Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020388.1 Corchorus olitorius cultivar O-4 contig20421, 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: 77775
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:2785 original size:31 final size:31
Alignment explanation
Indices: 2723--2831 Score: 137
Period size: 31 Copynumber: 3.5 Consensus size: 31
2713 GGTATTACTG
* *
2723 ACGTGGCAATATCATGTCGAACCAAAAATGCC
1 ACGTGGCAATATCATGTTGGACC-AAAATGCC
* *
2755 ACGTGACAATTTCATGTTGGACCAAAATGCC
1 ACGTGGCAATATCATGTTGGACCAAAATGCC
* **
2786 ACGTGGCAATGTCACATTGGACCAAAATGCC
1 ACGTGGCAATATCATGTTGGACCAAAATGCC
*
2817 ACGTGGCAAGATCAT
1 ACGTGGCAATATCAT
2832 ATCAGACCAA
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
31 47 0.71
32 19 0.29
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (31 bp):
ACGTGGCAATATCATGTTGGACCAAAATGCC
Found at i:4957 original size:132 final size:130
Alignment explanation
Indices: 4704--4957 Score: 404
Period size: 132 Copynumber: 1.9 Consensus size: 130
4694 GCATAACTTG
*
4704 GTTGTGAATGGATTGTAATGAGATTCCCGATTATTGTATTCTTTGGGAAAAAAAAAGGAAAAACA
1 GTTGTGAATGGATTGTAATGAGATTCCCGATTATTGTATTCTTTGGGAAAAAAAAAAGAAAAACA
* * * *
4769 TCAAGCATAACTTGGTTCAAGTGGTTTGACGCTTGTTCCCCTTAAGCGAGGTCTCGAATTCGTGT
66 TCAAGCATAACTTGGTTCAAGTGGTTTGACACTTCTTCCACTTAAGCGAAGTCTCGAATTCGTGT
4834 GTTGTGAAT-GACTTGTAATGAGATTCCCGATTATTGTATTCTTTGGGAAAAAGAAAAAAGAAAA
1 GTTGTGAATGGA-TTGTAATGAGATTCCCGATTATTGTATTCTTTGGG-AAAA-AAAAAAGAAAA
*
4898 ACATCAAGCATAACTTGGTTCAAGTGGTTTGACACTTCTTCCATTTAAAG-GAAGTCTCGA
63 ACATCAAGCATAACTTGGTTCAAGTGGTTTGACACTTCTTCCACTT-AAGCGAAGTCTCGA
4958 GTTTGAGTCT
Statistics
Matches: 114, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
129 2 0.02
130 44 0.39
131 4 0.04
132 61 0.54
133 3 0.03
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (130 bp):
GTTGTGAATGGATTGTAATGAGATTCCCGATTATTGTATTCTTTGGGAAAAAAAAAAGAAAAACA
TCAAGCATAACTTGGTTCAAGTGGTTTGACACTTCTTCCACTTAAGCGAAGTCTCGAATTCGTGT
Found at i:10525 original size:22 final size:25
Alignment explanation
Indices: 10472--10520 Score: 89
Period size: 26 Copynumber: 1.9 Consensus size: 25
10462 ACTAGAAACT
10472 ATACCATAAATAAACTACATACCGAC
1 ATACCATAAATAAACTACATACC-AC
10498 ATACCATAAATAAACTACATACC
1 ATACCATAAATAAACTACATACC
10521 TACCAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.51, C:0.27, G:0.02, T:0.20
Consensus pattern (25 bp):
ATACCATAAATAAACTACATACCAC
Found at i:12128 original size:19 final size:19
Alignment explanation
Indices: 12085--12122 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12075 ACCATGATGA
12085 TCCTTGAGCTATATAGATC
1 TCCTTGAGCTATATAGATC
*
12104 TCCTTGAGCTATGTAGATC
1 TCCTTGAGCTATATAGATC
12123 ATCTTGGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (19 bp):
TCCTTGAGCTATATAGATC
Found at i:26994 original size:42 final size:42
Alignment explanation
Indices: 26935--27108 Score: 280
Period size: 42 Copynumber: 4.1 Consensus size: 42
26925 CCTATTGTAT
26935 AACCCAATTTCAATATTATGATATTATGTTAATGAGTAGAAA
1 AACCCAATTTCAATATTATGATATTATGTTAATGAGTAGAAA
26977 AACCCAATTTCAATATTATGATATTATGTTAATGAGTAGAAA
1 AACCCAATTTCAATATTATGATATTATGTTAATGAGTAGAAA
*
27019 AACCCAATTTCAATATTATGATATTATGTTAAAGAGTAGAAA
1 AACCCAATTTCAATATTATGATATTATGTTAATGAGTAGAAA
27061 AACCCATGCAATTTCAATA-TAT-ATTATTATGTTAATGAGTAGAAA
1 AA-CC---CAATTTCAATATTATGA-TATTATGTTAATGAGTAGAAA
27106 AAC
1 AAC
27109 AACCCAATTT
Statistics
Matches: 125, Mismatches: 2, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
42 85 0.68
43 2 0.02
44 2 0.02
45 25 0.20
46 11 0.09
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (42 bp):
AACCCAATTTCAATATTATGATATTATGTTAATGAGTAGAAA
Found at i:27127 original size:84 final size:82
Alignment explanation
Indices: 26945--27132 Score: 222
Period size: 84 Copynumber: 2.2 Consensus size: 82
26935 AACCCAATTT
* *
26945 CAATATTATGATATTATGTTAATGAGTAGAAAAACCCAATTTCAATATTATGATATTATGTTAAT
1 CAATATTATAATATTATGTTAAAGAGTAGAAAAACCCAATTTCAATATTAT-ATATTATGTTAAT
**
27010 GAGTAGAAAAACCCAATTT
65 GAGTAGAAAAA-CCAATCC
*
27029 CAATATTATGATATTATGTTAAAGAGTAGAAAAACCCATGCAATTTCAATA-TATATTATTATGT
1 CAATATTATAATATTATGTTAAAGAGTAGAAAAA-CC---CAATTTCAATATTATA-TATTATGT
27093 TAATGAGTAGAAAAA-CAA-CC
61 TAATGAGTAGAAAAACCAATCC
*
27113 CAAT-TTTTCAATATTATGTT
1 CAATATTAT-AATATTATGTT
27133 TTTTTTGGTC
Statistics
Matches: 93, Mismatches: 5, Indels: 12
0.85 0.05 0.11
Matches are distributed among these distances:
83 3 0.03
84 47 0.51
85 5 0.05
86 1 0.01
87 26 0.28
88 11 0.12
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (82 bp):
CAATATTATAATATTATGTTAAAGAGTAGAAAAACCCAATTTCAATATTATATATTATGTTAATG
AGTAGAAAAACCAATCC
Found at i:34701 original size:26 final size:26
Alignment explanation
Indices: 34665--34714 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
34655 AAAGTTCGGC
34665 ATAAGTCTCATTTTGCCCCTTGAAAA
1 ATAAGTCTCATTTTGCCCCTTGAAAA
34691 ATAAGTCTCATTTTGCCCCTTGAA
1 ATAAGTCTCATTTTGCCCCTTGAA
34715 GTTGTAGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (26 bp):
ATAAGTCTCATTTTGCCCCTTGAAAA
Found at i:35328 original size:30 final size:29
Alignment explanation
Indices: 35289--35359 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
35279 GCGGGGCACA
* *
35289 AAAAAGTCCAAAATTGAGAGTTTAAAG-GGC
1 AAAACGTCCAAAATT-AAAG-TTAAAGAGGC
* *
35319 AAAACGTCCAAAATTAAAGTTCAGGAGGC
1 AAAACGTCCAAAATTAAAGTTAAAGAGGC
35348 AAAACGTCCAAA
1 AAAACGTCCAAA
35360 CCGTACAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 4 0.11
29 18 0.50
30 14 0.39
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.17
Consensus pattern (29 bp):
AAAACGTCCAAAATTAAAGTTAAAGAGGC
Found at i:40184 original size:17 final size:16
Alignment explanation
Indices: 40132--40180 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
40122 TCACCCCCAA
*
40132 ATCACTAGTGATCTAAG
1 ATCACCAGTGATC-AAG
40149 ATCACCAGTGATGCAAG
1 ATCACCAGTGAT-CAAG
*
40166 ATCACCGGTGATCAA
1 ATCACCAGTGATCAA
40181 AGATTATATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (16 bp):
ATCACCAGTGATCAAG
Found at i:50995 original size:22 final size:22
Alignment explanation
Indices: 50970--51047 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
50960 TATTTTTATG
*
50970 AAATTTTGATAACTATCCTATT
1 AAATTTTGATAACTATCCTATA
* *
50992 AAATTTTGATAACCA-CGCTATG
1 AAATTTTGATAACTATC-CTATA
*
51014 AAATTTTGATAA-TTTACCTATA
1 AAATTTTGATAACTAT-CCTATA
*
51036 AAATTGTGATAA
1 AAATTTTGATAA
51048 ACTCCATACA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.02
22 45 0.96
23 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACTATCCTATA
Found at i:51117 original size:21 final size:21
Alignment explanation
Indices: 51091--51137 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
51081 AATTTTAATA
*
51091 AACCTTTCTATGAACTTTTG-T
1 AACCTTCCTATG-ACTTTTGAT
*
51112 AACCTTCCTATGATTTTTGAT
1 AACCTTCCTATGACTTTTGAT
51133 AACCT
1 AACCT
51138 CCTTGTGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.45
Consensus pattern (21 bp):
AACCTTCCTATGACTTTTGAT
Found at i:51888 original size:20 final size:18
Alignment explanation
Indices: 51866--51906 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
51856 CGATCCTTTA
*
51866 TATATATAATAATATTAT
1 TATATATATTAATATTAT
51884 TATAT-TATTAATATTA-
1 TATATATATTAATATTAT
51900 TATATAT
1 TATATAT
51907 CTATCTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 5 0.24
17 11 0.52
18 5 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATATATATTAATATTAT
Found at i:52046 original size:10 final size:10
Alignment explanation
Indices: 52031--52055 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
52021 CATCTTCTCC
52031 TTCTCTCTTT
1 TTCTCTCTTT
52041 TTCTCTCTTT
1 TTCTCTCTTT
52051 TTCTC
1 TTCTC
52056 AGATCTCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TTCTCTCTTT
Found at i:60269 original size:10 final size:10
Alignment explanation
Indices: 60254--60278 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
60244 TGTGAGATCT
60254 GAGAAAAAGA
1 GAGAAAAAGA
60264 GAGAAAAAGA
1 GAGAAAAAGA
60274 GAGAA
1 GAGAA
60279 GGTGAAGACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
GAGAAAAAGA
Found at i:60406 original size:2 final size:2
Alignment explanation
Indices: 60399--60451 Score: 50
Period size: 2 Copynumber: 30.5 Consensus size: 2
60389 ATATAAACGG
60399 AT AT AT AT AT AT A- AT AT AT -T A- AT A- AT AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60435 -T AT -T AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
60452 GGATCGGTCG
Statistics
Matches: 43, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
1 8 0.19
2 35 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:61109 original size:2 final size:2
Alignment explanation
Indices: 61102--61140 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
61092 TTGCATTATT
*
61102 TA TA TA TA CA 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
61141 TTGCATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:63542 original size:13 final size:13
Alignment explanation
Indices: 63526--63556 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
63516 TAAATTTTAC
63526 TACTATATATATA
1 TACTATATATATA
63539 TACTATATATATA
1 TACTATATATATA
*
63552 CACTA
1 TACTA
63557 GGAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (13 bp):
TACTATATATATA
Found at i:64086 original size:21 final size:21
Alignment explanation
Indices: 64060--64101 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
64050 CCATGTGGCG
64060 CACCATCATTGTCCCAAAATC
1 CACCATCATTGTCCCAAAATC
64081 CACCATCATTGTCCCAAAATC
1 CACCATCATTGTCCCAAAATC
64102 AATCCCAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.38, G:0.05, T:0.24
Consensus pattern (21 bp):
CACCATCATTGTCCCAAAATC
Found at i:65349 original size:24 final size:24
Alignment explanation
Indices: 65317--65370 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
65307 GGCTTTGTTA
65317 TTGCTTTGTTGATGGAGAAGAACT
1 TTGCTTTGTTGATGGAGAAGAACT
*
65341 TTGCTTTGTTGATGGATAAGAACT
1 TTGCTTTGTTGATGGAGAAGAACT
65365 TTGCTT
1 TTGCTT
65371 CAGATTTGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (24 bp):
TTGCTTTGTTGATGGAGAAGAACT
Found at i:67918 original size:17 final size:16
Alignment explanation
Indices: 67878--67920 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
67868 CATGTAATCT
*
67878 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
67894 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
67911 TTAGATCACT
1 TT-GATCACT
67921 AATGATTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:71344 original size:2 final size:2
Alignment explanation
Indices: 71337--71378 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
71327 AATAGGCGTT
71337 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
71379 GTAATAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 36 0.95
3 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:71384 original size:12 final size:11
Alignment explanation
Indices: 71337--71384 Score: 62
Period size: 12 Copynumber: 4.2 Consensus size: 11
71327 AATAGGCGTT
71337 TATATATAT-A
1 TATATATATAA
71347 TATATATATATA
1 TATATATATA-A
71359 TATATATATCAA
1 TATATATAT-AA
71371 TATATATAGTAA
1 TATATATA-TAA
71383 TA
1 TA
71385 AAGACTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 9 0.26
12 23 0.68
13 2 0.06
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (11 bp):
TATATATATAA
Found at i:77529 original size:342 final size:341
Alignment explanation
Indices: 77115--77775 Score: 795
Period size: 340 Copynumber: 1.9 Consensus size: 341
77105 TGATTATTAT
* * *
77115 ACGATTTCGGCTAGAATTTTGCAAAAATTGACTCGAAAGTTATTTCCTCTATTTTTAGCCACAAT
1 ACGATTTCGGCTAGAATTTTGCAAAAATTGACTCGAAAATTATTTCCTCTAATTTTAGCCAAAAT
* *
77180 ACTCATAAAA-ATTATATAATTTAAAGCCAAAAAGATTGAAAGG-CTTTTCATGCTTCTAATAAC
66 ACTCATAAAATA-TATATAATTCAAAGCCAAAAAGATTG-AAGGACTCTTCATGCTTCTAATAAC
* * * **
77243 GTTTTTCGTATTATTTTTC-GAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTGGTTT
129 GTTTTTC--A-TATTTTTCTGAATTAATTTCTAATTAAACCGAAACAAGATTCAGATGCTCGTAA
* * *
77307 TACAAATCCTTAAAT-CTAATGTGGCTGAGATCTAG-TTAGACGAATATAGATATTTCAAGGAGT
191 AAAAAATCCTGAAATGC-AATGTGGCTGAGAT-TAGATTAGACGAATATAGATATTTCAAGGAGT
* * * * * * *
77370 CTCGGCACCCAAAATCATGCAACACTAA-ACTGGGACCCTGGAATGC-GTTTTTAGCAAAAAAAA
254 CCCGACACCAAAAATCATACAAAACTAAGACGGGGACCC-GAAATGCGGTTTTTAGCAAAAAAAA
77433 AAAAAGTGATTTCGACTAACGTAC
318 AAAAAGTGATTTCGACTAACGTAC
* *
77457 ACGATTTCGGCTA-ATATTTTGCAAAAATTTGAC-CAGAAAAATT-TTTCCTC-AATTTTATCTA
1 ACGATTTCGGCTAGA-ATTTTGCAAAAA-TTGACTC-G-AAAATTATTTCCTCTAATTTTAGCCA
** * * *
77518 AAATACTCATAAAATATATATAATTCAACTCCAAAAAGATTGGAGGACTCTTCATGTTTTTAATA
62 AAATACTCATAAAATATATATAATTCAAAGCCAAAAAGATTGAAGGACTCTTCATGCTTCTAATA
* * *
77583 TCGTTTTTCATATTTTTCTGATTTAATTTCTAATTAAACCGAAACAAGATTCGGATGCTCGTAAA
127 ACGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAACCGAAACAAGATTCAGATGCTCGTAAA
* * * *
77648 AAAAATCCTGAAATGCAATGTGGCTGAGATTTGATTATATGAATATAGATATTTTAAGGAGTCCC
192 AAAAATCCTGAAATGCAATGTGGCTGAGATTAGATTAGACGAATATAGATATTTCAAGGAGTCCC
** * *
77713 GATGCCAAAAATCATACAAAACTAAGTCGGGGTCCCGAAATGCGGTTTTTAGCAAAAAAAAAA
257 GACACCAAAAATCATACAAAACTAAGACGGGGACCCGAAATGCGGTTTTTAGCAAAAAAAAAA
Statistics
Matches: 270, Mismatches: 38, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
339 10 0.04
340 117 0.43
341 31 0.11
342 93 0.34
343 14 0.05
344 5 0.02
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (341 bp):
ACGATTTCGGCTAGAATTTTGCAAAAATTGACTCGAAAATTATTTCCTCTAATTTTAGCCAAAAT
ACTCATAAAATATATATAATTCAAAGCCAAAAAGATTGAAGGACTCTTCATGCTTCTAATAACGT
TTTTCATATTTTTCTGAATTAATTTCTAATTAAACCGAAACAAGATTCAGATGCTCGTAAAAAAA
ATCCTGAAATGCAATGTGGCTGAGATTAGATTAGACGAATATAGATATTTCAAGGAGTCCCGACA
CCAAAAATCATACAAAACTAAGACGGGGACCCGAAATGCGGTTTTTAGCAAAAAAAAAAAAAGTG
ATTTCGACTAACGTAC
Found at i:77775 original size:340 final size:327
Alignment explanation
Indices: 76473--77771 Score: 1001
Period size: 343 Copynumber: 3.9 Consensus size: 327
76463 TAAAAATAAT
* * * * ** *
76473 CCGAAAGATTTTTCCTCAATTTTTGGCAAAAGAAACTTTTAAAATATATATAATTC-AGTGCCAA
1 CCGAAAAATTTTTCCTCAA-TTTTAGCTAAA-ATACTCATAAAATATATATAATTCAACT-CCAA
* * * ** **
76537 AAAAATTGGAGGACTTTTCACACTTTTAATATTATTTTTCATATTTTTCTGAATTAATTTCTCTT
63 AAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAAT
* * * *
76602 TAAATCGAAACAAGATTCAGATGCACATAAATACAAATCCTTG-AATCCAATGTAGCCT-AGATT
128 TAAATCGAAACAAGATTCAGATGCTCGTAAA-AAAAATCC-TGAAAT-CAATGT-GGCTGAGATT
* * * * * * *
76665 TGA-TTAGATAAATAAAGATATTTTAAGGAGTCCGGCT-CCAAAAATCATGCAAAA-TAGAGTTG
189 TGAGTTAGATGAATATAGATATTTCAAGGAGTCCCGATGCCAAAAATCATACAAAACTA-AGTCG
* * * * * * *
76727 TGACCCCGAAACGCGTTTTTCGCCAAAAATCGCGATG-GTCAATAAACGATTTCAGCTAAAATTT
253 GGGCCCCGAAACGCGTTTTTAGCAAAAAATCGTGATGACT-AATAAACGATTTCGGCT-AAATTT
*
76791 TGCAAAAAATGA
316 TGCAAAAATTGA
* * * *
76803 CCCGAAAAAATTTTCCAACAATTTTGGCTAAAATACTCATTATATATATATATATGTAATTTAAC
1 -CCGAAAAATTTTTCC-TCAATTTTAGCTAAAATACTCA-TA-A-A-ATATATA--TAATTCAAC
* * * * *
76868 ACCAAAAATATTGAAAGACTTTTCACGCTTTTAATATCGTTTTTCATATATTTCTGAACTAATTT
58 TCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTT
* * * * * * * ** * *
76933 CTGATTAAATTGGAATAAGATTTAGATGATCGTAAAAACAAGTTTTTAAATTCAATGTAGCTGAG
123 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAATCCTGAAA-TCAATGTGGCTGAG
* * * * * ***
76998 ATTTTATAATTTATTAGATGAATATGGATATCTCAAAGAGTTTTGA-GCCAAAAATCATACAAAA
186 A--TT-TGA---GTTAGATGAATATAGATATTTCAAGGAGTCCCGATGCCAAAAATCATACAAAA
* * * * *
77062 CTTAG-CTGGGGCCCCGAAACGCGTTTTTAGCCAAAAATCGTGATGATTATTATACGATTTCGGC
245 CTAAGTC-GGGGCCCCGAAACGCGTTTTTAGCAAAAAATCGTGATGACTAATAAACGATTTCGGC
77126 TAGAATTTTGCAAAAATTGA
309 TA-AATTTTGCAAAAATTGA
* * * * * **
77146 CTCG-AAAGTTATTTCCTCTATTTTTAGCCACAATACTCATAAAA-ATTATATAATTTAAAGCCA
1 C-CGAAAAATT-TTTCCTC-AATTTTAGCTAAAATACTCATAAAATA-TATATAATTCAACTCCA
* * *
77209 AAAAGATTGAAAGG-CTTTTCATGCTTCTAATAACGTTTTTCGTATTATTTTTC-GAATTAATTT
62 AAAAGATTG-AAGGACTTTTCACGCTTTTAATATCGTTTTTC--A-TATTTTTCTGAATTAATTT
* * *** * *
77272 CTAATTAAATCGAAACATGATTCAGATGCTGGTTTTACAAATCCTTAAATCTAATGTGGCTGAGA
123 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAATCCTGAAATC-AATGTGGCTGAGA
* * * *** * * * *
77337 TCT-AGTTAGACGAATATAGATATTTCAAGGAGTCTCGGCACCCAAAATCATGCAACACTAA-AC
187 TTTGAGTTAGATGAATATAGATATTTCAAGGAGTCCCGATGCCAAAAATCATACAAAACTAAGTC
* * * * ** *
77400 TGGGACCCTGGAATGCGTTTTTAGCAAAAAAAAAAAAAGTGATTTCGACTAACGTACACGATTTC
252 -GGGGCCCCGAAACGCGTTTTTAGC-----AAAAAATCGTGA--T-GACTAA--TAAACGATTTC
77465 GGCTAATATTTTGCAAAAATTTGA
306 GGCTAA-ATTTTGCAAAAA-TTGA
*
77489 CCAGAAAAATTTTTCCTCAATTTTATCTAAAATACTCATAAAATATATATAATTCAACTCCAAAA
1 CC-GAAAAATTTTTCCTCAATTTTAGCTAAAATACTCATAAAATATATATAATTCAACTCCAAAA
* * * * *
77554 AGATTGGAGGACTCTTCATGTTTTTAATATCGTTTTTCATATTTTTCTGATTTAATTTCTAATTA
65 AGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTA
* *
77619 AACCGAAACAAGATTCGGATGCTCGTAAAAAAAATCCTGAAATGCAATGTGGCTGAGATTTGA-T
130 AATCGAAACAAGATTCAGATGCTCGTAAAAAAAATCCTGAAAT-CAATGTGGCTGAGATTTGAGT
* * *
77683 TATATGAATATAGATATTTTAAGGAGTCCCGATGCCAAAAATCATACAAAACTAAGTCGGGGTCC
194 TAGATGAATATAGATATTTCAAGGAGTCCCGATGCCAAAAATCATACAAAACTAAGTCGGGGCCC
*
77748 CGAAATGCGGTTTTTAGCAAAAAA
259 CGAAACGC-GTTTTTAGCAAAAAA
77772 AAAA
Statistics
Matches: 760, Mismatches: 152, Indels: 107
0.75 0.15 0.11
Matches are distributed among these distances:
330 4 0.01
331 51 0.07
332 43 0.06
333 1 0.00
334 8 0.01
335 5 0.01
336 109 0.14
337 56 0.07
338 26 0.03
339 52 0.07
340 135 0.18
341 17 0.02
342 104 0.14
343 142 0.19
344 7 0.01
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (327 bp):
CCGAAAAATTTTTCCTCAATTTTAGCTAAAATACTCATAAAATATATATAATTCAACTCCAAAAA
GATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAA
ATCGAAACAAGATTCAGATGCTCGTAAAAAAAATCCTGAAATCAATGTGGCTGAGATTTGAGTTA
GATGAATATAGATATTTCAAGGAGTCCCGATGCCAAAAATCATACAAAACTAAGTCGGGGCCCCG
AAACGCGTTTTTAGCAAAAAATCGTGATGACTAATAAACGATTTCGGCTAAATTTTGCAAAAATT
GA
Done.