Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1762
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: 92833
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1229 original size:30 final size:30
Alignment explanation
Indices: 1195--1291 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
1185 AGCTCACTCC
1195 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
1225 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
1255 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
1285 TAGCTCA
1 TAGCTCA
1292 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:7910 original size:22 final size:24
Alignment explanation
Indices: 7876--7920 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
7866 CTTGGACCAA
7876 GATTTTCAAGA-T-TTGAAATCTT
1 GATTTTCAAGATTCTTGAAATCTT
**
7898 GATTTTCCTGATTCTTGAAATCT
1 GATTTTCAAGATTCTTGAAATCT
7921 CTTCGAACAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 1 0.05
24 9 0.47
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (24 bp):
GATTTTCAAGATTCTTGAAATCTT
Found at i:10907 original size:17 final size:17
Alignment explanation
Indices: 10862--10915 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
10852 AGAAAAGAGC
* *
10862 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
* *
10879 GAAAAATGAAAAAAAAA
1 GAAAATTCAAAAAAAAA
*
10896 GAAAATTCAAAAAAAGA
1 GAAAATTCAAAAAAAAA
10913 GAA
1 GAA
10916 TGAAAAGAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (17 bp):
GAAAATTCAAAAAAAAA
Found at i:10946 original size:15 final size:16
Alignment explanation
Indices: 10918--10953 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
10908 AAAGAGAATG
*
10918 AAAAGAGAGTAAAAGA
1 AAAAGAGAGAAAAAGA
10934 AAAAGA-AGAAAAAGA
1 AAAAGAGAGAAAAAGA
10949 AAAAG
1 AAAAG
10954 TGAGTGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (16 bp):
AAAAGAGAGAAAAAGA
Found at i:13672 original size:10 final size:10
Alignment explanation
Indices: 13657--13691 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
13647 AGTGAGCAAA
13657 AAAAAAAAGT
1 AAAAAAAAGT
*
13667 AAAAAAAAGA
1 AAAAAAAAGT
13677 AAAAAAAAGT
1 AAAAAAAAGT
13687 GAAAA
1 -AAAA
13692 GTCTTGCGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (10 bp):
AAAAAAAAGT
Found at i:14784 original size:48 final size:47
Alignment explanation
Indices: 14705--14810 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
14695 GAGTGTCATG
*
14705 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
14753 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
14801 GAAAAAGAAA
1 GAAAAAGAAA
14811 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:16526 original size:20 final size:20
Alignment explanation
Indices: 16480--16526 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
16470 AGCTCGTTTC
*
16480 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
16500 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
16520 CAGCTCA
1 CAGCTCA
16527 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:19355 original size:48 final size:48
Alignment explanation
Indices: 19300--19405 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
19290 TTGTCTTTTC
*
19300 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
19348 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
19396 TTTCTTTTTC
1 TTTCTTTTTC
19406 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:22034 original size:20 final size:20
Alignment explanation
Indices: 22011--22057 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
22001 GGGTTAAGAT
*
22011 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
22031 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
22051 TGAGCTG
1 TGAGCTG
22058 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:23946 original size:12 final size:12
Alignment explanation
Indices: 23929--23958 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
23919 CCTCACATGC
23929 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
23941 CCGTGTGCTAGG
1 CCGTGTGCCAGG
23953 CCGTGT
1 CCGTGT
23959 AACAGCCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:29503 original size:12 final size:11
Alignment explanation
Indices: 29480--29512 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
29470 GTTGTAAAGT
29480 TTTATT-TTTA
1 TTTATTATTTA
29490 TTTATTTATTTA
1 TTTA-TTATTTA
29502 TTTATTATTTA
1 TTTATTATTTA
29513 CTTAGTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.19
11 9 0.43
12 8 0.38
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:30760 original size:12 final size:12
Alignment explanation
Indices: 30743--30768 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30733 CCTTAAACAC
30743 ATTACATTGAAT
1 ATTACATTGAAT
30755 ATTACATTGAAT
1 ATTACATTGAAT
30767 AT
1 AT
30769 CCTACTTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
ATTACATTGAAT
Found at i:31536 original size:16 final size:15
Alignment explanation
Indices: 31515--31554 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
31505 CTATTGTAAT
*
31515 TAAAAAAATTTCGAAG
1 TAAAAAAA-TACGAAG
31531 TAAAAAGAATACGAAG
1 TAAAAA-AATACGAAG
31547 TAAAAAAA
1 TAAAAAAA
31555 AGTAAAGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 2 0.09
16 18 0.82
17 2 0.09
ACGTcount: A:0.65, C:0.05, G:0.12, T:0.17
Consensus pattern (15 bp):
TAAAAAAATACGAAG
Found at i:37682 original size:13 final size:12
Alignment explanation
Indices: 37646--37685 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
37636 TGAGAGTGAG
37646 GAAG-TGAAAAA
1 GAAGTTGAAAAA
*
37657 GAAATTGAAAAA
1 GAAGTTGAAAAA
37669 GAAGTTGAAGAAA
1 GAAGTTGAA-AAA
37682 GAAG
1 GAAG
37686 AGAAATGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 3 0.12
12 15 0.60
13 7 0.28
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (12 bp):
GAAGTTGAAAAA
Found at i:42228 original size:19 final size:18
Alignment explanation
Indices: 42192--42231 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42182 TTTCCACTCG
*
42192 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
42210 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
42229 TTT
1 TTT
42232 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:42341 original size:18 final size:17
Alignment explanation
Indices: 42304--42348 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
42294 GCACTCTTTC
* *
42304 TTTTCTTTCTCCAATCT
1 TTTTCTTTTTTCAATCT
*
42321 TTTTCTCTTTTTCAATTT
1 TTTTCT-TTTTTCAATCT
42339 TTTTCTTTTT
1 TTTTCTTTTT
42349 CGGTTTCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCTTTTTTCAATCT
Found at i:43302 original size:12 final size:13
Alignment explanation
Indices: 43285--43321 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
43275 TAGCTCTCTC
43285 TTTTTTTCACAATT
1 TTTTTTTCACAA-T
43299 TTTTTTTCA-AAT
1 TTTTTTTCACAAT
43311 TTTTTTT-ACAA
1 TTTTTTTCACAA
43322 CTTGATATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 1 0.05
12 10 0.45
13 2 0.09
14 9 0.41
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTTTTCACAAT
Found at i:43303 original size:13 final size:14
Alignment explanation
Indices: 43285--43317 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
43275 TAGCTCTCTC
43285 TTTTTTTCACAATT
1 TTTTTTTCACAATT
43299 TTTTTTTCA-AATT
1 TTTTTTTCACAATT
43312 TTTTTT
1 TTTTTT
43318 ACAACTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTTTTCACAATT
Found at i:43406 original size:12 final size:12
Alignment explanation
Indices: 43360--43406 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
43350 GGAAACTAGT
43360 TTTTTTTTCGA-
1 TTTTTTTTCGAG
*
43371 TTTTTTTT-GAAT
1 TTTTTTTTCG-AG
43383 TTTTTTTTCGAG
1 TTTTTTTTCGAG
43395 TTTTTTTTCGAG
1 TTTTTTTTCGAG
43407 AAACTACTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
10 1 0.03
11 9 0.28
12 21 0.66
13 1 0.03
ACGTcount: A:0.11, C:0.06, G:0.13, T:0.70
Consensus pattern (12 bp):
TTTTTTTTCGAG
Found at i:48178 original size:18 final size:18
Alignment explanation
Indices: 48149--48193 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
48139 TACTTCCTTT
48149 TCTTTCTTCAATCTCACTC
1 TCTTT-TTCAATCTCACTC
* **
48168 TCTTTTTCAATTTCTTTC
1 TCTTTTTCAATCTCACTC
48186 TCTTTTTC
1 TCTTTTTC
48194 TTCTTTTGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (18 bp):
TCTTTTTCAATCTCACTC
Found at i:51029 original size:12 final size:12
Alignment explanation
Indices: 51012--51036 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51002 CCTTATACAC
51012 ATTACACATTGA
1 ATTACACATTGA
51024 ATTACACATTGA
1 ATTACACATTGA
51036 A
1 A
51037 ATCAGATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
ATTACACATTGA
Found at i:52042 original size:20 final size:20
Alignment explanation
Indices: 52017--52064 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
52007 AGCTAATAAC
52017 GAGCTGAATTGAGCTCGAA-T
1 GAGCTGAATTGAGCTC-AAGT
* *
52037 GAGCTGACTTGAGTTCAAGT
1 GAGCTGAATTGAGCTCAAGT
52057 GAGCTGAA
1 GAGCTGAA
52065 CAACATGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (20 bp):
GAGCTGAATTGAGCTCAAGT
Found at i:53431 original size:19 final size:21
Alignment explanation
Indices: 53350--53425 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
53340 ATTTTCGAGG
*
53350 ATATACAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
53369 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
53390 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
53411 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
53426 AGATATGATT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
19 18 0.33
21 36 0.67
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:53461 original size:21 final size:23
Alignment explanation
Indices: 53402--53461 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
53392 ATGCAATCTT
* *
53402 AGATATGATATATGCAATCTTAGA
1 AGATATGA-ATTTGTAATCTTAGA
*
53426 AGATATGATTTTGTAATCTTA-A
1 AGATATGAATTTGTAATCTTAGA
*
53448 AGAT-TTAATTTGTA
1 AGATATGAATTTGTA
53462 GATACCCTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 8 0.26
22 5 0.16
23 10 0.32
24 8 0.26
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (23 bp):
AGATATGAATTTGTAATCTTAGA
Found at i:53895 original size:3 final size:3
Alignment explanation
Indices: 53887--53920 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
53877 ATTAATTTTG
53887 TTA TTA TTA TTA TTA TTA -TA TTA TATA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T
53921 ACCTACATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:59173 original size:34 final size:34
Alignment explanation
Indices: 59125--59192 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
59115 TATTTTTGAA
* *
59125 TATCACTCACTTTCACCTCA-TTTTCTTTGCTTTT
1 TATCACTCAATTTCAACTCACTTTTCTTTG-TTTT
* *
59159 TATCTCTCAATTTCAACTCACTTTTTTTTGTTTT
1 TATCACTCAATTTCAACTCACTTTTCTTTGTTTT
59193 CTCACTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 21 0.72
35 8 0.28
ACGTcount: A:0.16, C:0.25, G:0.03, T:0.56
Consensus pattern (34 bp):
TATCACTCAATTTCAACTCACTTTTCTTTGTTTT
Found at i:59198 original size:18 final size:19
Alignment explanation
Indices: 59175--59211 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
59165 TCAATTTCAA
*
59175 CTCACT-TTTTTTTGTTTT
1 CTCACTCTTTTTTTCTTTT
59193 CTCACTCTTTTTTTCTTTT
1 CTCACTCTTTTTTTCTTTT
59212 TCCATCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.05, C:0.22, G:0.03, T:0.70
Consensus pattern (19 bp):
CTCACTCTTTTTTTCTTTT
Found at i:59204 original size:20 final size:17
Alignment explanation
Indices: 59179--59232 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 17
59169 TTTCAACTCA
59179 CTTTTTTTTGTTTTCTCACT
1 CTTTTTTTT-TTTTC-CA-T
59199 CTTTTTTTCTTTTTCCAT
1 CTTTTTTT-TTTTTCCAT
*
59217 CTTTTCTTTTTGTTCC
1 CTTTT-TTTTTTTTCC
59233 TTTGCCTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 12 0.39
19 5 0.16
20 13 0.42
21 1 0.03
ACGTcount: A:0.04, C:0.22, G:0.04, T:0.70
Consensus pattern (17 bp):
CTTTTTTTTTTTTCCAT
Found at i:59219 original size:18 final size:20
Alignment explanation
Indices: 59179--59226 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
59169 TTTCAACTCA
59179 CTTTTTTTTGTTTTCTCACT
1 CTTTTTTTTGTTTTCTCACT
59199 CTTTTTTTCT-TTTTC-CA-T
1 CTTTTTTT-TGTTTTCTCACT
59217 CTTTTCTTTT
1 CTTTT-TTTT
59227 TGTTCCTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.27
19 5 0.19
20 13 0.50
21 1 0.04
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.73
Consensus pattern (20 bp):
CTTTTTTTTGTTTTCTCACT
Found at i:62272 original size:20 final size:20
Alignment explanation
Indices: 62249--62295 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
62239 GGGTTAAGAT
*
62249 TGAGCTGAATTGAGCTTGAC
1 TGAGCTGAATTGAGCTCGAC
* * *
62269 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAC
62289 TGAGCTG
1 TGAGCTG
62296 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAC
Found at i:62761 original size:20 final size:20
Alignment explanation
Indices: 62738--62791 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
62728 AGTTTTTCCC
*
62738 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
62758 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
62778 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
62792 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:62773 original size:30 final size:30
Alignment explanation
Indices: 62738--62811 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
62728 AGTTTTTCCC
62738 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
62768 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
62798 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
62812 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:62801 original size:20 final size:20
Alignment explanation
Indices: 62738--62802 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
62728 AGTTTTTCCC
* * * *
62738 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
62758 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
62777 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
62798 AGCTC
1 AGCTC
62803 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:75008 original size:12 final size:13
Alignment explanation
Indices: 74981--75013 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
74971 GTTGTAAAGT
*
74981 TTTATTTTTATTA
1 TTTATTTATATTA
74994 TTTATTTAT-TTA
1 TTTATTTATATTA
75006 TTTATTTA
1 TTTATTTA
75014 CTTAGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTATATTA
Found at i:76238 original size:15 final size:15
Alignment explanation
Indices: 76218--76251 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
76208 TTTATAAAAA
*
76218 AAAAGAGAAAGAAAG
1 AAAAGAAAAAGAAAG
76233 AAAAGAAAAAGAAAG
1 AAAAGAAAAAGAAAG
76248 AAAA
1 AAAA
76252 AGGAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAGAAAG
Found at i:76245 original size:19 final size:20
Alignment explanation
Indices: 76213--76250 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
76203 CAAATTTTAT
76213 AAAAAAAAAGAGAAAGAAAG
1 AAAAAAAAAGAGAAAGAAAG
*
76233 AAAAGAAAA-AGAAAGAAA
1 AAAAAAAAAGAGAAAGAAA
76251 AAGGAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGAGAAAGAAAG
Found at i:77753 original size:132 final size:132
Alignment explanation
Indices: 77516--78976 Score: 2517
Period size: 132 Copynumber: 11.1 Consensus size: 132
77506 GTGAAACACT
77516 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* *
77581 TAGTAGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAACAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
77646 CC
131 CC
77648 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * *
77713 TAGTGAAACAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
77778 CC
131 CC
* *
77780 AAGCCTTGTCTCCCTGAGCAGCAGCGGATTAGGTTAAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
*
77845 TAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
77910 CC
131 CC
*
77912 AAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* *
77977 TAGTGAAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
78042 CC
131 CC
* * * *
78044 AAGCCTTGTCTTCCTGAGCAGCTGCGGAGTAGATTGAAGATTGTAGATCTTATCTCCCTAAGTAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
** * *
78109 TAGTGGAGCAGATCAAAGATAACAAATCTTATCTTTCGAAGATAGTGGGAAGCAAATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
78174 CC
131 CC
*
78176 AAGCCTTGTCTCCCTGAGCAGTAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* *
78241 TAGTAGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAACAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
78306 CC
131 CC
* *
78308 AAGCCTTGTCTTCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGAAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * * *
78373 TAGTGAAACATATCAAAGATGGCAAATCTTATCTTTTCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
78438 CC
131 CC
* *
78440 AAGCCTTGTCTCCCTGAGCAGCAGCGGATTAGGTTGAAGATTTTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
*
78505 TAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
78570 CC
131 CC
* *
78572 AAGCCTTGTCTCCCTAAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCTTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
*
78637 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
78702 CC
131 CC
*
78704 AAGCCTTGTCTTCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* *
78769 TAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCGAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
78834 CC
131 CC
* *
78836 AAGCCTTGTCTCCCTAAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATATCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * ** *
78901 TAGGGGAGCAGATCGAAGACAGCAAATATTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
*
78966 GC
131 CC
78968 AAGCCTTGT
1 AAGCCTTGT
78977 GATACGACCA
Statistics
Matches: 1253, Mismatches: 76, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 1253 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (132 bp):
AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
CC
Found at i:77863 original size:44 final size:44
Alignment explanation
Indices: 77560--78274 Score: 138
Period size: 44 Copynumber: 16.2 Consensus size: 44
77550 TGAAGATTGT
*
77560 AGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCAAAGATGGC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
* * * ** ****
77604 AAATCTTATCTTTCC-AAG-A-TAGTGGGAAACAGATTTAAGCCACC
1 AGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGATGGC
* * * * * * * ** * *
77648 A-AGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGT
1 AGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
* *
77692 AGATCTTATCTCCCTAAGCAGTAGTGAAACAGATCAAAGATGGC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
* * * ** ****
77736 AAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAAATTTAAGCCACC
1 AGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGATGGC
* * * * * ** * * * *
77780 A-AGCCTTGTCTCCCTGAGCAGCAGCGGATTAGGTTAAAGATTGT
1 AGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
*
77824 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
* * ** ****
77868 AAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACC
1 AGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGATGGC
* * * * * * ** * *
77912 A-AGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGT
1 AGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
*
77956 AGATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCAAAGATGGC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
* * * ** ****
78000 AAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAAATTTAAGCCACC
1 AGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGATGGC
* * * * * * ** * *
78044 A-AGCCTTGTCTTCCTGAGCAGCT-GCGGAGTAGATTGAAGATTGT
1 AGA-TCTTATCTCCCTAAGCAG-TAGTGGAGCAGATCAAAGATGGC
* **
78088 AGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCAAAGATAAC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
* ** * * ** ****
78132 AAATCTTATCTTTCGAAG-A-TAGTGGGAAGCAAATTTAAGCCACC
1 AGATCTTATCTCCCTAAGCAGTAGT-GG-AGCAGATCAAAGATGGC
* * * * * * ** * *
78176 A-AGCCTTGTCTCCCTGAGCAGTAGCGGAGTAGGTTGAAGATTGT
1 AGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
*
78220 AGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCAAAGATGGC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
*
78264 AAATCTTATCT
1 AGATCTTATCT
78275 TTCCAAGATA
Statistics
Matches: 451, Mismatches: 180, Indels: 80
0.63 0.25 0.11
Matches are distributed among these distances:
42 20 0.04
43 31 0.07
44 356 0.79
45 32 0.07
46 11 0.02
47 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (44 bp):
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
Found at i:78534 original size:44 final size:44
Alignment explanation
Indices: 78486--78934 Score: 167
Period size: 44 Copynumber: 10.2 Consensus size: 44
78476 AAGATTTTAG
*
78486 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGCAA
* * * **
78530 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTAAAGACGGCAA
** * * * * * * ** * *
78574 GCCTTGTCTCCCTAAGCAGCAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGCAA
* * *
78618 ATCTTATCTCCTTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGCAA
* * * * **
78662 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAAATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTAAAGACGGCAA
** * * * * * * * * ** * *
78706 GCCTTGTCTTCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGCAA
*
78750 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGCAA
** * * * **
78794 ATCTTATCTTTCGAAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTAAAGACGGCAA
** * * * * * * ** * *
78838 GCCTTGTCTCCCTAAGCAGCAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGCAA
* * ** *
78882 ATCTTATATCCCTAAGCAGTAGGGGAGCAGATCGAAGACAGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGCAA
*
78926 ATATTATCT
1 ATCTTATCT
78935 TTCCAAGATA
Statistics
Matches: 275, Mismatches: 114, Indels: 32
0.65 0.27 0.08
Matches are distributed among these distances:
42 12 0.04
43 16 0.06
44 227 0.83
45 14 0.05
46 6 0.02
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGCAA
Found at i:80907 original size:44 final size:44
Alignment explanation
Indices: 80727--81175 Score: 158
Period size: 44 Copynumber: 10.2 Consensus size: 44
80717 AAGATTGTAG
* * *
80727 ATCTTATCTCCCTAAGCAGTAGTGAAACAGATCAAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGCAA
* * * **
80771 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTAAAGACGGCAA
** * * * ** ** * * ** * *
80815 GCCTTGTCTCCCTGAGCAGCAGCAGATTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGCAA
*
80859 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGCAA
* * * * **
80903 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGTAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTAAAGACGGCAA
** * * * * * * * ** * *
80947 GCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGCAA
* *
80991 ATCTTATATCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGCAA
** * * * **
81035 ATCTTATCTTTCGAAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTAAAGACGGCAA
** * * * * * * * ** * *
81079 GCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGCAA
* * *
81123 ATCTTATATCCCTAAGCAGTAGGGGAGCAGATTGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGCAA
81167 ATCTTATCT
1 ATCTTATCT
81176 TTCCAAGATA
Statistics
Matches: 269, Mismatches: 120, Indels: 32
0.64 0.29 0.08
Matches are distributed among these distances:
42 12 0.04
43 14 0.05
44 223 0.83
45 14 0.05
46 6 0.02
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGCAA
Found at i:81257 original size:44 final size:45
Alignment explanation
Indices: 81195--81293 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 45
81185 AGTGGGAAGT
* *
81195 AGATTTAAGCTAGCAAGTCTTATCGT-CCTGAAGTTGCAGTGGAGC
1 AGATTAAAGCTAGCAAGTCTTATC-TCCCTGAAGTTACAGTGGAGC
* * *
81240 AGATTAAAGCTA-TAAGTCTTTTCTCCCTGAAGTTACAGTGGAGT
1 AGATTAAAGCTAGCAAGTCTTATCTCCCTGAAGTTACAGTGGAGC
*
81284 AGATTGAAGC
1 AGATTAAAGC
81294 ATGAATTCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
43 1 0.02
44 35 0.74
45 11 0.23
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (45 bp):
AGATTAAAGCTAGCAAGTCTTATCTCCCTGAAGTTACAGTGGAGC
Found at i:81267 original size:132 final size:132
Alignment explanation
Indices: 80684--81204 Score: 934
Period size: 132 Copynumber: 3.9 Consensus size: 132
80674 GGTCACATCA
80684 CCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
1 CCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
* *
80749 TGAAACAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
66 TGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
80814 AG
131 AG
* *
80816 CCTTGTCTCCCTGAGCAGCAGCAGATTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
1 CCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
*
80881 TGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCACCA
66 TGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
80946 AG
131 AG
*
80948 CCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATATCCCTAAGCAGTAG
1 CCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
*
81013 TGGAGCAGATCAAAGACGGCAAATCTTATCTTTCGAAGATAGTGGGAAGCAGATTTAAGCCACCA
66 TGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
81078 AG
131 AG
*
81080 CCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATATCCCTAAGCAGTAG
1 CCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
* ** *
81145 GGGAGCAGATTGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGC
66 TGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGC
81205 TAGCAAGTCT
Statistics
Matches: 374, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 374 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (132 bp):
CCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
AG
Found at i:81524 original size:19 final size:19
Alignment explanation
Indices: 81496--81559 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
81486 AATTTTCGAG
*
81496 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
81515 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
*
81534 GATATATGTAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
81555 GATAT
1 GATAT
81560 ATACAATCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 22 0.56
21 17 0.44
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:81578 original size:19 final size:21
Alignment explanation
Indices: 81497--81572 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
81487 ATTTTCGAGG
81497 ATATACAATCTTAGATATG--
1 ATATACAATCTTAGATATGAT
* *
81516 ATATGCAATCCTAGATATGAT
1 ATATACAATCTTAGATATGAT
**
81537 ATATGTAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
81558 ATATACAATCTTAGA
1 ATATACAATCTTAGA
81573 AGATATGATT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
19 17 0.35
21 32 0.65
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:81608 original size:21 final size:23
Alignment explanation
Indices: 81564--81608 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
81554 TGATATATAC
*
81564 AATCTTAGAAGATATGATTTTGT
1 AATCTTAGAAGATATGAATTTGT
*
81587 AATCTTA-AAGAT-TTAATTTGT
1 AATCTTAGAAGATATGAATTTGT
81608 A
1 A
81609 GATACCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 5 0.25
23 7 0.35
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (23 bp):
AATCTTAGAAGATATGAATTTGT
Found at i:82037 original size:15 final size:15
Alignment explanation
Indices: 82013--82050 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
82003 GTTTTTAGTC
82013 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
82027 TGTTATTATTATTTT
1 TATTATTATTAATTT
82042 TATTATTAT
1 TATTATTAT
82051 ATTATATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:82044 original size:12 final size:12
Alignment explanation
Indices: 82015--82065 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
82005 TTTTAGTCTA
82015 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
82027 TGTTATTATTAT
1 TTTTATTATTAT
82039 TTTTATTATTAT
1 TTTTATTATTAT
82051 ATTATATATTATTAT
1 -TT-T-TATTATTAT
82066 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 3 0.09
12 18 0.55
13 2 0.06
14 1 0.03
15 9 0.27
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:82060 original size:15 final size:13
Alignment explanation
Indices: 82029--82066 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
82019 ATTAATTTTG
82029 TTATTATTAT-TT
1 TTATTATTATATT
82041 TTATTATTATATT
1 TTATTATTATATT
82054 ATATATTATTATA
1 -T-TATTATTATA
82067 CCTACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
13 2 0.09
14 1 0.04
15 10 0.43
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTATTATATT
Found at i:88902 original size:22 final size:24
Alignment explanation
Indices: 88856--88902 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
88846 CACCTGCAAT
* *
88856 AAACACATTAAAATGAGTTTATTA
1 AAACACATTAAAATCAGCTTATTA
88880 AAACACATTAAAA-CA-CTTATTA
1 AAACACATTAAAATCAGCTTATTA
88902 A
1 A
88903 TCATAACACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 1 0.05
24 13 0.62
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.30
Consensus pattern (24 bp):
AAACACATTAAAATCAGCTTATTA
Done.