Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1336
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: 32331
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Found at i:21 original size:3 final size:3
Alignment explanation
Indices: 13--61 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
3 TCCGAGTCAC
13 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
61 C
1 C
62 TTCCTCTTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:1694 original size:13 final size:13
Alignment explanation
Indices: 1653--1701 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
1643 CCTTTACAAG
*
1653 CAATGCATCGATA
1 CAATGTATCGATA
1666 CAAT-T-TC-AT-
1 CAATGTATCGATA
1675 C-ATGTATCGATA
1 CAATGTATCGATA
1687 CAATGTATCGATA
1 CAATGTATCGATA
1700 CA
1 CA
1702 TTATCCCATG
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
8 2 0.07
9 2 0.07
10 4 0.13
11 4 0.13
12 1 0.03
13 17 0.57
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1720 original size:33 final size:34
Alignment explanation
Indices: 1653--1722 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
1643 CCTTTACAAG
*
1653 CAATGCATCGATACAATTTCATCATGTATCGATA
1 CAATGCATCGATACAATTTCACCATGTATCGATA
* *
1687 CAATGTATCGATAC-ATTATC-CCATGTATTGATA
1 CAATGCATCGATACAATT-TCACCATGTATCGATA
1720 CAA
1 CAA
1723 ATAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 17 0.53
34 15 0.47
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (34 bp):
CAATGCATCGATACAATTTCACCATGTATCGATA
Found at i:1795 original size:19 final size:19
Alignment explanation
Indices: 1751--1806 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
1741 CTGCCAATAT
*
1751 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAC
*
1771 CATGTATCGATACAATGAG
1 CATGTATCGATACAATGAC
1790 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1807 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:1809 original size:13 final size:13
Alignment explanation
Indices: 1791--1817 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1781 TACAATGAGC
1791 ATGTATCGATACA
1 ATGTATCGATACA
1804 ATGTATCGATACA
1 ATGTATCGATACA
1817 A
1 A
1818 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3291 original size:30 final size:30
Alignment explanation
Indices: 3253--3310 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
3243 AATTTGTTGG
3253 AAATAAACC-ATCAGC-TTTCTTGTCAAAAA
1 AAATAAACCAATCA-CATTTCTTGTCAAAAA
3282 AAATCAAACCATATCACATTTCTTGTCAA
1 AAAT-AAACCA-ATCACATTTCTTGTCAA
3311 GTAAGCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
29 4 0.16
30 5 0.20
31 1 0.04
32 15 0.60
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.29
Consensus pattern (30 bp):
AAATAAACCAATCACATTTCTTGTCAAAAA
Found at i:3889 original size:62 final size:62
Alignment explanation
Indices: 3814--4007 Score: 307
Period size: 62 Copynumber: 3.1 Consensus size: 62
3804 AATTTGGTGG
* * **
3814 ATTTCATGCTTAATTTGCTGCCACCTAAGCTTTTTAGACGTCATTGCATTACATTGCATTGC
1 ATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCATTGCATTACATTGCATTGC
* *
3876 ATTTCATGTTTAATTTGTTGCCACCTAAGCTTTCTAGGTGTCATTGCATTACATTGCATTGG
1 ATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCATTGCATTACATTGCATTGC
** *
3938 ATTTCATGTTTAATTTGCTGCCATATAAGCTTTCTAGGTGTCATTGCATAACATTGCATTGC
1 ATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCATTGCATTACATTGCATTGC
4000 ATTTCATG
1 ATTTCATG
4008 CATGCTTTCA
Statistics
Matches: 121, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 121 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (62 bp):
ATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCATTGCATTACATTGCATTGC
Found at i:4400 original size:33 final size:33
Alignment explanation
Indices: 4363--4431 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
4353 ACTGCAAGCA
4363 AATGAATGCAATCAAAATAGCAATTCAAAGGAG
1 AATGAATGCAATCAAAATAGCAATTCAAAGGAG
* * **
4396 AATGAATGTAATCGAAATAGCGGTTCAAAGGAG
1 AATGAATGCAATCAAAATAGCAATTCAAAGGAG
4429 AAT
1 AAT
4432 AAAAGCAGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.48, C:0.10, G:0.22, T:0.20
Consensus pattern (33 bp):
AATGAATGCAATCAAAATAGCAATTCAAAGGAG
Found at i:12218 original size:16 final size:16
Alignment explanation
Indices: 12197--12229 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12187 ATTCAATAAC
12197 TCAGATGAGTATGAGA
1 TCAGATGAGTATGAGA
12213 TCAGATGAGTATGAGA
1 TCAGATGAGTATGAGA
12229 T
1 T
12230 TCTGAATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.30, T:0.27
Consensus pattern (16 bp):
TCAGATGAGTATGAGA
Found at i:12546 original size:18 final size:17
Alignment explanation
Indices: 12512--12548 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
12502 AATTCGAGCA
*
12512 AAAAAATAGATATATTT
1 AAAAAATAGATAGATTT
12529 AAAAAATAGATAAGATTT
1 AAAAAATAGAT-AGATTT
12547 AA
1 AA
12549 TTTTAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (17 bp):
AAAAAATAGATAGATTT
Found at i:12653 original size:27 final size:27
Alignment explanation
Indices: 12597--12653 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
12587 TATTTTTTAA
* * * *
12597 TTATATAAAATATATATAATGTAATTT
1 TTATATAAAAAATAAATAATATAATAT
12624 TTATATAAAAAATAAATATATATAA-AT
1 TTATATAAAAAATAAATA-ATATAATAT
12651 TTA
1 TTA
12654 GAATGTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
TTATATAAAAAATAAATAATATAATAT
Found at i:23450 original size:3 final size:3
Alignment explanation
Indices: 23442--23486 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
23432 TTATCTAATA
*
23442 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
23487 AGTGTGGGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:24369 original size:11 final size:10
Alignment explanation
Indices: 24349--24414 Score: 50
Period size: 9 Copynumber: 6.9 Consensus size: 10
24339 TTCTTCGGTT
24349 TTTATTATTA
1 TTTATTATTA
24359 TTTATTTATTA
1 TTTA-TTATTA
* *
24370 TTT-TGACT-
1 TTTATTATTA
*
24378 TTCATT-TTA
1 TTTATTATTA
*
24387 TTTTTTATTA
1 TTTATTATTA
*
24397 TTTATTACT-
1 TTTATTATTA
24406 TTTATTATT
1 TTTATTATT
24415 TCTTTTTAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
8 3 0.07
9 16 0.38
10 14 0.33
11 9 0.21
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTATTATTA
Found at i:24405 original size:138 final size:138
Alignment explanation
Indices: 24241--24489 Score: 421
Period size: 138 Copynumber: 1.8 Consensus size: 138
24231 TCCATTAGGC
24241 TCATTTTATTTTTTATTATTTATTACTTTTATTATTTCTTTTTTAA-CTCAATTTAATTTTGA-T
1 TCATTTTATTTTTTATTATTTATTACTTTTATTATTTC-TTTTTAACCT-AATTTAATTTTGATT
* * *
24304 TTTGTTTTGATTTTCATTTTTTTATTACTTATTTGTTCTTCGGTTTTTATTATTATTTATTTATT
64 TTTATTTTGATTTTCATTTATTTATTACTTATTTGTTCTTCCGTTTTTATTATTATTTATTTATT
24369 ATTTTGACTT
129 ATTTTGACTT
*
24379 TCATTTTATTTTTTATTATTTATTACTTTTATTATTTCTTTTTAACCTAATTTAGTTTTGATTTT
1 TCATTTTATTTTTTATTATTTATTACTTTTATTATTTCTTTTTAACCTAATTTAATTTTGATTTT
*
24444 TATTTTGATTTTCATTTATTTATTATTTATTTGTTCTTCCGTTTTT
66 TATTTTGATTTTCATTTATTTATTACTTATTTGTTCTTCCGTTTTT
24490 TCTCTTTTGG
Statistics
Matches: 104, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
137 19 0.18
138 85 0.82
ACGTcount: A:0.19, C:0.08, G:0.05, T:0.68
Consensus pattern (138 bp):
TCATTTTATTTTTTATTATTTATTACTTTTATTATTTCTTTTTAACCTAATTTAATTTTGATTTT
TATTTTGATTTTCATTTATTTATTACTTATTTGTTCTTCCGTTTTTATTATTATTTATTTATTAT
TTTGACTT
Found at i:24411 original size:9 final size:8
Alignment explanation
Indices: 24348--24415 Score: 54
Period size: 7 Copynumber: 8.4 Consensus size: 8
24338 GTTCTTCGGT
24348 TTTTATTA
1 TTTTATTA
*
24356 TTAT-TTA
1 TTTTATTA
24363 -TTTATTA
1 TTTTATTA
24370 TTTTGACTTTCA
1 TTTT-A--TT-A
24382 TTTTATT-
1 TTTTATTA
24389 TTTTATTA
1 TTTTATTA
24397 -TTTATTA
1 TTTTATTA
24404 CTTTTATTA
1 -TTTTATTA
24413 TTT
1 TTT
24416 CTTTTTAACC
Statistics
Matches: 49, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
6 2 0.04
7 20 0.41
8 9 0.18
9 10 0.20
11 3 0.06
12 5 0.10
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.72
Consensus pattern (8 bp):
TTTTATTA
Found at i:27518 original size:15 final size:15
Alignment explanation
Indices: 27494--27529 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
27484 ACTATACTAT
* *
27494 AAATTCTTTCTTGTG
1 AAATTTTTTCTAGTG
27509 AAATTTTTTCTAGTG
1 AAATTTTTTCTAGTG
27524 AAATTT
1 AAATTT
27530 ATTCCAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.53
Consensus pattern (15 bp):
AAATTTTTTCTAGTG
Found at i:28725 original size:96 final size:97
Alignment explanation
Indices: 28454--28788 Score: 505
Period size: 97 Copynumber: 3.5 Consensus size: 97
28444 TGAAAAACGG
* * *
28454 GGTTGGAGTATCTTCTCGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTGAGTGAGAA
1 GGTTGGAGTATCTCCTCGGAGGAATAGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAGAA
* *
28519 TAAGATCTAAACTTTGATGTGTTTAAAAGCAA
66 TAAGATTTAAACTTTGATGTGTTTAAAAGCGA
* * *
28551 GGTTGGAGTATC-CTCTCGGAGGAATAGGGTTGGAGTGTCCTCGATAATGACAATTTAGGTGAGA
1 GGTTGGAGTATCTC-CTCGGAGGAATAGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAGA
* **
28615 ACAAGATTTAAACTTTGACATGTTTAAAAGCGA
65 ATAAGATTTAAACTTTGATGTGTTTAAAAGCGA
28648 GGTTGGAGTATCTCCTCGGAGGAAT-GGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAGAA
1 GGTTGGAGTATCTCCTCGGAGGAATAGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAGAA
28712 TAAGATTTAAACTTTGATGTGTTTAAAAGCGA
66 TAAGATTTAAACTTTGATGTGTTTAAAAGCGA
* * *
28744 GGTTGGAGTATCAT-CTCGGAGGAATAGGGTTAGAGTATCCTCGAT
1 GGTTGGAGTATC-TCCTCGGAGGAATAGGGTTGGAGTGTCCCCGAT
28789 AAATAGAATT
Statistics
Matches: 214, Mismatches: 20, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
96 88 0.41
97 125 0.58
98 1 0.00
ACGTcount: A:0.29, C:0.12, G:0.30, T:0.30
Consensus pattern (97 bp):
GGTTGGAGTATCTCCTCGGAGGAATAGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAGAA
TAAGATTTAAACTTTGATGTGTTTAAAAGCGA
Found at i:30224 original size:14 final size:13
Alignment explanation
Indices: 30196--30220 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30186 AAAAAAATTT
30196 ACGGAGTTGAAAC
1 ACGGAGTTGAAAC
30209 ACGGAGTTGAAA
1 ACGGAGTTGAAA
30221 ACACCGTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.32, T:0.16
Consensus pattern (13 bp):
ACGGAGTTGAAAC
Found at i:30989 original size:31 final size:32
Alignment explanation
Indices: 30954--31054 Score: 118
Period size: 32 Copynumber: 3.2 Consensus size: 32
30944 AATGCCACAA
*
30954 ACTTGTGTGGGCCTT-GAAGGGGTTGCCACCG
1 ACTTGTGTGGGCCTTGGAAAGGGTTGCCACCG
* *
30985 ACTTGTGTGGACTTTGGAAAGGGTTGCCACCG
1 ACTTGTGTGGGCCTTGGAAAGGGTTGCCACCG
* * *
31017 ACTTGTGTGGGCTTTAGAGAATGG-TGCCA-CG
1 ACTTGTGTGGGCCTTGGA-AAGGGTTGCCACCG
31048 ACTTGTG
1 ACTTGTG
31055 GGCTTTGAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
31 22 0.35
32 36 0.58
33 4 0.06
ACGTcount: A:0.17, C:0.19, G:0.36, T:0.29
Consensus pattern (32 bp):
ACTTGTGTGGGCCTTGGAAAGGGTTGCCACCG
Found at i:31109 original size:57 final size:55
Alignment explanation
Indices: 30959--31564 Score: 617
Period size: 57 Copynumber: 10.5 Consensus size: 55
30949 CACAAACTTG
* * * * *
30959 TGTGGGCCTTGAAGGGGTTGCCACCGACTTGTGTGGACTTTGGAAAGGGTTGCCACCGACTT
1 TGTGGGCTTTGAA-AGGATGCCACTGACTTGTG-GG-CTTT-GAAA-GG-TGCCACTGAC-T
* *
31021 GTGTGGGCTTTAGAGAATGG-TGCCAC-GACTTGTGGGCTTTGAAATGGTGCCACGGAGT
1 -TGTGGGCTTT-GA-AA-GGATGCCACTGACTTGTGGGCTTTGAAA-GGTGCCACTGACT
* * * *
31079 TATGGGCTTTTGAAAAGATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAA-GGTGCCACTGACT
* *
31136 TGTGGGCTTTTGAAAGGATGCCACTAACTTGTGGGCTTTTGAAAGGATGCCACTAACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACTTGTGGGC-TTTGAAAGG-TGCCACTGACT
* *
31194 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGAGTCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGTG-CCACTGACT
* * *
31250 TGTTAGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAGGGTGCCACAGAGC-
1 TG-TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGTGCCACTGA-CT
* * * * *
31306 TGTGGGCTTTGAAAAAAAGATGCCACTAACTTATGGGCTTTTGAAAAGATGCCACTAACT
1 TGTGGGCTTTG---AAAGGATGCCACTGACTTGTGGGC-TTTG-AAAGGTGCCACTGACT
* **
31366 TGTGGACTTTGAAAGGACACCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAA-GGTGCCACTGACT
* *
31422 TGTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTAAAATGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAA-GG-TGCCACTGACT
* * *
31479 TGTGGGCTTTGAAAGAATGTCATTGACTTGTGGGCTTTGAAAGGATGCCACTGA-T
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGG-TGCCACTGACT
* *
31534 TATGGGCTTTTGAAAAGATGCCACTGACTTG
1 TGTGGGC-TTTGAAAGGATGCCACTGACTTG
31565 GAGCTTTAAA
Statistics
Matches: 470, Mismatches: 53, Indels: 47
0.82 0.09 0.08
Matches are distributed among these distances:
55 20 0.04
56 120 0.26
57 207 0.44
58 50 0.11
59 13 0.03
60 26 0.06
61 4 0.01
62 2 0.00
63 17 0.04
64 8 0.02
65 3 0.01
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (55 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGTGCCACTGACT
Found at i:31128 original size:28 final size:28
Alignment explanation
Indices: 30959--31589 Score: 648
Period size: 28 Copynumber: 21.9 Consensus size: 28
30949 CACAAACTTG
* * * *
30959 TGTGGGCCTTGAAGGGGTTGCCACCGACT
1 TGTGGGCTTTGAA-AGGATGCCACTGACT
* *
30988 TGTGTGGACTTTGGAAAGGGTTGCCACCGACTT
1 TGTG-GG-CTTT-GAAA-GGATGCCACTGAC-T
31021 GTGTGGGCTTTAGAGAATGG-TGCCAC-GACT
1 -TGTGGGCTTT-GA-AA-GGATGCCACTGACT
* *
31051 TGTGGGCTTTGAAATGG-TGCCACGGAGT
1 TGTGGGCTTTGAAA-GGATGCCACTGACT
* * *
31079 TATGGGCTTTTGAAAAGATGCCACTAACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
* *
31108 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
31136 TGTGGGCTTTTGAAAGGATGCCACTAACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
*
31165 TGTGGGCTTTTGAAAGGATGCCACTAACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
31194 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
31222 TGTGGGCTTTGAAAGGA-GTCCACTAACT
1 TGTGGGCTTTGAAAGGATG-CCACTGACT
*
31250 TGTTAGGCTTTGAAAGGATGCCACTGACT
1 TG-TGGGCTTTGAAAGGATGCCACTGACT
* *
31279 TGTGGGCTTTG-AAGGGTGCCACAGAGC-
1 TGTGGGCTTTGAAAGGATGCCACTGA-CT
* *
31306 TGTGGGCTTTGAAAAAAAGATGCCACTAACT
1 TGTGGGCTTTG---AAAGGATGCCACTGACT
* * *
31337 TATGGGCTTTTGAAAAGATGCCACTAACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
* **
31366 TGTGGACTTTGAAAGGACACCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
31394 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
31422 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
31450 TATGGGCTTTAAAATGGATGCCACTGACT
1 TGTGGGCTTTGAAA-GGATGCCACTGACT
* * *
31479 TGTGGGCTTTGAAAGAATGTCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
31507 TGTGGGCTTTGAAAGGATGCCACTGA-T
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
31534 TATGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
* *
31563 TG-GAGCTTTAAAAAGGAATGCCACTGA
1 TGTGGGCTTT-GAAAGG-ATGCCACTGA
31590 ATCATGGACT
Statistics
Matches: 523, Mismatches: 53, Indels: 52
0.83 0.08 0.08
Matches are distributed among these distances:
27 45 0.09
28 233 0.45
29 175 0.33
30 5 0.01
31 22 0.04
32 32 0.06
33 7 0.01
34 4 0.01
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:31582 original size:85 final size:85
Alignment explanation
Indices: 31022--31587 Score: 641
Period size: 85 Copynumber: 6.6 Consensus size: 85
31012 CACCGACTTG
** * *
31022 TGTGGGCTTTAGAGAATGG-TGCCAC-GACTTGTGGGCTTTGAAATGG-TGCCACGGAGTTATGG
1 TGTGGGCTTT-GA-AA-GGATGCCACTGACTTGTGGGCTTTGAAA-GGATGCCACTAACTTGTGG
*
31084 GCTTTTGAAAAGATGCCACTAACT
62 GCTTTTGAAAGGATGCCACTAACT
* *
31108 TGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAGGATGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGC-TTTGAAAGGATGCCACTAACTTGTGGGCT
31173 TTTGAAAGGATGCCACTAACT
65 TTTGAAAGGATGCCACTAACT
*
31194 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGA-GTCCACTAACTTGTTAGGC
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATG-CCACTAACTTG-TGGGC
*
31258 -TTTGAAAGGATGCCACTGACT
64 TTTTGAAAGGATGCCACTAACT
* * * *
31279 TGTGGGCTTTG-AAGGGTGCCACAGAGC-TGTGGGCTTTGAAAAAAAGATGCCACTAACTTATGG
1 TGTGGGCTTTGAAAGGATGCCACTGA-CTTGTGGGCTTTG---AAAGGATGCCACTAACTTGTGG
*
31342 GCTTTTGAAAAGATGCCACTAACT
62 GCTTTTGAAAGGATGCCACTAACT
* ** * *
31366 TGTGGACTTTGAAAGGACACCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC-T
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTT
*
31430 TTGAAAGGATGCCACTGACT
66 TTGAAAGGATGCCACTAACT
* * * * * *
31450 TATGGGCTTTAAAATGGATGCCACTGACTTGTGGGCTTTGAAAGAATGTCATTGACTTGTGGGC-
1 TGTGGGCTTTGAAA-GGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCT
*
31514 TTTGAAAGGATGCCACTGA-T
65 TTTGAAAGGATGCCACTAACT
* * * *
31534 TATGGGCTTTTGAAAAGATGCCACTGACTTG-GAGCTTTAAAAAGGAATGCCACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACTTGTGGGCTTT-GAAAGG-ATGCCACT
31588 GAATCATGGA
Statistics
Matches: 418, Mismatches: 44, Indels: 37
0.84 0.09 0.07
Matches are distributed among these distances:
83 8 0.02
84 89 0.21
85 161 0.39
86 93 0.22
87 45 0.11
88 22 0.05
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (85 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTT
TTGAAAGGATGCCACTAACT
Done.