Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2242
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: 105331
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:7828 original size:27 final size:28
Alignment explanation
Indices: 7797--7867 Score: 110
Period size: 27 Copynumber: 2.6 Consensus size: 28
7787 TAATATGGAA
*
7797 ATAATTATATAATAAATTTTA-TTTTAT
1 ATAATAATATAATAAATTTTATTTTTAT
7824 ATAATAATAT-ATAAATTTTATTTTTAT
1 ATAATAATATAATAAATTTTATTTTTAT
*
7851 ATAATAATTTAATAAAT
1 ATAATAATATAATAAAT
7868 ATATAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 10 0.25
27 24 0.60
28 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATAATAATATAATAAATTTTATTTTTAT
Found at i:9430 original size:21 final size:20
Alignment explanation
Indices: 9399--9437 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
9389 TTTTTTATTT
9399 TTTAAATTTTTAAGTTTTAC
1 TTTAAATTTTTAAGTTTTAC
*
9419 TTTAAGATTTTTATGTTTT
1 TTTAA-ATTTTTAAGTTTT
9438 TAGATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTAAATTTTTAAGTTTTAC
Found at i:9564 original size:21 final size:22
Alignment explanation
Indices: 9521--9570 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
9511 TGTGAATAAA
*
9521 TTTATTATTAAATTTATAAATT
1 TTTATTATAAAATTTATAAATT
*
9543 TTTATTATAAAATTT-TACATT
1 TTTATTATAAAATTTATAAATT
*
9564 TTCATTA
1 TTTATTA
9571 ACCTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATTATAAAATTTATAAATT
Found at i:10032 original size:9 final size:9
Alignment explanation
Indices: 10018--10047 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
10008 ACTCCCAAAT
*
10018 TTCCTCCTC
1 TTCCTCTTC
10027 TTCCTCTTC
1 TTCCTCTTC
10036 TTCCTCTTC
1 TTCCTCTTC
10045 TTC
1 TTC
10048 TTCGTCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (9 bp):
TTCCTCTTC
Found at i:10591 original size:2 final size:2
Alignment explanation
Indices: 10584--10609 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10574 TTAACAATTG
10584 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
10610 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:13315 original size:3 final size:3
Alignment explanation
Indices: 13307--13350 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
13297 GTGTTACCTT
13307 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13351 TGTTAATAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:15537 original size:22 final size:22
Alignment explanation
Indices: 15502--15544 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
15492 AAATCTCTTT
** *
15502 TTTTTATTTGAATTCAAATATC
1 TTTTTATTCCAATTAAAATATC
15524 TTTTTATTCCAATTAAAATAT
1 TTTTTATTCCAATTAAAATAT
15545 TAACAATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTTATTCCAATTAAAATATC
Found at i:32420 original size:28 final size:28
Alignment explanation
Indices: 32339--32420 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
32329 TTTTGGAGAT
*
32339 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
32367 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
32395 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
32421 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:32563 original size:51 final size:51
Alignment explanation
Indices: 32403--32573 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
32393 GAAATAACGA
* * *
32403 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
32455 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
32508 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
32559 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
32574 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:32619 original size:27 final size:28
Alignment explanation
Indices: 32558--32631 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 28
32548 AATAAAGTCG
* *
32558 GGGTTGGAGTATCCCCTCA-GAAATAACG
1 GGGTTGGAGTATCCCC-GATGAAATAACA
*
32586 GGGTTGGAGTATCCCCGATG-ATTAACA
1 GGGTTGGAGTATCCCCGATGAAATAACA
*
32613 GGGTTGGAGTGTCCCCGAT
1 GGGTTGGAGTATCCCCGAT
32632 TGTGAAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGATGAAATAACA
Found at i:32674 original size:55 final size:51
Alignment explanation
Indices: 32615--32746 Score: 140
Period size: 51 Copynumber: 2.5 Consensus size: 51
32605 GATTAACAGG
* **
32615 GTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAATG---TTTTGAAAATAAAATCGGA
* *
32670 GTTGGAGTATCCCCGATTAT-AGAAAATTAATGTTTTGAAAGTAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAATGTTTTGAAAATAAAATCGGA
* *
32721 GTTGGAATATCCTCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
32747 TTGAGCAACT
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
51 35 0.53
52 2 0.03
53 4 0.06
54 7 0.11
55 18 0.27
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAATGTTTTGAAAATAAAATCGGA
Found at i:35114 original size:13 final size:13
Alignment explanation
Indices: 35096--35121 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35086 ACAAAGATCC
35096 ATGTATCGATACA
1 ATGTATCGATACA
35109 ATGTATCGATACA
1 ATGTATCGATACA
35122 CAGAAAAACG
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:35180 original size:19 final size:18
Alignment explanation
Indices: 35156--35223 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
35146 CAGTAGCCAA
35156 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
35175 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
35190 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
35207 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
35224 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:35196 original size:13 final size:13
Alignment explanation
Indices: 35178--35202 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35168 ACAATACTTA
35178 TGTATCGATACAT
1 TGTATCGATACAT
35191 TGTATCGATACA
1 TGTATCGATACA
35203 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:35197 original size:32 final size:32
Alignment explanation
Indices: 35159--35221 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
35149 TAGCCAATTA
*
35159 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
35191 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
35222 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:35285 original size:21 final size:21
Alignment explanation
Indices: 35259--35336 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
35249 GTTGGGACCC
35259 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
35280 TGTATCGATACATTTGT-GAA
1 TGTATCGATACATTTGTAGAA
* *
35300 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTA-GAA
35321 TGTATCGATACATTTG
1 TGTATCGATACATTTG
35337 GAATTTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
19 3 0.06
20 15 0.29
21 31 0.61
22 2 0.04
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:35323 original size:41 final size:40
Alignment explanation
Indices: 35259--35340 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
35249 GTTGGGACCC
* *
35259 TGTATCGATACATTTGTAGAATGTATCGATACATTTGTGAA
1 TGTATCGATACATTTCTAAAATGTATCGATACATTTG-GAA
35300 TGTATCGATACA-TTCTACAAATGTATCGATACATTTGGAA
1 TGTATCGATACATTTCTA-AAATGTATCGATACATTTGGAA
35340 T
1 T
35341 TTTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (40 bp):
TGTATCGATACATTTCTAAAATGTATCGATACATTTGGAA
Found at i:39577 original size:28 final size:28
Alignment explanation
Indices: 39516--39597 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
39506 TTTTGGAGAT
*
39516 AATAACGGGGTTGGAGTGTTCCCTC-A-GA
1 AATAACGGGGTTGGAGT-ATCCC-CGATGA
*
39544 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGGGGTTGGAGTATCCCCGATGA
* *
39572 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGGGGTTGGAGTATCCCCGAT
39598 TGTGAAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.02
27 5 0.11
28 41 0.87
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGGGGTTGGAGTATCCCCGATGA
Found at i:39735 original size:51 final size:51
Alignment explanation
Indices: 39580--39749 Score: 214
Period size: 52 Copynumber: 3.3 Consensus size: 51
39570 GAAATAACGA
* * *
39580 GGTTGGAGTATCCTCGATTGTGAAAATTTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGGAAATAAAATCGG
* * * * *
39632 TGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTGGAAATAAAATCGG
*** *
39684 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAATCGG
39735 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
39750 TCGAAAATAA
Statistics
Matches: 100, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
51 39 0.39
52 52 0.52
53 9 0.09
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.32
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAATCGG
Found at i:39795 original size:27 final size:28
Alignment explanation
Indices: 39732--39798 Score: 93
Period size: 27 Copynumber: 2.4 Consensus size: 28
39722 GAAATAAAGT
39732 CGGGGTTGGAGTATCCCCTCGAAAATAA
1 CGGGGTTGGAGTATCCCCTCGAAAATAA
* *
39760 CGGGGTTGGAGTAT-CCC-CGATGATTAA
1 CGGGGTTGGAGTATCCCCTCGA-AAATAA
39787 CGGGGTTGGAGT
1 CGGGGTTGGAGT
39799 GCCCACGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 3 0.08
27 19 0.53
28 14 0.39
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAA
Found at i:39872 original size:211 final size:211
Alignment explanation
Indices: 39521--39913 Score: 594
Period size: 211 Copynumber: 1.9 Consensus size: 211
39511 GAGATAATAA
* * *
39521 CGGGGTTGGAGTGTTCCCTCAGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
1 CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
* * * *
39586 AGTATCCTCGATTGTGAAAATTTGGTATTTTTGGAAATAAAATCGGTGTTGGAGTATCCCCGATT
66 AGTACCCACGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
* * * *
39651 AAAGGAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTATGAAAAATCAAT
131 AAAGGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTAGAATATCCCCGATTATGAAAAATCAAT
39716 ATTTTGGAAATAAAGT
196 ATTTTGGAAATAAAGT
* *
39732 CGGGGTTGGAGTATCCCCTC-GAAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTG
1 CGGGGTTGGAGTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTG
* *
39795 GAGTGCCCACGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCG
65 GAGTACCCACGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCG
*
39860 ATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTAGAATATCCCCGATT
128 ATTAAAGGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTAGAATATCCCCGATT
39914 GTGGAGAATT
Statistics
Matches: 163, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
210 28 0.17
211 96 0.59
212 39 0.24
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (211 bp):
CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
AGTACCCACGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
AAAGGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTAGAATATCCCCGATTATGAAAAATCAAT
ATTTTGGAAATAAAGT
Found at i:42295 original size:13 final size:13
Alignment explanation
Indices: 42277--42302 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42267 ACAAAGATCC
42277 ATGTATCGATACA
1 ATGTATCGATACA
42290 ATGTATCGATACA
1 ATGTATCGATACA
42303 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:42295 original size:33 final size:33
Alignment explanation
Indices: 42257--42320 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
42247 AAAATTCCAT
***
42257 ATGTATCGATACAAAGATCCATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCGATACA
*
42290 ATGTATCGATACACAGAAAAATGTATCGATA
1 ATGTATCGATACAAAGAAAAATGTATCGATA
42321 TATTTCCTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.27
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATACA
Found at i:42366 original size:19 final size:18
Alignment explanation
Indices: 42342--42409 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
42332 CAGTAGCTAA
42342 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
42361 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
42376 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
42393 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
42410 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:42382 original size:13 final size:13
Alignment explanation
Indices: 42364--42388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42354 ACAATACTTA
42364 TGTATCGATACAT
1 TGTATCGATACAT
42377 TGTATCGATACA
1 TGTATCGATACA
42389 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:42386 original size:32 final size:32
Alignment explanation
Indices: 42345--42407 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
42335 TAGCTAATTA
*
42345 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
42377 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
42408 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:42489 original size:21 final size:21
Alignment explanation
Indices: 42465--42521 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
42455 CATTTGTAGG
42465 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
42486 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
42507 ATGTATCGATACATT
1 ATGTATCGATACATT
42522 TGGATAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:43198 original size:119 final size:116
Alignment explanation
Indices: 42987--43198 Score: 252
Period size: 119 Copynumber: 1.8 Consensus size: 116
42977 AGGTGTCCAC
* * * *
42987 TTTTCAAGGACAAAGGAAAAGAGAATGAAATAGGTCTTGCTCCTTGAAGACCAAGGAAGAGAAGA
1 TTTTCAAGGACAAAGGAAAAGAGAATGAAATACGTCCTGCTCCTTGAAGACAAAAGAAGAGAAGA
*
43052 AAAGCAAAGTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTACGTCCCA
66 AAAGCAAAGTGTCCTACTTCTTGAGGACAAAGTGAAAAAGAGTACGTCCCA
* *
43103 TTTTCCAAGGACAAAGGAAAAAGGGGAATGAAATACGTCCTGCT-CTCTGAGGACAAAAGAA-AG
1 TTTT-CAAGGACAAAGG-AAAA-GAGAATGAAATACGTCCTGCTCCT-TGAAGACAAAAGAAGAG
* *
43166 AGGAAAA-TAAAGTGTATCCTAC-TCTTTGAGGAC
62 AAGAAAAGCAAAGTG--TCCTACTTC-TTGAGGAC
43199 TAAAAAGTGC
Statistics
Matches: 80, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
116 4 0.05
117 18 0.22
118 16 0.20
119 42 0.52
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.20
Consensus pattern (116 bp):
TTTTCAAGGACAAAGGAAAAGAGAATGAAATACGTCCTGCTCCTTGAAGACAAAAGAAGAGAAGA
AAAGCAAAGTGTCCTACTTCTTGAGGACAAAGTGAAAAAGAGTACGTCCCA
Found at i:43360 original size:26 final size:26
Alignment explanation
Indices: 43331--43470 Score: 63
Period size: 26 Copynumber: 5.2 Consensus size: 26
43321 CCAACTTGTG
43331 TGGGCTTTGAAAGGTGTCCTGCTCTT
1 TGGGCTTTGAAAGGTGTCCTGCTCTT
*** * ** *
43357 TGGGGACTGAAAGGTGCCACCAACTTCTG
1 TGGGCTTTGAAAGGTG--TCCTGC-TCTT
43386 TGGGCTTT-AAGAGGTGTCCTGCTCTT
1 TGGGCTTTGAA-AGGTGTCCTGCTCTT
** *
43412 TGGAGAC--TGAAAGGTG-CCACCAACTTGT
1 TGG-G-CTTTGAAAGGTGTCCTGC-TC-T-T
*
43440 GTGGGCTTTGAAAGGGGTCCTGCTCTT
1 -TGGGCTTTGAAAGGTGTCCTGCTCTT
43467 TGGG
1 TGGG
43471 GACTGAAAGG
Statistics
Matches: 79, Mismatches: 21, Indels: 28
0.62 0.16 0.22
Matches are distributed among these distances:
25 3 0.04
26 30 0.38
27 9 0.11
28 9 0.11
29 25 0.32
30 3 0.04
ACGTcount: A:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (26 bp):
TGGGCTTTGAAAGGTGTCCTGCTCTT
Found at i:43584 original size:59 final size:58
Alignment explanation
Indices: 43187--44248 Score: 1280
Period size: 59 Copynumber: 18.2 Consensus size: 58
43177 GTGTATCCTA
* * * * *
43187 CTCTTTGAGGACTAAAAAGTGCCACCGACTCGTGTGGGCTTT----G-AAAGACGTCCTG
1 CTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCC-G
*
43242 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTGTCCTG
1 CTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCC-G
** *
43297 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTG
1 CTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCC-G
* * *
43352 CTCTTTGGGGACTGAAAGGTGCCACCAACTTCTGTGGGCTTT--AAG---AGGTGTCCTG
1 CTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCC-G
*
43407 CTCTTTG-GAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGGGTCCTG
1 CTCTTTGAG-GACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCC-G
*
43462 CTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGCGTCCCG
1 CTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGT-CCG
* * *
43523 CTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGGTTTTAAAAGAAAAGGCGTCTCG
1 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTC-CG
* *
43582 CTCTTTGAGGACTAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCTCG
1 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTC-CG
*
43641 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGACGTCCCG
1 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGT-CCG
*
43700 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCG
1 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGT-CCG
* *
43759 CACTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTA
1 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCC-G
* *
43818 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAGGTGTCCTG
1 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCC-G
* *
43877 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAAGCGTCCCG
1 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGT-CCG
*
43936 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAGAAA-GCGTCCCG
1 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA-AAAGGCGT-CCG
**
43995 CTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCTCG
1 CTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCGTC-CG
*
44056 CTCTTTGAGGACGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCGTCTCG
1 CTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAG-AAAAGGCGTC-CG
* *
44117 CTCTTTGAGGA-TGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGCGTCCCA
1 CTCTTTGAGGACT-G-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGT-CCG
** **
44177 CTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTATCCTG
1 CTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCGTCC-G
44238 CTCTTTGAGGA
1 CTCTTTGAGGA
44249 TTAAAAAGCA
Statistics
Matches: 918, Mismatches: 53, Indels: 66
0.89 0.05 0.06
Matches are distributed among these distances:
53 2 0.00
54 2 0.00
55 227 0.25
56 2 0.00
57 2 0.00
58 3 0.00
59 411 0.45
60 119 0.13
61 148 0.16
62 2 0.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (58 bp):
CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCG
Found at i:45228 original size:1 final size:1
Alignment explanation
Indices: 45218--45265 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
45208 CTTAAGCAGA
* * * * *
45218 TTTTTCTTTTTTTTTGTTTTTTTTTGTTTTTGTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
45266 GAAGAGAAGG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.04, G:0.06, T:0.90
Consensus pattern (1 bp):
T
Found at i:45247 original size:16 final size:15
Alignment explanation
Indices: 45218--45264 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 15
45208 CTTAAGCAGA
45218 TTTTTCTTTTTTTTTG
1 TTTTT-TTTTTTTTTG
45234 TTTTTTTTTGTTTTTG
1 TTTTTTTTT-TTTTTG
45250 TTTTTTTTCTTTTTT
1 TTTTTTTT-TTTTTT
45265 TGAAGAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.14
16 24 0.83
17 1 0.03
ACGTcount: A:0.00, C:0.04, G:0.06, T:0.89
Consensus pattern (15 bp):
TTTTTTTTTTTTTTG
Found at i:45265 original size:10 final size:10
Alignment explanation
Indices: 45218--45263 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
45208 CTTAAGCAGA
*
45218 TTTTTCTTTT
1 TTTTTGTTTT
45228 TTTTTGTTTT
1 TTTTTGTTTT
45238 TTTTTGTTTT
1 TTTTTGTTTT
45248 TGTTTT-TTTT
1 T-TTTTGTTTT
45258 CTTTTT
1 -TTTTT
45264 TTGAAGAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
10 28 0.85
11 5 0.15
ACGTcount: A:0.00, C:0.04, G:0.07, T:0.89
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:57786 original size:52 final size:50
Alignment explanation
Indices: 57725--58061 Score: 182
Period size: 51 Copynumber: 6.4 Consensus size: 50
57715 GAAATAACGA
*
57725 GGTTGGAGTATCCTCGATTGTGAAAATTTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAA-TTGGTA-TTTTGGAAATAAAATCGG
* * * *
57777 TGTTGGAGTATCCCCGATTAAAG-GAAAATTGGTGTTTAGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT---GTGAAAATTGGTATTTTGGAAATAAAATCGG
* * * *** *
57829 GGTTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTGTG-AAAATTGGTATTTTGGAAATAAAATCGG
* **** * *
57880 GGTTGGAGTATCCCC--TCG-GAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTGTG-AA-AA-----TT-G-GTATTTTGGA-AATAAAATCGG
** *
57935 GGTTGGAGTGCCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTG-A-AAATT-G-GTATTTTGGAAATAAAATCGG
* * * * *
57989 AGTTGGAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAATTGGTATTTTGGAAATAAAATCGG
* *
58040 AGTTGGAATATCCCCGATTGTG
1 GGTTGGAGTATCCCCGATTGTG
58062 GAGAATTGAG
Statistics
Matches: 215, Mismatches: 49, Indels: 44
0.70 0.16 0.14
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
50 2 0.01
51 73 0.34
52 51 0.24
53 21 0.10
54 27 0.13
55 18 0.08
56 6 0.03
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.30
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTGTGAAAATTGGTATTTTGGAAATAAAATCGG
Found at i:57940 original size:27 final size:28
Alignment explanation
Indices: 57877--57952 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 28
57867 GAAATAAAGT
***
57877 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
57905 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
**
57932 CGGGGTTGGAGTGCCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
57953 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.55
28 19 0.45
ACGTcount: A:0.20, C:0.22, G:0.36, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:58032 original size:211 final size:211
Alignment explanation
Indices: 57666--58054 Score: 595
Period size: 211 Copynumber: 1.8 Consensus size: 211
57656 GAGATAATAA
* * *
57666 CGGGGTTGGAGTGTTCCCTCGAAAGTAATGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
1 CGGGGTTGGAGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
* * * *
57731 AGTATCCTCGATTGTGAAAATTTGGTATTTTTGGAAATAAAATCGGTGTTGGAGTATCCCCGATT
66 AGTACCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
* *
57796 AAAGGAAAATTGGTGTTTAGAAAATAAAATCGGGGTTGGAATATCCCCAATTATGAAAAATCAAT
131 AAAGGAAAATTAGTGTTTAGAAAATAAAATCGGAGTTGGAATATCCCCAATTATGAAAAATCAAT
57861 ATTTTGGAAATAAAGT
196 ATTTTGGAAATAAAGT
* *
57877 CGGGGTTGGAGTATCCCCTCGGAAA-TAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTG
1 CGGGGTTGGAGTATCCCCTC-GAAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTG
* *
57940 GAGTGCCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCG
65 GAGTACCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCG
* *
58005 ATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCC
128 ATTAAAGGAAAATTAGTGTTTAGAAAATAAAATCGGAGTTGGAATATCCCC
58055 GATTGTGGAG
Statistics
Matches: 160, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
210 27 0.17
211 90 0.56
212 43 0.27
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (211 bp):
CGGGGTTGGAGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
AGTACCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
AAAGGAAAATTAGTGTTTAGAAAATAAAATCGGAGTTGGAATATCCCCAATTATGAAAAATCAAT
ATTTTGGAAATAAAGT
Found at i:64568 original size:27 final size:28
Alignment explanation
Indices: 64537--64607 Score: 110
Period size: 27 Copynumber: 2.6 Consensus size: 28
64527 TAATATGGAA
*
64537 ATAATTATATAATAAATTTTA-TTTTAT
1 ATAATAATATAATAAATTTTATTTTTAT
64564 ATAATAATAT-ATAAATTTTATTTTTAT
1 ATAATAATATAATAAATTTTATTTTTAT
*
64591 ATAATAATTTAATAAAT
1 ATAATAATATAATAAAT
64608 ATATAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 10 0.25
27 24 0.60
28 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATAATAATATAATAAATTTTATTTTTAT
Found at i:66170 original size:21 final size:20
Alignment explanation
Indices: 66139--66177 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
66129 ATTTTTATTT
66139 TTTAAATTTTTAAGTTTTAC
1 TTTAAATTTTTAAGTTTTAC
*
66159 TTTAAGATTTTTATGTTTT
1 TTTAA-ATTTTTAAGTTTT
66178 TAGATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTAAATTTTTAAGTTTTAC
Found at i:66304 original size:21 final size:22
Alignment explanation
Indices: 66261--66310 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
66251 TGTGAATAAA
*
66261 TTTATTATTAAATTTATAAATT
1 TTTATTATAAAATTTATAAATT
*
66283 TTTATTATAAAATTT-TACATT
1 TTTATTATAAAATTTATAAATT
*
66304 TTCATTA
1 TTTATTA
66311 ACTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATTATAAAATTTATAAATT
Found at i:66772 original size:9 final size:9
Alignment explanation
Indices: 66758--66787 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
66748 ACTCCCAAAT
*
66758 TTCCTCCTC
1 TTCCTCTTC
66767 TTCCTCTTC
1 TTCCTCTTC
66776 TTCCTCTTC
1 TTCCTCTTC
66785 TTC
1 TTC
66788 TTCGTCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (9 bp):
TTCCTCTTC
Found at i:70063 original size:3 final size:3
Alignment explanation
Indices: 70055--70095 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
70045 GTGTTACCTT
70055 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
70096 TGTTAATAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:72282 original size:22 final size:22
Alignment explanation
Indices: 72247--72289 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
72237 AAATCTCTTT
** *
72247 TTTTTATTTGAATTCAAATATC
1 TTTTTATTCCAATTAAAATATC
72269 TTTTTATTCCAATTAAAATAT
1 TTTTTATTCCAATTAAAATAT
72290 TAACAATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTTATTCCAATTAAAATATC
Found at i:85487 original size:52 final size:52
Alignment explanation
Indices: 85421--85535 Score: 194
Period size: 52 Copynumber: 2.2 Consensus size: 52
85411 ATTTATCTGT
* *
85421 ATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCTTGC
1 ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTGC
* *
85473 ATGTATCGATACATTTTATAATGTATCGATACATCTTGGCAAATTTGCCTGC
1 ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTGC
85525 ATGTATCGATA
1 ATGTATCGATA
85536 TAAAGATCGG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (52 bp):
ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTGC
Found at i:85550 original size:52 final size:52
Alignment explanation
Indices: 85421--85557 Score: 161
Period size: 52 Copynumber: 2.6 Consensus size: 52
85411 ATTTATCTGT
* *
85421 ATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGCTTGC
1 ATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
*** * *
85473 ATGTATCGATACATTTTATAATGTATCGATACATCTTGGCAAATTTGCCTGC
1 ATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
* *
85525 ATGTATCGATATA-AAGATCGGTGTATCGATACA
1 ATGTATCGATACATAAGAT-AGTGTATCGATACA
85558 ATGTATTGAT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
51 4 0.05
52 69 0.95
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (52 bp):
ATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
Found at i:85652 original size:13 final size:13
Alignment explanation
Indices: 85634--85658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85624 CAAAAAAATA
85634 TGTATCGATACAT
1 TGTATCGATACAT
85647 TGTATCGATACA
1 TGTATCGATACA
85659 ACATTTTATG
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:85654 original size:33 final size:33
Alignment explanation
Indices: 85612--85678 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
85602 AGTAGCTTAA
85612 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
85645 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
85678 A
1 A
85679 AATCGTTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:86576 original size:55 final size:52
Alignment explanation
Indices: 86476--86907 Score: 374
Period size: 49 Copynumber: 8.7 Consensus size: 52
86466 GAAAAGTGAT
* * * * * * **
86476 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G-A
* *
86530 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
86583 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
86626 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGGT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
86676 --AGGTGCCAATGTGCTGATTCAAGACCAGCTATATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* **
86724 -AAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGAT---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
86772 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-ATGGT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
86821 GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
86871 -AAGGTGCCAATATGCTGATTCAGGGCCAGCTATATTG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTG
86908 GGCTTAGAAG
Statistics
Matches: 325, Mismatches: 37, Indels: 37
0.81 0.09 0.09
Matches are distributed among these distances:
43 38 0.12
44 1 0.00
46 3 0.01
47 1 0.00
48 44 0.14
49 154 0.47
51 3 0.01
52 34 0.10
53 6 0.02
54 5 0.02
55 36 0.11
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
Found at i:86747 original size:49 final size:49
Alignment explanation
Indices: 86539--86913 Score: 494
Period size: 49 Copynumber: 7.7 Consensus size: 49
86529 AAAAGGATGT
* *
86539 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
*
86591 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
86634 CAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGGTG-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
86682 CAATGTGCTGATTCAAGACCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
86731 CAATATGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
86780 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
86829 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
86878 CAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
86914 GAAGGGTTGC
Statistics
Matches: 283, Mismatches: 33, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
43 39 0.14
48 45 0.16
49 167 0.59
52 32 0.11
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:86813 original size:98 final size:98
Alignment explanation
Indices: 86473--86913 Score: 554
Period size: 98 Copynumber: 4.5 Consensus size: 98
86463 TGAGAAAAGT
* * * * * *
86473 GATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG-TG
* * *
86538 TCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
60 CCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
86577 GATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCA
1 GAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCA
* *
86636 ATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAA
63 ATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* * * * *
86672 GGT-GAGGTGCCAATGTGCTGATTCAAGACCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
*
86736 TGCTGAGTCAAGGCCAGCTACATTGGTCTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* *
86769 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
86834 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* * *
86867 GATGAAGGTGCCAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
86914 GAAGGGTTGC
Statistics
Matches: 299, Mismatches: 28, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
91 39 0.13
95 41 0.14
96 4 0.01
97 43 0.14
98 131 0.44
103 1 0.00
104 3 0.01
107 37 0.12
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (98 bp):
GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
Found at i:86873 original size:147 final size:142
Alignment explanation
Indices: 86539--86913 Score: 547
Period size: 147 Copynumber: 2.6 Consensus size: 142
86529 AAAAGGATGT
*
86539 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATATGCTGATT
* *
86604 CAAGGCCAGCTATATTGGAC-T-TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGAC
63 CAAGGCCAGCTATATTGGACTTATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGAC
86667 TTAAAGGTGAGGTGC
128 TTAAAGGTGAGGTGC
* * *
86682 CAATGTGCTGATTCAAGACCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGAGTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
* * *
86747 GGCCAGCTACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
66 GGCCAGCTATATTGGACTT----ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGA
*
86812 CTTAATGGTGAAGGTGC
127 CTTAAAGGTG-AGGTGC
* *
86829 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAG
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
*
86894 GGCCAGCTATATTGGGCTTA
66 GGCCAGCTATATTGGACTTA
86914 GAAGGGTTGC
Statistics
Matches: 208, Mismatches: 17, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
140 37 0.18
141 1 0.00
142 1 0.00
143 39 0.19
146 47 0.23
147 83 0.40
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (142 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
AAGGTGAGGTGC
Found at i:100621 original size:26 final size:27
Alignment explanation
Indices: 100571--100639 Score: 97
Period size: 26 Copynumber: 2.6 Consensus size: 27
100561 TTAATATGAA
* *
100571 ATAATTATATAATACATTTTATTTTAT
1 ATAATAATATAATAAATTTTATTTTAT
100598 ATAATAATAT-ATAAATTTTATTTTAT
1 ATAATAATATAATAAATTTTATTTTAT
*
100624 ATAAT-ATTTAATAAAT
1 ATAATAATATAATAAAT
100640 ATATAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 3 0.08
26 26 0.68
27 9 0.24
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (27 bp):
ATAATAATATAATAAATTTTATTTTAT
Found at i:100669 original size:34 final size:34
Alignment explanation
Indices: 100599--100670 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 34
100589 TTATTTTATA
* *
100599 TAAT-AATATATAAATTTTATTTTATATAATATT
1 TAATAAATATATAAAATTTATTTTATATAATAAT
100632 TAATAAATATATAAAATTTATTATTAT-T-ATGAAT
1 TAATAAATATATAAAATTTATT-TTATATAAT-AAT
100666 TAATA
1 TAATA
100671 TGAATTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 6 0.18
34 24 0.71
35 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (34 bp):
TAATAAATATATAAAATTTATTTTATATAATAAT
Found at i:102817 original size:9 final size:9
Alignment explanation
Indices: 102803--102832 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
102793 ACTCCCAAAT
*
102803 TTCCTCCTC
1 TTCCTCTTC
102812 TTCCTCTTC
1 TTCCTCTTC
102821 TTCCTCTTC
1 TTCCTCTTC
102830 TTC
1 TTC
102833 TTCGTCCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (9 bp):
TTCCTCTTC
Found at i:103379 original size:2 final size:2
Alignment explanation
Indices: 103372--103396 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
103362 AACAATTGCT
103372 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
103397 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.