Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2560
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: 63793
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:285 original size:7 final size:6
Alignment explanation
Indices: 254--283 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
244 TAGTATTAAT
254 ATAAAA AT-AAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A
284 ATTATGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:4468 original size:22 final size:22
Alignment explanation
Indices: 4443--4487 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4433 AGTTATTGTT
4443 AAATTGCCTT-ATTAAGGGGGAG
1 AAATT-CCTTGATTAAGGGGGAG
**
4465 AAATTTTTTGATTAAGGGGGAG
1 AAATTCCTTGATTAAGGGGGAG
4487 A
1 A
4488 GATAAGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.31
Consensus pattern (22 bp):
AAATTCCTTGATTAAGGGGGAG
Found at i:4922 original size:21 final size:22
Alignment explanation
Indices: 4882--4923 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4872 GATAAGTATA
4882 AATGTTTTCAAGGCTTAAAATG
1 AATGTTTTCAAGGCTTAAAATG
4904 AATGATTTTCAA-G-TTAAAAT
1 AATG-TTTTCAAGGCTTAAAAT
4924 ATATCAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (22 bp):
AATGTTTTCAAGGCTTAAAATG
Found at i:5185 original size:13 final size:13
Alignment explanation
Indices: 5167--5192 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5157 TACACACAAG
5167 ATGTATCGATACA
1 ATGTATCGATACA
5180 ATGTATCGATACA
1 ATGTATCGATACA
5193 TCCCAAAATG
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:5209 original size:33 final size:32
Alignment explanation
Indices: 5150--5212 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
5140 TTAACTGTTC
*
5150 GTATCGATACACACAAGATGTATCGATACAAT
1 GTATCGATACACACAAAATGTATCGATACAAT
*
5182 GTATCGATACATCCCAAAATGTATCGATACA
1 GTATCGATACA-CACAAAATGTATCGATACA
5213 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (32 bp):
GTATCGATACACACAAAATGTATCGATACAAT
Found at i:10513 original size:25 final size:25
Alignment explanation
Indices: 10479--10528 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
10469 AAACTAATTC
*
10479 TCCTAATCTATTTACAGCACATCTA
1 TCCTAATCTATTTACAACACATCTA
*
10504 TCCTAATCTATTTACAACTCATCTA
1 TCCTAATCTATTTACAACACATCTA
10529 CACCCCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.28, G:0.02, T:0.38
Consensus pattern (25 bp):
TCCTAATCTATTTACAACACATCTA
Found at i:19338 original size:20 final size:20
Alignment explanation
Indices: 19313--19366 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
19303 GTTTGAAGCA
19313 ATGTATCGATACAATTCAT-C
1 ATGTATCGATACAATT-ATCC
19333 ATGTATCGATAC-ATTATGCC
1 ATGTATCGATACAATTAT-CC
*
19353 AAGTATCGATACAA
1 ATGTATCGATACAA
19367 ATAGTGGTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.07
19 3 0.10
20 24 0.80
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATTATCC
Found at i:19420 original size:20 final size:19
Alignment explanation
Indices: 19395--19432 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
19385 CTGCTAGTTT
19395 CATGTATCGATACAATTGTC
1 CATGTATCGATAC-ATTGTC
19415 CATGTATCGATACATTGT
1 CATGTATCGATACATTGT
19433 ATCGATACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (19 bp):
CATGTATCGATACATTGTC
Found at i:19435 original size:13 final size:13
Alignment explanation
Indices: 19417--19441 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19407 CAATTGTCCA
19417 TGTATCGATACAT
1 TGTATCGATACAT
19430 TGTATCGATACA
1 TGTATCGATACA
19442 AAGCATAATG
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:20599 original size:20 final size:20
Alignment explanation
Indices: 20566--20626 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
20556 AAAGGTCAAA
20566 ACCTTGAAAAGTATCGATAC
1 ACCTTGAAAAGTATCGATAC
* *
20586 ACCTTTAAATGTATCGATAC
1 ACCTTGAAAAGTATCGATAC
** * *
20606 AGATTGCACAGTATCGATAC
1 ACCTTGAAAAGTATCGATAC
20626 A
1 A
20627 TTGTATCGAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (20 bp):
ACCTTGAAAAGTATCGATAC
Found at i:20634 original size:13 final size:13
Alignment explanation
Indices: 20616--20640 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20606 AGATTGCACA
20616 GTATCGATACATT
1 GTATCGATACATT
20629 GTATCGATACAT
1 GTATCGATACAT
20641 GACCAAATGT
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):
GTATCGATACATT
Found at i:20653 original size:20 final size:21
Alignment explanation
Indices: 20628--20680 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
20618 ATCGATACAT
**
20628 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
20648 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
20669 TGTATCGATACA
1 TGTATCGATACA
20681 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:25367 original size:79 final size:79
Alignment explanation
Indices: 25256--25462 Score: 236
Period size: 79 Copynumber: 2.6 Consensus size: 79
25246 GAGATAATAA
* * * * * * * *
25256 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTAGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
25321 -TTAGAAAAAAAAAT
65 TTTAGAAAAAAAAAC
* **
25335 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCTAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
* * * *
25400 TTTGGAAATAAAGC
66 TTAGAAAAAAAAAC
* *
25414 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
25463 GAAATAACAA
Statistics
Matches: 106, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 1 0.01
79 105 0.99
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAAC
Found at i:25470 original size:28 final size:28
Alignment explanation
Indices: 25414--25485 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
25404 GAAATAAAGC
** *
25414 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
25442 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
**
25470 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
25486 TCGACTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:25589 original size:51 final size:51
Alignment explanation
Indices: 25508--25692 Score: 146
Period size: 51 Copynumber: 3.6 Consensus size: 51
25498 AATTGGTATT
* * *
25508 TTTG-GAAATAAAATCGGAGTTGGAGTATCCCAATTAAAGG-AAAATTGGTG
1 TTTGAGAAATAAAACCGGGGTTGGAGTATCCCAATT-AAGGAAAAATTAGTG
* **
25558 TTTCGA-AAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTG
1 TTT-GAGAAATAAAACCGGGGTTGGAGTAT-CCCAATTAAGGAAAAATTAGTG
* * * * * * * *
25610 TTTTAGCAATAAAACCGGGGTTGGAATATCCCCGATT-ATGAAAAATCAATAT
1 TTTGAGAAATAAAACCGGGGTTGGAGTAT-CCCAATTAAGGAAAAATTAGT-G
**
25662 TTTG-GAAATAAAGTCGGGGTTGGAGTATCCC
1 TTTGAGAAATAAAACCGGGGTTGGAGTATCCC
25693 CTCGGAAATA
Statistics
Matches: 110, Mismatches: 19, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
50 6 0.05
51 54 0.49
52 50 0.45
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (51 bp):
TTTGAGAAATAAAACCGGGGTTGGAGTATCCCAATTAAGGAAAAATTAGTG
Found at i:25655 original size:103 final size:103
Alignment explanation
Indices: 25473--25693 Score: 230
Period size: 103 Copynumber: 2.1 Consensus size: 103
25463 GAAATAACAA
* * * * * *
25473 GGTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCC
1 GGTTGGAGTATCCCCGACTGTGAAAAATTAGTAGTTTTAGAAATAAAACCGGAGTTGGAATATCC
* *** *
25538 CAATTAAAGGAAAATTGGTGTTTCGAAAATAAAACCGG
66 CAATTAAAGAAAAATCAATATTTCGAAAATAAAACCGG
* * *
25576 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGT-GTTTTAGCAATAAAACCGGGGTTGGAATATC
1 GGTTGGAGTATCCCCGACTGT-GAAAAATTAGTAGTTTTAGAAATAAAACCGGAGTTGGAATAT-
* * * * **
25640 CCCGATT-ATGAAAAATCAATATTTTGGAAATAAAGTCGG
64 CCCAATTAAAGAAAAATCAATATTTCGAAAATAAAACCGG
25679 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
25694 TCGGAAATAA
Statistics
Matches: 96, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
103 80 0.83
104 16 0.17
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (103 bp):
GGTTGGAGTATCCCCGACTGTGAAAAATTAGTAGTTTTAGAAATAAAACCGGAGTTGGAATATCC
CAATTAAAGAAAAATCAATATTTCGAAAATAAAACCGG
Found at i:25693 original size:51 final size:51
Alignment explanation
Indices: 25473--25693 Score: 210
Period size: 52 Copynumber: 4.3 Consensus size: 51
25463 GAAATAACAA
* * * * *
25473 GGTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTA-TTTTGGAAATAAAACCGG
* * * * * * * *
25525 AGTTGGAGTAT-CCCAATTAAAGGAAAATTGGTGTTTCGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTATTTTGGAAATAAAACCGG
* * * *
25576 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTATTTTGGAAATAAAACCGG
* * * **
25628 GGTTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAACCGG
25679 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
25694 TCGGAAATAA
Statistics
Matches: 135, Mismatches: 31, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
51 66 0.49
52 69 0.51
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAACCGG
Found at i:25694 original size:262 final size:263
Alignment explanation
Indices: 25363--25862 Score: 783
Period size: 262 Copynumber: 1.9 Consensus size: 263
25353 TCGAAAATAA
* * *
25363 CGGGGTTGGAGTATCCCTAATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
* *
25428 CCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAAT-AACAAGGTTGGAGTATCCTCGACT
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG--ATCAACAAGGTTGGAGTATCCCCGACT
25492 GTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCC-CAATTAAAGGAAAATT
129 GTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCTCAATTAAA-GAAAATT
* * * *
25554 GGTGTTTCGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAA
193 AGTGTTTCAAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAA
25619 TAAAAC
258 TAAAAC
* *
25625 CGGGGTTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTAT
1 CGGGGTTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
** *
25690 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATCAACGGGGTTGGAGTATCCCCGATTGT
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATCAACAAGGTTGGAGTATCCCCGACTGT
* * *
25755 GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCTCGATTATAGAAAATTAGT
131 GAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCTCAATTAAAGAAAATTAGT
*
25820 GTTTCAAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
196 GTTTCAAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
25863 GAATTGAGAA
Statistics
Matches: 216, Mismatches: 18, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
260 2 0.01
261 25 0.12
262 103 0.48
263 80 0.37
264 6 0.03
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (263 bp):
CGGGGTTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATCAACAAGGTTGGAGTATCCCCGACTGT
GAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCTCAATTAAAGAAAATTAGT
GTTTCAAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
AAC
Found at i:25740 original size:27 final size:26
Alignment explanation
Indices: 25676--25751 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 26
25666 GAAATAAAGT
25676 CGGGGTTGGAGTATCCCCTCGGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATAATAA
*
25704 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
25731 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
25752 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:28240 original size:13 final size:13
Alignment explanation
Indices: 28222--28247 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28212 ACAAAGATCC
28222 ATGTATCGATACA
1 ATGTATCGATACA
28235 ATGTATCGATACA
1 ATGTATCGATACA
28248 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:28243 original size:33 final size:33
Alignment explanation
Indices: 28201--28267 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
28191 AAAATTTCCA
***
28201 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
28234 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
28267 A
1 A
28268 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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:28311 original size:19 final size:18
Alignment explanation
Indices: 28287--28354 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
28277 CAGTAGCTAA
28287 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
28306 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
28321 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
28338 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
28355 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:28327 original size:13 final size:13
Alignment explanation
Indices: 28309--28333 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28299 ACAATACTTA
28309 TGTATCGATACAT
1 TGTATCGATACAT
28322 TGTATCGATACA
1 TGTATCGATACA
28334 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:28331 original size:32 final size:32
Alignment explanation
Indices: 28290--28352 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
28280 TAGCTAATTA
*
28290 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
28322 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
28353 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:28434 original size:21 final size:21
Alignment explanation
Indices: 28410--28485 Score: 143
Period size: 21 Copynumber: 3.6 Consensus size: 21
28400 CATTTGTAGG
28410 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
28431 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
28452 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
28473 ATGTATCGATACA
1 ATGTATCGATACA
28486 CTTGGATAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:29416 original size:29 final size:29
Alignment explanation
Indices: 29329--29417 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 29
29319 CTTTGAGGAC
29329 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
* ** * ***
29358 T-AAGAGGTG--TCCTGCTCGT-TGGGGAC
1 TGAA-AGGTGCCACCAACTTGTGTGGGCTT
29384 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
29413 TGAAA
1 TGAAA
29418 AGAAAAAGCA
Statistics
Matches: 41, Mismatches: 14, Indels: 10
0.63 0.22 0.15
Matches are distributed among these distances:
26 10 0.24
27 8 0.20
28 8 0.20
29 15 0.37
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.27
Consensus pattern (29 bp):
TGAAAGGTGCCACCAACTTGTGTGGGCTT
Found at i:29482 original size:116 final size:114
Alignment explanation
Indices: 29257--29828 Score: 641
Period size: 116 Copynumber: 5.0 Consensus size: 114
29247 ATAAAGTGTA
* * * * *
29257 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTG-AAAG----GCGTCCTG
1 TCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGCGTCCTG
*
29317 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
66 CTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* * *
29367 TCCTGCTCGTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
1 TCCTGCTCTTTGAGGACTAGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAAG-AAAAGCGTCC
** *
29431 TGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
64 TGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* * *
29483 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG----GTGTCCTG
1 TCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGCGTCCTG
*
29543 CTCTTTGAGGATTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAGGTG
66 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT-----AAAAGGTG
* * * *
29597 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGAAAAAGTGTCCC
1 TCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAG-AAAAGCGTCCT
* * *
29660 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTTTGGGCTTTAAGAGAAAAAGCG
65 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT-----AAAAGGTG
*
29715 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCT
1 TCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAA-GCGTCCT
** *
29779 GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGGGGGCTTTTAAAAGG
65 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGC-TTTAAAAGG
29829 AAAAGGCATC
Statistics
Matches: 401, Mismatches: 38, Indels: 40
0.84 0.08 0.08
Matches are distributed among these distances:
109 27 0.07
110 57 0.14
111 4 0.01
113 29 0.07
114 26 0.06
115 4 0.01
116 98 0.24
117 4 0.01
118 79 0.20
119 49 0.12
120 21 0.05
121 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (114 bp):
TCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGCGTCCTG
CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTG
Found at i:29612 original size:59 final size:58
Alignment explanation
Indices: 29280--29854 Score: 651
Period size: 55 Copynumber: 9.9 Consensus size: 58
29270 GGAGTAAAAA
*
29280 GTGCCACCAACTCGTGTGGGCTTT---G-AAAGGCGTCCTGCTCTTTGAGGACTGAAAG
1 GTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCGTCCTGCTCTTTGAGGACTG-AAG
* * *
29335 GTGCCACCAACTTGTGTGGGCTTT-AAG---AGGTGTCCTGCTCGTTGGGGACTGAAAG
1 GTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCGTCCTGCTCTTTGAGGACTG-AAG
* * *
29390 GTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAA
1 GTGCCACCAACTTGTGTGGGCTTT--AAAGAAAAGGCGTCCTGCTCTTTGAGGACTG-AAG
* * * *
29451 ATGCCACCAACCTGTGTGGGCTTT----AAAAGGTGTCCTGCTCTTTGAGGACTGGAAA
1 GTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAG
* * *
29506 ATGCCACCAACTTGTGTGGGCTTT---G-AAAGGTGTCCTGCTCTTTGAGGATTGAAG
1 GTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGAAG
*
29560 GTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAGGTGTCCTGCTCTTTGAGGACTGAAG
1 GTGCCACCAACTTGTGTGGGCTTTAA-AGAAAAGGCGTCCTGCTCTTTGAGGACTGAAG
* * *
29619 GTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAAGTGTCCCGCTCTTTGAGGACTGAAG
1 GTGCCACCAACTTGTGTGGGCTTTAA-AGAAAAGGCGTCCTGCTCTTTGAGGACTGAAG
* * *
29678 GTGCCACCAACTTGTTTGGGCTTTAAGAGAAAAAGCGTCCTGCTCTTTGAGGACTAGAAA
1 GTGCCACCAACTTGTGTGGGCTTTAA-AGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAG
* *
29738 ATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAA
1 GTGCCACCAACTTGTGTGGGCTTT-AAAGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAG
* * * * *
29798 ATGCCACCAACTTGTGGGGGCTTTTAAAAGGAAAAGGCATCCTGCTCTCTAAGGACT
1 GTGCCACCAACTTGTGTGGGC-TTT-AAA-GAAAAGGCGTCCTGCTCTTTGAGGACT
29855 AAAAAGCGGA
Statistics
Matches: 467, Mismatches: 34, Indels: 31
0.88 0.06 0.06
Matches are distributed among these distances:
54 26 0.06
55 145 0.31
56 1 0.00
57 1 0.00
58 4 0.01
59 137 0.29
60 76 0.16
61 53 0.11
62 24 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (58 bp):
GTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGAAG
Found at i:30841 original size:15 final size:15
Alignment explanation
Indices: 30820--30889 Score: 60
Period size: 15 Copynumber: 4.7 Consensus size: 15
30810 CTTAAGTAGG
30820 TTTTTTCTTTT-CTT
1 TTTTTTCTTTTCCTT
30834 TCTTTTTCTTTGT--TT
1 T-TTTTTCTTT-TCCTT
30849 TGTTTTT-TTTTCCGTT
1 T-TTTTTCTTTTCC-TT
*
30865 TTTTTTCTTTTGCTT
1 TTTTTTCTTTTCCTT
30880 TTTTTT-TTTT
1 TTTTTTCTTTT
30890 GAAGAGAAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
13 1 0.02
14 8 0.17
15 30 0.62
16 9 0.19
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (15 bp):
TTTTTTCTTTTCCTT
Found at i:30842 original size:10 final size:9
Alignment explanation
Indices: 30822--30889 Score: 50
Period size: 10 Copynumber: 6.9 Consensus size: 9
30812 TAAGTAGGTT
30822 TTTTCTTTTC
1 TTTT-TTTTC
30832 TTTCTTTTTC
1 TTT-TTTTTC
30842 TTTGTTTTGT-
1 TTT-TTTT-TC
30852 TTTTTTTTCC
1 TTTTTTTT-C
30862 GTTTTTTTTC
1 -TTTTTTTTC
30872 TTTTGCTTTT-
1 TTTT--TTTTC
30882 TTTTTTTT
1 TTTTTTTT
30890 GAAGAGAAGG
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
8 5 0.10
9 8 0.16
10 23 0.46
11 14 0.28
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:30854 original size:31 final size:32
Alignment explanation
Indices: 30819--30889 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
30809 GCTTAAGTAG
*
30819 GTTTTTTCTTTTC-TTTCTTTTTC-TTTG-TTTT
1 GTTTTTT-TTTCCGTTT-TTTTTCTTTTGCTTTT
30850 GTTTTTTTTTCCGTTTTTTTTCTTTTGCTTTT
1 GTTTTTTTTTCCGTTTTTTTTCTTTTGCTTTT
30882 -TTTTTTTT
1 GTTTTTTTT
30890 GAAGAGAAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 10 0.28
31 22 0.61
32 4 0.11
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.82
Consensus pattern (32 bp):
GTTTTTTTTTCCGTTTTTTTTCTTTTGCTTTT
Found at i:30885 original size:30 final size:28
Alignment explanation
Indices: 30820--30889 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 28
30810 CTTAAGTAGG
* *
30820 TTTTTTCTTTTCTTTCTTTTTCTTTGTT
1 TTTTTTTTTTTCTTTCTTTTTCTTTGCT
30848 TTGTTTTTTTTTCCGTTT-TTTTTCTTTTGCT
1 TT-TTTTTTTTT-C-TTTCTTTTTC-TTTGCT
30879 TTTTTTTTTTT
1 TTTTTTTTTTT
30890 GAAGAGAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
28 2 0.06
29 8 0.22
30 16 0.44
31 10 0.28
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (28 bp):
TTTTTTTTTTTCTTTCTTTTTCTTTGCT
Found at i:34834 original size:13 final size:13
Alignment explanation
Indices: 34816--34853 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
34806 CAGCATTCTC
*
34816 TGTATCGATACAT
1 TGTATCGATACAG
*
34829 TGTATCGATATAG
1 TGTATCGATACAG
34842 TGTATCGATACA
1 TGTATCGATACA
34854 AAGGGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:35020 original size:20 final size:20
Alignment explanation
Indices: 34985--35025 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
34975 CAAATTTCTT
34985 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
35007 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
35026 AACAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:35319 original size:20 final size:21
Alignment explanation
Indices: 35287--35327 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
35277 CCTCTAGGCA
*
35287 GCACCCACTAGGTCGCGACCG
1 GCACCCACTAGGTCGCAACCG
35308 GCACCC-CTAGGTCGCAACCG
1 GCACCCACTAGGTCGCAACCG
35328 AGTAGCCCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.20, C:0.44, G:0.27, T:0.10
Consensus pattern (21 bp):
GCACCCACTAGGTCGCAACCG
Found at i:37350 original size:20 final size:21
Alignment explanation
Indices: 37325--37377 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
37315 ATCGATGCAT
**
37325 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
37345 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
37366 TGTATCGATACA
1 TGTATCGATACA
37378 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:37456 original size:13 final size:13
Alignment explanation
Indices: 37438--37462 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37428 ACACACAATA
37438 TGTATCGATACAC
1 TGTATCGATACAC
37451 TGTATCGATACA
1 TGTATCGATACA
37463 TCCCAAAATG
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:37479 original size:33 final size:32
Alignment explanation
Indices: 37419--37482 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
37409 CTTAACTGTT
*
37419 TGTATCGATACACACAATATGTATCGATACAC
1 TGTATCGATACACACAAAATGTATCGATACAC
*
37451 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
37483 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAC
Found at i:42693 original size:20 final size:20
Alignment explanation
Indices: 42664--42701 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42654 AAAAAAACCT
42664 AGAATATATCGATACAATAA
1 AGAATATATCGATACAATAA
*
42684 AGAATGTATCGATACAAT
1 AGAATATATCGATACAAT
42702 TGGGTCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (20 bp):
AGAATATATCGATACAATAA
Found at i:43472 original size:289 final size:289
Alignment explanation
Indices: 42953--43521 Score: 1129
Period size: 289 Copynumber: 2.0 Consensus size: 289
42943 TGACGATCGT
42953 TGTCCCCCTTTTATTCATTTAATCAATTATATTCAATCTAACCACCTTCTAGATATGCCTCTAGA
1 TGTCCCCCTTTTATTCATTTAATCAATTATATTCAATCTAACCACCTTCTAGATATGCCTCTAGA
43018 TATGTCCCCCTTTTATTCGTTTAATCAATACTAGCTTGACCTAGTTTCTTATGTCATATTCAAGA
66 TATGTCCCCCTTTTATTCGTTTAATCAATACTAGCTTGACCTAGTTTCTTATGTCATATTCAAGA
43083 CATGTCATTATTAGCAGCCATAAGACATATTTTGAGATGATAAGTAATTTGAATGAACAGTCTAA
131 CATGTCATTATTAGCAGCCATAAGACATATTTTGAGATGATAAGTAATTTGAATGAACAGTCTAA
43148 ATGTTTCCTTATCTTTAACTTATGAAAACAGCTTTATTAGTCTATATATCAACTACTTGACAACT
196 ATGTTTCCTTATCTTTAACTTATGAAAACAGCTTTATTAGTCTATATATCAACTACTTGACAACT
43213 TATGGACTTAAAGATGATGCCTCTAGATA
261 TATGGACTTAAAGATGATGCCTCTAGATA
*
43242 TGTCCCCCTTTTATTCATTTAATCAATTATATTCAATCTAACCACCTTTTAGATATGCCTCTAGA
1 TGTCCCCCTTTTATTCATTTAATCAATTATATTCAATCTAACCACCTTCTAGATATGCCTCTAGA
43307 TATGTCCCCCTTTTATTCGTTTAATCAATACTAGCTTGACCTAGTTTCTTATGTCATATTCAAGA
66 TATGTCCCCCTTTTATTCGTTTAATCAATACTAGCTTGACCTAGTTTCTTATGTCATATTCAAGA
43372 CATGTCATTATTAGCAGCCATAAGACATATTTTGAGATGATAAGTAATTTGAATGAACAGTCTAA
131 CATGTCATTATTAGCAGCCATAAGACATATTTTGAGATGATAAGTAATTTGAATGAACAGTCTAA
43437 ATGTTTCCTTATCTTTAACTTATGAAAACAGCTTTATTAGTCTATATATCAACTACTTGACAACT
196 ATGTTTCCTTATCTTTAACTTATGAAAACAGCTTTATTAGTCTATATATCAACTACTTGACAACT
43502 TATGGACTTAAAGATGATGC
261 TATGGACTTAAAGATGATGC
43522 AGCCTTTATC
Statistics
Matches: 279, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
289 279 1.00
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (289 bp):
TGTCCCCCTTTTATTCATTTAATCAATTATATTCAATCTAACCACCTTCTAGATATGCCTCTAGA
TATGTCCCCCTTTTATTCGTTTAATCAATACTAGCTTGACCTAGTTTCTTATGTCATATTCAAGA
CATGTCATTATTAGCAGCCATAAGACATATTTTGAGATGATAAGTAATTTGAATGAACAGTCTAA
ATGTTTCCTTATCTTTAACTTATGAAAACAGCTTTATTAGTCTATATATCAACTACTTGACAACT
TATGGACTTAAAGATGATGCCTCTAGATA
Found at i:48695 original size:166 final size:166
Alignment explanation
Indices: 48420--48838 Score: 435
Period size: 166 Copynumber: 2.5 Consensus size: 166
48410 AAAATTATTT
* * *
48420 AAATATTATCATTTATTTACCATCAAATCAGTTTTGAAAAATTCATTTTATTTTCATGAGTTATT
1 AAATATTATCATTTAATTACCATTAAATCAGTTTTGAAAAATTCA-TTTATTTTCATGA-TTTTT
* * ** * *
48485 AATTTTCTT--TTGGAATTCCCTTTGCTTTCGAAATATTGAGTTTTCT-TCTCCGTA-AAT-TTT
64 CATTTTTTTCCTTAAAATTCCCTTTGCTTTCGAAAAATTGAGTTTTCTAT-TCC--ACAATGATT
* * **
48545 TTCGAGGGCATTTTTCTTGGTTTATAAA-TTTAAAATTCATC
126 TTCGAGGGCATTTTTCTCGATCCA-AAATTTTAAAATTCATC
* * * *
48586 AAATTTTATTATTTAATCACCATTAAATCAGTTTTGAAAAATTCATTGATTTTCATGACTTTTTC
1 AAATATTATCATTTAATTACCATTAAATCAGTTTTGAAAAATTCATTTATTTTCATGA-TTTTTC
*
48651 TTTTTTTTCCTTAAAATT-CCTTTG-TTTCTGAAAAATCT-AGTTTTCTATTCCACAATGATTTT
65 ATTTTTTTCCTTAAAATTCCCTTTGCTTTC-GAAAAAT-TGAGTTTTCTATTCCACAATGATTTT
**
48713 CGAGGGGGTTTTTCTCGATCCAAAATTTTTAAAATTCATC
128 CGAGGGCATTTTTCTCGATCCAAAA-TTTTAAAATTCATC
* ** * *
48753 AAATATAATCATTTAATTTA-TTTTAAATTAGTTTTGAAAAATTCATTTATTTTCATGAGTTTTC
1 AAATATTATCATTTAA-TTACCATTAAATCAGTTTTGAAAAATTCATTTATTTTCATGATTTTTC
*
48817 ATTTTTTTCCTTAAAATGCCCT
65 ATTTTTTTCCTTAAAATTCCCT
48839 ATTTTCAAAA
Statistics
Matches: 210, Mismatches: 32, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
164 1 0.00
165 32 0.15
166 104 0.50
167 71 0.34
168 2 0.01
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (166 bp):
AAATATTATCATTTAATTACCATTAAATCAGTTTTGAAAAATTCATTTATTTTCATGATTTTTCA
TTTTTTTCCTTAAAATTCCCTTTGCTTTCGAAAAATTGAGTTTTCTATTCCACAATGATTTTCGA
GGGCATTTTTCTCGATCCAAAATTTTAAAATTCATC
Found at i:49326 original size:18 final size:19
Alignment explanation
Indices: 49305--49345 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
49295 AAATCTCATT
49305 AAAAATG-CAT-AAAAATA
1 AAAAATGCCATGAAAAATA
49322 GAAAAATGCCATGAAAAATA
1 -AAAAATGCCATGAAAAATA
49342 AAAA
1 AAAA
49346 GAAAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
19 7 0.33
20 7 0.33
ACGTcount: A:0.68, C:0.07, G:0.10, T:0.15
Consensus pattern (19 bp):
AAAAATGCCATGAAAAATA
Found at i:50584 original size:142 final size:141
Alignment explanation
Indices: 50292--50630 Score: 362
Period size: 142 Copynumber: 2.4 Consensus size: 141
50282 AAAAGACTTT
* * * * * ** *
50292 AAAAGTTTTCGTATCTTTTCAAG-TCTCCTTTAAGATGCGAAATGAATTTTTTTAAATTTAAAAA
1 AAAAATTTTCGTATCTTTT-AGGTTCTCCATTAAGGTACGAAATGAATTTTTAAAAATTAAAAAA
* *
50356 TAAACTAAAAATTGTTATCTTAATTTTTCAAGATTTCTAATATTCCCATAGGTATCCATGGGGGT
65 TAAACTAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCCATAGGTATCCATAGGGGT
*
50421 ATAGAAATATTT
130 ATAGAAATATTC
*
50433 AAAAATTTTCGTATCTTTTTGGTTCTCCATTAAGGTACGAAATGAATTTTTCAAAAATTAAAGAA
1 AAAAATTTTCGTATCTTTTAGGTTCTCCATTAAGGTACGAAATGAATTTTT-AAAAATTAAA-AA
* ** * * *
50498 ATTAAA-TAAAAA-TATTATCTTAATTTTTTAAGATTTCTAATATTCTTAT-GGTTTTTCGTAGG
64 A-TAAACTAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCCATAGG-TATCCATAGG
* *
50560 GGTTTAGAAATCTTC
127 GGTATAGAAATATTC
* * * * * *
50575 AAAACTTTTCGTATCCTTTCGATTCTCCATTAAAGTATGAAATGAGATTTTTAAAA
1 AAAAATTTTCGTATCTTTTAGGTTCTCCATTAAGGTACGAAATGA-ATTTTTAAAA
50631 TTTATAACTT
Statistics
Matches: 166, Mismatches: 26, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
140 1 0.01
141 45 0.27
142 101 0.61
143 15 0.09
144 4 0.02
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (141 bp):
AAAAATTTTCGTATCTTTTAGGTTCTCCATTAAGGTACGAAATGAATTTTTAAAAATTAAAAAAT
AAACTAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCCATAGGTATCCATAGGGGTA
TAGAAATATTC
Found at i:53065 original size:52 final size:52
Alignment explanation
Indices: 53003--53101 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
52993 CGACACTAGT
*
53003 CTTAAAGATGAT-AAGGCTACCATTATGCTGATTCATGGCCAATGACATTGGA
1 CTTAAAGATGATAAAGG-TACCAATATGCTGATTCATGGCCAATGACATTGGA
* * *
53055 CTTAGAGATGATAAAGGTGCCAATATGCTGATTCATGGCCAGTGACA
1 CTTAAAGATGATAAAGGTACCAATATGCTGATTCATGGCCAATGACA
53102 CTAGTCTTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 38 0.90
53 4 0.10
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (52 bp):
CTTAAAGATGATAAAGGTACCAATATGCTGATTCATGGCCAATGACATTGGA
Found at i:53535 original size:59 final size:58
Alignment explanation
Indices: 53428--53571 Score: 162
Period size: 59 Copynumber: 2.4 Consensus size: 58
53418 TTACAAGGAA
* *
53428 ATGCCACCAACTTGTGTGGGCTTTTGGGTGCCGCCAACTCATGCGAACTTTGAAAAAGG
1 ATGCCA-CAACTTGTGTGGGCTTTTAGGTGCCGCCAACTCATACGAACTTTGAAAAAGG
** * ** *
53487 ATGCCATCAACTTGTGTGGGCTTTTAGGTGCCGTTAGCTTGTATGAACTTTGAAAAAGG
1 ATGCCA-CAACTTGTGTGGGCTTTTAGGTGCCGCCAACTCATACGAACTTTGAAAAAGG
* * *
53546 ATGACACTAGCTTGTGTAGGCTTTTA
1 ATGCCAC-AACTTGTGTGGGCTTTTA
53572 AAAGGGTGTC
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
58 1 0.01
59 71 0.99
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (58 bp):
ATGCCACAACTTGTGTGGGCTTTTAGGTGCCGCCAACTCATACGAACTTTGAAAAAGG
Found at i:53606 original size:29 final size:29
Alignment explanation
Indices: 53566--53830 Score: 209
Period size: 29 Copynumber: 9.2 Consensus size: 29
53556 CTTGTGTAGG
* * *
53566 CTTTTAAAAGGGTGTCACTAAGTCTTGGA
1 CTTTGAAAAGGGTGCCACTAAGTCATGGA
*
53595 CTTTGAAAAGGGTGCCACTAAATCATGGA
1 CTTTGAAAAGGGTGCCACTAAGTCATGGA
* *
53624 CTTTGATAAGGGTGCCACTAAGTCATGGG
1 CTTTGAAAAGGGTGCCACTAAGTCATGGA
* *
53653 CTTTGAAAATGGTACCACTAAGTCAT-GA
1 CTTTGAAAAGGGTGCCACTAAGTCATGGA
** **
53681 GCTTTGAGAAA-AATGCCACTAAGTTGTAGG-
1 -CTTTGA-AAAGGGTGCCACTAAGTCAT-GGA
* ** *
53711 CTTTGAGAA--GTGCCACTAAGTTGTGGG
1 CTTTGAAAAGGGTGCCACTAAGTCATGGA
* * * **
53738 CTTT-AAGAAGGGTGCTACTGACTTGTGGA
1 CTTTGAA-AAGGGTGCCACTAAGTCATGGA
*
53767 CTTTGAGAAGGGTGCCACTAAGTCATGGA
1 CTTTGAAAAGGGTGCCACTAAGTCATGGA
* ** * *
53796 CTTTGAGAAGGGCACTAGTAAGTCATGGA
1 CTTTGAAAAGGGTGCCACTAAGTCATGGA
53825 CTTTGA
1 CTTTGA
53831 GAAGAGGGCC
Statistics
Matches: 194, Mismatches: 33, Indels: 18
0.79 0.13 0.07
Matches are distributed among these distances:
26 3 0.02
27 20 0.10
28 3 0.02
29 163 0.84
30 4 0.02
31 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (29 bp):
CTTTGAAAAGGGTGCCACTAAGTCATGGA
Found at i:56805 original size:13 final size:13
Alignment explanation
Indices: 56787--56811 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56777 ATATTGCACA
56787 GTATCGATACATT
1 GTATCGATACATT
56800 GTATCGATACAT
1 GTATCGATACAT
56812 GACCAAATGT
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):
GTATCGATACATT
Found at i:56933 original size:32 final size:33
Alignment explanation
Indices: 56892--56955 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
56882 CTTAACTGTT
56892 TGTATCGATACA-CACAAAATGCATCGATACAA
1 TGTATCGATACATCACAAAATGCATCGATACAA
* *
56924 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACATCACAAAATGCATCGATACA
56956 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (33 bp):
TGTATCGATACATCACAAAATGCATCGATACAA
Done.