Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1009
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: 25281
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1442 original size:21 final size:21
Alignment explanation
Indices: 1418--1472 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
1408 AGTTTTGTCC
1418 AAATGTATCGATACATTGTTT
1 AAATGTATCGATACATTGTTT
1439 AAATGTATCGATACATTGTTT
1 AAATGTATCGATACATTGTTT
*
1460 GAATGTATCGATA
1 AAATGTATCGATA
1473 TAAGGTCCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (21 bp):
AAATGTATCGATACATTGTTT
Found at i:1530 original size:13 final size:13
Alignment explanation
Indices: 1512--1568 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1502 TTCAACGATT
1512 TGTATCGATACAA
1 TGTATCGATACAA
1525 TGTATCGATACATAA
1 TGTATCGATAC--AA
1540 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1557 TGTATCGATACA
1 TGTATCGATACA
1569 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1549 original size:19 final size:18
Alignment explanation
Indices: 1525--1587 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1515 ATCGATACAA
1525 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
1544 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
1557 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
1576 TGTATCGATACA
1 TGTATCGATACA
1588 ACGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:1552 original size:32 final size:32
Alignment explanation
Indices: 1511--1595 Score: 152
Period size: 32 Copynumber: 2.7 Consensus size: 32
1501 TTTCAACGAT
1511 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
1543 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
1575 TTGTATCGATACAACGTATCG
1 TTGTATCGATACAATGTATCG
1596 CTACGAAACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:1637 original size:13 final size:13
Alignment explanation
Indices: 1619--1643 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1609 GCCAAGAAAA
1619 TGTATCGATACAT
1 TGTATCGATACAT
1632 TGTATCGATACA
1 TGTATCGATACA
1644 CTGATCTTTG
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:3857 original size:24 final size:26
Alignment explanation
Indices: 3830--3883 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
3820 TCAAAATTTT
3830 ATTCAT-C-GGGGACACTCCAACCCC
1 ATTCATCCAGGGGACACTCCAACCCC
*
3854 ATTCTTCCGAGGGGACACTCCAACCCC
1 ATTCATCC-AGGGGACACTCCAACCCC
3881 ATT
1 ATT
3884 TTCAACCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 1 0.04
27 20 0.77
ACGTcount: A:0.24, C:0.39, G:0.17, T:0.20
Consensus pattern (26 bp):
ATTCATCCAGGGGACACTCCAACCCC
Found at i:7659 original size:21 final size:21
Alignment explanation
Indices: 7635--7690 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
7625 AGAGTGGTTT
7635 TGTATCGATACATTTCAAG-CA
1 TGTATCGATACATTTC-AGTCA
*
7656 TGTATCGATACA-TTCAGTTA
1 TGTATCGATACATTTCAGTCA
7676 TGTATCGATACATTT
1 TGTATCGATACATTT
7691 ACTATTTGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 2 0.06
20 16 0.50
21 14 0.44
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTTCAGTCA
Found at i:7747 original size:49 final size:49
Alignment explanation
Indices: 7675--7773 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
7665 ACATTCAGTT
7675 ATGTATCGATACATTTACTATTTGTATTGATAGAAATTGTAAAAATTTG
1 ATGTATCGATACATTTACTATTTGTATTGATAGAAATTGTAAAAATTTG
7724 ATGTATCGATACATTTACTATTTGTATTGATAGAAATTGTAAAAATTTG
1 ATGTATCGATACATTTACTATTTGTATTGATAGAAATTGTAAAAATTTG
7773 A
1 A
7774 AATTTTTAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.42
Consensus pattern (49 bp):
ATGTATCGATACATTTACTATTTGTATTGATAGAAATTGTAAAAATTTG
Found at i:8371 original size:52 final size:52
Alignment explanation
Indices: 8306--8880 Score: 296
Period size: 52 Copynumber: 10.8 Consensus size: 52
8296 ATGAGAAGGG
* * * * *
8306 TGCCAATGTGTTGATTCAAGGCCAATGACATTGGACTTGAAGATGAGAAAAA
1 TGCCAATGTGCTGATTCAAGGCCAGTGACATTAGACTTAAAAATGAGAAAAA
* ** * ***
8358 TGCCAATGTGTTGATTCAAGGCCAGCAACATTAGACTTAAAAATGACAAGGG
1 TGCCAATGTGCTGATTCAAGGCCAGTGACATTAGACTTAAAAATGAGAAAAA
* ** * * * **
8410 TGCTAATGTGCTGATTCAAGGCCAGCAACATTGGGCTTAAAAATGATAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGTGACATTAGACTTAAAAATGAGAAAAA
* ** *
8462 TGCCTATGTGCTGATTCAAGGCCAGCAACATTAGACTTAAAAA-GAGATAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGTGACATTAGACTTAAAAATGAGA-AAA-A
* ** * *
8515 TGCCGATATGT-C-GATTCAAGGCCAATGATGTCAGACTTAAAGATGATAAGGGTAAGAAGA
1 TGCC-A-ATGTGCTGATTCAAGGCCAGTGACATTAGACTTAAA-A--AT--GAG-AA-AA-A
* * * * *
8575 GTGCCAATGTGCTGATTCATGGCTAGTGACATTAGACTTGAAGATGAAAAAAA
1 -TGCCAATGTGCTGATTCAAGGCCAGTGACATTAGACTTAAAAATGAGAAAAA
* * * ** * * *
8628 TGCTAATGTGCTGATTGAAGGCCTGCAACATTGGACTTAAAAATTAGAAGAA
1 TGCCAATGTGCTGATTCAAGGCCAGTGACATTAGACTTAAAAATGAGAAAAA
* * * * *** * *
8680 TGCCAATCTGCTGATTCAAGGCTAGTGACATTGGGCTTAGGGATGATAAAGA
1 TGCCAATGTGCTGATTCAAGGCCAGTGACATTAGACTTAAAAATGAGAAAAA
* * * * * * * * * ***
8732 TGCCAATATACTGATCCAAGGCTAGCGATATCAGACTTAAAGATGACAACCG
1 TGCCAATGTGCTGATTCAAGGCCAGTGACATTAGACTTAAAAATGAGAAAAA
* ** * * * * *
8784 TGTCAAAAATGCTGATTCAAGGCTAGTGATACTGGACTTAAGAAA-GA-AAAAGG
1 TG-CCAATGTGCTGATTCAAGGCCAGTGACATTAGACTTAA-AAATGAGAAAA-A
* * *
8837 TGCCAATGTGCTGATTCAAGGCCAGCGATATTAGGCTTAGAAAA
1 TGCCAATGTGCTGATTCAAGGCCAGTGACATTAGACTTA-AAAA
8881 AGATGGTTTG
Statistics
Matches: 402, Mismatches: 102, Indels: 38
0.74 0.19 0.07
Matches are distributed among these distances:
51 3 0.01
52 279 0.69
53 65 0.16
54 6 0.01
55 6 0.01
56 2 0.00
58 2 0.00
59 7 0.02
60 6 0.01
61 26 0.06
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (52 bp):
TGCCAATGTGCTGATTCAAGGCCAGTGACATTAGACTTAAAAATGAGAAAAA
Found at i:8770 original size:270 final size:270
Alignment explanation
Indices: 8277--8772 Score: 659
Period size: 270 Copynumber: 1.8 Consensus size: 270
8267 CTACGATAGT
* * * *
8277 AGACTTAAAGATAATAAAGATGAGAAGGGTGCCAATGTGTTGATTCAAGGCCAATGACATTGGAC
1 AGACTTAAAGATAATAAAGATAAGAAGAGTGCCAATGTGCTGATTCAAGGCCAATGACATTAGAC
* *
8342 TTGAAGATGAGAAAAATGCCAATGTGTTGATTCAAGGCCAGCAACATTAGACTTAAAAATGACAA
66 TTGAAGATGAAAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTAGACTTAAAAATGACAA
** * * * * * *
8407 GGGTGCTAATGTGCTGATTCAAGGCCAGCAACATTGGGCTTAAAAATGATAAAGGTGCCTATGTG
131 GAATGCCAATCTGCTGATTCAAGGCCAGCAACATTGGGCTTAAAAATGATAAAGATGCCAATATA
* *
8472 CTGATTCAAGGCCAGCAACATTAGACTTAAAAAGAGATAAAGGTGCCGATATGTCGATTCAAGGC
196 CTGATCCAAGGCCAGCAACATCAGACTTAAAAAGAGATAAAGGTGCCGATATGTCGATTCAAGGC
8537 CAATGATGTC
261 CAATGATGTC
* * * * * *
8547 AGACTTAAAGATGATAAGGGTAAGAAGAGTGCCAATGTGCTGATTCATGGCTAGTGACATTAGAC
1 AGACTTAAAGATAATAAAGATAAGAAGAGTGCCAATGTGCTGATTCAAGGCCAATGACATTAGAC
* * * * * *
8612 TTGAAGATGAAAAAAATGCTAATGTGCTGATTGAAGGCCTGCAACATTGGACTTAAAAATTAGAA
66 TTGAAGATGAAAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTAGACTTAAAAATGACAA
* ** ***
8677 GAATGCCAATCTGCTGATTCAAGGCTAGTGACATTGGGCTTAGGGATGATAAAGATGCCAATATA
131 GAATGCCAATCTGCTGATTCAAGGCCAGCAACATTGGGCTTAAAAATGATAAAGATGCCAATATA
* * *
8742 CTGATCCAAGGCTAGCGATATCAGACTTAAA
196 CTGATCCAAGGCCAGCAACATCAGACTTAAA
8773 GATGACAACC
Statistics
Matches: 189, Mismatches: 37, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
270 189 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (270 bp):
AGACTTAAAGATAATAAAGATAAGAAGAGTGCCAATGTGCTGATTCAAGGCCAATGACATTAGAC
TTGAAGATGAAAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTAGACTTAAAAATGACAA
GAATGCCAATCTGCTGATTCAAGGCCAGCAACATTGGGCTTAAAAATGATAAAGATGCCAATATA
CTGATCCAAGGCCAGCAACATCAGACTTAAAAAGAGATAAAGGTGCCGATATGTCGATTCAAGGC
CAATGATGTC
Found at i:8824 original size:270 final size:269
Alignment explanation
Indices: 8277--8860 Score: 616
Period size: 270 Copynumber: 2.2 Consensus size: 269
8267 CTACGATAGT
* * * *
8277 AGACTTAAAGATAATAAAGATGAGAAGGGTGCCAATGTGTTGATTCAAGGCCAATGACATTGGAC
1 AGACTTAAAGATAATAAAGATAAGAAGAGTGCCAATGTGCTGATTCAAGGCCAATGACATTAGAC
* *
8342 TTGAAGATGAGAAAAATGCCAATGTGTTGATTCAAGGCCAGCAACATTAGACTTAAAAATGACAA
66 TTGAAGATGAAAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTAGACTTAAAAATGACAA
** * * * * * *
8407 GGGTGCTAATGTGCTGATTCAAGGCCAGCAACATTGGGCTTAAAAATGATAAAGGTGCCTATGTG
131 GAATGCCAATCTGCTGATTCAAGGCCAGCAACATTGGGCTTAAAAATGATAAAGATGCCAATATA
* * * * ** *
8472 CTGATTCAAGGCCAGCAACATTAGACTTAAAAAGAGATAAAGGTGCCGATATGTCGATTCAAGGC
196 CTGATCCAAGGCCAGCAACATCAGACTT-AAAAGAGACAAACGTGCAAAAATGTCGATTCAAGGC
*
8537 CAATGATGTC
260 CAATGATCTC
* * * * * *
8547 AGACTTAAAGATGATAAGGGTAAGAAGAGTGCCAATGTGCTGATTCATGGCTAGTGACATTAGAC
1 AGACTTAAAGATAATAAAGATAAGAAGAGTGCCAATGTGCTGATTCAAGGCCAATGACATTAGAC
* * * * * *
8612 TTGAAGATGAAAAAAATGCTAATGTGCTGATTGAAGGCCTGCAACATTGGACTTAAAAATTAGAA
66 TTGAAGATGAAAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTAGACTTAAAAATGACAA
* ** ***
8677 GAATGCCAATCTGCTGATTCAAGGCTAGTGACATTGGGCTTAGGGATGATAAAGATGCCAATATA
131 GAATGCCAATCTGCTGATTCAAGGCCAGCAACATTGGGCTTAAAAATGATAAAGATGCCAATATA
* * * *
8742 CTGATCCAAGGCTAGCGATATCAGACTT-AAAGATGACAACCGTGTCAAAAATG-CTGATTCAAG
196 CTGATCCAAGGCCAGCAACATCAGACTTAAAAGA-GACAAACGTG-CAAAAATGTC-GATTCAAG
* *
8805 GCTAGTGATACT-
258 GCCAATGAT-CTC
*
8817 GGACTT-AAG-----AAAGA-AA-AAG-GTGCCAATGTGCTGATTCAAGGCCA
1 AGACTTAAAGATAATAAAGATAAGAAGAGTGCCAATGTGCTGATTCAAGGCCA
8861 GCGATATTAG
Statistics
Matches: 259, Mismatches: 51, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
261 23 0.09
262 3 0.01
263 2 0.01
264 3 0.01
268 5 0.02
269 11 0.04
270 211 0.81
271 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (269 bp):
AGACTTAAAGATAATAAAGATAAGAAGAGTGCCAATGTGCTGATTCAAGGCCAATGACATTAGAC
TTGAAGATGAAAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTAGACTTAAAAATGACAA
GAATGCCAATCTGCTGATTCAAGGCCAGCAACATTGGGCTTAAAAATGATAAAGATGCCAATATA
CTGATCCAAGGCCAGCAACATCAGACTTAAAAGAGACAAACGTGCAAAAATGTCGATTCAAGGCC
AATGATCTC
Found at i:9030 original size:33 final size:33
Alignment explanation
Indices: 8943--9097 Score: 156
Period size: 33 Copynumber: 4.8 Consensus size: 33
8933 TAGAAGAAGA
* *
8943 TGCCACCAACTTGTGTGGGCTATT-G-AGAGGGT
1 TGCCACCGACTTGTGTGGGCT-TTAGAAGGGGGT
* * ** *
8975 TGCCATCGACTCGTGTATGCTTTTGAAGGGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGGGT
* ** *
9008 TGTCACTAACTTGTGTGGGCTTTAGAAAGGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGGGT
* *
9041 TACCACCGACTTGTGTGGACTTTAGAA--GGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGGGT
9072 TGCCACCGACTTGTGTGGGCTTTAGA
1 TGCCACCGACTTGTGTGGGCTTTAGA
9098 GAAGGGTGCC
Statistics
Matches: 99, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
31 30 0.30
32 17 0.17
33 52 0.53
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.31
Consensus pattern (33 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAGGGGGT
Found at i:9138 original size:32 final size:32
Alignment explanation
Indices: 9102--9453 Score: 156
Period size: 33 Copynumber: 11.0 Consensus size: 32
9092 TTTAGAGAAG
* * *
9102 GGTGCCATAGTGTTGTGGACTTTGAAGAAAAA
1 GGTGCCATAGAGTTATGGACTTTAAAGAAAAA
*
9134 GGTGCCATGGAGTTATGGA-TTTAAAAGGAAAAA
1 GGTGCCATAGAGTTATGGACTTT-AAA-GAAAAA
* **
9167 GGTGCCGTAGAGTTATGGACATCAAAAGAAAAA
1 GGTGCCATAGAGTTATGGAC-TTTAAAGAAAAA
* * * *
9200 GAGTGCCATGGAGTTGTAGAC-TT----AAAAG
1 G-GTGCCATAGAGTTATGGACTTTAAAGAAAAA
** * ** * *
9228 GGCACCACAGAGTCGTAGACTTT---G-AAAG
1 GGTGCCATAGAGTTATGGACTTTAAAGAAAAA
** *
9256 GGTGCCACGGAGTTGTGGACTTTAAA-AAAAA
1 GGTGCCATAGAGTTATGGACTTTAAAGAAAAA
* *
9287 GGTGCCATGGAGTTATGGACTTTGAAGAAAAA
1 GGTGCCATAGAGTTATGGACTTTAAAGAAAAA
* ** *
9319 TGTGCCACGGAGTTGTGGACTTTAAA-AAGGAAA
1 GGTGCCATAGAGTTATGGACTTTAAAGAA--AAA
** *
9352 GAGT-CCACGGAGTTATGGACTTCAAAGGGAAGAAA
1 G-GTGCCATAGAGTTATGGACTTTAAA--GAA-AAA
* * **
9387 GGTGCCA-CGAAGTTGTGGACTTTAAAAGGGAAA
1 GGTGCCATAG-AGTTATGGACTTT-AAAGAAAAA
* * *
9420 TGTGCCATAGAGTTGTGGACTTAAAAAGAAAAA
1 GGTGCCATAGAGTTATGGACTT-TAAAGAAAAA
9453 G
1 G
9454 AGTTATGGAC
Statistics
Matches: 250, Mismatches: 47, Indels: 45
0.73 0.14 0.13
Matches are distributed among these distances:
27 14 0.06
28 29 0.12
31 31 0.12
32 45 0.18
33 81 0.32
34 25 0.10
35 20 0.08
36 5 0.02
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (32 bp):
GGTGCCATAGAGTTATGGACTTTAAAGAAAAA
Found at i:9227 original size:27 final size:28
Alignment explanation
Indices: 9196--9345 Score: 95
Period size: 32 Copynumber: 5.1 Consensus size: 28
9186 CATCAAAAGA
*
9196 AAAAGAGTGCCATGGAGTTGTAGAC-TT
1 AAAAGAGTGCCACGGAGTTGTAGACTTT
* ** * *
9223 AAAAGGGCACCACAGAGTCGTAGACTTT
1 AAAAGAGTGCCACGGAGTTGTAGACTTT
* * *
9251 GAAAGGGTGCCACGGAGTTGTGGACTTT
1 AAAAGAGTGCCACGGAGTTGTAGACTTT
* * * *
9279 AAAAAAAAGGTGCCATGGAGTTATGGACTTT
1 --AAAAGA-GTGCCACGGAGTTGTAGACTTT
* *
9310 GAAGAAAAATGTGCCACGGAGTTGTGGACTTT
1 --A-AAAGA-GTGCCACGGAGTTGTAGACTTT
9342 AAAA
1 AAAA
9346 AGGAAAGAGT
Statistics
Matches: 97, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
27 19 0.20
28 24 0.25
29 3 0.03
30 4 0.04
31 22 0.23
32 25 0.26
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.23
Consensus pattern (28 bp):
AAAAGAGTGCCACGGAGTTGTAGACTTT
Found at i:9268 original size:28 final size:28
Alignment explanation
Indices: 9196--9345 Score: 95
Period size: 28 Copynumber: 5.1 Consensus size: 28
9186 CATCAAAAGA
* *
9196 AAAAGAGTGCCATGGAGTTGTAGAC-TT
1 AAAAGGGTGCCACGGAGTTGTAGACTTT
** * *
9223 AAAAGGGCACCACAGAGTCGTAGACTTT
1 AAAAGGGTGCCACGGAGTTGTAGACTTT
* *
9251 GAAAGGGTGCCACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTAGACTTT
* * * *
9279 AAAAAAAAGGTGCCATGGAGTTATGGACTTT
1 ---AAAAGGGTGCCACGGAGTTGTAGACTTT
** *
9310 GAAGAAAAATGTGCCACGGAGTTGTGGACTTT
1 ----AAAAGGGTGCCACGGAGTTGTAGACTTT
9342 AAAA
1 AAAA
9346 AGGAAAGAGT
Statistics
Matches: 98, Mismatches: 20, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
27 19 0.19
28 28 0.29
31 24 0.24
32 27 0.28
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.23
Consensus pattern (28 bp):
AAAAGGGTGCCACGGAGTTGTAGACTTT
Found at i:9364 original size:33 final size:32
Alignment explanation
Indices: 9251--9450 Score: 201
Period size: 33 Copynumber: 6.1 Consensus size: 32
9241 CGTAGACTTT
9251 GAAAGGGTGCCACGGAGTTGTGGACTTTAAAAA
1 GAAA-GGTGCCACGGAGTTGTGGACTTTAAAAA
* * *
9284 -AAAGGTGCCATGGAGTTATGGACTTTGAAGAA
1 GAAAGGTGCCACGGAGTTGTGGACTTT-AAAAA
*
9316 -AAATGTGCCACGGAGTTGTGGACTTTAAAAA
1 GAAAGGTGCCACGGAGTTGTGGACTTTAAAAA
* *
9347 GGAAAGAGT-CCACGGAGTTATGGACTTCAAAGGGAA
1 -GAAAG-GTGCCACGGAGTTGTGGACTTTAAA---AA
* *
9383 GAAAGGTGCCACGAAGTTGTGGACTTTAAAAGG
1 GAAAGGTGCCACGGAGTTGTGGACTTTAAAA-A
* **
9416 GAAATGTGCCATAGAGTTGTGGAC-TTAAAAA
1 GAAAGGTGCCACGGAGTTGTGGACTTTAAAAA
9447 GAAA
1 GAAA
9451 AAGAGTTATG
Statistics
Matches: 139, Mismatches: 19, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
31 29 0.21
32 37 0.27
33 43 0.31
34 4 0.03
35 24 0.17
36 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (32 bp):
GAAAGGTGCCACGGAGTTGTGGACTTTAAAAA
Found at i:9409 original size:68 final size:66
Alignment explanation
Indices: 9251--9450 Score: 232
Period size: 68 Copynumber: 3.1 Consensus size: 66
9241 CGTAGACTTT
* **
9251 GAAAGGGTGCCACGGAGTTGTGGACTTTAAAAA--AAAGGTGCCATGGAGTTATGGACTTTGAAG
1 GAAA-GGTGCCACGGAGTTGTGGACTTTAAAAAGGAAAGGTGCCACGGAGTTATGGACTTCAAAG
9314 AA
65 AA
*
9316 -AAATGTGCCACGGAGTTGTGGACTTTAAAAAGGAAAGAGT-CCACGGAGTTATGGACTTCAAAG
1 GAAAGGTGCCACGGAGTTGTGGACTTTAAAAAGGAAAG-GTGCCACGGAGTTATGGACTTCAAA-
9379 GGAA
64 -GAA
* * * ** *
9383 GAAAGGTGCCACGAAGTTGTGGACTTTAAAAGGGAAATGTGCCATAGAGTTGTGGACTT-AAA-A
1 GAAAGGTGCCACGGAGTTGTGGACTTTAAAAAGGAAAGGTGCCACGGAGTTATGGACTTCAAAGA
9446 A
66 A
9447 GAAA
1 GAAA
9451 AAGAGTTATG
Statistics
Matches: 117, Mismatches: 11, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
63 27 0.23
64 9 0.08
65 23 0.20
66 2 0.02
67 8 0.07
68 48 0.41
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (66 bp):
GAAAGGTGCCACGGAGTTGTGGACTTTAAAAAGGAAAGGTGCCACGGAGTTATGGACTTCAAAGA
A
Found at i:9462 original size:24 final size:24
Alignment explanation
Indices: 9428--9477 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
9418 AATGTGCCAT
* *
9428 AGAGTTGTGGACTTAAAAAGAAAA
1 AGAGTTATGGACATAAAAAGAAAA
**
9452 AGAGTTATGGACATAAATGGAAAA
1 AGAGTTATGGACATAAAAAGAAAA
9476 AG
1 AG
9478 GTGCCATGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.04, G:0.26, T:0.20
Consensus pattern (24 bp):
AGAGTTATGGACATAAAAAGAAAA
Found at i:9541 original size:90 final size:92
Alignment explanation
Indices: 9361--9532 Score: 222
Period size: 90 Copynumber: 1.9 Consensus size: 92
9351 AGAGTCCACG
* * ** *
9361 GAGTTATGGACTTCAAAGGGAAGAAAGGTGCCACGAAGTTGTGGACTTTAAAAGGGAAATGTGCC
1 GAGTTATGGACATCAAAGGGAAGAAAGGTGCCACGAAGTTGTGGACTTAAAAAGAAAAAGGTGCC
* *
9426 ATAGAGTTGTGGACTTAAAAAGAAAAA
66 ACAGAGTCGTGGACTTAAAAAGAAAAA
* * *
9453 GAGTTATGGACAT-AAATGGAA-AAAGGTGCCATGGAGTTGTGGACTTAAAAAGAAAAAGGGTGC
1 GAGTTATGGACATCAAAGGGAAGAAAGGTGCCACGAAGTTGTGGACTTAAAAAGAAAAA-GGTGC
*
9516 TACAGAGTCGTGGACTT
65 CACAGAGTCGTGGACTT
9533 TGAAGAAAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
90 31 0.46
91 25 0.37
92 12 0.18
ACGTcount: A:0.38, C:0.10, G:0.30, T:0.22
Consensus pattern (92 bp):
GAGTTATGGACATCAAAGGGAAGAAAGGTGCCACGAAGTTGTGGACTTAAAAAGAAAAAGGTGCC
ACAGAGTCGTGGACTTAAAAAGAAAAA
Found at i:9556 original size:30 final size:31
Alignment explanation
Indices: 9520--9668 Score: 159
Period size: 30 Copynumber: 5.0 Consensus size: 31
9510 GGGTGCTACA
*
9520 GAGTCGTGGACTTTGAAGAA-A-ATTGCCATT
1 GAGTCGTGGACTTTGAAGAAGAGA-TGCCACT
* *
9550 GAGTCGTGGACTTTGAAAAAG-GATACCACT
1 GAGTCGTGGACTTTGAAGAAGAGATGCCACT
* *
9580 GAGTCATGGAC-TTGGAGAAGAGATGCCACT
1 GAGTCGTGGACTTTGAAGAAGAGATGCCACT
* *
9610 AAGTCGTGGACTTAG-AGAAGAGATGCCA-T
1 GAGTCGTGGACTTTGAAGAAGAGATGCCACT
*
9639 AGAGTCGTGGACTTAG-AGAAGAGATGCCAC
1 -GAGTCGTGGACTTTGAAGAAGAGATGCCAC
9669 CATGGGAGTT
Statistics
Matches: 102, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
29 8 0.08
30 91 0.89
31 3 0.03
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.22
Consensus pattern (31 bp):
GAGTCGTGGACTTTGAAGAAGAGATGCCACT
Found at i:14756 original size:19 final size:19
Alignment explanation
Indices: 14732--14799 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
14722 AATTCAACGA
14732 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
14751 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
14766 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
14783 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
14800 TTAGCTACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:14770 original size:32 final size:32
Alignment explanation
Indices: 14734--14796 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
14724 TTCAACGATT
*
14734 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
14766 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
14797 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:14771 original size:13 final size:13
Alignment explanation
Indices: 14753--14777 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14743 ACATAAGTTT
14753 TGTATCGATACAA
1 TGTATCGATACAA
14766 TGTATCGATACA
1 TGTATCGATACA
14778 TAAGTATTGT
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):
TGTATCGATACAA
Found at i:14857 original size:13 final size:13
Alignment explanation
Indices: 14839--14864 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14829 CATTTTTCTG
14839 TGTATCGATACAT
1 TGTATCGATACAT
14852 TGTATCGATACAT
1 TGTATCGATACAT
14865 GGATCTTTGT
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:14861 original size:33 final size:33
Alignment explanation
Indices: 14819--14885 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
14809 ACCAAGGAAA
***
14819 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
14852 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
14885 T
1 T
14886 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:16274 original size:31 final size:31
Alignment explanation
Indices: 16232--16376 Score: 179
Period size: 31 Copynumber: 4.7 Consensus size: 31
16222 ATACCTTTTT
16232 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
* *
16263 AAAGTCGACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
* *
16294 AAAGTCCACGACTCAGTGGC-ATCTTTTCCTTT
1 AAAGTCCACGACTCAGTGGCAATCTCTT-C-TC
* * *
16326 AAAGTCCATGACTCAATGGC-AT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCT-TCTC
16356 AAAGTCCACGACTCAGTGGCA
1 AAAGTCCACGACTCAGTGGCA
16377 TTTTTTTCTT
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
30 24 0.24
31 53 0.54
32 22 0.22
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCAATCTCTTCTC
Found at i:16377 original size:62 final size:62
Alignment explanation
Indices: 16232--16396 Score: 201
Period size: 62 Copynumber: 2.6 Consensus size: 62
16222 ATACCTTTTT
* * *
16232 AAAGTCCACGACTCAGTGGCAATCTCTTC-TCAAAGTCGACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTCTTCAAAGTCCACGACTCAATGGCAATCTCTGCTC
* * *
16294 AAAGTCCACGACTCAGTGGCATCTTTTCCTTTAAAGTCCATGACTCAATGGC-AT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCATCTTTT-CTTCAAAGTCCACGACTCAATGGCAATCTCTG-CTC
* *
16356 AAAGTCCACGACTCAGTGGCATTTTTTTCTTCAAAGCCCAC
1 AAAGTCCACGACTCAGTGGCA-TCTTTTCTTCAAAGTCCAC
16397 AACTTCGTGG
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
61 9 0.10
62 57 0.64
63 23 0.26
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.29
Consensus pattern (62 bp):
AAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAATGGCAATCTCTGCTC
Found at i:16390 original size:94 final size:94
Alignment explanation
Indices: 16229--16514 Score: 245
Period size: 94 Copynumber: 3.0 Consensus size: 94
16219 CAAATACCTT
* *
16229 TTTAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCGACGACTCAGTGGCAATCTCTGCTC
1 TTTAAAGTCCACGACTCAATGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
* * *
16294 AAAGTCCACGAC-TCAGTGGCATCTTTTCC
66 AAAGCCCACAACTTC-GTGGCACCTTTTCC
* * * * * *
16323 TTTAAAGTCCATGACTCAATGGC-AT-TTTGTCTCAAAGTCCACGACTCAGTGGCATTTTTTTCT
1 TTTAAAGTCCACGACTCAATGGCAATCTCT-TCTCAAAGTCCACGACTCAGTGGCAATCTCTGC-
16386 TCAAAGCCCACAACTTCGTGGCACCTTTTCC
64 TCAAAGCCCACAACTTCGTGGCACCTTTTCC
* * ** * * * * * *
16417 TTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTT
1 TTTAAAGTCCACGACTCAATGGCA--ATC-TCTTCTCAAAGTCCACGACTCAGTGGCA--ATC-T
** * *
16482 CTTTTCAAAGCCCACAACTCCGTGGCACTTTTT
60 CTGCTCAAAGCCCACAACTTCGTGGCACCTTTT
16515 TCATCTTTAA
Statistics
Matches: 154, Mismatches: 27, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
92 2 0.01
93 30 0.19
94 64 0.42
95 2 0.01
97 1 0.01
98 21 0.14
99 2 0.01
100 29 0.19
101 3 0.02
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (94 bp):
TTTAAAGTCCACGACTCAATGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
AAAGCCCACAACTTCGTGGCACCTTTTCC
Found at i:16408 original size:62 final size:61
Alignment explanation
Indices: 16232--16474 Score: 188
Period size: 62 Copynumber: 3.9 Consensus size: 61
16222 ATACCTTTTT
* * * * * *
16232 AAAGTCCACGACTCAGTGGCAATCTCTTC-TCAAAGTCGACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGCATTTTCTTCTTCAAAGCCCACAACTCAGTGGC-AT-TTTGCTC
* * * ** *
16294 AAAGTCCACGACTCAGTGGCATCTTT-TCCTTTAAAGTCCATGACTCAATGGCATTTTGTCTC
1 AAAGTCCACGACTCAGTGGCAT-TTTCTTCTTCAAAGCCCACAACTCAGTGGCATTTTG-CTC
* * *
16356 AAAGTCCACGACTCAGTGGCATTTTTTTCTTCAAAGCCCACAACTTC-GTGGCACCTTTTCCTTT
1 AAAGTCCACGACTCAGTGGCATTTTCTTCTTCAAAGCCCACAAC-TCAGTGGCA--TTTTGC-TC
* * * *
16420 AAAGCCCACAACTCCGTGGCACCTTCTTCTT-TTCAAAGCCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCA--TT-TTCTTCTTCAAAGCCCACAACTCAGTGGCA
16475 CCTTCTTCTT
Statistics
Matches: 149, Mismatches: 20, Indels: 20
0.79 0.11 0.11
Matches are distributed among these distances:
61 6 0.04
62 68 0.46
63 23 0.15
64 23 0.15
65 2 0.01
66 23 0.15
67 4 0.03
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (61 bp):
AAAGTCCACGACTCAGTGGCATTTTCTTCTTCAAAGCCCACAACTCAGTGGCATTTTGCTC
Found at i:16704 original size:33 final size:33
Alignment explanation
Indices: 16356--17290 Score: 1005
Period size: 34 Copynumber: 27.8 Consensus size: 33
16346 ATTTTGTCTC
* * * ** *
16356 AAAGTCCACGACTCAGTGGCATTTTTTTC-TTC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
* *
16388 AAAGCCCACAACTTCGTGGCACC-TTTTCCTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
16420 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
16453 CAAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
16487 CAAAGCCCACAACTCCGTGGCACTTTTTTCATCTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTC-T-TTT
*
16523 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTC-TTTT
*
16556 AAAGCCCACAACTCCATGGCACCTTTTTCTGTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTT
*
16590 AAAGCCCACAACTCTGTGGCACACTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTC-TTTT
16625 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTT
16661 CAAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
16695 AAAGCCCACAACTCTGTGGCACACTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTC-TTTT
*
16730 AAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTT
16766 CAAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
16800 AAAGCCCACAACTCTGTGGCACACTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTC-TTTT
16835 AAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTTT
1 AAAGCCCACAACTCCGTGGCA-CCTTTTT-C-TTTT
16871 CAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTC-TTTT
16906 AAAGCCCACAACTCCGTGGCACC-----CTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
* * *
16934 -AAGTCCACGACTCCGTGGCA-CTCTTTTCCTTT
1 AAAGCCCACAACTCCGTGGCACCT-TTTTCTTTT
* * *
16966 AAAGCCCACAACTACGTGGCACTCTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTT
*
17000 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTT
17034 -AAGCCCACAACTCCGTGGCACC-----CTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
* * *
17061 -AAGTCCACGACTCCGTGGCA-CTCTTTTCCTTT
1 AAAGCCCACAACTCCGTGGCACCT-TTTTCTTTT
* * *
17093 AAAGCCCACAACTACGTGGCACTCTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTT
*
17127 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTT
*
17161 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTT
*
17195 -AAGCCTACAACTCCGTGGCACTCTTTTTTTCCTTTTT
1 AAAGCCCACAACTCCGTGGCAC-C--TTTTT-C-TTTT
* *
17232 AAAGCCCACAACTCTGTGGCACCTTGTTCTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
* * * *
17265 TAAGTCCACAACTTCGTGGCATCTTT
1 AAAGCCCACAACTCCGTGGCACCTTT
17291 CACCCTTTCT
Statistics
Matches: 797, Mismatches: 60, Indels: 91
0.84 0.06 0.10
Matches are distributed among these distances:
26 2 0.00
27 40 0.05
28 4 0.01
29 1 0.00
31 5 0.01
32 49 0.06
33 164 0.21
34 284 0.36
35 114 0.14
36 45 0.06
37 70 0.09
38 19 0.02
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (33 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
Found at i:16725 original size:105 final size:102
Alignment explanation
Indices: 16354--17290 Score: 1042
Period size: 105 Copynumber: 9.3 Consensus size: 102
16344 GCATTTTGTC
* * * ** * *
16354 TCAAAGTCCACGACTCAGTGGCATTTTTTTC-TTCAAAGCCCACAACTTCGTGGCACC-TTTTC-
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCT
* *
16416 CTTTAAAGCCCACAACTCCGTGGCACCTTCTT-CTTT
66 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTT
* *
16452 TCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTC
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
* *
16517 ATCTTT-AAGTCCACAACTCCGTGGCACCTTTTT-CTTT
65 -TTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTT
* * *
16554 TTAAAGCCCACAACTCCATGGCACCTTTTTCTGTTTAAAGCCCACAACTCTGTGGCACACTTTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT
16619 CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
64 CTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTT
*
16660 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACACTTTTTC
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTC
*
16725 TTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTT
65 TTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTT
*
16765 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACACTTTTTC
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTC
16830 TTTTTAAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTT
65 TTTTTAAAGCCCACAACTCCGTGGCA-CCTTTTTCC-TTT
16870 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACC-----C
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTC-TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* *
16930 -TTTT-AAGTCCACGACTCCGTGGCA-CTCTTTTCC-TT
65 TTTTTAAAGCCCACAACTCCGTGGCACCT-TTTTCCTTT
* * *
16965 T-AAAGCCCACAACTACGTGGCACTCTTTTCCTTCT-AAGCCCACAACTCCGTGGCACTCTTTTT
1 TCAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT
* *
17028 CCTTCT-AAGCCCACAACTCCGTGGCA-C-----CCTTT
64 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTT
* * * *
17060 T--AAGTCCACGACTCCGTGGCA-CTCTTTTCCTTTAAAGCCCACAACTACGTGGCA-CTCTTTT
1 TCAAAGCCCACAACTCCGTGGCACCT-TTTTCTTTTAAAGCCCACAACTCCGTGGCACCT-TTTT
* *
17121 CCTTCT-AAGCCCACAACTCCGTGGCACTCTTTTTCC--T
64 CTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCCTTT
* * *
17158 TCTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGCCTACAACTCCGTGGCACTCTTTT
1 TCAAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTAAAGCCCACAACTCCGTGGCAC-C--TT
* *
17222 TTTCCTTTTTAAAGCCCACAACTCTGTGGCACCTTGTT-CTTT
61 TTT-CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTT
* * * *
17264 T-TAAGTCCACAACTTCGTGGCATCTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTT
17291 CACCCTTTCT
Statistics
Matches: 741, Mismatches: 51, Indels: 88
0.84 0.06 0.10
Matches are distributed among these distances:
92 4 0.01
93 57 0.08
94 63 0.09
95 13 0.02
96 2 0.00
97 6 0.01
98 45 0.06
99 7 0.01
100 64 0.09
101 27 0.04
102 88 0.12
103 34 0.05
104 17 0.02
105 232 0.31
106 82 0.11
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.33
Consensus pattern (102 bp):
TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCT
TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTT
Found at i:16946 original size:27 final size:28
Alignment explanation
Indices: 16867--17153 Score: 128
Period size: 33 Copynumber: 9.1 Consensus size: 28
16857 CCTTTTTCCT
16867 TTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACC-----C
16901 TTTTTAAAGCCCACAACTCCGTGGCACCC
1 -TTTTAAAGCCCACAACTCCGTGGCACCC
* *
16930 TTTT-AAGTCCACGACTCCGTGGCACTCTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCAC-C----C
* * *
16962 CTTTAAAGCCCACAACTACGTGGCACTCTT
1 TTTTAAAGCCCACAACTCCGTGGCAC-C-C
* *
16992 TTCCTTCTAAGCCCACAACTCCGTGGCACTCTTT
1 TT--TT-AAAGCCCACAACTCCGTGGCAC-C--C
*
17026 TTCCTTCTAAGCCCACAACTCCGTGGCACCC
1 TT--TT-AAAGCCCACAACTCCGTGGCACCC
* *
17057 TTTT-AAGTCCACGACTCCGTGGCACTCTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCAC-C----C
* * *
17089 CTTTAAAGCCCACAACTACGTGGCACTCTT
1 TTTTAAAGCCCACAACTCCGTGGCAC-C-C
* *
17119 TTCCTTCTAAGCCCACAACTCCGTGGCACTC
1 TT--TT-AAAGCCCACAACTCCGTGGCACCC
17150 TTTT
1 TTTT
17154 TCCTTCTAAG
Statistics
Matches: 210, Mismatches: 23, Indels: 44
0.76 0.08 0.16
Matches are distributed among these distances:
27 38 0.18
28 6 0.03
29 5 0.02
30 4 0.02
31 4 0.02
32 12 0.06
33 83 0.40
34 54 0.26
35 4 0.02
ACGTcount: A:0.20, C:0.36, G:0.13, T:0.31
Consensus pattern (28 bp):
TTTTAAAGCCCACAACTCCGTGGCACCC
Found at i:17328 original size:32 final size:32
Alignment explanation
Indices: 17292--17370 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 32
17282 GGCATCTTTC
17292 ACCCTTTCTAAAGCCCACACAAGTCGATGGCA
1 ACCCTTTCTAAAGCCCACACAAGTCGATGGCA
* *
17324 ACCCTCTCTAAAGCCCACACAAGTCGGTGGCA
1 ACCCTTTCTAAAGCCCACACAAGTCGATGGCA
17356 ACCC-TTCT-AAGCCCA
1 ACCCTTTCTAAAGCCCA
17371 ATGTAGCTGG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 7 0.16
31 3 0.07
32 34 0.77
ACGTcount: A:0.29, C:0.38, G:0.15, T:0.18
Consensus pattern (32 bp):
ACCCTTTCTAAAGCCCACACAAGTCGATGGCA
Found at i:17425 original size:49 final size:49
Alignment explanation
Indices: 17363--17835 Score: 726
Period size: 49 Copynumber: 9.7 Consensus size: 49
17353 GCAACCCTTC
* *
17363 TAAGCCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
17412 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATAGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
17461 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
17510 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
17559 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
17608 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
17657 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
17705 TAAGTCCAATGTAGCTGGCTTTGAATCAGCACATT-G-A----CACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
17748 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
*
17800 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
17836 ACATCCTTTT
Statistics
Matches: 388, Mismatches: 27, Indels: 15
0.90 0.06 0.03
Matches are distributed among these distances:
43 37 0.10
44 1 0.00
45 1 0.00
46 1 0.00
47 1 0.00
48 41 0.11
49 268 0.69
52 38 0.10
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:17763 original size:43 final size:43
Alignment explanation
Indices: 17654--17844 Score: 193
Period size: 43 Copynumber: 4.1 Consensus size: 43
17644 GCACCTTCAT
*
17654 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT-G-A---CAC
*
17702 CTTTAAGTCCAATGTAGCTGGCTTTGAATCAGCACATTGACAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACAC
* * *
17745 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT-G-A-------CAC
*
17797 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACA-C
17841 CTTT
1 CTTT
17845 TTCTCATCTT
Statistics
Matches: 123, Mismatches: 10, Indels: 24
0.78 0.06 0.15
Matches are distributed among these distances:
43 39 0.32
44 5 0.04
45 1 0.01
46 1 0.01
47 1 0.01
48 37 0.30
50 1 0.01
51 1 0.01
52 37 0.30
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACAC
Found at i:17784 original size:91 final size:94
Alignment explanation
Indices: 17654--17844 Score: 307
Period size: 95 Copynumber: 2.0 Consensus size: 94
17644 GCACCTTCAT
*
17654 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-T-CATCTTTAAGTCCAATGT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCCATCTTTAAGTCCAATGT
*
17717 AGCTGGCTTTGAATCAGCACATTGACA-C
66 AGCTGGCCTTGAATCAGCACATTGACATC
* *
17745 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TTCCATCTTTAAGTCCAAT
17810 GTAGCTGGCCTTGAATCAGCACATTGACATC
64 GTAGCTGGCCTTGAATCAGCACATTGACATC
17841 CTTT
1 CTTT
17845 TTCTCATCTT
Statistics
Matches: 91, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
91 42 0.46
94 1 0.01
95 43 0.47
96 5 0.05
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (94 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGACATC
Found at i:17823 original size:52 final size:53
Alignment explanation
Indices: 17745--17898 Score: 186
Period size: 52 Copynumber: 2.9 Consensus size: 53
17735 ACATTGACAC
17745 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * *
17797 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * * * *
17852 CTTTAAG-CCTAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCC-AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
17899 ATCACTTTTC
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
52 38 0.45
53 5 0.06
54 7 0.08
55 35 0.41
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:18555 original size:34 final size:35
Alignment explanation
Indices: 18517--18583 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
18507 CCTTACAACA
18517 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
18551 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
18584 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:19060 original size:13 final size:13
Alignment explanation
Indices: 19042--19067 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19032 CAATTTTTTG
19042 TGTATCGATACAT
1 TGTATCGATACAT
19055 TGTATCGATACAT
1 TGTATCGATACAT
19068 ACTTGCTGTA
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:20736 original size:13 final size:13
Alignment explanation
Indices: 20718--20742 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20708 ACTGAAGCAA
20718 TGTATCGATACAT
1 TGTATCGATACAT
20731 TGTATCGATACA
1 TGTATCGATACA
20743 ATTTGGAAAA
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:21374 original size:23 final size:24
Alignment explanation
Indices: 21329--21375 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
21319 CAAAGAATTG
*
21329 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
21353 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
21376 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:23968 original size:34 final size:35
Alignment explanation
Indices: 23930--23996 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
23920 CCTTACAACA
23930 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
23964 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
23997 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:24473 original size:13 final size:13
Alignment explanation
Indices: 24455--24480 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24445 CAATTTTTTG
24455 TGTATCGATACAT
1 TGTATCGATACAT
24468 TGTATCGATACAT
1 TGTATCGATACAT
24481 ACTTGCTGTA
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
Done.