Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2577
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: 31891
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Found at i:1186 original size:28 final size:27
Alignment explanation
Indices: 1146--1268 Score: 135
Period size: 28 Copynumber: 4.5 Consensus size: 27
1136 CTCGTAATCA
*
1146 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGC-ACATAGTCAAATT
* * *
1174 CGCACACTTAGTGCCGCATGGTCAATTT
1 CGCACACTTAGTG-CACATAGTCAAATT
* *
1202 CGCCACACTTAGTGCATCATATTCATATT
1 CG-CACACTTAGTGCA-CATAGTCAAATT
1231 CGCACAC-TAGTGCACATAGTC-AA-T
1 CGCACACTTAGTGCACATAGTCAAATT
1255 CGCACACTTAGTGC
1 CGCACACTTAGTGC
1269 TTGTAACAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
24 8 0.10
25 7 0.09
26 6 0.08
27 7 0.09
28 30 0.38
29 22 0.28
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCACATAGTCAAATT
Found at i:1236 original size:57 final size:52
Alignment explanation
Indices: 1146--1269 Score: 142
Period size: 57 Copynumber: 2.3 Consensus size: 52
1136 CTCGTAATCA
* *
1146 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATTT
1 CGCACACTTAGTGCTACATAGTCAAACTCGCACAC-TAGTG-CACATAGTCAA--T
* * *
1202 CGCCACACTTAGTGC-ATCATATTCATATTCGCACACTAGTGCACATAGTCAAT
1 CG-CACACTTAGTGCTA-CATAGTCAAACTCGCACACTAGTGCACATAGTCAAT
1255 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1270 TGTAACAATT
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
52 12 0.20
53 3 0.05
55 9 0.15
56 8 0.13
57 28 0.47
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.27
Consensus pattern (52 bp):
CGCACACTTAGTGCTACATAGTCAAACTCGCACACTAGTGCACATAGTCAAT
Found at i:9309 original size:27 final size:27
Alignment explanation
Indices: 9279--9455 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
9269 ATATTGAGTC
* * * *
9279 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
9306 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
9333 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
* * *
9361 CGCACACTTAGTGCTGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
9388 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
9415 CGCACA-TTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
9441 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9456 GTACAATTTA
Statistics
Matches: 129, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
26 21 0.16
27 84 0.65
28 24 0.19
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:9371 original size:55 final size:54
Alignment explanation
Indices: 9279--9455 Score: 214
Period size: 55 Copynumber: 3.3 Consensus size: 54
9269 ATATTGAGTC
* * * *
9279 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAGTCAAAT
* * * *
9333 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCTACATAGTCAAAT
* ** *
9388 CGCACACTTAGTGC-ATCATATTCATTTCGCACA-TTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCTACATAGTCAAAT
9441 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9456 GTACAATTTA
Statistics
Matches: 105, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
53 30 0.29
54 29 0.28
55 46 0.44
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAGTCAAAT
Found at i:12116 original size:48 final size:47
Alignment explanation
Indices: 12062--12167 Score: 126
Period size: 48 Copynumber: 2.2 Consensus size: 47
12052 TTGTCTTTTC
* *
12062 TTTCTTTTTCAATTT-TCTCTTTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTT--TCACATCCTTT-TTCAATCTCAA
* *
12110 TTTCTTTTTTCGATTTCTTTCTCTTTTCACATCCTTTTTCAATCTCAA
1 TTTC-TTTTTCAATTTCTCTCTCTTTTCACATCCTTTTTCAATCTCAA
12158 TTTCTTTTTC
1 TTTCTTTTTC
12168 CATGACACTC
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
47 6 0.12
48 24 0.47
49 14 0.27
50 7 0.14
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (47 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTCACATCCTTTTTCAATCTCAA
Found at i:12260 original size:21 final size:21
Alignment explanation
Indices: 12231--12366 Score: 51
Period size: 21 Copynumber: 6.7 Consensus size: 21
12221 CAAGCTCTCT
*
12231 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
12252 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
*
12273 TTCATTTTCTTTTTCTCTCACTT-
1 TTCATTTTCTTTTT-TC-C-TTTC
12296 TTCGA-TTTC-TTTTT-CTTT-
1 TTC-ATTTTCTTTTTTCCTTTC
* *
12314 TGCAATTTC-TTTTT-C-TTC
1 TTCATTTTCTTTTTTCCTTTC
12332 TTCATTTTCTTTTTGT--TTTC
1 TTCATTTTCTTTTT-TCCTTTC
*
12352 TTTCAATTTCTTTTT
1 -TTCATTTTCTTTTT
12367 CAATCTCTTT
Statistics
Matches: 89, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
17 3 0.03
18 21 0.24
19 5 0.06
20 7 0.08
21 37 0.42
22 6 0.07
23 7 0.08
24 3 0.03
ACGTcount: A:0.09, C:0.19, G:0.03, T:0.69
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:12279 original size:14 final size:14
Alignment explanation
Indices: 12230--12286 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
12220 TCAAGCTCTC
12230 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
12243 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
12257 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
12271 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
12285 TT
1 TT
12287 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:12323 original size:18 final size:17
Alignment explanation
Indices: 12293--12351 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 17
12283 TTTTCTCTCA
*
12293 CTTTTCGATTTCTTTTT
1 CTTTTCAATTTCTTTTT
12310 CTTTTGCAATTTCTTTTT
1 CTTTT-CAATTTCTTTTT
*
12328 CTTCTTCATTTTCTTTTT
1 CTT-TTCAATTTCTTTTT
*
12346 GTTTTC
1 CTTTTC
12352 TTTCAATTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 8 0.22
18 27 0.73
19 2 0.05
ACGTcount: A:0.07, C:0.19, G:0.05, T:0.69
Consensus pattern (17 bp):
CTTTTCAATTTCTTTTT
Found at i:12367 original size:6 final size:6
Alignment explanation
Indices: 12248--12354 Score: 56
Period size: 6 Copynumber: 17.7 Consensus size: 6
12238 TCTTTTTTCG
* * * **
12248 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA C-TTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
12298 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CATTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
12346 -GTTTT CTTT
1 CTTTTT CTTT
12355 CAATTTCTTT
Statistics
Matches: 71, Mismatches: 26, Indels: 8
0.68 0.25 0.08
Matches are distributed among these distances:
5 6 0.08
6 53 0.75
7 9 0.13
8 3 0.04
ACGTcount: A:0.07, C:0.20, G:0.03, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:13498 original size:31 final size:31
Alignment explanation
Indices: 13391--13505 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
13381 TTAAACTTGA
13391 TTTTTTTTGCTCACCTTTTTTTTTCTTTTC-T
1 TTTTTTTTGCTCACC-TTTTTTTTCTTTTCTT
** *
13422 TTTTTTTTGCTCGATTTTTTTTCACTTTTTTTTAAACTT
1 TTTTTTTTGCTC-A-CCTTTTT---TTTCTTTT---CTT
13461 GATTTTTTTTGCTCACCTTTTTTTTCTTTTCTT
1 --TTTTTTTTGCTCACCTTTTTTTTCTTTTCTT
13494 TTTTTTTTGCTC
1 TTTTTTTTGCTC
13506 GATTTTTTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
31 24 0.36
32 6 0.09
33 3 0.04
35 7 0.10
36 7 0.10
38 1 0.01
39 6 0.09
40 1 0.01
41 12 0.18
ACGTcount: A:0.07, C:0.17, G:0.05, T:0.71
Consensus pattern (31 bp):
TTTTTTTTGCTCACCTTTTTTTTCTTTTCTT
Found at i:13540 original size:72 final size:72
Alignment explanation
Indices: 13368--13526 Score: 302
Period size: 72 Copynumber: 2.2 Consensus size: 72
13358 CTCGCAAGAC
13368 TTTTCACTTTTTTTTAAACTTGATTTTTTTTGCTCACCTTTTTTTTTCTTTTCTTTTTTTTTGCT
1 TTTTCACTTTTTTTTAAACTTGATTTTTTTTGCTCACCTTTTTTTTTCTTTTCTTTTTTTTTGCT
13433 CGATTTT
66 CGATTTT
13440 TTTTCACTTTTTTTTAAACTTGATTTTTTTTGCTCACC-TTTTTTTTCTTTTCTTTTTTTTTTGC
1 TTTTCACTTTTTTTTAAACTTGATTTTTTTTGCTCACCTTTTTTTTTCTTTTC-TTTTTTTTTGC
13504 TCGATTTT
65 TCGATTTT
13512 TTTTCACTTTTTTTT
1 TTTTCACTTTTTTTT
13527 TGAATTTTTT
Statistics
Matches: 86, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
71 14 0.16
72 72 0.84
ACGTcount: A:0.09, C:0.15, G:0.05, T:0.70
Consensus pattern (72 bp):
TTTTCACTTTTTTTTAAACTTGATTTTTTTTGCTCACCTTTTTTTTTCTTTTCTTTTTTTTTGCT
CGATTTT
Found at i:13553 original size:71 final size:70
Alignment explanation
Indices: 13368--13556 Score: 258
Period size: 72 Copynumber: 2.6 Consensus size: 70
13358 CTCGCAAGAC
*
13368 TTTTCACTTTTTTTTAAACTTGATTTTTTTTGCTCACCTTTTTTTTTCTTTTCTTTTTTTTTGCT
1 TTTTCACTTTTTTTTAAACTT-ATTTTTTTTGCTCA-ATTTTTTTTTCTTTTCTTTTTTTTTGCT
13433 CGATTTT
64 CGATTTT
**
13440 TTTTCACTTTTTTTTAAACTTGATTTTTTTTGCTCACCTTTTTTTTCTTTTCTTTTTTTTTTGCT
1 TTTTCACTTTTTTTTAAACTT-ATTTTTTTTGCTCAATTTTTTTTTCTTTTC-TTTTTTTTTGCT
13505 CGATTTT
64 CGATTTT
*
13512 TTTTCACTTTTTTTTTGAA-TT-TTTTTTTT-CAATCAATTTTTTTTT
1 TTTTCAC-TTTTTTTTAAACTTATTTTTTTTGC--TCAATTTTTTTTT
13557 GATTTTTTTT
Statistics
Matches: 109, Mismatches: 4, Indels: 9
0.89 0.03 0.07
Matches are distributed among these distances:
69 1 0.01
70 8 0.07
71 26 0.24
72 64 0.59
73 10 0.09
ACGTcount: A:0.11, C:0.14, G:0.05, T:0.70
Consensus pattern (70 bp):
TTTTCACTTTTTTTTAAACTTATTTTTTTTGCTCAATTTTTTTTTCTTTTCTTTTTTTTTGCTCG
ATTTT
Found at i:15393 original size:4 final size:4
Alignment explanation
Indices: 15384--15411 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
15374 TATTTTTATT
15384 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
15412 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:16372 original size:30 final size:31
Alignment explanation
Indices: 16338--16434 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
16328 AGCTCACTCC
*
16338 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
16368 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
16398 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
16428 TAGCTCA
1 TAGCTCA
16435 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:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:18386 original size:132 final size:132
Alignment explanation
Indices: 18149--18413 Score: 512
Period size: 132 Copynumber: 2.0 Consensus size: 132
18139 GTTGAAATGA
*
18149 TAATTTATACGACAGAAGTAGAAGATATCAATTCTTTTTACACATTGGAATCTTTAAAAGAGGTC
1 TAATTTATACGACAGAAGTAGAAGATATCAATTCCTTTTACACATTGGAATCTTTAAAAGAGGTC
*
18214 TATGGGATCATATGGATGTTGGTCCCTATTTTGACTCTTGTATTGGGAATCATAATAGGTGTACT
66 TATGGGATCATATGGATGTTGGTCCCTATTTTGACTCTTGTATTGGGAATCACAATAGGTGTACT
18279 AG
131 AG
18281 TAATTTATACGACAGAAGTAGAAGATATCAATTCCTTTTACACATTGGAATCTTTAAAAGAGGTC
1 TAATTTATACGACAGAAGTAGAAGATATCAATTCCTTTTACACATTGGAATCTTTAAAAGAGGTC
18346 TATGGGATCATATGGATGTTGGTCCCTATTTTGACTCTTGTATTGGGAATCACAATAGGTGTACT
66 TATGGGATCATATGGATGTTGGTCCCTATTTTGACTCTTGTATTGGGAATCACAATAGGTGTACT
18411 AG
131 AG
18413 T
1 T
18414 TGTATGGTTA
Statistics
Matches: 131, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 131 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (132 bp):
TAATTTATACGACAGAAGTAGAAGATATCAATTCCTTTTACACATTGGAATCTTTAAAAGAGGTC
TATGGGATCATATGGATGTTGGTCCCTATTTTGACTCTTGTATTGGGAATCACAATAGGTGTACT
AG
Found at i:19288 original size:30 final size:30
Alignment explanation
Indices: 19254--19350 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
19244 AGCTCACTCC
19254 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
19284 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
19314 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
19344 TAGCTCA
1 TAGCTCA
19351 TTTTAGTTTA
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:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:23375 original size:27 final size:27
Alignment explanation
Indices: 23338--23542 Score: 216
Period size: 27 Copynumber: 7.6 Consensus size: 27
23328 TAAATTGTAC
*
23338 AGCACTAAGTGTGCGATTTGGCTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
23365 AGCACTAAGTGTGCGATTTGACCATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** **
23392 TGCACTAAGTGTGCGAAATGAAAATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
23418 ATGCACTAAGTGTGCGAATTGACCATG-
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
23445 CGACACTAAGTGTGCGAGTTGACTATGT
1 AG-CACTAAGTGTGCGATTTGACTATGT
*
23473 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * * *
23501 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
23528 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
23543 GACTTAATAT
Statistics
Matches: 152, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.01
27 126 0.83
28 25 0.16
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:23399 original size:54 final size:54
Alignment explanation
Indices: 23339--23542 Score: 241
Period size: 54 Copynumber: 3.8 Consensus size: 54
23329 AAATTGTACA
* * *
23339 GCACTAAGTGTGCGATTTGGCTATGTAGCACTAAGTGTGCGATTTGACCATGTT
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTC
** ** *
23393 GCACTAAGTGTGCGAAATGAAAATG-ATGCACTAAGTGTGCGAATTGACCATG-C
1 GCACTAAGTGTGCGAGTTGACTATGTA-GCACTAAGTGTGCGATTTGACCATGTC
** *
23446 GACACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTG
1 G-CACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGA-TTTGACCATGTC
* * *
23502 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
23543 GACTTAATAT
Statistics
Matches: 127, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
53 2 0.02
54 79 0.62
55 45 0.35
56 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTC
Found at i:31503 original size:27 final size:27
Alignment explanation
Indices: 31469--31670 Score: 198
Period size: 27 Copynumber: 7.6 Consensus size: 27
31459 GTAAATGTAC
*
31469 AGCACTAAGTGTGCGATTTGGCTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
31496 AGCACTAAGTGTGCGATTTGACCATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
31523 TGCACTAAGTGTGCGAAATGA-AATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
31548 ATGCACTAAGTGTGCGAATTGACCATG-
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
31575 CGACACTAAGTGTGCGA--GGACTATGT
1 AG-CACTAAGTGTGCGATTTGACTATGT
*
31601 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * * *
31629 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
31656 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31671 GACTTAATAT
Statistics
Matches: 148, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
25 20 0.14
26 24 0.16
27 82 0.55
28 22 0.15
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:31645 original size:53 final size:52
Alignment explanation
Indices: 31470--31670 Score: 201
Period size: 53 Copynumber: 3.8 Consensus size: 52
31460 TAAATGTACA
*
31470 GCACTAAGTGTGCGATTTGG-CTATGTAGCACTAAGTGTGCGATTTGACCATGTT
1 GCACTAAGTGTGCGA---GGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
* * * *
31524 GCACTAAGTGTGCGAAATGA-AATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCG--AGGACTATGTA-GCACTAAGTGTGCGATTTGACCATGTG
* **
31577 ACACTAAGTGTGCGAGGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTG
1 GCACTAAGTGTGCGAGGACTATGTAGCACTAAGTGTGCGA-TTTGACCATGTG
* * *
31630 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAG--GACTATGTAGCACTAAGTGTGCG
31671 GACTTAATAT
Statistics
Matches: 122, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
51 3 0.02
52 19 0.16
53 65 0.53
54 14 0.11
55 20 0.16
56 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (52 bp):
GCACTAAGTGTGCGAGGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
Found at i:31667 original size:80 final size:78
Alignment explanation
Indices: 31470--31670 Score: 199
Period size: 80 Copynumber: 2.5 Consensus size: 78
31460 TAAATGTACA
* * * *
31470 GCACTAAGTGTGCGATTTGGCTATGTAGCACTAAGTGTGCGATTTGACCATGTTGCACTAAGTGT
1 GCACTAAGTGTGCGAATTGACTAT-TAGCACTAAGTGTGCGA-TGGACCATGTAGCACTAAGTGT
31535 GCGAAATGAAATGAT
64 GCGAAATGAAATGAT
* ** *
31550 GCACTAAGTGTGCGAATTGACCATGCGACACTAAGTGTGCGA-GGACTATGTAGCACTAAGTGTG
1 GCACTAAGTGTGCGAATTGACTATTAG-CACTAAGTGTGCGATGGACCATGTAGCACTAAGTGTG
** *
31614 CGAGTTTGATTATG-T
65 CGA-AATGA-AATGAT
* * *
31629 GGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 -GCACTAAGTGTGCGAATTGACTAT-TAGCACTAAGTGTGCG
31671 GACTTAATAT
Statistics
Matches: 99, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
78 22 0.22
79 5 0.05
80 71 0.72
81 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (78 bp):
GCACTAAGTGTGCGAATTGACTATTAGCACTAAGTGTGCGATGGACCATGTAGCACTAAGTGTGC
GAAATGAAATGAT
Done.