Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold694
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: 127048
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1064 original size:15 final size:15
Alignment explanation
Indices: 1044--1080 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1034 TGCTTTTCAA
1044 TTCTATCTATATATC
1 TTCTATCTATATATC
*
1059 TTCTATCTATCTATC
1 TTCTATCTATATATC
1074 -TCTATCT
1 TTCTATCT
1081 CAATCCAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (15 bp):
TTCTATCTATATATC
Found at i:3651 original size:23 final size:23
Alignment explanation
Indices: 3625--3668 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3615 TTTCTTTTGT
3625 TTCTTT-TTCTAATTCATTTTCTC
1 TTCTTTCTTC-AATTCATTTTCTC
*
3648 TTCTTTCTTCAATTCTTTTTC
1 TTCTTTCTTCAATTCATTTTC
3669 ACTCTCAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.11, C:0.23, G:0.00, T:0.66
Consensus pattern (23 bp):
TTCTTTCTTCAATTCATTTTCTC
Found at i:18260 original size:12 final size:11
Alignment explanation
Indices: 18235--18259 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18225 TACTTCAAAA
18235 TTTGAATTTTT
1 TTTGAATTTTT
18246 TTTGAATTTTT
1 TTTGAATTTTT
18257 TTT
1 TTT
18260 TCAAATTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTGAATTTTT
Found at i:20645 original size:30 final size:29
Alignment explanation
Indices: 20545--20647 Score: 80
Period size: 30 Copynumber: 3.4 Consensus size: 29
20535 TGAGTTTAAA
* * * *
20545 CTAAAATGAGATAAGCTTTAGTTCGTGAG
1 CTAAATTGAGCTAAGGTTTAGCTCGTGAG
* * * * * *
20574 CTAAAGTTGAGCTGAGGCTAAACTCCTAAG
1 CTAAA-TTGAGCTAAGGTTTAGCTCGTGAG
*
20604 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGGTTTAGCTCGTGAG
20634 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
20648 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 18, Indels: 5
0.70 0.24 0.07
Matches are distributed among these distances:
29 8 0.15
30 43 0.81
31 2 0.04
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGTTTAGCTCGTGAG
Found at i:22828 original size:12 final size:12
Alignment explanation
Indices: 22813--22843 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
22803 TTATTTTTGC
22813 TTTTCAAAGGCT
1 TTTTCAAAGGCT
22825 TTTTCAAAGGCT
1 TTTTCAAAGGCT
22837 TTTTCAA
1 TTTTCAA
22844 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:22901 original size:5 final size:5
Alignment explanation
Indices: 22891--22957 Score: 59
Period size: 5 Copynumber: 13.0 Consensus size: 5
22881 CTCTTGCCTC
*
22891 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
22938 TCTTT TCTTT T-TTT CTCTTT
1 TCTTT TCTTT TCTTT -TCTTT
22958 ACAAGAATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
4 7 0.13
5 31 0.60
6 9 0.17
7 5 0.10
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:22933 original size:31 final size:29
Alignment explanation
Indices: 22891--22953 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
22881 CTCTTGCCTC
22891 TCTTTTCTTTTT-ATTTCATTTTCTTTTTCT
1 TCTTTTCTTTTTCATTTC-TTTTCTTTTT-T
*
22921 TCTTTTGCTTTTTCTTTTCTTTTCTTTTTT
1 TCTTTT-CTTTTTCATTTCTTTTCTTTTTT
22951 TCT
1 TCT
22954 CTTTACAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 10 0.33
31 16 0.53
32 4 0.13
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (29 bp):
TCTTTTCTTTTTCATTTCTTTTCTTTTTT
Found at i:22956 original size:15 final size:16
Alignment explanation
Indices: 22889--22957 Score: 81
Period size: 15 Copynumber: 4.4 Consensus size: 16
22879 GCCTCTTGCC
*
22889 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
22905 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
22921 TCT-TTTGCTTTTTCT
1 TCTCTTTTCTTTTTCT
*
22936 TTTCTTTTCTTTTT-T
1 TCTCTTTTCTTTTTCT
22951 TCTCTTT
1 TCTCTTT
22958 ACAAGAATGT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
15 22 0.49
16 22 0.49
17 1 0.02
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:23888 original size:17 final size:17
Alignment explanation
Indices: 23855--23893 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
23845 CATTAAACAC
*
23855 TTTTTTTTCAGATTTTT
1 TTTTTTTTCAGAATTTT
23872 TTTTCTTTTC-GAATTTT
1 TTTT-TTTTCAGAATTTT
23889 TTTTT
1 TTTTT
23894 GAATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 14 0.70
18 5 0.25
ACGTcount: A:0.10, C:0.08, G:0.05, T:0.77
Consensus pattern (17 bp):
TTTTTTTTCAGAATTTT
Found at i:26252 original size:30 final size:31
Alignment explanation
Indices: 26218--26314 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 31
26208 AGCTCACTCC
*
26218 TAGCTC-ACTTTCAACTCATGAGCTAAACCT
1 TAGCTCAACTTTCAACTCACGAGCTAAACCT
* * * * *
26248 TAGCTCAAC-TTCAACTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAACTCACGAGCTAAACCT
* * *
26278 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAACTCACGAGCTAAACCT
26308 TAGCTCA
1 TAGCTCA
26315 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAACTCACGAGCTAAACCT
Found at i:29024 original size:19 final size:20
Alignment explanation
Indices: 29002--29047 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
28992 AGCTCCGTCC
29002 AGCTCAATTCA-CTCATTTG
1 AGCTCAATTCAGCTCATTTG
* *
29021 AGCTCATTTCAGCTCGTTTG
1 AGCTCAATTCAGCTCATTTG
29041 AGCTCAA
1 AGCTCAA
29048 CCGAGCTTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (20 bp):
AGCTCAATTCAGCTCATTTG
Found at i:29028 original size:10 final size:10
Alignment explanation
Indices: 29013--29046 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
29003 GCTCAATTCA
29013 CTCATTTGAG
1 CTCATTTGAG
*
29023 CTCATTTCAG
1 CTCATTTGAG
*
29033 CTCGTTTGAG
1 CTCATTTGAG
29043 CTCA
1 CTCA
29047 ACCGAGCTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (10 bp):
CTCATTTGAG
Found at i:33195 original size:30 final size:30
Alignment explanation
Indices: 33110--33206 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
33100 TAAACTAAAA
* *
33110 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
33140 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* *
33170 TGAGCTAAGGTTTAGCTAGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
33199 ATGAGCTA
1 -TGAGCTA
33207 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:34783 original size:14 final size:14
Alignment explanation
Indices: 34766--34805 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
34756 CGAATGGAAT
*
34766 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
34780 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
34794 GATATGAACAAA
1 GGTAGGAACAAA
34806 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:38483 original size:42 final size:42
Alignment explanation
Indices: 38437--38522 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
38427 CTCCAAAATC
38437 CTGCAACAAAGAAACAATAAGAGAAGGTAAATATTTTTCTAT
1 CTGCAACAAAGAAACAATAAGAGAAGGTAAATATTTTTCTAT
38479 CTGCAACAAAGAAACAATAAGAGAAGGTAAATATTTTTCTAT
1 CTGCAACAAAGAAACAATAAGAGAAGGTAAATATTTTTCTAT
38521 CT
1 CT
38523 CATTAGTTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.27
Consensus pattern (42 bp):
CTGCAACAAAGAAACAATAAGAGAAGGTAAATATTTTTCTAT
Found at i:38723 original size:15 final size:14
Alignment explanation
Indices: 38699--38738 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
38689 TTTTCCACTA
*
38699 TTTTTCTTTTCGTTC
1 TTTTTCTTTT-GCTC
*
38714 TTTTTATTTTGCTC
1 TTTTTCTTTTGCTC
38728 TTTTTCTTTTG
1 TTTTTCTTTTG
38739 ATATTTCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.03, C:0.15, G:0.07, T:0.75
Consensus pattern (14 bp):
TTTTTCTTTTGCTC
Found at i:44043 original size:23 final size:22
Alignment explanation
Indices: 43991--44043 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
43981 TCCACGTCTT
*
43991 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
44013 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
44036 TTTCTTTT
1 TTTCTTTT
44044 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:46415 original size:6 final size:6
Alignment explanation
Indices: 46404--46429 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
46394 ATAAATAAAT
46404 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
46430 CTTTACAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:58037 original size:21 final size:21
Alignment explanation
Indices: 58013--58080 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
58003 GATTTTGAAT
58013 GAAATCGAGAGAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
***** *
58034 GAAAAT-GAGAGAATCTTGAAT
1 G-AAATCGAGAGAAGAAACAAA
*
58055 GAAATCGAGAAAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
58076 GAAAT
1 GAAAT
58081 GAAAGAAAAA
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.59, C:0.07, G:0.22, T:0.12
Consensus pattern (21 bp):
GAAATCGAGAGAAGAAACAAA
Found at i:58053 original size:42 final size:42
Alignment explanation
Indices: 57991--58087 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
57981 AGATTATGAG
* * *
57991 AGAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
58033 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
58075 AG-AAATGAAAGAA
1 AGAAAATGAGAGAA
58088 AAAGAAAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 10 0.20
42 41 0.80
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (42 bp):
AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
Found at i:58114 original size:18 final size:18
Alignment explanation
Indices: 58091--58140 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
58081 GAAAGAAAAA
*
58091 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
58109 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
58127 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
58141 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:60007 original size:30 final size:30
Alignment explanation
Indices: 59973--60069 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
59963 TAAACTAAAA
59973 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
60003 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
60033 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
60063 TGAGCTA
1 TGAGCTA
60070 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:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:62231 original size:30 final size:30
Alignment explanation
Indices: 62176--62261 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 30
62166 TTCTTTTGTT
* *
62176 TCAATTTCTTTTT-TTATCTTCTTTTTCACTC
1 TCAATTTCTTTTTCAT-TC-TCTTTTTCAATC
62207 TCAAATTTC-TTTTCATTCTCTTTTTCAATC
1 TC-AATTTCTTTTTCATTCTCTTTTTCAATC
* *
62237 TCATTTTCTTTTTCATTTTCTTTTT
1 TCAATTTCTTTTTCATTCTCTTTTT
62262 GCTTTTAAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 5 0.10
30 28 0.58
31 8 0.17
32 7 0.15
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.65
Consensus pattern (30 bp):
TCAATTTCTTTTTCATTCTCTTTTTCAATC
Found at i:62261 original size:18 final size:18
Alignment explanation
Indices: 62212--62267 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
62202 CACTCTCAAA
*
62212 TTTC-TTTTCATTCTCTT
1 TTTCATTTTCATTTTCTT
* *
62229 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
62247 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
62266 TT
1 TT
62268 AAAGGCTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 4 0.13
18 22 0.71
19 5 0.16
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:62267 original size:12 final size:12
Alignment explanation
Indices: 62237--62261 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62227 TTTTTCAATC
62237 TCATTTTCTTTT
1 TCATTTTCTTTT
62249 TCATTTTCTTTT
1 TCATTTTCTTTT
62261 T
1 T
62262 GCTTTTAAAG
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:62283 original size:12 final size:12
Alignment explanation
Indices: 62264--62293 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
62254 TTCTTTTTGC
62264 TTTT-AAAGGCT
1 TTTTCAAAGGCT
62275 TTTTCAAAGGCT
1 TTTTCAAAGGCT
62287 TTTTCAA
1 TTTTCAA
62294 GTTCTCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:62351 original size:5 final size:5
Alignment explanation
Indices: 62341--62391 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
62331 CTCTTGCCTC
*
62341 TCTTT TCTTT T-TATT TCTTT T-TCT TCTTT TGCTTTT TCTTT TCTTT
1 TCTTT TCTTT TCT-TT TCTTT TCTTT TCTTT T-C-TTT TCTTT TCTTT
62387 TCTTT
1 TCTTT
62392 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 4 0.10
5 28 0.72
6 3 0.08
7 4 0.10
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:63327 original size:17 final size:16
Alignment explanation
Indices: 63302--63340 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
63292 CATTAAACAC
*
63302 TTTTTTTTTCAGATTT
1 TTTTTTTTTCAAATTT
63318 TTTTTCTTTTCAAATTT
1 TTTTT-TTTTCAAATTT
63335 TTTTTT
1 TTTTTT
63341 GAATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTTTTTTCAAATTT
Found at i:63335 original size:16 final size:16
Alignment explanation
Indices: 63302--63340 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
63292 CATTAAACAC
*
63302 TTTTTTTTTCAGATTT
1 TTTTTTTTTCAGAATT
63318 TTTTTCTTTTCA-AATT
1 TTTTT-TTTTCAGAATT
63334 TTTTTTT
1 TTTTTTT
63341 GAATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 13 0.62
17 6 0.29
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTTTTTTCAGAATT
Found at i:65075 original size:30 final size:30
Alignment explanation
Indices: 65041--65137 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
65031 TAAACTAAAA
65041 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
65071 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
65101 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
65131 TGAGCTA
1 TGAGCTA
65138 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:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:65766 original size:19 final size:19
Alignment explanation
Indices: 65742--65778 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
65732 TACTACAACA
65742 ATTTAAGTTGTCTTAGTTC
1 ATTTAAGTTGTCTTAGTTC
*
65761 ATTTAATTTGTCTTAGTT
1 ATTTAAGTTGTCTTAGTT
65779 TAATGCATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.08, G:0.14, T:0.57
Consensus pattern (19 bp):
ATTTAAGTTGTCTTAGTTC
Found at i:68061 original size:17 final size:17
Alignment explanation
Indices: 68041--68099 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
68031 AAAAATTTGA
68041 AAAAATAAAAAAAGTTC
1 AAAAATAAAAAAAGTTC
*
68058 AAAAA-ACAAAAAAATTC
1 AAAAATA-AAAAAAGTTC
*
68075 AAAAATTCAAAAAAAGTTA
1 AAAAA-T-AAAAAAAGTTC
68094 AAAAAT
1 AAAAAT
68100 TAGAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 1 0.03
17 19 0.54
18 1 0.03
19 13 0.37
20 1 0.03
ACGTcount: A:0.73, C:0.07, G:0.03, T:0.17
Consensus pattern (17 bp):
AAAAATAAAAAAAGTTC
Found at i:68062 original size:19 final size:18
Alignment explanation
Indices: 68040--68099 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
68030 TAAAAATTTG
68040 AAAAAATAAAAAAAGTTC
1 AAAAAATAAAAAAAGTTC
*
68058 AAAAAACAAAAAAA-TTC
1 AAAAAATAAAAAAAGTTC
*
68075 AAAAATTCAAAAAAAGTT-
1 AAAAAAT-AAAAAAAGTTC
68093 AAAAAAT
1 AAAAAAT
68100 TAGAAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 8 0.22
18 26 0.72
19 2 0.06
ACGTcount: A:0.73, C:0.07, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAAAATAAAAAAAGTTC
Found at i:68073 original size:36 final size:35
Alignment explanation
Indices: 68031--68098 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
68021 GTTTCAAAAT
* *
68031 AAAAATTTGAAAAAAT-AAAAAAAGTTCAAAAAACA
1 AAAAAATTCAAAAAATCAAAAAAAGTT-AAAAAACA
*
68066 AAAAAATTCAAAAATTCAAAAAAAGTTAAAAAA
1 AAAAAATTCAAAAAATCAAAAAAAGTTAAAAAA
68099 TTAGAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 19 0.66
36 10 0.34
ACGTcount: A:0.72, C:0.06, G:0.04, T:0.18
Consensus pattern (35 bp):
AAAAAATTCAAAAAATCAAAAAAAGTTAAAAAACA
Found at i:70177 original size:30 final size:30
Alignment explanation
Indices: 70143--70239 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
70133 TAAACTAAAA
* *
70143 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * *
70173 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* *
70203 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGCT-AAAGT
70233 TGAGCTA
1 TGAGCTA
70240 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 47 0.94
31 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:82489 original size:20 final size:20
Alignment explanation
Indices: 82442--82489 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
82432 AGTAAGCTCG
82442 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
82462 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
82482 GTTGAGCT
1 GTTGAGCT
82490 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:83768 original size:23 final size:22
Alignment explanation
Indices: 83716--83768 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
83706 TCCACGTCTT
*
83716 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
83738 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
83761 TTTCTTTT
1 TTTCTTTT
83769 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:86551 original size:11 final size:11
Alignment explanation
Indices: 86535--86573 Score: 78
Period size: 11 Copynumber: 3.5 Consensus size: 11
86525 TCAAAATATA
86535 TTTTTTTCGAT
1 TTTTTTTCGAT
86546 TTTTTTTCGAT
1 TTTTTTTCGAT
86557 TTTTTTTCGAT
1 TTTTTTTCGAT
86568 TTTTTT
1 TTTTTT
86574 GAATCTACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTTTTCGAT
Found at i:90735 original size:10 final size:11
Alignment explanation
Indices: 90719--90749 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
90709 TTCAAAATAT
90719 TTTTTTTTCGA
1 TTTTTTTTCGA
90730 TTTTTTTTCGA
1 TTTTTTTTCGA
90741 TTTTGTTTT
1 TTTT-TTTT
90750 TTTTGAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.06, C:0.06, G:0.10, T:0.77
Consensus pattern (11 bp):
TTTTTTTTCGA
Found at i:91747 original size:25 final size:24
Alignment explanation
Indices: 91713--91760 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
91703 CAACTTCTAA
91713 AGAAAACTCAAGAGAGAAA-TCTTGG
1 AGAAAACTCAA-AGA-AAATTCTTGG
91738 AGAAAACTCAAAGAAAATTCTTG
1 AGAAAACTCAAAGAAAATTCTTG
91761 ATACGAGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.14
24 8 0.36
25 11 0.50
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (24 bp):
AGAAAACTCAAAGAAAATTCTTGG
Found at i:98190 original size:23 final size:22
Alignment explanation
Indices: 98138--98190 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
98128 TCCACGTCTT
*
98138 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
98160 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
98183 TTTCTTTT
1 TTTCTTTT
98191 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:99497 original size:18 final size:19
Alignment explanation
Indices: 99466--99507 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
99456 TTTTTTTAAA
*
99466 TTTTTATTGAATTTTGTCTT
1 TTTTTATT-AATTTTGACTT
99486 TTTTTATT-ATTTTGACTT
1 TTTTTATTAATTTTGACTT
99504 TTTT
1 TTTT
99508 GACTGATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.62
20 8 0.38
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (19 bp):
TTTTTATTAATTTTGACTT
Found at i:115143 original size:30 final size:30
Alignment explanation
Indices: 115109--115205 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
115099 AGCTCACTCC
115109 TAGCTCATA-TTTAGCTCACGAGCTAAAGCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
* * * **
115139 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
115169 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
115199 TAGCTCA
1 TAGCTCA
115206 TTTTAGTTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 4 0.08
30 45 0.87
31 3 0.06
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:118738 original size:20 final size:21
Alignment explanation
Indices: 118694--118755 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
118684 TTTGAACCAT
* *
118694 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
118716 TACCATTTCGTA-CAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
118736 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
118756 CAAATACCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 16 0.46
21 8 0.23
22 11 0.31
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.31
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:120629 original size:20 final size:20
Alignment explanation
Indices: 120606--120658 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
120596 AGTTTTTCCC
120606 AGCTCAATTTAGCACACATG
1 AGCTCAATTTAGCACACATG
* * ***
120626 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCACACATG
120646 AGCTCAATTTAGC
1 AGCTCAATTTAGC
120659 TTACTTTAGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (20 bp):
AGCTCAATTTAGCACACATG
Found at i:120669 original size:20 final size:19
Alignment explanation
Indices: 120606--120670 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
120596 AGTTTTTCCC
* * *
120606 AGCTCAATTTAGCACACATG
1 AGCTCAATTTAGC-TACTTT
*
120626 AGCTTAATTTAGCT-CGTTT
1 AGCTCAATTTAGCTAC-TTT
120645 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGC-TACTTT
120666 AGCTC
1 AGCTC
120671 GTTTGAGCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 29 0.81
21 4 0.11
22 1 0.03
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (19 bp):
AGCTCAATTTAGCTACTTT
Found at i:122303 original size:12 final size:12
Alignment explanation
Indices: 122286--122312 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
122276 CAAAAAAATC
122286 AAAATTCAAAAA
1 AAAATTCAAAAA
122298 AAAATTCAAAAA
1 AAAATTCAAAAA
122310 AAA
1 AAA
122313 GTGAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATTCAAAAA
Found at i:122308 original size:11 final size:11
Alignment explanation
Indices: 122286--122324 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
122276 CAAAAAAATC
122286 AAAATTCAAAAA
1 AAAATTC-AAAA
122298 AAAATTCAAAA
1 AAAATTCAAAA
* *
122309 AAAAGTGAAAA
1 AAAATTCAAAA
122320 AAAAT
1 AAAAT
122325 CGAGCAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 17 0.71
12 7 0.29
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.15
Consensus pattern (11 bp):
AAAATTCAAAA
Found at i:123381 original size:17 final size:17
Alignment explanation
Indices: 123355--123444 Score: 87
Period size: 17 Copynumber: 5.4 Consensus size: 17
123345 CATTGAGCGA
* *
123355 GAAAAGGAAAAGAGATT
1 GAAAAAGAAAAGAAATT
*
123372 GAAAAAGAAATTGAAA--
1 GAAAAAGAAA-AGAAATT
*
123388 GAAAACA-AAAAGAAAAT
1 GAAAA-AGAAAAGAAATT
123405 GAAAAAGAAAAGAAATT
1 GAAAAAGAAAAGAAATT
* *
123422 GCAAAAGAAAAGAAATC
1 GAAAAAGAAAAGAAATT
123439 GAAAAA
1 GAAAAA
123445 CTGAGAGAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.07
16 9 0.15
17 44 0.73
18 3 0.05
ACGTcount: A:0.69, C:0.03, G:0.19, T:0.09
Consensus pattern (17 bp):
GAAAAAGAAAAGAAATT
Found at i:123472 original size:14 final size:13
Alignment explanation
Indices: 123451--123488 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
123441 AAAACTGAGA
123451 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
123463 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
123478 GAAAAAGAAAA
1 GAAAAAGAAAA
123489 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:123485 original size:13 final size:12
Alignment explanation
Indices: 123371--123488 Score: 65
Period size: 12 Copynumber: 10.0 Consensus size: 12
123361 GAAAAGAGAT
*
123371 TGAAAAAGAAAT
1 TGAAAAAGAAAA
123383 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
123393 -CAAAAAGAAAA
1 TGAAAAAGAAAA
123404 TGAAAAAGAAAA
1 TGAAAAAGAAAA
**
123416 -GAAATTGCAAAA
1 TGAAAAAG-AAAA
123428 -G-AAAAG-AAA
1 TGAAAAAGAAAA
*
123437 TCGAAAAACTG-AGA
1 T-GAAAAA--GAAAA
123451 -GAAAAAGAAAA
1 TGAAAAAGAAAA
123462 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
123476 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
123489 AGCGAAAAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 27
0.70 0.08 0.23
Matches are distributed among these distances:
9 3 0.04
10 8 0.10
11 19 0.23
12 28 0.34
13 10 0.12
14 13 0.16
15 2 0.02
ACGTcount: A:0.69, C:0.03, G:0.18, T:0.09
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:123502 original size:21 final size:21
Alignment explanation
Indices: 123452--123502 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
123442 AAACTGAGAG
*
123452 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
123473 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
123494 AAAAAGAAA
1 AAAAAGAAA
123503 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:123542 original size:33 final size:33
Alignment explanation
Indices: 123505--123567 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
123495 AAAAGAAATT
123505 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
123538 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
123568 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:125353 original size:20 final size:20
Alignment explanation
Indices: 125330--125383 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
125320 AGTTTTTCCC
*
125330 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
125350 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
125370 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
125384 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:125365 original size:30 final size:30
Alignment explanation
Indices: 125330--125403 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
125320 AGTTTTTCCC
125330 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
125360 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
125390 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
125404 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:125393 original size:20 final size:20
Alignment explanation
Indices: 125330--125394 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
125320 AGTTTTTCCC
* * * *
125330 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
125350 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
125369 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
125390 AGCTC
1 AGCTC
125395 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.