Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019994.1 Corchorus olitorius cultivar O-4 contig20027, 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: 51762
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:860 original size:12 final size:12
Alignment explanation
Indices: 843--870 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
833 TACTTGTCAG
843 ATTTGACATAAT
1 ATTTGACATAAT
855 ATTTGACATAAT
1 ATTTGACATAAT
867 ATTT
1 ATTT
871 TGATCGCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (12 bp):
ATTTGACATAAT
Found at i:1851 original size:27 final size:27
Alignment explanation
Indices: 1814--1869 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1804 CTAAAAACTA
1814 AAATATTTAATAATCTAGCCCCTCATT
1 AAATATTTAATAATCTAGCCCCTCATT
1841 AAATATTTAATAATCTAGCCCCTCATT
1 AAATATTTAATAATCTAGCCCCTCATT
1868 AA
1 AA
1870 CCCAAACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (27 bp):
AAATATTTAATAATCTAGCCCCTCATT
Found at i:4055 original size:48 final size:46
Alignment explanation
Indices: 3974--4080 Score: 142
Period size: 48 Copynumber: 2.3 Consensus size: 46
3964 ACTCAAAGCA
* * **
3974 ATCTTTTACTTTTCTGCACTTTTTCTCAGTTTTTACTACAAAATTG
1 ATCTTTAACTTTTCTGCACTTTTTCTCAATTTTTAAGACAAAATTG
*
4020 ATCTTTAATTTTTCTCGCACCTTTTTCTCAATTTTTAAGACAAAATTG
1 ATCTTTAACTTTTCT-GCA-CTTTTTCTCAATTTTTAAGACAAAATTG
*
4068 ATCTTTTACTTTT
1 ATCTTTAACTTTT
4081 TATTGTTCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
46 13 0.25
47 3 0.06
48 36 0.69
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (46 bp):
ATCTTTAACTTTTCTGCACTTTTTCTCAATTTTTAAGACAAAATTG
Found at i:4099 original size:48 final size:47
Alignment explanation
Indices: 4011--4114 Score: 111
Period size: 48 Copynumber: 2.2 Consensus size: 47
4001 AGTTTTTACT
* * *
4011 ACAAAATTGATCTTTAATTTTTCTCGCACCTTTTTCTCAATTTTTAAG
1 ACAAAATTGATCTTTAATTTTTATCGCACCTTTTTATCAATTTCT-AG
* * **
4059 ACAAAATTGATCTTTTACTTTTTATTGTTCC-TTTTATCAATTTCTAG
1 ACAAAATTGATC-TTTAATTTTTATCGCACCTTTTTATCAATTTCTAG
*
4106 TCAAAATTG
1 ACAAAATTG
4115 GTTGGCATGC
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
47 10 0.21
48 24 0.51
49 13 0.28
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (47 bp):
ACAAAATTGATCTTTAATTTTTATCGCACCTTTTTATCAATTTCTAG
Found at i:6867 original size:13 final size:13
Alignment explanation
Indices: 6839--6868 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
6829 TATTCCAAAA
6839 TTTCTATTTAATT
1 TTTCTATTTAATT
6852 TTTCTTATTTAATT
1 TTTC-TATTTAATT
6866 TTT
1 TTT
6869 TTTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTCTATTTAATT
Found at i:7107 original size:3 final size:3
Alignment explanation
Indices: 7101--7125 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
7091 CAACCTTTTT
7101 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
7126 CCCTCTCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:7699 original size:19 final size:19
Alignment explanation
Indices: 7672--7708 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
7662 CGGTGGAGAA
7672 AACAAAAATGAAGAAAATT
1 AACAAAAATGAAGAAAATT
*
7691 AACACAAATGAAGAAAAT
1 AACAAAAATGAAGAAAAT
7709 GAAGTAACGG
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:0.68, C:0.08, G:0.11, T:0.14
Consensus pattern (19 bp):
AACAAAAATGAAGAAAATT
Found at i:11588 original size:21 final size:21
Alignment explanation
Indices: 11547--11589 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
11537 CTTTATAGCA
**
11547 TTATTATCTTTTTTTGTACCT
1 TTATTATCTTTTTGAGTACCT
11568 TTATTA-CTTTTTGAGTAACCT
1 TTATTATCTTTTTGAGT-ACCT
11589 T
1 T
11590 ACATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.19, C:0.14, G:0.07, T:0.60
Consensus pattern (21 bp):
TTATTATCTTTTTGAGTACCT
Found at i:11974 original size:22 final size:22
Alignment explanation
Indices: 11947--11992 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
11937 AACTTAGTAA
11947 TAACATT-ATATAAGAAAATTGG
1 TAACATTCAT-TAAGAAAATTGG
* *
11969 TAACATTCATTAATAATATTGG
1 TAACATTCATTAAGAAAATTGG
11991 TA
1 TA
11993 GATATGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (22 bp):
TAACATTCATTAAGAAAATTGG
Found at i:12900 original size:22 final size:22
Alignment explanation
Indices: 12875--12920 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
12865 TTTTTTTTAA
12875 TAACCTTGAATAAGAAGAATGG
1 TAACCTTGAATAAGAAGAATGG
*
12897 TAACCTTGAATAAGAAGATTGG
1 TAACCTTGAATAAGAAGAATGG
12919 TA
1 TA
12921 TAACCTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (22 bp):
TAACCTTGAATAAGAAGAATGG
Found at i:14326 original size:2 final size:2
Alignment explanation
Indices: 14319--14355 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
14309 AACCAAAATA
14319 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14356 CAAAGAGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16676 original size:32 final size:31
Alignment explanation
Indices: 16625--16712 Score: 92
Period size: 32 Copynumber: 2.9 Consensus size: 31
16615 CTTAACTTTG
**
16625 GGAAGTTTA-GGGGGTAAAATATCCTTATTTT
1 GGAAGTTTATGGGGACAAAATATCCTTA-TTT
*
16656 GGAAGTTTATGGGGACAAAATATCCTGATTT
1 GGAAGTTTATGGGGACAAAATATCCTTATTT
* * *
16687 -GAAGTTCAT-GAGACAAAACATCCTTA
1 GGAAGTTTATGGGGACAAAATATCCTTA
16713 ACGCAATATT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
29 14 0.29
30 8 0.16
31 12 0.24
32 15 0.31
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (31 bp):
GGAAGTTTATGGGGACAAAATATCCTTATTT
Found at i:22134 original size:43 final size:43
Alignment explanation
Indices: 22023--22325 Score: 393
Period size: 43 Copynumber: 7.1 Consensus size: 43
22013 CATATATAAT
* *
22023 GGGCACCTTTATTACAAAGTCCTCAAACACATATATAACACA-
1 GGGCAACTCTATTACAAAGTCCTCAAACACATATATAACACAG
* * * *
22065 GAGCCA-TCTA-TATCATAGTCCCCAAACACATATATAACACAG
1 GGGCAACTCTATTA-CAAAGTCCTCAAACACATATATAACACAG
*
22107 GGGCAACTCTACTACAAAGTCCTCAAACACATATATAACACAG
1 GGGCAACTCTATTACAAAGTCCTCAAACACATATATAACACAG
* * *
22150 AGGCATCTATATTACAAAGTCCTCAAACACATATATAACACAG
1 GGGCAACTCTATTACAAAGTCCTCAAACACATATATAACACAG
22193 GGGCAACTCTATTACAAAGTCCTCAAACACATATATAACACA-
1 GGGCAACTCTATTACAAAGTCCTCAAACACATATATAACACAG
* * * *
22235 GAGCCA-TTTA-TATCAAAGTCCCCAAACACATATATAACACAG
1 GGGCAACTCTATTA-CAAAGTCCTCAAACACATATATAACACAG
*
22277 GGGCATCTCTATTACAAAAGTCCTCAAACACATATATAACACAG
1 GGGCAACTCTATTAC-AAAGTCCTCAAACACATATATAACACAG
*
22321 AGGCA
1 GGGCA
22326 TTTCTCCTTA
Statistics
Matches: 225, Mismatches: 27, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
40 4 0.02
41 59 0.26
42 14 0.06
43 113 0.50
44 35 0.16
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (43 bp):
GGGCAACTCTATTACAAAGTCCTCAAACACATATATAACACAG
Found at i:22198 original size:86 final size:84
Alignment explanation
Indices: 21999--22322 Score: 503
Period size: 84 Copynumber: 3.9 Consensus size: 84
21989 CAATAGCCAA
* * * *
21999 AAAGTCCCCAAATACATATAT---A-ATGGGCACCTTTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
22060 ACACAGAGCCATCTATATC
66 ACACAGAGCCATCTATATC
* *
22079 ATAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
22144 ACACAGAGGCATCTATATTAC
66 ACACAGAGCCATCTATA-T-C
*
22165 AAAGTCCTCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
22230 ACACAGAGCCATTTATATC
66 ACACAGAGCCATCTATATC
*
22249 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
22314 AACACAGAG
65 AACACAGAG
22323 GCATTTCTCC
Statistics
Matches: 223, Mismatches: 14, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
80 19 0.09
83 1 0.00
84 93 0.42
85 32 0.14
86 78 0.35
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.22
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGCCATCTATATC
Found at i:22447 original size:2 final size:2
Alignment explanation
Indices: 22435--22474 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
22425 ACCAAATTCC
*
22435 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22475 GTGACAAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34256 original size:43 final size:41
Alignment explanation
Indices: 34209--34537 Score: 403
Period size: 41 Copynumber: 7.8 Consensus size: 41
34199 CAATAGCCAA
* *
34209 AAAGTCCACAAACACATATATAACACAGGGGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCA-CTTTA-TAC
* *
34252 AAAGTCCACAAACACATATATAACACAGAGGCA-TCTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACTTTATA-C
*
34293 AAAGTCCCCAAACACATATATAACACAGGGGCAACTTTACTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-ACTTTA-TAC
* *
34336 AAAGTCCTCAAACACATATATAACACAGAAGCA-TTTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACTTTATA-C
* *
34377 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-ACTTTA-TAC
*
34420 AAAGTCCTCAAACACATATATAACACAGAGGCA-TTTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACTTTATA-C
* *
34461 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCA-CTTTA-TAC
**
34504 AAAAGTCTTCAAACACATATATAACACAGAGGCA
1 -AAAGTCCCCAAACACATATATAACACAGAGGCA
34538 TTTCTCCTTA
Statistics
Matches: 252, Mismatches: 21, Indels: 25
0.85 0.07 0.08
Matches are distributed among these distances:
40 6 0.02
41 103 0.41
42 4 0.02
43 103 0.41
44 36 0.14
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.21
Consensus pattern (41 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCACTTTATAC
Found at i:34298 original size:84 final size:84
Alignment explanation
Indices: 34209--34540 Score: 565
Period size: 84 Copynumber: 3.9 Consensus size: 84
34199 CAATAGCCAA
* * * *
34209 AAAGTCCACAAACACATATATAACACAGGGGCACCTTTATTACAAAGTCCACAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
34274 ACACAGAGGCATCTATATC
66 ACACAGAGGCATTTATATC
* *
34293 AAAGTCCCCAAACACATATATAACACAGGGGCAACTTTACTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
34358 ACACAGAAGCATTTATATC
66 ACACAGAGGCATTTATATC
34377 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
34442 ACACAGAGGCATTTATATC
66 ACACAGAGGCATTTATATC
* *
34461 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCTTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
34526 AACACAGAGGCATTT
65 AACACAGAGGCATTT
34541 CTCCTTATGG
Statistics
Matches: 236, Mismatches: 11, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
84 201 0.85
85 35 0.15
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATTTATATC
Found at i:38463 original size:396 final size:386
Alignment explanation
Indices: 37735--38516 Score: 1359
Period size: 396 Copynumber: 2.0 Consensus size: 386
37725 TTGTTCTTTC
37735 AGAAATTCTGGTCCACTGTTGGGGAATCGGTGACTAAGGCTGTGCAAAGTTTCTTCCATAGTGGC
1 AGAAATTCTGGTCCACTGTTGGGGAATCGGTGACTAAGGCTGTGCAAAGTTTCTTCCATAGTGGC
37800 CATATGCTCAGAGAGCTCAACCAGACTAATATTGTCTTAATCCCTAAGGTAAAATCCCCCGAGCT
66 CATATGCTCAGAGAGCTCAACCAGACTAATATTGTCTTAATCCCTAAGGTAAAATCCCCCGAGCT
37865 GGTTTCCCAATTTCGTCCCATAAGCTGTGTAACTATGCTTACAAGGTTATATCTAAAGTCCTAGC
131 GGTTTCCCAATTTCGTCCCATAAGCTGTGTAACTATGCTTACAAGGTTATATCTAAAGTCCTAGC
37930 TAATCGACTTAAGCATTATATGAATTTAATCATCTCGCAGCATCAAAGTGCCTTTGTAGAGGGTA
196 TAATCGACTTAAGCATTATATGAATTTAATCATCTCGCAGCATCAAAGTGCCTTTGTAGAGGGTA
37995 GGCTTATACAAGATAATATACTGGTGGAAAATGAGATCTTTCATGATTTTAAGATCAGAAAAAGG
261 GGCTTATACAAGATAATATACTGGTGGAAAATGAGATCTTTCATGATTTTAAGATCAGAAAAAGG
* *
38060 GGTAAGAATTATGATGCAGCTGTGAAACTTGACCTTAACAAGGCCTGCGATCAGGTTGATT
326 AGTAAGAATTATGATGCAGCTGTGAAACTTGACCTTAACAAGGCCTACGATCAGGTTGATT
* *
38121 AGAAATTCTGGTCCATTGTTGGGGAATCGGTGACTAGGGCTGTGCAAAGTTTCTTCCATAGTGGC
1 AGAAATTCTGGTCCACTGTTGGGGAATCGGTGACTAAGGCTGTGCAAAGTTTCTTCCATAGTGGC
38186 CATATGCTCAGAGAGCTCAACCAGCTCAACCAGACTAATATTGTCTTAATCCCTAAGGTAGAAA-
66 CATATGCTC--AGAG-------AGCTCAACCAGACTAATATTGTCTTAATCCCTAAGGTA-AAAT
*
38250 CCCCCGAGCTGGTTTCCCAATTTCGTCCCATAAGCCTGTGTAACTATGCTTATAAGGTTATATCT
121 CCCCCGAGCTGGTTTCCCAATTTCGTCCCATAAG-CTGTGTAACTATGCTTACAAGGTTATATCT
38315 AAAGTCCTAGCTAATCGACTTAAGCATTATATGAATTTAATCATCTCGCAGCATCAAAGTGCCTT
185 AAAGTCCTAGCTAATCGACTTAAGCATTATATGAATTTAATCATCTCGCAGCATCAAAGTGCCTT
* * *
38380 TGTGGAGGGTAGGCTTATACAAGATAATATATTGGTGGCAAATGAGATCTTTCATGATTTTAAGA
250 TGTAGAGGGTAGGCTTATACAAGATAATATACTGGTGGAAAATGAGATCTTTCATGATTTTAAGA
* **
38445 TCAGAAAAAGGAGTAAGAATTATGATGCAGTTGTGAAACTTGACCTTAACAAGGCCTACGATTGG
315 TCAGAAAAAGGAGTAAGAATTATGATGCAGCTGTGAAACTTGACCTTAACAAGGCCTACGATCAG
38510 GTTGATT
380 GTTGATT
38517 GGAAGTTCCT
Statistics
Matches: 374, Mismatches: 11, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
386 72 0.19
388 4 0.01
395 72 0.19
396 226 0.60
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (386 bp):
AGAAATTCTGGTCCACTGTTGGGGAATCGGTGACTAAGGCTGTGCAAAGTTTCTTCCATAGTGGC
CATATGCTCAGAGAGCTCAACCAGACTAATATTGTCTTAATCCCTAAGGTAAAATCCCCCGAGCT
GGTTTCCCAATTTCGTCCCATAAGCTGTGTAACTATGCTTACAAGGTTATATCTAAAGTCCTAGC
TAATCGACTTAAGCATTATATGAATTTAATCATCTCGCAGCATCAAAGTGCCTTTGTAGAGGGTA
GGCTTATACAAGATAATATACTGGTGGAAAATGAGATCTTTCATGATTTTAAGATCAGAAAAAGG
AGTAAGAATTATGATGCAGCTGTGAAACTTGACCTTAACAAGGCCTACGATCAGGTTGATT
Found at i:45336 original size:22 final size:22
Alignment explanation
Indices: 45309--45354 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
45299 AACTTAGTAA
45309 TAACATT-ATATAAGAAAATTGG
1 TAACATTCAT-TAAGAAAATTGG
* *
45331 TAACATTCATTAATAATATTGG
1 TAACATTCATTAAGAAAATTGG
45353 TA
1 TA
45355 GATATGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (22 bp):
TAACATTCATTAAGAAAATTGG
Found at i:46983 original size:320 final size:318
Alignment explanation
Indices: 46399--47043 Score: 1204
Period size: 320 Copynumber: 2.0 Consensus size: 318
46389 ATAGAATTTG
46399 TAAA-GAATTAAGTAGTATAAAGTAGAAAAGTATGAGGGCCATTTGATAAATAATTCAAATAAGA
1 TAAATGAATTAAGTAGTATAAAGTAGAAAAGTATGAGGGCCATTTGATAAATAATTCAAATAAGA
*
46463 AAATGTTTGTTAATGGAGATCTTGAAACATAAAAAATTTTTTTAACCCTTAACGAAACTCGTAGA
66 AAATGTTTGTTAATGGAGATCTTGAAACATAAAAAATTTTTTGAACCCTTAACGAAACTCGTAGA
*
46528 TCAAATTTAGCTTTCGGGTCCTTCATGAAAGTCGTAAATCATGCAATAACCTTTAAACCGACACT
131 TCAAATTTAGCTTTCGGGCCCTTCATGAAAGTCGTAAATCATGCAATAACCTTTAAACCGACACT
46593 TCAATAACTTCAATCGGAGATGTGGACAAAAAATTATACGATATTAAATTAACCGGCAATCAAAA
196 TCAATAACTTCAATCGGAGATGTGGACAAAAAATTATACGATATTAAATTAACCGGCAATCAAAA
46658 CCACAAAATTTCAGAAGCAATTTTTAGAATCAAAACATTAAAATTGACTTTTGAGTTC
261 CCACAAAATTTCAGAAGCAATTTTTAGAATCAAAACATTAAAATTGACTTTTGAGTTC
46716 TAAATGAATTAAGTAGTATAAAGTAGAAAAGTATGAGGGCCATTTGATAAATAATTCAAATAAGA
1 TAAATGAATTAAGTAGTATAAAGTAGAAAAGTATGAGGGCCATTTGATAAATAATTCAAATAAGA
* * *
46781 AAATGTTTGTTAATGGAGATCTTGGAACAT-GAAAATTCCCTTTTGAACCCTTAATGAAACTCGT
66 AAATGTTTGTTAATGGAGATCTTGAAACATAAAAAATT---TTTTGAACCCTTAACGAAACTCGT
46845 AGATCAAATTTAGCTTTCGGGCCCTTCATGAAAGTCGTAAATCATGCAATAACCTTTAAACCGAC
128 AGATCAAATTTAGCTTTCGGGCCCTTCATGAAAGTCGTAAATCATGCAATAACCTTTAAACCGAC
46910 ACTTCAATAACTTCAATCGGAGATGTGGACAAAAAATTATACGATATTAAATTAACCGGCAATCA
193 ACTTCAATAACTTCAATCGGAGATGTGGACAAAAAATTATACGATATTAAATTAACCGGCAATCA
46975 AAACCACAAAATTTCAGAAGCAATTTTTAGAATCAAAACATTAAAATTGACTTTTGAGTTC
258 AAACCACAAAATTTCAGAAGCAATTTTTAGAATCAAAACATTAAAATTGACTTTTGAGTTC
47036 TAAATGAA
1 TAAATGAA
47044 AATTGTAGAT
Statistics
Matches: 319, Mismatches: 5, Indels: 5
0.97 0.02 0.02
Matches are distributed among these distances:
317 10 0.03
318 89 0.28
320 220 0.69
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (318 bp):
TAAATGAATTAAGTAGTATAAAGTAGAAAAGTATGAGGGCCATTTGATAAATAATTCAAATAAGA
AAATGTTTGTTAATGGAGATCTTGAAACATAAAAAATTTTTTGAACCCTTAACGAAACTCGTAGA
TCAAATTTAGCTTTCGGGCCCTTCATGAAAGTCGTAAATCATGCAATAACCTTTAAACCGACACT
TCAATAACTTCAATCGGAGATGTGGACAAAAAATTATACGATATTAAATTAACCGGCAATCAAAA
CCACAAAATTTCAGAAGCAATTTTTAGAATCAAAACATTAAAATTGACTTTTGAGTTC
Found at i:48265 original size:19 final size:18
Alignment explanation
Indices: 48233--48277 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
48223 TGTTTTAAGT
48233 TTTCTT-TTTTCTTTATC
1 TTTCTTCTTTTCTTTATC
* *
48250 TTTCTTCTTTTCCTTTGTT
1 TTTCTTCTTTT-CTTTATC
48269 TTTCTTCTT
1 TTTCTTCTT
48278 CAATTTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 6 0.25
18 4 0.17
19 14 0.58
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTCTTCTTTTCTTTATC
Found at i:49857 original size:130 final size:128
Alignment explanation
Indices: 49712--49970 Score: 403
Period size: 130 Copynumber: 2.0 Consensus size: 128
49702 CATTGTTTAA
* * *
49712 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
1 ACTTTTACAATTTTACTCAACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCCTTACAAC
* * *
49777 TATTTTATTTTTACCATTTTACTATTTTATTTAAAAAAACTTAGGTATATTACAAAT-TTTTAAA
66 TATTTTATTTTTACCATTTTACTA-ATTAATT-AAAAAACTTAGATATATTA-AAATCTTTTAAA
49841 T
128 T
*
49842 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCCTTACAAC
1 ACTTTTACAATTTTACTCAACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCCTTACAAC
* *
49907 TATTTTATTTTTACCATTTTTCTAATTAATTAAAAAACTTAGATATATTAGAATCTTTTAAAT
66 TATTTTATTTTTACCATTTTACTAATTAATTAAAAAACTTAGATATATTAAAATCTTTTAAAT
49970 A
1 A
49971 TATTTCTTAA
Statistics
Matches: 119, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
127 3 0.03
128 27 0.23
129 5 0.04
130 84 0.71
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.47
Consensus pattern (128 bp):
ACTTTTACAATTTTACTCAACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCCTTACAAC
TATTTTATTTTTACCATTTTACTAATTAATTAAAAAACTTAGATATATTAAAATCTTTTAAAT
Found at i:50025 original size:128 final size:128
Alignment explanation
Indices: 49728--50018 Score: 369
Period size: 130 Copynumber: 2.3 Consensus size: 128
49718 ATAATTTTAC
*
49728 TCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTTTTACCA
1 TCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTACAACTATTTTATTTTTACCA
* * * * *
49793 TTTTACTATTTTATTTAAAAAAACTTAGGTATATTACAAATTTTTAAATACTTTTACAGTTTTAC
66 TTTTACTATATTAATTAAAAAAACTTAGATATATTACAAATTTTTAAATACTTTTACA--TTAAA
*
49858 TCAACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCCTTACAACTATTTTATTTTTACCA
1 TCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTACAACTATTTTATTTTTACCA
* *
49923 TTTTTCTA-ATTAATT-AAAAAACTTAGATATATTA-GAATCTTTTAAATA-TATTT-C-TTAAA
66 TTTTACTATATTAATTAAAAAAACTTAGATATATTACAAAT-TTTTAAATACT-TTTACATTAAA
* *
49982 TGACATTCTTAAAAACTATATTTTTATTTAATTAAAT
1 T--CA-AC-TAAAAACTCTATTTTTATTTAATTAAAT
50019 TCAATATTTT
Statistics
Matches: 143, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
124 4 0.03
126 2 0.01
127 6 0.04
128 56 0.39
129 5 0.03
130 70 0.49
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.47
Consensus pattern (128 bp):
TCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTACAACTATTTTATTTTTACCA
TTTTACTATATTAATTAAAAAAACTTAGATATATTACAAATTTTTAAATACTTTTACATTAAA
Found at i:50042 original size:128 final size:128
Alignment explanation
Indices: 49728--50055 Score: 373
Period size: 128 Copynumber: 2.5 Consensus size: 128
49718 ATAATTTTAC
49728 TCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTTTTACCA
1 TCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTTTTACCA
* * * * *
49793 TTTTACTATTTTATTTAAAAAAACTTAGGTATATTACAAATTTTTAAATACTTTTACAGTTTTAC
66 TTTTACTATATTAATTAAAAAAACTTAGATATATTACAAATTTTTAAATACTTTTACA--TTAAA
* *
49858 TCAACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCCTTACAACTATTTTATTTTTACCA
1 TCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTTTTACCA
* *
49923 TTTTTCTA-ATTAATT-AAAAAACTTAGATATATTA-GAATCTTTTAAATA-TATTT-C-TTAAA
66 TTTTACTATATTAATTAAAAAAACTTAGATATATTACAAAT-TTTTAAATACT-TTTACATTAAA
* * ** ** *
49982 TGACATTCTTAAAAACTATATTTTTATTTAATTAAAT-TCAATATTTTTATAAAAAGTTTATTTT
1 T--CA-AC-TAAAAACTCTATTTTTATTTAATTAAATCT-AATATCCTTATAACTATTTTATTTT
*
50046 TTCCATTTTA
61 TACCATTTTA
50056 ATTTTAAAAA
Statistics
Matches: 171, Mismatches: 20, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
124 4 0.02
126 2 0.01
127 7 0.04
128 83 0.49
129 5 0.03
130 70 0.41
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (128 bp):
TCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTTTTACCA
TTTTACTATATTAATTAAAAAAACTTAGATATATTACAAATTTTTAAATACTTTTACATTAAA
Done.