Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015371.1 Corchorus capsularis cultivar CVL-1 contig15392, 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: 15034
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Found at i:550 original size:36 final size:36
Alignment explanation
Indices: 508--658 Score: 223
Period size: 36 Copynumber: 4.2 Consensus size: 36
498 CTCTTCTTAG
* *
508 ATTAAG-CTCTTTATTGACTCCACTTAATTACCCTGA
1 ATTAAGCCT-TTTATTGACGCTACTTAATTACCCTGA
**
544 ATTAAGCCTTTTATTGACATTACTTAATTACCCTGA
1 ATTAAGCCTTTTATTGACGCTACTTAATTACCCTGA
580 ATTAAGCCTTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGCCTTTTATTGACGCTACTTAATTACCCTGA
* *
616 ATTAAGTCCCTTTATTGACGCTACTTAATTACCCCGA
1 ATTAAG-CCTTTTATTGACGCTACTTAATTACCCTGA
653 ATTAAG
1 ATTAAG
659 TCCCTAACTT
Statistics
Matches: 106, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
36 70 0.66
37 36 0.34
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (36 bp):
ATTAAGCCTTTTATTGACGCTACTTAATTACCCTGA
Found at i:693 original size:37 final size:37
Alignment explanation
Indices: 651--930 Score: 343
Period size: 37 Copynumber: 7.8 Consensus size: 37
641 TAATTACCCC
* * *
651 GAATTAAGTCCCTAACT-TGACTTAATTTCCTTCCTTG
1 GAATCAAGTCCCTTACTCT-ACTTAATTCCCTTCCTTG
* *
688 AAATTAAGT-CCTTAACTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCCTT-ACTCTACTTAATTCCCTTCCTTG
725 GAATCAAGT--C---CTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTG
757 GAATCAAGT--C---CTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTG
789 GAATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTG
*
826 GAATCAAGTCCTTTACTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTG
* *
863 GAATCAAGTCCTTTGCTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTG
* * *
900 GAACCAAGTCCTTTATCTTTACTTAA-TCCCT
1 GAATCAAGTCCCTTA-CTCTACTTAATTCCCT
931 GGAGGTTAAG
Statistics
Matches: 225, Mismatches: 10, Indels: 16
0.90 0.04 0.06
Matches are distributed among these distances:
32 63 0.28
34 1 0.00
36 4 0.02
37 147 0.65
38 10 0.04
ACGTcount: A:0.23, C:0.29, G:0.09, T:0.39
Consensus pattern (37 bp):
GAATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTG
Found at i:802 original size:19 final size:19
Alignment explanation
Indices: 778--873 Score: 65
Period size: 19 Copynumber: 5.2 Consensus size: 19
768 TCTACTTAAT
778 TCCCTTCCTTGGAATCAAG
1 TCCCTTCCTTGGAATCAAG
* * * *
797 TCCCTTACTCT--ACTTAAT
1 TCCCTTCCT-TGGAATCAAG
815 TCCCTTCCTTGGAATCAAG
1 TCCCTTCCTTGGAATCAAG
* * * * *
834 TCCTTTACTCT--ACTTAAT
1 TCCCTTCCT-TGGAATCAAG
852 TCCCTTCCTTGGAATCAAG
1 TCCCTTCCTTGGAATCAAG
871 TCC
1 TCC
874 TTTGCTCTAC
Statistics
Matches: 53, Mismatches: 18, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
17 2 0.04
18 23 0.43
19 26 0.49
20 2 0.04
ACGTcount: A:0.21, C:0.32, G:0.09, T:0.38
Consensus pattern (19 bp):
TCCCTTCCTTGGAATCAAG
Found at i:820 original size:18 final size:18
Alignment explanation
Indices: 797--857 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
787 TGGAATCAAG
797 TCCCTTACTCTACTTAAT
1 TCCCTTACTCTACTTAAT
* * * *
815 TCCCTTCCT-TGGAATCAAG
1 TCCCTTACTCT--ACTTAAT
*
834 TCCTTTACTCTACTTAAT
1 TCCCTTACTCTACTTAAT
852 TCCCTT
1 TCCCTT
858 CCTTGGAATC
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
17 1 0.03
18 17 0.57
19 11 0.37
20 1 0.03
ACGTcount: A:0.20, C:0.33, G:0.05, T:0.43
Consensus pattern (18 bp):
TCCCTTACTCTACTTAAT
Found at i:1051 original size:76 final size:78
Alignment explanation
Indices: 971--1260 Score: 328
Period size: 76 Copynumber: 3.7 Consensus size: 78
961 ATCATCCTGG
*
971 ATTAAGTATGTGCTTGCCTTTACCTAATT-CTTATGAAATTAAGTCTATGCTGTCTTTACCTAA-
1 ATTAAGTCTGTGCTTGCCTTTACCTAATTACTTATGAAATTAAGTCTATGCTGTCTTTACCTAAT
*
1034 TTACTTCACTGAA
66 TTCCTTCACTGAA
* *
1047 ATTAAGTCTGTGCTTGCCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTATGCTCGTCTTTACC
1 ATTAAGTCTGTGCTTGCCTTTACCTAA-TTACTT--ATGAAATTAAGTCTATGCT-GTCTTTACC
1112 TAATTTCCTTCACTGAA
62 TAATTTCCTTCACTGAA
* * ***
1129 ATTAAGTCTGTGCTT-ACTTTACTTAATTAC-CCCG-AATTAAGTCTATGCTTGTCTTTACCTAA
1 ATTAAGTCTGTGCTTGCCTTTACCTAATTACTTATGAAATTAAGTCTATGC-TGTCTTTACCTAA
1191 TTTCCTTC-CTTGAA
65 TTTCCTTCAC-TGAA
* * * **
1205 ATTAAGTCTGTGCTT-ACTTTACTTAACTAC-CCTG-AATTAAGTCTATGCTTGTCTTT
1 ATTAAGTCTGTGCTTGCCTTTACCTAATTACTTATGAAATTAAGTCTATGC-TGTCTTT
1261 GACCATGTTT
Statistics
Matches: 195, Mismatches: 11, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
75 1 0.01
76 118 0.61
77 4 0.02
78 3 0.02
80 21 0.11
81 21 0.11
82 27 0.14
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.43
Consensus pattern (78 bp):
ATTAAGTCTGTGCTTGCCTTTACCTAATTACTTATGAAATTAAGTCTATGCTGTCTTTACCTAAT
TTCCTTCACTGAA
Found at i:1095 original size:41 final size:40
Alignment explanation
Indices: 971--1260 Score: 286
Period size: 41 Copynumber: 7.5 Consensus size: 40
961 ATCATCCTGG
* * *
971 ATTAAGTATGTGCTTGCCTTTACCTAA-TT-CTT-ATGAA
1 ATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCCTGAA
* *
1008 ATTAAGTCTATGC-TGTCTTTACCTAA-TTACTTCACTGAA
1 ATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTC-CTGAA
*
1047 ATTAAGTCTGTGCTTGCCTTTACCTAATTTCCTTCCTTGAA
1 ATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCC-TGAA
* *
1088 ATTAAGTCTATGCTCGTCTTTACCTAATTTCCTTCACTGAA
1 ATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTC-CTGAA
* * *
1129 ATTAAGTCTGTGCTT-ACTTTACTTAATTACC--CC-G-A
1 ATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCCTGAA
*
1164 ATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAA
1 ATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCC-TGAA
* * * *
1205 ATTAAGTCTGTGCTT-ACTTTACTTAA-CTAC--CCTG-A
1 ATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCCTGAA
*
1240 ATTAAGTCTATGCTTGTCTTT
1 ATTAAGTCTGTGCTTGTCTTT
1261 GACCATGTTT
Statistics
Matches: 213, Mismatches: 26, Indels: 29
0.79 0.10 0.11
Matches are distributed among these distances:
35 30 0.14
36 34 0.16
37 17 0.08
38 3 0.01
39 18 0.08
40 36 0.17
41 74 0.35
42 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.43
Consensus pattern (40 bp):
ATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCCTGAA
Found at i:1178 original size:35 final size:35
Alignment explanation
Indices: 1128--1254 Score: 137
Period size: 35 Copynumber: 3.5 Consensus size: 35
1118 CCTTCACTGA
*
1128 AATTAAGTCTGTGCTTACTTTACTTAATTACCCCG
1 AATTAAGTCTATGCTTACTTTACTTAATTACCCCG
* * *
1163 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTG
1 AATTAAGTCTATGCTT-ACTTTACTTAATTACC--CC--G
* * *
1203 AAATTAAGTCTGTGCTTACTTTACTTAACTACCCTG
1 -AATTAAGTCTATGCTTACTTTACTTAATTACCCCG
1239 AATTAAGTCTATGCTT
1 AATTAAGTCTATGCTT
1255 GTCTTTGACC
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
35 30 0.40
36 14 0.19
38 3 0.04
40 13 0.17
41 15 0.20
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (35 bp):
AATTAAGTCTATGCTTACTTTACTTAATTACCCCG
Found at i:1178 original size:117 final size:116
Alignment explanation
Indices: 988--1218 Score: 326
Period size: 117 Copynumber: 2.0 Consensus size: 116
978 ATGTGCTTGC
*
988 CTTTACCTAATTCTTATGAAATTAAGTCTATGCTGTCTTTACCTAATTACTTCACTGAAATTAAG
1 CTTTACCTAATTCTTATGAAATTAAGTCTATGCTGTCTTTACCTAATTAC-TCACCGAAATTAAG
*
1053 TCTGTGCTTGCCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTATGCTCGT
65 TCTATGCTTGCCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTATGCTCGT
* *
1105 CTTTACCTAATTTCCTTCACTGAAATTAAGTCTGTGCT-TACTTTACTTAATTAC-C-CCG-AAT
1 CTTTACCTAA-TT-CTT-A-TGAAATTAAGTCTATGCTGT-CTTTACCTAATTACTCACCGAAAT
* *
1166 TAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCT
61 TAAGTCTATGCTTGCCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTATGCT
1219 TACTTTACTT
Statistics
Matches: 103, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
117 63 0.61
118 4 0.04
119 4 0.04
120 2 0.02
121 30 0.29
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (116 bp):
CTTTACCTAATTCTTATGAAATTAAGTCTATGCTGTCTTTACCTAATTACTCACCGAAATTAAGT
CTATGCTTGCCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTATGCTCGT
Found at i:1436 original size:37 final size:37
Alignment explanation
Indices: 1350--1580 Score: 231
Period size: 37 Copynumber: 6.3 Consensus size: 37
1340 ACTATGTTTA
* *
1350 CTTTT-CTTAATTGCCCTGAATTAAG-ATTTTGACTG
1 CTTTTACTTAATTGCCCTGAATTAAGTTTTTTAACTG
* *
1385 TTTTTACTTAATTGCCCTGAATTAAGTTTTTTACCTG
1 CTTTTACTTAATTGCCCTGAATTAAGTTTTTTAACTG
* * *
1422 CTTTTACTTAATTGCGCTGAATTAAG-TTCTTAACCTA
1 CTTTTACTTAATTGCCCTGAATTAAGTTTTTTAA-CTG
* *
1459 TTTTTACTTAATTAG-CCTGAATTAAG-TTCTTAACTG
1 CTTTTACTTAATT-GCCCTGAATTAAGTTTTTTAACTG
* * * *
1495 CTTATACTTAATTGTCCTGAACTAAG-TTCTTAACTG
1 CTTTTACTTAATTGCCCTGAATTAAGTTTTTTAACTG
** * *
1531 CTTTTTACTTAATTATCCTGAATTAAGTTCTTTAACTA
1 C-TTTTACTTAATTGCCCTGAATTAAGTTTTTTAACTG
*
1569 CTCTTACTTAAT
1 CTTTTACTTAAT
1581 CACCTTGGAT
Statistics
Matches: 167, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
35 5 0.03
36 59 0.35
37 94 0.56
38 9 0.05
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.47
Consensus pattern (37 bp):
CTTTTACTTAATTGCCCTGAATTAAGTTTTTTAACTG
Found at i:1497 original size:73 final size:71
Alignment explanation
Indices: 1350--1580 Score: 270
Period size: 73 Copynumber: 3.2 Consensus size: 71
1340 ACTATGTTTA
* *
1350 CTTTT-CTTAATTGCCCTGAATTAAGATT-TTGACTGTTTTTACTTAATT-GCCCTGAATTAAGT
1 CTTTTACTTAATTG-CCTGAATTAAG-TTCTTAACTATTTTTACTTAATTAG-CCTGAATTAAG-
* *
1412 TTTTTACCTG
62 TTCTTAACTG
1422 CTTTTACTTAATTGCGCTGAATTAAGTTCTTAACCTATTTTTACTTAATTAGCCTGAATTAAGTT
1 CTTTTACTTAATTGC-CTGAATTAAGTTCTTAA-CTATTTTTACTTAATTAGCCTGAATTAAGTT
1487 CTTAACTG
64 CTTAACTG
* * * *
1495 CTTATACTTAATTGTCCTGAACTAAGTTCTTAACTGCTTTTTACTTAATTATCCTGAATTAAGTT
1 CTTTTACTTAATTG-CCTGAATTAAGTTCTTAACT-ATTTTTACTTAATTAGCCTGAATTAAGTT
*
1560 CTTTAACTA
64 C-TTAACTG
*
1569 CTCTTACTTAAT
1 CTTTTACTTAAT
1581 CACCTTGGAT
Statistics
Matches: 140, Mismatches: 11, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
72 10 0.07
73 86 0.61
74 43 0.31
75 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.47
Consensus pattern (71 bp):
CTTTTACTTAATTGCCTGAATTAAGTTCTTAACTATTTTTACTTAATTAGCCTGAATTAAGTTCT
TAACTG
Found at i:1552 original size:110 final size:110
Alignment explanation
Indices: 1348--1580 Score: 289
Period size: 110 Copynumber: 2.1 Consensus size: 110
1338 TGACTATGTT
* * * *
1348 TACTTTT-CTTAATTGCCCTGAATTAAGATTTTGACTGTTTTTACTTAATTGCCCTGAATTAAGT
1 TACTTTTACTTAATTGCCCTGAATTAAGATTTTAACTGCTTATACTTAATTGCCCTGAACTAAGT
* *
1412 TTTTTACCTGCTTTTACTTAATTGCGCTGAATTAAGTTC-TTAACC
66 TTCTTAACTGCTTTTACTTAATTGCGCTGAATTAAGTTCTTTAA-C
* *
1457 TATTTTTACTTAATTAG-CCTGAATTAAG-TTCTTAACTGCTTATACTTAATTGTCCTGAACTAA
1 TACTTTTACTTAATT-GCCCTGAATTAAGATT-TTAACTGCTTATACTTAATTGCCCTGAACTAA
*
1520 G-TTCTTAACTGCTTTTTACTTAATTATC-CTGAATTAAGTTCTTTAAC
64 GTTTCTTAACTGC-TTTTACTTAATT-GCGCTGAATTAAGTTCTTTAAC
*
1567 TACTCTTACTTAAT
1 TACTTTTACTTAAT
1581 CACCTTGGAT
Statistics
Matches: 107, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
109 17 0.16
110 84 0.79
111 6 0.06
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.47
Consensus pattern (110 bp):
TACTTTTACTTAATTGCCCTGAATTAAGATTTTAACTGCTTATACTTAATTGCCCTGAACTAAGT
TTCTTAACTGCTTTTACTTAATTGCGCTGAATTAAGTTCTTTAAC
Found at i:1602 original size:110 final size:110
Alignment explanation
Indices: 1389--1603 Score: 251
Period size: 110 Copynumber: 2.0 Consensus size: 110
1379 TGACTGTTTT
* * *
1389 TACTTAATTGCCCTGAATTAAGTTTTTTACCTGCTTTTACTTAATTGCGCTGAATTAAGTTCTTA
1 TACTTAATTGCCCTGAACTAAGTTTCTTAACTGCTTTTACTTAATTGCGCTGAATTAAGTTCTTA
* * * **
1454 ACCTATTTTTACTTAATTAGCCTGAATTAAGTTCTTAACTGCTTA
66 ACCTACTCTTACTTAATCAGCCTGAATTAAACTCTTAACTGCTTA
* *
1499 TACTTAATTGTCCTGAACTAAG-TTCTTAACTGCTTTTTACTTAATTATC-CTGAATTAAGTTCT
1 TACTTAATTGCCCTGAACTAAGTTTCTTAACTGC-TTTTACTTAATT-GCGCTGAATTAAGTTC-
*
1562 TTAA-CTACTCTTACTTAATCA-CCTTGGATTAGAACT-TTAACT
63 TTAACCTACTCTTACTTAATCAGCC-TGAATTA-AACTCTTAACT
1604 AATCTGACTT
Statistics
Matches: 89, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
109 11 0.12
110 71 0.80
111 7 0.08
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (110 bp):
TACTTAATTGCCCTGAACTAAGTTTCTTAACTGCTTTTACTTAATTGCGCTGAATTAAGTTCTTA
ACCTACTCTTACTTAATCAGCCTGAATTAAACTCTTAACTGCTTA
Found at i:1604 original size:36 final size:39
Alignment explanation
Indices: 1560--1722 Score: 127
Period size: 41 Copynumber: 4.1 Consensus size: 39
1550 GAATTAAGTT
* *
1560 CTTTAACT-A-CT-CTTACTTAATCACCTTGGATTAGAA
1 CTTTAACTAATCTACTTACTTAATCACCCTGGATTAAAA
*
1596 CTTTAACTAATCTGACTTTCTTAATCACCCTGGATTAAAA
1 CTTTAACTAATCT-ACTTACTTAATCACCCTGGATTAAAA
* * * * *
1636 CCTTAACTGTATTTGACTTTCTTAATCGCCCTGGATTAAAA
1 CTTTAACT-AATCT-ACTTACTTAATCACCCTGGATTAAAA
* * * * *
1677 CCTTAACTATGTTTGACCTT-CTTAATCGCCCTGGATTAAGA
1 CTTTAACTA-ATCT-A-CTTACTTAATCACCCTGGATTAAAA
1718 CTTTA
1 CTTTA
1723 CTTTTCTTAA
Statistics
Matches: 109, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
36 8 0.07
37 1 0.01
38 2 0.02
40 29 0.27
41 66 0.61
42 3 0.03
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.39
Consensus pattern (39 bp):
CTTTAACTAATCTACTTACTTAATCACCCTGGATTAAAA
Found at i:1668 original size:41 final size:40
Alignment explanation
Indices: 1575--1715 Score: 183
Period size: 41 Copynumber: 3.5 Consensus size: 40
1565 ACTACTCTTA
* * * * *
1575 CTTAATCACCTTGGATTAGAACTTTAACTAATCTGACTTT
1 CTTAATCACCCTGGATTAAAACCTTAACTTATTTGACTTT
1615 CTTAATCACCCTGGATTAAAACCTTAACTGTATTTGACTTT
1 CTTAATCACCCTGGATTAAAACCTTAACT-TATTTGACTTT
* * *
1656 CTTAATCGCCCTGGATTAAAACCTTAACTATGTTTGACCTT
1 CTTAATCACCCTGGATTAAAACCTTAACT-TATTTGACTTT
*
1697 CTTAATCGCCCTGGATTAA
1 CTTAATCACCCTGGATTAA
1716 GACTTTACTT
Statistics
Matches: 91, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 26 0.29
41 65 0.71
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (40 bp):
CTTAATCACCCTGGATTAAAACCTTAACTTATTTGACTTT
Found at i:4825 original size:13 final size:13
Alignment explanation
Indices: 4807--4841 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
4797 AATCAAAATC
4807 ATAAACCAACATA
1 ATAAACCAACATA
*
4820 ATAAACCAAGATA
1 ATAAACCAACATA
4833 ATAAACCAA
1 ATAAACCAA
4842 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.63, C:0.20, G:0.03, T:0.14
Consensus pattern (13 bp):
ATAAACCAACATA
Found at i:5465 original size:12 final size:12
Alignment explanation
Indices: 5450--5491 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
5440 TTCTCTTAAA
*
5450 TTCCCTTCCTTT
1 TTCCTTTCCTTT
**
5462 TTCCTTTTATTT
1 TTCCTTTCCTTT
5474 TTCCTTTCC-TT
1 TTCCTTTCCTTT
5485 TTCCTTT
1 TTCCTTT
5492 TCTTCATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (12 bp):
TTCCTTTCCTTT
Found at i:6626 original size:15 final size:15
Alignment explanation
Indices: 6608--6641 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
6598 AAGTGAATAT
*
6608 GACACAAGTGGAAAC
1 GACACAAGTGCAAAC
6623 GACACAAGTGCAAAC
1 GACACAAGTGCAAAC
6638 GACA
1 GACA
6642 AGTTGGGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.24, G:0.24, T:0.06
Consensus pattern (15 bp):
GACACAAGTGCAAAC
Found at i:8429 original size:20 final size:21
Alignment explanation
Indices: 8391--8432 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
8381 TGTGCCTTGT
* *
8391 TTTATATGTGATATGTTTATG
1 TTTACATGTGATATATTTATG
8412 TTTACATGT-ATATATTTATG
1 TTTACATGTGATATATTTATG
8432 T
1 T
8433 ATGTATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.57
Consensus pattern (21 bp):
TTTACATGTGATATATTTATG
Found at i:8497 original size:85 final size:85
Alignment explanation
Indices: 8271--8705 Score: 710
Period size: 85 Copynumber: 5.1 Consensus size: 85
8261 ATAATTTGTA
* *
8271 ATATATAACATAAAATATTAAC-TCGTGCGTTGTTTTATATGTGATATGTATATGTTTACATGTA
1 ATATATAACATGAAATATTGACGT-GTGCGTTGTTTTATATGTGATATGTATATGTTTACATGTA
* *
8335 GGTATTTATATATGTATAAATAT
65 TGTATTTATGTATGTAT-AA-AT
* * *
8358 ATATATAACATGAAATATTGATGTGTGCCTTGTTTTATATGTGATATGTTTATGTTTACATGTAT
1 ATATATAACATGAAATATTGACGTGTGCGTTGTTTTATATGTGATATGTATATGTTTACATGTAT
*
8423 ATATTTATGTATGTATAAAT
66 GTATTTATGTATGTATAAAT
8443 ATATATAACATGAAATATTGACGTGTGCGTTGTTTTATATGTGATATGTATATGTTTACATGTAT
1 ATATATAACATGAAATATTGACGTGTGCGTTGTTTTATATGTGATATGTATATGTTTACATGTAT
8508 GTATTTATGTATGTATAAAT
66 GTATTTATGTATGTATAAAT
* *
8528 ATATATAGCATGAAATATTGACTTGTGCGTTGTTTTATATGTGATATGTATATGTTTACATGTAT
1 ATATATAACATGAAATATTGACGTGTGCGTTGTTTTATATGTGATATGTATATGTTTACATGTAT
8593 GTATTTATGTATGTATAAAT
66 GTATTTATGTATGTATAAAT
* * * *
8613 ATATACAACATGAAATATTGACTTATGTGTTGTTTTATATGTGATATGTATATGTTTACATGTAT
1 ATATATAACATGAAATATTGACGTGTGCGTTGTTTTATATGTGATATGTATATGTTTACATGTAT
8678 GTATTTATGTATGTATAAAT
66 GTATTTATGTATGTATAAAT
8698 ATATATAA
1 ATATATAA
8706 TATCTACATA
Statistics
Matches: 328, Mismatches: 19, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
85 254 0.77
86 2 0.01
87 71 0.22
88 1 0.00
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.46
Consensus pattern (85 bp):
ATATATAACATGAAATATTGACGTGTGCGTTGTTTTATATGTGATATGTATATGTTTACATGTAT
GTATTTATGTATGTATAAAT
Found at i:8750 original size:12 final size:12
Alignment explanation
Indices: 8696--8751 Score: 60
Period size: 12 Copynumber: 4.6 Consensus size: 12
8686 GTATGTATAA
8696 ATATATATA-AT
1 ATATATATACAT
* *
8707 ATCTACATACAT
1 ATATATATACAT
*
8719 ATATACATACATGT
1 ATATATATACA--T
8733 ATATATATACAT
1 ATATATATACAT
8745 ATATATA
1 ATATATA
8752 ATAAACCTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
11 7 0.18
12 20 0.53
14 11 0.29
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (12 bp):
ATATATATACAT
Found at i:9343 original size:85 final size:85
Alignment explanation
Indices: 9203--9377 Score: 271
Period size: 85 Copynumber: 2.1 Consensus size: 85
9193 ATAATTTGTA
* * * *
9203 ATATATAACATGTAATATTAACTCGTGCATTGTTTGATATGAGATATGTATATGTTTACATGTAT
1 ATATATAACATGAAATATTAACTCATGCATCGTTTGATATGAGATATATATATGTTTACATGTAT
*
9268 GTATTTATGTATGTATAAAT
66 GTATTTATGAATGTATAAAT
* *
9288 ATATATAACATGAAATATTGACTCATGCATCGTTTTATAT-ATGATATATATATGTTTACATGTA
1 ATATATAACATGAAATATTAACTCATGCATCGTTTGATATGA-GATATATATATGTTTACATGTA
9352 TGTATTTATGAATGTATAAAT
65 TGTATTTATGAATGTATAAAT
9373 ATATA
1 ATATA
9378 ATATCTACAT
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
84 1 0.01
85 81 0.99
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (85 bp):
ATATATAACATGAAATATTAACTCATGCATCGTTTGATATGAGATATATATATGTTTACATGTAT
GTATTTATGAATGTATAAAT
Found at i:9395 original size:2 final size:2
Alignment explanation
Indices: 9366--9501 Score: 98
Period size: 2 Copynumber: 69.0 Consensus size: 2
9356 TTTATGAATG
* * * * * * *
9366 TA TA AA TA TA TA -A TA TC TA CA TA CA TA TA TA CA TA CA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
9407 TA TA TA TA TA T- TCA TA TA TA CA TA TA TA TA TA TT TG TG TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
9449 TA TA TA TA TA TA TC TA TA TG TA TA -A TA TA TA TA TG TA TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
9490 TA TA TG TA TA TA
1 TA TA TA TA TA TA
9502 CAATAGCCAT
Statistics
Matches: 101, Mismatches: 29, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
1 3 0.03
2 97 0.96
3 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:9488 original size:12 final size:12
Alignment explanation
Indices: 9323--9501 Score: 83
Period size: 12 Copynumber: 14.2 Consensus size: 12
9313 TGCATCGTTT
9323 TATATATG-ATA
1 TATATATGTATA
*
9334 TATATATGTTTA
1 TATATATGTATA
* * *
9346 CATGTATGTATT
1 TATATATGTATA
9358 TATGA-ATGTATAAA
1 TAT-ATATGTAT--A
* *
9372 TATATAATATCTA
1 TATAT-ATGTATA
* * *
9385 CATACATATATA
1 TATATATGTATA
* *
9397 CATACATGTATA
1 TATATATGTATA
*
9409 TATATATATTCATA
1 TATATAT-GT-ATA
*
9423 TATACATATATATA
1 TAT--ATATGTATA
* *
9437 TATTTGTGTATA
1 TATATATGTATA
*
9449 TATATATATATA
1 TATATATGTATA
*
9461 TCTATATGTATAATA
1 TATATATG--T-ATA
9476 TATATATGTATA
1 TATATATGTATA
*
9488 TCTATATGTATA
1 TATATATGTATA
9500 TA
1 TA
9502 CAATAGCCAT
Statistics
Matches: 126, Mismatches: 29, Indels: 25
0.70 0.16 0.14
Matches are distributed among these distances:
11 8 0.06
12 76 0.60
13 7 0.06
14 16 0.13
15 15 0.12
16 4 0.03
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (12 bp):
TATATATGTATA
Found at i:9705 original size:21 final size:21
Alignment explanation
Indices: 9679--9722 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
9669 ACAATCTGGA
9679 TTGCTAAACACCACCCCATTT
1 TTGCTAAACACCACCCCATTT
** *
9700 TTGCTATTCACCGCCCCATTT
1 TTGCTAAACACCACCCCATTT
9721 TT
1 TT
9723 TACGCTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.36, G:0.07, T:0.36
Consensus pattern (21 bp):
TTGCTAAACACCACCCCATTT
Found at i:10115 original size:33 final size:33
Alignment explanation
Indices: 10059--10123 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
10049 AGGGCTGCCT
10059 GCCGTGGCGAAGCCGCCCCAGTGGGGAGGCTCC
1 GCCGTGGCGAAGCCGCCCCAGTGGGGAGGCTCC
* *
10092 GCCGTGGCTGAA-CCGTCCTAGTGGGGAGGCTC
1 GCCGTGGC-GAAGCCGCCCCAGTGGGGAGGCTC
10124 TGTGTAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.12, C:0.32, G:0.42, T:0.14
Consensus pattern (33 bp):
GCCGTGGCGAAGCCGCCCCAGTGGGGAGGCTCC
Done.