGGCCCC-ACTTCAGTTTCGAATAATTT
255 TAATCATCACA--ATTTTTGGATAAAAA-ACGTCTTGGGGCCCCGAC-TCAGTTTCGAATAATTT
* * *
16553 TTGACGCTAAG-CTACTTTATATATCCATATTCATCTAATCAAATCTCAACCACATTGCATTTAA
316 TTGACGCCAAGACTACTTGAGATATCCATATTCATCTAATCAAATCTCAACCACATTGCATTTAA
* * * *
16617 AGATTTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTAATTCAAAAAAATAT
381 AAATTTGTTTTTACAAGCATCTAAATCTTATTTCAATTTAATTAGAAATTAATACAAAAAAATAT
* *
16682 GAAAAATGAAATGAAAAGCATGAAAAGTCCTCCAATCTTTTTGACGTTAAATTTTATATATTTCA
446 GAAAAACGAAATGAAAAGCATGAAAAGTCCTCCAATCTTTTTGACATTAAATTTTATATATTTCA
* * *
16747 TGAGTATTTTAGCCAAAAAATTGAGACAAAAAATTTTGGTCATTTTTTTCAAAATTTTAGGCGAA
511 TGAGTATTTTAGCCAAAAAATTGAGACAAAAAATTTTAGTCATTTTTTTCAAAATTTTAGCCAAA
*
16812 ATCGTGTACTAACCATCACGGGTTTTTT
576 ATCGTATACTAACCATCACGGGTTTTTT
16840 TTTTCTAAAA
Statistics
Matches: 512, Mismatches: 77, Indels: 32
0.82 0.12 0.05
Matches are distributed among these distances:
667 1 0.00
668 53 0.10
669 62 0.12
670 10 0.02
671 207 0.40
672 90 0.18
673 88 0.17
674 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (669 bp):
CTTGAAATAACCATATTCATCTAATAAAATCTCACCAACATTACATTTAAGGATTTGTTTTTACA
AGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATCAAAAAAATAGGAAAAACAATATTAGA
AACGGAAAAAGCCCTTCAATCTTTTTGGCATTGAGATATATATTTTTTATGAGTATTTGAGCCAA
AAATTGAGAAAATATCTTTCGGGTCAATTTTTTACAAAATTTTAACCAAAATCATGTAATAATCA
TCACAATTTTTGGATAAAAAACGTCTTGGGGCCCCGACTCAGTTTCGAATAATTTTTGACGCCAA
GACTACTTGAGATATCCATATTCATCTAATCAAATCTCAACCACATTGCATTTAAAAATTTGTTT
TTACAAGCATCTAAATCTTATTTCAATTTAATTAGAAATTAATACAAAAAAATATGAAAAACGAA
ATGAAAAGCATGAAAAGTCCTCCAATCTTTTTGACATTAAATTTTATATATTTCATGAGTATTTT
AGCCAAAAAATTGAGACAAAAAATTTTAGTCATTTTTTTCAAAATTTTAGCCAAAATCGTATACT
AACCATCACGGGTTTTTTGCTAAAAAGTAAAAACGCATTTAGGGGCACCAGCTTAGTTTTGCATG
ATTTTTTGCGCTAACACTC
Found at i:16914 original size:2 final size:2
Alignment explanation
Indices: 16907--16932 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16897 ACTCCTTGAA
16907 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
16933 TCATCTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18930 original size:324 final size:327
Alignment explanation
Indices: 18112--19239 Score: 862
Period size: 327 Copynumber: 3.5 Consensus size: 327
18102 CCCGGCTTAG
* ** * * * *
18112 TTTTGCATCATTTTTTGCACCGAGACTCCTTGGAATATCTATATTCATTTAATCAAATCTCAGCC
1 TTTTGCATGATTTTTTGCGGCAAGACTCCTTAGAATATCTATATTCATCTAACCAAATCTCAGCC
* * * *
18177 ACATTGAAGTTAAGGAATTGTTTCTACGA-ACATCTGAATCTTTTTTCGATTTAATTACAAATTA
66 ACATTGAAGTTAAGG-ATTTTTTCTACGAGA-TTCTGAATCTTGTTTCGATTTAATTAAAAATTA
* * * * * *
18241 A--T-ACAGAAAATTATGAAAAACGATATTAAAAGCGTGAAGAGTCCTCCAATCTTCTTGGCTTT
129 ATTTGAAACAAAA-TAGGAAAAACGATATTAGAAGCGTGAAGAGACCTCCAATCTTCTTGGCATT
* * * * *
18303 TAATTATATATATTATATGAGTATTGTGGCTAAAAATGGAGGGAAAATATTTCTGATCAATTTTT
193 GAATTATATATATTATATGAGTATTGTGGCTAAAAATGGAGGAAAAATAATTCGGATAAATTTTT
* * * * ** *
18368 GTAAAATTTTAGCCGACATTGTCTAGCATCACGGCTTTTTGGTTAAAAACGCGTTTTGTGTCCCA
258 GTAAAATTTTAGCCAAAATTGTCTACCATCAC-GCTTTTTGGCTAAAAACGCGTTCAGGGTCCCA
*
18433 GGTCAG
322 GGTCAA
* * * * * *
18439 TTTTGCATGATTTTTAGTGGCAACACTCCTTAAAATATCTATATTCATCAAACCAAATCTTAGCC
1 TTTTGCATGATTTTTTGCGGCAAGACTCCTTAGAATATCTATATTCATCTAACCAAATCTCAGCC
* * * * * * * **
18504 ATATTGGATTTAAGGATTTTTTTTACAAGCATT-TGAATCATGTTTCAATTTAATTGGAAATTAA
66 ACATTGAAGTTAAGGATTTTTTCTACGAG-ATTCTGAATCTTGTTTCGATTTAATTAAAAATTAA
* *
18568 TTTGAAAACAAAATAGGAAAAACGATATTAGAAGCGTG-AGAAGACCTTCAATCTTTTTGGCATT
130 TTTG-AAACAAAATAGGAAAAACGATATTAGAAGCGTGAAG-AGACCTCCAATCTTCTTGGCATT
* * * * *
18632 GAATTATATATTTTTTTTGAGTATTGTGGCTAAAAATTGA-GAAAAATAATT-GGCTAAATTTTT
193 GAATTATATATATTATATGAGTATTGTGGCTAAAAATGGAGGAAAAATAATTCGGATAAATTTTT
* * ** * *
18695 GTAAAATTTTAGCCAAAATTGTGTACCTTCA-TTTTTTTTGCTAAAAACGCGTTCCAGGG-CTCT
258 GTAAAATTTTAGCCAAAATTGTCTACCATCACGCTTTTTGGCTAAAAACGCGTT-CAGGGTC-CC
18758 AGGTCAA
321 AGGTCAA
* *
18765 TTTTGCATGATTTTTTGCGGCAAGACT-CTT-GAATATATATATGCATCTAACCAAATCTCAGCC
1 TTTTGCATGATTTTTTGCGGCAAGACTCCTTAGAATATCTATATTCATCTAACCAAATCTCAGCC
* * * * * * *
18828 ACATTGTA-TTAAGGATTTATTTGTATGAGTTTCTAAAACTTGTTTCGATTTAATCAAAAATTAA
66 ACATTGAAGTTAAGGATTT-TTTCTACGAGATTCTGAATCTTGTTTCGATTTAATTAAAAATTAA
* * * * *
18892 TTTTGAAATAAAATAGGAAAAATGATATTAGCAGCGT---GA-A-----AA------TGGCTTTC
130 -TTTGAAACAAAATAGGAAAAACGATATTAGAAGCGTGAAGAGACCTCCAATCTTCTTGGCATTG
* * * * ** * *
18942 AATTAT-T-T-TT-TATGAGTATTTTTGCTAGAAATCGAGGAAAAATCTTTCAGG-TCAATTTTG
194 AATTATATATATTATATGAGTATTGTGGCTAAAAATGGAGGAAAAATAATTC-GGATAAATTTTT
* * * *
19002 GCAAAA-TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCGGCTAAAAACGCGTTGC-GAGG
258 GTAAAATTTTAGCCAAAAT--TGT-CT-ACCATCACGCTTTTTGGCTAAAAACGCGTT-CAG-GG
* * *
19065 -CCC-GACTTAG
317 TCCCAG-GTCAA
* * *
19075 TTTTGCATGATTTTTGGTGCCAAGACTCCTT-GATATATCTATATTCATCTAACCAAATCTCAGC
1 TTTTGCATGATTTTTTGCGGCAAGACTCCTTAGA-ATATCTATATTCATCTAACCAAATCTCAGC
* * * * ** *
19139 CACATT-AGATTTAAGGATTTGTTTTTATGAGCA-TATGAATCTTGTTTTAATTTAATTAGAAAT
65 CACATTGA-AGTTAAGGATTT-TTTCTACGAG-ATTCTGAATCTTGTTTCGATTTAATTAAAAAT
* * *
19202 TAATTCGGAA-AAAATAGGAAAAACAATATTAGAAGCGT
127 TAATTTGAAACAAAATAGGAAAAACGATATTAGAAGCGT
19240 TAAAAGCCCT
Statistics
Matches: 648, Mismatches: 126, Indels: 70
0.77 0.15 0.08
Matches are distributed among these distances:
305 20 0.03
306 22 0.03
307 13 0.02
308 6 0.01
309 14 0.02
310 34 0.05
311 52 0.08
312 40 0.06
313 45 0.07
315 2 0.00
320 1 0.00
321 1 0.00
322 1 0.00
323 12 0.02
324 94 0.15
325 26 0.04
326 69 0.11
327 100 0.15
328 13 0.02
329 77 0.12
330 6 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (327 bp):
TTTTGCATGATTTTTTGCGGCAAGACTCCTTAGAATATCTATATTCATCTAACCAAATCTCAGCC
ACATTGAAGTTAAGGATTTTTTCTACGAGATTCTGAATCTTGTTTCGATTTAATTAAAAATTAAT
TTGAAACAAAATAGGAAAAACGATATTAGAAGCGTGAAGAGACCTCCAATCTTCTTGGCATTGAA
TTATATATATTATATGAGTATTGTGGCTAAAAATGGAGGAAAAATAATTCGGATAAATTTTTGTA
AAATTTTAGCCAAAATTGTCTACCATCACGCTTTTTGGCTAAAAACGCGTTCAGGGTCCCAGGTC
AA
Found at i:19583 original size:6 final size:6
Alignment explanation
Indices: 19572--19598 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19562 AAAGCAAAGC
19572 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
19599 GCAAATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:19613 original size:13 final size:13
Alignment explanation
Indices: 19595--19629 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
19585 AATCTAAATC
19595 TAAAGCAAATTAA
1 TAAAGCAAATTAA
*
19608 TAAAGCAATTTAA
1 TAAAGCAAATTAA
19621 TAAAGCAAA
1 TAAAGCAAA
19630 CAATAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.23
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:26355 original size:43 final size:43
Alignment explanation
Indices: 26272--26356 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
26262 AAAATTAATT
* *
26272 AATTTTTTTTAAAGAAAAATCGGAAACCCTAAAAATAAAAACG
1 AATTTTTTTTAAAGAAAAATCGGAAAACCGAAAAATAAAAACG
** *
26315 AATTTTTTTTTTAGAAAAATCGGAAAAACGGAAAAA-AAAAAC
1 AATTTTTTTTAAAGAAAAATCGG-AAAACCGAAAAATAAAAAC
26357 TTTTTTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 27 0.75
44 9 0.25
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (43 bp):
AATTTTTTTTAAAGAAAAATCGGAAAACCGAAAAATAAAAACG
Found at i:26715 original size:6 final size:6
Alignment explanation
Indices: 26704--26730 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
26694 AAAGCAAAGC
26704 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
26731 GCAAATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:26745 original size:13 final size:13
Alignment explanation
Indices: 26727--26774 Score: 87
Period size: 13 Copynumber: 3.7 Consensus size: 13
26717 AATCTAAATC
26727 TAAAGCAAATTAA
1 TAAAGCAAATTAA
26740 TAAAGCAAATTAA
1 TAAAGCAAATTAA
*
26753 TAAAGCAATTTAA
1 TAAAGCAAATTAA
26766 TAAAGCAAA
1 TAAAGCAAA
26775 CAATAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:27699 original size:10 final size:10
Alignment explanation
Indices: 27684--27708 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
27674 GAGGACTCTA
27684 GAATTTTCTG
1 GAATTTTCTG
27694 GAATTTTCTG
1 GAATTTTCTG
27704 GAATT
1 GAATT
27709 GAGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:31207 original size:16 final size:16
Alignment explanation
Indices: 31186--31220 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
31176 ATCTGAAATA
31186 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
31202 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
31218 CTT
1 CTT
31221 TTTGAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:44709 original size:7 final size:6
Alignment explanation
Indices: 44687--44735 Score: 53
Period size: 6 Copynumber: 7.5 Consensus size: 6
44677 TCTATTTTCA
*
44687 TTTCCT TTTCAGT TTTCCCT TTTCCT TTTCCT TTTCCT ATTTCCAT TTT
1 TTTCCT TTTC-CT TTT-CCT TTTCCT TTTCCT TTTCCT -TTTCC-T TTT
44736 ATTATCTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
6 19 0.51
7 16 0.43
8 2 0.05
ACGTcount: A:0.06, C:0.29, G:0.02, T:0.63
Consensus pattern (6 bp):
TTTCCT
Found at i:47444 original size:8 final size:8
Alignment explanation
Indices: 47431--47461 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
47421 TCTTCCTATG
47431 CTTATGTT
1 CTTATGTT
47439 CTTATGTT
1 CTTATGTT
47447 CTTATGTT
1 CTTATGTT
47455 CTTATGT
1 CTTATGT
47462 ATAATAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (8 bp):
CTTATGTT
Found at i:51057 original size:4 final size:4
Alignment explanation
Indices: 51048--51081 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
51038 TGAAGAGGGG
*
51048 AATA AATA AATA CATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
51082 ATGTAGGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:51441 original size:49 final size:48
Alignment explanation
Indices: 51372--51465 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 48
51362 GACAGAAAAG
*
51372 AAAACAAACAGAAATCTTCATATTAATAAACCACGGCATATAGGATGA
1 AAAACAAACAGAAATCTTCATATTAATAAACCACGGCATACAGGATGA
* *
51420 AAAACAAGACAGAAATCTTCATATTAATAAAGCAGGGCATACAGGA
1 AAAACAA-ACAGAAATCTTCATATTAATAAACCACGGCATACAGGA
51466 AGGATAAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 7 0.17
49 35 0.83
ACGTcount: A:0.50, C:0.16, G:0.15, T:0.19
Consensus pattern (48 bp):
AAAACAAACAGAAATCTTCATATTAATAAACCACGGCATACAGGATGA
Found at i:51841 original size:84 final size:83
Alignment explanation
Indices: 51685--51850 Score: 208
Period size: 84 Copynumber: 2.0 Consensus size: 83
51675 AAAAGAAGGT
* * *
51685 TGAAGAACTTTTCTATCTATATTCAACATTGAAAACATCTAGTATGTCTGACATAAAATGGGATG
1 TGAAGAACTTTTCTATCTATATTCAACATTGAAAACATCTAATACGTCTGACAT-AAATGGGATA
*
51750 TCATGTGCTTCGATATGTC
65 TCATGTGCTTCAATATGTC
* * * * *
51769 TGAAGACCTTTTCTATCTATATTTAACATTGAGAGCATCTAATACGTCTTGACAT-AATGGGGTT
1 TGAAGAACTTTTCTATCTATATTCAACATTGAAAACATCTAATACGTC-TGACATAAAT-GGGAT
*
51833 ATCGTGTGCTTCAATATG
64 ATCATGTGCTTCAATATG
51851 CCAATTGCCA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
83 3 0.04
84 61 0.87
85 6 0.09
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (83 bp):
TGAAGAACTTTTCTATCTATATTCAACATTGAAAACATCTAATACGTCTGACATAAATGGGATAT
CATGTGCTTCAATATGTC
Found at i:71663 original size:16 final size:16
Alignment explanation
Indices: 71642--71674 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
71632 GATAGCCAAA
71642 AACCAAACATAATAAC
1 AACCAAACATAATAAC
71658 AACCAAACATAATAAC
1 AACCAAACATAATAAC
71674 A
1 A
71675 TCAGTATCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.64, C:0.24, G:0.00, T:0.12
Consensus pattern (16 bp):
AACCAAACATAATAAC
Found at i:72649 original size:21 final size:19
Alignment explanation
Indices: 72623--72661 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
72613 GAGTTATCTA
72623 TCTATAATTCTATATCTATAG
1 TCTATAA-TCTATA-CTATAG
72644 TCTATAATCTATACTATA
1 TCTATAATCTATACTATA
72662 TCTGTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.46
Consensus pattern (19 bp):
TCTATAATCTATACTATAG
Found at i:87233 original size:3 final size:3
Alignment explanation
Indices: 87225--87249 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
87215 TAATCTAAAA
87225 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
87250 TTGAACTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:95524 original size:17 final size:18
Alignment explanation
Indices: 95492--95525 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
95482 AAAATATATG
95492 AAGTAAAATAATTTTTAA
1 AAGTAAAATAATTTTTAA
*
95510 AAGTAACAT-ATTTTTA
1 AAGTAAAATAATTTTTA
95526 GCACATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (18 bp):
AAGTAAAATAATTTTTAA
Found at i:99157 original size:16 final size:18
Alignment explanation
Indices: 99138--99174 Score: 53
Period size: 15 Copynumber: 2.2 Consensus size: 18
99128 TATCCTTTTC
99138 TTTAATTTTA-TAA-TTA
1 TTTAATTTTAGTAACTTA
99154 TTT-ATTTTAGTAACTTA
1 TTTAATTTTAGTAACTTA
99171 TTTA
1 TTTA
99175 TAATAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 6 0.33
16 6 0.33
17 6 0.33
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTAATTTTAGTAACTTA
Found at i:99173 original size:17 final size:15
Alignment explanation
Indices: 99142--99175 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
99132 CTTTTCTTTA
99142 ATTTTATAATTATTT
1 ATTTTATAATTATTT
99157 ATTTTAGTAACTTATTT
1 ATTTTA-TAA-TTATTT
99174 AT
1 AT
99176 AATAAACAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 3 0.18
17 8 0.47
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
ATTTTATAATTATTT
Found at i:100147 original size:2 final size:2
Alignment explanation
Indices: 100140--100186 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
100130 TTCTTACTCG
100140 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
100182 TA TA T
1 TA TA T
100187 NTTTTTAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.