Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2254
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: 42973
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:4782 original size:29 final size:31
Alignment explanation
Indices: 4748--4808 Score: 108
Period size: 29 Copynumber: 2.0 Consensus size: 31
4738 ATAGTGTGAT
4748 CGTGTGTCACACAC-GCCTAGACA-CACGCC
1 CGTGTGTCACACACGGCCTAGACACCACGCC
4777 CGTGTGTCACACACGGCCTAGACACCACGCC
1 CGTGTGTCACACACGGCCTAGACACCACGCC
4808 C
1 C
4809 ATGTCTGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 14 0.47
30 9 0.30
31 7 0.23
ACGTcount: A:0.23, C:0.43, G:0.21, T:0.13
Consensus pattern (31 bp):
CGTGTGTCACACACGGCCTAGACACCACGCC
Found at i:6429 original size:84 final size:83
Alignment explanation
Indices: 6238--6430 Score: 205
Period size: 84 Copynumber: 2.3 Consensus size: 83
6228 ATAACCTGAT
* * *
6238 TTCATCACTGGCAATAAGCCTGCTAGACCTTTAAGTCTGATATCATTCACTGGCATTACGCCTGC
1 TTCATCACCGGCAA-AAGCCTGCTAGACCTTTAAGTCTGATATCATTCACCGGCATTACACCTGC
** **
6303 TAGGCTCGGAGCTTGATAA
65 TAGGCTCAAAGCCCGATAA
* * *
6322 -T-ATTCACCAGCTTAAAGCTTGCTAGACCTTTAAGTC-GATATCATTTTCACCGGCATTACACC
1 TTCA-TCACCGGC-AAAAGCCTGCTAGACCTTTAAGTCTGATATCA--TTCACCGGCATTACACC
6384 TGCTAGGCTCAAAGCCCGA-AA
62 TGCTAGGCTCAAAGCCCGATAA
*
6405 TTCATCACCGGCACAAGGCCTGCTAG
1 TTCATCACCGGCA-AAAGCCTGCTAG
6431 GTTTGAAACC
Statistics
Matches: 88, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
82 8 0.09
83 30 0.34
84 49 0.56
85 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (83 bp):
TTCATCACCGGCAAAAGCCTGCTAGACCTTTAAGTCTGATATCATTCACCGGCATTACACCTGCT
AGGCTCAAAGCCCGATAA
Found at i:8268 original size:14 final size:15
Alignment explanation
Indices: 8239--8268 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
8229 TAAAATTAAG
8239 ACATGATACTTTCAC
1 ACATGATACTTTCAC
8254 ACATGATAC-TTCAC
1 ACATGATACTTTCAC
8268 A
1 A
8269 TATAATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (15 bp):
ACATGATACTTTCAC
Found at i:9983 original size:67 final size:69
Alignment explanation
Indices: 9831--10017 Score: 256
Period size: 67 Copynumber: 2.7 Consensus size: 69
9821 AGAATCTATA
* *
9831 GGCTACAATACAGTGGTAGCTTCGACTACATCTCAGTGGTAGCTTCAGCTACAATACAGTGGTAG
1 GGCTACAATACAGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTTCAGCTACAATACAATGGTAG
9896 CTTC
66 CTTC
*
9900 GGCTAC-ATCTCAGTGGTAGCTTCGGCTACATCTCA-TGGTAGCTTC-GCTACAATACAATGGTA
1 GGCTACAAT-ACAGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTTCAGCTACAATACAATGGTA
* *
9962 GGTTT
65 GCTTC
* * *
9967 GGCTGCAATACAGTGGTAGCTTCGGCTACGT-TACAGTGATAGCTTCAGCTA
1 GGCTACAATACAGTGGTAGCTTCGGCTACATCT-CAGTGGTAGCTTCAGCTA
10018 TATTACAGTG
Statistics
Matches: 104, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
66 1 0.01
67 46 0.44
68 23 0.22
69 34 0.33
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (69 bp):
GGCTACAATACAGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTTCAGCTACAATACAATGGTAG
CTTC
Found at i:9993 original size:23 final size:23
Alignment explanation
Indices: 9831--10027 Score: 197
Period size: 23 Copynumber: 8.7 Consensus size: 23
9821 AGAATCTATA
9831 GGCTACAATACAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
* *
9854 GACTAC-ATCTCAGTGGTAGCTTC
1 GGCTACAAT-ACAGTGGTAGCTTC
*
9877 AGCTACAATACAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
*
9900 GGCTAC-ATCTCAGTGGTAGCTTC
1 GGCTACAAT-ACAGTGGTAGCTTC
*
9923 GGCTAC-ATCTCA-TGGTAGCTTC
1 GGCTACAAT-ACAGTGGTAGCTTC
* * *
9945 -GCTACAATACAATGGTAGGTTT
1 GGCTACAATACAGTGGTAGCTTC
*
9967 GGCTGCAATACAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
** *
9990 GGCTACGTTACAGTGATAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
* * *
10013 AGCTATATTACAGTG
1 GGCTACAATACAGTG
10028 TAGTACTTTG
Statistics
Matches: 147, Mismatches: 21, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
21 7 0.05
22 24 0.16
23 114 0.78
24 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (23 bp):
GGCTACAATACAGTGGTAGCTTC
Found at i:11680 original size:29 final size:28
Alignment explanation
Indices: 11648--11735 Score: 88
Period size: 29 Copynumber: 3.1 Consensus size: 28
11638 TAAAAAATAA
*
11648 AAATTGCATTTTGACCCCTAAATTTTCCT
1 AAATTTCATTTTGA-CCCTAAATTTTCCT
* * * *
11677 AAATTTCACTTAGACCCTAAACTTTCATT
1 AAATTTCATTTTGACCCTAAATTTTC-CT
* *
11706 AAATTTCATTTTAATCCTAAATTTT-CT
1 AAATTTCATTTTGACCCTAAATTTTCCT
11733 AAA
1 AAA
11736 AATTACATTT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
27 4 0.09
28 11 0.23
29 32 0.68
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.42
Consensus pattern (28 bp):
AAATTTCATTTTGACCCTAAATTTTCCT
Found at i:12268 original size:12 final size:12
Alignment explanation
Indices: 12251--12318 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 12
12241 TAACCCGAAG
12251 AAGAAAGGAAAA
1 AAGAAAGGAAAA
12263 AAGAAA-G-AAA
1 AAGAAAGGAAAA
12273 AAGAAA-GAAAA
1 AAGAAAGGAAAA
* *
12284 AAGGAGAGAAAAAA
1 AA-GAAAG-GAAAA
12298 ATAGAAAAGGAAGAA
1 A-AG-AAAGGAA-AA
12313 AAGAAA
1 AAGAAA
12319 ATAAAAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
10 10 0.22
11 6 0.13
12 9 0.20
13 3 0.07
14 10 0.22
15 7 0.16
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (12 bp):
AAGAAAGGAAAA
Found at i:12275 original size:10 final size:10
Alignment explanation
Indices: 12260--12318 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 10
12250 GAAGAAAGGA
12260 AAAAAGAAAG
1 AAAAAGAAAG
12270 AAAAAGAAAG
1 AAAAAGAAAG
*
12280 AAAAAAGGAGAG
1 -AAAAA-GAAAG
12292 AAAAA-AATAG
1 AAAAAGAA-AG
*
12302 -AAAAGGAAG
1 AAAAAGAAAG
12311 -AAAAGAAA
1 AAAAAGAAA
12319 ATAAAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
9 14 0.34
10 13 0.32
11 10 0.24
12 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:12277 original size:22 final size:22
Alignment explanation
Indices: 12251--12319 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
12241 TAACCCGAAG
* *
12251 AAGAAAGGAAAAAAGAAAGAAA
1 AAGAAAGAAAAAAGGAAAGAAA
*
12273 AAGAAAGAAAAAAGGAGAGAAA
1 AAGAAAGAAAAAAGGAAAGAAA
*
12295 AA-AATAGAAAAGGAAGAAAAGAAA
1 AAGAA-AGAAAA--AAGGAAAGAAA
12319 A
1 A
12320 TAAAAAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
21 2 0.05
22 27 0.69
24 10 0.26
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.01
Consensus pattern (22 bp):
AAGAAAGAAAAAAGGAAAGAAA
Found at i:12325 original size:20 final size:20
Alignment explanation
Indices: 12260--12325 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
12250 GAAGAAAGGA
*
12260 AAAAAGAAAGAAAAAGAAAGA-
1 AAAAAGGAAG-AAAAGAAA-AT
12281 AAAAAGG-AGAGAAA-AAAAT
1 AAAAAGGAAGA-AAAGAAAAT
12300 AGAAAAGGAAGAAAAGAAAAT
1 A-AAAAGGAAGAAAAGAAAAT
12321 AAAAA
1 AAAAA
12326 AATAAAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
18 1 0.03
19 5 0.13
20 18 0.46
21 15 0.38
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (20 bp):
AAAAAGGAAGAAAAGAAAAT
Found at i:12332 original size:13 final size:13
Alignment explanation
Indices: 12311--12344 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12301 GAAAAGGAAG
*
12311 AAAAGAAAATAAA
1 AAAATAAAATAAA
12324 AAAATAAAATAAA
1 AAAATAAAATAAA
*
12337 AAGATAAA
1 AAAATAAA
12345 CAAAAATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (13 bp):
AAAATAAAATAAA
Found at i:12490 original size:24 final size:24
Alignment explanation
Indices: 12452--12506 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
12442 AGCAAAAAAA
12452 AAGCAGCAAAAAAGAAGAAGAAAG
1 AAGCAGCAAAAAAGAAGAAGAAAG
12476 AAGCAG-AAAACAAGAAGAAGAAAG
1 AAGCAGCAAAA-AAGAAGAAGAAAG
12500 AAGCAGC
1 AAGCAGC
12507 CCACTTTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.64, C:0.11, G:0.25, T:0.00
Consensus pattern (24 bp):
AAGCAGCAAAAAAGAAGAAGAAAG
Found at i:13218 original size:17 final size:18
Alignment explanation
Indices: 13198--13263 Score: 55
Period size: 18 Copynumber: 3.8 Consensus size: 18
13188 TAAAAAAATC
13198 CGTG-TTTCAAAAATTCT
1 CGTGATTTCAAAAATTCT
* **
13215 CGTGAATAAAAAAATT-T
1 CGTGATTTCAAAAATTCT
* *
13232 CGTGTTTTCAAAAATTCC
1 CGTGATTTCAAAAATTCT
* *
13250 CGTGTTTTTAAAAA
1 CGTGATTTCAAAAA
13264 AACATTTCGT
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
17 17 0.45
18 21 0.55
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (18 bp):
CGTGATTTCAAAAATTCT
Found at i:13244 original size:18 final size:18
Alignment explanation
Indices: 13223--13449 Score: 85
Period size: 17 Copynumber: 12.2 Consensus size: 18
13213 CTCGTGAATA
13223 AAAAAATTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
* *
13241 -AAAAATTCCCGTGTTTTTAA
1 AAAAAATT-TCGTG-TTTT-C
*
13261 AAAAACATTTCGTGTTTTTTTTTT
1 AAAAA-ATTTCGTG-----TTTTC
* *
13285 AAAAAAATTCATGTTTT-
1 AAAAAATTTCGTGTTTTC
* *
13302 AAAAAAATTCATGTTTTC
1 AAAAAATTTCGTGTTTTC
* *
13320 -GAAATTTTCGTGTTTTTC
1 AAAAAATTTCGTG-TTTTC
* *
13338 -AAAAATTT-TTG-TGTC
1 AAAAAATTTCGTGTTTTC
* *
13353 AAAAAATTCTCATG-TATC
1 AAAAAATT-TCGTGTTTTC
* *
13371 -GAAAATTTCCTTGTTTTC
1 AAAAAATTT-CGTGTTTTC
*
13389 AAAAAAAATTCCGTGTTTTC
1 --AAAAAATTTCGTGTTTTC
*
13409 AAAAAAAAATTCGTGTTTTC
1 --AAAAAATTTCGTGTTTTC
13429 -AAAAATCTTCGTGTTTTC
1 AAAAAAT-TTCGTGTTTTC
13447 AAA
1 AAA
13450 CATTATTATT
Statistics
Matches: 163, Mismatches: 25, Indels: 41
0.71 0.11 0.18
Matches are distributed among these distances:
15 3 0.02
16 8 0.05
17 49 0.30
18 38 0.23
19 6 0.04
20 26 0.16
21 14 0.09
22 3 0.02
23 6 0.04
24 5 0.03
25 5 0.03
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (18 bp):
AAAAAATTTCGTGTTTTC
Found at i:13263 original size:35 final size:34
Alignment explanation
Indices: 13188--13253 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
13178 GTTTCTTCTT
* *
13188 TAAAAAAA-TCCGTGTTTCAAAAATTCTCGTGAA
1 TAAAAAAATTTCGTGTTTCAAAAATTCCCGTGAA
13221 TAAAAAAATTTCGTGTTTTCAAAAATTCCCGTG
1 TAAAAAAATTTCGTG-TTTCAAAAATTCCCGTG
13254 TTTTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 8 0.28
34 5 0.17
35 16 0.55
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (34 bp):
TAAAAAAATTTCGTGTTTCAAAAATTCCCGTGAA
Found at i:13299 original size:23 final size:25
Alignment explanation
Indices: 13254--13301 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
13244 AATTCCCGTG
*
13254 TTTTTAAAAAAACATTTCGTGTTTT
1 TTTTTAAAAAAACATTTCATGTTTT
*
13279 TTTTTTAAAAAA-A-TTCATGTTTT
1 TTTTTAAAAAAACATTTCATGTTTT
13302 AAAAAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 1 0.05
25 11 0.52
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.54
Consensus pattern (25 bp):
TTTTTAAAAAAACATTTCATGTTTT
Found at i:13400 original size:20 final size:20
Alignment explanation
Indices: 13372--13433 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
13362 TCATGTATCG
* *
13372 AAAATTTCCTTGTTTTCAAA
1 AAAAATTCCGTGTTTTCAAA
13392 AAAAATTCCGTGTTTTCAAAA
1 AAAAATTCCGTGTTTTC-AAA
13413 AAAAATT-CGTGTTTTCAAA
1 AAAAATTCCGTGTTTTCAAA
13432 AA
1 AA
13434 TCTTCGTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
19 5 0.13
20 24 0.62
21 10 0.26
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (20 bp):
AAAAATTCCGTGTTTTCAAA
Found at i:13434 original size:16 final size:17
Alignment explanation
Indices: 13412--13449 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
13402 TGTTTTCAAA
*
13412 AAAAAATTCGTGTTTTC
1 AAAAACTTCGTGTTTTC
13429 AAAAATCTTCGTGTTTTC
1 AAAAA-CTTCGTGTTTTC
13447 AAA
1 AAA
13450 CATTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (17 bp):
AAAAACTTCGTGTTTTC
Found at i:25351 original size:19 final size:21
Alignment explanation
Indices: 25327--25386 Score: 74
Period size: 19 Copynumber: 3.0 Consensus size: 21
25317 AACACGAAGA
25327 TTTTTG-AAACAC-GAATTTT
1 TTTTTGAAAACACGGAATTTT
25346 TTTTTGAAAACACGGAA--TT
1 TTTTTGAAAACACGGAATTTT
* *
25365 TTTTTGAAAACAAGGAAATTT
1 TTTTTGAAAACACGGAATTTT
25386 T
1 T
25387 CGATACATGA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 24 0.67
20 6 0.17
21 6 0.17
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (21 bp):
TTTTTGAAAACACGGAATTTT
Found at i:25356 original size:20 final size:20
Alignment explanation
Indices: 25327--25369 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
25317 AACACGAAGA
25327 TTTTTGAAACAC-GAATTTT
1 TTTTTGAAACACGGAATTTT
25346 TTTTTGAAAACACGGAATTTT
1 TTTTTG-AAACACGGAATTTT
25367 TTT
1 TTT
25370 GAAAACAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 6 0.27
21 10 0.45
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (20 bp):
TTTTTGAAACACGGAATTTT
Found at i:25529 original size:17 final size:17
Alignment explanation
Indices: 25311--25532 Score: 83
Period size: 17 Copynumber: 12.2 Consensus size: 17
25301 AATAATAATG
25311 TTTGAAAACACGAAGATT
1 TTTGAAAACACGAA-ATT
*
25329 TTTG-AAACACGAATTTTTT
1 TTTGAAAACACGAA---ATT
*
25348 TTTGAAAACACGGAATTTT
1 TTTGAAAACAC-GAA-ATT
*
25367 TTTGAAAACAAGGAAATT
1 TTTGAAAAC-ACGAAATT
* * *
25385 TTCG-ATACATGAGAATTT
1 TTTGAAAACACGA-AA-TT
* *
25403 TTTG-ACACA-AAAATT
1 TTTGAAAACACGAAATT
*
25418 TTTGAAAACACGAAAAT
1 TTTGAAAACACGAAATT
* * *
25435 TTCGAAAACATGAATTT
1 TTTGAAAACACGAAATT
* * *
25452 TTTTAAAACATGAATTTT
1 TTTGAAAACACGAA-ATT
*
25470 TTTAAAAAAAAACACGAAAATGTTT
1 TTT----GAAAACACG-AAA---TT
* *
25495 TTTTAAAACACGGGAATT
1 TTTGAAAACAC-GAAATT
25513 TTTGAAAACACGAAATT
1 TTTGAAAACACGAAATT
25530 TTT
1 TTT
25533 TTATTCACGA
Statistics
Matches: 159, Mismatches: 26, Indels: 39
0.71 0.12 0.17
Matches are distributed among these distances:
15 6 0.04
16 9 0.06
17 52 0.33
18 36 0.23
19 22 0.14
20 7 0.04
21 12 0.08
22 8 0.05
23 2 0.01
25 5 0.03
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (17 bp):
TTTGAAAACACGAAATT
Found at i:25533 original size:18 final size:18
Alignment explanation
Indices: 25311--25533 Score: 97
Period size: 18 Copynumber: 12.2 Consensus size: 18
25301 AATAATAATG
25311 TTTGAAAACACGAAGA-TT
1 TTTGAAAACACGAA-ATTT
*
25329 TTTG-AAACACGAATTTTTT
1 TTTGAAAACACGAA--ATTT
*
25348 TTTGAAAACACGGAATTTT
1 TTTGAAAACAC-GAAATTT
*
25367 TTTGAAAACAAGGAAA-TT
1 TTTGAAAAC-ACGAAATTT
* * *
25385 TTCG-ATACATGAGAATTT
1 TTTGAAAACACGA-AATTT
* *
25403 TTTG---ACACAAAAATT
1 TTTGAAAACACGAAATTT
*
25418 TTTGAAAACACGAAA-AT
1 TTTGAAAACACGAAATTT
* *
25435 TTCGAAAACATG-AATTT
1 TTTGAAAACACGAAATTT
* * *
25452 TTTTAAAACATGAATTTT
1 TTTGAAAACACGAAATTT
*
25470 TTTAAAAAAAAACACGAAAATGTTT
1 TTT----GAAAACACG-AAA--TTT
* *
25495 TTTTAAAACACGGGAA-TT
1 TTTGAAAACAC-GAAATTT
25513 TTTGAAAACACGAAATTT
1 TTTGAAAACACGAAATTT
25531 TTT
1 TTT
25534 TATTCACGAG
Statistics
Matches: 158, Mismatches: 26, Indels: 42
0.70 0.12 0.19
Matches are distributed among these distances:
15 8 0.05
16 9 0.06
17 39 0.25
18 45 0.28
19 22 0.14
20 7 0.04
21 12 0.08
22 8 0.05
23 2 0.01
25 6 0.04
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (18 bp):
TTTGAAAACACGAAATTT
Found at i:25547 original size:35 final size:34
Alignment explanation
Indices: 25503--25569 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
25493 TTTTTTAAAA
*
25503 CACGGGAATTTTTGAAAACACGAAATTTTTTTATT
1 CACGAGAATTTTTG-AAACACGAAATTTTTTTATT
* *
25538 CACGAGAATTTTTGAAACACGGATTTTTTTTA
1 CACGAGAATTTTTGAAACACGAAATTTTTTTA
25570 AAGAAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (34 bp):
CACGAGAATTTTTGAAACACGAAATTTTTTTATT
Found at i:25558 original size:17 final size:17
Alignment explanation
Indices: 25494--25558 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
25484 CGAAAATGTT
* *
25494 TTTTTAAAACACGGGAA
1 TTTTTGAAACACGAGAA
25511 TTTTTGAAAACACGA-AA
1 TTTTTG-AAACACGAGAA
* **
25528 TTTTTTTATTCACGAGAA
1 -TTTTTGAAACACGAGAA
25546 TTTTTGAAACACG
1 TTTTTGAAACACG
25559 GATTTTTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
17 23 0.62
18 14 0.38
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (17 bp):
TTTTTGAAACACGAGAA
Found at i:25645 original size:17 final size:19
Alignment explanation
Indices: 25623--25668 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
25613 ATTATTATTA
25623 TTTGAAACACGTG-AAA-T
1 TTTGAAACACGTGAAAATT
25640 TTTGAAGACA--TGAAAATT
1 TTTGAA-ACACGTGAAAATT
25658 TTTGAAACACG
1 TTTGAAACACG
25669 ATTTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
16 2 0.08
17 12 0.50
18 10 0.42
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.30
Consensus pattern (19 bp):
TTTGAAACACGTGAAAATT
Found at i:26117 original size:15 final size:16
Alignment explanation
Indices: 26097--26133 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
26087 CCCCTTTTCC
26097 TTTTTT-CTT-TTTCTT
1 TTTTTTCCTTATTT-TT
26112 TTTTTTCCTTATTTTT
1 TTTTTTCCTTATTTTT
26128 TTTTTT
1 TTTTTT
26134 GCTGGGCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 11 0.55
17 3 0.15
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTTCCTTATTTTT
Found at i:26284 original size:24 final size:24
Alignment explanation
Indices: 26255--26309 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
26245 CACAAAGTGG
26255 GCTGCTTCTTTCTTCTTCTTGTTTT
1 GCTGCTTCTTTCTTCTTCTT-TTTT
26280 -CTGCTTCTTTCTTCTTCTTTTTT
1 GCTGCTTCTTTCTTCTTCTTTTTT
26303 GCTGCTT
1 GCTGCTT
26310 TTTTTTTGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.00, C:0.25, G:0.11, T:0.64
Consensus pattern (24 bp):
GCTGCTTCTTTCTTCTTCTTTTTT
Found at i:26293 original size:21 final size:21
Alignment explanation
Indices: 26267--26310 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
26257 TGCTTCTTTC
* *
26267 TTCTTCTTGTTTTCTGCTTCT
1 TTCTTCTTCTTTTCTGCTGCT
*
26288 TTCTTCTTCTTTTTTGCTGCT
1 TTCTTCTTCTTTTCTGCTGCT
26309 TT
1 TT
26311 TTTTTTGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.23, G:0.09, T:0.68
Consensus pattern (21 bp):
TTCTTCTTCTTTTCTGCTGCT
Found at i:26493 original size:12 final size:12
Alignment explanation
Indices: 26466--26514 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
26456 TCCTTTTCTA
*
26466 TTTTTTTCTCTCC
1 TTTTTTTCT-TTC
26479 TTTTTTTCTTTC
1 TTTTTTTCTTTC
26491 --TTTTTCTTTC
1 TTTTTTTCTTTC
*
26501 TTTTTTCCTTTC
1 TTTTTTTCTTTC
26513 TT
1 TT
26515 CTTCGGGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 10 0.31
12 13 0.41
13 9 0.28
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTTCTTTC
Found at i:26494 original size:10 final size:10
Alignment explanation
Indices: 26445--26505 Score: 54
Period size: 10 Copynumber: 5.9 Consensus size: 10
26435 ATTTTTTTAT
26445 TTTC-TTTTC
1 TTTCTTTTTC
*
26454 TTTCCTTTTC
1 TTTCTTTTTC
26464 TATT-TTTTTC
1 T-TTCTTTTTC
*
26474 TCTCCTTTTTTTC
1 T-T--TCTTTTTC
26487 TTTCTTTTTC
1 TTTCTTTTTC
26497 TTTCTTTTT
1 TTTCTTTTT
26506 TCCTTTCTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
9 4 0.09
10 29 0.66
11 2 0.05
12 2 0.05
13 7 0.16
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:26506 original size:22 final size:22
Alignment explanation
Indices: 26444--26514 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 22
26434 TATTTTTTTA
26444 TTTTCTTTTCTTTCCTTTTCTATT-T
1 TTTTC-TTTCTTT--TTTTCT-TTCT
*
26469 TTTTCTCTCCTTTTTTTCTTTCT
1 TTTTCT-TTCTTTTTTTCTTTCT
*
26492 TTTTCTTTCTTTTTTCCTTTCT
1 TTTTCTTTCTTTTTTTCTTTCT
26514 T
1 T
26515 CTTCGGGTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 17 0.41
23 13 0.32
24 1 0.02
25 10 0.24
ACGTcount: A:0.01, C:0.23, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTCTTTCTTTTTTTCTTTCT
Found at i:27150 original size:14 final size:16
Alignment explanation
Indices: 27125--27160 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
27115 GTCAAAATGC
27125 AATTTTTATTTTTT-A
1 AATTTTTATTTTTTGA
27140 AATTTTT-TTTTTTGA
1 AATTTTTATTTTTTGA
27155 AATTTT
1 AATTTT
27161 GAAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
AATTTTTATTTTTTGA
Found at i:28781 original size:23 final size:23
Alignment explanation
Indices: 28755--28953 Score: 224
Period size: 23 Copynumber: 8.7 Consensus size: 23
28745 CAAAGTACTA
* * *
28755 CACTGTAATATAGCTGAAGCTAT
1 CACTGTAATGTAGCCGAAGCTAC
*
28778 CACTGTAACGTAGCCGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
* * * *
28801 CACTGTATTGCAGCCAAACCTAC
1 CACTGTAATGTAGCCGAAGCTAC
* *
28824 CATTGTATTGTAGCCGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
28847 CACTG-AGATGTAGCCGAAGCTAC
1 CACTGTA-ATGTAGCCGAAGCTAC
28870 CACTG-AGATGTAGCCGAAGCTAC
1 CACTGTA-ATGTAGCCGAAGCTAC
* *
28893 CACTGTATTGTAGCTGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
*
28916 CACTG-AGATGTAGTCGAAGCTAC
1 CACTGTA-ATGTAGCCGAAGCTAC
*
28939 CACTGTATTGTAGCC
1 CACTGTAATGTAGCC
28954 TATAGATTCC
Statistics
Matches: 150, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
22 2 0.01
23 146 0.97
24 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (23 bp):
CACTGTAATGTAGCCGAAGCTAC
Found at i:28951 original size:69 final size:69
Alignment explanation
Indices: 28755--28953 Score: 267
Period size: 69 Copynumber: 2.9 Consensus size: 69
28745 CAAAGTACTA
* * * * *
28755 CACTGTAATATAGCTGAAGCTATCACTGTA-ACGTAGCCGAAGCTACCACTGTATTGCAGCCAAA
1 CACTGTATTGTAGCTGAAGCTACCACTG-AGATGTAGCCGAAGCTACCACTGTATTGTAGCCAAA
28819 CCTAC
65 CCTAC
* * * *
28824 CATTGTATTGTAGCCGAAGCTACCACTGAGATGTAGCCGAAGCTACCACTG-AGATGTAGCCGAA
1 CACTGTATTGTAGCTGAAGCTACCACTGAGATGTAGCCGAAGCTACCACTGTA-TTGTAGCCAAA
*
28888 GCTAC
65 CCTAC
*
28893 CACTGTATTGTAGCTGAAGCTACCACTGAGATGTAGTCGAAGCTACCACTGTATTGTAGCC
1 CACTGTATTGTAGCTGAAGCTACCACTGAGATGTAGCCGAAGCTACCACTGTATTGTAGCC
28954 TATAGATTCC
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
68 2 0.02
69 110 0.97
70 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (69 bp):
CACTGTATTGTAGCTGAAGCTACCACTGAGATGTAGCCGAAGCTACCACTGTATTGTAGCCAAAC
CTAC
Found at i:30550 original size:14 final size:15
Alignment explanation
Indices: 30531--30560 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30521 GTTTATTATA
30531 TGTG-AAGTATCATG
1 TGTGAAAGTATCATG
30545 TGTGAAAGTATCATG
1 TGTGAAAGTATCATG
30560 T
1 T
30561 CTTAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.37
Consensus pattern (15 bp):
TGTGAAAGTATCATG
Found at i:32581 original size:43 final size:43
Alignment explanation
Indices: 32450--32598 Score: 119
Period size: 43 Copynumber: 3.5 Consensus size: 43
32440 GGCTTTGAGC
* * *
32450 CTAGCAGGTGTAATGCCGGTGAAATGATATCGGACTTAAAGGT
1 CTAGCAGGCGTAATGCCAGTGAAATGATATCAGACTTAAAGGT
* * ** *** *
32493 CTAGCAAGCTTTAA-GCTGGTG-AAT-ATTATCA-AGCTCCGA-GC
1 CTAGCAGGC-GTAATGCCAGTGAAATGA-TATCAGA-CTTAAAGGT
32534 CTAGCAGGCGTAATGCCAGTGAAATGATATCAGACTTAAAGGT
1 CTAGCAGGCGTAATGCCAGTGAAATGATATCAGACTTAAAGGT
* *
32577 CTAGCAGGCTTATTGCCAGTGA
1 CTAGCAGGCGTAATGCCAGTGA
32599 TGAAATCAGG
Statistics
Matches: 79, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
40 3 0.04
41 16 0.20
42 21 0.27
43 36 0.46
44 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (43 bp):
CTAGCAGGCGTAATGCCAGTGAAATGATATCAGACTTAAAGGT
Found at i:34080 original size:30 final size:30
Alignment explanation
Indices: 34046--34113 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
34036 CACATGGATA
*
34046 GACACATGGGCGTGTGTCTAGGCCGTGTGT
1 GACACACGGGCGTGTGTCTAGGCCGTGTGT
34076 GACACACGGGCGTGTGTCTAGGCCGTGTGT
1 GACACACGGGCGTGTGTCTAGGCCGTGTGT
34106 GACACACG
1 GACACACG
34114 ATCACACTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.16, C:0.24, G:0.38, T:0.22
Consensus pattern (30 bp):
GACACACGGGCGTGTGTCTAGGCCGTGTGT
Found at i:39084 original size:23 final size:23
Alignment explanation
Indices: 39058--39279 Score: 252
Period size: 23 Copynumber: 9.7 Consensus size: 23
39048 CAAAGTGCCA
* * *
39058 CACTGTAATATAGCTGAAGCTAT
1 CACTGTAATGTAGCCGAAGCTAC
* *
39081 CACTTTAACGTAGCCGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
* *
39104 CACTGTATTGTAGCCAAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
*
39127 CACTGTATTGTAGCCGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
* *
39150 CACTG-AGATATAGCCAAAGCTAC
1 CACTGTA-ATGTAGCCGAAGCTAC
*
39173 CACTGTATTGTAGCCGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
*
39196 CACTG-AGATGTAGCTGAAGCTAC
1 CACTGTA-ATGTAGCCGAAGCTAC
* * *
39219 CACTATATTGTAGCTGAAGCTAC
1 CACTGTAATGTAGCCGAAGCTAC
39242 CACTG-AGATGTAGCCGAAGCTAC
1 CACTGTA-ATGTAGCCGAAGCTAC
*
39265 CACTGTATTGTAGCC
1 CACTGTAATGTAGCC
39280 TATAGATTCC
Statistics
Matches: 169, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
22 3 0.02
23 163 0.96
24 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (23 bp):
CACTGTAATGTAGCCGAAGCTAC
Found at i:39125 original size:46 final size:46
Alignment explanation
Indices: 39090--39279 Score: 301
Period size: 46 Copynumber: 4.1 Consensus size: 46
39080 TCACTTTAAC
*
39090 GTAGCCGAAGCTACCACTGTA-TTGTAGCCAAAGCTACCACTGTATT
1 GTAGCCGAAGCTACCACTG-AGATGTAGCCAAAGCTACCACTGTATT
*
39136 GTAGCCGAAGCTACCACTGAGATATAGCCAAAGCTACCACTGTATT
1 GTAGCCGAAGCTACCACTGAGATGTAGCCAAAGCTACCACTGTATT
** *
39182 GTAGCCGAAGCTACCACTGAGATGTAGCTGAAGCTACCACTATATT
1 GTAGCCGAAGCTACCACTGAGATGTAGCCAAAGCTACCACTGTATT
* *
39228 GTAGCTGAAGCTACCACTGAGATGTAGCCGAAGCTACCACTGTATT
1 GTAGCCGAAGCTACCACTGAGATGTAGCCAAAGCTACCACTGTATT
39274 GTAGCC
1 GTAGCC
39280 TATAGATTCC
Statistics
Matches: 133, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.01
46 132 0.99
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (46 bp):
GTAGCCGAAGCTACCACTGAGATGTAGCCAAAGCTACCACTGTATT
Done.