Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021248.1 Corchorus olitorius cultivar O-4 contig21281, 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: 71125
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:5457 original size:31 final size:31
Alignment explanation
Indices: 5360--5459 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 31
5350 TGTTGCTTAG
* *
5360 GGGGCAAAACATACAAAA-T-TA-AAGTTCAG
1 GGGGCAAAACGT-CAAAACTGTACAAGTTCAA
* *
5389 GGGGCAAAATGTCAAAACTGTACAAGTT-TA
1 GGGGCAAAACGTCAAAACTGTACAAGTTCAA
* *
5419 GAAGGCAAAACGTCCAAA-TCGTACAAGTTCAA
1 G-GGGCAAAACGTCAAAACT-GTACAAGTTCAA
5451 GGGGCAAAA
1 GGGGCAAAA
5460 AGTGCATTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
28 5 0.09
29 11 0.20
30 4 0.07
31 34 0.61
32 2 0.04
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (31 bp):
GGGGCAAAACGTCAAAACTGTACAAGTTCAA
Found at i:5586 original size:30 final size:31
Alignment explanation
Indices: 5550--5641 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 31
5540 ACAGAAACTC
*
5550 AAATTGAGAGTTCAGG-GGGCAAAATATCGA
1 AAATTGAGAGTTCAGGAGGGCAAAATATCCA
* *
5580 AAATTGAGAGTTTAGGAGGGCAAAATGTCCA
1 AAATTGAGAGTTCAGGAGGGCAAAATATCCA
* ** *
5611 AAATTTA-AGTTC-GTTGGGCAAAATGTCCA
1 AAATTGAGAGTTCAGGAGGGCAAAATATCCA
5640 AA
1 AA
5642 CTTTACAAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 17 0.31
30 19 0.35
31 18 0.33
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (31 bp):
AAATTGAGAGTTCAGGAGGGCAAAATATCCA
Found at i:8138 original size:12 final size:12
Alignment explanation
Indices: 8121--8145 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8111 CAAATTCTTT
8121 TACTAAAAATTA
1 TACTAAAAATTA
8133 TACTAAAAATTA
1 TACTAAAAATTA
8145 T
1 T
8146 CGAATCCAAA
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (12 bp):
TACTAAAAATTA
Found at i:16240 original size:3 final size:3
Alignment explanation
Indices: 16191--16228 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
16181 TGTGATTCTT
16191 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
16229 CTTCCTGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:19212 original size:178 final size:179
Alignment explanation
Indices: 18890--19285 Score: 474
Period size: 178 Copynumber: 2.2 Consensus size: 179
18880 TATCCGATCA
* * **
18890 AGATGATTGAAGTGTCTATTAAAATATTGTTCCATGATCTACAACTCTCATGAAGGACTTGAAAA
1 AGATGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTCTCATGAAGGACTCAAAAA
* * * *
18955 CTAAATTTAATGTTTCAAGTATCAAAAATACTTCCAAAAAATTAGTATTTTCGGTTAACAAGAAT
66 CTAAATTCAATGTTTAAAGTATAAAAAATACTTACAAAAAATTAGTATTTTCGGTTAACAAGAAT
** * *
19020 GGACGGTTTACTTAATA-TTACATAACTTTTGCTTCAGATGTCTGATTG
131 GGACAATCTACTTAATACTTACATAACTTTTGCTTCAGATATCTGATTG
* * * * *
19068 AGGTGATTCAAGTGTCTCTTAAAAGGTTGTTCCATGATCTACAACTTTTATG-AGGACTCAAAAA
1 AGATGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTCTCATGAAGGACTCAAAAA
* ** * **
19132 CTAAATTCAATGTTTAAAGTATAAAAAAATGCTTATGAAGAATTAGT-TGTTTCGGTTAACGGGA
66 CTAAATTCAATGTTTAAAGTAT-AAAAAATACTTACAAAAAATTAGTAT-TTTCGGTTAACAAGA
* * *
19196 ATGTACAATCTACTTAATACTCTTACATAATTTTTGCTTCATATATCTGATTG
129 ATGGACAATCTACTTAATA--CTTACATAACTTTTGCTTCAGATATCTGATTG
* * *
19249 AGATAATTCAAGTGTCTGTTAAAAGATTATTCCATGA
1 AGATGATTCAAGTGTCTATTAAAAGATTGTTCCATGA
19286 CTATGACCGA
Statistics
Matches: 182, Mismatches: 31, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
177 31 0.17
178 91 0.50
181 60 0.33
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (179 bp):
AGATGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTCTCATGAAGGACTCAAAAA
CTAAATTCAATGTTTAAAGTATAAAAAATACTTACAAAAAATTAGTATTTTCGGTTAACAAGAAT
GGACAATCTACTTAATACTTACATAACTTTTGCTTCAGATATCTGATTG
Found at i:20689 original size:27 final size:29
Alignment explanation
Indices: 20631--20690 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
20621 TGCTACTAAC
** * *
20631 AAAGAGTTCCATATATTTTTTTTTAGGTA
1 AAAGAGTTCCATATATTTGGTTTAAAGTA
*
20660 AAAGAGTTCCATAT-TTTGGTTTAAAGAA
1 AAAGAGTTCCATATATTTGGTTTAAAGTA
20688 AAA
1 AAA
20691 CAAGAAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 12 0.46
29 14 0.54
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (29 bp):
AAAGAGTTCCATATATTTGGTTTAAAGTA
Found at i:21038 original size:13 final size:13
Alignment explanation
Indices: 21020--21045 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21010 GACTCCCTCT
21020 ACTATATGATTTC
1 ACTATATGATTTC
21033 ACTATATGATTTC
1 ACTATATGATTTC
21046 TGCAGTTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
ACTATATGATTTC
Found at i:22738 original size:40 final size:40
Alignment explanation
Indices: 22694--22779 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 40
22684 GTCCGCCTCG
* * *
22694 TTATCTCAAATTTGCTTCGTGCAACAACTAAGCTTCGTGC
1 TTATCTCAAACTTGCTCCGTGCAACAACTAAGCTCCGTGC
22734 TTATCTCAAACTTGCTCCGTGCAACAACTAAGCTCCGTGC
1 TTATCTCAAACTTGCTCCGTGCAACAACTAAGCTCCGTGC
22774 TTATCT
1 TTATCT
22780 TATCTCAGGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (40 bp):
TTATCTCAAACTTGCTCCGTGCAACAACTAAGCTCCGTGC
Found at i:29234 original size:29 final size:28
Alignment explanation
Indices: 29190--29283 Score: 116
Period size: 29 Copynumber: 3.1 Consensus size: 28
29180 AATAATAATA
29190 ATTTTATAATTATTATAATTATAACTATTATT
1 ATTTTATAATTA-T-T-ATTATAA-TATTATT
* *
29222 ATTTTATAATTATTATTATTATAATTATA
1 ATTTTATAATTATTATTATAAT-ATTATT
29251 ATTTTATAATTATTATTATAATTATTATT
1 ATTTTATAATTATTATTATAA-TATTATT
29280 ATTT
1 ATTT
29284 CAGTAAATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
28 1 0.02
29 40 0.71
30 2 0.04
31 1 0.02
32 12 0.21
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTTTATAATTATTATTATAATATTATT
Found at i:29282 original size:6 final size:6
Alignment explanation
Indices: 29193--29282 Score: 85
Period size: 6 Copynumber: 15.3 Consensus size: 6
29183 AATAATAATT
* * * * *
29193 TTATAA TTATTA TAATTA TAACTA TTATTA TT-TTA TAATTA TTATTA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
* * * *
29240 TTATAA TTATAA TT-TTA TAATTA TTATTA TAATTA TTATTA TT
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TT
29283 TCAGTAAATA
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
5 7 0.10
6 62 0.90
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (6 bp):
TTATTA
Found at i:30410 original size:25 final size:25
Alignment explanation
Indices: 30356--30415 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
30346 ATTCTTTCTC
* *
30356 CAGGCCCTGCGCCACTTCTTTTATT
1 CAGGCCCTGCGCCACTTCTCTCATT
30381 CAGGCCCTGCGCCACCTTTCTCTCA-T
1 CAGGCCCTGCGCCA-C-TTCTCTCATT
30407 -AGGCCCTGC
1 CAGGCCCTGC
30416 ACCATCCTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 23 0.74
26 2 0.06
27 6 0.19
ACGTcount: A:0.12, C:0.42, G:0.18, T:0.28
Consensus pattern (25 bp):
CAGGCCCTGCGCCACTTCTCTCATT
Found at i:30501 original size:22 final size:22
Alignment explanation
Indices: 30473--30516 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
30463 GTCCGCCTCG
*
30473 TTATCTCAAATTTGCTCCGTGC
1 TTATCTCAAACTTGCTCCGTGC
30495 TTATCTCAAACTTGCTCCGTGC
1 TTATCTCAAACTTGCTCCGTGC
30517 AATAACTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.30, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCTCAAACTTGCTCCGTGC
Found at i:31221 original size:19 final size:19
Alignment explanation
Indices: 31194--31248 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
31184 AAGTTGTCCA
* *
31194 TATTTGGTGTAATGATCCC
1 TATTAGGTGTAATGATCAC
*
31213 TATTAGGTGTAATGGTATCAT
1 TATTAGGTGTAAT-G-ATCAC
31234 TATTAGGTGTAATGA
1 TATTAGGTGTAATGA
31249 AAAATTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 13 0.42
20 2 0.06
21 16 0.52
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.42
Consensus pattern (19 bp):
TATTAGGTGTAATGATCAC
Found at i:31755 original size:31 final size:31
Alignment explanation
Indices: 31720--31779 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
31710 TCTACCATTA
*
31720 AACATAAATATAGATAAATGGAAAAATTTGT
1 AACATAAAGATAGATAAATGGAAAAATTTGT
*
31751 AACATGAAGATAGATAAATGGAAAAATTT
1 AACATAAAGATAGATAAATGGAAAAATTT
31780 AACAAATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.55, C:0.03, G:0.15, T:0.27
Consensus pattern (31 bp):
AACATAAAGATAGATAAATGGAAAAATTTGT
Found at i:33605 original size:13 final size:13
Alignment explanation
Indices: 33587--33618 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
33577 GAAATCGTTA
*
33587 AAATCAATGTCAT
1 AAATCAAAGTCAT
33600 AAATCAAAGTCAT
1 AAATCAAAGTCAT
33613 AAATCA
1 AAATCA
33619 GAGTAAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.16, G:0.06, T:0.25
Consensus pattern (13 bp):
AAATCAAAGTCAT
Found at i:34708 original size:19 final size:19
Alignment explanation
Indices: 34686--34723 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
34676 GTTTTATTTC
34686 CTTTTCCCTCTTT-TTTTTT
1 CTTTTCCCT-TTTCTTTTTT
*
34705 CTTTTTCCTTTTCTTTTTT
1 CTTTTCCCTTTTCTTTTTT
34724 TTCTTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
CTTTTCCCTTTTCTTTTTT
Found at i:34721 original size:21 final size:21
Alignment explanation
Indices: 34671--34728 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
34661 AATCCTAAAA
*
34671 TTTCTGTTTTATTTCCTTTTCCC
1 TTTCT-TTTT-TTTCTTTTTCCC
* *
34694 TCT-TTTTTTTTCTTTTTCCT
1 TTTCTTTTTTTTCTTTTTCCC
34714 TTTCTTTTTTTTCTT
1 TTTCTTTTTTTTCTT
34729 ATATTGGGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 12 0.40
21 15 0.50
22 1 0.03
23 2 0.07
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTCTTTTTTTTCTTTTTCCC
Found at i:34836 original size:12 final size:12
Alignment explanation
Indices: 34821--34849 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
34811 CCGCGCCTTG
34821 GCTGGTCCAAGC
1 GCTGGTCCAAGC
34833 GCTGGTCCAAGC
1 GCTGGTCCAAGC
34845 GCTGG
1 GCTGG
34850 GCCACGCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.31, G:0.38, T:0.17
Consensus pattern (12 bp):
GCTGGTCCAAGC
Found at i:34909 original size:41 final size:41
Alignment explanation
Indices: 34807--34915 Score: 134
Period size: 41 Copynumber: 2.7 Consensus size: 41
34797 GCCAGGAGCT
* *
34807 TGGGCCGCGC-CTTGGCTGGTCCAAGCGCTGGTCCAAGCGC
1 TGGGCCACGCACTTGGCTGGCCCAAGCGCTGGTCCAAGCGC
34847 TGGGCCACGCACTTGGCTGGCCCAAGCGCTGGTCC-AGCCGC
1 TGGGCCACGCACTTGGCTGGCCCAAGCGCTGGTCCAAG-CGC
* * *
34888 TGGGCCGC-CAAGTTGGTTGGCCCAAGCG
1 TGGGCCACGC-ACTTGGCTGGCCCAAGCG
34916 GCCTGTTCTT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
40 12 0.20
41 49 0.80
ACGTcount: A:0.12, C:0.35, G:0.37, T:0.17
Consensus pattern (41 bp):
TGGGCCACGCACTTGGCTGGCCCAAGCGCTGGTCCAAGCGC
Found at i:34964 original size:21 final size:21
Alignment explanation
Indices: 34921--34965 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
34911 AAGCGGCCTG
** **
34921 TTCTTCTTCTTCTTTTTTTTT
1 TTCTTCTTCTTCTTCCTCCTT
34942 TTCTTCTTCTTCTTCCTCCTT
1 TTCTTCTTCTTCTTCCTCCTT
34963 TTC
1 TTC
34966 CGGTAGCCGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (21 bp):
TTCTTCTTCTTCTTCCTCCTT
Found at i:39769 original size:16 final size:15
Alignment explanation
Indices: 39731--39772 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
39721 ACAGAGATTG
*
39731 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
39746 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
39761 ACTAGAAAACAA
1 AC-AGAAAACAA
39773 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:47781 original size:118 final size:118
Alignment explanation
Indices: 47564--47783 Score: 341
Period size: 118 Copynumber: 1.9 Consensus size: 118
47554 TTATGTCCAA
* * * *
47564 AAGAAAGAGAAAGCGCTTTTAAGTGATCAAACAATCAATTACCAAAAAGGGCAGGGAGAAAAGGA
1 AAGAAAGAGAAAACGCTTTTAAGTGACCAAACAATCAATTAACAAAAAGGACAGGGAGAAAAGGA
* *
47629 AGTGAAGAAAACTGATTGAGGGGCTTCTTGGTAATCCCTACATAAATTCCTAG
66 AGTGAAGAAAACTAATTGAGGGGCTTCTTAGTAATCCCTACATAAATTCCTAG
* * *
47682 AAGACAGAGAAAACGCTTTTAAGTGGCCAAACAGTCAATTAACAAAAAGGACAGGGAGAAAAGGA
1 AAGAAAGAGAAAACGCTTTTAAGTGACCAAACAATCAATTAACAAAAAGGACAGGGAGAAAAGGA
**
47747 AGTGCTGAAAACTAATTGAGGGGCTTCTTAGTAATCC
66 AGTGAAGAAAACTAATTGAGGGGCTTCTTAGTAATCC
47784 GACAAACGAG
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
118 91 1.00
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.20
Consensus pattern (118 bp):
AAGAAAGAGAAAACGCTTTTAAGTGACCAAACAATCAATTAACAAAAAGGACAGGGAGAAAAGGA
AGTGAAGAAAACTAATTGAGGGGCTTCTTAGTAATCCCTACATAAATTCCTAG
Found at i:48188 original size:125 final size:125
Alignment explanation
Indices: 47966--48201 Score: 357
Period size: 125 Copynumber: 1.9 Consensus size: 125
47956 ATTAATGTCT
** *
47966 AGAAGAAAGAGAAAATGCTTTTAAGTGGTCAAACAGTCAATTACCAAAAAGGGCAGGAAGAAAAG
1 AGAAGAAAGAGAAAACACTTTTAAGTGGTCAAACAGTCAATTACCAAAAAGGACAGGAAGAAAAG
* * * * *
48031 GAAGTGTAGCAAATTGATTGAGGGGCTTCTTAGTAATCTGGCAAGCTACATAAATATCCC
66 GAAGTGCAGAAAACTGATTGAGGGGCTTCTTAGTAACCCGGCAAGCTACATAAATATCCC
* * *
48091 AGAAGAAAGAGAAACCACTTTTAAGTGGTCAAACAGTCCATTACCAAGAAA-GACAGGGAGAAAA
1 AGAAGAAAGAGAAAACACTTTTAAGTGGTCAAACAGTCAATTACCAA-AAAGGACAGGAAGAAAA
48155 GGAAGTGCAGAAAACTGATTGAGGGGCTTCTTAGTAACCCGGCAAGC
65 GGAAGTGCAGAAAACTGATTGAGGGGCTTCTTAGTAACCCGGCAAGC
48202 GAGAAAAGAC
Statistics
Matches: 99, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
125 96 0.97
126 3 0.03
ACGTcount: A:0.41, C:0.15, G:0.25, T:0.19
Consensus pattern (125 bp):
AGAAGAAAGAGAAAACACTTTTAAGTGGTCAAACAGTCAATTACCAAAAAGGACAGGAAGAAAAG
GAAGTGCAGAAAACTGATTGAGGGGCTTCTTAGTAACCCGGCAAGCTACATAAATATCCC
Found at i:48731 original size:21 final size:21
Alignment explanation
Indices: 48705--48762 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
48695 CACATCTTTG
* *
48705 TCCTCATCATTCTCATTTGCC
1 TCCTCATCATTATCATATGCC
* *
48726 TTCTCAACATTATCATATGCC
1 TCCTCATCATTATCATATGCC
* *
48747 TCCTCATTATCATCAT
1 TCCTCATCATTATCAT
48763 CTACAAGTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.33, G:0.03, T:0.41
Consensus pattern (21 bp):
TCCTCATCATTATCATATGCC
Found at i:49778 original size:21 final size:19
Alignment explanation
Indices: 49753--49808 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
49743 GTTGTTCTAA
49753 TAATCTCATATGTACAATACC
1 TAATCTCATATGTACAAT--C
* * *
49774 TAATCTAATATGTACAGTG
1 TAATCTCATATGTACAATC
49793 TAATCTCATATGTACA
1 TAATCTCATATGTACA
49809 GTTGCTAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (19 bp):
TAATCTCATATGTACAATC
Found at i:49798 original size:19 final size:19
Alignment explanation
Indices: 49774--49810 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
49764 GTACAATACC
49774 TAATCTAATATGTACAGTG
1 TAATCTAATATGTACAGTG
*
49793 TAATCTCATATGTACAGT
1 TAATCTAATATGTACAGT
49811 TGCTAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATATGTACAGTG
Found at i:65775 original size:2 final size:2
Alignment explanation
Indices: 65768--65812 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
65758 TCAGAGAATA
65768 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T- TGC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T-C TC TC TC
65810 TC T
1 TC T
65813 AGTTTTGGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:66992 original size:18 final size:19
Alignment explanation
Indices: 66960--67000 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
66950 AAAGAAGCAA
*
66960 AAAACGAAAGTAAAGATTG
1 AAAACGAAAGCAAAGATTG
66979 AAAA-GAAAGCAAAGATTG
1 AAAACGAAAGCAAAGATTG
66997 AAAA
1 AAAA
67001 TTTCTGGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.63, C:0.05, G:0.20, T:0.12
Consensus pattern (19 bp):
AAAACGAAAGCAAAGATTG
Found at i:67954 original size:6 final size:6
Alignment explanation
Indices: 67943--67990 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
67933 ATGGTTATAT
* *
67943 TATCTA TATCTA TATCTATA TATCTA TATTTA TATTTA TATACTA TAT
1 TATCTA TATCTA TATC--TA TATCTA TATCTA TATCTA TAT-CTA TAT
67991 AAGTCTAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
6 26 0.70
7 5 0.14
8 6 0.16
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.54
Consensus pattern (6 bp):
TATCTA
Found at i:67966 original size:14 final size:14
Alignment explanation
Indices: 67947--67991 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
67937 TTATATTATC
67947 TATATCTATATCTA
1 TATATCTATATCTA
67961 TATATCTATAT-T-
1 TATATCTATATCTA
*
67973 TATATTTATATACTA
1 TATATCTATAT-CTA
67988 TATA
1 TATA
67992 AGTCTAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 10 0.37
13 1 0.04
14 12 0.44
15 4 0.15
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
TATATCTATATCTA
Found at i:67968 original size:20 final size:20
Alignment explanation
Indices: 67938--67990 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
67928 TGAAGATGGT
67938 TATATTATCTATATCTATATC
1 TATA-TATCTATATCTATATC
* *
67959 TATATATCTATATTTATATT
1 TATATATCTATATCTATATC
67979 TATATA-CTATAT
1 TATATATCTATAT
67991 AAGTCTAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 6 0.20
20 20 0.67
21 4 0.13
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATATCTATATCTATATC
Found at i:68319 original size:30 final size:27
Alignment explanation
Indices: 68269--68351 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 27
68259 GTTAATTTAG
68269 ACTTATTATTATTATAATAATTATTAA
1 ACTTATTATTATTATAATAATTATTAA
*
68296 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTA-T--TATAATAATTATTAA
* * *
68326 ATTTATTATTATAATAATTATTATTA
1 ACTTATTATTATTATAATAATTATTA
68352 TTAGTGGTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
27 22 0.46
28 1 0.02
29 1 0.02
30 24 0.50
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (27 bp):
ACTTATTATTATTATAATAATTATTAA
Done.