Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010478.1 Corchorus capsularis cultivar CVL-1 contig10499, 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: 37496
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1365 original size:19 final size:18
Alignment explanation
Indices: 1341--1376 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1331 TGAAGATTTC
1341 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
1360 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
1377 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:5334 original size:170 final size:170
Alignment explanation
Indices: 4958--5486 Score: 819
Period size: 170 Copynumber: 3.1 Consensus size: 170
4948 CAAGTTTTTA
* * * * *
4958 TCATGTTTAAGTTTAAAATCCTTGTTCAAGGTCTCTATTTAGAGTTTGCATTTGTAAGACCTCCG
1 TCATGTTTAAGTTTAAAATCCTTGTTAAAGGTCTCTATTCAAAGTTTGCATTGGTAAGTCCTCCG
* *
5023 GGCAAAAGTTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCTAGGCAATTGGTAAAACCTC
66 GGCAAAATTTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCAGGCAATTGGTAAAACCTC
* *
5088 -CGAGTACC-GTTTCATTTCATCAAGTTTTTCATCAAAGAT
131 TAG-GTACCATTTTCATTTCATCAAGTTTTTCATCAAAGAT
** * * *
5127 TCAAATTTAAGTTTGAAATCCTTGTCAAAGGTCTCTATTCAAAGTTTGCATTGGTAAGTCCTCCA
1 TCATGTTTAAGTTTAAAATCCTTGTTAAAGGTCTCTATTCAAAGTTTGCATTGGTAAGTCCTCCG
* * *
5192 GACAAAATTTCAGAAACCTCCGGGTATTAATTTTGATAAGTCCTCCAGGTAATTGGTAAAACCTC
66 GGCAAAATTTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCAGGCAATTGGTAAAACCTC
5257 TAGGTACCATTTTCATTTCATCAAGTTTTTCATCAAAGAT
131 TAGGTACCATTTTCATTTCATCAAGTTTTTCATCAAAGAT
5297 TCATGTTTAAGTTTAAAATCCTTGTTAAAGGTCTCTATTCAAAGTTTGCATTGGTAAGTCCTCCG
1 TCATGTTTAAGTTTAAAATCCTTGTTAAAGGTCTCTATTCAAAGTTTGCATTGGTAAGTCCTCCG
* * * *
5362 GGCACAATTTCAGAAACCTCCGAGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAACCTT
66 GGCAAAATTTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCAGGCAATTGGTAAAACCTC
*
5427 TGGGTACCATTTTCATTTCATCAAGTTTTTCATCAAAGAAT
131 TAGGTACCATTTTCATTTCATCAAGTTTTTCATCAAAG-AT
*
5468 TCATGTATAAGTTTAAAAT
1 TCATGTTTAAGTTTAAAAT
5487 TATGGGGAGC
Statistics
Matches: 326, Mismatches: 31, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
169 120 0.37
170 186 0.57
171 20 0.06
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
Consensus pattern (170 bp):
TCATGTTTAAGTTTAAAATCCTTGTTAAAGGTCTCTATTCAAAGTTTGCATTGGTAAGTCCTCCG
GGCAAAATTTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCAGGCAATTGGTAAAACCTC
TAGGTACCATTTTCATTTCATCAAGTTTTTCATCAAAGAT
Found at i:8435 original size:16 final size:16
Alignment explanation
Indices: 8416--8463 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
8406 AACCCGCCCG
8416 AACCCGAACCCAAAAA
1 AACCCGAACCCAAAAA
*
8432 AACCCGAACCCGAAAA
1 AACCCGAACCCAAAAA
* *
8448 AATCAGAACCCAAAAA
1 AACCCGAACCCAAAAA
8464 TCTGAAACCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.56, C:0.33, G:0.08, T:0.02
Consensus pattern (16 bp):
AACCCGAACCCAAAAA
Found at i:9787 original size:27 final size:27
Alignment explanation
Indices: 9736--9787 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
9726 TAGTTGCGAC
**
9736 AATTTTGGCTAGTTGTAGGGTTTTTAT
1 AATTTTGGCTAGTTGTAGGAATTTTAT
9763 AATTTTGGCTAGTTGT-GGCAATTTT
1 AATTTTGGCTAGTTGTAGG-AATTTT
9788 GCAAGGGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (27 bp):
AATTTTGGCTAGTTGTAGGAATTTTAT
Found at i:9849 original size:26 final size:27
Alignment explanation
Indices: 9801--9856 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
9791 AGGGGACTTC
*
9801 TTGCAATTTTAGGTTGCTGTGGCAACT
1 TTGCAATTTTACGTTGCTGTGGCAACT
* *
9828 TTGCAATTTT-CGTTGTTGTGGCATCT
1 TTGCAATTTTACGTTGCTGTGGCAACT
9854 TTG
1 TTG
9857 GCTAGCTGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.14, C:0.14, G:0.25, T:0.46
Consensus pattern (27 bp):
TTGCAATTTTACGTTGCTGTGGCAACT
Found at i:9898 original size:27 final size:27
Alignment explanation
Indices: 9863--9916 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
9853 TTTGGCTAGC
9863 TGCGACAATTGTGCAATTTCT-GGTACT
1 TGCGACAATTGTGCAATTT-TGGGTACT
* *
9890 TGCGGCAATTTTGCAATTTTGGGTACT
1 TGCGACAATTGTGCAATTTTGGGTACT
9917 AGCTCAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (27 bp):
TGCGACAATTGTGCAATTTTGGGTACT
Found at i:13473 original size:23 final size:23
Alignment explanation
Indices: 13447--13510 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 23
13437 AAATCTGTAG
13447 AAAATTTAGAAAATTTATGTGTT
1 AAAATTTAGAAAATTTATGTGTT
* *
13470 AAAA-ATAAAAACATTTATGTGTT
1 AAAATTTAGAAA-ATTTATGTGTT
13493 -AAATCTGTAGAAAATTTA
1 AAAAT-T-TAGAAAATTTA
13511 GAATTTTACC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
22 8 0.24
23 15 0.45
24 5 0.15
25 5 0.15
ACGTcount: A:0.48, C:0.03, G:0.11, T:0.38
Consensus pattern (23 bp):
AAAATTTAGAAAATTTATGTGTT
Found at i:14814 original size:42 final size:42
Alignment explanation
Indices: 14754--14842 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
14744 GTGCCCGGGT
* * *
14754 TGTGCTCGGTCATATGCGATTGCCCCATGCAATGGCTGGTCA
1 TGTGCCCGGTCATATGCGATTGCCCCATGCAATGGCCGATCA
* * *
14796 TGTGCCCGGTCTTGTGCGATTGCTCCATGCAATGGCCGATCA
1 TGTGCCCGGTCATATGCGATTGCCCCATGCAATGGCCGATCA
14838 TGTGC
1 TGTGC
14843 GATCCCTTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (42 bp):
TGTGCCCGGTCATATGCGATTGCCCCATGCAATGGCCGATCA
Found at i:19926 original size:469 final size:469
Alignment explanation
Indices: 19048--19990 Score: 1886
Period size: 469 Copynumber: 2.0 Consensus size: 469
19038 TGATTCCACC
19048 AATTCAAAGCATTCTCCGTAAATTCAAGAGTAGCAATTTGCACTTTCTTAGGCTCGGCATGAGGA
1 AATTCAAAGCATTCTCCGTAAATTCAAGAGTAGCAATTTGCACTTTCTTAGGCTCGGCATGAGGA
19113 TAATAATCAAAGTACATATCCAATTTGTCTCCCACTCCAAGTAATCCGATGGTGACCCTCTCCCA
66 TAATAATCAAAGTACATATCCAATTTGTCTCCCACTCCAAGTAATCCGATGGTGACCCTCTCCCA
19178 TTGAATTTAGGGATTTTGTACTTGATGTTATCTTTAGGCTTTTCTCTTTCAACTCCCCTCCTAGG
131 TTGAATTTAGGGATTTTGTACTTGATGTTATCTTTAGGCTTTTCTCTTTCAACTCCCCTCCTAGG
19243 CCGCATGTTTTCATTGATTGTTTGACCTCCAAGCTCTTGTTGCCTCAATCTCTCCATGGGATCCA
196 CCGCATGTTTTCATTGATTGTTTGACCTCCAAGCTCTTGTTGCCTCAATCTCTCCATGGGATCCA
19308 ACCTAGCAACTTGCCTCGGTGGTGGAAGTTGAATTCTCTCATTGTTGATTGCGGCATTGGCTCCA
261 ACCTAGCAACTTGCCTCGGTGGTGGAAGTTGAATTCTCTCATTGTTGATTGCGGCATTGGCTCCA
19373 TGTTGAGCTTGTTGATTTCGAGTTTCTAATGCCTCCAATCTCGTTGTCATGGTACCAAGTTGTTG
326 TGTTGAGCTTGTTGATTTCGAGTTTCTAATGCCTCCAATCTCGTTGTCATGGTACCAAGTTGTTG
19438 CATGATTTGTTGCCACATGATTTTGTTCTTCTTGTCTATCTCCCATTGTACCTACAAAAGAGCAA
391 CATGATTTGTTGCCACATGATTTTGTTCTTCTTGTCTATCTCCCATTGTACCTACAAAAGAGCAA
19503 AGATTAGTAGTAAA
456 AGATTAGTAGTAAA
19517 AATTCAAAGCATTCTCCGTAAATTCAAGAGTAGCAATTTGCACTTTCTTAGGCTCGGCATGAGGA
1 AATTCAAAGCATTCTCCGTAAATTCAAGAGTAGCAATTTGCACTTTCTTAGGCTCGGCATGAGGA
19582 TAATAATCAAAGTACATATCCAATTTGTCTCCCACTCCAAGTAATCCGATGGTGACCCTCTCCCA
66 TAATAATCAAAGTACATATCCAATTTGTCTCCCACTCCAAGTAATCCGATGGTGACCCTCTCCCA
19647 TTGAATTTAGGGATTTTGTACTTGATGTTATCTTTAGGCTTTTCTCTTTCAACTCCCCTCCTAGG
131 TTGAATTTAGGGATTTTGTACTTGATGTTATCTTTAGGCTTTTCTCTTTCAACTCCCCTCCTAGG
19712 CCGCATGTTTTCATTGATTGTTTGACCTCCAAGCTCTTGTTGCCTCAATCTCTCCATGGGATCCA
196 CCGCATGTTTTCATTGATTGTTTGACCTCCAAGCTCTTGTTGCCTCAATCTCTCCATGGGATCCA
19777 ACCTAGCAACTTGCCTCGGTGGTGGAAGTTGAATTCTCTCATTGTTGATTGCGGCATTGGCTCCA
261 ACCTAGCAACTTGCCTCGGTGGTGGAAGTTGAATTCTCTCATTGTTGATTGCGGCATTGGCTCCA
19842 TGTTGAGCTTGTTGATTTCGAGTTTCTAATGCCTCCAATCTCGTTGTCATGGTACCAAGTTGTTG
326 TGTTGAGCTTGTTGATTTCGAGTTTCTAATGCCTCCAATCTCGTTGTCATGGTACCAAGTTGTTG
19907 CATGATTTGTTGCCACATGATTTTGTTCTTCTTGTCTATCTCCCATTGTACCTACAAAAGAGCAA
391 CATGATTTGTTGCCACATGATTTTGTTCTTCTTGTCTATCTCCCATTGTACCTACAAAAGAGCAA
19972 AGATTAGTAGTAAA
456 AGATTAGTAGTAAA
19986 AATTC
1 AATTC
19991 CTCACAAGTG
Statistics
Matches: 474, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
469 474 1.00
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (469 bp):
AATTCAAAGCATTCTCCGTAAATTCAAGAGTAGCAATTTGCACTTTCTTAGGCTCGGCATGAGGA
TAATAATCAAAGTACATATCCAATTTGTCTCCCACTCCAAGTAATCCGATGGTGACCCTCTCCCA
TTGAATTTAGGGATTTTGTACTTGATGTTATCTTTAGGCTTTTCTCTTTCAACTCCCCTCCTAGG
CCGCATGTTTTCATTGATTGTTTGACCTCCAAGCTCTTGTTGCCTCAATCTCTCCATGGGATCCA
ACCTAGCAACTTGCCTCGGTGGTGGAAGTTGAATTCTCTCATTGTTGATTGCGGCATTGGCTCCA
TGTTGAGCTTGTTGATTTCGAGTTTCTAATGCCTCCAATCTCGTTGTCATGGTACCAAGTTGTTG
CATGATTTGTTGCCACATGATTTTGTTCTTCTTGTCTATCTCCCATTGTACCTACAAAAGAGCAA
AGATTAGTAGTAAA
Found at i:21792 original size:42 final size:42
Alignment explanation
Indices: 21740--21828 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
21730 AATGTCCGGT
*
21740 TGTGCCCGGTCATATGCGATTGCCCCATGCAATGGCCGGTCA
1 TGTGCCCGGTCATATGCGAGTGCCCCATGCAATGGCCGGTCA
* * * *
21782 TGTGCCCGGTCTTGTGCGAGTGCTCCATTCAATGGCCGGTCA
1 TGTGCCCGGTCATATGCGAGTGCCCCATGCAATGGCCGGTCA
21824 TGTGC
1 TGTGC
21829 GATCCCTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.13, C:0.29, G:0.30, T:0.27
Consensus pattern (42 bp):
TGTGCCCGGTCATATGCGAGTGCCCCATGCAATGGCCGGTCA
Found at i:22058 original size:25 final size:25
Alignment explanation
Indices: 22029--22095 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
22019 CTTGTTTCGT
*
22029 TGTTGCGCTGCGTCTCATTGTGTTG
1 TGTTGCGCTGCATCTCATTGTGTTG
*
22054 TGTTGCGCCGCATCTCATTGTGTTG
1 TGTTGCGCTGCATCTCATTGTGTTG
22079 TG-TGCGCTGCATCTCAT
1 TGTTGCGCTGCATCTCAT
22096 GTCTTACGCC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
24 14 0.36
25 25 0.64
ACGTcount: A:0.07, C:0.24, G:0.28, T:0.40
Consensus pattern (25 bp):
TGTTGCGCTGCATCTCATTGTGTTG
Found at i:22205 original size:35 final size:35
Alignment explanation
Indices: 22135--22226 Score: 114
Period size: 35 Copynumber: 2.6 Consensus size: 35
22125 CCCATGTGGC
* **
22135 CATGTCTAATGCCATAAACGTCTTGTGCCATATCT
1 CATGTCTAATGCCATAAATGTCTAATGCCATATCT
*
22170 CATGTCTGATGCCATAAATGTCTAATGCCGA-ATCT
1 CATGTCTAATGCCATAAATGTCTAATGCC-ATATCT
* *
22205 CGTGTCTAATGCAATAAATGTC
1 CATGTCTAATGCCATAAATGTC
22227 GTATGCGATA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
35 48 0.98
36 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (35 bp):
CATGTCTAATGCCATAAATGTCTAATGCCATATCT
Found at i:30449 original size:5 final size:6
Alignment explanation
Indices: 30419--30446 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
30409 CACTAAAACG
30419 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
30447 TAACGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:32582 original size:24 final size:25
Alignment explanation
Indices: 32542--32640 Score: 80
Period size: 24 Copynumber: 4.0 Consensus size: 25
32532 ATAGATATTT
*
32542 GGCTGCCACATTCTCTTCATTG-TTG
1 GGCTGCGACATT-TCTTCATTGCTTG
*
32567 GGCTGCGACATTTCTTAATTGCTT-
1 GGCTGCGACATTTCTTCATTGCTTG
* * *
32591 GGCTAC-ATCATTTCTTCCTTG-TTT
1 GGCTGCGA-CATTTCTTCATTGCTTG
* * *
32615 GGCTGTGGCATCTCTTCATTGCTTG
1 GGCTGCGACATTTCTTCATTGCTTG
32640 G
1 G
32641 TTACGGCATT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
23 3 0.05
24 39 0.67
25 16 0.28
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.42
Consensus pattern (25 bp):
GGCTGCGACATTTCTTCATTGCTTG
Found at i:32651 original size:48 final size:48
Alignment explanation
Indices: 32550--32651 Score: 114
Period size: 48 Copynumber: 2.1 Consensus size: 48
32540 TTGGCTGCCA
* *
32550 CATTCTCTTCATTGTTGGGCTGCGACATTTCTTAATTGCTTGGCTACAT
1 CATT-TCTTCATTGTTGGGCTGCGACATCTCTTAATTGCTTGGCTACAG
* * * * * * *
32599 CATTTCTTCCTTGTTTGGCTGTGGCATCTCTTCATTGCTTGGTTACGG
1 CATTTCTTCATTGTTGGGCTGCGACATCTCTTAATTGCTTGGCTACAG
32647 CATTT
1 CATTT
32652 ACAACGGTGC
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
48 40 0.91
49 4 0.09
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.45
Consensus pattern (48 bp):
CATTTCTTCATTGTTGGGCTGCGACATCTCTTAATTGCTTGGCTACAG
Found at i:32717 original size:27 final size:27
Alignment explanation
Indices: 32667--32718 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
32657 GGTGCAACAT
*
32667 GGCTTGGGCGCGGGATCGCCTGGGCAC
1 GGCTTGGGCGCGGGAACGCCTGGGCAC
* * *
32694 GGCTTGGGTGCGGTAACGCTTGGGC
1 GGCTTGGGCGCGGGAACGCCTGGGC
32719 GCGACATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.08, C:0.25, G:0.48, T:0.19
Consensus pattern (27 bp):
GGCTTGGGCGCGGGAACGCCTGGGCAC
Found at i:32734 original size:17 final size:17
Alignment explanation
Indices: 32712--32825 Score: 81
Period size: 16 Copynumber: 6.9 Consensus size: 17
32702 TGCGGTAACG
*
32712 CTTGGGCGCGACATTTA
1 CTTGGGTGCGACATTTA
**
32729 CTTGGGTGCGACATCCA
1 CTTGGGTGCGACATTTA
*
32746 -TTGGGTGCGGCATTTA
1 CTTGGGTGCGACATTTA
* * *
32762 CTTGGATGCGGCA-TTG
1 CTTGGGTGCGACATTTA
* * **
32778 CTTGGCTGCGGCA-TCG
1 CTTGGGTGCGACATTTA
* *
32794 CTTGGGCGCGGCATTTA
1 CTTGGGTGCGACATTTA
*
32811 CTTGGGTGCGGCATT
1 CTTGGGTGCGACATT
32826 GTTTAGGTGC
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
16 40 0.50
17 40 0.50
ACGTcount: A:0.12, C:0.23, G:0.35, T:0.30
Consensus pattern (17 bp):
CTTGGGTGCGACATTTA
Found at i:32782 original size:49 final size:49
Alignment explanation
Indices: 32729--32835 Score: 144
Period size: 49 Copynumber: 2.2 Consensus size: 49
32719 GCGACATTTA
*
32729 CTTGGGTGCGACATC-CATTGGGTGCGGCATTTACTTGGATGCGGCATTG
1 CTTGGGTGCGACATCGC-TTGGGCGCGGCATTTACTTGGATGCGGCATTG
* * *
32778 CTTGGCTGCGGCATCGCTTGGGCGCGGCATTTACTTGGGTGCGGCATTG
1 CTTGGGTGCGACATCGCTTGGGCGCGGCATTTACTTGGATGCGGCATTG
* *
32827 TTTAGGTGC
1 CTTGGGTGC
32836 CGTAGTCTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
49 49 0.98
50 1 0.02
ACGTcount: A:0.11, C:0.21, G:0.36, T:0.31
Consensus pattern (49 bp):
CTTGGGTGCGACATCGCTTGGGCGCGGCATTTACTTGGATGCGGCATTG
Found at i:32788 original size:33 final size:33
Alignment explanation
Indices: 32723--32791 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
32713 TTGGGCGCGA
* *
32723 CATTTACTTGGGTGCGACATCCATTGGGTGCGG
1 CATTTACTTGGATGCGACATCCATTGGCTGCGG
* *
32756 CATTTACTTGGATGCGGCATTGC-TTGGCTGCGG
1 CATTTACTTGGATGCGACA-TCCATTGGCTGCGG
32789 CAT
1 CAT
32792 CGCTTGGGCG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.14, C:0.22, G:0.32, T:0.32
Consensus pattern (33 bp):
CATTTACTTGGATGCGACATCCATTGGCTGCGG
Found at i:33043 original size:32 final size:32
Alignment explanation
Indices: 33002--33075 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
32992 ACCTACTCCT
* *
33002 GCAAATCTCCACAGCCGTATCTCACCACTGTC
1 GCAAATCTCCACAACCATATCTCACCACTGTC
*
33034 GCAAATCTCCACAACCATGTCTCACCACTGTC
1 GCAAATCTCCACAACCATATCTCACCACTGTC
33066 GCAAATCTCC
1 GCAAATCTCC
33076 GTTGTCGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.27, C:0.41, G:0.11, T:0.22
Consensus pattern (32 bp):
GCAAATCTCCACAACCATATCTCACCACTGTC
Found at i:33222 original size:32 final size:32
Alignment explanation
Indices: 33138--33213 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
33128 CTAACTACTA
33138 CCGCAAATCTCCACAGCCGTATCACACCACTG
1 CCGCAAATCTCCACAGCCGTATCACACCACTG
* *
33170 CCACAAATCTCCACAGCCGTATCTCACCACTG
1 CCGCAAATCTCCACAGCCGTATCACACCACTG
*
33202 TCGCAAATCTCC
1 CCGCAAATCTCC
33214 GTTGCCGTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.28, C:0.43, G:0.11, T:0.18
Consensus pattern (32 bp):
CCGCAAATCTCCACAGCCGTATCACACCACTG
Found at i:33331 original size:141 final size:137
Alignment explanation
Indices: 32905--33321 Score: 550
Period size: 138 Copynumber: 3.1 Consensus size: 137
32895 TCACTTATGT
*
32905 CGCAAATCTCCACTA-CCGTATCTCACCACTGTCGCAAA--T---AT--C-TAAGCCATTCTTTG
1 CGCAAATCTCCAC-AGCCGTATCTCACCACTGTCGCAAATCTCCGTTGCCGTAAGCCATTCTTTG
*
32961 --TTTTTTTTAATAATGGGTCGTGGCTTCCACTACCTACTCCTGCAAATCTCCACAGCCGTATCT
65 TTTTTTTTTTAATAATGTGTCGTGGCTTCCACTACCTACTCC-GCAAATCTCCACAGCCGTATCT
*
33024 CACCACTGT
129 CACCACTGC
* * * *
33033 CGCAAATCTCCACAACCATGTCTCACCACTGTCGCAAATCTCCGTTGTCGTAAGCCATTCTTTGT
1 CGCAAATCTCCACAGCCGTATCTCACCACTGTCGCAAATCTCCGTTGCCGTAAGCCATTCTTTGT
* *
33098 TTTTTTTTTAATAATGTGTCGTGGCTTCCACTAACTACTACCGCAAATCTCCACAGCCGTATCAC
66 TTTTTTTTTAATAATGTGTCGTGGCTTCCACTACCTACT-CCGCAAATCTCCACAGCCGTATCTC
33163 ACCACTGC
130 ACCACTGC
*
33171 CACAAATCTCCACAGCCGTATCTCACCACTGTCGCAAATCTCCGTTGCCGTAAGCCATTCTTTGT
1 CGCAAATCTCCACAGCCGTATCTCACCACTGTCGCAAATCTCCGTTGCCGTAAGCCATTCTTTG-
* * * * *
33236 TTTTGTTATTTTAATAATGTGCCGTGGCTTCCAATACCTACTGCCACAAATCCCCACAGTCGTAT
65 TTTT-TT-TTTTAATAATGTGTCGTGGCTTCCACTACCTACT-CCGCAAATCTCCACAGCCGTAT
*
33301 CTCACTACTGC
127 CTCACCACTGC
33312 CGCAAATCTC
1 CGCAAATCTC
33322 AATTGCCGTA
Statistics
Matches: 252, Mismatches: 22, Indels: 17
0.87 0.08 0.06
Matches are distributed among these distances:
127 1 0.00
128 34 0.13
130 1 0.00
133 1 0.00
135 1 0.00
136 14 0.06
138 124 0.49
139 6 0.02
140 2 0.01
141 68 0.27
ACGTcount: A:0.24, C:0.32, G:0.13, T:0.31
Consensus pattern (137 bp):
CGCAAATCTCCACAGCCGTATCTCACCACTGTCGCAAATCTCCGTTGCCGTAAGCCATTCTTTGT
TTTTTTTTTAATAATGTGTCGTGGCTTCCACTACCTACTCCGCAAATCTCCACAGCCGTATCTCA
CCACTGC
Found at i:33397 original size:104 final size:107
Alignment explanation
Indices: 33166--33427 Score: 386
Period size: 104 Copynumber: 2.5 Consensus size: 107
33156 GTATCACACC
* ** *
33166 ACTGCCACAAATCTCCACAGCCGTATCTCACCACTGTCGCAAATCTCCGTTGCCGTAAGCCATTC
1 ACTGCCACAAATCTCCACAGCCGTATCTCACCACTGCCGCAAATCTCAATTGCCGTAAGCCAGTC
*
33231 TTTGTTTTTGTTATTTTAATAATGTGCCGTGGCTTCCAATACCT
66 TTAG--TTTGTTATTTTAATAATGTGCCGTGGCTTCCAATACCT
* * *
33275 ACTGCCACAAATCCCCACAGTCGTATCTCACTACTGCCGCAAATCTCAATTGCCGTAAGCCAGTC
1 ACTGCCACAAATCTCCACAGCCGTATCTCACCACTGCCGCAAATCTCAATTGCCGTAAGCCAGTC
* *
33340 TTAG-TT-TT-TTTTAATAATGTGTCGTGGCTTCCACTACCT
66 TTAGTTTGTTATTTTAATAATGTGCCGTGGCTTCCAATACCT
*
33379 ACTGCCGCAAATCTCCACAGCCGTATCTCACCACTGCCGCAAATCTCAA
1 ACTGCCACAAATCTCCACAGCCGTATCTCACCACTGCCGCAAATCTCAA
33428 CAGCCATATC
Statistics
Matches: 139, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
104 74 0.53
105 2 0.01
106 2 0.01
109 61 0.44
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.30
Consensus pattern (107 bp):
ACTGCCACAAATCTCCACAGCCGTATCTCACCACTGCCGCAAATCTCAATTGCCGTAAGCCAGTC
TTAGTTTGTTATTTTAATAATGTGCCGTGGCTTCCAATACCT
Found at i:33426 original size:18 final size:18
Alignment explanation
Indices: 33379--33426 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 18
33369 TCCACTACCT
33379 ACTGCCGCAAATCT--CC
1 ACTGCCGCAAATCTCACC
* *
33395 ACAGCCG--TATCTCACC
1 ACTGCCGCAAATCTCACC
33411 ACTGCCGCAAATCTCA
1 ACTGCCGCAAATCTCA
33427 ACAGCCATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
14 4 0.17
16 14 0.58
18 6 0.25
ACGTcount: A:0.27, C:0.42, G:0.12, T:0.19
Consensus pattern (18 bp):
ACTGCCGCAAATCTCACC
Found at i:33492 original size:16 final size:16
Alignment explanation
Indices: 33449--33500 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
33439 CACGACTACT
* *
33449 GTAAATCTCCATAGCT
1 GTAAATCTCCATTGCC
** *
33465 GTATCTCACCATTGCC
1 GTAAATCTCCATTGCC
*
33481 GTAAATCTCCATTGTC
1 GTAAATCTCCATTGCC
33497 GTAA
1 GTAA
33501 GTCATTCTTT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (16 bp):
GTAAATCTCCATTGCC
Found at i:33492 original size:32 final size:32
Alignment explanation
Indices: 33379--33491 Score: 136
Period size: 32 Copynumber: 3.5 Consensus size: 32
33369 TCCACTACCT
33379 ACTGCCGCAAATCTCCACAGCCGTATCTCACC
1 ACTGCCGCAAATCTCCACAGCCGTATCTCACC
* * *
33411 ACTGCCGCAAATCTCAACAGCCATATCTCACG
1 ACTGCCGCAAATCTCCACAGCCGTATCTCACC
* * * * *
33443 ACTACTGTAAATCTCCATAGCTGTATCTCACC
1 ACTGCCGCAAATCTCCACAGCCGTATCTCACC
* *
33475 ATTGCCGTAAATCTCCA
1 ACTGCCGCAAATCTCCA
33492 TTGTCGTAAG
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.28, C:0.36, G:0.12, T:0.24
Consensus pattern (32 bp):
ACTGCCGCAAATCTCCACAGCCGTATCTCACC
Done.