Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012484.1 Corchorus olitorius cultivar O-4 contig12517, whole genome shotgun sequence
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: 36737
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1334 original size:21 final size:21
Alignment explanation
Indices: 1305--1400 Score: 146
Period size: 21 Copynumber: 4.8 Consensus size: 21
1295 ATTTAACGTG
*
1305 TTGACTATCAAACTTTGGGGT
1 TTGACTATCAAAATTTGGGGT
*
1326 TTTACTATCAAAATTTGGGGT
1 TTGACTATCAAAATTTGGGGT
1347 TTGACTATCAAAATTTGGGGT
1 TTGACTATCAAAATTTGGGGT
1368 TTGACTATC--AA--TGGGGT
1 TTGACTATCAAAATTTGGGGT
1385 TTGACTATCAAAATTT
1 TTGACTATCAAAATTT
1401 AATTAATTGT
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
17 15 0.22
19 4 0.06
21 49 0.72
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (21 bp):
TTGACTATCAAAATTTGGGGT
Found at i:1518 original size:21 final size:21
Alignment explanation
Indices: 1493--1700 Score: 213
Period size: 21 Copynumber: 9.9 Consensus size: 21
1483 TCAAATCGCA
* *
1493 TTGATGGTCAACCCCCAAATT
1 TTGATAGTCAAACCCCAAATT
*
1514 TTGATAGTCAAACCCCAAAGT
1 TTGATAGTCAAACCCCAAATT
*
1535 TTGATGGTC-AACCCCTAAATT
1 TTGATAGTCAAACCCC-AAATT
* *
1556 TTGATATTC-AACACCCAAAGT
1 TTGATAGTCAAAC-CCCAAATT
* *
1577 TTGATGGTCAAACCCCAAAAT
1 TTGATAGTCAAACCCCAAATT
* * *
1598 TCGATAGTTAAACCCCAAAAT
1 TTGATAGTCAAACCCCAAATT
* * *
1619 TTGATAGTCAATCCTCGAATT
1 TTGATAGTCAAACCCCAAATT
*
1640 TTGATAGTCAAACCCCAAAGT
1 TTGATAGTCAAACCCCAAATT
* * *
1661 TTGATGGTCAACCCCCGAATT
1 TTGATAGTCAAACCCCAAATT
*
1682 TTAATAGTCAAACCCCAAA
1 TTGATAGTCAAACCCCAAA
1701 GTTTCATATA
Statistics
Matches: 152, Mismatches: 32, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
20 6 0.04
21 140 0.92
22 6 0.04
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (21 bp):
TTGATAGTCAAACCCCAAATT
Found at i:1546 original size:42 final size:42
Alignment explanation
Indices: 1493--1704 Score: 291
Period size: 42 Copynumber: 5.0 Consensus size: 42
1483 TCAAATCGCA
1493 TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
1 TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
* *
1535 TTGATGGTCAACCCCTAAATTTTGATATTC-AACACCCAAAGT
1 TTGATGGTCAACCCCCAAATTTTGATAGTCAAAC-CCCAAAGT
* * * * *
1577 TTGATGGTCAAACCCCAAAATTCGATAGTTAAACCCCAAAAT
1 TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
* * * *
1619 TTGATAGTCAATCCTCGAATTTTGATAGTCAAACCCCAAAGT
1 TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
* *
1661 TTGATGGTCAACCCCCGAATTTTAATAGTCAAACCCCAAAGT
1 TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
1703 TT
1 TT
1705 CATATATTTC
Statistics
Matches: 147, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
41 3 0.02
42 141 0.96
43 3 0.02
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.28
Consensus pattern (42 bp):
TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
Found at i:3214 original size:10 final size:10
Alignment explanation
Indices: 3187--3217 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3177 CACCTGTTAA
*
3187 TGTAATTAAT
1 TGTAATTGAT
3197 TGTAATTGAT
1 TGTAATTGAT
3207 TGTAATTGAT
1 TGTAATTGAT
3217 T
1 T
3218 TTGGTATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (10 bp):
TGTAATTGAT
Found at i:6377 original size:5 final size:5
Alignment explanation
Indices: 6363--6395 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
6353 CATATTAACA
6363 ATTTT A-TTT ATTTT ATTTT ATTTT ATTTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
6396 CCTTTTCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:6401 original size:15 final size:15
Alignment explanation
Indices: 6363--6395 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
6353 CATATTAACA
6363 ATTTTATTT-ATTTT
1 ATTTTATTTCATTTT
*
6377 ATTTTATTTTATTTT
1 ATTTTATTTCATTTT
6392 ATTT
1 ATTT
6396 CCTTTTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
ATTTTATTTCATTTT
Found at i:8411 original size:20 final size:20
Alignment explanation
Indices: 8388--8426 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
8378 AGCAAAACGA
8388 GAATAAAACATTGAAAACAG
1 GAATAAAACATTGAAAACAG
*
8408 GAATGAAACATTGAAAACA
1 GAATAAAACATTGAAAACA
8427 ACACCTTCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.10, G:0.15, T:0.15
Consensus pattern (20 bp):
GAATAAAACATTGAAAACAG
Found at i:8464 original size:68 final size:67
Alignment explanation
Indices: 8372--8542 Score: 261
Period size: 68 Copynumber: 2.5 Consensus size: 67
8362 CCTTCTGATG
* *
8372 GGGAAGAGCAAAACGAGAATAAAACATTGAAAACAGGAATGAAACATTGAAAACAACACCTTCCG
1 GGGAAGGGCAAAAC-AGAATAAAACATTGAAAACAAGAATGAAACATTGAAAACAACACCTTCCG
8437 ACC
65 ACC
*
8440 GGGAAGGGCAAAACAAGAATAAAACATTGAAAACAAGAATGAAATATTGAAAACAACACCTTCCG
1 GGGAAGGGCAAAAC-AGAATAAAACATTGAAAACAAGAATGAAACATTGAAAACAACACCTTCCG
8505 ACC
65 ACC
** * *
8508 AAGAAGGGCAAAACGGGATAAAACATTGAAAACAA
1 GGGAAGGGCAAAACAGAATAAAACATTGAAAACAA
8543 CACCTTCCGA
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 19 0.20
68 76 0.80
ACGTcount: A:0.52, C:0.17, G:0.19, T:0.12
Consensus pattern (67 bp):
GGGAAGGGCAAAACAGAATAAAACATTGAAAACAAGAATGAAACATTGAAAACAACACCTTCCGA
CC
Found at i:8474 original size:20 final size:20
Alignment explanation
Indices: 8449--8495 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
8439 CGGGAAGGGC
8449 AAAACAAGAATAAAACATTG
1 AAAACAAGAATAAAACATTG
* *
8469 AAAACAAGAATGAAATATTG
1 AAAACAAGAATAAAACATTG
8489 AAAACAA
1 AAAACAA
8496 CACCTTCCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.66, C:0.09, G:0.11, T:0.15
Consensus pattern (20 bp):
AAAACAAGAATAAAACATTG
Found at i:8521 original size:48 final size:47
Alignment explanation
Indices: 8476--8614 Score: 215
Period size: 48 Copynumber: 2.9 Consensus size: 47
8466 TTGAAAACAA
* * **
8476 GAATGAAATATTGAAAACAACACCTTCCGACCAAGAAGGGCAAAACG
1 GAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
*
8523 GGATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGG
1 GAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAAC-G
*
8571 GAATAAAACATTGAAAACAACACCTTCCGATCGGGAAGGGCAAA
1 GAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
8615 TTGGGGATAT
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
47 41 0.49
48 43 0.51
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (47 bp):
GAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
Found at i:8539 original size:47 final size:48
Alignment explanation
Indices: 8476--8614 Score: 226
Period size: 47 Copynumber: 2.9 Consensus size: 48
8466 TTGAAAACAA
* * **
8476 GAATGAAATATTGAAAACAACACCTTCCGACCAAGAAGGGCAAAACGG
1 GAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGG
8524 G-ATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGG
1 GAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGG
*
8571 GAATAAAACATTGAAAACAACACCTTCCGATCGGGAAGGGCAAA
1 GAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
8615 TTGGGGATAT
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
47 43 0.51
48 42 0.49
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (48 bp):
GAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGG
Found at i:8690 original size:40 final size:41
Alignment explanation
Indices: 8586--9012 Score: 330
Period size: 41 Copynumber: 10.7 Consensus size: 41
8576 AAACATTGAA
* * *
8586 AACAACACCTTCCGATCG-GGAAGGGCAAATTGGGGATATGCT
1 AACAACACCTTCCGAT-GAGGAAGGGCAAATT-GGTAAAGGCT
*
8628 GACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAAGGC-
1 AACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAAGGCT
* * *
8668 AACAACACCTCCCAAT-AGGGAAGGGCAAATTGGT-AATGCT
1 AACAACACCTTCCGATGA-GGAAGGGCAAATTGGTAAAGGCT
* * ** *
8708 GACAACGCCTTCTAATGAGGAAGGGCAAATTGGACAAAGGC-
1 AACAACACCTTCCGATGAGGAAGGGCAAATTGG-TAAAGGCT
* * *
8749 AACAACACCTCCCGATGAGGAAGGGCAAACTGGT-AATGCT
1 AACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAAGGCT
* ** *
8789 GACAACACCTTCTAATGAGGAAGGGCAAATTGGACAAAGGC-
1 AACAACACCTTCCGATGAGGAAGGGCAAATTGG-TAAAGGCT
* * * *
8830 AACAACACCTCCCGATGAGGAAGGGCAAATTGGCAAATGAT
1 AACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAAGGCT
* * * ***
8871 GACAACACCTTCCGATGAGGAAGGGCAGACTGGTAAACTTT
1 AACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAAGGCT
* * *
8912 GACAACACCTTCC-A--AAG-A-GG--AA-TGGCAAA--CT
1 AACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAAGGCT
* * ***
8943 GACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTT
1 AACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAAGGCT
* * *
8984 GACAACACCTTCCAAAGAGGAAGGGCAAA
1 AACAACACCTTCCGATGAGGAAGGGCAAA
9013 CTGACAACAC
Statistics
Matches: 313, Mismatches: 52, Indels: 41
0.77 0.13 0.10
Matches are distributed among these distances:
31 14 0.04
32 1 0.00
33 6 0.02
34 3 0.01
35 1 0.00
36 4 0.01
37 1 0.00
38 4 0.01
39 15 0.05
40 90 0.29
41 138 0.44
42 36 0.12
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.16
Consensus pattern (41 bp):
AACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAAGGCT
Found at i:8783 original size:81 final size:81
Alignment explanation
Indices: 8586--8897 Score: 450
Period size: 81 Copynumber: 3.8 Consensus size: 81
8576 AAACATTGAA
* * *
8586 AACAACACCTTCCGATCG-GGAAGGGCAAATTGGGGATATGCTGACAACACCTTCCGATGAGGAA
1 AACAACACCTCCCGAT-GAGGAAGGGCAAATT-GGTA-ATGCTGACAACACCTTCCAATGAGGAA
*
8650 GGGCAAATTGG-TAAAGGC
63 GGGCAAATTGGACAAAGGC
* * *
8668 AACAACACCTCCCAAT-AGGGAAGGGCAAATTGGTAATGCTGACAACGCCTTCTAATGAGGAAGG
1 AACAACACCTCCCGATGA-GGAAGGGCAAATTGGTAATGCTGACAACACCTTCCAATGAGGAAGG
8732 GCAAATTGGACAAAGGC
65 GCAAATTGGACAAAGGC
* *
8749 AACAACACCTCCCGATGAGGAAGGGCAAACTGGTAATGCTGACAACACCTTCTAATGAGGAAGGG
1 AACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATGCTGACAACACCTTCCAATGAGGAAGGG
8814 CAAATTGGACAAAGGC
66 CAAATTGGACAAAGGC
* * *
8830 AACAACACCTCCCGATGAGGAAGGGCAAATTGGCAAATGATGACAACACCTTCCGATGAGGAAGG
1 AACAACACCTCCCGATGAGGAAGGGCAAATTGG-TAATGCTGACAACACCTTCCAATGAGGAAGG
8895 GCA
65 GCA
8898 GACTGGTAAA
Statistics
Matches: 210, Mismatches: 15, Indels: 10
0.89 0.06 0.04
Matches are distributed among these distances:
80 35 0.17
81 117 0.56
82 58 0.28
ACGTcount: A:0.36, C:0.22, G:0.27, T:0.15
Consensus pattern (81 bp):
AACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATGCTGACAACACCTTCCAATGAGGAAGGG
CAAATTGGACAAAGGC
Found at i:8896 original size:122 final size:121
Alignment explanation
Indices: 8586--9015 Score: 433
Period size: 122 Copynumber: 3.6 Consensus size: 121
8576 AAACATTGAA
* * *
8586 AACAACACCTTCCGATCG-GGAAGGGCAAATTGGGGATATGCTGACAACACCTTCCGATGAGGAA
1 AACAACACCTTCCGAT-GAGGAAGGGCAAATT-GGCAAATGATGACAACACCTTCCGATGAGGAA
* * * * * *
8650 GGGCAAATTGGTAAAGGC-AACAACACCTCCCAATAGGGAAGGGCAAATTGGTAATGCT
64 GGGCAAACTGGTAAATGCTGACAACACCTTCCAATA-GGAAGGGCAAATTGGCAAAGCT
* * ** * *
8708 GACAACGCCTTCTAATGAGGAAGGGCAAATTGGACAAAGGCA--ACAACACCTCCCGATGAGGAA
1 AACAACACCTTCCGATGAGGAAGGGCAAATTGG-CAAATG-ATGACAACACCTTCCGATGAGGAA
*
8771 GGGCAAACTGGT-AATGCTGACAACACCTTCTAATGAGGAAGGGCAAATTGGACAAAGGC-
64 GGGCAAACTGGTAAATGCTGACAACACCTTCCAAT-AGGAAGGGCAAATTGG-CAAA-GCT
*
8830 AACAACACCTCCCGATGAGGAAGGGCAAATTGGCAAATGATGACAACACCTTCCGATGAGGAAGG
1 AACAACACCTTCCGATGAGGAAGGGCAAATTGGCAAATGATGACAACACCTTCCGATGAGGAAGG
* *
8895 GCAGACTGGTAAACT-TTGACAACACCTTCCAA-A-G-A-GG--AA-TGGCAAA-CT
66 GCAAACTGGTAAA-TGCTGACAACACCTTCCAATAGGAAGGGCAAATTGGCAAAGCT
* * * * * *
8943 GACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACT-TTGACAACACCTTCCAAAGAGGAAG
1 AACAACACCTTCCGATGAGGAAGGGCAAATTGGCAAA-TGATGACAACACCTTCCGATGAGGAAG
9007 GGCAAACTG
65 GGCAAACTG
9016 ACAACACCTT
Statistics
Matches: 261, Mismatches: 34, Indels: 35
0.79 0.10 0.11
Matches are distributed among these distances:
112 1 0.00
113 63 0.24
114 5 0.02
115 3 0.01
116 2 0.01
118 2 0.01
119 1 0.00
120 6 0.02
121 68 0.26
122 90 0.34
123 19 0.07
124 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.26, T:0.16
Consensus pattern (121 bp):
AACAACACCTTCCGATGAGGAAGGGCAAATTGGCAAATGATGACAACACCTTCCGATGAGGAAGG
GCAAACTGGTAAATGCTGACAACACCTTCCAATAGGAAGGGCAAATTGGCAAAGCT
Found at i:8946 original size:31 final size:32
Alignment explanation
Indices: 8911--9046 Score: 127
Period size: 31 Copynumber: 4.1 Consensus size: 32
8901 TGGTAAACTT
*
8911 TGACAACACCTTCC-AAAGAGGAATGGCAAAC
1 TGACAACACCTTCCGAAAGAGGAAGGGCAAAC
*
8942 TGACAACACCTTCCG-ATGAGGAAGGGCAAACTGGTAAAC
1 TGACAACACCTTCCGAAAGAGGAAGGG----C----AAAC
8981 TTTGACAACACCTTCC-AAAGAGGAAGGGCAAAC
1 --TGACAACACCTTCCGAAAGAGGAAGGGCAAAC
*
9014 TGACAACACCTTCCGATA-AGGAAGGGCAAAC
1 TGACAACACCTTCCGAAAGAGGAAGGGCAAAC
9045 TG
1 TG
9047 GAAAAGTAGA
Statistics
Matches: 88, Mismatches: 4, Indels: 26
0.75 0.03 0.22
Matches are distributed among these distances:
31 52 0.59
32 2 0.02
33 4 0.05
35 1 0.01
37 1 0.01
39 4 0.05
41 24 0.27
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (32 bp):
TGACAACACCTTCCGAAAGAGGAAGGGCAAAC
Found at i:8987 original size:72 final size:72
Alignment explanation
Indices: 8870--9047 Score: 329
Period size: 72 Copynumber: 2.5 Consensus size: 72
8860 TGGCAAATGA
* *
8870 TGACAACACCTTCCGATGAGGAAGGGCAGACTGGTAAACTTTGACAACACCTTCCAAAGAGGAAT
1 TGACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTTGACAACACCTTCCAAAGAGGAAG
8935 GGCAAAC
66 GGCAAAC
8942 TGACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTTGACAACACCTTCCAAAGAGGAAG
1 TGACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTTGACAACACCTTCCAAAGAGGAAG
9007 GGCAAAC
66 GGCAAAC
*
9014 TGACAACACCTTCCGATAAGGAAGGGCAAACTGG
1 TGACAACACCTTCCGATGAGGAAGGGCAAACTGG
9048 AAAAGTAGAC
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 103 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.16
Consensus pattern (72 bp):
TGACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACTTTGACAACACCTTCCAAAGAGGAAG
GGCAAAC
Found at i:9119 original size:46 final size:46
Alignment explanation
Indices: 9069--9780 Score: 652
Period size: 46 Copynumber: 15.9 Consensus size: 46
9059 TAAACAACAT
* * *
9069 CTTCCGACCAGGAATGTGCATTTTTGGAATGAAAGAAAACAGTGAC
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGTGAC
* * * *
9115 CTTCCAATCAGGAAGGAGCATTTTTGG-A--AATGAAAACAGGGAC
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGTGAC
* * *
9158 CTTCCAACCAAGAAGGGGCATTTTTGGAAAGAAAGAAAACTGTGAC
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGTGAC
* * * *
9204 CTTCCGACCGGGAAGGGGCATTTTT-G---GAAATAAAACAGGGAC
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGTGAC
* * *
9246 CTTCAAACTAGGAAGGGGCATTTTTGGAAT-AAGAGAAAACTGTGAC
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAA-AGAAAACAGTGAC
*
9292 CTT-CAACCAGGAAGGGGCATTTTTGGAAAGAAAGAAAACTAG-GAC
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAAC-AGTGAC
* * * * * *
9337 TTTCCGACCAGGAATGGGCATTTTTGGAAAGAAAGAAAACTGGGAC
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGTGAC
* ** *
9383 CTTCCAACCAGGAAGGGGCTATTTTTGG-A--AATGAAAATTGGGAC
1 CTTCCAACCAGGAAGGGGC-ATTTTTGGAATGAAAGAAAACAGTGAC
* *
9427 CTTCCAACCAGGCAAGGGGCGTTTTTGGAAT-AGAAGAAAACAGGGAC
1 CTTCCAACCAGG-AAGGGGCATTTTTGGAATGA-AAGAAAACAGTGAC
* * * * *
9474 CTTCCATCCAGGAAGGGCCATTTTTGGAAAGAGAGAAAACTGTGAC
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGTGAC
* * * *
9520 CTTCCGATCGGGAAGGGGCATTTTTGGAAT---A-AAAACAGAGAC
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGTGAC
9562 CTTCCAACCAGGAAGGGGCATTTTT----TGAAATGAAAACAAG-GAC
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAA-GAAAAC-AGTGAC
* * * *
9605 CTTCCAATCAGGAAGGGGCATTTTTGGAAAGAGAGAAAACTGTGAC
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGTGAC
* * * * * *
9651 CATCCGACCGGGAAGGGGCATTTTTGGAAAGAAAGAAAGCTGTGAC
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGTGAC
* ** * * *
9697 CTTCCGACTGGGAAAGGTCATTTTTGGAAT-----AAAACAGAGAC
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGTGAC
* *
9738 CTTCCAACCAGGAAGGGGCATTTTTGGTATAAAAGAAAACAGT
1 CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGT
9781 TCTTTTGAAT
Statistics
Matches: 547, Mismatches: 85, Indels: 68
0.78 0.12 0.10
Matches are distributed among these distances:
38 1 0.00
41 33 0.06
42 65 0.12
43 71 0.13
44 35 0.06
45 49 0.09
46 259 0.47
47 34 0.06
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (46 bp):
CTTCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACAGTGAC
Found at i:9675 original size:177 final size:181
Alignment explanation
Indices: 9077--9764 Score: 809
Period size: 177 Copynumber: 3.9 Consensus size: 181
9067 ATCTTCCGAC
* * * * *
9077 CAGGAATGTGCATTTTTGGAAT-GAAAGAAAACAGTGACCTTCCAATCAGGAAGGAGCATTTTTG
1 CAGGAAGGGGCATTTTTGGAATAGAGAGAAAACAGTGACCTTCCAACCAGGAAGGGGCATTTTTG
* * * * * * *
9141 G--A-AATGAAAACAGGGACCTTCCAACCAAGAAGGGGCATTTTTGGAAAGAAAGAAAACTGTGA
66 GAAAGAAAGAAAACTGTGACCTTCCGACCAGGAAGGGGCATTTTTGG-AAGAAAGAAAACAGAGA
* *
9203 CCTTCCGACCGGGAAGGGGCATTTTTGGAAAT-AAAACAGGGACCTT-CAAA
130 CCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCAAA
*
9253 CTAGGAAGGGGCATTTTTGGAATA-AGAGAAAACTGTGACCTT-CAACCAGGAAGGGGCATTTTT
1 C-AGGAAGGGGCATTTTTGGAATAGAGAGAAAACAGTGACCTTCCAACCAGGAAGGGGCATTTTT
* * * *
9316 GGAAAGAAAGAAAACTAG-GACTTTCCGACCAGGAATGGGCATTTTTGGAAAGAAAGAAAACTGG
65 GGAAAGAAAGAAAACT-GTGACCTTCCGACCAGGAAGGGGCATTTTTGG-AAGAAAGAAAACAGA
** *
9380 GACCTTCCAACCAGGAAGGGGCTATTTTTGGAAATGAAAATTGGGACCTTCCAAC
128 GACCTTCCAACCAGGAAGGGGC-ATTTTTGGAAATGAAAACAGGGACCTTCCAAA
* * * *
9435 CAGGCAAGGGGCGTTTTTGGAATAGA-AGAAAACAGGGACCTTCCATCCAGGAAGGGCCATTTTT
1 CAGG-AAGGGGCATTTTTGGAATAGAGAGAAAACAGTGACCTTCCAACCAGGAAGGGGCATTTTT
* * * *
9499 GGAAAGAGAGAAAACTGTGACCTTCCGATCGGGAAGGGGCATTTTTGG-A-ATA-AAAACAGAGA
65 GGAAAGAAAGAAAACTGTGACCTTCCGACCAGGAAGGGGCATTTTTGGAAGAAAGAAAACAGAGA
* * *
9561 CCTTCCAACCAGGAAGGGGCATTTTTTGAAATGAAAACAAGGACCTTCCAAT
130 CCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCAAA
* * * *
9613 CAGGAAGGGGCATTTTTGGAA-AGAGAGAAAACTGTGACCATCCGACCGGGAAGGGGCATTTTTG
1 CAGGAAGGGGCATTTTTGGAATAGAGAGAAAACAGTGACCTTCCAACCAGGAAGGGGCATTTTTG
* ** * * *
9677 GAAAGAAAGAAAGCTGTGACCTTCCGACTGGGAAAGGTCATTTTT-G--G-AATAAAACAGAGAC
66 GAAAGAAAGAAAACTGTGACCTTCCGACCAGGAAGGGGCATTTTTGGAAGAAAGAAAACAGAGAC
9738 CTTCCAACCAGGAAGGGGCATTTTTGG
131 CTTCCAACCAGGAAGGGGCATTTTTGG
9765 TATAAAAGAA
Statistics
Matches: 444, Mismatches: 52, Indels: 32
0.84 0.10 0.06
Matches are distributed among these distances:
175 1 0.00
176 63 0.14
177 122 0.27
178 32 0.07
179 97 0.22
180 15 0.03
181 16 0.04
182 37 0.08
183 61 0.14
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (181 bp):
CAGGAAGGGGCATTTTTGGAATAGAGAGAAAACAGTGACCTTCCAACCAGGAAGGGGCATTTTTG
GAAAGAAAGAAAACTGTGACCTTCCGACCAGGAAGGGGCATTTTTGGAAGAAAGAAAACAGAGAC
CTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCAAA
Found at i:17953 original size:15 final size:15
Alignment explanation
Indices: 17920--17962 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
17910 GTTTCTTCTC
17920 TAATTTTT-T-TTTT
1 TAATTTTTGTGTTTT
*
17933 TTATTTTTGTGTTTT
1 TAATTTTTGTGTTTT
17948 TAATTTTTGTGTTTT
1 TAATTTTTGTGTTTT
17963 GCGTTTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 7 0.27
14 1 0.04
15 18 0.69
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (15 bp):
TAATTTTTGTGTTTT
Found at i:24495 original size:15 final size:16
Alignment explanation
Indices: 24461--24502 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
24451 TTACTTTGCT
*
24461 TTGTTTTCTAGTATAA
1 TTGTTTTCTTGTATAA
*
24477 TTGTTTTCTTTTA-AA
1 TTGTTTTCTTGTATAA
24492 TTGTTCTTCTT
1 TTGTT-TTCTT
24503 AACCCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.64
Consensus pattern (16 bp):
TTGTTTTCTTGTATAA
Found at i:26554 original size:904 final size:907
Alignment explanation
Indices: 24664--29784 Score: 6948
Period size: 904 Copynumber: 5.7 Consensus size: 907
24654 CGATCAATTA
*
24664 TTTTCTGAGTTCACCATCTCTATTCTAAGCACCCATGACTTAAAAGATATATTTGGACTCTGATA
1 TTTTCTGAGTTCACCATCTCTATACTAAGCACCCATGACTTAAAAGATATATTTGGACTCTGATA
* * * * *
24729 TCACATTA-GATAAATAAAACATTAAAAATAAATTATTTTCTAATTTACAAATATATTTAAATAC
66 TCACA-TAGGATAAATAAAAAATTAAAAATAATTTATTTTTTAATGTACAAATATATTTAAATAT
* *
24793 ATATACCTATATATATATATATATACATATGAATTTAAATTAATATTTTCCAATATTTATATATA
130 ATATA-CTATATATATA-AT-T-T-C---T--A-CT-AA-T-AT-TCTTCCAATATTTATATATA
* * *
24858 ATTTATTTTCCTTAAAAAAATTAAAAAAGTTTCACAGGTGACAAAAAAAGGTCCAGCCACTGAAA
180 ATTGATTTTCCTT-AAAAAATTAAAAAACTTTCACAGGTGACAAAAAAAGGTCCAGCCACTAAAA
* *
24923 TACTCAGCAGAACACTATATATCATTTAGGCTCCAATAAATGCAGCAATGTTTATAGGATGAATC
244 TACTCAACAGAACACTATATATCATTTGGGCTCCAATAAATGCAGCAATGTTTATAGGATGAATC
* *
24988 GGAATGCTATATGGCCGTGTAACTTGCTTGATTGCTTCTGTTGTTTTTTTTATTCGTTTCAAGGA
309 GAAATGCTATATGGCCGTGTAACTTGCTTGATTGCTTCTGTTG-TTGTTTTATTCGTTTCAAGGA
*
25053 TATTATACAACATCATTTTGTTGGCATAAACTATATATGAG-AAGAAACCTGATGAGCGATGTTG
373 TATTATACGACATCATTTTGTTGGCATAAACTATATATGAGAAAGAAACCTGATGAGCGATGTTG
*
25117 ATAAAGCTTTAATCATTCTGTTGGTTTCCGCCTTCGCTTTCTTAGT-AAAAACCTGATAATACCC
438 ATAAAGCTTTAATCATTCTGTTGGTTTCCGCCTTCGCTTTCTTAGTAAAAAACTTGATAATACCC
** * * * *
25181 AACGTTGAAAAGAAGGGCACTGTGACCCTTTATTCGAATGAAACTGTGAATTTTGTTTTGGAGCT
503 AACGTTGAAAAGAAGGGCACAATGACCCTTTATTTGAATCAGACTGTGAATTTTGTGTTGGAGCT
* *
25246 ATTAACCATAGCCATGATCATGACCTGGACCACTATCATTCCAGATTGAGGAGTTGGAATCCTAG
568 ATTAACCATAGCCATGATCATGACCTGGACCACTCTCATTCCAGATTGAGGAGTTGGAATCTTAG
** *
25311 CAACGCATTTCACACTGTTCGTCCAATGTTATCAATACATTATCAGGAAGCGTCTGAAAAACTTG
633 CAAC-CATTTCACGTTGTTCGTCCAATATTATCAATACATTATCAGGAAGCGTCTGAAAAACTTG
* *
25376 AACTTTGCCTTCGGCATAAATTCCTTTGATAGAAATGACGTGATATCAATAAAACCAAAAGCCCA
697 AACTTTGTCTTCGGCATAAATTCCTTTGATAGAAATGACGTGATATCAATAAAACTAAAAGCCCA
* *
25441 CCCAATGAACCTATATTATATCTTAACAACATTATGAACTAGTGTGTATCTCATATGTCACACAT
762 CCCAATGAACCTATATCATATCTTAACAACATTATGAACTAGTGTGTATCTCATATGTCTCACAT
** * * * *
25506 AAGTGAAAGAATATTAATAAAAAAGAAAATATCTTAAGTTATAATATCACCTATTAAATAGCCAC
827 AAGTGAAAGAATAAAAAAAAAAAAGAAATTATCTAAAGTCATAATATCACCTATTAAATAGCCAC
25571 CATACTGAACGGATTG
892 CATACTGAACGGATTG
*
25587 TTTTCTGAGTTCACCATCTCTATACTAAGCACCCATGACTTAAAATATATATTTGGACTCTGATA
1 TTTTCTGAGTTCACCATCTCTATACTAAGCACCCATGACTTAAAAGATATATTTGGACTCTGATA
*
25652 TGACATAGGATAAATAAAAAATTAAAAATAATTTATTTTTTAATGTA-AAATATATTTAAATATA
66 TCACATAGGATAAATAAAAAATTAAAAATAATTTATTTTTTAATGTACAAATATATTTAAATATA
25716 TATAC-ATATATA-AATTTCTACTAAT-TTCTTCCAATATTTATATATAATTGATTTTCCATTAA
131 TATACTATATATATAATTTCTACTAATATTCTTCCAATATTTATATATAATTGATTTTCC-TTAA
*
25778 AAAATTAAAAAACTTTCACAGGTGACAAAAAAAGGTCCAACCACTAAAATACTCAACAGAACACT
195 AAAATTAAAAAACTTTCACAGGTGACAAAAAAAGGTCCAGCCACTAAAATACTCAACAGAACACT
* * *
25843 ATATATCAGTTGGGCTACAATAAATGCAGCAATTTTTATAGGATGAATCGAAATGCTATATGGCC
260 ATATATCATTTGGGCTCCAATAAATGCAGCAATGTTTATAGGATGAATCGAAATGCTATATGGCC
* *
25908 GTGAAACTTGCTTGATTGCTTCTGTTGTTGTTTTATTCGTTTCAAGGATATTATACGACATTA-T
325 GTGTAACTTGCTTGATTGCTTCTGTTGTTGTTTTATTCGTTTCAAGGATATTATACGACATCATT
* * * *
25972 TTATTGGCATAAACTATATATGACAAACAAAGCTGATGAGCGATGTTGATAAAGCTTTAATCATT
390 TTGTTGGCATAAACTATATATGAGAAAGAAACCTGATGAGCGATGTTGATAAAGCTTTAATCATT
*
26037 CTTTTGGTTTCCGCCTTCGCTTTCTTAGTAAAAAACTTGATAATACCCAACGTTGAAAAGAAGGG
455 CTGTTGGTTTCCGCCTTCGCTTTCTTAGTAAAAAACTTGATAATACCCAACGTTGAAAAGAAGGG
** * * * * * *
26102 CACTGTGACCCTTTATTCGAATGAGACTGTAAATATTGTTTTGG-GCCTATTAACCATAGTCATG
520 CACAATGACCCTTTATTTGAATCAGACTGTGAATTTTGTGTTGGAG-CTATTAACCATAGCCATG
* * * *
26166 ATCATGATCTGGACCATTCTCATTCCAGATTGAGGAGTTGGAATCCTAGCAACTCATTTCACGCT
584 ATCATGACCTGGACCACTCTCATTCCAGATTGAGGAGTTGGAATCTTAGCAAC-CATTTCACGTT
* * * * *
26231 GTTCGTCCCATTTTATCAATACATTATCAGGATGTGTCTCAAAAACTTGAACTTTGTCTTCGGCA
648 GTTCGTCCAATATTATCAATACATTATCAGGAAGCGTCTGAAAAACTTGAACTTTGTCTTCGGCA
* * * * *
26296 TAAATTCCTTTGATAAAAATGACGTTATATTAATAAAACCAAAATCCCACCCAATGAAACC-ATA
713 TAAATTCCTTTGATAGAAATGACGTGATATCAATAAAACTAAAAGCCCACCCAATG-AACCTATA
* * * * *
26360 TGATATCTTAACAGCATTATGAACTAGTGTGTTTCTCATATGCCTCACATAAGTGAATGAATAAA
777 TCATATCTTAACAACATTATGAACTAGTGTGTATCTCATATGTCTCACATAAGTGAAAGAATAAA
* *
26425 AACAAAAAAGAAATTATCTAAAGTCATAATATCACCTATTAAATAGCCACCATACTGATCGGATT
842 AAAAAAAAAGAAATTATCTAAAGTCATAATATCACCTATTAAATAGCCACCATACTGAACGGATT
26490 G
907 G
* *
26491 TTTTCTGAGTTCACCATCTCTATACTAAGGACTCATGACTTAAAAGATATATTTGGACTCTGATA
1 TTTTCTGAGTTCACCATCTCTATACTAAGCACCCATGACTTAAAAGATATATTTGGACTCTGATA
* *
26556 TGACTTAGGATAAATAAAAAATTAAAAATAATTTATTTTTTAATGTA-AAATATATTTAAATATA
66 TCACATAGGATAAATAAAAAATTAAAAATAATTTATTTTTTAATGTACAAATATATTTAAATATA
* *
26620 TATAC-ATATATA-AATTTCTACTAAT-TTCTTCCAATATTTATAAATAATTGATTTTCTTTTAA
131 TATACTATATATATAATTTCTACTAATATTCTTCCAATATTTATATATAATTGATTTTC-CTTAA
** * * * * * *
26682 AAAATTTTAAAACTTTCACAGGTCAC-AAAAACGGTCTAGGCACTAAAATA-TTAAGCATAACAC
195 AAAATTAAAAAACTTTCACAGGTGACAAAAAAAGGTCCAGCCACTAAAATACTCAA-CAGAACAC
* * * ***
26745 TATATATAATTTGGGCTCCAATAAATGCAGCAATATTTACAGGATGAATCGAAATGCTATATATT
259 TATATATCATTTGGGCTCCAATAAATGCAGCAATGTTTATAGGATGAATCGAAATGCTATATGGC
* * * * * *
26810 CGTGTAACATGCGTAATTGTTTCTGTTGTTGTTTTATTCGTTTCCAGGATATTATACTACATCAT
324 CGTGTAACTTGCTTGATTGCTTCTGTTGTTGTTTTATTCGTTTCAAGGATATTATACGACATCAT
* *
26875 TTTGTTGGCATAAACAATATATGAGAAAGAAACCTGATGAACGATGTTGATAAAG-TTT--TCCA
389 TTTGTTGGCATAAACTATATATGAGAAAGAAACCTGATGAGCGATGTTGATAAAGCTTTAAT-CA
* * * ** * *
26937 -TC--------T--G-----GCTTTGTTACTAAAAAACTTGATAATATCCAGTGTTGAGAAGAAC
453 TTCTGTTGGTTTCCGCCTTCGCTTTCTTAGTAAAAAACTTGATAATACCCAACGTTGAAAAGAAG
** *
26986 AACACAATGACCCTTTATTTGAATCAGA-TCGTGAATTTTGTGTTGGAGCTATTACCCATAGCCA
518 GGCACAATGACCCTTTATTTGAATCAGACT-GTGAATTTTGTGTTGGAGCTATTAACCATAGCCA
*
27050 TGATCATGACCTGGACCACTCTCATTCCAGATTAAGGAGTTGGAATCTTAGCAACCTATTTCACG
582 TGATCATGACCTGGACCACTCTCATTCCAGATTGAGGAGTTGGAATCTTAGCAACC-ATTTCACG
* * * *
27115 TTGTTCGTCCAATATTATCAATGCATTACCAGGCA-CGTCTGAAAAACTTGAACTTTGTCTTTGG
646 TTGTTCGTCCAATATTATCAATACATTATCAGGAAGCGTCTGAAAAACTTGAACTTTGTCTTCGG
* * *
27179 CATAAATTCCTTTGATAGATATGGCGTGATATCAATAAAACTAAAAGCTCACCCAATGAACCTAT
711 CATAAATTCCTTTGATAGAAATGACGTGATATCAATAAAACTAAAAGCCCACCCAATGAACCTAT
* *
27244 ATCATATCTTAACAACATTATGAACTAGTGTGTATCTCATATGTCTCATATAAGTGAAAGAATAT
776 ATCATATCTTAACAACATTATGAACTAGTGTGTATCTCATATGTCTCACATAAGTGAAAGAATAA
** * * * *
27309 AAATTAAAAAGAAATTATTTGAAGTCATAATATCACCTACTAAATAGCCACCATACTGAAAGGAT
841 AAAAAAAAAAGAAATTATCTAAAGTCATAATATCACCTATTAAATAGCCACCATACTGAACGGAT
*
27374 TA
906 TG
27376 TTTTCTGAGTTCACCATCTCTATACTAAGCACCCATGACTTAAAAGATATATTTGGACTCTGATA
1 TTTTCTGAGTTCACCATCTCTATACTAAGCACCCATGACTTAAAAGATATATTTGGACTCTGATA
* * * *
27441 TCACATAAGATAAATAAAACATTAAAAATAATTTATTTTCTAATGTACGAATATATTTAAATATA
66 TCACATAGGATAAATAAAAAATTAAAAATAATTTATTTTTTAATGTACAAATATATTTAAATATA
* * *
27506 TATACATATATATATATATATGAATTTCAATTAATATT-TTCCAACATTTATATATAATTGATTT
131 TATAC-------TATATATAT-AATTTCTACTAATATTCTTCCAATATTTATATATAATTGATTT
* * * * *
27570 TCCTGAAAAAAATT-AAAAACTTTCACAGGAGACAAAACAAGGTCCAGCCACTGAAATACACAAC
188 TCCT-TAAAAAATTAAAAAACTTTCACAGGTGACAAAAAAAGGTCCAGCCACTAAAATACTCAAC
* *
27634 AGACCACTATATATCATTTGGGCTCCAATAAATGCAGCAATGTTTATAGGATGAATTGAAATGCT
252 AGAACACTATATATCATTTGGGCTCCAATAAATGCAGCAATGTTTATAGGATGAATCGAAATGCT
* **
27699 ATATTGCCGTGTAACTTGCTTGATTGCTTC---TGTTGTTTTATTCGTTTCATTGATATTATACG
317 ATATGGCCGTGTAACTTGCTTGATTGCTTCTGTTGTTGTTTTATTCGTTTCAAGGATATTATACG
*
27761 ACATCATTTTGTTGGCATAAACTATATATGAGAAAGAAACCTGATGAGCGATATTGATAAAGCTT
382 ACATCATTTTGTTGGCATAAACTATATATGAGAAAGAAACCTGATGAGCGATGTTGATAAAGCTT
* *
27826 TAATTATTCTGTTGGTTTCCGCCTTCGCTTTCTTAGTAAAAAAC-TGATAATACCCAACATTGAA
447 TAATCATTCTGTTGGTTTCCGCCTTCGCTTTCTTAGTAAAAAACTTGATAATACCCAACGTTGAA
** * * *
27890 AAGAAGGGCACTTTGACCCTTTATTTGAATGAGACTGCGAATTTTGTTTTGGAGCTATTAACCAT
512 AAGAAGGGCACAATGACCCTTTATTTGAATCAGACTGTGAATTTTGTGTTGGAGCTATTAACCAT
* * *
27955 AGCCATGATCATGACCTGGACCACACTCAATCCAGATTGAGGAGTTGGAATCTTAGCAACGTATT
577 AGCCATGATCATGACCTGGACCACTCTCATTCCAGATTGAGGAGTTGGAATCTTAGCAAC-CATT
* * * **
28020 TTACATTGTTCGTCCAATGTTATCAATACATTATCAGGAAGCGTCTGAAAAAAGTGAACTTTGTC
641 TCACGTTGTTCGTCCAATATTATCAATACATTATCAGGAAGCGTCTGAAAAACTTGAACTTTGTC
* * *
28085 TTCGGCATAAATTCCTTTAATAGAAATGACGTTATATCAATAAAACTAAAATCCCACCCAATGAA
706 TTCGGCATAAATTCCTTTGATAGAAATGACGTGATATCAATAAAACTAAAAGCCCACCCAATGAA
* * * * * *
28150 CCCATATGATATCTTAACAACATTATGAACTAGTGTCTTTCTCATATGCCTCACATGAGTGAAAG
771 CCTATATCATATCTTAACAACATTATGAACTAGTGTGTATCTCATATGTCTCACATAAGTGAAAG
* *
28215 AATAAAAATGAAAAAAAGTAATTATCTAAAGTCATAATATCACATATTAAATAGCCACCATACTG
836 AATAAAAA--AAAAAAAGAAATTATCTAAAGTCATAATATCACCTATTAAATAGCCACCATACTG
*
28280 AACGAATTG
899 AACGGATTG
*
28289 TTTTCTGAGTTCACTATCTCTATACTAAGCACCCATGACTTAAAAGATATATTTGGACTCTGATA
1 TTTTCTGAGTTCACCATCTCTATACTAAGCACCCATGACTTAAAAGATATATTTGGACTCTGATA
* *
28354 TGACATAGAATAAATAAAAAATTAAAAATAATTTATTTTTTAATGTA-AAATATATTTAAATATA
66 TCACATAGGATAAATAAAAAATTAAAAATAATTTATTTTTTAATGTACAAATATATTTAAATATA
* * *
28418 TATAC-ATATATA-AATTTCTACTAAT-TTCTTCAAATATTTATATATAATTTATTTTCTTTTAA
131 TATACTATATATATAATTTCTACTAATATTCTTCCAATATTTATATATAATTGATTTTC-CTTAA
** * * * * * * * * **
28480 AAAATT-TTAAACTTTCATATGTCAC-AAAAACGGTCTAGACACTAAAATATTTAGTAGAACACT
195 AAAATTAAAAAACTTTCACAGGTGACAAAAAAAGGTCCAGCCACTAAAATACTCAACAGAACACT
* * * * ***
28543 ATATATAATTTGGGCTCCAATAAATACAGCAATATTTACAGGATGAATCGAAATGCTATATATTC
260 ATATATCATTTGGGCTCCAATAAATGCAGCAATGTTTATAGGATGAATCGAAATGCTATATGGCC
* * * * * *
28608 GTGTAACATGCATGATTGTTTCTGTTGTTGTTTTATTCGTTGCCAGGATATTATACTACATCATT
325 GTGTAACTTGCTTGATTGCTTCTGTTGTTGTTTTATTCGTTTCAAGGATATTATACGACATCATT
* *
28673 TCGTTGGCATAAACTATATATGAGAAAGAAACCTGATGAGCGATATTGATAAAGC-TT--TC---
390 TTGTTGGCATAAACTATATATGAGAAAGAAACCTGATGAGCGATGTTGATAAAGCTTTAATCATT
* * * * ** * **
28732 C-----ATTT--G-----GCTTTGTTAGTAAAAAACTTAATAATATCCAGTGTTGAGAAGAAGAA
455 CTGTTGGTTTCCGCCTTCGCTTTCTTAGTAAAAAACTTGATAATACCCAACGTTGAAAAGAAGGG
** * *
28785 CACAATGACCCTTTATTTGAATCAGACCATGAATCTTGTGTTGGAGCTATTACCCATAGCCATGA
520 CACAATGACCCTTTATTTGAATCAGACTGTGAATTTTGTGTTGGAGCTATTAACCATAGCCATGA
*
28850 TCATGACCTGGACCACTCTCATTCCAGATTAAGGAGTTGGAATCTTAGCGCAACCTATTTCACGT
585 TCATGACCTGGACCACTCTCATTCCAGATTGAGGAGTTGGAATCTTA--GCAACC-ATTTCACGT
* * *
28915 TGTTCGCCCAATATTATCAATACATTATC-GGACA-CGTCTGAAAAACTTGAACTTTCTCTTCAG
647 TGTTCGTCCAATATTATCAATACATTATCAGGA-AGCGTCTGAAAAACTTGAACTTTGTCTTCGG
28978 CATAAATTCCTTTGATAGAAATGACGTGATATCAATAAAACTAAAAGCCCACCCAATGAACCTAT
711 CATAAATTCCTTTGATAGAAATGACGTGATATCAATAAAACTAAAAGCCCACCCAATGAACCTAT
29043 ATCATATCTTAACAACATTATGAACTAGTGTGTATCTCATATGTCTCACATAAGTGAAAGAATAT
776 ATCATATCTTAACAACATTATGAACTAGTGTGTATCTCATATGTCTCACATAAGTGAAAGAATA-
* * * *
29108 AAATAAAAAAAAAAAACTATCTGAAGTCATAATATCACCTATTAAATAGCCACCATACTGAAAGG
840 AAA-AAAAAAAAGAAATTATCTAAAGTCATAATATCACCTATTAAATAGCCACCATACTGAACGG
*
29173 ATTA
904 ATTG
* *
29177 TTTTTTGAGTTCACCATCTCTATACTAAGCACCCATGACTTAAAAGATATATTTGGGCTCTGATA
1 TTTTCTGAGTTCACCATCTCTATACTAAGCACCCATGACTTAAAAGATATATTTGGACTCTGATA
* *
29242 TCACATAAGATAAATAAAACATTAAAAATAATTTATTTTTTAATGTACAAATATATTTAAATATA
66 TCACATAGGATAAATAAAAAATTAAAAATAATTTATTTTTTAATGTACAAATATATTTAAATATA
* *
29307 TATACCTATATATATGAATTTCAATTAATATT-TTCCAATATTTATATATAATTGATTTTCCTTA
131 TATA-CTATATATAT-AATTTCTACTAATATTCTTCCAATATTTATATATAATTGATTTTCCTT-
* * * * *
29371 AAAAAATAAAAAAAGTTTCACTGGTGACAAAAAAAAGGTCCAGCCACTGAAATACTCAGCAGAAC
193 AAAAAATTAAAAAACTTTCACAGGTGAC-AAAAAAAGGTCCAGCCACTAAAATACTCAACAGAAC
29436 ACTATATATC-TTTGGGCTCCAATAAATGCAGCAATGTTTATAGGATGAATCGAAATGCTATATG
257 ACTATATATCATTTGGGCTCCAATAAATGCAGCAATGTTTATAGGATGAATCGAAATGCTATATG
* *
29500 TCCGTGTAACTTGCTTGATTGCTTCTGTTGTTGTTTTATTCCTTTCAAGGATATTATACGACATC
322 GCCGTGTAACTTGCTTGATTGCTTCTGTTGTTGTTTTATTCGTTTCAAGGATATTATACGACATC
* * *
29565 ATTTTGTTTGCATAAACTATATATGAGAAAGAAACCTAAGGAGCGATGTTGATAAAGCTTTAATC
387 ATTTTGTTGGCATAAACTATATATGAGAAAGAAACCTGATGAGCGATGTTGATAAAGCTTTAATC
* *
29630 ATTCTGTTGGTTTCCGCCTTGGCTTTCTTAGTAAAAAAAC-TGATAATACCTAACGTTGAAAAGA
452 ATTCTGTTGGTTTCCGCCTTCGCTTTCTTAGT-AAAAAACTTGATAATACCCAACGTTGAAAAGA
** * * *
29694 AGGGCACAATGACTTTTTTTTTTAATCAGACCGTGAATTTTGTGTTGGAGCTATTAACCATAGCC
516 AGGGCACAATGACCCTTTATTTGAATCAGACTGTGAATTTTGTGTTGGAGCTATTAACCATAGCC
29759 ATGATCATGACCTGGACCACTCTCAT
581 ATGATCATGACCTGGACCACTCTCAT
29785 CCCAAGTTGT
Statistics
Matches: 3693, Mismatches: 411, Indels: 198
0.86 0.10 0.05
Matches are distributed among these distances:
884 4 0.00
885 302 0.08
886 212 0.06
887 121 0.03
888 309 0.08
889 64 0.02
890 2 0.00
891 9 0.00
892 2 0.00
893 135 0.04
894 24 0.01
895 178 0.05
896 189 0.05
897 4 0.00
898 3 0.00
901 110 0.03
902 85 0.02
903 246 0.07
904 915 0.25
905 7 0.00
906 4 0.00
907 1 0.00
908 3 0.00
909 1 0.00
910 164 0.04
911 162 0.04
912 22 0.01
913 270 0.07
914 7 0.00
915 1 0.00
916 1 0.00
917 1 0.00
918 2 0.00
919 1 0.00
920 7 0.00
921 1 0.00
922 22 0.01
923 102 0.03
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (907 bp):
TTTTCTGAGTTCACCATCTCTATACTAAGCACCCATGACTTAAAAGATATATTTGGACTCTGATA
TCACATAGGATAAATAAAAAATTAAAAATAATTTATTTTTTAATGTACAAATATATTTAAATATA
TATACTATATATATAATTTCTACTAATATTCTTCCAATATTTATATATAATTGATTTTCCTTAAA
AAATTAAAAAACTTTCACAGGTGACAAAAAAAGGTCCAGCCACTAAAATACTCAACAGAACACTA
TATATCATTTGGGCTCCAATAAATGCAGCAATGTTTATAGGATGAATCGAAATGCTATATGGCCG
TGTAACTTGCTTGATTGCTTCTGTTGTTGTTTTATTCGTTTCAAGGATATTATACGACATCATTT
TGTTGGCATAAACTATATATGAGAAAGAAACCTGATGAGCGATGTTGATAAAGCTTTAATCATTC
TGTTGGTTTCCGCCTTCGCTTTCTTAGTAAAAAACTTGATAATACCCAACGTTGAAAAGAAGGGC
ACAATGACCCTTTATTTGAATCAGACTGTGAATTTTGTGTTGGAGCTATTAACCATAGCCATGAT
CATGACCTGGACCACTCTCATTCCAGATTGAGGAGTTGGAATCTTAGCAACCATTTCACGTTGTT
CGTCCAATATTATCAATACATTATCAGGAAGCGTCTGAAAAACTTGAACTTTGTCTTCGGCATAA
ATTCCTTTGATAGAAATGACGTGATATCAATAAAACTAAAAGCCCACCCAATGAACCTATATCAT
ATCTTAACAACATTATGAACTAGTGTGTATCTCATATGTCTCACATAAGTGAAAGAATAAAAAAA
AAAAAGAAATTATCTAAAGTCATAATATCACCTATTAAATAGCCACCATACTGAACGGATTG
Found at i:30429 original size:28 final size:27
Alignment explanation
Indices: 30383--30442 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
30373 AGTTACAATT
*
30383 TTACCCTTAGATGGGTAAAATTACTAAA
1 TTACCCTTAGATGGGT-AAATTACAAAA
* *
30411 TTACCCTTAAGAT-GTTAAATTAGAAAA
1 TTACCCTT-AGATGGGTAAATTACAAAA
30438 TTACC
1 TTACC
30443 TATAGAAGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 14 0.50
28 10 0.36
29 4 0.14
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (27 bp):
TTACCCTTAGATGGGTAAATTACAAAA
Done.