Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2016
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: 30654
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1725 original size:20 final size:22
Alignment explanation
Indices: 1693--1739 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
1683 TTTTTTTTTC
1693 TTTTTGTATTTTTCGTAATT-T
1 TTTTTGTATTTTTCGTAATTCT
1714 TTTTTGTATTTTT-GTAATTCT
1 TTTTTGTATTTTTCGTAATTCT
1735 TTTTT
1 TTTTT
1740 TATGTACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.13, C:0.04, G:0.09, T:0.74
Consensus pattern (22 bp):
TTTTTGTATTTTTCGTAATTCT
Found at i:2424 original size:14 final size:14
Alignment explanation
Indices: 2377--2424 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2367 GTACGAATGG
*
2377 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
2391 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
2405 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
2419 ATTGGT
1 AATGGT
2425 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:7123 original size:30 final size:30
Alignment explanation
Indices: 7089--7185 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
7079 TAAACTAAAA
7089 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
* * * * * *
7119 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCATGAGCTAAAGT
* * *
7149 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCATGAGCT-AAAGT
7179 TGAGCTA
1 TGAGCTA
7186 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
Found at i:9810 original size:30 final size:30
Alignment explanation
Indices: 9724--9821 Score: 106
Period size: 30 Copynumber: 3.3 Consensus size: 30
9714 TTAAACTAAA
* *
9724 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
9754 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* *
9784 CTGAGCTAAGATTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
9814 ATGAGCTA
1 ATGAGCTA
9822 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:12102 original size:30 final size:30
Alignment explanation
Indices: 12031--12113 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
12021 CTTTTGTTTC
* *
12031 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
12062 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
12091 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
12114 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:12113 original size:18 final size:18
Alignment explanation
Indices: 12064--12119 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
12054 CACTCTCAAA
* *
12064 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
12081 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
12099 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
12118 TT
1 TT
12120 CAAAGACTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:12120 original size:12 final size:12
Alignment explanation
Indices: 12089--12113 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12079 TTTTTCAATC
12089 TCATTTTCTTTT
1 TCATTTTCTTTT
12101 TCATTTTCTTTT
1 TCATTTTCTTTT
12113 T
1 T
12114 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:12131 original size:12 final size:12
Alignment explanation
Indices: 12116--12146 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
12106 TTCTTTTTGC
12116 TTTTCAAAGACT
1 TTTTCAAAGACT
*
12128 TTTTCAAAGGCT
1 TTTTCAAAGACT
12140 TTTTCAA
1 TTTTCAA
12147 GTTCTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGACT
Found at i:12204 original size:5 final size:5
Alignment explanation
Indices: 12194--12250 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
12184 CTCTTGCCTC
* * *
12194 TCTTT TCTTTT TATTT TGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TC-TTT TCTTT TCTTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
12241 TCTTT TCTTT
1 TCTTT TCTTT
12251 GTTTTCTCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
4 3 0.07
5 30 0.70
6 6 0.14
7 4 0.09
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:12226 original size:25 final size:25
Alignment explanation
Indices: 12198--12246 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
12188 TGCCTCTCTT
*
12198 TTCTTTT-TATTTTGTTTTCTTTTTC
1 TTCTTTTCT-TTTTCTTTTCTTTTTC
12223 TTCTTTTGCTTTTTCTTTTCTTTT
1 TTCTTTT-CTTTTTCTTTTCTTTT
12247 CTTTGTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 13 0.62
27 1 0.05
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.80
Consensus pattern (25 bp):
TTCTTTTCTTTTTCTTTTCTTTTTC
Found at i:12251 original size:21 final size:20
Alignment explanation
Indices: 12207--12261 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
12197 TTTCTTTTTA
12207 TTTTG-TTTTCTTTTTCTTC
1 TTTTGTTTTTCTTTTTCTTC
*
12226 TTTTGCTTTTTC-TTTTCTTT
1 TTTTG-TTTTTCTTTTTCTTC
12246 TCTTTGTTTTCTCTTT
1 T-TTTGTTTT-TCTTT
12262 ACAAGAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 5 0.17
20 12 0.40
21 11 0.37
22 2 0.07
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTTGTTTTTCTTTTTCTTC
Found at i:13183 original size:13 final size:13
Alignment explanation
Indices: 13161--13192 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
13151 TCACTTCTTA
13161 TTTTTT-GAATTT
1 TTTTTTCGAATTT
13173 TTTTTTCGAATTT
1 TTTTTTCGAATTT
13186 TTTTTTC
1 TTTTTTC
13193 AAACTTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.75
Consensus pattern (13 bp):
TTTTTTCGAATTT
Found at i:14927 original size:30 final size:30
Alignment explanation
Indices: 14842--14929 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
14832 TAAACTAAAA
* * *
14842 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGC
* * * * *
14872 TGAGCTGAGATTAAACTCCTAAGCTGAAGC
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGC
*
14902 TGAGCTAAGGTTTAGCTCGTGAGCTGAA
1 TGAGCTAAGATTTAGCTCGTGAGCTGAA
14930 TTTGCGCTAG
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGC
Found at i:15994 original size:28 final size:27
Alignment explanation
Indices: 15939--16003 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
15929 TTCTTTTTCA
*
15939 TCTTCT-TTTTCACTCTCAAATTTCTT
1 TCTTCTCTTTTCAATCTCAAATTTCTT
*
15965 TCGTTCTCTTTTCAATCTC-ATTTTCTTT
1 TC-TTCTCTTTTCAATCTCAAATTTC-TT
*
15993 TCTTTTCTTTT
1 TCTTCTCTTTT
16004 GCTTTTCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 2 0.06
27 17 0.52
28 14 0.42
ACGTcount: A:0.11, C:0.25, G:0.02, T:0.63
Consensus pattern (27 bp):
TCTTCTCTTTTCAATCTCAAATTTCTT
Found at i:16003 original size:27 final size:28
Alignment explanation
Indices: 15941--15992 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
15931 CTTTTTCATC
*
15941 TTCT-TTTTCACTCTCAAATTTCTTTCG
1 TTCTCTTTTCAATCTCAAATTTCTTTCG
*
15968 TTCTCTTTTCAATCTC-ATTTTCTTT
1 TTCTCTTTTCAATCTCAAATTTCTTT
15993 TCTTTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.13, C:0.25, G:0.02, T:0.60
Consensus pattern (28 bp):
TTCTCTTTTCAATCTCAAATTTCTTTCG
Found at i:16095 original size:15 final size:14
Alignment explanation
Indices: 16075--16131 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 14
16065 CTTGCCTCTC
16075 CTTTTTTTTCATTTT
1 CTTTTTTTTC-TTTT
*
16090 CTTTTTCTTCTTTT
1 CTTTTTTTTCTTTT
16104 GCTTTTTCTTTTCTTTT
1 -C-TTTT-TTTTCTTTT
*
16121 CTTTGTTTTCT
1 CTTTTTTTTCT
16132 CTTAACAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 10 0.28
15 13 0.36
16 5 0.14
17 8 0.22
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
CTTTTTTTTCTTTT
Found at i:16117 original size:5 final size:5
Alignment explanation
Indices: 16075--16124 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
16065 CTTGCCTCTC
*
16075 CTTTT -TTTT CATTTT CTTTT -TCTT CTTTT GCTTTTT CTTTT CTTTT
1 CTTTT CTTTT C-TTTT CTTTT CTTTT CTTTT -C-TTTT CTTTT CTTTT
16121 CTTT
1 CTTT
16125 GTTTTCTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 7 0.18
5 20 0.53
6 7 0.18
7 4 0.11
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (5 bp):
CTTTT
Found at i:16125 original size:21 final size:20
Alignment explanation
Indices: 16086--16134 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
16076 TTTTTTTTCA
16086 TTTTCTTTTTCTTCTTTTGCT
1 TTTTCTTTTTCTTCTTTTG-T
*
16107 TTTTC-TTTTCTTTTCTTTGT
1 TTTTCTTTTTCTTCT-TTTGT
16127 TTTCTCTT
1 TTT-TCTT
16135 AACAAGAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 12 0.50
21 11 0.46
22 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTTCTTCTTTTGT
Found at i:17950 original size:29 final size:30
Alignment explanation
Indices: 17916--17978 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
17906 AGCTCGAATT
17916 AGCTCACA-TGAGCTTAATTTAGCTCG-TTG
1 AGCTCA-ATTGAGCTTAATTTAGCTCGTTTG
* *
17945 AGCTCAATTTAGCTTACTTTAGCTCGTTTG
1 AGCTCAATTGAGCTTAATTTAGCTCGTTTG
17975 AGCT
1 AGCT
17979 TGGCTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 1 0.03
29 22 0.73
30 7 0.23
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCAATTGAGCTTAATTTAGCTCGTTTG
Found at i:22080 original size:17 final size:17
Alignment explanation
Indices: 22058--22090 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22048 TGAAGGCGAG
22058 GCCCAAT-AAGCAAATCA
1 GCCCAATCAAG-AAATCA
22075 GCCCAATCAAGAAATC
1 GCCCAATCAAGAAATC
22091 CATCCATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.45, C:0.30, G:0.12, T:0.12
Consensus pattern (17 bp):
GCCCAATCAAGAAATCA
Found at i:25362 original size:12 final size:12
Alignment explanation
Indices: 25341--25504 Score: 54
Period size: 12 Copynumber: 13.7 Consensus size: 12
25331 AGAAAAGGAG
*
25341 AAAGAGATTGAA
1 AAAGAAATTGAA
25353 AAAGAAATTG--
1 AAAGAAATTGAA
**
25363 AAAGAAA-ACAA
1 AAAGAAATTGAA
**
25374 AAAGAAAACG-A
1 AAAGAAATTGAA
**
25385 AAAGAAAAAG-A
1 AAAGAAATTGAA
*
25396 AAAGAAATTGCA
1 AAAGAAATTGAA
**
25408 AAAGAAAAAGAA
1 AAAGAAATTGAA
*
25420 ATCAA-AAAGTGAGAA
1 A--AAGAAA-T-TGAA
*
25435 AAAGAAAATGAAGA
1 AAAGAAATTG-A-A
25449 AAAGAAAATTGAA
1 AAAG-AAATTGAA
* **
25462 AAAAAAAGCGAA
1 AAAGAAATTGAA
25474 AAAGAAATTGAA
1 AAAGAAATTGAA
* **
25486 AGAGAGCTTG-A
1 AAAGAAATTGAA
25497 AAAGAAAT
1 AAAGAAAT
25505 CAAGTGAAAA
Statistics
Matches: 113, Mismatches: 27, Indels: 25
0.68 0.16 0.15
Matches are distributed among these distances:
10 7 0.06
11 32 0.28
12 43 0.38
13 10 0.09
14 11 0.10
15 10 0.09
ACGTcount: A:0.68, C:0.04, G:0.19, T:0.10
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:25376 original size:22 final size:21
Alignment explanation
Indices: 25351--25416 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 21
25341 AAAGAGATTG
25351 AAAAAGAAATTG-AAAGAAAA
1 AAAAAGAAATTGAAAAGAAAA
**
25371 CAAAAAGAAAACGAAAAGAAAA
1 -AAAAAGAAATTGAAAAGAAAA
25393 AGAAAAGAAATTGCAAAAGAAAA
1 A-AAAAGAAATTG-AAAAGAAAA
25416 A
1 A
25417 GAAATCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.29
22 17 0.45
23 10 0.26
ACGTcount: A:0.74, C:0.05, G:0.15, T:0.06
Consensus pattern (21 bp):
AAAAAGAAATTGAAAAGAAAA
Found at i:25379 original size:11 final size:11
Alignment explanation
Indices: 25363--25402 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
25353 AAAGAAATTG
25363 AAAGAAAACAA
1 AAAGAAAACAA
*
25374 AAAGAAAACGA
1 AAAGAAAACAA
25385 AAAGAAAA-AGA
1 AAAGAAAACA-A
25396 AAAGAAA
1 AAAGAAA
25403 TTGCAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAGAAAACAA
Found at i:25416 original size:6 final size:6
Alignment explanation
Indices: 25363--25420 Score: 50
Period size: 6 Copynumber: 10.2 Consensus size: 6
25353 AAAGAAATTG
* * ** *
25363 AAAG-A AAACAA AAAGAA AACG-A AAAGAA AAAG-A AAAGAA ATTGCA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
25408 AAAGAA AAAGAA A
1 AAAGAA AAAGAA A
25421 TCAAAAAGTG
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
5 12 0.30
6 28 0.70
ACGTcount: A:0.76, C:0.05, G:0.16, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:25427 original size:17 final size:17
Alignment explanation
Indices: 25363--25428 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
25353 AAAGAAATTG
25363 AAAGAAAACAAAAAGAA
1 AAAGAAAACAAAAAGAA
* *
25380 AACGAAAAGAAAAAG-A
1 AAAGAAAACAAAAAGAA
*
25396 AAAGAAATTGC-AAAAGAA
1 AAAGAAA--ACAAAAAGAA
*
25414 AAAGAAATCAAAAAG
1 AAAGAAAACAAAAAG
25429 TGAGAAAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 8 0.21
17 23 0.59
18 8 0.21
ACGTcount: A:0.74, C:0.06, G:0.15, T:0.05
Consensus pattern (17 bp):
AAAGAAAACAAAAAGAA
Found at i:27335 original size:20 final size:20
Alignment explanation
Indices: 27312--27365 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
27302 AGTTTTTCCC
*
27312 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
27332 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
27352 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
27366 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:27347 original size:30 final size:30
Alignment explanation
Indices: 27312--27385 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
27302 AGTTTTTCCC
27312 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
27342 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
27372 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
27386 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:27375 original size:20 final size:20
Alignment explanation
Indices: 27312--27376 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
27302 AGTTTTTCCC
* * * *
27312 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
27332 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
27351 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
27372 AGCTC
1 AGCTC
27377 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
Done.