Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2020
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: 103352
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1336 original size:13 final size:13
Alignment explanation
Indices: 1318--1389 Score: 63
Period size: 13 Copynumber: 5.0 Consensus size: 13
1308 ACAGCATTCT
1318 TTGTATCGATACA
1 TTGTATCGATACA
1331 TTGTATCGATAGAGCA
1 TTGTATCGAT--A-CA
*
1347 TTCTCTGTATCAATACA
1 ---T-TGTATCGATACA
1364 TTGTATCGATACA
1 TTGTATCGATACA
*
1377 GTGTATCGATACA
1 TTGTATCGATACA
1390 AAAGGTTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
13 33 0.67
14 1 0.02
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 1 0.02
20 8 0.16
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1347 original size:33 final size:33
Alignment explanation
Indices: 1299--1377 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
1289 AAAACTCAGA
* * *
1299 TGTATCAATACAGCATTCTTTGTATCGATACAT
1 TGTATCGATACAGCATTCTCTGTATCAATACAT
*
1332 TGTATCGATAGAGCATTCTCTGTATCAATACAT
1 TGTATCGATACAGCATTCTCTGTATCAATACAT
1365 TGTATCGATACAG
1 TGTATCGATACAG
1378 TGTATCGATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAGCATTCTCTGTATCAATACAT
Found at i:3656 original size:13 final size:13
Alignment explanation
Indices: 3638--3663 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3628 ACATACAAGA
3638 TGTATCGATACAT
1 TGTATCGATACAT
3651 TGTATCGATACAT
1 TGTATCGATACAT
3664 GACCAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3679 original size:33 final size:32
Alignment explanation
Indices: 3618--3685 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
3608 CCTTAACTGT
3618 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
3650 TTGTATCGATACATGACCAA-ATGTATCGATACA
1 TTGTATCGATACAT-A-CAAGATGTATCGATACA
3683 TTG
1 TTG
3686 GCTTGTAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 17 0.50
34 3 0.09
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:4461 original size:18 final size:18
Alignment explanation
Indices: 4422--4461 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4412 TTCAATACCC
* *
4422 AAAAAAAACAAAAAATAG
1 AAAAAAAACAAAAAACAA
*
4440 AAAAAAAATAAAAAACAA
1 AAAAAAAACAAAAAACAA
4458 AAAA
1 AAAA
4462 CTAAGGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.88, C:0.05, G:0.03, T:0.05
Consensus pattern (18 bp):
AAAAAAAACAAAAAACAA
Found at i:5635 original size:28 final size:28
Alignment explanation
Indices: 5595--5979 Score: 430
Period size: 28 Copynumber: 13.4 Consensus size: 28
5585 CATTCATCTC
* *
5595 TTCAAAGACCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
5623 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
5651 TTCAAAGCCTACAAAAGTCGGAGGCAACTCTT
1 TTCAAAGCC--CACAAGTCAGTGGC-AC-CCT
*
5683 TTCAAAGCCCACAAGTCAGTGGTACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
**
5711 TTCAAAGCCCACAAGTCAGTGGCATTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
5739 TTCAAAGCCCATAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
5767 TTCAAAGCCCACGAGTCAGTGGCATTCCT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCCT
* *
5796 TTCAAAGCCCACGAGTCAGTGGCATTCCT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCCT
* * * *
5825 TTCAAAACCCACGAGTCGGTGGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-AC-CCT
* *
5855 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
**
5883 TTCAAAGCCCACAAGTCAGAAGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
5911 TTCAAAGCCCACAAGTCAGTGGC-CCTCT
1 TTCAAAGCCCACAAGTCAGTGGCACC-CT
* * **
5939 TTCAATGCCCATAAGTCAGTGGCACTATT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
5968 TTCAAAGCCCAC
1 TTCAAAGCCCAC
5980 TCGAGTCGGT
Statistics
Matches: 307, Mismatches: 40, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
27 2 0.01
28 181 0.59
29 68 0.22
30 43 0.14
31 2 0.01
32 11 0.04
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:5851 original size:172 final size:171
Alignment explanation
Indices: 5595--5993 Score: 505
Period size: 172 Copynumber: 2.3 Consensus size: 171
5585 CATTCATCTC
* * * * * *
5595 TTCAAAGACCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGGCACCCTTTCAAAACC
*
5660 TACAAAAGTCGGAGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGTACCCTTTCAAAGCCCACAA
66 -ACAAAAGTCGGAGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAA
** ** *
5725 GTCAGTGGCATTCTTTCAAAGCCCATAAGTCAGTGGCACC-CT
130 GTCAGAAGCACCCTTTCAAAGCCCACAAGTCAGTGGC-CCTCT
* *
5767 TTCAAAGCCCACGAGTCAGTGGCATTCCTTTCAAAGCCCACGAGTCAGTGGCATTCCTTTCAAAA
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACGAGTCAGTGGCA-CCCTTTCAAAA
** * * *
5832 CC-CACGAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACA
64 CCACAAAAGTCGGAGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACA
5896 AGTCAGAAGCACCCTTTCAAAGCCCACAAGTCAGTGGCCCTCT
129 AGTCAGAAGCACCCTTTCAAAGCCCACAAGTCAGTGGCCCTCT
* * ** *
5939 TTCAATGCCCATAAGTCAGTGGCACTATTTTCAAAGCCCACTCGAGTCGGTGGCA
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCA--CGAGTCAGTGGCA
5994 ACTCTTTTCA
Statistics
Matches: 196, Mismatches: 26, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
171 2 0.01
172 146 0.74
173 25 0.13
174 23 0.12
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (171 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGGCACCCTTTCAAAACC
ACAAAAGTCGGAGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
TCAGAAGCACCCTTTCAAAGCCCACAAGTCAGTGGCCCTCT
Found at i:5858 original size:144 final size:143
Alignment explanation
Indices: 5589--6031 Score: 525
Period size: 144 Copynumber: 3.1 Consensus size: 143
5579 CTAGAACATT
* * * * *
5589 CATCTCTTCAAAGACCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTC
1 CATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
* * * * * *
5654 AAAGCCTACAAAAGTCGGAGGCAACTCTTTTCAAAGCCCACAAGTCAGTGG-TAC-CCTTTCAAA
66 AAAGCC--CAAAAGTCAGTGGC-ACTCTTTTCAAAGCCCACGAGTCGGTGGCAACTCTTTTCAAA
5717 GCCCACAAGTCAGTGG
128 GCCCACAAGTCAGTGG
* *
5733 CAT-TCTTTCAAAGCCCATAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCAGTGGCATTCCTT
1 CATCT-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTT
** * * *
5797 TCAAAGCCCACGAGTCAGTGGCATTCCTTTCAAAACCCACGAGTCGGTGGCAACTCTTTTCAAAG
64 TCAAAGCCCAAAAGTCAGTGGCACTCTTTTCAAAGCCCACGAGTCGGTGGCAACTCTTTTCAAAG
5862 CCCACAAGTCAGTGG
129 CCCACAAGTCAGTGG
** *
5877 CATCTTTTCAAAGCCCACAAGTCAGAAGCACCCTTTCAAAGCCCACAAGTCAGTGGC-CCTCTTT
1 CATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATC-CTTT
* * *
5941 CAATGCCCATAAGTCAGTGGCACTATTTTCAAAGCCCACTCGAGTCGGTGGCAACTCTTTTCAAA
65 CAAAGCCCAAAAGTCAGTGGCACTCTTTTCAAAGCCCA--CGAGTCGGTGGCAACTCTTTTCAAA
* *
6006 GCTTACACAAGTTAGTGG
128 GC--CCACAAGTCAGTGG
*
6024 CACCTTTT
1 CATCTTTT
6032 TTAAAAAAAG
Statistics
Matches: 256, Mismatches: 33, Indels: 17
0.84 0.11 0.06
Matches are distributed among these distances:
142 24 0.09
143 48 0.19
144 125 0.49
145 40 0.16
147 19 0.07
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (143 bp):
CATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
AAAGCCCAAAAGTCAGTGGCACTCTTTTCAAAGCCCACGAGTCGGTGGCAACTCTTTTCAAAGCC
CACAAGTCAGTGG
Found at i:6900 original size:20 final size:20
Alignment explanation
Indices: 6877--6951 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
6867 AAGTATCTAG
6877 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
6897 ATGTATCTATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
6917 ATGTATC-ACTACATTCTTCA
1 ATGTATCGA-TACATTTTTCA
*
6937 ATGTATTGATACATT
1 ATGTATCGATACATT
6952 CTGTCTTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:8467 original size:97 final size:97
Alignment explanation
Indices: 8343--8574 Score: 329
Period size: 97 Copynumber: 2.4 Consensus size: 97
8333 TATCGGGGAT
* *
8343 ACTCCAACCCTATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATC
1 ACTCCAACCCCATTCCTCTGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATC
8408 TTATTCTCACTTAAATTATCACCATCAAGGAC
66 TTATTCTCACTTAAATTATCACCATCAAGGAC
* * * ** * *
8440 ACTTCAACCCCATTCCTCTGAGGGGATACTCTAACACCGCTTTTAAATGCCTCAAAGTTTAAATT
1 ACTCCAACCCCATTCCTCTGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATC
* * **
8505 TTATTCTCACTTAAATTGTCATCATCGGGGAC
66 TTATTCTCACTTAAATTATCACCATCAAGGAC
* *
8537 ACTCCAAACCCACTCCTCTGAGGGGATACTCCAACCCC
1 ACTCCAACCCCATTCCTCTGAGGGGATACTCCAACCCC
8575 ATTTTTCAAT
Statistics
Matches: 117, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
97 117 1.00
ACGTcount: A:0.29, C:0.31, G:0.12, T:0.28
Consensus pattern (97 bp):
ACTCCAACCCCATTCCTCTGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATC
TTATTCTCACTTAAATTATCACCATCAAGGAC
Found at i:11519 original size:20 final size:20
Alignment explanation
Indices: 11485--11526 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
11475 AATGAGATGT
*
11485 TGAAAAT-ATTAAAAATGCA
1 TGAAAATAATAAAAAATGCA
11504 TGAAACATAATAAAAAATGCA
1 TGAAA-ATAATAAAAAATGCA
11525 TG
1 TG
11527 GTCAAAGGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.57, C:0.07, G:0.12, T:0.24
Consensus pattern (20 bp):
TGAAAATAATAAAAAATGCA
Found at i:12414 original size:20 final size:20
Alignment explanation
Indices: 12363--12437 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
12353 AAAAAGACAT
12363 AATGTATCGATACATT-AAA
1 AATGTATCGATACATTCAAA
* *
12382 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCAAA
* * * *
12403 CATGTATTGATATATTGAAA
1 AATGTATCGATACATTCAAA
12423 AATGTATCGATACAT
1 AATGTATCGATACAT
12438 CTGGGTAAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:12431 original size:40 final size:39
Alignment explanation
Indices: 12360--12437 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
12350 GGTAAAAAGA
12360 CATAATGTATCGATACATTAAAGAATATATCGATACATT
1 CATAATGTATCGATACATTAAAGAATATATCGATACATT
* * *
12399 CATACATGTATTGATATATTGAAA-AATGTATCGATACAT
1 CATA-ATGTATCGATACATT-AAAGAATATATCGATACAT
12438 CTGGGTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 4 0.12
40 27 0.79
41 3 0.09
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTAAAGAATATATCGATACATT
Found at i:13132 original size:28 final size:28
Alignment explanation
Indices: 12994--14145 Score: 1142
Period size: 28 Copynumber: 40.2 Consensus size: 28
12984 TTTTTTAAAA
* *
12994 AAAATGTGCCACTAACTTGTGTAGGCTTTG
1 AAAAGGTGCCACTGACTTGTG--GGCTTTG
* * *
13024 AAAAAAGTTGCCACCGACACGTGTGGGCTTTG
1 --AAAAGGTGCCACTG--ACTTGTGGGCTTTG
* * * * *
13056 AAAAGAGTTACTAATGGCTTATGGGCTTTG
1 AAAAG-G-TGCCACTGACTTGTGGGCTTTG
* *
13086 AAAAGGGTGTCACTAACTTGTGGGCTTTG
1 AAAA-GGTGCCACTGACTTGTGGGCTTTG
13115 AAAAGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
*
13143 -AAAGGATGCCACTAACTTGTGGGCTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
*
13171 AAAAAGTGCCA--GACTTGTGGGC-TTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* * *
13196 AAAAAGTGCCACTAACTTCTGGGC-TTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
**
13223 AAAAGGTGCCACTGACTCATGGGCTTT-
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
**
13250 AAAAGGGTGCCACTGACTCATGGGCTTTG
1 AAAA-GGTGCCACTGACTTGTGGGCTTTG
*
13279 AAATGAGTGCCACTGACTTACGTGGGCTTTG
1 AAAAG-GTGCCACTGACTT--GTGGGCTTTG
*
13310 AAAAGAGTGCCACTAACTTGCGTGGGCTTT-
1 AAAAG-GTGCCACTGACTT--GTGGGCTTTG
13340 AAAAGGGTGCCACTGACTTGCGTGGGCTTTG
1 AAAA-GGTGCCACTGACTT--GTGGGCTTTG
13371 -AAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
* *
13399 -AAAGAGTGCCACTGGCTCGTGGGC-TTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
13426 AAAAGGTGCCACTGACTTGCGTGGGCTTT-
1 AAAAGGTGCCACTGACTT--GTGGGCTTTG
* *
13455 AAAAGGGTGCCACTAACTTGCGTGAGCTTTG
1 AAAA-GGTGCCACTGACTT--GTGGGCTTTG
* *
13486 AAATGATGCCACTGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* *
13514 -AAAGAGTGCCACTGACTCGTAGGCTTTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
* * * *
13542 AAAAGAGTGCCACCGACCTATGGTCTTTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
* *
13571 AAATGAGTTGCCACCGACTTGTGTGGGCTTTG
1 AAA--AGGTGCCACTGAC-T-TGTGGGCTTTG
13603 -AAAGGAATGCCACTGACTTGTGTAGGCTTTG
1 AAAAGG--TGCCACTGACTTGTG--GGCTTTG
* *
13634 -AAAGGATGCCACTAACTTGTGTGCTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
*
13662 -AAAGAGTGCCACTGACTCGTGGGC-TTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
* *
13689 AAATGGTGCCACTGACTCGTGGGC-TTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
*
13716 AAATGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* *
13744 -AAAGAGTGCCACTAACTTATGGGCTTTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
* * *
13772 AAAAGAGTGCCACTAAATTATGGGCTTTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
*
13801 AAAAGAGTGCCACTGACTTGTGGGCTTCG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
* *
13830 AAAGGGTGCCACTGACTTGTGGGCTCTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* * *
13858 AAAGGGTGCCATTGACTTATGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
*
13886 AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
*
13914 -AAAGAGTGCCACTAACTTGTGGGC-TTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
13941 AAAAGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
13969 -AAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
13997 -AAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
*
14025 AAAAGAGTGCCACTAACTTGTGGGCTTTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
*
14054 AAAAGGGTGTCACTGACTTGTGGGCTTTG
1 AAAA-GGTGCCACTGACTTGTGGGCTTTG
* * *
14083 AAAGGGTGCCACTAACTTGTAGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* * *
14111 AAAAGACTACCACTGACTTGTGGACTTTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
14140 AAAAGG
1 AAAAGG
14146 GTGAACATTC
Statistics
Matches: 969, Mismatches: 104, Indels: 98
0.83 0.09 0.08
Matches are distributed among these distances:
25 14 0.01
26 10 0.01
27 137 0.14
28 362 0.37
29 217 0.22
30 127 0.13
31 66 0.07
32 30 0.03
34 6 0.01
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (28 bp):
AAAAGGTGCCACTGACTTGTGGGCTTTG
Found at i:13465 original size:57 final size:56
Alignment explanation
Indices: 13077--14148 Score: 1069
Period size: 57 Copynumber: 18.8 Consensus size: 56
13067 TAATGGCTTA
* *
13077 TGGGCTTTGAAAAGGGTGTCACTAACTTGTGGGCTTTGAAAA-GGTGCCACTGACTTG
1 TGGGCTTTGAAAA-GGTGCCACTGACTTGTGGGCTTT-AAAAGGGTGCCACTGACTTG
* *
13134 TGGGCTTTG-AAAGGATGCCACTAACTTGTGGGCTTTGAAAA-AGTGCCA--GACTTG
1 TGGGCTTTGAAAAGG-TGCCACTGACTTGTGGGCTTT-AAAAGGGTGCCACTGACTTG
* * * * **
13188 TGGGC-TTGAAAAAGTGCCACTAACTTCTGGGCTTGAAAA-GGTGCCACTGACTCA
1 TGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTG
** * *
13242 TGGGCTTT-AAAAGGGTGCCACTGACTCATGGGCTTTGAAATGAGTGCCACTGACTTACG
1 TGGGCTTTGAAAA-GGTGCCACTGACTTGTGGGCTTT-AAAAGGGTGCCACTGACTT--G
*
13301 TGGGCTTTGAAAAGAGTGCCACTAACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCG
1 TGGGCTTTGAAAAG-GTGCCACTGACTT--GTGGGCTTTAAAAGGGTGCCACTGACTT--G
* * * *
13362 TGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGGCTCG
1 TGGGCTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTG
*
13418 TGGGC-TTGAAAAGGTGCCACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTAACTTGCG
1 TGGGCTTTGAAAAGGTGCCACTGACTT--GTGGGCTTTAAAAGGGTGCCACTGACTT--G
* * * * * *
13477 TGAGCTTTGAAATGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCG
1 TGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTG
* * * * * * * *
13533 TAGGCTTTGAAAAGAGTGCCACCGACCTATGGTCTTTGAAATGAGTTGCCACCGACTTGTG
1 TGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTT-AAAAG-GGTGCCACTGAC-T-TG
* * *
13594 TGGGCTTTG-AAAGGAATGCCACTGACTTGTGTAGGCTTTGAAAGGATGCCACTAACTTG
1 TGGGCTTTGAAAAGG--TGCCACTGACTTGTG--GGCTTTAAAAGGGTGCCACTGACTTG
* * * * *
13653 TGTGCTTTG-AAAGAGTGCCACTGACTCGTGGGC-TTGAAATGGTGCCACTGACTCG
1 TGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTG
* * * * *
13708 TGGGC-TTGAAATGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTAACTTA
1 TGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTG
* * * *
13763 TGGGCTTTGAAAAGAGTGCCACTAAATTATGGGCTTTGAAAAGAGTGCCACTGACTTG
1 TGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTT-AAAAGGGTGCCACTGACTTG
* * * * * *
13821 TGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCATTGACTTA
1 TGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTG
* * * *
13877 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTAACTTG
1 TGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTG
* *
13933 TGGGC-TTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG
1 TGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTG
* *
13988 TGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTG
1 TGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTT-AAAAGGGTGCCACTGACTTG
* * *
14045 TGGGCTTTGAAAAGGGTGTCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTG
1 TGGGCTTTGAAAA-GGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTG
* * * *
14102 TAGGCTTTGAAAAGACTACCACTGACTTGTGGACTTTGAAAAGGGTG
1 TGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTT-AAAAGGGTG
14149 AACATTCTAG
Statistics
Matches: 858, Mismatches: 114, Indels: 85
0.81 0.11 0.08
Matches are distributed among these distances:
52 10 0.01
53 22 0.03
54 49 0.06
55 141 0.16
56 167 0.19
57 173 0.20
58 126 0.15
59 40 0.05
60 56 0.07
61 58 0.07
62 11 0.01
63 5 0.01
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.28
Consensus pattern (56 bp):
TGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTG
Found at i:17676 original size:16 final size:17
Alignment explanation
Indices: 17645--17677 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
17635 TTAAAGGACG
17645 ACCAAGCACCGGCGGGT
1 ACCAAGCACCGGCGGGT
*
17662 ACCAA-CACTGGCGGGT
1 ACCAAGCACCGGCGGGT
17678 TTGACAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.24, C:0.33, G:0.33, T:0.09
Consensus pattern (17 bp):
ACCAAGCACCGGCGGGT
Found at i:29440 original size:20 final size:19
Alignment explanation
Indices: 29407--29481 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
29397 AAAAAGACAT
*
29407 AATGTATTGATACATTGAA
1 AATGTATCGATACATTGAA
* *
29426 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
29447 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
29467 AATGTATCGATACAT
1 AATGTATCGATACAT
29482 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:29464 original size:40 final size:39
Alignment explanation
Indices: 29404--29481 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
29394 GGTAAAAAGA
* *
29404 CATAATGTATTGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
29443 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
29482 CTGGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:30080 original size:12 final size:12
Alignment explanation
Indices: 30063--30095 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
30053 TGGGCAGCTG
30063 AGAAAGAAAAAA
1 AGAAAGAAAAAA
30075 AGAAAG-AAAAA
1 AGAAAGAAAAAA
30086 A-AAAGAAAAA
1 AGAAAGAAAAA
30096 TGTAAGCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.20
11 10 0.50
12 6 0.30
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAAA
Found at i:33638 original size:48 final size:48
Alignment explanation
Indices: 33548--33640 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
33538 TATATAGTCG
* * *
33548 AAATGTATCGATACAAATTGCATTGTATCGATATAATCTGGAAAACCT
1 AAATGTATCGATACAAATTGCAATGTATCGATACAATATGGAAAACCT
** *
33596 AAATGTATCGATACATTTTGCAATGTATCGATACATTATGGAAAA
1 AAATGTATCGATACAAATTGCAATGTATCGATACAATATGGAAAA
33641 ATCTAGAAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (48 bp):
AAATGTATCGATACAAATTGCAATGTATCGATACAATATGGAAAACCT
Found at i:44080 original size:13 final size:13
Alignment explanation
Indices: 44062--44087 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44052 TACAGCAAGT
44062 ATGTATCGATACA
1 ATGTATCGATACA
44075 ATGTATCGATACA
1 ATGTATCGATACA
44088 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:46340 original size:21 final size:21
Alignment explanation
Indices: 46307--46351 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
46297 TTGCAAGTTG
*
46307 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
46329 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
46349 AAA
1 AAA
46352 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:48172 original size:15 final size:15
Alignment explanation
Indices: 48152--48182 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
48142 TAAAAATGTC
*
48152 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
48167 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
48182 C
1 C
48183 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:52863 original size:33 final size:33
Alignment explanation
Indices: 52821--52890 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
52811 GGCAGTAGCT
52821 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
52854 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
52887 TACA
1 TACA
52891 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:52864 original size:13 final size:13
Alignment explanation
Indices: 52846--52870 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52836 CAAAAAAATA
52846 TGTATCGATACAT
1 TGTATCGATACAT
52859 TGTATCGATACA
1 TGTATCGATACA
52871 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:53850 original size:13 final size:13
Alignment explanation
Indices: 53832--53857 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53822 ACATTTTTCT
53832 TTGTATCGATACA
1 TTGTATCGATACA
53845 TTGTATCGATACA
1 TTGTATCGATACA
53858 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:57946 original size:20 final size:20
Alignment explanation
Indices: 57921--57958 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
57911 GTAAAAAAAT
57921 AGAATGTATCGATACATTAC
1 AGAATGTATCGATACATTAC
57941 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
57959 CATGCATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTAC
Found at i:59746 original size:21 final size:22
Alignment explanation
Indices: 59722--59780 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 22
59712 CAAGTTTTTG
59722 TTTTCCTTTATTAATTCA-TTA
1 TTTTCCTTTATTAATTCATTTA
*
59743 TTTT-CTTCT-TGCAATTCATTTA
1 TTTTCCTT-TAT-TAATTCATTTA
*
59765 TTTTCTTTTA-TAATTC
1 TTTTCCTTTATTAATTC
59781 GGTCATTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
20 4 0.13
21 16 0.53
22 8 0.27
23 2 0.07
ACGTcount: A:0.20, C:0.15, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTCCTTTATTAATTCATTTA
Found at i:62111 original size:13 final size:13
Alignment explanation
Indices: 62093--62117 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62083 ATTTTGCTAA
62093 GTATCGATACATT
1 GTATCGATACATT
62106 GTATCGATACAT
1 GTATCGATACAT
62118 AGCATTGGCA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:64086 original size:13 final size:13
Alignment explanation
Indices: 64068--64093 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
64058 TACACCAAGT
64068 ATGTATCGATACA
1 ATGTATCGATACA
64081 ATGTATCGATACA
1 ATGTATCGATACA
64094 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:64112 original size:34 final size:32
Alignment explanation
Indices: 64050--64114 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
64040 TAGCCAAACT
**
64050 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
64082 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
64115 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:65933 original size:15 final size:14
Alignment explanation
Indices: 65915--65950 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
65905 TTTATATTAT
65915 AAAAAAAGAAAAAGG
1 AAAAAAAGAAAAA-G
65930 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
65944 AAAAAAA
1 AAAAAAA
65951 TTTATGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:66686 original size:36 final size:34
Alignment explanation
Indices: 66603--66700 Score: 116
Period size: 36 Copynumber: 3.0 Consensus size: 34
66593 CCTTACAACA
*
66603 CTATC-TTTC-AAGGCTAAGATAGAA-AC-CTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACTCTCTCC
**
66633 CTATCTTTTCACGGGCTAAGATAGAACCTCTCTCC
1 CTATCTTTTCAAAGGCTAAGATAGAA-CTCTCTCC
66668 CTATCTTTTTCAAAGGCTAAGATAGAACT-TCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACTCTCTC
66701 AATCACTTCG
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
30 5 0.09
31 4 0.07
32 13 0.23
34 5 0.09
35 11 0.19
36 19 0.33
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (34 bp):
CTATCTTTTCAAAGGCTAAGATAGAACTCTCTCC
Found at i:67582 original size:13 final size:13
Alignment explanation
Indices: 67564--67589 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
67554 CTATTTATGA
67564 TGTATCGATACAC
1 TGTATCGATACAC
67577 TGTATCGATACAC
1 TGTATCGATACAC
67590 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:67694 original size:22 final size:22
Alignment explanation
Indices: 67641--67694 Score: 101
Period size: 21 Copynumber: 2.5 Consensus size: 22
67631 TTTAACACGG
67641 GAACAGTGATGTATCGATACAT
1 GAACAGTGATGTATCGATACAT
67663 GAA-AGTGATGTATCGATACAT
1 GAACAGTGATGTATCGATACAT
67684 GAACAGTGATG
1 GAACAGTGATG
67695 AATAGTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (22 bp):
GAACAGTGATGTATCGATACAT
Found at i:67792 original size:53 final size:53
Alignment explanation
Indices: 67726--67862 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
67716 CTACTTCCAA
*
67726 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCACTGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
*
67779 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
67832 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
67863 TATGCAATTT
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
53 68 0.84
54 13 0.16
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:67895 original size:20 final size:20
Alignment explanation
Indices: 67832--67902 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
67822 GCCAATGTCC
**
67832 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
67852 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
67872 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
67892 TGTATCGATAC
1 TGTATCGATAC
67903 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:67968 original size:21 final size:21
Alignment explanation
Indices: 67942--67982 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
67932 GTCAACCTTG
67942 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
67963 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
67983 TTTTACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:68598 original size:13 final size:13
Alignment explanation
Indices: 68580--68608 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
68570 GATATTATTC
68580 ACAATGTATCGAT
1 ACAATGTATCGAT
68593 ACAATGTATCGAT
1 ACAATGTATCGAT
68606 ACA
1 ACA
68609 TGATTAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
ACAATGTATCGAT
Found at i:68637 original size:32 final size:32
Alignment explanation
Indices: 68596--68686 Score: 164
Period size: 32 Copynumber: 2.8 Consensus size: 32
68586 TATCGATACA
68596 ATGTATCGATACATGATTAGTGATGAACAGTG
1 ATGTATCGATACATGATTAGTGATGAACAGTG
68628 ATGTATCGATACATGATTAGTGATGAACAGTG
1 ATGTATCGATACATGATTAGTGATGAACAGTG
**
68660 ATGTATCGATACATGAACAGTGATGAA
1 ATGTATCGATACATGATTAGTGATGAA
68687 TAGGGATGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (32 bp):
ATGTATCGATACATGATTAGTGATGAACAGTG
Found at i:69595 original size:87 final size:87
Alignment explanation
Indices: 69492--69675 Score: 332
Period size: 87 Copynumber: 2.1 Consensus size: 87
69482 ATAACCATTG
* *
69492 TCTCCCCCTTACTAAAATATCTCCCCCAAAATTATAATTTTTTTCCCCCTTAATACGTTCTCACC
1 TCTCCCCCTTACTAAAATATCTCCCCCAAAATTATAAATTTTCTCCCCCTTAATACGTTCTCACC
69557 CTTAAACCAATACACAAAAATC
66 CTTAAACCAATACACAAAAATC
* *
69579 TCTCCCCCTTACTAAAATATCTCTCCCAAAATTATAAATTTTCTCCCCTTTAATACGTTCTCACC
1 TCTCCCCCTTACTAAAATATCTCCCCCAAAATTATAAATTTTCTCCCCCTTAATACGTTCTCACC
69644 CTTAAACCAATACACAAAAATC
66 CTTAAACCAATACACAAAAATC
69666 TCTCCCCCTT
1 TCTCCCCCTT
69676 TATGTTATCA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 93 1.00
ACGTcount: A:0.32, C:0.34, G:0.01, T:0.33
Consensus pattern (87 bp):
TCTCCCCCTTACTAAAATATCTCCCCCAAAATTATAAATTTTCTCCCCCTTAATACGTTCTCACC
CTTAAACCAATACACAAAAATC
Found at i:72064 original size:21 final size:21
Alignment explanation
Indices: 72023--72081 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
72013 CACTTGCAAC
* *
72023 TCATTTCTTTTCTCCTT-TAAT
1 TCATTTATTTTCT-TTTCTAAT
72044 TCATTTATTTTCTTTTCTAAT
1 TCATTTATTTTCTTTTCTAAT
* *
72065 TCACTTAATTTCTTTTC
1 TCATTTATTTTCTTTTC
72082 AAGAATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 2 0.06
21 31 0.94
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.63
Consensus pattern (21 bp):
TCATTTATTTTCTTTTCTAAT
Found at i:74151 original size:32 final size:32
Alignment explanation
Indices: 74060--74158 Score: 153
Period size: 32 Copynumber: 3.1 Consensus size: 32
74050 ACTATTCACA
* *
74060 ATGTATCGATACATGATTAGTGATGAACAGTA
1 ATGTATCGATACATGATTAGTGATGAATAGTG
74092 ATGTATCGATACATGATTAGTGATGAATAGTG
1 ATGTATCGATACATGATTAGTGATGAATAGTG
** *
74124 ATGTATCGATACATGAACAGTGATGAATAATG
1 ATGTATCGATACATGATTAGTGATGAATAGTG
74156 ATG
1 ATG
74159 AGCAGTGAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.31
Consensus pattern (32 bp):
ATGTATCGATACATGATTAGTGATGAATAGTG
Found at i:74212 original size:13 final size:13
Alignment explanation
Indices: 74194--74218 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74184 TGTCAATTTT
74194 ATGTATCGATACA
1 ATGTATCGATACA
74207 ATGTATCGATAC
1 ATGTATCGATAC
74219 TAAGCAAAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:74669 original size:16 final size:16
Alignment explanation
Indices: 74648--74690 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
74638 TTATTTTTAA
74648 ATAAATTTTATTAATT
1 ATAAATTTTATTAATT
74664 ATAAATTTCT-TTAATT
1 ATAAATTT-TATTAATT
74680 A-AAACTTTTAT
1 ATAAA-TTTTAT
74691 AAATATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 4 0.17
16 19 0.79
17 1 0.04
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAAATTTTATTAATT
Found at i:75440 original size:2 final size:2
Alignment explanation
Indices: 75433--75467 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
75423 GTTTTCGTTC
75433 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
75468 AATGATCTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:79353 original size:18 final size:18
Alignment explanation
Indices: 79331--79364 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
79321 CATTTGCTTT
79331 TTTTTTC-TTTTCTTTTA
1 TTTTTTCTTTTTCTTTTA
79348 TTTTTTCTTTTTCTTTT
1 TTTTTTCTTTTTCTTTT
79365 TCAAAAGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTTCTTTTTCTTTTA
Found at i:88952 original size:15 final size:16
Alignment explanation
Indices: 88932--88964 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
88922 AGCGCATAGA
88932 CATTAGACATCAT-TT
1 CATTAGACATCATGTT
*
88947 CATTAGAGATCATGTT
1 CATTAGACATCATGTT
88963 CA
1 CA
88965 AAAAGGAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (16 bp):
CATTAGACATCATGTT
Found at i:94677 original size:13 final size:13
Alignment explanation
Indices: 94659--94684 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
94649 CAATTTTTTG
94659 TGTATCGATACAT
1 TGTATCGATACAT
94672 TGTATCGATACAT
1 TGTATCGATACAT
94685 ATTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:94700 original size:32 final size:33
Alignment explanation
Indices: 94639--94702 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
94629 TACAAGCTAA
*
94639 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTATTTGTGTATCGATACAT
94672 TGTATCGATAC-A-TATTTGCTGTATCGATACA
1 TGTATCGATACAATTATTTG-TGTATCGATACA
94703 AGTTTGGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 5 0.17
32 13 0.45
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATTATTTGTGTATCGATACAT
Found at i:97251 original size:13 final size:13
Alignment explanation
Indices: 97233--97258 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
97223 ATAATCACCC
97233 TGTATCGATACAA
1 TGTATCGATACAA
97246 TGTATCGATACAA
1 TGTATCGATACAA
97259 AGAAAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:99356 original size:15 final size:15
Alignment explanation
Indices: 99336--99366 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
99326 ATTTCGTTTG
*
99336 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
99351 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
99366 G
1 G
99367 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Done.