Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016744.1 Corchorus olitorius cultivar O-4 contig16777, 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: 35891
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--34 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35 GAAAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1005 original size:22 final size:23
Alignment explanation
Indices: 978--1021 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
968 GTGATAAATA
*
978 AGAGAAA-AAGCGCAGAGCTTTG
1 AGAGAAATAAGCACAGAGCTTTG
*
1000 AGAGAAATAAGCACGGAGCTTT
1 AGAGAAATAAGCACAGAGCTTT
1022 TTTTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.41, C:0.14, G:0.30, T:0.16
Consensus pattern (23 bp):
AGAGAAATAAGCACAGAGCTTTG
Found at i:1203 original size:18 final size:20
Alignment explanation
Indices: 1170--1209 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
1160 AAGGCAATTT
*
1170 CAACTTCTTCAGGAAGGTGA
1 CAACTTCTTCAGGAAGGAGA
1190 CAACTTC-T-AGGAAGGAGA
1 CAACTTCTTCAGGAAGGAGA
1208 CA
1 CA
1210 GGAAGCTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 1 0.05
20 7 0.37
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (20 bp):
CAACTTCTTCAGGAAGGAGA
Found at i:2387 original size:16 final size:17
Alignment explanation
Indices: 2368--2401 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2358 TGATATTTTG
2368 AAGAATAAT-AAAAGTA
1 AAGAATAATAAAAAGTA
*
2384 AAGAATGATAAAAAGTA
1 AAGAATAATAAAAAGTA
2401 A
1 A
2402 GAAAATTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.18
Consensus pattern (17 bp):
AAGAATAATAAAAAGTA
Found at i:2647 original size:22 final size:22
Alignment explanation
Indices: 2599--2808 Score: 178
Period size: 22 Copynumber: 9.4 Consensus size: 22
2589 TTGGAAACAT
* *
2599 CTTTGCAGAG-ATT-CTTTCTT
1 CTTTGCAGAGCATTATTTTCTA
2619 CTTTGCAGAGCATTATTTTCTA
1 CTTTGCAGAGCATTATTTTCTA
*
2641 CTCTGCAGAGCATTATTTTCTA
1 CTTTGCAGAGCATTATTTTCTA
*
2663 CTTTGCAGAGCATTATTTTCCA
1 CTTTGCAGAGCATTATTTTCTA
2685 CTTTGCAGAGCATTATTTTCTTCAA
1 CTTTGCAGAGCATTATTTTC-T--A
** *** * **
2710 CTTCACCTTTGCACTATTGGAAAC-A
1 CTT-TGCAGAGCATTATT---TTCTA
* *
2735 TCTTTGCAGAG-ATT-CTTTCTT
1 -CTTTGCAGAGCATTATTTTCTA
2756 CTTTGCAGAGCATTATTTTCTA
1 CTTTGCAGAGCATTATTTTCTA
*
2778 CTTTGCAGAGCATTATTTTCCA
1 CTTTGCAGAGCATTATTTTCTA
2800 CTTTGCAGA
1 CTTTGCAGA
2809 ACACTTCTTG
Statistics
Matches: 150, Mismatches: 27, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
20 21 0.14
21 6 0.04
22 101 0.67
23 1 0.01
24 2 0.01
25 7 0.05
26 11 0.07
29 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43
Consensus pattern (22 bp):
CTTTGCAGAGCATTATTTTCTA
Found at i:5485 original size:2 final size:2
Alignment explanation
Indices: 5480--5506 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5470 ACACACACAG
5480 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 A
5507 ATACACACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6240 original size:18 final size:18
Alignment explanation
Indices: 6217--6251 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6207 TCGTCGTGAA
6217 CAAAACCAAAACATTATG
1 CAAAACCAAAACATTATG
*
6235 CAAAACCGAAACATTAT
1 CAAAACCAAAACATTAT
6252 ATAAAAGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.23, G:0.06, T:0.17
Consensus pattern (18 bp):
CAAAACCAAAACATTATG
Found at i:6257 original size:18 final size:18
Alignment explanation
Indices: 6216--6257 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
6206 TTCGTCGTGA
6216 ACAAAACCAAAACATTAT
1 ACAAAACCAAAACATTAT
* *
6234 GCAAAACCGAAACATTAT
1 ACAAAACCAAAACATTAT
*
6252 ATAAAA
1 ACAAAA
6258 GACATTAAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.60, C:0.19, G:0.05, T:0.17
Consensus pattern (18 bp):
ACAAAACCAAAACATTAT
Found at i:6467 original size:18 final size:18
Alignment explanation
Indices: 6444--6480 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
6434 TATAAGTGGA
6444 ATTTAACAGACTGTATAT
1 ATTTAACAGACTGTATAT
6462 ATTTAACAGACTGTATAT
1 ATTTAACAGACTGTATAT
6480 A
1 A
6481 CAGGATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (18 bp):
ATTTAACAGACTGTATAT
Found at i:12387 original size:37 final size:37
Alignment explanation
Indices: 12332--12404 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
12322 ATGCCGCTAA
*
12332 ATGTTTTTAGCGACTGGACTATTGAGAACAGATGTCC
1 ATGTTTTTAGCAACTGGACTATTGAGAACAGATGTCC
*
12369 ATGTTTTTAGCAATTGGACTATTGAGAACAGATGTC
1 ATGTTTTTAGCAACTGGACTATTGAGAACAGATGTC
12405 TTAATTGCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (37 bp):
ATGTTTTTAGCAACTGGACTATTGAGAACAGATGTCC
Found at i:12739 original size:22 final size:22
Alignment explanation
Indices: 12711--12755 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
12701 GCATTGCAAG
12711 ACCCATGAAGCAATCCCAATCA
1 ACCCATGAAGCAATCCCAATCA
12733 ACCCATGAAGCAATCCCAATCA
1 ACCCATGAAGCAATCCCAATCA
12755 A
1 A
12756 ATAACATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.36, G:0.09, T:0.13
Consensus pattern (22 bp):
ACCCATGAAGCAATCCCAATCA
Found at i:13240 original size:23 final size:23
Alignment explanation
Indices: 13214--13264 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
13204 AAAAAAGGAA
13214 GGTAAGCTTTATAAAATAGAGTT
1 GGTAAGCTTTATAAAATAGAGTT
13237 GGTAAGCTTTATAAAATAGAGTT
1 GGTAAGCTTTATAAAATAGAGTT
13260 GGTAA
1 GGTAA
13265 ATAATCAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (23 bp):
GGTAAGCTTTATAAAATAGAGTT
Found at i:16515 original size:15 final size:15
Alignment explanation
Indices: 16497--16526 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
16487 TATTATTATA
16497 TAATAATTAATTAAT
1 TAATAATTAATTAAT
16512 TAATAATTAATTAAT
1 TAATAATTAATTAAT
16527 GTATTTTTAC
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATAATTAATTAAT
Found at i:18163 original size:40 final size:40
Alignment explanation
Indices: 18119--18198 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
18109 TTTCACATAA
* * *
18119 ATGTTACGATAAATCCTATCCCCCTTAATTATCTATAATT
1 ATGTTACAATAAATCATATCCCCCTTAATTATCTAGAATT
* *
18159 ATGTTATAATAAATCATATCTCCCTTAATTATCTAGAATT
1 ATGTTACAATAAATCATATCCCCCTTAATTATCTAGAATT
18199 GTAATCTCTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (40 bp):
ATGTTACAATAAATCATATCCCCCTTAATTATCTAGAATT
Found at i:19939 original size:41 final size:41
Alignment explanation
Indices: 19892--19969 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
19882 CAAAAAAAAT
19892 TCTAAATCCA-GGACAAAATTGAATCAATAAATAAATATTAC
1 TCTAAAT-CAGGGACAAAATTGAATCAATAAATAAATATTAC
* * *
19933 TCTAAATTAGGGACACAATTGAATCAATGAATAAATA
1 TCTAAATCAGGGACAAAATTGAATCAATAAATAAATA
19970 ACAACCTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 1 0.03
41 32 0.97
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (41 bp):
TCTAAATCAGGGACAAAATTGAATCAATAAATAAATATTAC
Found at i:19979 original size:41 final size:41
Alignment explanation
Indices: 19902--19997 Score: 131
Period size: 41 Copynumber: 2.3 Consensus size: 41
19892 TCTAAATCCA
* **
19902 GGACAAAATTGAATCAATAAATAAATATTACTCTAAATTAG
1 GGACACAATTGAATCAATAAATAAATACAACTCTAAATTAG
*
19943 GGACACAATTGAATCAATGAATAAATAACAAC-CTAAATTAG
1 GGACACAATTGAATCAATAAATAAAT-ACAACTCTAAATTAG
*
19984 GGACCCAATTGAAT
1 GGACACAATTGAAT
19998 GAAATCACAC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
41 46 0.94
42 3 0.06
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (41 bp):
GGACACAATTGAATCAATAAATAAATACAACTCTAAATTAG
Found at i:22190 original size:22 final size:22
Alignment explanation
Indices: 22165--22215 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
22155 TAAAAGGATG
22165 GATGCAAAAGATACCATGCAAA
1 GATGCAAAAGATACCATGCAAA
* *
22187 GATGCAAAAGGTGCCATGCAAA
1 GATGCAAAAGATACCATGCAAA
*
22209 AATGCAA
1 GATGCAA
22216 CTATTAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (22 bp):
GATGCAAAAGATACCATGCAAA
Found at i:22610 original size:27 final size:27
Alignment explanation
Indices: 22568--22664 Score: 97
Period size: 27 Copynumber: 3.6 Consensus size: 27
22558 AATGAGCTTA
**
22568 AAATGACCAATGTGCCCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAACATGC
* * ** **
22595 GAATGACCAAAATGCCCAT-AATGTAA
1 AAATGACCAAAATGCCCCTGAACATGC
**
22621 AAATGACCAACGTGCCCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAACATGC
22648 AAATGACCAAAATGCCC
1 AAATGACCAAAATGCCC
22665 TTGGATGACC
Statistics
Matches: 51, Mismatches: 18, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
26 18 0.35
27 33 0.65
ACGTcount: A:0.39, C:0.28, G:0.16, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAACATGC
Found at i:23017 original size:22 final size:22
Alignment explanation
Indices: 22925--23376 Score: 203
Period size: 22 Copynumber: 20.9 Consensus size: 22
22915 TTAACATTCT
* * *
22925 TATGAAATTTTGTTAATCTCCT
1 TATGAAATTTTGATAACCTCCA
* * *
22947 TAAGGAATTTTGA-AGACAT-CA
1 TATGAAATTTTGATA-ACCTCCA
*
22968 CTATGAAATTTTGATAACTTCCGA
1 -TATGAAATTTTGATAACCTCC-A
22992 -ATGAAATTTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCA
* * * * **
23013 TATGATATATTGATAAACACGT
1 TATGAAATTTTGATAACCTCCA
* * *
23035 TATGAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCA
*
23057 TATG-AATGGTT-AGTAA--TCACA
1 TATGAAAT-TTTGA-TAACCTC-CA
* *
23078 CTCTGAAATTTTGATAA--TCAAA
1 -TATGAAATTTTGATAACCTC-CA
*
23100 CTATGAAATTGTGATAACCTCGC-
1 -TATGAAATTTTGATAACCTC-CA
* * *
23123 TATAAAATTTTAATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCA
* * * *
23146 TATAAAATTTTAATAACCTTCT
1 TATGAAATTTTGATAACCTCCA
*
23168 TATGAAATCTTGATAA----C-
1 TATGAAATTTTGATAACCTCCA
* *
23185 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCA
**
23206 TATGATTTTTTGATAACCT-CA
1 TATGAAATTTTGATAACCTCCA
* *
23227 TTATGAAATTTT-ATTAATCTCCC
1 -TATGAAATTTTGA-TAACCTCCA
*
23250 TATGAAATTTTGATAACC-CTCT
1 TATGAAATTTTGATAACCTC-CA
* **
23272 TATGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAACCTCCA
*
23293 CTATGAAATTTTGATAACCTTCA
1 -TATGAAATTTTGATAACCTCCA
*
23316 TATGAAATTTTGATATCCTCC-
1 TATGAAATTTTGATAACCTCCA
*
23337 T-TGAAATTTTGATTA-CTCCA
1 TATGAAATTTTGATAACCTCCA
* * *
23357 TAGTAAAAGTTTAATAACCT
1 TA-TGAAATTTTGATAACCT
23377 TCCTAATTTG
Statistics
Matches: 326, Mismatches: 70, Indels: 67
0.70 0.15 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
19 4 0.01
20 16 0.05
21 17 0.05
22 237 0.73
23 35 0.11
24 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:23148 original size:23 final size:23
Alignment explanation
Indices: 23115--23161 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
23105 AAATTGTGAT
*
23115 AACCTCGCTATAAAATTTTAATA
1 AACCTCCCTATAAAATTTTAATA
23138 AACCTCCCTATAAAATTTTAATA
1 AACCTCCCTATAAAATTTTAATA
23161 A
1 A
23162 CCTTCTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (23 bp):
AACCTCCCTATAAAATTTTAATA
Found at i:23254 original size:82 final size:83
Alignment explanation
Indices: 23105--23266 Score: 191
Period size: 82 Copynumber: 2.0 Consensus size: 83
23095 TCAAACTATG
* * * *
23105 AAATTGTGATAACCTCGCTATAAAATTTTAATAAACCTCCCTATAAAATTTTAATAACCTTCTTA
1 AAATTGTGATAACCTCCCTATAAAATTTTAATAAACCTCACTATAAAATTTTAATAACCTCCCTA
23170 TGAAATCTTGATAACTAC
66 TGAAATCTTGATAACTAC
* * ** * * * * *
23188 AAATTTTGATAACCTCCCTATGATTTTTTGAT-AACCTCATTATGAAATTTTATTAATCTCCCTA
1 AAATTGTGATAACCTCCCTATAAAATTTTAATAAACCTCACTATAAAATTTTAATAACCTCCCTA
*
23252 TGAAATTTTGATAAC
66 TGAAATCTTGATAAC
23267 CCTCTTATGA
Statistics
Matches: 65, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
82 39 0.60
83 26 0.40
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (83 bp):
AAATTGTGATAACCTCCCTATAAAATTTTAATAAACCTCACTATAAAATTTTAATAACCTCCCTA
TGAAATCTTGATAACTAC
Found at i:23343 original size:20 final size:22
Alignment explanation
Indices: 22842--23349 Score: 148
Period size: 22 Copynumber: 23.5 Consensus size: 22
22832 CCTCCTTATA
* *
22842 AAATTTTAATAACCTTCCTATG
1 AAATTTTGATAACCTTCATATG
* ** *
22864 AAAATTTGATAACGAT-ACTATC
1 AAATTTTGATAACCTTCA-TATG
* * *
22886 AAATTTCGAGAACCCTT-TTAT-
1 AAATTTTGATAA-CCTTCATATG
** * *
22907 AAATTTTTTTAACATTCTTATG
1 AAATTTTGATAACCTTCATATG
* * * * *
22929 AAATTTTGTTAATCTCCTTAAG
1 AAATTTTGATAACCTTCATATG
* *
22951 GAATTTTGA-AGA-CATCACTATG
1 AAATTTTGATA-ACCTTCA-TATG
22973 AAATTTTGATAA-CTTCCGA-ATG
1 AAATTTTGATAACCTT-C-ATATG
*
22995 AAATTTTGATAACCTCCATATG
1 AAATTTTGATAACCTTCATATG
* * *
23017 ATATATTGATAAACACGT--TATG
1 AAATTTTGAT-AAC-CTTCATATG
* * * *
23039 AAAATTTAAAAACCTCCATATG
1 AAATTTTGATAACCTTCATATG
* * * *
23061 -AATGGTT-AGTAATC-ACACTCTG
1 AAAT-TTTGA-TAACCTTCA-TATG
* **
23083 AAATTTTGATAATC-AAACTATG
1 AAATTTTGATAACCTTCA-TATG
* * *
23105 AAATTGTGATAACC-TCGCTATA
1 AAATTTTGATAACCTTC-ATATG
* * * *
23127 AAATTTTAATAAACCTCCCTATA
1 AAATTTTGAT-AACCTTCATATG
* *
23150 AAATTTTAATAACCTTCTTATG
1 AAATTTTGATAACCTTCATATG
* *
23172 AAATCTTGATAA----C-TA-C
1 AAATTTTGATAACCTTCATATG
* *
23188 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTTCATATG
**
23210 ATTTTTTGATAACC-TCATTATG
1 AAATTTTGATAACCTTCA-TATG
* * *
23232 AAATTTT-ATTAATCTCCCTATG
1 AAATTTTGA-TAACCTTCATATG
* *
23254 AAATTTTGATAACCCTCTTATG
1 AAATTTTGATAACCTTCATATG
* **
23276 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCTTCA-TATG
23298 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACCTTCATATG
* *
23320 AAATTTTGATATCC-TCCT-TG
1 AAATTTTGATAACCTTCATATG
23340 AAATTTTGAT
1 AAATTTTGAT
23350 TACTCCATAG
Statistics
Matches: 360, Mismatches: 91, Indels: 72
0.69 0.17 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 17 0.05
21 34 0.09
22 253 0.70
23 39 0.11
24 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAACCTTCATATG
Found at i:23489 original size:22 final size:22
Alignment explanation
Indices: 23431--23508 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
23421 TAAATACCAC
* * *
23431 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGATAACCTC-TT
23454 T-TGGAAA-TTTGATAACCTCTT
1 TAT-GAAATTTTGATAACCTCTT
* *
23475 TATGAAATTTTGATAACTTCTC
1 TATGAAATTTTGATAACCTCTT
*
23497 TATAAAATTTTG
1 TATGAAATTTTG
23509 TTGACAAGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
21 7 0.15
22 34 0.74
23 5 0.11
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTT
Found at i:23565 original size:22 final size:21
Alignment explanation
Indices: 23535--23695 Score: 98
Period size: 22 Copynumber: 7.4 Consensus size: 21
23525 ATATTTTCAT
* *
23535 TATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACATC-C
* *
23557 TTTGAAATTTTGATAACAACAC
1 TATGAAATTTTGATAACATC-C
*
23579 TATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAA-CATCC
23601 TAT-AAATTTTGATAATTCGATCTC
1 TATGAAATTTTGATAA--C-ATC-C
*
23625 TATGAAATTTCGATAATCA-CTC
1 TATGAAATTTTGATAA-CATC-C
* * *
23647 TATGAGA-TTTGATAACCTTC
1 TATGAAATTTTGATAACATCC
* *
23667 TATCAAATTTTGGT-AC-TCC
1 TATGAAATTTTGATAACATCC
23686 TTATGAAATT
1 -TATGAAATT
23696 AAGACTTTTA
Statistics
Matches: 112, Mismatches: 19, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
19 2 0.02
20 17 0.15
21 24 0.21
22 47 0.42
23 5 0.04
24 6 0.05
25 11 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (21 bp):
TATGAAATTTTGATAACATCC
Found at i:23730 original size:22 final size:22
Alignment explanation
Indices: 23530--23788 Score: 83
Period size: 22 Copynumber: 11.5 Consensus size: 22
23520 TTATGATATT
*
23530 TTCATTATGTAATTTTGATAACC
1 TTCA-TATGAAATTTTGATAACC
* *
23553 -TCGCTTTGAAATTTTGATAA-C
1 TTC-ATATGAAATTTTGATAACC
** *
23574 AACACTATGAAATTTTGATAATC
1 TTCA-TATGAAATTTTGATAACC
* *
23597 TTCCTAT-AAATTTTGATAATTCGA
1 TTCATATGAAATTTTGATAA--C-C
*
23621 TCTC-TATGAAATTTCGATAATCAC
1 T-TCATATGAAATTTTGATAA-C-C
*
23645 -TC-TATGAGA-TTTGATAACC
1 TTCATATGAAATTTTGATAACC
* * *
23664 TTC-TATCAAATTTTGGTACTCC
1 TTCATATGAAATTTTGATA-ACC
*
23686 TT-ATGAAATTAAGACTTTT-ATAACC
1 TTCAT---ATGAA-A-TTTTGATAACC
23711 TTCATATGAAATTTTGATAACC
1 TTCATATGAAATTTTGATAACC
* ** *
23733 -ACACTAAAAAATTTTAATAACC
1 TTCA-TATGAAATTTTGATAACC
* *
23755 -ACACTATGCAATTTTGATAACC
1 TTCA-TATGAAATTTTGATAACC
* *
23777 TCCCTATGAAAT
1 TTCATATGAAAT
23789 ACTCCCTCTG
Statistics
Matches: 179, Mismatches: 35, Indels: 45
0.69 0.14 0.17
Matches are distributed among these distances:
19 1 0.01
20 8 0.04
21 32 0.18
22 95 0.53
23 7 0.04
24 6 0.03
25 21 0.12
26 5 0.03
27 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.39
Consensus pattern (22 bp):
TTCATATGAAATTTTGATAACC
Found at i:24273 original size:22 final size:22
Alignment explanation
Indices: 24165--24397 Score: 172
Period size: 22 Copynumber: 10.5 Consensus size: 22
24155 TGATAATCTC
* * *
24165 TTTGATAACCTTTCTATAAAAT
1 TTTGATAACCATCCTATGAAAT
*
24187 TGTGATAACCA-CACTATGAAAT
1 TTTGATAACCATC-CTATGAAAT
** * ** *
24209 TTCAATAACCTTCCTAAAAAAA
1 TTTGATAACCATCCTATGAAAT
* *
24231 TTTAATAACTTGATCCTATGAAATT
1 TTTGATAAC--CATCCTATGAAA-T
*
24256 TTTG-TAACCATACTATGAAAT
1 TTTGATAACCATCCTATGAAAT
* *
24277 TTTGATAACCTTCCCATGAAAT
1 TTTGATAACCATCCTATGAAAT
*
24299 TTTGATAA-CTTCCATATGAAATT
1 TTTGATAACCATCC-TATGAAA-T
*
24322 TTTG-TAACCA-CACTATGGAAT
1 TTTGATAACCATC-CTATGAAAT
24343 TTTGATAACC-TCCTCATGAAAT
1 TTTGATAACCATCCT-ATGAAAT
* * *
24365 TATAATAACCATCTTATGAAAT
1 TTTGATAACCATCCTATGAAAT
24387 TTTGATAACCA
1 TTTGATAACCA
24398 CACAGAGACA
Statistics
Matches: 165, Mismatches: 32, Indels: 28
0.73 0.14 0.12
Matches are distributed among these distances:
21 17 0.10
22 122 0.74
23 11 0.07
24 12 0.07
25 3 0.02
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (22 bp):
TTTGATAACCATCCTATGAAAT
Found at i:24344 original size:66 final size:65
Alignment explanation
Indices: 24192--24400 Score: 233
Period size: 66 Copynumber: 3.1 Consensus size: 65
24182 AAAATTGTGA
** * ** *
24192 TAACCACACTATGAAATTTCAATAACCTTCCTAAAAAAATTTAATAACTTGATCCTATGAAATTT
1 TAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTAATAAC-T--TCCTATGAAATTT
24257 TTG
63 TTG
* *
24260 TAACCATACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACTTCCATATGAAATTTTT
1 TAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTAATAACTTCC-TATGAAATTTTT
24325 G
65 G
* * * *
24326 TAACCACACTATGGAATTTTGATAACC-TCCTCATGAAATTATAATAACCATCTTATGAAA-TTT
1 TAACCACACTATGAAATTTTGATAACCTTCC-CATGAAATTTTAATAA-CTTCCTATGAAATTTT
24389 TG
64 TG
24391 ATAACCACAC
1 -TAACCACAC
24401 AGAGACAAGA
Statistics
Matches: 123, Mismatches: 14, Indels: 10
0.84 0.10 0.07
Matches are distributed among these distances:
65 11 0.09
66 68 0.55
67 4 0.03
68 40 0.33
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (65 bp):
TAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTAATAACTTCCTATGAAATTTTTG
Found at i:27648 original size:16 final size:17
Alignment explanation
Indices: 27616--27648 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27606 GATGACTAAT
*
27616 GGGATTGACTTGGCTTG
1 GGGATTGACTTGACTTG
27633 GGGATTGAC-TGACTTG
1 GGGATTGACTTGACTTG
27649 AATCTGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.15, C:0.12, G:0.39, T:0.33
Consensus pattern (17 bp):
GGGATTGACTTGACTTG
Found at i:33058 original size:28 final size:28
Alignment explanation
Indices: 32978--33064 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
32968 ATAGATAGAT
32978 AATCCTATGTGATGCATCCTATTGGGAAAAA
1 AATCCTATGTGATGCATCCTATT-GG--AAA
* *
33009 AATCCTA--TAAAG--TCC-ATTGGAAA
1 AATCCTATGTGATGCATCCTATTGGAAA
33032 AATCCTATGTGATGCATCCTATTGGAAA
1 AATCCTATGTGATGCATCCTATTGGAAA
33060 AATCC
1 AATCC
33065 AAAATTTATG
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
23 10 0.21
25 5 0.11
26 3 0.06
27 6 0.13
28 13 0.28
29 3 0.06
31 7 0.15
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (28 bp):
AATCCTATGTGATGCATCCTATTGGAAA
Done.