Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024251.1 Corchorus olitorius cultivar O-4 contig24284, 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: 60952
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:284 original size:2 final size:2
Alignment explanation
Indices: 277--315 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
267 TATTCTTTCT
277 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
316 TTCTTTCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:973 original size:63 final size:63
Alignment explanation
Indices: 870--1237 Score: 559
Period size: 63 Copynumber: 5.9 Consensus size: 63
860 TATCTGTTTC
* *
870 AATCTTGTTTTATTTTAAAATCCTGCTCGAGGTCTCTGGTCGACAGTTTTCCATTTCAATTCAA
1 AATC-TGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCATTTCAATTCAA
* *
934 AATTTGTTTCATTATAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCATTTCAATTCAA
1 AATCTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCATTTCAATTCAA
*
997 AATCTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGATCGAGAGTTTTCCATTTCAATTCAA
1 AATCTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCATTTCAATTCAA
*
1060 AATCAGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCATTTCAATTCAA
1 AATCTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCATTTCAATTCAA
* *
1123 AATCTGTTTCATTTTAAAAATCCTGCGCGAGGTCTCTGGTCGAGAGTTTT---TTGC--TTCAGA
1 AATCTGTTTCATTTT-AAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCATTTCAATTCA-A
* **
1183 AATCTTGTTTAATTTTAAAATCCTGCTCGAGGTCTCTAATCGAGAGTTTT-CATTT
1 AATC-TGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCATTT
1238 TAAAGTCTAA
Statistics
Matches: 282, Mismatches: 17, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
59 4 0.01
60 36 0.13
61 13 0.05
62 2 0.01
63 191 0.68
64 36 0.13
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.40
Consensus pattern (63 bp):
AATCTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCATTTCAATTCAA
Found at i:1045 original size:126 final size:127
Alignment explanation
Indices: 803--1237 Score: 594
Period size: 126 Copynumber: 3.5 Consensus size: 127
793 TCTGTTTCTG
* * * * * **
803 TTTCAATTCCAAGTCTTGTTTCGTTTTAAAATCCTGTTCGAGGTCTCTGGTCGAGAG-TATCTGT
1 TTTCAATTCAAAATCTTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCAT
* *
867 TTCAA-TC----T-TGTTTTATTTTAAAATCCTGCTCGAGGTCTCTGGTCGACAGTTTTCCA
66 TTCAATTCAAAATCTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCA
*
923 TTTCAATTCAAAAT-TTGTTTCATTATAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCAT
1 TTTCAATTCAAAATCTTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCAT
*
987 TTCAATTCAAAATCTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGATCGAGAGTTTTCCA
66 TTCAATTCAAAATCTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCA
*
1049 TTTCAATTCAAAATC-AGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCAT
1 TTTCAATTCAAAATCTTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCAT
*
1113 TTCAATTCAAAATCTGTTTCATTTTAAAAATCCTGCGCGAGGTCTCTGGTCGAGAGTTTT---
66 TTCAATTCAAAATCTGTTTCATTTT-AAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCA
* * **
1173 TTGC--TTCAGAAATCTTGTTTAATTTTAAAATCCTGCTCGAGGTCTCTAATCGAGAGTTTT-CA
1 TTTCAATTCA-AAATCTTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCA
1235 TTT
65 TTT
1238 TAAAGTCTAA
Statistics
Matches: 284, Mismatches: 20, Indels: 19
0.88 0.06 0.06
Matches are distributed among these distances:
119 39 0.14
120 21 0.07
121 2 0.01
122 4 0.01
123 10 0.04
124 44 0.15
125 1 0.00
126 131 0.46
127 32 0.11
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (127 bp):
TTTCAATTCAAAATCTTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCAT
TTCAATTCAAAATCTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCA
Found at i:1117 original size:189 final size:182
Alignment explanation
Indices: 803--1237 Score: 585
Period size: 189 Copynumber: 2.4 Consensus size: 182
793 TCTGTTTCTG
* * * * * * **
803 TTTCAATTCCAAGTCTTGTTTCGTTTTAAAATCCTGTTCGAGGTCTCTGGTCGAGAG-TATCTGT
1 TTTCAATTCAAAATCTTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGATCGAGAGTTTTCCAT
* *
867 TTCAATCTTGTTTTATTTTAAAATCCTGCTCGAGGTCTCTGGTCGACAGTTTTCCATTTCAATTC
66 TTCAATCTAGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGACAGTTTTCCATTTCAATTC
* *
932 AAAATTTGTTTCATTAT-AAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTT
131 AAAATCTGTTTCATTATAAAAATCCTGCGCGAGGTCTCTGGTCGAGAGTTTT
983 CCATTTCAATTCAAAATC-TGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGATCGAGAGTTTTC
1 ---TTTCAATTCAAAATCTTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGATCGAGAGTTTTC
*
1047 CATTTCAATTCAAAATCAGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCA
63 CATTTCAA-TC----T-AGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGACAGTTTTCCA
*
1112 TTTCAATTCAAAATCTGTTTCATTTTAAAAATCCTGCGCGAGGTCTCTGGTCGAGAGTTTT
122 TTTCAATTCAAAATCTGTTTCATTATAAAAATCCTGCGCGAGGTCTCTGGTCGAGAGTTTT
* * *
1173 TTGC--TTCAGAAATCTTGTTTAATTTTAAAATCCTGCTCGAGGTCTCTAATCGAGAGTTTT-CA
1 TTTCAATTCA-AAATCTTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGATCGAGAGTTTTCCA
1235 TTT
65 TTT
1238 TAAAGTCTAA
Statistics
Matches: 225, Mismatches: 17, Indels: 17
0.87 0.07 0.07
Matches are distributed among these distances:
182 38 0.17
183 22 0.10
184 2 0.01
185 4 0.02
186 10 0.04
187 46 0.20
188 1 0.00
189 69 0.31
190 33 0.15
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (182 bp):
TTTCAATTCAAAATCTTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGATCGAGAGTTTTCCAT
TTCAATCTAGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGACAGTTTTCCATTTCAATTC
AAAATCTGTTTCATTATAAAAATCCTGCGCGAGGTCTCTGGTCGAGAGTTTT
Found at i:1294 original size:189 final size:185
Alignment explanation
Indices: 870--1297 Score: 549
Period size: 189 Copynumber: 2.3 Consensus size: 185
860 TATCTGTTTC
* *
870 AATCTTGTTTTATTTTAAAATCCTGCTCGAGGTCTCTGGTCGACAGTTTTCCATTTCAATTCAAA
1 AATCTTGTCTT-TTTT-AAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCATTTCAATTCAAA
* * *
935 ATTTGTTTCATTATAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCATTTCAATTCAAAAT
64 ATCTGTTTCATTATAAAATCCTGCGCGAGGTCTCTGGTCGAGAGTTTT-C-TTGC-ATTCAAAAT
* * * *
1000 CTGTTTCATTTTAAAATCCTGCTCGAGGTCTCTGATCGAGAGTTTTCCATTTCAATTCAA
126 CTGTTTAATTTTAAAATCCTGCTCGAGGTCTCTAATCGAGAGTTTTCCATTTAAATTAAA
* *
1060 AATCAGTT-TCATTTTAAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCATTTCAATTCAAA
1 AATC--TTGTCTTTTTTAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCATTTCAATTCAAA
*
1124 ATCTGTTTCATTTTAAAAATCCTGCGCGAGGTCTCTGGTCGAGAGTTTT-TTGC-TTCAGAAATC
64 ATCTGTTTCATTAT-AAAATCCTGCGCGAGGTCTCTGGTCGAGAGTTTTCTTGCATTCA-AAATC
1187 TTGTTTAATTTTAAAATCCTGCTCGAGGTCTCTAATCGAGAGTTTT-CATTTTAAAGTCTAAA
127 -TGTTTAATTTTAAAATCCTGCTCGAGGTCTCTAATCGAGAGTTTTCCA-TTTAAA-T-TAAA
* * * * *
1249 AATCTTGTCTTGTTTTAAATCTTGTTTGAGGCCTCTGTTCGAGAGTTTT
1 AATCTTGTCTT-TTTTAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTT
1298 GTTTCAAAAT
Statistics
Matches: 209, Mismatches: 19, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
185 4 0.02
186 7 0.03
187 53 0.25
188 4 0.02
189 97 0.46
190 40 0.19
191 2 0.01
192 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.41
Consensus pattern (185 bp):
AATCTTGTCTTTTTTAAATCCTGCTCGAGGTCTCTGGTCGAGAGTTTTCCATTTCAATTCAAAAT
CTGTTTCATTATAAAATCCTGCGCGAGGTCTCTGGTCGAGAGTTTTCTTGCATTCAAAATCTGTT
TAATTTTAAAATCCTGCTCGAGGTCTCTAATCGAGAGTTTTCCATTTAAATTAAA
Found at i:1649 original size:63 final size:66
Alignment explanation
Indices: 1574--1713 Score: 205
Period size: 63 Copynumber: 2.2 Consensus size: 66
1564 TACATCCAAT
* *
1574 TTACTTTCATTCATATTAATCATATTAAGCATATTCATGTTCA-TT-TC-TTAAACATGCTCATA
1 TTACTTTCATTCATATTAATCACATTAAGCATAATCATGTTCATTTCTCATTAAACATGCTCATA
1636 C
66 C
* * *
1637 TTACTTTCATTCATATTAATCACATTAAGCATAATCTTGTTCATTTCTCATTAACCATGTTCATA
1 TTACTTTCATTCATATTAATCACATTAAGCATAATCATGTTCATTTCTCATTAAACATGCTCATA
*
1702 T
66 C
1703 TTACTTTCATT
1 TTACTTTCATT
1714 TGCCCATTAC
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
63 40 0.59
64 2 0.03
65 2 0.03
66 24 0.35
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.46
Consensus pattern (66 bp):
TTACTTTCATTCATATTAATCACATTAAGCATAATCATGTTCATTTCTCATTAAACATGCTCATA
C
Found at i:4377 original size:12 final size:12
Alignment explanation
Indices: 4360--4404 Score: 90
Period size: 12 Copynumber: 3.8 Consensus size: 12
4350 ATTAACTACT
4360 TCAGTTTGACCA
1 TCAGTTTGACCA
4372 TCAGTTTGACCA
1 TCAGTTTGACCA
4384 TCAGTTTGACCA
1 TCAGTTTGACCA
4396 TCAGTTTGA
1 TCAGTTTGA
4405 GGATGACAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (12 bp):
TCAGTTTGACCA
Found at i:14363 original size:15 final size:15
Alignment explanation
Indices: 14339--14371 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
14329 CGACTTGAGC
14339 TTGGAATATTTGTAG
1 TTGGAATATTTGTAG
*
14354 TTGGAGTATTTGTAG
1 TTGGAATATTTGTAG
14369 TTG
1 TTG
14372 CATTTTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.48
Consensus pattern (15 bp):
TTGGAATATTTGTAG
Found at i:15410 original size:19 final size:19
Alignment explanation
Indices: 15386--15459 Score: 103
Period size: 19 Copynumber: 3.8 Consensus size: 19
15376 TTAGTAACTG
15386 TACAGATGAGATTATACTT
1 TACAGATGAGATTATACTT
*
15405 TACAGATTAGATTATACTT
1 TACAGATGAGATTATACTT
* *
15424 TACAGATTAGATTAGGTACTG
1 TACAGATGAGATTA--TACTT
15445 TACAGATGAGATTAT
1 TACAGATGAGATTAT
15460 TAGAGCAGTG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 33 0.66
21 17 0.34
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (19 bp):
TACAGATGAGATTATACTT
Found at i:15656 original size:3 final size:3
Alignment explanation
Indices: 15643--15683 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
15633 TATATATATA
15643 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
15684 ATATATCATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:16093 original size:21 final size:20
Alignment explanation
Indices: 16065--16126 Score: 97
Period size: 20 Copynumber: 3.0 Consensus size: 20
16055 ATCGCTGCTC
16065 TAATAATCTCATCTGTACAG
1 TAATAATCTCATCTGTACAG
* *
16085 TACCTAATCTAATCTGTACAG
1 TA-ATAATCTCATCTGTACAG
16106 TAATAATCTCATCTGTACAG
1 TAATAATCTCATCTGTACAG
16126 T
1 T
16127 TACTAAACAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 19 0.51
21 18 0.49
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.35
Consensus pattern (20 bp):
TAATAATCTCATCTGTACAG
Found at i:19808 original size:15 final size:15
Alignment explanation
Indices: 19788--19879 Score: 96
Period size: 15 Copynumber: 5.9 Consensus size: 15
19778 GGTAATGGTG
* *
19788 ATGGTGCATAAGTAA
1 ATGGTGCAGAAGTTA
19803 ATGGTGAAGCAGAAGTTA
1 ATGGT---GCAGAAGTTA
19821 ATGGTGCAGAAGTTA
1 ATGGTGCAGAAGTTA
19836 ATGGT-CAAGAAGTTA
1 ATGGTGC-AGAAGTTA
*
19851 ATGGTGAAGAAGTTA
1 ATGGTGCAGAAGTTA
* *
19866 ATGCTGAAGAAGTT
1 ATGGTGCAGAAGTT
19880 GAGGATGATG
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
14 1 0.01
15 54 0.79
18 13 0.19
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.26
Consensus pattern (15 bp):
ATGGTGCAGAAGTTA
Found at i:19839 original size:33 final size:32
Alignment explanation
Indices: 19788--19875 Score: 108
Period size: 30 Copynumber: 2.8 Consensus size: 32
19778 GGTAATGGTG
* *
19788 ATGGTGCATAAGTAAATGGTGAAGCAGAAGTTA
1 ATGGTGCAGAAGTTAATGGTGAAG-AGAAGTTA
*
19821 ATGGTGCAGAAGTTAATGGT-CA-AGAAGTTA
1 ATGGTGCAGAAGTTAATGGTGAAGAGAAGTTA
* *
19851 ATGGTGAAGAAGTTAATGCTGAAGA
1 ATGGTGCAGAAGTTAATGGTGAAGA
19876 AGTTGAGGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
30 26 0.55
31 1 0.02
32 2 0.04
33 18 0.38
ACGTcount: A:0.39, C:0.06, G:0.31, T:0.25
Consensus pattern (32 bp):
ATGGTGCAGAAGTTAATGGTGAAGAGAAGTTA
Found at i:23944 original size:43 final size:44
Alignment explanation
Indices: 23885--23979 Score: 131
Period size: 43 Copynumber: 2.2 Consensus size: 44
23875 TGCTTAGATA
*
23885 TGGACAAATCATGGGTGTCTA-AATTTATTTTGG-ATGGTTATGC
1 TGGACAAATCATGGGTGTC-AGAATTTATTTTGGAATGGTTAAGC
* *
23928 TGGACATATTATGGGTGTCAGAATTTATTTTGGATATGGTTAAGC
1 TGGACAAATCATGGGTGTCAGAATTTATTTTGGA-ATGGTTAAGC
23973 TGGACAA
1 TGGACAA
23980 GTTATGAGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
42 1 0.02
43 29 0.64
45 15 0.33
ACGTcount: A:0.27, C:0.08, G:0.26, T:0.38
Consensus pattern (44 bp):
TGGACAAATCATGGGTGTCAGAATTTATTTTGGAATGGTTAAGC
Found at i:23985 original size:45 final size:42
Alignment explanation
Indices: 23864--23985 Score: 129
Period size: 43 Copynumber: 2.8 Consensus size: 42
23854 ATGTCATGAC
* ** *
23864 TTTATTTTGGATGCTTAGATATGGACAAATCATGGGTGTCTAAA
1 TTTATTTTGGATGGTTA-AGCTGGAC-AATTATGGGTGTCTAAA
*
23908 TTTATTTTGGATGGTTATGCTGGACATATTATGGGTGTC-AGAA
1 TTTATTTTGGATGGTTAAGCTGGACA-ATTATGGGTGTCTA-AA
23951 TTTATTTTGGATATGGTTAAGCTGGACAAGTTATG
1 TTTATTTTGG--ATGGTTAAGCTGGACAA-TTATG
23986 AGTTTCAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
42 2 0.03
43 28 0.42
44 17 0.25
45 20 0.30
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.41
Consensus pattern (42 bp):
TTTATTTTGGATGGTTAAGCTGGACAATTATGGGTGTCTAAA
Found at i:25028 original size:25 final size:24
Alignment explanation
Indices: 25000--25056 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
24990 GTGGATTGTA
*
25000 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
25025 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
25049 AAA-AAATT
1 AAATAAATT
25057 CAAGGCTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:44921 original size:439 final size:440
Alignment explanation
Indices: 44097--45045 Score: 1467
Period size: 439 Copynumber: 2.2 Consensus size: 440
44087 AAATCATTTT
* * * * * *
44097 TTATTTATGAAATGATTCATATACTTTTATACTTTATGTTATTTAGTCCCTCACAATTTATGGGT
1 TTATTTATCAAATGATCCTTAGACTTTTATGCTTTATGCTATTTAGTCCCTCACAATTTATGGGT
44162 TGGACAACTAAACGTTTCAACTTTAATTCTTTTATTTTTTTTATTTTGCTTATCCGATCAAGGTG
66 TGGACAACTAAACGTTTCAACTTTAATTCTTTTA-TTTTTTTATTTTGCTTATCCGATCAAGGTG
** * * *
44227 ATTCAAGTGTCTATTAAAACGTAATTTTGTGATCTACAACTTCCATAAAGGATTCAAAACTAATT
130 ATTCAAGTGTCTATTAAAACGTAATTTCATGATCTACAACTTCCATAAAGGACTCAAAACCAAAT
* * * *
44292 TTAATGTTTTGATTTAAAAAAATGCTTTTGAAATTGTGTGGTCTTGATTGTCGGTTTATTTGATA
195 TTAATGTTTTGATTTAAAAAAATACTTTTGAAATTGTATGGTCTTGATTGTCGATCTATTTGATA
44357 TCGTATAATTTTTGTTCCACTTGTCCGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGTG
260 TCGTATAATTTTTGTTCCACTTGTCCGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGTG
* *
44422 TGATCTATGGCTTTCGTTAAGGGCTTCAAAGCTGAATTTGATTAATGAGTTTCGTGGAGGGTTCA
325 TGATCTACGGCTTTCGTTAAGGGCTTCAAAGCTGAATTTGATTAATGAGTTTCATGGAGGGTTCA
*
44487 AGAGGGAAATTTTATGTTTGGTCTCCATAAACAAATATTT-TTTTGCTGGA
390 AGAGGGAAATTTTATGTTTGATCTCCATAAACAAATATTTGTTTTGCTGGA
* *
44537 TTATTTATCAAATGATCCTTAGACTTTTGTGCTTTATGCTATTTAGTCCCTCACAATTTCTGGGT
1 TTATTTATCAAATGATCCTTAGACTTTTATGCTTTATGCTATTTAGTCCCTCACAATTTATGGGT
* * *** * *
44602 TGGACGACTGAACGTTTTGGCTTTAATTCTTTTA-TTTTTTCTTTTGCTTGTCCGATCAAGGTGA
66 TGGACAACTAAACGTTTCAACTTTAATTCTTTTATTTTTTTATTTTGCTTATCCGATCAAGGTGA
* *
44666 TTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTCCATGAAGGACTCAAAAGCCAAAT
131 TTCAAGTGTCTATTAAAACGTAATTTCATGATCTACAACTTCCATAAAGGACTCAAAA-CCAAAT
* * *
44731 TTAATGTTTTGATTTTAAAAAATACTTTTGAAATTTTATGGTCTTGATTGTCGATCTATTTGTTA
195 TTAATGTTTTGATTTAAAAAAATACTTTTGAAATTGTATGGTCTTGATTGTCGATCTATTTGATA
44796 TCGTATAATTTTATG-TCCACTTGTCCGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGT
260 TCGTATAATTTT-TGTTCCACTTGTCCGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGT
*
44860 GTGATTTACGGCTTTCGTTAAGGG-TCTCAAAGCTGAATTTGATTAATGAGTTTCATGGAGGGTT
324 GTGATCTACGGCTTTCGTTAAGGGCT-TCAAAGCTGAATTTGATTAATGAGTTTCATGGAGGGTT
* *
44924 CAAGAGGGAATTTTTATGTTTGATCTTCATAAACAAATATTTGTTTTGCTGGA
388 CAAGAGGGAAATTTTATGTTTGATCTCCATAAACAAATATTTGTTTTGCTGGA
* * * * *
44977 TTATTTATCAAATAATCCTCAGATTTTTATGCTTTATGCTATTTAATCCCTCATAA-TTATGGGT
1 TTATTTATCAAATGATCCTTAGACTTTTATGCTTTATGCTATTTAGTCCCTCACAATTTATGGGT
45041 TGGAC
66 TGGAC
45046 CATTTAATGC
Statistics
Matches: 463, Mismatches: 42, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
438 82 0.18
439 233 0.50
440 148 0.32
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.43
Consensus pattern (440 bp):
TTATTTATCAAATGATCCTTAGACTTTTATGCTTTATGCTATTTAGTCCCTCACAATTTATGGGT
TGGACAACTAAACGTTTCAACTTTAATTCTTTTATTTTTTTATTTTGCTTATCCGATCAAGGTGA
TTCAAGTGTCTATTAAAACGTAATTTCATGATCTACAACTTCCATAAAGGACTCAAAACCAAATT
TAATGTTTTGATTTAAAAAAATACTTTTGAAATTGTATGGTCTTGATTGTCGATCTATTTGATAT
CGTATAATTTTTGTTCCACTTGTCCGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGTGT
GATCTACGGCTTTCGTTAAGGGCTTCAAAGCTGAATTTGATTAATGAGTTTCATGGAGGGTTCAA
GAGGGAAATTTTATGTTTGATCTCCATAAACAAATATTTGTTTTGCTGGA
Found at i:48128 original size:56 final size:56
Alignment explanation
Indices: 48052--48163 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
48042 TAGAGTAGGC
48052 TTATGTGTTTGACAGGTTGTCAATGGATGATTAAAGGCTATATATCAGTAGGCTAA
1 TTATGTGTTTGACAGGTTGTCAATGGATGATTAAAGGCTATATATCAGTAGGCTAA
48108 TTATGTGTTTGACAGGTTGTCAATGGATGATTAAAGGCTATATATCAGTAGGCTAA
1 TTATGTGTTTGACAGGTTGTCAATGGATGATTAAAGGCTATATATCAGTAGGCTAA
48164 CATCTGCGAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (56 bp):
TTATGTGTTTGACAGGTTGTCAATGGATGATTAAAGGCTATATATCAGTAGGCTAA
Found at i:53364 original size:27 final size:27
Alignment explanation
Indices: 53303--53377 Score: 123
Period size: 27 Copynumber: 2.7 Consensus size: 27
53293 TTTCAAAATC
*
53303 CAGGGGCATTTTGGTCATTTTTTACATT
1 CAGGGGCATTTTGGTCA-TTTGTACATT
*
53331 CAAGGGCATTTTGGTCATTTGTACATT
1 CAGGGGCATTTTGGTCATTTGTACATT
53358 CAGGGGCATTTTGGTCATTT
1 CAGGGGCATTTTGGTCATTT
53378 TAAGTTCACT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
27 28 0.64
28 16 0.36
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.43
Consensus pattern (27 bp):
CAGGGGCATTTTGGTCATTTGTACATT
Done.