Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018077.1 Corchorus olitorius cultivar O-4 contig18110, 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: 119356
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6661 original size:6 final size:6
Alignment explanation
Indices: 6650--6677 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6640 ACCAAAATGC
6650 ACCCCA ACCCCA ACCCCA ACCCCA ACCC
1 ACCCCA ACCCCA ACCCCA ACCCCA ACCC
6678 ATTATCATAA
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:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCCCA
Found at i:19803 original size:144 final size:144
Alignment explanation
Indices: 19562--20257 Score: 999
Period size: 144 Copynumber: 4.9 Consensus size: 144
19552 CTGGATTCTC
19562 TCACTGCTTCGATCCCGTTTGAAGCTTGAGGAGTGCCT-C--CTATCTGATCTTTCGCCTGAATT
1 TCACTGCTTCGATCCCGTTTGAAGCTTGAGGAGTGCCTCCGTCTATCTGATCTTTCGCCTGAATT
19624 TTTTGTTTGCCATCTGTCATTATGCTTAACCCTTTGACTGTCTGAGTAACCATCATCAGAACTTG
66 TTTTGTTTGCCATCTGTCATTATGCTTAACCCTTTGACTGTCTGAGTAACCATCATCAGAACTTG
*
19689 TATCATGGACCCTC
131 TATCATGGACCCTA
* * *
19703 TCACTGTTTCGATCCCGTTTGAAGCTTGAGGAGTGCCTCCGTCTATCTGATCTTTCGTCTGGATT
1 TCACTGCTTCGATCCCGTTTGAAGCTTGAGGAGTGCCTCCGTCTATCTGATCTTTCGCCTGAATT
* *
19768 TTTTGTTTGCCATCTGTCATTCTGCTTAACCCTTTGACTATCTGAGTAACCATCATCAGAACTTG
66 TTTTGTTTGCCATCTGTCATTATGCTTAACCCTTTGACTGTCTGAGTAACCATCATCAGAACTTG
19833 TATCATGGACCCTA
131 TATCATGGACCCTA
*
19847 TCACTGCTTCGATCCCGTTTGAAGCTT--GCA----CTCCGTCTATCTGATCTTTCGCCTGAATT
1 TCACTGCTTCGATCCCGTTTGAAGCTTGAGGAGTGCCTCCGTCTATCTGATCTTTCGCCTGAATT
* * *
19906 TTTTGTTTGCCATCTTTCATTATGCTTAACCTTTTGACTGTCAGAGTAACCATCATCAGAACTTG
66 TTTTGTTTGCCATCTGTCATTATGCTTAACCCTTTGACTGTCTGAGTAACCATCATCAGAACTTG
19971 TATCATGGACCCTA
131 TATCATGGACCCTA
* * * *
19985 TCACTGTTTCGATACCGTTTGAAGCTTGAGGAGTGCCTCCGTCTATCTGATCTTTCACCTGGATT
1 TCACTGCTTCGATCCCGTTTGAAGCTTGAGGAGTGCCTCCGTCTATCTGATCTTTCGCCTGAATT
* *
20050 TTTTGTTTGCCATCTATCATTATGCTTAACCCTTTGACTGTCTGAGTAACCATTATCAGAACTTG
66 TTTTGTTTGCCATCTGTCATTATGCTTAACCCTTTGACTGTCTGAGTAACCATCATCAGAACTTG
20115 TATCATGGACCCTA
131 TATCATGGACCCTA
* * * * * *
20129 TCACTGCTTCGATCCCGTTTGAAGCTT--GCA----CTCCGTTTATCTGATCTTCCACCTAAATC
1 TCACTGCTTCGATCCCGTTTGAAGCTTGAGGAGTGCCTCCGTCTATCTGATCTTTCGCCTGAATT
** * * * * ** * *
20188 TTTTGTTTGCTTTCTGTCATTACGCCTAAACCTTTCACTGTCCAAGTAACCTTCATCAGAACTGG
66 TTTTGTTTGCCATCTGTCATTATGCTTAACCCTTTGACTGTCTGAGTAACCATCATCAGAACTTG
20253 TATCA
131 TATCA
20258 AAGATTCTCC
Statistics
Matches: 502, Mismatches: 44, Indels: 21
0.89 0.08 0.04
Matches are distributed among these distances:
138 208 0.41
140 2 0.00
141 37 0.07
142 5 0.01
144 250 0.50
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38
Consensus pattern (144 bp):
TCACTGCTTCGATCCCGTTTGAAGCTTGAGGAGTGCCTCCGTCTATCTGATCTTTCGCCTGAATT
TTTTGTTTGCCATCTGTCATTATGCTTAACCCTTTGACTGTCTGAGTAACCATCATCAGAACTTG
TATCATGGACCCTA
Found at i:19955 original size:282 final size:281
Alignment explanation
Indices: 19562--20294 Score: 1094
Period size: 282 Copynumber: 2.6 Consensus size: 281
19552 CTGGATTCTC
* *
19562 TCACTGCTTCGATCCCGTTTGAAGCTTGAGGAGTGCC-TCCTATCTGATCTTTCGCCTGAATTTT
1 TCACTGCTTCGATCCCGTTTGAAGCTT--GCACT-CCGT-CTATCTGATCTTTCGCCTGAATTTT
*
19626 TTGTTTGCCATCTGTCATTATGCTTAACCCTTTGACTGTCTGAGTAACCATCATCAGAACTTGTA
62 TTGTTTGCCATCTGTCATTATGCTTAA-CCTTTGACTGTCAGAGTAACCATCATCAGAACTTGTA
19691 TCATGGACCCTCTCACTGTTTCGATCCCGTTTGAAGCTTGAGGAGTGCCTCCGTCTATCTGATCT
126 TCATGGACCCTCTCACTGTTTCGATCCCGTTTGAAGCTTGAGGAGTGCCTCCGTCTATCTGATCT
** * *
19756 TTCGTCTGGATTTTTTGTTTGCCATCTGTCATTCTGCTTAACCCTTTGACTATCTGAGTAACCAT
191 TTCACCTGGATTTTTTGTTTGCCATCTATCATTATGCTTAACCCTTTGACTATCTGAGTAACCAT
19821 CATCAGAACTTGTATCATGGACCCTA
256 CATCAGAACTTGTATCATGGACCCTA
19847 TCACTGCTTCGATCCCGTTTGAAGCTTGCACTCCGTCTATCTGATCTTTCGCCTGAATTTTTTGT
1 TCACTGCTTCGATCCCGTTTGAAGCTTGCACTCCGTCTATCTGATCTTTCGCCTGAATTTTTTGT
*
19912 TTGCCATCTTTCATTATGCTTAACCTTTTGACTGTCAGAGTAACCATCATCAGAACTTGTATCAT
66 TTGCCATCTGTCATTATGCTTAACC-TTTGACTGTCAGAGTAACCATCATCAGAACTTGTATCAT
* *
19977 GGACCCTATCACTGTTTCGATACCGTTTGAAGCTTGAGGAGTGCCTCCGTCTATCTGATCTTTCA
130 GGACCCTCTCACTGTTTCGATCCCGTTTGAAGCTTGAGGAGTGCCTCCGTCTATCTGATCTTTCA
* *
20042 CCTGGATTTTTTGTTTGCCATCTATCATTATGCTTAACCCTTTGACTGTCTGAGTAACCATTATC
195 CCTGGATTTTTTGTTTGCCATCTATCATTATGCTTAACCCTTTGACTATCTGAGTAACCATCATC
20107 AGAACTTGTATCATGGACCCTA
260 AGAACTTGTATCATGGACCCTA
* * * * *
20129 TCACTGCTTCGATCCCGTTTGAAGCTTGCACTCCGTTTATCTGATCTTCCACCTAAATCTTTTGT
1 TCACTGCTTCGATCCCGTTTGAAGCTTGCACTCCGTCTATCTGATCTTTCGCCTGAATTTTTTGT
** * * * * *
20194 TTGCTTTCTGTCATTACGCCTAAACCTTTCACTGTCCA-AGTAACCTTCATCAGAACTGGTATCA
66 TTGCCATCTGTCATTATG-CTTAACCTTTGACTGT-CAGAGTAACCATCATCAGAACTTGTATCA
** ** * *
20258 AAGATTCTCCCACTGTTTTGATCCCGTTTTGAA-CTTG
129 TGGACCCTCTCACTGTTTCGATCCCG-TTTGAAGCTTG
20295 TGCTCTGTCT
Statistics
Matches: 410, Mismatches: 33, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
281 2 0.00
282 363 0.89
283 18 0.04
285 27 0.07
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38
Consensus pattern (281 bp):
TCACTGCTTCGATCCCGTTTGAAGCTTGCACTCCGTCTATCTGATCTTTCGCCTGAATTTTTTGT
TTGCCATCTGTCATTATGCTTAACCTTTGACTGTCAGAGTAACCATCATCAGAACTTGTATCATG
GACCCTCTCACTGTTTCGATCCCGTTTGAAGCTTGAGGAGTGCCTCCGTCTATCTGATCTTTCAC
CTGGATTTTTTGTTTGCCATCTATCATTATGCTTAACCCTTTGACTATCTGAGTAACCATCATCA
GAACTTGTATCATGGACCCTA
Found at i:20281 original size:138 final size:138
Alignment explanation
Indices: 19361--20294 Score: 904
Period size: 138 Copynumber: 6.7 Consensus size: 138
19351 TCGCTTTCTA
*** * ** * *
19361 TCATTATGCTTGCTCCTTCGACTGTCTAAGTAATATTCATCAGAACTGGTATCATGGATTCC-CT
1 TCATTATGCTTAAACCTTTGACTGTCTAAGTAACCTTCATCAGAACTTGTATCATGGA-CCCTCT
* *
19425 CACTCTTTTGATCCCGTTTGAAGCTTG-AGCTCCG-CATATCTGATC-TTCTGCCT-AATTTTTT
65 CACTGTTTCGATCCCGTTTGAAGCTTGCA-CTCCGTC-TATCTGATCTTTC-GCCTGAA-TTTTT
* **
19486 TGTTCGCTTTCTG
126 TGTTTGCCATCTG
* * ** ** * * **
19499 TCATTATGCTCGATA-CTTTGACCATAC-AAGTAGTCTTCATCA-AGACTAGTATCCTGGATTCT
1 TCATTATGCT-TAAACCTTTGACTGT-CTAAGTAACCTTCATCAGA-ACTTGTATCATGGACCCT
* * *
19561 CTCACTGCTTCGATCCCGTTTGAAGCTTGAGGAGTGCC-TCCTATCTGATCTTTCGCCTGAATTT
63 CTCACTGTTTCGATCCCGTTTGAAGCTT--GCACT-CCGT-CTATCTGATCTTTCGCCTGAATTT
19625 TTTGTTTGCCATCTG
124 TTTGTTTGCCATCTG
* * *
19640 TCATTATGCTTAACCCTTTGACTGTCTGAGTAACCATCATCAGAACTTGTATCATGGACCCTCTC
1 TCATTATGCTTAAACCTTTGACTGTCTAAGTAACCTTCATCAGAACTTGTATCATGGACCCTCTC
* * *
19705 ACTGTTTCGATCCCGTTTGAAGCTTGAGGAGTGCCTCCGTCTATCTGATCTTTCGTCTGGATTTT
66 ACTGTTTCGATCCCGTTTGAAGCTT--GCA----CTCCGTCTATCTGATCTTTCGCCTGAATTTT
19770 TTGTTTGCCATCTG
125 TTGTTTGCCATCTG
* * * * * *
19784 TCATTCTGCTTAACCCTTTGACTATCTGAGTAACCATCATCAGAACTTGTATCATGGACCCTATC
1 TCATTATGCTTAAACCTTTGACTGTCTAAGTAACCTTCATCAGAACTTGTATCATGGACCCTCTC
*
19849 ACTGCTTCGATCCCGTTTGAAGCTTGCACTCCGTCTATCTGATCTTTCGCCTGAATTTTTTGTTT
66 ACTGTTTCGATCCCGTTTGAAGCTTGCACTCCGTCTATCTGATCTTTCGCCTGAATTTTTTGTTT
*
19914 GCCATCTT
131 GCCATCTG
* *
19922 TCATTATGCTT-AACCTTTTGACTGTC-AGAGTAACCATCATCAGAACTTGTATCATGGACCCTA
1 TCATTATGCTTAAACC-TTTGACTGTCTA-AGTAACCTTCATCAGAACTTGTATCATGGACCCTC
* * * *
19985 TCACTGTTTCGATACCGTTTGAAGCTTGAGGAGTGCCTCCGTCTATCTGATCTTTCACCTGGATT
64 TCACTGTTTCGATCCCGTTTGAAGCTT--GCA----CTCCGTCTATCTGATCTTTCGCCTGAATT
*
20050 TTTTGTTTGCCATCTA
123 TTTTGTTTGCCATCTG
* * *
20066 TCATTATGCTTAACCCTTTGACTGTCTGAGTAACCATT-ATCAGAACTTGTATCATGGACCCTAT
1 TCATTATGCTTAAACCTTTGACTGTCTAAGTAACC-TTCATCAGAACTTGTATCATGGACCCTCT
* * * * * *
20130 CACTGCTTCGATCCCGTTTGAAGCTTGCACTCCGTTTATCTGATCTTCCACCTAAATCTTTTGTT
65 CACTGTTTCGATCCCGTTTGAAGCTTGCACTCCGTCTATCTGATCTTTCGCCTGAATTTTTTGTT
**
20195 TGCTTTCTG
130 TGCCATCTG
* * * * * ** ** *
20204 TCATTACGCCTAAACCTTTCACTGTCCAAGTAACCTTCATCAGAACTGGTATCAAAGATTCTCCC
1 TCATTATGCTTAAACCTTTGACTGTCTAAGTAACCTTCATCAGAACTTGTATCATGGACCCTCTC
*
20269 ACTGTTTTGATCCCGTTTTGAA-CTTG
66 ACTGTTTCGATCCCG-TTTGAAGCTTG
20295 TGCTCTGTCT
Statistics
Matches: 680, Mismatches: 83, Indels: 66
0.82 0.10 0.08
Matches are distributed among these distances:
137 8 0.01
138 291 0.43
139 7 0.01
140 6 0.01
141 106 0.16
142 11 0.02
144 245 0.36
145 6 0.01
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.38
Consensus pattern (138 bp):
TCATTATGCTTAAACCTTTGACTGTCTAAGTAACCTTCATCAGAACTTGTATCATGGACCCTCTC
ACTGTTTCGATCCCGTTTGAAGCTTGCACTCCGTCTATCTGATCTTTCGCCTGAATTTTTTGTTT
GCCATCTG
Found at i:20366 original size:138 final size:136
Alignment explanation
Indices: 20079--20681 Score: 441
Period size: 138 Copynumber: 4.4 Consensus size: 136
20069 TTATGCTTAA
* ** * * ** *
20079 CCCTTTGACTGTCTGAGTAACCATT-ATCAGAACTTGTATCATGGACCCTATCACTGCTTCGATC
1 CCCTCTGACTGTCCAAGTAACC-TTCATCAGAACTGGTATCAAGGATTCTCTCACTGCTTCGATC
* ** * ** * * * * *
20143 CCGTTTGAAGCTTGCACTCCGTTTATCTGATCTTCCACCTAAATCTTTTGTTTGCTT-TCTGTCA
65 CCGTTTTAA-CTTGTGCTCTGCCTCTCTGACCTTCCATCTAAAACTTTTGCTTG-TTCTCTGTCA
** **
20207 TTACGCCTAA
128 TTA-TTCTTG
* * * * * * *
20217 ACCTTTCACTGTCCAAGTAACCTTCATCAGAACTGGTATCAAAGATTCTCCCACTGTTTTGATCC
1 CCCTCTGACTGTCCAAGTAACCTTCATCAGAACTGGTATCAAGGATTCTCTCACTGCTTCGATCC
* * * * * *
20282 CGTTTTGAACTTGTGCTCTGTCTCTCTGACCTTCCATCTATAGCATTTGCCTGTTTTCTGTCATT
66 CGTTTT-AACTTGTGCTCTGCCTCTCTGACCTTCCATCTAAAACTTTTGCTTGTTCTCTGTCATT
20347 ATTCTTG
130 ATTCTTG
* * *
20354 CTCCTCTGACTGTCTGAA-TAACCTTCATCAGAGCTGGTAT-AATGGATTCTCTTA-TGGCTTCG
1 C-CCTCTGACTGTC-CAAGTAACCTTCATCAGAACTGGTATCAA-GGATTCTCTCACT-GCTTCG
* ** * * *
20416 A-CACTGTTTTAAGCTTGTAATCTGCCTCTCTGATCTCCCATCTAAAATTTTTGCTTGTTCTCTG
62 ATC-CCGTTTTAA-CTTGTGCTCTGCCTCTCTGACCTTCCATCTAAAACTTTTGCTTGTTCTCTG
20480 TCATTATTCTTG
125 TCATTATTCTTG
* ** * * * * *
20492 CCC-CTTCGACAGTCTGAGTAACTTTCATCAGAACTGGTGTCATGGACTCTCTCACTCCTTCGAT
1 CCCTC-T-GACTGTCCAAGTAACCTTCATCAGAACTGGTATCAAGGATTCTCTCACTGCTTCGAT
* * *
20556 CCCATTTTAAACTTGTGCTATGCCTGC-CTGACCTTCCATCTAAAACTTTTGTTTGTTCTCTGTC
64 CCCGTTTT-AACTTGTGCTCTGCCT-CTCTGACCTTCCATCTAAAACTTTTGCTTGTTCTCTGTC
20620 ATTATTCTTG
127 ATTATTCTTG
** * * *
20630 CCC-CTTTCGTAGTCCAAGTAACCTCCATCAGAACTTGTATCATGGATTCTCT
1 CCCTCTGAC-T-GTCCAAGTAACCTTCATCAGAACTGGTATCAAGGATTCTCT
20682 GATCCCATTT
Statistics
Matches: 365, Mismatches: 81, Indels: 38
0.75 0.17 0.08
Matches are distributed among these distances:
136 2 0.01
137 17 0.05
138 336 0.92
139 10 0.03
ACGTcount: A:0.20, C:0.27, G:0.14, T:0.39
Consensus pattern (136 bp):
CCCTCTGACTGTCCAAGTAACCTTCATCAGAACTGGTATCAAGGATTCTCTCACTGCTTCGATCC
CGTTTTAACTTGTGCTCTGCCTCTCTGACCTTCCATCTAAAACTTTTGCTTGTTCTCTGTCATTA
TTCTTG
Found at i:21410 original size:27 final size:26
Alignment explanation
Indices: 21360--21411 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
21350 AATTAGCATA
21360 AAAAATAAAATGCAAGACGATTTTTC
1 AAAAATAAAATGCAAGACGATTTTTC
*
21386 AAAAATAAAATGCAAGATGATTTTTC
1 AAAAATAAAATGCAAGACGATTTTTC
21412 TGATCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (26 bp):
AAAAATAAAATGCAAGACGATTTTTC
Found at i:29140 original size:16 final size:18
Alignment explanation
Indices: 29109--29141 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
29099 TTAACAAGCT
29109 TTACTCTGTGAATTGTGA
1 TTACTCTGTGAATTGTGA
29127 TTACTCT-T-AATTGTG
1 TTACTCTGTGAATTGTG
29142 CTGCAGCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.48
Consensus pattern (18 bp):
TTACTCTGTGAATTGTGA
Found at i:35808 original size:42 final size:41
Alignment explanation
Indices: 35709--35830 Score: 185
Period size: 41 Copynumber: 3.0 Consensus size: 41
35699 AAACACACCT
* *
35709 ATTTGATAGATAG--TATCTCTTTAATTAAAGAAAAAATCA
1 ATTTGATAGATAGTATATCTATTTATTTAAAGAAAAAATCA
35748 ATTTGATAGATAGTATATCTATTTATTTAAAGAAAAAATCA
1 ATTTGATAGATAGTATATCTATTTATTTAAAGAAAAAATCA
* *
35789 ATTTGATAGATGATTATATCTATTTATTTAAAGGAAAAATCA
1 ATTTGATAGAT-AGTATATCTATTTATTTAAAGAAAAAATCA
35831 TTCGATTAAT
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
39 13 0.17
41 35 0.46
42 28 0.37
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.39
Consensus pattern (41 bp):
ATTTGATAGATAGTATATCTATTTATTTAAAGAAAAAATCA
Found at i:41163 original size:29 final size:30
Alignment explanation
Indices: 41095--41167 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
41085 CTCATAGCAG
* * *
41095 AAGGGTTTATTTGGCCAAAATTGATAGTTC
1 AAGGGCTTATTTGACCAAAATTGAAAGTTC
41125 AAGGGCTTATTTGACCAAAATT-AAAGTT-
1 AAGGGCTTATTTGACCAAAATTGAAAGTTC
*
41153 TAGGGACTTATTTGA
1 AAGGG-CTTATTTGA
41168 TTGTTGATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 4 0.11
29 14 0.37
30 20 0.53
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.36
Consensus pattern (30 bp):
AAGGGCTTATTTGACCAAAATTGAAAGTTC
Found at i:54849 original size:2 final size:2
Alignment explanation
Indices: 54844--54869 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54834 AAAAAATAAA
54844 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
54870 GTAAGTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55490 original size:14 final size:14
Alignment explanation
Indices: 55471--55498 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55461 TAACTCTTCG
55471 TTCATATGACGCAA
1 TTCATATGACGCAA
55485 TTCATATGACGCAA
1 TTCATATGACGCAA
55499 CAAGATGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (14 bp):
TTCATATGACGCAA
Found at i:67627 original size:17 final size:15
Alignment explanation
Indices: 67605--67642 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
67595 ATTTTCTCAG
67605 TTCTTTTCTTCTTCTTT
1 TTCTTTTCTT-TT-TTT
67622 TTCTTTTCTTTTTTT
1 TTCTTTTCTTTTTTT
67637 TT-TTTT
1 TTCTTTT
67643 GTTTATGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 5 0.24
16 2 0.10
17 10 0.48
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTCTTTTCTTTTTTT
Found at i:82553 original size:147 final size:147
Alignment explanation
Indices: 82351--82646 Score: 466
Period size: 147 Copynumber: 2.0 Consensus size: 147
82341 GTGTTAACTA
* * * ** *
82351 TCGGTTCAACTGGGTACCGGTGGCCTCACCGATATGGCCTCTGGTCCGGTATTTTATTCATTGGT
1 TCGGTTCAACCGGATACCGCTGGCCTCACCGATATCACCTCCGGTCCGGTATTTTATTCATTGGT
* * * *
82416 CAAATTTCTATTCATTAACCTTCCAAAATCAAGGTTAAGTCGTAATTGAAGAGTTGTTTAGGGGG
66 CAAATTTCTATTCATTAACCTTCCAAAATCAAGATTAAGTCATAATTGAAGAGTTATTTAAGGGG
82481 TTGTGAAGTATGTCATT
131 TTGTGAAGTATGTCATT
* * *
82498 TCGGTTCAACCGGATACCGCTGGCCTCATCGGTATCATCTCCGGTCCGGTATTTTATTCATTGGT
1 TCGGTTCAACCGGATACCGCTGGCCTCACCGATATCACCTCCGGTCCGGTATTTTATTCATTGGT
*
82563 CAAATTTCTATTTATTAACCTTCCAAAATCAAGATTAAGTCATAATTGAAGAGTTATTTAAGGGG
66 CAAATTTCTATTCATTAACCTTCCAAAATCAAGATTAAGTCATAATTGAAGAGTTATTTAAGGGG
82628 TTGTGAAGTATGTCATT
131 TTGTGAAGTATGTCATT
82645 TC
1 TC
82647 TCATCATTAT
Statistics
Matches: 135, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
147 135 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (147 bp):
TCGGTTCAACCGGATACCGCTGGCCTCACCGATATCACCTCCGGTCCGGTATTTTATTCATTGGT
CAAATTTCTATTCATTAACCTTCCAAAATCAAGATTAAGTCATAATTGAAGAGTTATTTAAGGGG
TTGTGAAGTATGTCATT
Found at i:83929 original size:7 final size:7
Alignment explanation
Indices: 83917--83943 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
83907 TTTAGATCTG
83917 CTTTCTA
1 CTTTCTA
83924 CTTTCTA
1 CTTTCTA
83931 CTTTCTA
1 CTTTCTA
83938 CTTTCT
1 CTTTCT
83944 TTTCTTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.30, G:0.00, T:0.59
Consensus pattern (7 bp):
CTTTCTA
Found at i:95455 original size:25 final size:25
Alignment explanation
Indices: 95426--95489 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
95416 ATCGAATTTT
*
95426 TCTAATTAGGTTTTTTTTGGCCAAA
1 TCTAATTAGGGTTTTTTTGGCCAAA
95451 TCTAATTAGGGTTTTTTTGGCCAAA
1 TCTAATTAGGGTTTTTTTGGCCAAA
*
95476 CCTAATTAGGGTTT
1 TCTAATTAGGGTTT
95490 GATCTTGATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.45
Consensus pattern (25 bp):
TCTAATTAGGGTTTTTTTGGCCAAA
Found at i:103671 original size:5 final size:5
Alignment explanation
Indices: 103661--103685 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
103651 ATGATGGATG
103661 GGGTT GGGTT GGGTT GGGTT GGGTT
1 GGGTT GGGTT GGGTT GGGTT GGGTT
103686 ATCTTTGCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (5 bp):
GGGTT
Found at i:112257 original size:35 final size:35
Alignment explanation
Indices: 112217--112286 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
112207 TTTAAATGCC
112217 AAACTCCTTTTATCATCTTATTACCACCTTGAAGA
1 AAACTCCTTTTATCATCTTATTACCACCTTGAAGA
*
112252 AAACTCCTTTTATCATCTTATTAGCACCTTGAAGA
1 AAACTCCTTTTATCATCTTATTACCACCTTGAAGA
112287 TTTGTTGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.37
Consensus pattern (35 bp):
AAACTCCTTTTATCATCTTATTACCACCTTGAAGA
Found at i:114100 original size:27 final size:27
Alignment explanation
Indices: 114044--114100 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
114034 GGCATTCCAG
*
114044 AGTTAGGTAACCTAAGGATGACTATCA
1 AGTTAGGTAACCTAAGGATGACGATCA
114071 AGTTAGGTAACCTAAGGATGACAGAT-A
1 AGTTAGGTAACCTAAGGATGAC-GATCA
114098 AGT
1 AGT
114101 CTATGAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 26 0.93
28 2 0.07
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.25
Consensus pattern (27 bp):
AGTTAGGTAACCTAAGGATGACGATCA
Done.