Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2714
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: 41377
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Found at i:8562 original size:51 final size:50
Alignment explanation
Indices: 8481--8642 Score: 137
Period size: 50 Copynumber: 3.2 Consensus size: 50
8471 GGGACGATGG
* * *
8481 GGAGTAT-CCGGATTAAAGGAAAATTGGTGTTTCAAAAATAAAACCGGGGTT
1 GGAGTATCCCCGATT-ATGGAAAATTAGTGTTTCAAAAATAAAA-CGGGGTT
* * * ** *
8532 GGAGTATCCCCGATTGTGGAAAATTCGTGTTTTAGCAATAAAACGGGATT
1 GGAGTATCCCCGATTATGGAAAATTAGTGTTTCAAAAATAAAACGGGGTT
* * * * * ** **
8582 GGAATATCACCGATTATGAAAAATTAATATTTGGAAAATAAGTCGGGGTT
1 GGAGTATCCCCGATTATGGAAAATTAGTGTTTCAAAAATAAAACGGGGTT
8632 GGAGTATCCCC
1 GGAGTATCCCC
8643 TCGGAAATAA
Statistics
Matches: 86, Mismatches: 24, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
50 51 0.59
51 29 0.34
52 6 0.07
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (50 bp):
GGAGTATCCCCGATTATGGAAAATTAGTGTTTCAAAAATAAAACGGGGTT
Found at i:8689 original size:27 final size:26
Alignment explanation
Indices: 8625--8701 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 26
8615 GAAAATAAGT
*
8625 CGGGGTTGGAGTATCCCCTCGGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATGATAA
8653 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATGAT-AA
8680 CGGGGTTGGAGTATCCCCGATG
1 CGGGGTTGGAGTATCCCCGATG
8702 TGAAGAAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 27 0.59
28 14 0.30
ACGTcount: A:0.21, C:0.22, G:0.35, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATGATAA
Found at i:8763 original size:52 final size:49
Alignment explanation
Indices: 8684--8804 Score: 129
Period size: 50 Copynumber: 2.4 Consensus size: 49
8674 GATCAACGGG
* * *
8684 GTTGGAGTATCCCCGATGTGAAGAAATTGGTATTTTTTG-GAATAAAATCGGA
1 GTTGGAGTATCCCCGAT-TGAAGAAATTAG--TGTTTTGAAAAT-AAATCGGA
8736 GTTGGAGTATCCCCGATT-ATAGAAAATTAGTGTTTTGAAAATAAATCGGA
1 GTTGGAGTATCCCCGATTGA-AG-AAATTAGTGTTTTGAAAATAAATCGGA
* *
8786 GTTGGAATATCTCCGATTG
1 GTTGGAGTATCCCCGATTG
8805 TGGGAATTGA
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
50 31 0.52
51 6 0.10
52 23 0.38
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (49 bp):
GTTGGAGTATCCCCGATTGAAGAAATTAGTGTTTTGAAAATAAATCGGA
Found at i:11212 original size:13 final size:13
Alignment explanation
Indices: 11194--11219 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11184 ACATAGATCC
11194 ATGTATCGATACA
1 ATGTATCGATACA
11207 ATGTATCGATACA
1 ATGTATCGATACA
11220 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:11215 original size:33 final size:33
Alignment explanation
Indices: 11173--11239 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
11163 AAAATTTCCA
* ***
11173 AATGTATCGATACATAGATCCATGTATCGATAC
1 AATGTATCGATACACAGAAAAATGTATCGATAC
11206 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACACAGAAAAATGTATCGATAC
11239 A
1 A
11240 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACACAGAAAAATGTATCGATAC
Found at i:11283 original size:19 final size:18
Alignment explanation
Indices: 11259--11326 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
11249 CAGTAGCTAA
11259 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
11278 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
11293 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
11310 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
11327 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:11299 original size:13 final size:13
Alignment explanation
Indices: 11281--11305 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11271 ACAATACTTA
11281 TGTATCGATACAT
1 TGTATCGATACAT
11294 TGTATCGATACA
1 TGTATCGATACA
11306 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11303 original size:32 final size:32
Alignment explanation
Indices: 11262--11324 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
11252 TAGCTAATTA
*
11262 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
11294 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
11325 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:11555 original size:51 final size:51
Alignment explanation
Indices: 11499--11627 Score: 143
Period size: 52 Copynumber: 2.5 Consensus size: 51
11489 GGTGTTTCAA
* * *
11499 AAATAAAACCGGGTTGGAGTATCCCCGATTGTGGAAAAATT-AGTGTTTTAG
1 AAATAAAACCGGGTTGGAGTATCCCCGATTAT-GAAAAATTAAATATTTTAG
* * * *
11550 CAATAAAACCGGGATTGGAATATCACCGATTATGAAAAATTAAATATTTTGG
1 AAATAAAACCGGG-TTGGAGTATCCCCGATTATGAAAAATTAAATATTTTAG
* *
11602 AAATAAAGTCGGGGTTGGAGTATCCC
1 AAATAAA-ACCGGGTTGGAGTATCCC
11628 TCGGAAATAA
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
51 20 0.32
52 39 0.62
53 4 0.06
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (51 bp):
AAATAAAACCGGGTTGGAGTATCCCCGATTATGAAAAATTAAATATTTTAG
Found at i:11672 original size:26 final size:25
Alignment explanation
Indices: 11611--11683 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 25
11601 GAAATAAAGT
11611 CGGGGTTGGAGTATCCCTCGGA-AATAA
1 CGGGGTTGGAGTAT-CC-C-GATAATAA
*
11638 CGGGGTTGGAGTATCCCGATGATCAA
1 CGGGGTTGGAGTATCCCGATAAT-AA
11664 CGGGGTTGGAGTATCCCGAT
1 CGGGGTTGGAGTATCCCGAT
11684 TGTGAAGAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
24 2 0.05
25 3 0.07
26 24 0.56
27 14 0.33
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (25 bp):
CGGGGTTGGAGTATCCCGATAATAA
Found at i:11725 original size:53 final size:51
Alignment explanation
Indices: 11668--11797 Score: 147
Period size: 51 Copynumber: 2.5 Consensus size: 51
11658 GATCAACGGG
* * *
11668 GTTGGAGTATCCCGATTGTGA-AGAAATTGGTATTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCGATTGTGAGA-AAATTAG--TGTTTTGAAAATAAAATCGGA
*
11721 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTAT-CCCGATTGTGAGAAAATTAGTGTTTTGAAAATAAAATCGGA
*
11772 GTTGGAATATCTCCGATTGTGGAGAA
1 GTTGGAGTATC-CCGATTGT-GAGAA
11798 TTGAGAAACT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
50 1 0.02
51 35 0.53
53 21 0.32
54 9 0.14
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCGATTGTGAGAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:14181 original size:13 final size:13
Alignment explanation
Indices: 14163--14188 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14153 ACATAGATCC
14163 ATGTATCGATACA
1 ATGTATCGATACA
14176 ATGTATCGATACA
1 ATGTATCGATACA
14189 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:14184 original size:33 final size:33
Alignment explanation
Indices: 14142--14208 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
14132 AAAATTTCCA
* ***
14142 AATGTATCGATACATAGATCCATGTATCGATAC
1 AATGTATCGATACACAGAAAAATGTATCGATAC
14175 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACACAGAAAAATGTATCGATAC
14208 A
1 A
14209 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACACAGAAAAATGTATCGATAC
Found at i:14252 original size:19 final size:18
Alignment explanation
Indices: 14228--14295 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
14218 CAGTAGCTAA
14228 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
14247 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
14262 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
14279 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
14296 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:14268 original size:13 final size:13
Alignment explanation
Indices: 14250--14274 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14240 ACAATACTTA
14250 TGTATCGATACAT
1 TGTATCGATACAT
14263 TGTATCGATACA
1 TGTATCGATACA
14275 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:14272 original size:32 final size:32
Alignment explanation
Indices: 14231--14293 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
14221 TAGCTAATTA
*
14231 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
14263 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
14294 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:14523 original size:51 final size:50
Alignment explanation
Indices: 14467--14595 Score: 141
Period size: 51 Copynumber: 2.5 Consensus size: 50
14457 GGTGTTTCGA
* * * *
14467 AAATAAAACCGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAG
1 AAATAAAACCGGGTTGGAGTATCCCCGATTAT-GAAAAATCAATATTTTAG
* * * *
14518 CAATAAAATCGGGATTGGAATATCCCCGATTATGAAAAATCAATATTTTGG
1 AAATAAAACCGGG-TTGGAGTATCCCCGATTATGAAAAATCAATATTTTAG
* *
14569 AAATAAAGTCGGGGTTGGAGTATCCCC
1 AAATAAA-ACCGGGTTGGAGTATCCCC
14596 TCGGAAATAA
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
51 43 0.68
52 20 0.32
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (50 bp):
AAATAAAACCGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTAG
Found at i:14642 original size:27 final size:26
Alignment explanation
Indices: 14578--14653 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 26
14568 GAAATAAAGT
14578 CGGGGTTGGAGTATCCCCTCGGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATAATAA
*
14606 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
14633 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
14654 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 26 0.58
28 14 0.31
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATAATAA
Found at i:14741 original size:51 final size:53
Alignment explanation
Indices: 14637--14759 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 53
14627 GATCAACGGG
* * * *
14637 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATTAG-ATGTTTTGAAAATAAAATCGGA
14691 GTTGGAGTATCCCCGATTAT--AGAAAATTAG-TGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAG-AAATTAGATGTTTTGAAAATAAAATCGGA
* *
14742 GTTGGAATATCTCCGATT
1 GTTGGAGTATCCCCGATT
14760 GTGGAGAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
51 35 0.56
52 2 0.03
53 6 0.10
54 19 0.31
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTATGAAGAAATTAGATGTTTTGAAAATAAAATCGGA
Found at i:17150 original size:13 final size:13
Alignment explanation
Indices: 17132--17157 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17122 ACATAGATCC
17132 ATGTATCGATACA
1 ATGTATCGATACA
17145 ATGTATCGATACA
1 ATGTATCGATACA
17158 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:17153 original size:33 final size:33
Alignment explanation
Indices: 17111--17177 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
17101 AAAATTTCCA
* ***
17111 AATGTATCGATACATAGATCCATGTATCGATAC
1 AATGTATCGATACACAGAAAAATGTATCGATAC
17144 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACACAGAAAAATGTATCGATAC
17177 A
1 A
17178 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACACAGAAAAATGTATCGATAC
Found at i:17221 original size:19 final size:18
Alignment explanation
Indices: 17197--17264 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
17187 CAGTAGCTAA
17197 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
17216 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
17231 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
17248 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
17265 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:17237 original size:13 final size:13
Alignment explanation
Indices: 17219--17243 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17209 ACAATACTTA
17219 TGTATCGATACAT
1 TGTATCGATACAT
17232 TGTATCGATACA
1 TGTATCGATACA
17244 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:17241 original size:32 final size:32
Alignment explanation
Indices: 17200--17262 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
17190 TAGCTAATTA
*
17200 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
17232 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
17263 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:17557 original size:51 final size:52
Alignment explanation
Indices: 17436--17565 Score: 163
Period size: 51 Copynumber: 2.5 Consensus size: 52
17426 GGTGTTTCGA
* * * *
17436 AAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAG
1 AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
* * * *
17488 CAATAAAACCGGGATTGGAATATCCCCGATTAT-GAAAAATCAATATTTTGG
1 AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
**
17539 AAATAAAGTCGGGGTTGGAGTATCCCC
1 AAATAAAACCGGGGTTGGAGTATCCCC
17566 TCGGAAATAA
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
51 36 0.55
52 29 0.45
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (52 bp):
AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
Found at i:17612 original size:27 final size:26
Alignment explanation
Indices: 17548--17623 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 26
17538 GAAATAAAGT
17548 CGGGGTTGGAGTATCCCCTCGGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATAATAA
*
17576 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
17603 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
17624 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 26 0.58
28 14 0.31
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATAATAA
Found at i:17711 original size:51 final size:53
Alignment explanation
Indices: 17607--17729 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 53
17597 GATCAACGGG
* * * *
17607 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATTAG-ATGTTTTGAAAATAAAATCGGA
17661 GTTGGAGTATCCCCGATTAT--AGAAAATTAG-TGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAG-AAATTAGATGTTTTGAAAATAAAATCGGA
* *
17712 GTTGGAATATCTCCGATT
1 GTTGGAGTATCCCCGATT
17730 GTGGAGAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
51 35 0.56
52 2 0.03
53 6 0.10
54 19 0.31
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTATGAAGAAATTAGATGTTTTGAAAATAAAATCGGA
Found at i:20119 original size:13 final size:13
Alignment explanation
Indices: 20101--20126 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20091 ACATAGATCC
20101 ATGTATCGATACA
1 ATGTATCGATACA
20114 ATGTATCGATACA
1 ATGTATCGATACA
20127 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:20122 original size:33 final size:33
Alignment explanation
Indices: 20080--20146 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
20070 AAAATTTCCA
* ***
20080 AATGTATCGATACATAGATCCATGTATCGATAC
1 AATGTATCGATACACAGAAAAATGTATCGATAC
20113 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACACAGAAAAATGTATCGATAC
20146 A
1 A
20147 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACACAGAAAAATGTATCGATAC
Found at i:20190 original size:19 final size:18
Alignment explanation
Indices: 20166--20233 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
20156 CAGTAGCTAA
20166 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
20185 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
20200 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
20217 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
20234 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:20206 original size:13 final size:13
Alignment explanation
Indices: 20188--20212 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20178 ACAATACTTA
20188 TGTATCGATACAT
1 TGTATCGATACAT
20201 TGTATCGATACA
1 TGTATCGATACA
20213 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:20210 original size:32 final size:32
Alignment explanation
Indices: 20169--20231 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
20159 TAGCTAATTA
*
20169 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
20201 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
20232 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:20526 original size:51 final size:52
Alignment explanation
Indices: 20405--20534 Score: 163
Period size: 51 Copynumber: 2.5 Consensus size: 52
20395 GGTGTTTCGA
* * * *
20405 AAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAG
1 AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
* * * *
20457 CAATAAAACCGGGATTGGAATATCCCCGATTAT-GAAAAATCAATATTTTGG
1 AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
**
20508 AAATAAAGTCGGGGTTGGAGTATCCCC
1 AAATAAAACCGGGGTTGGAGTATCCCC
20535 TCGGAAATAA
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
51 36 0.55
52 29 0.45
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (52 bp):
AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
Found at i:20581 original size:27 final size:26
Alignment explanation
Indices: 20517--20592 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 26
20507 GAAATAAAGT
20517 CGGGGTTGGAGTATCCCCTCGGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATAATAA
*
20545 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
20572 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
20593 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 26 0.58
28 14 0.31
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATAATAA
Found at i:20680 original size:51 final size:53
Alignment explanation
Indices: 20576--20698 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 53
20566 GATCAACGGG
* * * *
20576 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATTAG-ATGTTTTGAAAATAAAATCGGA
20630 GTTGGAGTATCCCCGATTAT--AGAAAATTAG-TGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAG-AAATTAGATGTTTTGAAAATAAAATCGGA
* *
20681 GTTGGAATATCTCCGATT
1 GTTGGAGTATCCCCGATT
20699 GTGGAGAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
51 35 0.56
52 2 0.03
53 6 0.10
54 19 0.31
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTATGAAGAAATTAGATGTTTTGAAAATAAAATCGGA
Found at i:23089 original size:13 final size:13
Alignment explanation
Indices: 23071--23096 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23061 ACATAGATCC
23071 ATGTATCGATACA
1 ATGTATCGATACA
23084 ATGTATCGATACA
1 ATGTATCGATACA
23097 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:23092 original size:33 final size:33
Alignment explanation
Indices: 23050--23116 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
23040 AAAATTTCCA
* ***
23050 AATGTATCGATACATAGATCCATGTATCGATAC
1 AATGTATCGATACACAGAAAAATGTATCGATAC
23083 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACACAGAAAAATGTATCGATAC
23116 A
1 A
23117 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACACAGAAAAATGTATCGATAC
Found at i:23160 original size:19 final size:18
Alignment explanation
Indices: 23136--23202 Score: 90
Period size: 18 Copynumber: 3.9 Consensus size: 18
23126 CAGTAGCTAA
23136 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
23155 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
23170 -T-TGTATCGATACAAAC
1 TTATGTATCGATACAAAC
23186 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
23203 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 14 0.33
19 14 0.33
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:23176 original size:13 final size:13
Alignment explanation
Indices: 23158--23182 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23148 ACAATACTTA
23158 TGTATCGATACAT
1 TGTATCGATACAT
23171 TGTATCGATACA
1 TGTATCGATACA
23183 AACTTATGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:23191 original size:31 final size:32
Alignment explanation
Indices: 23139--23200 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 32
23129 TAGCTAATTA
23139 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAATACTTATGTATCGATACAT
23171 TGTATCGATACAA-ACTTATGTATCGATACA
1 TGTATCGATACAATACTTATGTATCGATACA
23201 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAATACTTATGTATCGATACAT
Found at i:23501 original size:51 final size:52
Alignment explanation
Indices: 23374--23503 Score: 145
Period size: 51 Copynumber: 2.5 Consensus size: 52
23364 GGTGTTTCGA
* * * *
23374 AAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAG
1 AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
* * * * *
23426 CAATAAAACCGGGATTAGAATATCCCCGATTAT-GAAAAATCAATATTTTGG
1 AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
***
23477 AAATAAAGTTGGGGTTGGAGTATCCCC
1 AAATAAAACCGGGGTTGGAGTATCCCC
23504 TCGGAAATAA
Statistics
Matches: 62, Mismatches: 16, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
51 34 0.55
52 28 0.45
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (52 bp):
AAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
Found at i:23550 original size:27 final size:26
Alignment explanation
Indices: 23487--23561 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 26
23477 AAATAAAGTT
23487 GGGGTTGGAGTATCCCCTCGGA-AATAAC
1 GGGGTTGGAGTAT-CCC-C-GATAATAAC
*
23515 GGGGTTGGAGTATCCCCGATGATCAAC
1 GGGGTTGGAGTATCCCCGATAAT-AAC
23542 GGGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
23562 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.05
26 3 0.07
27 26 0.59
28 13 0.30
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.23
Consensus pattern (26 bp):
GGGGTTGGAGTATCCCCGATAATAAC
Found at i:23649 original size:51 final size:53
Alignment explanation
Indices: 23545--23667 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 53
23535 GATCAACGGG
* * * *
23545 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATTAG-ATGTTTTGAAAATAAAATCGGA
23599 GTTGGAGTATCCCCGATTAT--AGAAAATTAG-TGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAG-AAATTAGATGTTTTGAAAATAAAATCGGA
* *
23650 GTTGGAATATCTCCGATT
1 GTTGGAGTATCCCCGATT
23668 GTGGAGAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
51 35 0.56
52 2 0.03
53 6 0.10
54 19 0.31
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTATGAAGAAATTAGATGTTTTGAAAATAAAATCGGA
Found at i:26060 original size:13 final size:13
Alignment explanation
Indices: 26042--26067 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26032 ACATAGATCC
26042 ATGTATCGATACA
1 ATGTATCGATACA
26055 ATGTATCGATACA
1 ATGTATCGATACA
26068 CAAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:26130 original size:19 final size:18
Alignment explanation
Indices: 26106--26173 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
26096 CAGTAGCTAA
26106 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
26125 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
26140 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
26157 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
26174 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:26146 original size:13 final size:13
Alignment explanation
Indices: 26128--26152 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26118 ACAATACTTA
26128 TGTATCGATACAT
1 TGTATCGATACAT
26141 TGTATCGATACA
1 TGTATCGATACA
26153 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:26150 original size:32 final size:32
Alignment explanation
Indices: 26109--26171 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
26099 TAGCTAATTA
*
26109 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
26141 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
26172 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:26517 original size:28 final size:27
Alignment explanation
Indices: 26457--26550 Score: 117
Period size: 27 Copynumber: 3.6 Consensus size: 27
26447 AAATAAAGTC
26457 GGGTTGGAGTATCCCTCGG-AAT-AC-
1 GGGTTGGAGTATCCCTCGGAAATAACG
26481 GGGTTGGAGTATCCCCTCGGAAATAACG
1 GGGTTGGAGTAT-CCCTCGGAAATAACG
*
26509 GGGTTGGAGTATCCC-C-GATGATCAACG
1 GGGTTGGAGTATCCCTCGGA-AAT-AACG
26536 GGGTTGGAGTATCCC
1 GGGTTGGAGTATCCC
26551 CGATTGTGAA
Statistics
Matches: 63, Mismatches: 1, Indels: 9
0.86 0.01 0.12
Matches are distributed among these distances:
24 12 0.19
25 9 0.14
26 6 0.10
27 24 0.38
28 12 0.19
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGTTGGAGTATCCCTCGGAAATAACG
Found at i:26606 original size:54 final size:51
Alignment explanation
Indices: 26538--26670 Score: 169
Period size: 51 Copynumber: 2.5 Consensus size: 51
26528 GATCAACGGG
* *
26538 GTTGGAGTATCCCCGATTGTGAAGAAGTTAGTATTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAGAA-TTAG--TGTTTTGAAAATAAAATCGGA
*
26592 GTTGGAGTATCCCCGATTATAGAA-AATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGT-GAAGAATTAGTGTTTTGAAAATAAAATCGGA
* * *
26643 GTTGGAATATCTCCGATTGTGGAGAATT
1 GTTGGAGTATCCCCGATTGTGAAGAATT
26671 GAGAAACTCA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
50 2 0.03
51 40 0.57
53 4 0.06
54 21 0.30
55 3 0.04
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAGAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:29053 original size:13 final size:13
Alignment explanation
Indices: 29035--29060 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29025 ACATAGATCC
29035 ATGTATCGATACA
1 ATGTATCGATACA
29048 ATGTATCGATACA
1 ATGTATCGATACA
29061 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:29056 original size:33 final size:33
Alignment explanation
Indices: 29014--29080 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
29004 AAATTTTCCA
* ***
29014 AATGTATCGATACATAGATCCATGTATCGATAC
1 AATGTATCGATACACAGAAAAATGTATCGATAC
29047 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACACAGAAAAATGTATCGATAC
29080 A
1 A
29081 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACACAGAAAAATGTATCGATAC
Found at i:29124 original size:19 final size:18
Alignment explanation
Indices: 29100--29167 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
29090 CAGTAGCTAA
29100 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
29119 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
29134 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
29151 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
29168 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:29140 original size:13 final size:13
Alignment explanation
Indices: 29122--29146 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29112 ACAATACTTA
29122 TGTATCGATACAT
1 TGTATCGATACAT
29135 TGTATCGATACA
1 TGTATCGATACA
29147 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:29144 original size:32 final size:32
Alignment explanation
Indices: 29103--29165 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
29093 TAGCTAATTA
*
29103 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
29135 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
29166 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:29923 original size:26 final size:26
Alignment explanation
Indices: 29840--29923 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
29830 GTGTCCTGCT
*
29840 CTTTGGGGACTGAAA-ATGCCACCAA
1 CTTTGGGGACTGAAAGGTGCCACCAA
* * * * *
29865 CTTGGGTGGGCTTTGAAAGGTGTCATGC-T
1 CTTTGG-GGAC--TGAAAGGTGCCA-CCAA
29894 CTTTGGGGACTGAAAGGTGCCACCAA
1 CTTTGGGGACTGAAAGGTGCCACCAA
29920 CTTT
1 CTTT
29924 TGTGGGCTTT
Statistics
Matches: 42, Mismatches: 11, Indels: 11
0.66 0.17 0.17
Matches are distributed among these distances:
25 6 0.14
26 18 0.43
28 8 0.19
29 9 0.21
30 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (26 bp):
CTTTGGGGACTGAAAGGTGCCACCAA
Found at i:30342 original size:226 final size:228
Alignment explanation
Indices: 29687--30505 Score: 1146
Period size: 226 Copynumber: 3.6 Consensus size: 228
29677 TGGGAAGGTT
* * *
29687 TGCCACTAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGGAA-ATGCCACCAAC
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAGACGCCACCAAC
*
29751 TTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGT
66 TTGTGTGGGCTTT--AAAG--AAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGT
** * * *
29816 GTGGGCTTT-AAAAG-----GTGTCCTGCTCTTTGGGGACTG-AAAATGCCACCAACTTGGGTGG
127 GTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGG
* * * * *
29874 GCTTTGAAAGGTGTCATGCTCTTTGGGGACT-GAAAGG
192 GCTTTAAAAGGTGTCCTGCTCTTTGAGGATTGGAAA-A
* *
29911 TGCCACCAACTTTTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAGGCGCCACCAAC
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAGACGCCACCAAC
*
29976 TTGTGTGGGCTTTGAAAAGACAAAGCATCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTG
66 TTGTGTGGGCTTT--AAAG--AAAGCATCCTGCTCTTTGAGGACTGAAAA-ATGCCACCAACTTG
30040 TGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTG
126 TGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTG
30105 GGCTTTAAAAGGTGTCCTGCTCTTTGAGGATTGGAAAA
191 GGCTTTAAAAGGTGTCCTGCTCTTTGAGGATTGGAAAA
*
30143 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAGGCGCCACCAAC
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAGACGCCACCAAC
* ** * * * *
30208 TTGTGTGGGCTTT-AAG-AGGTTTCCTCCTCTTTGAGGACTGGAAGACGCCACCAACTTGTGTGG
66 TTGTGTGGGCTTTAAAGAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGG
30271 GCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTT
131 GCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTT
30336 TAAAAGGTGTCCTGCTCTTTGAGGATTGGAAAA
196 TAAAAGGTGTCCTGCTCTTTGAGGATTGGAAAA
* * *
30369 TGCCACCGACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAGACGCCACCAAC
** * *
30434 TTGTGTGGGCTTT---GAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTATGTG
66 TTGTGTGGGCTTTAAAGAAA-GCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTG
30496 GGCTTTGAAA
130 GGCTTTGAAA
30506 GGTGTCCTGC
Statistics
Matches: 545, Mismatches: 37, Indels: 24
0.90 0.06 0.04
Matches are distributed among these distances:
224 55 0.10
225 76 0.14
226 262 0.48
227 2 0.00
229 3 0.01
231 19 0.03
232 124 0.23
233 4 0.01
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (228 bp):
TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAGACGCCACCAAC
TTGTGTGGGCTTTAAAGAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGG
GCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTT
TAAAAGGTGTCCTGCTCTTTGAGGATTGGAAAA
Found at i:30477 original size:27 final size:27
Alignment explanation
Indices: 30395--30477 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
30385 GGGCTTTAAG
30395 AGGTGTCCTGCTCTTTGAGGACTGGAA
1 AGGTGTCCTGCTCTTTGAGGACTGGAA
* ** * * * *
30422 A-ATG-CCACCAACTTGTGTGGGCTTTGAA
1 AGGTGTCCTGC-TCTT-TGAGGAC-TGGAA
30450 AGGTGTCCTGCTCTTTGAGGACTGGAA
1 AGGTGTCCTGCTCTTTGAGGACTGGAA
30477 A
1 A
30478 ATGCCACCAA
Statistics
Matches: 37, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.14
27 11 0.30
28 10 0.27
29 5 0.14
30 3 0.08
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (27 bp):
AGGTGTCCTGCTCTTTGAGGACTGGAA
Found at i:30534 original size:55 final size:55
Alignment explanation
Indices: 29687--30535 Score: 987
Period size: 55 Copynumber: 15.0 Consensus size: 55
29677 TGGGAAGGTT
* *
29687 TGCCACTAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGG-AAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
** *
29741 TGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAA
1 TGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCTTTGAGGACTGGAAAA
* * *
29802 TGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGGGGACT-GAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
* * * *
29856 TGCCACCAACTTGGGTGGGCTTTGAAAGGTGTCATGCTCTTTGGGGACT-GAAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-A
* **
29911 TGCCACCAACTTTTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGGAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGGAAAA
* **
29966 CGCCACCAACTTGTGTGGGCTTTGAAAAGACAAAGCATCCTGCTCTTTGAGGACT--AAAA
1 TGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCTTTGAGGACTGGAAAA
** *
30025 GGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAA
1 --TGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCTTTGAGGACTGGAAAA
* * *
30088 TGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGATTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
**
30143 TGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGGAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGGAAAA
* * * *
30198 CGCCACCAACTTGTGTGGGCTTT-AAGAGGTTTCCTCCTCTTTGAGGACTGGAAGA
1 TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGGAAAA
* ** *
30253 CGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAA
1 TGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCTTTGAGGACTGGAAAA
* * *
30314 TGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGATTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
*
30369 TGCCACCGACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGGAAAA
30424 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
* * *
30479 TGCCACCAACTTATGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
30534 TG
1 TG
30536 GACGGAGAAG
Statistics
Matches: 702, Mismatches: 62, Indels: 61
0.85 0.08 0.07
Matches are distributed among these distances:
54 81 0.12
55 408 0.58
56 9 0.01
57 4 0.01
59 2 0.00
60 32 0.05
61 162 0.23
63 4 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (55 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
Found at i:31544 original size:14 final size:14
Alignment explanation
Indices: 31539--31565 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31529 TTTGTTTTTT
31539 CCTTTTTTTTTTGC
1 CCTTTTTTTTTTGC
31553 CCTTTTTTTTTTG
1 CCTTTTTTTTTTG
31566 AAGAGAAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.19, G:0.07, T:0.74
Consensus pattern (14 bp):
CCTTTTTTTTTTGC
Done.