Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008710.1 Corchorus capsularis cultivar CVL-1 contig08731, 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: 58549
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:1518 original size:30 final size:32
Alignment explanation
Indices: 1482--1551 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 32
1472 GCCACTTGAT
* *
1482 CGGCCATCGCAT-GG-AGCAACCGGCCATAAC
1 CGGCCATCGCATAGGCAACAACCGGCCACAAC
1512 CGGCCATCGCATGAGGCAACAACCGGCCACAAC
1 CGGCCATCGCAT-AGGCAACAACCGGCCACAAC
1545 CGGCCAT
1 CGGCCAT
1552 TCGATCCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 12 0.34
32 2 0.06
33 21 0.60
ACGTcount: A:0.27, C:0.39, G:0.26, T:0.09
Consensus pattern (32 bp):
CGGCCATCGCATAGGCAACAACCGGCCACAAC
Found at i:8660 original size:48 final size:48
Alignment explanation
Indices: 8548--8850 Score: 509
Period size: 48 Copynumber: 6.3 Consensus size: 48
8538 TTAACTACTT
*
8548 TTTCCCAAAGCGTCCTTCCCAGACGGAAGCCA-TTCATCTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTT-AT-TTTACTTGCTA
* * *
8597 TTTCCCAAAACGCCCTTCCTAGACGGAAGCCACTTATTTGACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTTATTTTACTTGCTA
*
8645 TTTCACAAAGCGCCCTTCCCAGACGGAAGCCACTTATTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTTATTTTACTTGCTA
*
8693 TTTCCCAAAGCGCCATTCCCAGACGGAAGCCACTTATTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTTATTTTACTTGCTA
8741 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTTATTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTTATTTTACTTGCTA
*
8789 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTTATTTTACTTGCTA
*
8837 TTTCCCAAGGCGCC
1 TTTCCCAAAGCGCC
8851 AATTTTTATT
Statistics
Matches: 240, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
48 207 0.86
49 31 0.13
50 2 0.01
ACGTcount: A:0.23, C:0.32, G:0.15, T:0.29
Consensus pattern (48 bp):
TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTTATTTTACTTGCTA
Found at i:12521 original size:94 final size:93
Alignment explanation
Indices: 12261--12526 Score: 435
Period size: 93 Copynumber: 2.8 Consensus size: 93
12251 CAAAATTGTC
* * * *
12261 TTTGCAAAAGAAAAGTGTTTTTCTCGAAAAAGGTTTTTAGAGAAAATTGGTTTCGAAAGTTTTTC
1 TTTGCAGAAGAAACGTGTTTTTCTC-AAAAAGG-TTTTAGAGAAAACTGGTTTCAAAAGTTTTTC
* *
12326 AAAGGCAAGTGCATAGTACAAGAAATAGTT
64 AAAGGCAAGCGCATAGTACAAGAAATAATT
12356 TTTGCAGAAGAAACGTGTTTTTCTCAAAAAGGTTTTAGAGAAAACTGGTTTCAAAAGTTTTTCAA
1 TTTGCAGAAGAAACGTGTTTTTCTCAAAAAGGTTTTAGAGAAAACTGGTTTCAAAAGTTTTTCAA
12421 AGGCAAGCGCATAGTACAAGAAATAATT
66 AGGCAAGCGCATAGTACAAGAAATAATT
12449 TTTGCAGAAGAAACGTGTTTTTTCTCAAAAAGGTTTTAGAGAAAACTGGTTTCAAAAGTTTTTCG
1 TTTGCAGAAGAAACGTG-TTTTTCTCAAAAAGGTTTTAGAGAAAACTGGTTTCAAAAGTTTTTC-
12514 AAA-GCAAGCGCAT
64 AAAGGCAAGCGCAT
12527 GAAAAAGAGA
Statistics
Matches: 163, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
93 74 0.45
94 63 0.39
95 26 0.16
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (93 bp):
TTTGCAGAAGAAACGTGTTTTTCTCAAAAAGGTTTTAGAGAAAACTGGTTTCAAAAGTTTTTCAA
AGGCAAGCGCATAGTACAAGAAATAATT
Found at i:12542 original size:14 final size:15
Alignment explanation
Indices: 12525--12553 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12515 AAGCAAGCGC
12525 ATGAAAAAG-AGAAA
1 ATGAAAAAGAAGAAA
12539 ATGAAAAAGAAGAAA
1 ATGAAAAAGAAGAAA
12554 GAAGAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (15 bp):
ATGAAAAAGAAGAAA
Found at i:13419 original size:37 final size:36
Alignment explanation
Indices: 13359--13470 Score: 111
Period size: 37 Copynumber: 3.1 Consensus size: 36
13349 AAAATTCACA
** * *
13359 AAGATCAAC-AAGCGACCACGGATTGGTCTCTCCTC
1 AAGATCAACAAAATGACCATGGATTGGTCTCTTCTC
* * *
13394 ATGTATCGAAC-AACTGACCATGGATTGGTCGCTTCTC
1 AAG-ATC-AACAAAATGACCATGGATTGGTCTCTTCTC
*
13431 AAAGATCAACAAAATGACCATGGACTGGTCTCTTCTC
1 -AAGATCAACAAAATGACCATGGATTGGTCTCTTCTC
13468 AAG
1 AAG
13471 CTCCAGCAGT
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
35 2 0.03
36 9 0.14
37 50 0.79
38 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (36 bp):
AAGATCAACAAAATGACCATGGATTGGTCTCTTCTC
Found at i:13616 original size:38 final size:38
Alignment explanation
Indices: 13563--13653 Score: 146
Period size: 38 Copynumber: 2.4 Consensus size: 38
13553 TGGTCCCTTT
* *
13563 CAGGTCACCTCTCAACAATAATCAAAGTTGACTGGAAA
1 CAGGTCATCTTTCAACAATAATCAAAGTTGACTGGAAA
*
13601 CAGGTCATCTTTCAACAGTAATCAAAGTTGACTGGAAA
1 CAGGTCATCTTTCAACAATAATCAAAGTTGACTGGAAA
*
13639 TAGGTCATCTTTCAA
1 CAGGTCATCTTTCAA
13654 GTTATCAGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.26
Consensus pattern (38 bp):
CAGGTCATCTTTCAACAATAATCAAAGTTGACTGGAAA
Found at i:13877 original size:18 final size:18
Alignment explanation
Indices: 13854--13912 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
13844 AAGCGAAGCA
13854 TTTCAACAACTTTTCAAT
1 TTTCAACAACTTTTCAAT
* *
13872 TTT---CAACTTTACCGCA-
1 TTTCAACAACTTT-TC-AAT
13888 TTTCAACAACTTTTCAAT
1 TTTCAACAACTTTTCAAT
13906 TTTCAAC
1 TTTCAAC
13913 TTTACAGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
15 7 0.23
16 4 0.13
17 2 0.06
18 11 0.35
19 7 0.23
ACGTcount: A:0.31, C:0.25, G:0.02, T:0.42
Consensus pattern (18 bp):
TTTCAACAACTTTTCAAT
Found at i:13880 original size:15 final size:15
Alignment explanation
Indices: 13859--13986 Score: 63
Period size: 15 Copynumber: 8.5 Consensus size: 15
13849 AAGCATTTCA
13859 ACAACTTTTCAATTT
1 ACAACTTTTCAATTT
* * *
13874 TCAACTTTACCGCATTT
1 ACAACTTT-TC-AATTT
13891 CAACAACTTTTCAATTT
1 --ACAACTTTTCAATTT
* *
13908 TCAACTTTACAGCATTT
1 ACAACTTTTCA--ATTT
*
13925 CAACAACTTTTCGATTT
1 --ACAACTTTTCAATTT
13942 ACAACTTTTC-A---
1 ACAACTTTTCAATTT
* *
13953 GC-A--TTTCAATTC
1 ACAACTTTTCAATTT
13965 ACAACTTTTCAATTT
1 ACAACTTTTCAATTT
13980 ACAACTT
1 ACAACTT
13987 CCATGTGTCA
Statistics
Matches: 84, Mismatches: 14, Indels: 30
0.66 0.11 0.23
Matches are distributed among these distances:
8 4 0.05
9 1 0.01
10 1 0.01
11 1 0.01
12 1 0.01
13 1 0.01
14 1 0.01
15 41 0.49
16 1 0.01
17 16 0.19
18 1 0.01
19 15 0.18
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (15 bp):
ACAACTTTTCAATTT
Found at i:13889 original size:34 final size:34
Alignment explanation
Indices: 13850--13986 Score: 193
Period size: 34 Copynumber: 3.9 Consensus size: 34
13840 CCCTAAGCGA
*
13850 AGCATTTCAACAACTTTTCAATTTTCAACTTTAC
1 AGCATTTCAACAACTTTTCAATTTACAACTTTAC
* *
13884 CGCATTTCAACAACTTTTCAATTTTCAACTTTAC
1 AGCATTTCAACAACTTTTCAATTTACAACTTTAC
* *
13918 AGCATTTCAACAACTTTTCGATTTACAACTTTTC
1 AGCATTTCAACAACTTTTCAATTTACAACTTTAC
13952 AGCATTTCAATTCACAACTTTTCAATTTACAACTT
1 AGCATTTC-A---ACAACTTTTCAATTTACAACTT
13987 CCATGTGTCA
Statistics
Matches: 93, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
34 71 0.76
35 1 0.01
38 21 0.23
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (34 bp):
AGCATTTCAACAACTTTTCAATTTACAACTTTAC
Found at i:13899 original size:19 final size:19
Alignment explanation
Indices: 13875--13934 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
13865 TTTCAATTTT
13875 CAACTTTACCGCATTTCAA
1 CAACTTTACCGCATTTCAA
* * *
13894 CAACTTT-TC-AATTT--T
1 CAACTTTACCGCATTTCAA
*
13909 CAACTTTACAGCATTTCAA
1 CAACTTTACCGCATTTCAA
13928 CAACTTT
1 CAACTTT
13935 TCGATTTACA
Statistics
Matches: 30, Mismatches: 7, Indels: 8
0.67 0.16 0.18
Matches are distributed among these distances:
15 7 0.23
17 8 0.27
18 1 0.03
19 14 0.47
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.38
Consensus pattern (19 bp):
CAACTTTACCGCATTTCAA
Found at i:14128 original size:47 final size:47
Alignment explanation
Indices: 13993--14131 Score: 215
Period size: 48 Copynumber: 2.9 Consensus size: 47
13983 ACTTCCATGT
* *
13993 GTCAGCAATCCTTCGACCCAAGTTGGTCTTTCCTCACTTCCATGTGA
1 GTCAGAAATCCTTCGACCCAAGTTGGTCTTTCCTCACTTCTATGTGA
* *
14040 GTCAGAAATCGTTCTGACCCAAGTTGGTCTTTCCTCGCTTCTATGTGA
1 GTCAGAAATCCTTC-GACCCAAGTTGGTCTTTCCTCACTTCTATGTGA
* *
14088 GTCAGAAATCCTTCGACCAAAGTTGGTCTTTTCTCACTTCTATG
1 GTCAGAAATCCTTCGACCCAAGTTGGTCTTTCCTCACTTCTATG
14132 CAAAGTTACA
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
47 39 0.47
48 44 0.53
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (47 bp):
GTCAGAAATCCTTCGACCCAAGTTGGTCTTTCCTCACTTCTATGTGA
Found at i:14202 original size:47 final size:48
Alignment explanation
Indices: 14100--14212 Score: 108
Period size: 47 Copynumber: 2.4 Consensus size: 48
14090 CAGAAATCCT
* * *
14100 TCGACCAAAGTTGGTCTTTTCTCACTTCTATGCAAAGTTACAATTTGG
1 TCGACCACAGTTGGTCTTTGCTCACTTCTATGCAAAGTTACAATTTGA
* * *
14148 T-GGCCACAGTTGGTCTTTGCTCGCTT-TCATGC-GAGTATACAATTT-A
1 TCGACCACAGTTGGTCTTTGCTCACTTCT-ATGCAAAGT-TACAATTTGA
*
14194 TCGACCACAGACTGGTCTT
1 TCGACCACAG-TTGGTCTT
14213 CTTTAATTCC
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
46 5 0.09
47 40 0.75
48 8 0.15
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.35
Consensus pattern (48 bp):
TCGACCACAGTTGGTCTTTGCTCACTTCTATGCAAAGTTACAATTTGA
Found at i:17708 original size:48 final size:48
Alignment explanation
Indices: 17599--17968 Score: 483
Period size: 48 Copynumber: 7.6 Consensus size: 48
17589 TTACCTATTT
*
17599 TTTCCCAAAGCGCCCTTCCCAGACGGAAGTCA-TTCATCTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTT-AT-TTTACTTGCTA
*
17648 TTTCCCAAAGCGCCATTCCCAGACGGAAGCCACTTATTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTTATTTTACTTGCTA
17696 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTTATTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTTATTTTACTTGCTA
17744 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTTATTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTTATTTTACTTGCTA
* *
17792 TTTCCCAAAGCGCTCTTCCCAGACGGAAGCCATTTATTTT-CGTTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTTATTTTAC--TTGCTA
* * *
17841 TTTCCCAAAGCGCCCTTCCCGGACGGAAGCCATTTGTTTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTT-ATTTTACTTGCTA
* ** * * * * * * *
17890 CTTCCCAAAAATGCCCTTCTCGGATGGAAGACGCTTATTTTTACTTACTT
1 TTTCCC-AAAGCGCCCTTCCCAGACGGAAGCCACTTA-TTTTACTTGCTA
* * *
17940 TTTCCCAAAACGCCCTTCCCGGACAGAAG
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAG
17969 GCGCCAATTT
Statistics
Matches: 290, Mismatches: 24, Indels: 14
0.88 0.07 0.04
Matches are distributed among these distances:
47 1 0.00
48 144 0.50
49 101 0.35
50 43 0.15
51 1 0.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (48 bp):
TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCACTTATTTTACTTGCTA
Found at i:21221 original size:30 final size:31
Alignment explanation
Indices: 21186--21260 Score: 98
Period size: 33 Copynumber: 2.4 Consensus size: 31
21176 CATCGCATGC
* * *
21186 GCCATCGCATGG-AGCAACTGGCCATAACCG
1 GCCATCGCATGGCAACAACCGGCCACAACCG
21216 GCCATCGCATCAGGCAACAACCGGCCACAACCG
1 GCCATCGCAT--GGCAACAACCGGCCACAACCG
21249 GCCATCGCATGG
1 GCCATCGCATGG
21261 GGCATCCGCG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
30 10 0.26
31 2 0.05
32 2 0.05
33 25 0.64
ACGTcount: A:0.27, C:0.37, G:0.25, T:0.11
Consensus pattern (31 bp):
GCCATCGCATGGCAACAACCGGCCACAACCG
Found at i:24139 original size:37 final size:38
Alignment explanation
Indices: 24081--24152 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
24071 GTTATCTGTC
*
24081 CTCTGACATTGTAGCTTGAATTAG-AAAATGATCAGCG
1 CTCTGACATTGAAGCTTGAATTAGCAAAATGATCAGCG
24118 CTCTGACATTGAAG-TTCGAATTAGCAAAATGATCA
1 CTCTGACATTGAAGCTT-GAATTAGCAAAATGATCA
24153 TGTCTTTCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 2 0.06
37 20 0.62
38 10 0.31
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (38 bp):
CTCTGACATTGAAGCTTGAATTAGCAAAATGATCAGCG
Found at i:24365 original size:29 final size:29
Alignment explanation
Indices: 24323--24380 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
24313 TTTTTTTTTC
24323 GAACTTTCTGATTGCAGGTTTAGATCCAT
1 GAACTTTCTGATTGCAGGTTTAGATCCAT
*
24352 GAACTTTTTGATTGCAGGTTTAGATCCAT
1 GAACTTTCTGATTGCAGGTTTAGATCCAT
24381 CGATCTTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (29 bp):
GAACTTTCTGATTGCAGGTTTAGATCCAT
Found at i:38778 original size:14 final size:14
Alignment explanation
Indices: 38759--38794 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
38749 AAAATAATAA
38759 TTGTTCTTAATGCT
1 TTGTTCTTAATGCT
*
38773 TTGTTCTTAATGTT
1 TTGTTCTTAATGCT
38787 TTGTTCTT
1 TTGTTCTT
38795 TAGTGCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.14, T:0.64
Consensus pattern (14 bp):
TTGTTCTTAATGCT
Found at i:44722 original size:24 final size:24
Alignment explanation
Indices: 44677--44722 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
44667 ATGACCATCT
* *
44677 CCAACAAGTCAAAATGGTGAGCGA
1 CCAACAAGTCAAAAGGGCGAGCGA
44701 CCAACAAGTCAAAAGGGCGAGC
1 CCAACAAGTCAAAAGGGCGAGC
44723 AATTGTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.26, T:0.09
Consensus pattern (24 bp):
CCAACAAGTCAAAAGGGCGAGCGA
Found at i:44986 original size:53 final size:53
Alignment explanation
Indices: 44928--45096 Score: 136
Period size: 53 Copynumber: 3.2 Consensus size: 53
44918 AGTCAAAAGG
44928 GCGAGCTATTGTAAAATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTA
1 GCGAGCTATTGTAAAATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTA
* * * * * * * * * *
44981 GCGAGCGATTGGT----TT--CACTATCCTCGACCTAATAAAAGCACGAGTCAA-AA
1 GCGAGCTATT-GTAAAATTAGCTCTATACTTGACCT--CAAGACCA-AAGTTAATTA
45031 GGGCGAGCTATTGTAAAATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTA
1 --GCGAGCTATTGTAAAATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTA
*
45086 GCGAGCAATTG
1 GCGAGCTATTG
45097 GTTTCACTAT
Statistics
Matches: 82, Mismatches: 21, Indels: 26
0.64 0.16 0.20
Matches are distributed among these distances:
48 12 0.15
50 8 0.10
51 7 0.09
52 9 0.11
53 19 0.23
54 7 0.09
55 8 0.10
57 12 0.15
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (53 bp):
GCGAGCTATTGTAAAATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTA
Found at i:44997 original size:105 final size:106
Alignment explanation
Indices: 44707--45281 Score: 888
Period size: 105 Copynumber: 5.5 Consensus size: 106
44697 GCGACCAACA
*
44707 AGTCAAAAGGGCGAGCAATTGTAAA-ATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTGG
1 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTGG
* *
44771 CGAGCGATTGGTTTCACTATCCTAGACCCAATAAAAGCACG
66 CGAGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACG
** * * * *
44812 AGTCAAAAGGGCGAGCAATCACAAAGATTAGCTCTATACTTAACCTCATGACCAATGCTAATTGG
1 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTGG
* *
44877 CGAGCGATTGTTTTCATTATCCTCGACCTAATAAAAGCACG
66 CGAGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACG
* * *
44918 AGTCAAAAGGGCGAGCTATTGTAAA-ATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTAG
1 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTGG
44982 CGAGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACG
66 CGAGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACG
* * *
45023 AGTCAAAAGGGCGAGCTATTGTAAA-ATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTAG
1 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTGG
* *
45087 CGAGCAATTGGTTTCACTATCCTCGACCCAATAAAAGCACG
66 CGAGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACG
* * * * *
45128 AGTCAAAAGGGC-AGGCAATCGTAAAGCTTAGCTCTATACTTGACTTCAGGACCAATGCTAATTG
1 AGTCAAAAGGGCGA-GCAATCGTAAAGATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTG
45192 GCGAGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACG
65 GCGAGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACG
*
45234 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTTTATACTTGACCTCA
1 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACCTCA
45282 GAACTAAGGA
Statistics
Matches: 429, Mismatches: 37, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
104 1 0.00
105 219 0.51
106 208 0.48
107 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (106 bp):
AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTGG
CGAGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACG
Found at i:45161 original size:211 final size:211
Alignment explanation
Indices: 44707--45281 Score: 902
Period size: 211 Copynumber: 2.7 Consensus size: 211
44697 GCGACCAACA
44707 AGTCAAAAGGGCGAGCAATTGTAAAATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTGGC
1 AGTCAAAAGGGCGAGCAATTGTAAAATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTGGC
* * **
44772 GAGCGATTGGTTTCACTATCCTAGACCCAATAAAAGCACGAGTCAAAAGGGCGAGCAATCACAAA
66 GAGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACGAGTCAAAAGGGCGAGCAATCGTAAA
* * * * * * *
44837 GATTAGCTCTATACTTAACCTCATGACCAATGCTAATTGGCGAGCGATTGTTTTCATTATCCTCG
131 GATTAGCTCTATACTTGACCTCAAGACCAAAGCTAATTAGCGAGCAATTGGTTTCACTATCCTCG
*
44902 ACCTAATAAAAGCACG
196 ACCCAATAAAAGCACG
* *
44918 AGTCAAAAGGGCGAGCTATTGTAAAATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTAGC
1 AGTCAAAAGGGCGAGCAATTGTAAAATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTGGC
* *
44983 GAGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACGAGTCAAAAGGGCGAGCTATTGTAAA
66 GAGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACGAGTCAAAAGGGCGAGCAATCGTAAA
*
45048 -ATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTAGCGAGCAATTGGTTTCACTATCCTCG
131 GATTAGCTCTATACTTGACCTCAAGACCAAAGCTAATTAGCGAGCAATTGGTTTCACTATCCTCG
45112 ACCCAATAAAAGCACG
196 ACCCAATAAAAGCACG
* * * * * *
45128 AGTCAAAAGGGC-AGGCAATCGTAAAGCTTAGCTCTATACTTGACTTCAGGACCAATGCTAATTG
1 AGTCAAAAGGGCGA-GCAATTGTAAA-ATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTG
45192 GCGAGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACGAGTCAAAAGGGCGAGCAATCGTA
64 GCGAGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACGAGTCAAAAGGGCGAGCAATCGTA
*
45257 AAGATTAGCTTTATACTTGACCTCA
129 AAGATTAGCTCTATACTTGACCTCA
45282 GAACTAAGGA
Statistics
Matches: 333, Mismatches: 28, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
209 1 0.00
210 92 0.28
211 219 0.66
212 21 0.06
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (211 bp):
AGTCAAAAGGGCGAGCAATTGTAAAATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTGGC
GAGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACGAGTCAAAAGGGCGAGCAATCGTAAA
GATTAGCTCTATACTTGACCTCAAGACCAAAGCTAATTAGCGAGCAATTGGTTTCACTATCCTCG
ACCCAATAAAAGCACG
Found at i:45472 original size:24 final size:24
Alignment explanation
Indices: 45427--45472 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
45417 ATGACCATCT
*
45427 CCAACAAGTCAAAAAGGTGAGCTA
1 CCAACAAGTCAAAAAGGCGAGCTA
*
45451 CCAACAAGTCAAAAGGGCGAGC
1 CCAACAAGTCAAAAAGGCGAGC
45473 AATTGTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.24, G:0.24, T:0.09
Consensus pattern (24 bp):
CCAACAAGTCAAAAAGGCGAGCTA
Found at i:45720 original size:25 final size:25
Alignment explanation
Indices: 45686--45745 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
45676 TGCAAAAGAT
*
45686 CCGAATGCTCCTAGACCACAAACCG
1 CCGAGTGCTCCTAGACCACAAACCG
* * * * *
45711 CCGAGTGCTCGTCGATCACGAAGCG
1 CCGAGTGCTCCTAGACCACAAACCG
45736 CCGAGTGCTC
1 CCGAGTGCTC
45746 ATAAGACCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.23, C:0.37, G:0.25, T:0.15
Consensus pattern (25 bp):
CCGAGTGCTCCTAGACCACAAACCG
Found at i:46156 original size:119 final size:119
Alignment explanation
Indices: 46014--46468 Score: 723
Period size: 119 Copynumber: 3.9 Consensus size: 119
46004 CACGTGCGCA
*
46014 AAAGAAGAGTGCTCAGTGAAGAGTGCCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGA
1 AAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGA
*
46079 ATGCTCCCCTGAACACGTGCAACTCCCCTAAGCATGTGCAATCACCAACGCACG
66 ATGCTCCCCTGAACACGTGCAACTCCCCTAAGCACGTGCAATCACCAACGCACG
* * *
46133 AAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCGAGTGAACAATACTTAAGGAAGAGCACCGA
1 AAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGA
* *
46198 ATGCTACCCTGAACACGTGCAACTCCCCTAAGCACGTGCAATCACCAACGCGCG
66 ATGCTCCCCTGAACACGTGCAACTCCCCTAAGCACGTGCAATCACCAACGCACG
46252 AAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGA
1 AAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGA
*
46317 ATGCTCCCCTGAACACGTGCAACTCCCCTAAGCACGTGCAATCACCAACGCACA
66 ATGCTCCCCTGAACACGTGCAACTCCCCTAAGCACGTGCAATCACCAACGCACG
* *
46371 AAAGAAGAGTGCTCAATTAAGAGTGCCGACCGCGCGAGTGAAGAATGC-T-------AGCACCGA
1 AAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGA
* *
46428 ATGCT-CCCTGAACATGTGCAACT-CCCTCAAGCACGTTCAAT
66 ATGCTCCCCTGAACACGTGCAACTCCCCT-AAGCACGTGCAAT
46469 AACTAACTTA
Statistics
Matches: 318, Mismatches: 17, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
109 4 0.01
110 29 0.09
111 13 0.04
118 1 0.00
119 271 0.85
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.15
Consensus pattern (119 bp):
AAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGA
ATGCTCCCCTGAACACGTGCAACTCCCCTAAGCACGTGCAATCACCAACGCACG
Found at i:46207 original size:226 final size:229
Alignment explanation
Indices: 45813--46412 Score: 920
Period size: 226 Copynumber: 2.6 Consensus size: 229
45803 CGCATGATGA
* * * * *
45813 CCAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGGATGCTACCCTGAACAGGCGCAACTC
1 CCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
* * * *
45878 CCCCAAGCACGTGCAATCACCAATGCGCAAAAGAAGAGTGCTCAAGGAAGAGTGCCAACCGCGCG
66 CCCTAAGCACGTGCAATCACCAACGCACAAAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCG
* * *
45943 AGTGAATAATGCTTAAGGAAGAGCACCGAATGCTACCCTGAATACGTGCAACTCCCAC-AAGCAC
131 AGTGAACAATACTTAAGGAAGAGCACCGAATGCTACCCTGAACACGTGCAACTCCC-CTAAGCAC
*
46007 -G-T-GCGCAAAAGAAGAGTGCTCAGTGAAGAGTG
195 GGATCGCGCAAAAGAAGAGTGCTCAATGAAGAGTG
46039 CCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
1 CCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
* *
46104 CCCTAAGCATGTGCAATCACCAACGCACGAAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCG
66 CCCTAAGCACGTGCAATCACCAACGCACAAAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCG
46169 AGTGAACAATACTTAAGGAAGAGCACCGAATGCTACCCTGAACACGTGCAACTCCCCTAAGCACG
131 AGTGAACAATACTTAAGGAAGAGCACCGAATGCTACCCTGAACACGTGCAACTCCCCTAAGCACG
*
46234 TGCAATCACCAACGCGCGAAAGAAGAGTGCTCAATGAAGAGTG
196 -G--AT------CGCGCAAAAGAAGAGTGCTCAATGAAGAGTG
46277 CCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
1 CCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
* *
46342 CCCTAAGCACGTGCAATCACCAACGCACAAAAGAAGAGTGCTCAATTAAGAGTGCCGACCGCGCG
66 CCCTAAGCACGTGCAATCACCAACGCACAAAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCG
46407 AGTGAA
131 AGTGAA
46413 GAATGCTAGC
Statistics
Matches: 341, Mismatches: 20, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
225 1 0.00
226 178 0.52
228 1 0.00
231 1 0.00
238 160 0.47
ACGTcount: A:0.34, C:0.28, G:0.24, T:0.14
Consensus pattern (229 bp):
CCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
CCCTAAGCACGTGCAATCACCAACGCACAAAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCG
AGTGAACAATACTTAAGGAAGAGCACCGAATGCTACCCTGAACACGTGCAACTCCCCTAAGCACG
GATCGCGCAAAAGAAGAGTGCTCAATGAAGAGTG
Found at i:46295 original size:36 final size:35
Alignment explanation
Indices: 46242--46310 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
46232 CGTGCAATCA
* *
46242 CCAACGCGCGAAAGAAGAGTGCTCAATGAAGAGTG
1 CCAACGCGCGAAAGAAGAATGCTCAACGAAGAGTG
** *
46277 CCAACCGCGCGAGTGAAGAATGCTTAACGAAGAG
1 CCAA-CGCGCGAAAGAAGAATGCTCAACGAAGAG
46311 CACCGAATGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 4 0.14
36 24 0.86
ACGTcount: A:0.36, C:0.22, G:0.30, T:0.12
Consensus pattern (35 bp):
CCAACGCGCGAAAGAAGAATGCTCAACGAAGAGTG
Found at i:46344 original size:19 final size:19
Alignment explanation
Indices: 46320--46357 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
46310 GCACCGAATG
46320 CTCCCCTGAA-CACGTGCAA
1 CTCCCCT-AAGCACGTGCAA
46339 CTCCCCTAAGCACGTGCAA
1 CTCCCCTAAGCACGTGCAA
46358 TCACCAACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.26, C:0.42, G:0.16, T:0.16
Consensus pattern (19 bp):
CTCCCCTAAGCACGTGCAA
Found at i:51742 original size:31 final size:32
Alignment explanation
Indices: 51707--51767 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
51697 ATGTTTTTTA
*
51707 AAATGACCAAATAAGCCC-TCTACTTTTTTCT
1 AAATGACCAAATAAGCCCTTCAACTTTTTTCT
51738 AAATGACCAAATAAGCCCTTCAACTTTTTT
1 AAATGACCAAATAAGCCCTTCAACTTTTTT
51768 AAAAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (32 bp):
AAATGACCAAATAAGCCCTTCAACTTTTTTCT
Found at i:58369 original size:21 final size:22
Alignment explanation
Indices: 58345--58390 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
58335 AAAAAAAGGC
**
58345 TTTGCTATTTACCGCCC-CCCT
1 TTTGCTAAATACCGCCCTCCCT
58366 TTTGCTAAATACCGCCCTCCCT
1 TTTGCTAAATACCGCCCTCCCT
58388 TTT
1 TTT
58391 TATAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.13, C:0.39, G:0.09, T:0.39
Consensus pattern (22 bp):
TTTGCTAAATACCGCCCTCCCT
Done.