Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 97 of 97
Found at i:38619567 original size:33 final size:32
Alignment explanation
Indices: 38619502--38619568 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
38619492 AAAAAGCCTG
*
38619502 AAAAATGCTTTAAAAACTTCAAAAATCTTTAA
1 AAAAATGCTTTAAAAACTTCAAAAATCCTTAA
*
38619534 AAAAATGCTTTAAAAAATCTT-AACAATCCTTAA
1 AAAAATGCTTT-AAAAA-CTTCAAAAATCCTTAA
38619567 AA
1 AA
38619569 TTCAATGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 11 0.35
33 17 0.55
34 3 0.10
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.30
Consensus pattern (32 bp):
AAAAATGCTTTAAAAACTTCAAAAATCCTTAA
Found at i:38619714 original size:21 final size:21
Alignment explanation
Indices: 38619660--38619714 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
38619650 AAAAAATACT
*
38619660 TTTAAAAA-CC-TTAAAATTC
1 TTTAAAAATCCTTTAAAACTC
*
38619679 CTTAAAAAGTCCTTTAAAACTC
1 TTTAAAAA-TCCTTTAAAACTC
38619701 TTTAAAAATCCTTT
1 TTTAAAAATCCTTT
38619715 GAAATCCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 7 0.23
21 8 0.27
22 15 0.50
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (21 bp):
TTTAAAAATCCTTTAAAACTC
Found at i:38619964 original size:21 final size:21
Alignment explanation
Indices: 38619926--38620023 Score: 81
Period size: 21 Copynumber: 4.6 Consensus size: 21
38619916 CTTGAAAATG
* * *
38619926 CTTAAAAATCCATGAAAAAGC
1 CTTAAAAATCCTTCAAAAAAC
* *
38619947 CTTAAAAATACTTCAAAAATC
1 CTTAAAAATCCTTCAAAAAAC
* *
38619968 TTTAAATAATGCTTCAAAAAAC
1 CTTAAA-AATCCTTCAAAAAAC
* **
38619990 TTTAAAAATCCTT-AAAATTC
1 CTTAAAAATCCTTCAAAAAAC
38620010 CTTGAAAAATCCTT
1 CTT-AAAAATCCTT
38620024 TGAAATAAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
20 7 0.11
21 38 0.59
22 19 0.30
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.31
Consensus pattern (21 bp):
CTTAAAAATCCTTCAAAAAAC
Found at i:38620003 original size:53 final size:52
Alignment explanation
Indices: 38619940--38620166 Score: 126
Period size: 53 Copynumber: 4.3 Consensus size: 52
38619930 AAAATCCATG
* *
38619940 AAAAAGCCTTAAAAATACTTCAAAAAT-CTTT-AAAT-AATGCTTCAAAAAACTTT
1 AAAAATCCTTAAAAATACTTCAAAAATACTTTGAAATAAATG----AAAAAACCTT
* * * *
38619993 AAAAATCCTTAAAATTCCTTGAAAAATCCTTTGAAATAAATGAACAAAACCTT
1 AAAAATCCTTAAAAATACTTCAAAAATACTTTGAAATAAATGAA-AAAACCTT
* * * * * *
38620046 AAAAATGCTTCAAAAGACTGCAAAAATA-TTTTAAA-AAATGCTTTTAAAAACCTT
1 AAAAATCCTTAAAAATACTTCAAAAATACTTTGAAATAAATG----AAAAAACCTT
* * * ** *
38620100 GAAATTCCTTAAAAACTACTT-AAATAT-CATTTGAAATCCATGAAAAAAACTTT
1 AAAAATCCTTAAAAA-TACTTCAAAAATAC-TTTGAAATAAATG-AAAAAACCTT
*
38620153 AAAAATACTTAAAA
1 AAAAATCCTTAAAA
38620167 TGACCTTAAA
Statistics
Matches: 131, Mismatches: 31, Indels: 24
0.70 0.17 0.13
Matches are distributed among these distances:
51 5 0.04
52 8 0.06
53 69 0.53
54 28 0.21
55 14 0.11
56 7 0.05
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.30
Consensus pattern (52 bp):
AAAAATCCTTAAAAATACTTCAAAAATACTTTGAAATAAATGAAAAAACCTT
Found at i:38620004 original size:10 final size:10
Alignment explanation
Indices: 38619878--38620023 Score: 98
Period size: 10 Copynumber: 14.0 Consensus size: 10
38619868 AAATTTGATG
38619878 AAAAATCTCTT
1 AAAAATC-CTT
38619889 AAAAA-CCTT
1 AAAAATCCTT
* *
38619898 AAATATACTT
1 AAAAATCCTT
38619908 AAAAGGAT-CTT
1 AAAA--ATCCTT
* *
38619919 GAAAATGCTT
1 AAAAATCCTT
*
38619929 AAAAATCCATG
1 AAAAATCC-TT
*
38619940 AAAAAGCCTT
1 AAAAATCCTT
*
38619950 AAAAATACTT
1 AAAAATCCTT
*
38619960 CAAAAATCTTT
1 -AAAAATCCTT
*
38619971 AAATAATGCTT
1 AAA-AATCCTT
* *
38619982 CAAAAAACTTT
1 -AAAAATCCTT
38619993 AAAAATCCTT
1 AAAAATCCTT
*
38620003 AAAATTCCTT
1 AAAAATCCTT
38620013 GAAAAATCCTT
1 -AAAAATCCTT
38620024 TGAAATAAAT
Statistics
Matches: 104, Mismatches: 22, Indels: 18
0.72 0.15 0.12
Matches are distributed among these distances:
9 9 0.09
10 45 0.43
11 45 0.43
12 5 0.05
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (10 bp):
AAAAATCCTT
Found at i:38620095 original size:107 final size:105
Alignment explanation
Indices: 38619951--38620166 Score: 236
Period size: 107 Copynumber: 2.0 Consensus size: 105
38619941 AAAAGCCTTA
* * * * * *
38619951 AAAATACTTCAAAAATCTTTAAATAATGCTTCAAAAAACTTTAAAAATCCTT-AAAATTCCTTGA
1 AAAAGACTGCAAAAATCTTTAAAAAATGCTTCAAAAAACCTTAAAAATCCTTAAAAACTACTT-A
* * *
38620015 AAAATCCTTTGAAATAAATGAACAAAACCTTAAAAATGCTT
65 AAAATCATTTGAAATAAATGAAAAAAACCTTAAAAATACTT
* ** * *
38620056 CAAAAGACTGCAAAAATATTTTAAAAAATGCTTTTAAAAACCTTGAAATTCCTTAAAAACTACTT
1 -AAAAGACTGCAAAAAT-CTTTAAAAAATGCTTCAAAAAACCTTAAAAATCCTTAAAAACTACTT
* ** *
38620121 AAATATCATTTGAAATCCATGAAAAAAACTTTAAAAATACTT
64 AAAAATCATTTGAAATAAATGAAAAAAACCTTAAAAATACTT
38620163 AAAA
1 AAAA
38620167 TGACCTTAAA
Statistics
Matches: 90, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
106 18 0.20
107 64 0.71
108 8 0.09
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.30
Consensus pattern (105 bp):
AAAAGACTGCAAAAATCTTTAAAAAATGCTTCAAAAAACCTTAAAAATCCTTAAAAACTACTTAA
AAATCATTTGAAATAAATGAAAAAAACCTTAAAAATACTT
Found at i:38620406 original size:22 final size:22
Alignment explanation
Indices: 38620378--38620424 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
38620368 TAAATGCTTC
38620378 AAAATACTTCAA-AAATCTTAAA
1 AAAATACTTCAACAAA-CTTAAA
*
38620400 AAAATACTTCAACAAACTTTAA
1 AAAATACTTCAACAAACTTAAA
38620422 AAA
1 AAA
38620425 TCCCTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAATACTTCAACAAACTTAAA
Found at i:38620510 original size:106 final size:106
Alignment explanation
Indices: 38620369--38620562 Score: 230
Period size: 106 Copynumber: 1.8 Consensus size: 106
38620359 AAAAGTCTTT
* *
38620369 AAATGCTTCAAAATACTTCAAAAATCTTAAAAAAATACTTC-AACAAACTTTAAAAATCCCT-AA
1 AAATGCTTCAAAAGACTTCAAAAATCTTAAAAAAATACTTCAAAC-AACCTTAAAAATCCCTAAA
*
38620432 AATTTCTTTAAAAATCCTTTGAAATCAATGAACAAAACCTTAC
65 AATTTC-TTAAAAATACTTTGAAATCAATGAACAAAACCTTAC
* * * * * * * * * *
38620475 AAATGCTTCAAAAGACTTTAAAATTTTTTATAAAATGCTTTAAACAACCTTAAAATTTCTTAAAA
1 AAATGCTTCAAAAGACTTCAAAAATCTTAAAAAAATACTTCAAACAACCTTAAAAATCCCTAAAA
*
38620540 ATTTCTTAAAAGTACTTTGAAAT
66 ATTTCTTAAAAATACTTTGAAAT
38620563 ACAAGAAAAG
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
106 61 0.85
107 11 0.15
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.34
Consensus pattern (106 bp):
AAATGCTTCAAAAGACTTCAAAAATCTTAAAAAAATACTTCAAACAACCTTAAAAATCCCTAAAA
ATTTCTTAAAAATACTTTGAAATCAATGAACAAAACCTTAC
Found at i:38620511 original size:32 final size:31
Alignment explanation
Indices: 38620470--38620541 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
38620460 TGAACAAAAC
* *
38620470 CTTACAAATGCTTCAAA-AGACTTTAAAATTT
1 CTTAAAAATGCTTCAAACA-ACCTTAAAATTT
* *
38620501 TTTATAAAATGCTTTAAACAACCTTAAAATTT
1 CTTA-AAAATGCTTCAAACAACCTTAAAATTT
38620533 CTTAAAAAT
1 CTTAAAAAT
38620542 TTCTTAAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
31 8 0.24
32 25 0.74
33 1 0.03
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.38
Consensus pattern (31 bp):
CTTAAAAATGCTTCAAACAACCTTAAAATTT
Found at i:38620542 original size:11 final size:11
Alignment explanation
Indices: 38620526--38620550 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38620516 AAACAACCTT
38620526 AAAATTTCTTA
1 AAAATTTCTTA
38620537 AAAATTTCTTA
1 AAAATTTCTTA
38620548 AAA
1 AAA
38620551 GTACTTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAATTTCTTA
Found at i:38620821 original size:32 final size:33
Alignment explanation
Indices: 38620785--38620853 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 33
38620775 AAAATTCATG
* *
38620785 AAAAAAGCCTT-AAAAATGCTTCAAAATACTTT
1 AAAAAAGCCTTAAAAAATGATTCAAAAAACTTT
* * *
38620817 -AAAAATCTTTAAAAAATGATTCAAAAAAGTTT
1 AAAAAAGCCTTAAAAAATGATTCAAAAAACTTT
38620849 AAAAA
1 AAAAA
38620854 TCCTTTCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
31 8 0.27
32 18 0.60
33 4 0.13
ACGTcount: A:0.57, C:0.10, G:0.06, T:0.28
Consensus pattern (33 bp):
AAAAAAGCCTTAAAAAATGATTCAAAAAACTTT
Found at i:38621207 original size:10 final size:11
Alignment explanation
Indices: 38621170--38621276 Score: 55
Period size: 10 Copynumber: 10.2 Consensus size: 11
38621160 TAAAAGGATC
*
38621170 TTAAAAATG-A
1 TTAAAAATGCT
* *
38621180 TTAAAAATCCA
1 TTAAAAATGCT
* * *
38621191 TGAAAAAAGTT
1 TTAAAAATGCT
38621202 TTAAAAATGCT
1 TTAAAAATGCT
* *
38621213 TT-AAAATACC
1 TTAAAAATGCT
*
38621223 TCAAAAAT-CT
1 TTAAAAATGCT
38621233 TTAAAAAATGCT
1 TT-AAAAATGCT
* *
38621245 TCAAAAA-ACT
1 TTAAAAATGCT
*
38621255 TTAAAAAT-CC
1 TTAAAAATGCT
38621265 TTAAAAAT-CT
1 TTAAAAATGCT
38621275 TT
1 TT
38621277 TGAAATTAAT
Statistics
Matches: 73, Mismatches: 19, Indels: 10
0.72 0.19 0.10
Matches are distributed among these distances:
10 37 0.51
11 33 0.45
12 3 0.04
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (11 bp):
TTAAAAATGCT
Found at i:38621229 original size:32 final size:32
Alignment explanation
Indices: 38621170--38621251 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
38621160 TAAAAGGATC
* * *
38621170 TTAAAAATGATTAAAAATCCATGAAAAAAGTT
1 TTAAAAATGCTTAAAAATCCATCAAAAAACTT
* *
38621202 TTAAAAATGCTTTAAAATACC-TCAAAAATCTT
1 TTAAAAATGCTTAAAAAT-CCATCAAAAAACTT
*
38621234 TAAAAAATGCTTCAAAAA
1 TTAAAAATGCTT-AAAAA
38621252 ACTTTAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
32 35 0.85
33 6 0.15
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (32 bp):
TTAAAAATGCTTAAAAATCCATCAAAAAACTT
Found at i:38621240 original size:22 final size:20
Alignment explanation
Indices: 38621204--38621276 Score: 76
Period size: 22 Copynumber: 3.5 Consensus size: 20
38621194 AAAAAGTTTT
38621204 AAAAATGCTTT-AAAATACCTC
1 AAAAAT-CTTTAAAAAT-CCTC
*
38621225 AAAAATCTTTAAAAAATGCTTC
1 AAAAATCTTT-AAAAAT-CCTC
* *
38621247 AAAAAACTTTAAAAATCCTT
1 AAAAATCTTTAAAAATCCTC
38621267 AAAAATCTTT
1 AAAAATCTTT
38621277 TGAAATTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 15 0.34
21 12 0.27
22 17 0.39
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAAATCTTTAAAAATCCTC
Found at i:38621261 original size:32 final size:32
Alignment explanation
Indices: 38621204--38621271 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
38621194 AAAAAGTTTT
* * *
38621204 AAAAATGCTTTAAAATACCTCAAAAATCTTTA
1 AAAAATGCTTCAAAAAACCTCAAAAATCCTTA
* *
38621236 AAAAATGCTTCAAAAAACTTTAAAAATCCTTA
1 AAAAATGCTTCAAAAAACCTCAAAAATCCTTA
38621268 AAAA
1 AAAA
38621272 TCTTTTGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.28
Consensus pattern (32 bp):
AAAAATGCTTCAAAAAACCTCAAAAATCCTTA
Found at i:38621289 original size:95 final size:94
Alignment explanation
Indices: 38621184--38621402 Score: 262
Period size: 95 Copynumber: 2.3 Consensus size: 94
38621174 AAATGATTAA
* ** * * *
38621184 AAATCCATGAAAAAAGTTTTAAAAATGCTTTAAAATACCTCAAAAATCTTTAAAAAATGC-TTCA
1 AAATACATGAAAAAA-CCTTAAAAATGCTTCAAAAGACCTCAAAAATCTTTAAAAAATACATT-A
* *
38621248 AAAAACTTTAAAAATCCTTAAAAATCTTTTG
64 AAAAACCTTAAAAATCCTTAAAAATCCTTTG
* *
38621279 AAATTA-ATGAAGGAAACCTTAAAAATGCTTCAAAAGACTTCAAAAATCTTTAAAAAATACATTA
1 AAA-TACATGAA-AAAACCTTAAAAATGCTTCAAAAGACCTCAAAAATCTTTAAAAAATACATTA
* * *
38621343 ATAAACCTTAAAATTTCTTAAAAATCCTTTG
64 AAAAACCTTAAAAATCCTTAAAAATCCTTTG
*
38621374 AAATACATAAAAAAACCTTAAAAATGCTT
1 AAATACATGAAAAAACCTTAAAAATGCTT
38621403 AACATGACCT
Statistics
Matches: 105, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
94 19 0.18
95 80 0.76
96 6 0.06
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (94 bp):
AAATACATGAAAAAACCTTAAAAATGCTTCAAAAGACCTCAAAAATCTTTAAAAAATACATTAAA
AAACCTTAAAAATCCTTAAAAATCCTTTG
Found at i:38621335 original size:32 final size:30
Alignment explanation
Indices: 38621202--38621334 Score: 90
Period size: 32 Copynumber: 4.2 Consensus size: 30
38621192 GAAAAAAGTT
* * *
38621202 TTAAAAATGCTTTAAAATACCTCAAAAATCT
1 TTAAAAATGCTTCAAAA-ACTTCAAAAATCC
*
38621233 TTAAAAAATGCTTCAAAAAACTTTAAAAATCC
1 TT-AAAAATGCTTC-AAAAACTTCAAAAATCC
*** * *
38621265 TTAAAAAT-CTTTTGAAA-TTAATGAAGGAAACC
1 TTAAAAATGCTTCAAAAACTTCA--AA--AATCC
*
38621297 TTAAAAATGCTTCAAAAGACTTCAAAAATCT
1 TTAAAAATGCTTCAAAA-ACTTCAAAAATCC
38621328 TTAAAAA
1 TTAAAAA
38621335 ATACATTAAT
Statistics
Matches: 78, Mismatches: 15, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
28 3 0.04
29 3 0.04
30 5 0.06
31 18 0.23
32 34 0.44
33 11 0.14
34 1 0.01
35 3 0.04
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.30
Consensus pattern (30 bp):
TTAAAAATGCTTCAAAAACTTCAAAAATCC
Found at i:38621597 original size:22 final size:22
Alignment explanation
Indices: 38621578--38621637 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
38621568 TCTTAAAATA
38621578 CTTAAAAAT-CTTTGAAAAAAGT
1 CTTAAAAATGC-TTGAAAAAAGT
*
38621600 CTTAAAAATGCTTGAAAAAACT
1 CTTAAAAATGCTTGAAAAAAGT
*
38621622 -TTAAAAATCCTT-AAAA
1 CTTAAAAATGCTTGAAAA
38621638 TTCTTTGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.11
21 11 0.31
22 19 0.54
23 1 0.03
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.30
Consensus pattern (22 bp):
CTTAAAAATGCTTGAAAAAAGT
Found at i:38621635 original size:31 final size:31
Alignment explanation
Indices: 38621604--38621664 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
38621594 AAAAGTCTTA
*
38621604 AAAATGC-TTGAAAAAACTTTAAAAATCCTT
1 AAAATGCTTTGAAAAAACCTTAAAAATCCTT
* *
38621634 AAAATTCTTTGAAAAATCCTTAAAAATCCTT
1 AAAATGCTTTGAAAAAACCTTAAAAATCCTT
38621665 TGAAATCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 6 0.22
31 21 0.78
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.33
Consensus pattern (31 bp):
AAAATGCTTTGAAAAAACCTTAAAAATCCTT
Found at i:38621649 original size:22 final size:22
Alignment explanation
Indices: 38621603--38621669 Score: 77
Period size: 21 Copynumber: 3.1 Consensus size: 22
38621593 AAAAAGTCTT
* *
38621603 AAAAATGCTTGAAAAA-ACTTT-
1 AAAAATCCTT-AAAAATCCTTTG
*
38621624 AAAAATCCTT-AAAATTCTTTG
1 AAAAATCCTTAAAAATCCTTTG
38621645 AAAAATCCTTAAAAATCCTTTG
1 AAAAATCCTTAAAAATCCTTTG
38621667 AAA
1 AAA
38621670 TCAATGAACA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
19 4 0.10
20 4 0.10
21 19 0.47
22 13 0.32
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.31
Consensus pattern (22 bp):
AAAAATCCTTAAAAATCCTTTG
Found at i:38621671 original size:10 final size:10
Alignment explanation
Indices: 38621531--38621664 Score: 87
Period size: 10 Copynumber: 13.0 Consensus size: 10
38621521 TAAAAACATA
38621531 AAAAATCTCTT
1 AAAAATC-CTT
38621542 AAAAA-CCTT
1 AAAAATCCTT
* *
38621551 AAATATGCTT
1 AAAAATCCTT
38621561 AAAAGGAT-CTT
1 AAAA--ATCCTT
*
38621572 -AAAATACTT
1 AAAAATCCTT
*
38621581 AAAAATCTTT
1 AAAAATCCTT
38621591 GAAAAAAGT-CTT
1 --AAAAA-TCCTT
*
38621603 AAAAATGCTT
1 AAAAATCCTT
* *
38621613 GAAAAAACTTT
1 -AAAAATCCTT
38621624 AAAAATCCTT
1 AAAAATCCTT
* *
38621634 AAAATTCTTT
1 AAAAATCCTT
38621644 GAAAAATCCTT
1 -AAAAATCCTT
38621655 AAAAATCCTT
1 AAAAATCCTT
38621665 TGAAATCAAT
Statistics
Matches: 97, Mismatches: 15, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
8 2 0.02
9 11 0.11
10 51 0.53
11 23 0.24
12 9 0.09
13 1 0.01
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (10 bp):
AAAAATCCTT
Found at i:38621720 original size:31 final size:30
Alignment explanation
Indices: 38621678--38621753 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
38621668 AATCAATGAA
* * *
38621678 CAAAATC--TTAAAATACTTCGAAACACTT
1 CAAAATCTTTTAAAATACTTCAAAAAACAT
*
38621706 CAGAAATCTTTTAAAATTGCTTCAAAAAACAT
1 CA-AAATCTTTTAAAA-TACTTCAAAAAACAT
38621738 CAAAATCTTTTAAAAT
1 CAAAATCTTTTAAAAT
38621754 TCCTTAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 2 0.05
29 5 0.12
30 1 0.03
31 19 0.47
32 13 0.32
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.32
Consensus pattern (30 bp):
CAAAATCTTTTAAAATACTTCAAAAAACAT
Found at i:38622434 original size:31 final size:31
Alignment explanation
Indices: 38622367--38622443 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
38622357 GTTTTTAAGG
* * *
38622367 AATTTTAAAAGATTTTGATGTTTTTTGAAGC
1 AATTTTAAAAGATTTTGAAGTGTTTCGAAGC
38622398 AATTTTAAAAGATTTCTGAAGTGTTTCGAAG-
1 AATTTTAAAAGATTT-TGAAGTGTTTCGAAGC
*
38622429 TATTTT--AAGATTTTG
1 AATTTTAAAAGATTTTG
38622444 TTCATTGATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 2 0.05
29 7 0.17
31 20 0.49
32 12 0.29
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (31 bp):
AATTTTAAAAGATTTTGAAGTGTTTCGAAGC
Found at i:38622470 original size:10 final size:10
Alignment explanation
Indices: 38622457--38622590 Score: 87
Period size: 10 Copynumber: 13.0 Consensus size: 10
38622447 ATTGATTTCA
38622457 AAGGATTTTT
1 AAGGATTTTT
38622467 AAGGATTTTT
1 AAGGATTTTT
* *
38622477 CAAAGAATTTT
1 -AAGGATTTTT
38622488 AAGGATTTTT
1 AAGGATTTTT
* *
38622498 AAAGTTTTTT
1 AAGGATTTTT
*
38622508 CAAGCATTTTT
1 -AAGGATTTTT
38622519 AA-GACTTTTTT
1 AAGGA--TTTTT
*
38622530 CAAAGATTTTT
1 -AAGGATTTTT
*
38622541 AAGTA-TTTT
1 AAGGATTTTT
38622550 AA-GATCCTTTT
1 AAGGAT--TTTT
* *
38622561 AAGCATATTT
1 AAGGATTTTT
38622571 AAGG-TTTTT
1 AAGGATTTTT
38622580 AAGAGATTTTT
1 AAG-GATTTTT
38622591 TATGTTTTTA
Statistics
Matches: 95, Mismatches: 17, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
8 1 0.01
9 14 0.15
10 38 0.40
11 36 0.38
12 4 0.04
13 2 0.02
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (10 bp):
AAGGATTTTT
Found at i:38622489 original size:21 final size:21
Alignment explanation
Indices: 38622452--38622501 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
38622442 TGTTCATTGA
*
38622452 TTTCAAAGGATTTTTAAGGATT
1 TTTCAAA-GAATTTTAAGGATT
38622474 TTTCAAAGAATTTTAAGGATT
1 TTTCAAAGAATTTTAAGGATT
38622495 TTT-AAAG
1 TTTCAAAG
38622502 TTTTTTCAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 4 0.15
21 16 0.59
22 7 0.26
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (21 bp):
TTTCAAAGAATTTTAAGGATT
Found at i:38622516 original size:21 final size:20
Alignment explanation
Indices: 38622462--38622552 Score: 85
Period size: 21 Copynumber: 4.4 Consensus size: 20
38622452 TTTCAAAGGA
*
38622462 TTTTTAAGGATTTTTCAAAGA
1 TTTTTAAGGATTTTT-AAAGT
*
38622483 ATTTTAAGGATTTTTAAAGT
1 TTTTTAAGGATTTTTAAAGT
* *
38622503 TTTTTCAAGCATTTTTAAGACT
1 TTTTT-AAGGATTTTTAA-AGT
*
38622525 TTTTTCAAAGATTTTT-AAGT
1 TTTTT-AAGGATTTTTAAAGT
*
38622545 ATTTTAAG
1 TTTTTAAG
38622553 ATCCTTTTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.03
20 14 0.24
21 26 0.45
22 16 0.28
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (20 bp):
TTTTTAAGGATTTTTAAAGT
Found at i:38622528 original size:31 final size:29
Alignment explanation
Indices: 38622462--38622562 Score: 80
Period size: 31 Copynumber: 3.2 Consensus size: 29
38622452 TTTCAAAGGA
*
38622462 TTTTTAAGGATTTTTCAAAGAATTTTAAGGA-
1 TTTTTAAAGATTTTTC-AAG-ATTTTAA-GAC
*
38622493 TTTTTAAAGTTTTTTCAAGCATTTTTAAGAC
1 TTTTTAAAGATTTTTCAAG-A-TTTTAAGAC
38622524 TTTTTTCAAAGATTTTT-AAGTATTTTAAGATC
1 -TTTTT-AAAGATTTTTCAAG-ATTTTAAGA-C
*
38622556 CTTTTAA
1 TTTTTAA
38622563 GCATATTTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
30 8 0.14
31 32 0.54
32 10 0.17
33 9 0.15
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (29 bp):
TTTTTAAAGATTTTTCAAGATTTTAAGAC
Found at i:38622549 original size:22 final size:22
Alignment explanation
Indices: 38622484--38622543 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
38622474 TTTCAAAGAA
* *
38622484 TTTT-AAGGATTTTTAA-AGTT
1 TTTTCAAGCATTTTTAAGACTT
38622504 TTTTCAAGCATTTTTAAGACTT
1 TTTTCAAGCATTTTTAAGACTT
38622526 TTTTCAAAG-ATTTTTAAG
1 TTTTC-AAGCATTTTTAAG
38622544 TATTTTAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.11
21 11 0.31
22 17 0.49
23 3 0.09
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.52
Consensus pattern (22 bp):
TTTTCAAGCATTTTTAAGACTT
Found at i:38622666 original size:11 final size:11
Alignment explanation
Indices: 38622652--38622697 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
38622642 TTACTACGAA
38622652 TTTTAAGCTTT
1 TTTTAAGCTTT
*
38622663 TTTTAAGATTT
1 TTTTAAGCTTT
*
38622674 TTTCAAG-TTT
1 TTTTAAGCTTT
*
38622684 TTTT-TGCTTT
1 TTTTAAGCTTT
38622694 TTTT
1 TTTT
38622698 GAGGATGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 1 0.03
10 13 0.43
11 16 0.53
ACGTcount: A:0.15, C:0.07, G:0.09, T:0.70
Consensus pattern (11 bp):
TTTTAAGCTTT
Found at i:38622760 original size:7 final size:7
Alignment explanation
Indices: 38622745--38623239 Score: 405
Period size: 7 Copynumber: 71.3 Consensus size: 7
38622735 TTTTTATGTA
38622745 TTTAGGG
1 TTTAGGG
*
38622752 TTTAAGG
1 TTTAGGG
38622759 TTTAGGG
1 TTTAGGG
38622766 TTTAGGG
1 TTTAGGG
*
38622773 CTTAGGG
1 TTTAGGG
*
38622780 TTCAGGG
1 TTTAGGG
*
38622787 TTCAGGG
1 TTTAGGG
*
38622794 TTCA-GG
1 TTTAGGG
*
38622800 TTCAGGG
1 TTTAGGG
*
38622807 TTCAGGG
1 TTTAGGG
*
38622814 TTCAGGG
1 TTTAGGG
*
38622821 TTCA-GG
1 TTTAGGG
*
38622827 TTCAGGG
1 TTTAGGG
*
38622834 TTCAGGG
1 TTTAGGG
*
38622841 TTCAGGG
1 TTTAGGG
*
38622848 TTCAGGG
1 TTTAGGG
38622855 TTTAGGG
1 TTTAGGG
* *
38622862 TTCACGG
1 TTTAGGG
*
38622869 TTCAGGG
1 TTTAGGG
*
38622876 TTCAGGG
1 TTTAGGG
*
38622883 TTCAGGG
1 TTTAGGG
*
38622890 TTCAGGG
1 TTTAGGG
*
38622897 GTTAGGG
1 TTTAGGG
*
38622904 GTTAGGG
1 TTTAGGG
*
38622911 GTTAGGG
1 TTTAGGG
38622918 TTTAGGG
1 TTTAGGG
*
38622925 TTTCGGG
1 TTTAGGG
*
38622932 GTTAGGG
1 TTTAGGG
*
38622939 TTTCGGG
1 TTTAGGG
*
38622946 TTTCGGG
1 TTTAGGG
*
38622953 TTT-CGG
1 TTTAGGG
*
38622959 TTTCGGG
1 TTTAGGG
38622966 TTTA-GG
1 TTTAGGG
*
38622972 TTTCGGG
1 TTTAGGG
*
38622979 TTTCGGG
1 TTTAGGG
*
38622986 TTTCGGG
1 TTTAGGG
*
38622993 TTTCGGG
1 TTTAGGG
*
38623000 TTT-CGG
1 TTTAGGG
*
38623006 TTTCGGG
1 TTTAGGG
38623013 TTTA-GG
1 TTTAGGG
*
38623019 TTTCGGG
1 TTTAGGG
*
38623026 TTTCGGG
1 TTTAGGG
*
38623033 TTTTTAAGG
1 --TTTAGGG
*
38623042 TTTCGGG
1 TTTAGGG
38623049 TTTTTAGGG
1 --TTTAGGG
*
38623058 TTTCGGG
1 TTTAGGG
*
38623065 TTTCGGG
1 TTTAGGG
* *
38623072 TTTTGAG
1 TTTAGGG
* *
38623079 TTTCGAG
1 TTTAGGG
38623086 TTTAGGG
1 TTTAGGG
*
38623093 -TTCGGG
1 TTTAGGG
*
38623099 TTTCGGG
1 TTTAGGG
*
38623106 TTTCGGG
1 TTTAGGG
*
38623113 TTTCGGG
1 TTTAGGG
*
38623120 TTTCGGG
1 TTTAGGG
38623127 TTTAGGG
1 TTTAGGG
38623134 TTTTAGGG
1 -TTTAGGG
*
38623142 GTTAGGG
1 TTTAGGG
38623149 TTTAGGG
1 TTTAGGG
38623156 TTTAGGG
1 TTTAGGG
38623163 TTTAGGG
1 TTTAGGG
*
38623170 GTTAGGG
1 TTTAGGG
*
38623177 GTTAGGG
1 TTTAGGG
*
38623184 TTTTGGG
1 TTTAGGG
38623191 TTTAGGG
1 TTTAGGG
38623198 TTTAGGG
1 TTTAGGG
38623205 TTTA-GG
1 TTTAGGG
38623211 TTTAGGG
1 TTTAGGG
38623218 -TTAGGG
1 TTTAGGG
38623224 TTTAGGG
1 TTTAGGG
38623231 TTTAGGG
1 TTTAGGG
38623238 TT
1 TT
38623240 AGGTTTTTTT
Statistics
Matches: 430, Mismatches: 44, Indels: 28
0.86 0.09 0.06
Matches are distributed among these distances:
6 49 0.11
7 363 0.84
8 7 0.02
9 11 0.03
ACGTcount: A:0.10, C:0.08, G:0.42, T:0.40
Consensus pattern (7 bp):
TTTAGGG
Found at i:38623045 original size:16 final size:16
Alignment explanation
Indices: 38623024--38623067 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
38623014 TTAGGTTTCG
38623024 GGTTTCGGGTTTTTAA
1 GGTTTCGGGTTTTTAA
*
38623040 GGTTTCGGGTTTTTAG
1 GGTTTCGGGTTTTTAA
38623056 GGTTTCGGGTTT
1 GGTTTCGGGTTT
38623068 CGGGTTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.07, C:0.07, G:0.36, T:0.50
Consensus pattern (16 bp):
GGTTTCGGGTTTTTAA
Done.