Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023190.1 Corchorus olitorius cultivar O-4 contig23223, 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: 25307
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:137 original size:41 final size:41
Alignment explanation
Indices: 66--156 Score: 137
Period size: 41 Copynumber: 2.2 Consensus size: 41
56 CATATAATAA
* *
66 GCAACGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTC
1 GCAACGACTAACAAAACTCGCTGCGAAAAGTTTAAGATTTC
* *
107 GCAATGACTAACAAAACTCGCTGCGGAAAGTTTAAGATTTC
1 GCAACGACTAACAAAACTCGCTGCGAAAAGTTTAAGATTTC
*
148 ACAACGACT
1 GCAACGACT
157 TAATCTGTCG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (41 bp):
GCAACGACTAACAAAACTCGCTGCGAAAAGTTTAAGATTTC
Found at i:636 original size:22 final size:22
Alignment explanation
Indices: 611--653 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
601 GCTAAATTAG
611 ACTATGTTTAGGGATCTATTTT
1 ACTATGTTTAGGGATCTATTTT
**
633 ACTATGTTTTTGGATCTATTT
1 ACTATGTTTAGGGATCTATTT
654 ATGCTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.09, G:0.16, T:0.53
Consensus pattern (22 bp):
ACTATGTTTAGGGATCTATTTT
Found at i:2646 original size:38 final size:39
Alignment explanation
Indices: 2587--2693 Score: 157
Period size: 39 Copynumber: 2.8 Consensus size: 39
2577 ATGTTTTTAA
*
2587 TTAAG-TAATTCCAAAACAAGATTTTGGAAAATAAAAGT
1 TTAAGATAATTCCAAAAGAAGATTTTGGAAAATAAAAGT
*
2625 TT-AGATAATTCCAAAAGAAGATTTTCGAAAAATAAAAGT
1 TTAAGATAATTCCAAAAGAAGATTTT-GGAAAATAAAAGT
*
2664 TTAAGA-AATCCCAAAAGAAGATTTTGGAAA
1 TTAAGATAATTCCAAAAGAAGATTTTGGAAA
2694 TTAATAAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
37 2 0.03
38 25 0.40
39 32 0.52
40 3 0.05
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.27
Consensus pattern (39 bp):
TTAAGATAATTCCAAAAGAAGATTTTGGAAAATAAAAGT
Found at i:6437 original size:15 final size:14
Alignment explanation
Indices: 6417--6475 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
6407 CAAGAGACGT
*
6417 TTTTCAAGAAAATTG
1 TTTTCAAGAAAA-GG
6432 TTTTCAAGAAAAGG
1 TTTTCAAGAAAAGG
6446 TTTTCAA-AAATAGG
1 TTTTCAAGAAA-AGG
6460 TTTTC-A-AAAAGG
1 TTTTCAAGAAAAGG
6472 TTTT
1 TTTT
6476 GGGTTTTCTA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
12 7 0.17
13 7 0.17
14 16 0.38
15 12 0.29
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (14 bp):
TTTTCAAGAAAAGG
Found at i:8400 original size:105 final size:105
Alignment explanation
Indices: 8290--8700 Score: 418
Period size: 105 Copynumber: 3.9 Consensus size: 105
8280 ATAGTTTCGT
* * *
8290 ATTGA-CCAGGGCGGTCTTTTTTCAGTTGT-TTTCAAGTTGATCCAGGACGATCATTCTTCAGTT
1 ATTGACCCAGGGCGGTCTTTCTTCAGTT-TACTTCAA-TTGATCCAGGACGATCATTCTTCAATT
* *
8353 TATTTCAGTTGACCCAGGGCGATCATTCTTCAGTTTATTTCA
64 TATTTCAATTGATCCAGGGCGATCATTCTTCAGTTTATTTCA
* * * * ** *
8395 ATTGACCCAGGGCGGTCTTTCTTCAGTTTACTTCAGTTGACCCAGAACGTTGTTTATTCAATTTA
1 ATTGACCCAGGGCGGTCTTTCTTCAGTTTACTTCAATTGATCCAGGACGATCATTCTTCAATTTA
* * * ** *
8460 TGTT-AGAATGATCGAGGGTGGCCGTTCTTCAGTTTATTTCA
66 T-TTCA-ATTGATCCAGGGCGATCATTCTTCAGTTTATTTCA
* * * * * * *
8501 GTTCACCTAGGGCGGTCTTTCTTCAATTTACTTCAATTGATCCAGGGCGATCTTTCTTC-AGTTA
1 ATTGACCCAGGGCGGTCTTTCTTCAGTTTACTTCAATTGATCCAGGACGATCATTCTTCAATTTA
*
8565 GTTTCAATTGATCCAGGGCGATCATTCTTCAGTTTACTTCA
66 -TTTCAATTGATCCAGGGCGATCATTCTTCAGTTTATTTCA
* * *** *
8606 ATTGATCCAGGGCGATCTTTCTTCAGTTCGTTTCAATTGA-CCAAGGACGATTATTCTTCAATTT
1 ATTGACCCAGGGCGGTCTTTCTTCAGTTTACTTCAATTGATCC-AGGACGATCATTCTTCAATTT
* * *
8670 ACTTCAATTGATCCAGGGCAATCTTTCTTCA
65 ATTTCAATTGATCCAGGGCGATCATTCTTCA
8701 AATTGACTCA
Statistics
Matches: 245, Mismatches: 53, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
104 2 0.01
105 135 0.55
106 108 0.44
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (105 bp):
ATTGACCCAGGGCGGTCTTTCTTCAGTTTACTTCAATTGATCCAGGACGATCATTCTTCAATTTA
TTTCAATTGATCCAGGGCGATCATTCTTCAGTTTATTTCA
Found at i:8422 original size:70 final size:70
Alignment explanation
Indices: 8320--8700 Score: 406
Period size: 70 Copynumber: 5.4 Consensus size: 70
8310 TTCAGTTGTT
* *
8320 TTCAAGTTGATCCAGGACGATCATTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCATTCTTCA
1 TTCAA-TTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCATTCTTCA
* *
8385 GTTTAT
65 ATTTAC
* * * ** * ** *
8391 TTCAATTGACCCAGGGCGGTCTTTCTTCAGTTTACTTCAGTTGACCCAGAACGTTGTTTATTCAA
1 TTCAATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCATTCTTCAA
8456 TTTA-
66 TTTAC
* * * * ** * * * * *
8460 TGTTAGAATGATCGAGGGTGGCCGTTCTTCAGTTTATTTCAGTTCACCTAGGGCGGTCTTTCTTC
1 T-TCA-ATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCATTCTTC
8525 AATTTAC
64 AATTTAC
* *
8532 TTCAATTGATCCAGGGCGATCTTTCTTCAG-TTAGTTTCAATTGATCCAGGGCGATCATTCTTCA
1 TTCAATTGATCCAGGGCGATCTTTCTTCAGTTTA-TTTCAGTTGACCCAGGGCGATCATTCTTCA
*
8596 GTTTAC
65 ATTTAC
** * * * *
8602 TTCAATTGATCCAGGGCGATCTTTCTTCAGTTCGTTTCAATTGACCAAGGACGATTATTCTTCAA
1 TTCAATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCATTCTTCAA
8667 TTTAC
66 TTTAC
*
8672 TTCAATTGATCCAGGGCAATCTTTCTTCA
1 TTCAATTGATCCAGGGCGATCTTTCTTCA
8701 AATTGACTCA
Statistics
Matches: 256, Mismatches: 49, Indels: 11
0.81 0.16 0.03
Matches are distributed among these distances:
69 4 0.02
70 192 0.75
71 59 0.23
72 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (70 bp):
TTCAATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCATTCTTCAA
TTTAC
Found at i:8701 original size:35 final size:35
Alignment explanation
Indices: 8290--8700 Score: 368
Period size: 35 Copynumber: 11.7 Consensus size: 35
8280 ATAGTTTCGT
* *
8290 ATTGA-CCAGGGCGGTCTTTTTTCAGTTGT-TTTCA
1 ATTGATCCAGGGCGATCTTTCTTCAGTT-TATTTCA
* *
8324 AGTTGATCCAGGACGATCATTCTTCAGTTTATTTCA
1 A-TTGATCCAGGGCGATCTTTCTTCAGTTTATTTCA
* * *
8360 GTTGACCCAGGGCGATCATTCTTCAGTTTATTTCA
1 ATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCA
* * *
8395 ATTGACCCAGGGCGGTCTTTCTTCAGTTTACTTCA
1 ATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCA
* * ** * * * *
8430 GTTGACCCAGAACGTTGTTTATTCAATTTATGTT-A
1 ATTGATCCAGGGCGATCTTTCTTCAGTTTAT-TTCA
* * * ** *
8465 GAATGATCGAGGGTGGCCGTTCTTCAGTTTATTTCA
1 -ATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCA
* * * * *
8501 GTTCA-CCTAGGGCGGTCTTTCTTCAATTTACTTCA
1 ATTGATCC-AGGGCGATCTTTCTTCAGTTTATTTCA
8536 ATTGATCCAGGGCGATCTTTCTTCAG-TTAGTTTCA
1 ATTGATCCAGGGCGATCTTTCTTCAGTTTA-TTTCA
* *
8571 ATTGATCCAGGGCGATCATTCTTCAGTTTACTTCA
1 ATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCA
**
8606 ATTGATCCAGGGCGATCTTTCTTCAGTTCGTTTCA
1 ATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCA
* * *
8641 ATTGA-CCAAGGACGAT-TATTCTTCAATTTACTTCA
1 ATTGATCC-AGGGCGATCT-TTCTTCAGTTTATTTCA
*
8676 ATTGATCCAGGGCAATCTTTCTTCA
1 ATTGATCCAGGGCGATCTTTCTTCA
8701 AATTGACTCA
Statistics
Matches: 304, Mismatches: 59, Indels: 27
0.78 0.15 0.07
Matches are distributed among these distances:
34 8 0.03
35 244 0.80
36 52 0.17
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (35 bp):
ATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCA
Found at i:8793 original size:16 final size:16
Alignment explanation
Indices: 8768--8812 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
8758 CTCCATTATT
*
8768 CAATTATTCAATGT-TC
1 CAATTCTTCAAT-TCTC
8784 CAATTCTTCAATTCTC
1 CAATTCTTCAATTCTC
*
8800 CAATGCTTCAATT
1 CAATTCTTCAATT
8813 TACATCAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 1 0.04
16 25 0.96
ACGTcount: A:0.29, C:0.24, G:0.04, T:0.42
Consensus pattern (16 bp):
CAATTCTTCAATTCTC
Found at i:8803 original size:24 final size:24
Alignment explanation
Indices: 8753--8812 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
8743 TGGGGGTATG
* *
8753 CAATGCTCC-ATTATTCAATTATT
1 CAATGTTCCAATTATTCAATTATC
* *
8776 CAATGTTCCAATTCTTCAATTCTC
1 CAATGTTCCAATTATTCAATTATC
8800 CAATGCTT-CAATT
1 CAATG-TTCCAATT
8813 TACATCAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 8 0.26
24 21 0.68
25 2 0.06
ACGTcount: A:0.28, C:0.25, G:0.05, T:0.42
Consensus pattern (24 bp):
CAATGTTCCAATTATTCAATTATC
Found at i:9031 original size:52 final size:50
Alignment explanation
Indices: 8859--9087 Score: 307
Period size: 50 Copynumber: 4.5 Consensus size: 50
8849 TTCTGGTAGT
** *
8859 TTCAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTCGAGTTTATC
1 TTCAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTC
* * * *
8909 TTCAAGTGATCCAGTGCGTTCAATCAAATTTACAGTGGCTTAAGTTTTCC
1 TTCAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTC
*
8959 TTCAAGTGATGCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTTC
1 TTCAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAG-TTTTTC
* *
9010 TTCTAAGTGATCCAGTGCGATCAGTCAAGTTTACAGTGGTTTAAG-TTTCC
1 TTC-AAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTC
** *
9060 TAAAAGTGATCCAAGTGCGGTCAATCAA
1 TTCAAGTGATCC-AGTGCGATCAATCAA
9088 AGAAGTTTCT
Statistics
Matches: 157, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
49 9 0.06
50 101 0.64
51 8 0.05
52 39 0.25
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (50 bp):
TTCAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTC
Found at i:9077 original size:102 final size:100
Alignment explanation
Indices: 8862--9087 Score: 319
Period size: 102 Copynumber: 2.2 Consensus size: 100
8852 TGGTAGTTTC
*
8862 AAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTCGAGTTTATCTTCAAGTGATCCAGTGCG
1 AAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTCAAGTTTATCTTCAAGTGATCCAGTGCG
* **
8927 TTCAATCAAATTTACAGTGGCTTAAGTTTTCCTTC
66 ATCAATCAAATTTACAGTGGCTTAAGTTTTCCTAA
* * *
8962 AAGTGATGCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTTCTTCTAAGTGATCCAGTG
1 AAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTCAAG-TTTATCTTC-AAGTGATCCAGTG
* * *
9027 CGATCAGTCAAGTTTACAGTGGTTTAAG-TTTCCTAA
64 CGATCAATCAAATTTACAGTGGCTTAAGTTTTCCTAA
*
9063 AAGTGATCCAAGTGCGGTCAATCAA
1 AAGTGATCC-AGTGCGATCAATCAA
9088 AGAAGTTTCT
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
100 38 0.34
101 22 0.20
102 51 0.46
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (100 bp):
AAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTCAAGTTTATCTTCAAGTGATCCAGTGCG
ATCAATCAAATTTACAGTGGCTTAAGTTTTCCTAA
Found at i:9226 original size:54 final size:54
Alignment explanation
Indices: 9103--9258 Score: 215
Period size: 54 Copynumber: 2.9 Consensus size: 54
9093 TTTCTAAAGG
**
9103 TCCAGTGCGGTCAATCAATCAAATTTATAGTGGTTTAAGTTT-TCTTCAAGCGA
1 TCCAGTGCGGTCAATCAAGAAAATTTATAGTGGTTTAAGTTTATCTTCAAGCGA
* * *
9156 TCCAGTGCGATCAATCAAGAAAATTTACAGTGGTTTAAGTTTATCTTCAAGTGA
1 TCCAGTGCGGTCAATCAAGAAAATTTATAGTGGTTTAAGTTTATCTTCAAGCGA
* * * * *
9210 TCCAGTACGGCCAATCAAGGAAATTTTTAGTGGTTTAGGTTTATCTTCA
1 TCCAGTGCGGTCAATCAAGAAAATTTATAGTGGTTTAAGTTTATCTTCA
9259 GAGTTAGAAT
Statistics
Matches: 90, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
53 38 0.42
54 52 0.58
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (54 bp):
TCCAGTGCGGTCAATCAAGAAAATTTATAGTGGTTTAAGTTTATCTTCAAGCGA
Found at i:9307 original size:35 final size:35
Alignment explanation
Indices: 9252--9609 Score: 468
Period size: 35 Copynumber: 10.2 Consensus size: 35
9242 GTTTAGGTTT
*
9252 ATCTTCAGAGTTAGAATCAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
*
9287 ATCTTCAAAGTT-GAATTCAGATGACTTGGTGTAGC
1 ATCTTCAAAGTTAGAA-TCAGATGACTCGGTGTAGC
*
9322 ATCTTCAAAGTTAGAATTAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
* * *
9357 ATCTTCAAAG-TCGAATTCAGATGACTCAGTCTAGC
1 ATCTTCAAAGTTAGAA-TCAGATGACTCGGTGTAGC
* *
9392 ATCTTCAAAGTTAGAACCAGATGTCTCGGTGTAGC
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
* * * * * *
9427 ATCTTCAAAGTTGGATTTAGACGATTCAGTGTAGC
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
*
9462 ATCTTCAAAGTTGGAATCAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
*
9497 ATCTTCAAAGTTAGAACCAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
* * * *
9532 ATCTTCAAAGTTGGATTTAGATGACTCAGTGTAGC
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
* * *
9567 ATCTTCAAAGTTGGAATCAGACGACTCGGTGAAGC
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
*
9602 AACTTCAA
1 ATCTTCAA
9610 GTGGGATTTG
Statistics
Matches: 280, Mismatches: 39, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
34 7 0.03
35 266 0.95
36 7 0.03
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (35 bp):
ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
Found at i:9639 original size:42 final size:42
Alignment explanation
Indices: 9580--9694 Score: 167
Period size: 42 Copynumber: 2.7 Consensus size: 42
9570 TTCAAAGTTG
* * * *
9580 GAATCAGACGACTCGGTGAAGCAACTTCAAGTGGGATTTGGT
1 GAATCAGATGACTCGGTGAAGCATCTTCAAGTGGGATTCGAT
*
9622 GAATCAGATGACTCGGTGAAGCATCCTCAAGTGGGATTCGAT
1 GAATCAGATGACTCGGTGAAGCATCTTCAAGTGGGATTCGAT
* *
9664 GAATCAGATGAATCGGTGTAGCATCTTCAAG
1 GAATCAGATGACTCGGTGAAGCATCTTCAAG
9695 ATTGGAATTA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (42 bp):
GAATCAGATGACTCGGTGAAGCATCTTCAAGTGGGATTCGAT
Found at i:9817 original size:89 final size:88
Alignment explanation
Indices: 9656--9862 Score: 242
Period size: 89 Copynumber: 2.3 Consensus size: 88
9646 CCTCAAGTGG
* * * *
9656 GATTCGATGAATC-AGATGAAT-CGGTGTAGCATCTTCAAGATTGGAATTAGGTGAGCTCGGTCT
1 GATTCGATGAATCAAG-TTAATGCGGTGCATC-TCTTCAAGATTGGAATTAGGTAAGCTCGGTCT
* *
9719 AACATATTTTCAAATAGATCAGGG-T
64 AACACATTTTCAAACAGATC-GGGAT
* *
9744 GATTCGTTGAATCAAGTTAATGCGGTGCATCTCTTCAAAGATTGGAATTCGGTAAGCTCGGTGC-
1 GATTCGATGAATCAAGTTAATGCGGTGCATCTCTTC-AAGATTGGAATTAGGTAAGCTCGGT-CT
* *
9808 AACACATTTTGAAACAGTTCGGGAT
64 AACACATTTTCAAACAGATCGGGAT
*
9833 GATTCGATGAATCAAGTTGATGCGGTGCAT
1 GATTCGATGAATCAAGTTAATGCGGTGCAT
9863 TATTTCTTCA
Statistics
Matches: 102, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
88 24 0.24
89 77 0.75
90 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (88 bp):
GATTCGATGAATCAAGTTAATGCGGTGCATCTCTTCAAGATTGGAATTAGGTAAGCTCGGTCTAA
CACATTTTCAAACAGATCGGGAT
Found at i:15919 original size:16 final size:15
Alignment explanation
Indices: 15898--15937 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
15888 TTACTTTGTT
15898 TTGTTTTCTAGTATAA
1 TTGTTTTCT-GTATAA
* *
15914 TTGTTTTCTTTCTAA
1 TTGTTTTCTGTATAA
15929 TTGTTTTCT
1 TTGTTTTCT
15938 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.65
Consensus pattern (15 bp):
TTGTTTTCTGTATAA
Found at i:15931 original size:15 final size:15
Alignment explanation
Indices: 15911--15940 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15901 TTTTCTAGTA
15911 TAATTGTTTTCTTTC
1 TAATTGTTTTCTTTC
15926 TAATTGTTTTCTTTC
1 TAATTGTTTTCTTTC
15941 AACCTCTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (15 bp):
TAATTGTTTTCTTTC
Found at i:16719 original size:16 final size:15
Alignment explanation
Indices: 16698--16737 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
16688 TTACTTTATT
16698 TTGTTTTCTAGTATAA
1 TTGTTTTCT-GTATAA
* *
16714 TTGTTTTCTTTTTAA
1 TTGTTTTCTGTATAA
16729 TTGTTTTCT
1 TTGTTTTCT
16738 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (15 bp):
TTGTTTTCTGTATAA
Found at i:16731 original size:15 final size:15
Alignment explanation
Indices: 16711--16739 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16701 TTTTCTAGTA
16711 TAATTGTTTTCTTTT
1 TAATTGTTTTCTTTT
16726 TAATTGTTTTCTTT
1 TAATTGTTTTCTTT
16740 CAACCTCTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TAATTGTTTTCTTTT
Found at i:21206 original size:9 final size:9
Alignment explanation
Indices: 21192--21218 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
21182 AAATGGTTGC
21192 TTTGTTTTG
1 TTTGTTTTG
21201 TTTGTTTTG
1 TTTGTTTTG
21210 TTTGTTTTG
1 TTTGTTTTG
21219 ATATTTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (9 bp):
TTTGTTTTG
Found at i:23254 original size:3 final size:3
Alignment explanation
Indices: 23246--23275 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
23236 AAACAAAAAT
23246 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
23276 GACATGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:23316 original size:14 final size:14
Alignment explanation
Indices: 23283--23342 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
23273 CAAGACATGT
*
23283 TTTTCAAGAAAATTG
1 TTTTCAAGAAAA-GG
*
23298 TTTTCAAGAAGAGG
1 TTTTCAAGAAAAGG
23312 TTTTCAA-AAATAGG
1 TTTTCAAGAAA-AGG
23326 TTTTCAA-AAAAGG
1 TTTTCAAGAAAAGG
23339 TTTT
1 TTTT
23343 GAGTCTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
13 9 0.22
14 21 0.51
15 11 0.27
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (14 bp):
TTTTCAAGAAAAGG
Found at i:23641 original size:12 final size:12
Alignment explanation
Indices: 23624--23648 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23614 TATCAAGTAA
23624 TTCAAATCAAAG
1 TTCAAATCAAAG
23636 TTCAAATCAAAG
1 TTCAAATCAAAG
23648 T
1 T
23649 GAATCAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (12 bp):
TTCAAATCAAAG
Found at i:24370 original size:27 final size:27
Alignment explanation
Indices: 24340--24443 Score: 163
Period size: 27 Copynumber: 3.9 Consensus size: 27
24330 TAGAATCAAC
* *
24340 CAGGGGCATTTTAGTCATTTGCAAATT
1 CAGGGGCATTGTAGTCATTTGCACATT
24367 CAGGGGCATTGTAGTCATTTGCACATT
1 CAGGGGCATTGTAGTCATTTGCACATT
*
24394 TAGGGGCATTGTAGTCATTTGCACATT
1 CAGGGGCATTGTAGTCATTTGCACATT
* *
24421 TAGGGGCATTTTAGTCATTTGCA
1 CAGGGGCATTGTAGTCATTTGCA
24444 GTTCACTGTT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (27 bp):
CAGGGGCATTGTAGTCATTTGCACATT
Found at i:24614 original size:22 final size:23
Alignment explanation
Indices: 24584--24630 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
24574 TAATTCAGTA
*
24584 TTTTCGCACTTTGATCATATAGC
1 TTTTCGCACTTTGATCATACAGC
24607 TTTT-GCACTTTGATCATACAGC
1 TTTTCGCACTTTGATCATACAGC
24629 TT
1 TT
24631 AAGCCCTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (23 bp):
TTTTCGCACTTTGATCATACAGC
Done.