Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019874.1 Corchorus olitorius cultivar O-4 contig19907, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 87395
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Found at i:377 original size:21 final size:21
Alignment explanation
Indices: 353--402 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
343 CTTAGGCAAT
353 TCCAATGAGCTTGGAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
*
374 TCCAATAAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
395 TCCAATGA
1 TCCAATGA
403 ACTCCTAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:3961 original size:21 final size:21
Alignment explanation
Indices: 3932--3975 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3922 TCTTGCCCTT
* * *
3932 TTCATTGGACCTAATGGTATC
1 TTCAATGGACCAAATGGCATC
*
3953 TTCAATGGATCAAATGGCATC
1 TTCAATGGACCAAATGGCATC
3974 TT
1 TT
3976 AGGCAACTCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (21 bp):
TTCAATGGACCAAATGGCATC
Found at i:11565 original size:32 final size:32
Alignment explanation
Indices: 11529--11593 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
11519 CACATATAAT
* *
11529 TCTATCTTTTTGTGCATCATGTCGTGGAAAAG
1 TCTATCTCTTTGTGCATCATGTCGTCGAAAAG
11561 TCTATCTCTTTGTGCATCATGTCGTCGAAAAG
1 TCTATCTCTTTGTGCATCATGTCGTCGAAAAG
11593 T
1 T
11594 GCCACAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (32 bp):
TCTATCTCTTTGTGCATCATGTCGTCGAAAAG
Found at i:14748 original size:7 final size:7
Alignment explanation
Indices: 14738--14793 Score: 53
Period size: 7 Copynumber: 7.7 Consensus size: 7
14728 AAAATCAAAG
14738 TAAAAAT
1 TAAAAAT
14745 TAAAAATT
1 TAAAAA-T
14753 TAAAAAACTT
1 T-AAAAA--T
*
14763 TAGAAAT
1 TAAAAAT
14770 TAAAAAT
1 TAAAAAT
14777 T-AAAAT
1 TAAAAAT
14783 T-AAAAT
1 TAAAAAT
14789 TAAAA
1 TAAAA
14794 TTGGGTTGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
6 12 0.28
7 17 0.40
8 2 0.05
9 9 0.21
10 3 0.07
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (7 bp):
TAAAAAT
Found at i:14749 original size:6 final size:6
Alignment explanation
Indices: 14722--14795 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
14712 ACCTGTAAAA
* * * **
14722 AAAATT AAAATC AAAGTA AAAATT AAAAATTT AAAA-- AACTTT AGAAATT
1 AAAATT AAAATT AAAATT AAAATT -AAAA-TT AAAATT AAAATT A-AAATT
14771 AAAAATT AAAATT AAAATT AAAATT
1 -AAAATT AAAATT AAAATT AAAATT
14796 GGGTTGACTC
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
4 2 0.04
6 32 0.60
7 16 0.30
8 3 0.06
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:14794 original size:25 final size:24
Alignment explanation
Indices: 14721--14795 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 24
14711 AACCTGTAAA
* *
14721 AAAAATTAAAATCAAAGTAAAAATT
1 AAAAATTAAAAT-AAAATTAAAATT
**
14746 AAAAATTTAAAA-AACTTTAGAAATT
1 AAAAA-TTAAAATAAAATTA-AAATT
14771 AAAAATTAAAATTAAAATTAAAATT
1 AAAAATTAAAA-TAAAATTAAAATT
14796 GGGTTGACTC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
24 10 0.24
25 20 0.49
26 11 0.27
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (24 bp):
AAAAATTAAAATAAAATTAAAATT
Found at i:15783 original size:21 final size:21
Alignment explanation
Indices: 15759--15808 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
15749 CTTATGCAAT
*
15759 TCCAATGAGCTTGGAACCTT-C
1 TCCAATGAGCTTCGAA-CTTGC
15780 TCCAATGAGCTTCGAACTTGC
1 TCCAATGAGCTTCGAACTTGC
15801 TCCAATGA
1 TCCAATGA
15809 ACTCCTAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTCGAACTTGC
Found at i:17686 original size:33 final size:31
Alignment explanation
Indices: 17613--17753 Score: 120
Period size: 33 Copynumber: 4.3 Consensus size: 31
17603 GCTATGATCA
** *
17613 ACCAAAACAGATTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTG-TTTCATCACAAACAAC
17645 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC
*
17678 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC
** * * *
17711 ACTCAAATTAGTTTTAGTATCATCACTAACAAC
1 AC-CAAAACAGATTT-GTTTCATCACAAACAAC
*
17744 ATCTAAAACA
1 A-CCAAAACA
17754 CTCTTTGCAA
Statistics
Matches: 91, Mismatches: 12, Indels: 11
0.80 0.11 0.10
Matches are distributed among these distances:
32 7 0.08
33 77 0.85
34 7 0.08
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (31 bp):
ACCAAAACAGATTTGTTTCATCACAAACAAC
Found at i:18351 original size:15 final size:15
Alignment explanation
Indices: 18331--18362 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
18321 AAACTAAGTG
18331 GAGCTTGTTGATTTT
1 GAGCTTGTTGATTTT
18346 GAGCTTGTTGATTTT
1 GAGCTTGTTGATTTT
18361 GA
1 GA
18363 ACCCCCAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.28, T:0.50
Consensus pattern (15 bp):
GAGCTTGTTGATTTT
Found at i:30678 original size:14 final size:16
Alignment explanation
Indices: 30647--30680 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
30637 GAACTTAAGG
30647 AATAATTATTGAATAAT
1 AATAATTA-TGAATAAT
30664 AATAATTATGAAATAAT
1 AATAATTATG-AATAAT
30681 TATTATTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
AATAATTATGAATAAT
Found at i:33555 original size:21 final size:21
Alignment explanation
Indices: 33531--33597 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
33521 AATTCTCTGT
33531 AAATTAAGAAATACTCAATTC
1 AAATTAAGAAATACTCAATTC
* * * *
33552 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAATT-C
*
33573 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAATTC
33594 AAAT
1 AAAT
33598 CCTAATCCTT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 7 0.21
21 20 0.61
22 6 0.18
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (21 bp):
AAATTAAGAAATACTCAATTC
Found at i:33577 original size:42 final size:42
Alignment explanation
Indices: 33518--33598 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
33508 CCTAAGTCTT
*
33518 GAAAATTCTCTGTAAATTAAGAAATACTCAATTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
33560 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
33599 CTAATCCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:34252 original size:51 final size:51
Alignment explanation
Indices: 34192--34290 Score: 155
Period size: 51 Copynumber: 1.9 Consensus size: 51
34182 AAATCGAACC
34192 CAAGCTAGTATTAATTTTCTC-AAAAAAAAATGTAGTATATAAGAGTAGTGT
1 CAAGCTAGTATTAATTTTCTCAAAAAAAAAAT-TAGTATATAAGAGTAGTGT
* *
34243 CAAGTTAGTATTAATTTTCTCAAAAAAAAAAATTAGTGTATAAGAGTA
1 CAAGCTAGTATTAATTTTCTC-AAAAAAAAAATTAGTATATAAGAGTA
34291 ATGTGATTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
51 20 0.45
52 14 0.32
53 10 0.23
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.33
Consensus pattern (51 bp):
CAAGCTAGTATTAATTTTCTCAAAAAAAAAATTAGTATATAAGAGTAGTGT
Found at i:36257 original size:18 final size:18
Alignment explanation
Indices: 36236--36287 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
36226 AATCCTCCTA
*
36236 GACCTCCTGCGCCGCCTT
1 GACCTCCTGCACCGCCTT
*
36254 GACCTCCTGCACCGCCTA
1 GACCTCCTGCACCGCCTT
* *
36272 AACCTCCTCCACCGCC
1 GACCTCCTGCACCGCC
36288 AAGACCCCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.13, C:0.54, G:0.15, T:0.17
Consensus pattern (18 bp):
GACCTCCTGCACCGCCTT
Found at i:41615 original size:20 final size:20
Alignment explanation
Indices: 41590--41630 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
41580 CATTCATTTT
41590 CCTAAACGATGAAGAGATGA
1 CCTAAACGATGAAGAGATGA
41610 CCTAAACGATGAAGAGATGA
1 CCTAAACGATGAAGAGATGA
41630 C
1 C
41631 AAAGATAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (20 bp):
CCTAAACGATGAAGAGATGA
Found at i:42567 original size:18 final size:18
Alignment explanation
Indices: 42544--42580 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
42534 TAGACTCCGC
42544 TACATCTCTTATGAAAGA
1 TACATCTCTTATGAAAGA
*
42562 TACATCTCTTATGAGAGA
1 TACATCTCTTATGAAAGA
42580 T
1 T
42581 TCGATGTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (18 bp):
TACATCTCTTATGAAAGA
Found at i:43969 original size:15 final size:16
Alignment explanation
Indices: 43945--43984 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
43935 AGAGGTTGAA
*
43945 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
43960 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
43976 AGAAAACAA
1 AGAAAACAA
43985 AACAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:44068 original size:23 final size:23
Alignment explanation
Indices: 44042--44089 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
44032 ATAATTAAAG
44042 CATACTTCTCCAATGGTAGAAAA
1 CATACTTCTCCAATGGTAGAAAA
*
44065 CATACTTCTCCAATGGTAGTAAA
1 CATACTTCTCCAATGGTAGAAAA
44088 CA
1 CA
44090 ATCAAATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (23 bp):
CATACTTCTCCAATGGTAGAAAA
Found at i:45417 original size:29 final size:30
Alignment explanation
Indices: 45380--45439 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
45370 AATTCTTTCC
* *
45380 TCTTGAAATAATTCTTCAAT-GTCTTCAAA
1 TCTTCAAATAAGTCTTCAATAGTCTTCAAA
45409 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTCAAATAAGTCTTCAAT-AGTCTTCAAA
45440 CACGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
31 9 0.33
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (30 bp):
TCTTCAAATAAGTCTTCAATAGTCTTCAAA
Found at i:47262 original size:21 final size:19
Alignment explanation
Indices: 47212--47264 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 19
47202 GGCTTGGAAT
* *
47212 GGTGATGGCACGGGCATCC
1 GGTGGTGGCACGGGCAACC
* *
47231 GGTAGTAGCACGGGCTTAACC
1 GGTGGTGGCACGGGC--AACC
47252 GGTGGTGGCACGG
1 GGTGGTGGCACGG
47265 TGTATGGCCG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 12 0.46
21 14 0.54
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (19 bp):
GGTGGTGGCACGGGCAACC
Found at i:50428 original size:20 final size:20
Alignment explanation
Indices: 50392--50429 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
50382 TTTTTTTTCA
*
50392 AAAACGCAACACAAAAAATT
1 AAAACGCAACAAAAAAAATT
50412 AAAACGCAA-AAATAAAAA
1 AAAACGCAACAAA-AAAAA
50430 AAAATTAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.71, C:0.16, G:0.05, T:0.08
Consensus pattern (20 bp):
AAAACGCAACAAAAAAAATT
Found at i:50461 original size:30 final size:31
Alignment explanation
Indices: 50412--50481 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
50402 ACAAAAAATT
*
50412 AAAACGCA-AAAATAAAAAAAAATTA-G-AA
1 AAAACGCAGAAAAAAAAAAAAAATTAGGTAA
*
50440 AAAACGCAGAAAACAAAAAAAAAATTAGGTTA
1 AAAACGCAGAAAA-AAAAAAAAAATTAGGTAA
50472 AAAACGCAGA
1 AAAACGCAGA
50482 CACAAAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 8 0.22
29 4 0.11
30 12 0.33
31 1 0.03
32 11 0.31
ACGTcount: A:0.69, C:0.10, G:0.11, T:0.10
Consensus pattern (31 bp):
AAAACGCAGAAAAAAAAAAAAAATTAGGTAA
Found at i:51804 original size:29 final size:30
Alignment explanation
Indices: 51767--51826 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
51757 AATTCTTTCT
* *
51767 TCTTGAAATAATTCTTCGAT-GTCTTCAAA
1 TCTTGAAATAAGTCTTCAATAGTCTTCAAA
*
51796 TCTTTAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTGAAATAAGTCTTCAAT-AGTCTTCAAA
51827 CACGAACTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 17 0.65
31 9 0.35
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (30 bp):
TCTTGAAATAAGTCTTCAATAGTCTTCAAA
Found at i:54131 original size:27 final size:29
Alignment explanation
Indices: 54101--54168 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 29
54091 GCATTAGAAT
*
54101 CATTTTTGTCATTTTTACAC-T-AAGGGG
1 CATTTTAGTCATTTTTACACATCAAGGGG
* *
54128 CATTTTGGTCA--TTTACACATCCAGGGG
1 CATTTTAGTCATTTTTACACATCAAGGGG
54155 CATTTTAGTCATTT
1 CATTTTAGTCATTT
54169 CAAGTACACT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 7 0.21
26 1 0.03
27 25 0.74
29 1 0.03
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.43
Consensus pattern (29 bp):
CATTTTAGTCATTTTTACACATCAAGGGG
Found at i:54555 original size:25 final size:25
Alignment explanation
Indices: 54527--54577 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
54517 TTCTCAATAC
* *
54527 TAAGTCATTTTGGGAAATCCGATGT
1 TAAGTCATTGTGGGAAATCCAATGT
54552 TAAGTCATTGTGGGAAATCCAATGT
1 TAAGTCATTGTGGGAAATCCAATGT
54577 T
1 T
54578 GGTCCATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (25 bp):
TAAGTCATTGTGGGAAATCCAATGT
Found at i:58996 original size:5 final size:5
Alignment explanation
Indices: 58986--59022 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
58976 AAATGGTTGC
*
58986 TTTGT TTTGT TTTGG TTTGT TTTGT TTTG- TTTGT TTT
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTT
59023 AATGTTTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (5 bp):
TTTGT
Found at i:59006 original size:15 final size:14
Alignment explanation
Indices: 58986--59022 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
58976 AAATGGTTGC
58986 TTTGTTTTGTTTTGG
1 TTTGTTTTGTTTT-G
59001 TTTGTTTTGTTTTG
1 TTTGTTTTGTTTTG
59015 TTTGTTTT
1 TTTGTTTT
59023 AATGTTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (14 bp):
TTTGTTTTGTTTTG
Found at i:61090 original size:21 final size:22
Alignment explanation
Indices: 61066--61107 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
61056 TTTGCCTCAT
61066 GCATTCATTCAT-CATGCCATG
1 GCATTCATTCATGCATGCCATG
*
61087 GCATTCATTCATGCATTCCAT
1 GCATTCATTCATGCATGCCAT
61108 TAAAACCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36
Consensus pattern (22 bp):
GCATTCATTCATGCATGCCATG
Found at i:63121 original size:7 final size:7
Alignment explanation
Indices: 63104--63157 Score: 74
Period size: 7 Copynumber: 7.6 Consensus size: 7
63094 GATTTCCAAA
63104 AAAAATG
1 AAAAATG
63111 -AAAATG
1 AAAAATG
63117 AAAAAATG
1 -AAAAATG
63125 AAAAATG
1 AAAAATG
63132 AAAAATG
1 AAAAATG
63139 AAAAAATG
1 -AAAAATG
*
63147 AAAAAGG
1 AAAAATG
63154 AAAA
1 AAAA
63158 TAAAGGCACT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
6 6 0.14
7 24 0.56
8 13 0.30
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (7 bp):
AAAAATG
Found at i:63156 original size:22 final size:22
Alignment explanation
Indices: 63111--63157 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
63101 AAAAAAAATG
*
63111 AAAATGAAAAAATGAAAAATGA
1 AAAATGAAAAAATGAAAAAGGA
63133 AAAATGAAAAAATGAAAAAGGA
1 AAAATGAAAAAATGAAAAAGGA
63155 AAA
1 AAA
63158 TAAAGGCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (22 bp):
AAAATGAAAAAATGAAAAAGGA
Found at i:63583 original size:23 final size:24
Alignment explanation
Indices: 63548--63600 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
63538 TTCAATTAAA
63548 AAAAAATAACAAA-AATAATCAAAAT
1 AAAAAAT-ACAAATAA-AATCAAAAT
*
63573 AAAAAAT-CAAATCAAATCAAAAT
1 AAAAAATACAAATAAAATCAAAAT
*
63596 CAAAA
1 AAAAA
63601 GAGAATTGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 17 0.68
24 1 0.04
25 7 0.28
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.15
Consensus pattern (24 bp):
AAAAAATACAAATAAAATCAAAAT
Found at i:64183 original size:50 final size:49
Alignment explanation
Indices: 64119--64269 Score: 203
Period size: 50 Copynumber: 3.0 Consensus size: 49
64109 GAAGTTTTAT
* * *
64119 AATAAGATTTCTTTCCATCTATGAGTTCAAGATCAAAATTCGTTTTTCAA
1 AATAAGATTGCTTTCCAT-TGTGAGTTCAAGATCAAAATTCGCTTTTCAA
* *
64169 AATAAAATTGCTTTCCATTTGTGAGTTCAAGATTAAAATTCGCTTTTCAA
1 AATAAGATTGCTTTCCA-TTGTGAGTTCAAGATCAAAATTCGCTTTTCAA
* * *
64219 AGTAAGATTGCATTCCAGTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
1 AATAAGATTGCTTTCCA-TTGTGAGTTCAAGATCAAAATTCGCTTTTCAA
64269 A
1 A
64270 GGGCATTTAA
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 88 0.99
51 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (49 bp):
AATAAGATTGCTTTCCATTGTGAGTTCAAGATCAAAATTCGCTTTTCAA
Found at i:65145 original size:23 final size:23
Alignment explanation
Indices: 65119--65248 Score: 66
Period size: 23 Copynumber: 5.3 Consensus size: 23
65109 AGATTGAATT
65119 GGAAGACAGTTCAAAGGATAAGC
1 GGAAGACAGTTCAAAGGATAAGC
* ** **
65142 GGAAGACGGTCCTTTTAA-GATTGAATT
1 GGAAGACAG---TTCAAAGGA-T-AAGC
65169 GGAAGACAGTTCAAAGGATAAGC
1 GGAAGACAGTTCAAAGGATAAGC
* ** **
65192 GGAAGACGGTCCTTTTAA-GATTGAATT
1 GGAAGACAG---TTCAAAGGA-T-AAGC
65219 GGAAGACAGTTCAAAGGATAAGC
1 GGAAGACAGTTCAAAGGATAAGC
65242 GGAAGAC
1 GGAAGAC
65249 GGTCCTTTTA
Statistics
Matches: 75, Mismatches: 20, Indels: 24
0.63 0.17 0.20
Matches are distributed among these distances:
23 27 0.36
24 10 0.13
25 8 0.11
26 10 0.13
27 20 0.27
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (23 bp):
GGAAGACAGTTCAAAGGATAAGC
Found at i:65177 original size:50 final size:50
Alignment explanation
Indices: 65101--65282 Score: 312
Period size: 50 Copynumber: 3.6 Consensus size: 50
65091 CGGTACATTA
65101 CCTTTTAAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGT
1 CCTTTT-AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGT
65152 CCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGT
1 CCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGT
65202 CCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGT
1 CCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGT
* * *
65252 CCTTTTAATATT-AGATTGGAAAACAATTCAA
1 CCTTTTAAGATTGA-ATTGGAAGACAGTTCAA
65283 TGAAATTTAT
Statistics
Matches: 127, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
49 1 0.01
50 120 0.94
51 6 0.05
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (50 bp):
CCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGT
Found at i:66002 original size:25 final size:25
Alignment explanation
Indices: 65974--66025 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
65964 TTCTCAATAC
* *
65974 TTAAGTCATTTTGGGAAATCCGATG
1 TTAAGTCATTATGGGAAATCCAATG
65999 TTAAGTCATTATGGGAAATCCAATG
1 TTAAGTCATTATGGGAAATCCAATG
66024 TT
1 TT
66026 GGTCCATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.37
Consensus pattern (25 bp):
TTAAGTCATTATGGGAAATCCAATG
Found at i:74160 original size:11 final size:11
Alignment explanation
Indices: 74126--74167 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
74116 ACGATCTAGA
*
74126 GGTGATGGCAC
1 GGTGCTGGCAC
74137 GG-GCATGGC-C
1 GGTGC-TGGCAC
74147 GGTGCTGGCAC
1 GGTGCTGGCAC
74158 GGTGCTGGCA
1 GGTGCTGGCA
74168 TGGACTGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.17
Consensus pattern (11 bp):
GGTGCTGGCAC
Found at i:77446 original size:114 final size:110
Alignment explanation
Indices: 77209--77490 Score: 354
Period size: 114 Copynumber: 2.5 Consensus size: 110
77199 TGATTACCAT
* * * * *
77209 TTTTACTCTTTTTAGTTTAATAATTC-TGAATTAAACTATCTACTGATTACTTTTTCTTTACTTT
1 TTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAAATAACTACTGATTACTCTTTCTTTACTTT
* * * * *
77273 TTAGCTTAATTACTCTGAATTAAACTATCTATTGATTATTCTTTC
66 TTAACTTAATAACTCTGAATTAAACTATCTATTAATTACTCTCTC
*
77318 -TTTACTCTTTTTAGTTTAATTACTCTTGAATTAAAATAAACTACTGCTTACTCTTTCTTTTACT
1 TTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAAAT-AACTACTGATTACTCTTTC-TTTACT
77382 TTTTAACTTAATAACTCTTGAATTAAACTAATCT-TCTAATTACTCTCTC
64 TTTTAACTTAATAACTC-TGAATTAAACT-ATCTAT-TAATTACTCTCTC
* * * *
77431 TTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTATTCTTCTAATTACTCTTTCTT
1 TTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAAATA-ACTACTGATTACTCTTTCTT
77491 GTAGACACCC
Statistics
Matches: 149, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
108 23 0.15
109 10 0.07
110 16 0.11
111 21 0.14
112 12 0.08
113 17 0.11
114 50 0.34
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.52
Consensus pattern (110 bp):
TTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAAATAACTACTGATTACTCTTTCTTTACTTT
TTAACTTAATAACTCTGAATTAAACTATCTATTAATTACTCTCTC
Found at i:77464 original size:58 final size:58
Alignment explanation
Indices: 77209--77490 Score: 325
Period size: 56 Copynumber: 5.0 Consensus size: 58
77199 TGATTACCAT
* * * *
77209 TTTTACTCTTTTTAGTTTAATAATTC-TGAATTAAACT-ATCTACTGATTACTTTTTC
1 TTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTTCTGATTACTCTTTC
* *
77265 -TTTA--CTTTTTAGCTTAATTACTC-TGAATTAAACT-ATCTAT-TGATTATTCTTTC
1 TTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTAATCT-TCTGATTACTCTTTC
* * * *
77318 -TTTACTCTTTTTAGTTTAATTACTCTTGAATTAAAATAAACTACTGCTTACTCTTTC
1 TTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTTCTGATTACTCTTTC
** * * *
77375 TTTTA--CTTTTTAACTTAATAACTCTTGAATTAAACTAATCTTCTAATTACTCTCTC
1 TTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTTCTGATTACTCTTTC
* *
77431 TTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTATTCTTCTAATTACTCTTTC
1 TTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTTCTGATTACTCTTTC
77489 TT
1 TT
77491 GTAGACACCC
Statistics
Matches: 191, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
53 46 0.24
55 22 0.12
56 57 0.30
57 14 0.07
58 52 0.27
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.52
Consensus pattern (58 bp):
TTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTTCTGATTACTCTTTC
Found at i:77480 original size:28 final size:28
Alignment explanation
Indices: 77390--77486 Score: 79
Period size: 28 Copynumber: 3.4 Consensus size: 28
77380 CTTTTTAACT
* *
77390 TAATAACTCTTGAATTAAACTAATCTTC
1 TAATTACTCTTGAATTAAACTATTCTTC
*** ** * *
77418 TAATTACTCTCTCTTTTACTCT-TTTTAGTT
1 TAATTACTCT-TGAATTAAACTATTCT--TC
77448 TAATTACTCTTGAATTAAACTATTCTTC
1 TAATTACTCTTGAATTAAACTATTCTTC
77476 TAATTACTCTT
1 TAATTACTCTT
77487 TCTTGTAGAC
Statistics
Matches: 49, Mismatches: 16, Indels: 8
0.67 0.22 0.11
Matches are distributed among these distances:
28 23 0.47
29 12 0.24
30 14 0.29
ACGTcount: A:0.29, C:0.19, G:0.03, T:0.49
Consensus pattern (28 bp):
TAATTACTCTTGAATTAAACTATTCTTC
Found at i:83795 original size:13 final size:13
Alignment explanation
Indices: 83777--83801 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83767 TGAAGCAGCA
83777 GCAAGGCTGCCCT
1 GCAAGGCTGCCCT
83790 GCAAGGCTGCCC
1 GCAAGGCTGCCC
83802 CAGCATCCAG
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:0.16, C:0.40, G:0.32, T:0.12
Consensus pattern (13 bp):
GCAAGGCTGCCCT
Found at i:84384 original size:16 final size:15
Alignment explanation
Indices: 84352--84393 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
84342 TGTCGACTTA
*
84352 AAGGATCAAGTCGAT
1 AAGGATCAAGTCAAT
84367 AAGGATCAAAGTCAAT
1 AAGGATC-AAGTCAAT
*
84383 AAGGAGCAAGT
1 AAGGATCAAGT
84394 GTCGACTAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.45, C:0.12, G:0.26, T:0.17
Consensus pattern (15 bp):
AAGGATCAAGTCAAT
Found at i:84431 original size:21 final size:23
Alignment explanation
Indices: 84405--84458 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
84395 TCGACTAGGG
84405 AATTGTCAAC-CAAAT-GAAGCA
1 AATTGTCAACTCAAATAGAAGCA
* *
84426 AATTGTCGACTCAAGTAGAAGCA
1 AATTGTCAACTCAAATAGAAGCA
84449 AATTGTCAAC
1 AATTGTCAAC
84459 ACGTAGCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 9 0.32
22 4 0.14
23 15 0.54
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.22
Consensus pattern (23 bp):
AATTGTCAACTCAAATAGAAGCA
Done.