Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016382.1 Corchorus olitorius cultivar O-4 contig16415, 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: 117684
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1958 original size:332 final size:324
Alignment explanation
Indices: 932--2191 Score: 1267
Period size: 332 Copynumber: 3.8 Consensus size: 324
922 ATAATCATCA
* * *
932 CGGAGTCCCGGGTCAATTTTGCATGATTTTTGGCGCAAAAACTCCTTCAAATATCTATATCCATA
1 CGGAGTCCCGGCTCAGTTTTGCATGATTTTTGGCACAAAAACTCCTTCAAATATCTATATCCATA
* * *
997 TAACCAAATCTTAGCCACATTAGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTTCCA
66 TAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCCA
* * *
1062 TTTAATTAAAAATTAATTTGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCATCAA
131 TTTAATTAGAAATTAATTCGG-AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAA
* * * *
1127 TCTTTTTGGCATTGAATTA-TAAATTTTTTCTAAGCATTGTGGCAAAAAGTTCAGGAAAAAAAAT
195 TCTTTTTGGCATTGAATTATTTATTTTTTTCTAAGCATTGTGGCAAAAAGTTGAGG-AAAAAATT
* * * * * *
1191 TTCGAGTAAGT--TTTTAGCCAAAATCATGTACTAACCATCACAGTTTTTGGGATAAAAACGCGT
259 TTCGGGTCAGTAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT-GGCTAAAAACGCGT
1254 TT
323 TT
* * * **
1256 C-GTGTACTCGGCTCAGTTTTGCATGATTTTTGGCAGAAAAACTCCTTCAAATATCTATATTTAT
1 CGGAGT-CCCGGCTCAGTTTTGCATGATTTTTGGCACAAAAACTCCTTCAAATATCTATATCCAT
* ** * * * *
1320 CTTTCCAAATCTCAACCACATTGGAGA-TGAA-CATTTCTTTTTTACGAGCATCTGAATCATTGT
65 ATAACCAAATCTCAGCCACATT--AGATTTAAGGATTT-GTTTTTACGAGCATCTGAATC-TTGT
* * *
1383 TCCCATTTTAATTAGAAATTAATTC-GAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAGCTC
126 TTCCA-TTTAATTAGAAATTAATTCGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCC
* * * *
1447 GTCAATCTTTTTGGCGTTGAATTTATTATATATATATATATATATATATTAGTATTGTGGAAAAA
190 GTCAATCTTTTTGGCATTGAA-TTA-T-T-TAT-T-T-T-T-T-TCTA--AGCATTGTGGCAAAA
* * * * * *
1512 ATTTCG-GGAAAAAATTTTTCGGGACAGT--TTTTAGCTGAAATAGTTTACTAACCATCGCGGTT
243 AGTT-GAGGAAAAAA-TTTTCGGGTCAGTAATTTTAGCCGAAATCGTGTACTAACCATCACGGTT
**
1574 TAAGGCTAAAAACGCGTTT
306 TTTGGCTAAAAACGCGTTT
* ** * * * * * * **
1593 CGG-GGCTTTGACTCAGTTTTGCATGTTTTTTTGCATAAAAAATCCTTGAAATAAT-TATATTTA
1 CGGAGTC-CCGGCTCAGTTTTGCATGATTTTTGGCACAAAAACTCCTTCAAAT-ATCTATATCCA
* ** *
1656 TCTAATTAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTC
64 TATAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTC
* * * * * * * * * *
1721 GATTTAATTAGAAATAAATTCGGCAAAATTTGAAAAACGACATTAAAATCGTGAAAATCCCTTCA
129 CATTTAATTAGAAATTAATTCGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCA
* * * * *
1786 ATTTTTTTGGCGTTGAATTATTTATTTTTTTCTCAGTATTGTGGCAAAAA-TTGAGGAAAAACTT
194 ATCTTTTTGGCATTGAATTATTTATTTTTTTCTAAGCATTGTGGCAAAAAGTTGAGGAAAAAATT
* *
1850 TTCGGGTCAGTTTTTGTAAAATTTTAGCCGAAATCGTGCACTAATCATCAACGGTTTTTGGCTAA
259 TTCGGGTCA------GT--AATTTTAGCCGAAATCGTGTACTAACCATC-ACGGTTTTTGGCTAA
*
1915 AAACGCGTTC
315 AAACGCGTTT
* * * *
1925 CGGAGTCCCAGCTCAAG-TTTGCATGATTTTTTGCGCAAAAACTCCTTGAAATATCTATATCCAT
1 CGGAGTCCCGGCTC-AGTTTTGCATGATTTTTGGCACAAAAACTCCTTCAAATATCTATATCCAT
* *
1989 ATAACCAAATCTTAGCCACATTAGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCC
65 ATAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCC
*
2054 ATTTAATTAGAAATTAATTCGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCA
130 ATTTAATTAGAAATTAATTCG-GAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCA
* *
2119 ATCTTTTTGGCATTGAATTATATA-TTTTTTCTGAGCATTGTGGCAAAAA-TTGA-GAGAAAAAT
194 ATCTTTTTGGCATTGAATTATTTATTTTTTTCTAAGCATTGTGGCAAAAAGTTGAGGA-AAAAAT
*
2181 TTTTGGGTCAG
258 TTTCGGGTCAG
2192 CTTTTAGCCA
Statistics
Matches: 767, Mismatches: 125, Indels: 86
0.78 0.13 0.09
Matches are distributed among these distances:
321 11 0.01
322 9 0.01
323 18 0.02
324 73 0.10
325 79 0.10
326 17 0.02
327 20 0.03
328 1 0.00
329 2 0.00
330 2 0.00
331 31 0.04
332 186 0.24
333 61 0.08
334 22 0.03
335 59 0.08
336 27 0.04
337 91 0.12
338 58 0.08
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (324 bp):
CGGAGTCCCGGCTCAGTTTTGCATGATTTTTGGCACAAAAACTCCTTCAAATATCTATATCCATA
TAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCCA
TTTAATTAGAAATTAATTCGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAAT
CTTTTTGGCATTGAATTATTTATTTTTTTCTAAGCATTGTGGCAAAAAGTTGAGGAAAAAATTTT
CGGGTCAGTAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTT
Found at i:2676 original size:300 final size:300
Alignment explanation
Indices: 1906--2679 Score: 835
Period size: 308 Copynumber: 2.5 Consensus size: 300
1896 ATCAACGGTT
* * * *
1906 TTTGGCTAAAAACGCGTTCCGGAGTCCCAGCTCAAG-TTTGCATGATTTTTTGCGCAAAAACTCC
1 TTTGGCTAAAAACGCGTTCC-G-GTCCCGGCTC-AGTTTTGCATGATTTTTTGCGCCAAGACTCT
* * * * * *
1970 TTGAAATATCTATATCCATATAACCAAATCTTAGCCACATTAGATTTAAGGATTTATTTTTACGA
63 TTGAAATATCTATAT-TATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTT-GTTTTACGA
* *
2035 GCATCTGAATCTTGTTTCCATTTAATTAGAAATTAATTCGAAAAAAAATGGAAAAACGATATTAG
126 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAATGGAAAAACGATATTAA
* * * * *
2100 AAGCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGCATTGTGGCAA
191 AAGCGTGAAAAGCCCGTCAATCTTTTTGGCATTAAATTATATATATATTATGAGCATTGTGCCAA
*
2165 AAATTGAGAGAAAAATTTTTGGGTCAGCTTTTAGCCATCACAGTC
256 AAATTGAGAGAAAAATTTTCGGGTCAGCTTTTAGCCATCACAGTC
* * * * * * *
2210 TTTGACTAAAAACGCATTCTGAGGCCACGTACGGCTCTGTTTTGCATGATTTTTTGCGTCGAGAC
1 TTTGGCTAAAAACGCGTTC--CGGTC-C---CGGCTCAGTTTTGCATGATTTTTTGCGCCAAGAC
* * *
2275 TCTTTGAAATATCTTTATTCATCTAATTAAATTTCAGCCACATTGGATTTAAGGATTTGTGTTTA
60 TCTTTGAAATATCTATATT-ATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGT-TTTA
* * * **
2340 CGTGCATCTGAATCTTGTTTTGATTT-ATTAGAAATTAATTCTGAAAAAATAT-GAAATGCGATA
123 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAAATGGAAAAACGATA
* * * ** *
2403 TTAAAAGCGTGAAAAGTCCTTCTATCTTTTTGGTGTTAAATTTTATATATATATTATGAGTATTA
187 TTAAAAGCGTGAAAAGCCCGTCAATCTTTTTGGCATTAAA--TTATATATATATTATGAGCATT-
* * * *
2468 TTGCCAAAAATTGAG-GAAAAATATTTCGGGTCA-TTTTTA-CCATCA-TG-G
249 GTGCCAAAAATTGAGAGAAAAAT-TTTCGGGTCAGCTTTTAGCCATCACAGTC
* * *
2516 TTTGGTTAAAAACGTGTTCCGGTCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCTTTG
1 TTTGGCTAAAAACGCGTTCCGGTCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCTTTG
* * * * *
2581 AAATATCTATATTATCTAATGAAATCTCAGGCATATTGGATTTAAAGATTTGTTTTCACGAGTAT
66 AAATATCTATATTATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTT-ACGAGCAT
* * *
2646 TTAAATTTTGTTTCGATTTAATTAGAAATTAATT
130 CTGAATCTTGTTTCGATTTAATTAGAAATTAATT
2680 AATTCAAATA
Statistics
Matches: 389, Mismatches: 65, Indels: 36
0.79 0.13 0.07
Matches are distributed among these distances:
298 3 0.01
299 56 0.14
300 62 0.16
303 1 0.00
304 22 0.06
305 2 0.01
306 15 0.04
307 60 0.15
308 116 0.30
309 30 0.08
310 22 0.06
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (300 bp):
TTTGGCTAAAAACGCGTTCCGGTCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCTTTG
AAATATCTATATTATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTACGAGCATC
TGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAATGGAAAAACGATATTAAAAGCG
TGAAAAGCCCGTCAATCTTTTTGGCATTAAATTATATATATATTATGAGCATTGTGCCAAAAATT
GAGAGAAAAATTTTCGGGTCAGCTTTTAGCCATCACAGTC
Found at i:4602 original size:2 final size:2
Alignment explanation
Indices: 4597--4630 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4587 TTGCATCAAG
4597 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
4631 TAATACAACT
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:7486 original size:3 final size:3
Alignment explanation
Indices: 7478--7527 Score: 64
Period size: 3 Copynumber: 15.3 Consensus size: 3
7468 CCTCACAAAA
7478 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AGAG AGAG AGAG AGAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG A-AG A-AG A-AG AAG
7527 A
1 A
7528 GAAAGAAGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 31 0.67
4 15 0.33
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16154 original size:22 final size:22
Alignment explanation
Indices: 16126--16183 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
16116 GCAAGAGTGT
16126 GTGTGTGTGTGTGTACGCGCGC
1 GTGTGTGTGTGTGTACGCGCGC
16148 GTGTGTGTGTGTGTACGCGCGC
1 GTGTGTGTGTGTGTACGCGCGC
16170 GTGTGTGTGTGTGT
1 GTGTGTGTGTGTGT
16184 GAGAGAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.03, C:0.14, G:0.47, T:0.36
Consensus pattern (22 bp):
GTGTGTGTGTGTGTACGCGCGC
Found at i:16189 original size:2 final size:2
Alignment explanation
Indices: 16184--16217 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16174 GTGTGTGTGT
16184 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
16218 AAGTAATGAG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17370 original size:2 final size:2
Alignment explanation
Indices: 17365--17393 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17355 ATAATATATA
17365 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
17394 ATGTATGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:28262 original size:27 final size:27
Alignment explanation
Indices: 28224--28278 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
28214 GTTCATCACA
*
28224 TATATTTCGTAAAGGTAATAAATGTGT
1 TATATTTCGTAAAGATAATAAATGTGT
28251 TATATTTCGTAAAGATAATAAATGTGT
1 TATATTTCGTAAAGATAATAAATGTGT
28278 T
1 T
28279 GAGTCAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (27 bp):
TATATTTCGTAAAGATAATAAATGTGT
Found at i:29076 original size:14 final size:15
Alignment explanation
Indices: 29052--29081 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
29042 GTCCAAATCA
29052 AATATTTTGATTTGG
1 AATATTTTGATTTGG
29067 AATA-TTTGATTTGG
1 AATATTTTGATTTGG
29081 A
1 A
29082 GATGCAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (15 bp):
AATATTTTGATTTGG
Found at i:30727 original size:41 final size:38
Alignment explanation
Indices: 30670--30751 Score: 110
Period size: 38 Copynumber: 2.1 Consensus size: 38
30660 GTCTAACATC
* *
30670 CTTTTCTTAACGTATAGCTTGAATCGGTCAACCTCTGTTTT
1 CTTTTCTTAACGTATAGC---AACCAGTCAACCTCTGTTTT
*
30711 CTTTTCTTAATGTATAGCAACCAGTCAACCTCTGTTTT
1 CTTTTCTTAACGTATAGCAACCAGTCAACCTCTGTTTT
30749 CTT
1 CTT
30752 AGCATGACTG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 21 0.55
41 17 0.45
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (38 bp):
CTTTTCTTAACGTATAGCAACCAGTCAACCTCTGTTTT
Found at i:32116 original size:22 final size:22
Alignment explanation
Indices: 32043--32109 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
32033 AAAATGTTCA
32043 TAAAACAACAGACAGTTGTGTT
1 TAAAACAACAGACAGTTGTGTT
32065 TAAAACAACAGACAGTTGTGTT
1 TAAAACAACAGACAGTTGTGTT
32087 TAAAACAACAGACAGTTGTGTT
1 TAAAACAACAGACAGTTGTGTT
32109 T
1 T
32110 GGAACAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Consensus pattern (22 bp):
TAAAACAACAGACAGTTGTGTT
Found at i:33763 original size:22 final size:22
Alignment explanation
Indices: 33738--33781 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
33728 ATCAAAACTT
** *
33738 TGTTTCTTCTCATATTTTTAAA
1 TGTTTCTGATCATATTATTAAA
33760 TGTTTCTGATCATATTATTAAA
1 TGTTTCTGATCATATTATTAAA
33782 ATGAAATTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.07, T:0.55
Consensus pattern (22 bp):
TGTTTCTGATCATATTATTAAA
Found at i:39009 original size:12 final size:12
Alignment explanation
Indices: 38992--39018 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
38982 TCAATCGTCA
38992 CATCCCTTAATC
1 CATCCCTTAATC
39004 CATCCCTTAATC
1 CATCCCTTAATC
39016 CAT
1 CAT
39019 TTTGCTATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.41, G:0.00, T:0.33
Consensus pattern (12 bp):
CATCCCTTAATC
Found at i:52607 original size:22 final size:21
Alignment explanation
Indices: 52582--52622 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
52572 AATAATTGTA
*
52582 CATTTTCCGGATGAATGTGATC
1 CATTTT-CGGATGAAGGTGATC
*
52604 CATTTTGGGATGAAGGTGA
1 CATTTTCGGATGAAGGTGA
52623 AAACAATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.34
Consensus pattern (21 bp):
CATTTTCGGATGAAGGTGATC
Found at i:57772 original size:2 final size:2
Alignment explanation
Indices: 57765--57789 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57755 ACTATGCTGA
57765 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
57790 AGCCTCAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:59564 original size:25 final size:25
Alignment explanation
Indices: 59535--59585 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
59525 AGAAAAAAGC
*
59535 AAAGTTGATTTCTAATTTACCATTT
1 AAAGTTGATTTCTAATGTACCATTT
59560 AAAGTTGATTTCTAATGTACCATTT
1 AAAGTTGATTTCTAATGTACCATTT
59585 A
1 A
59586 CATTAACTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (25 bp):
AAAGTTGATTTCTAATGTACCATTT
Found at i:77066 original size:15 final size:15
Alignment explanation
Indices: 77043--77079 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
77033 GAGGAATGGA
77043 AAGAAAAAAAAAAA-
1 AAGAAAAAAAAAAAG
*
77057 AGGAAAAAAAAAAAG
1 AAGAAAAAAAAAAAG
77072 AAGAAAAA
1 AAGAAAAA
77080 GATAGATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAAAAG
Found at i:77078 original size:14 final size:13
Alignment explanation
Indices: 77042--77079 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
77032 AGAGGAATGG
77042 AAAGAAAAAAAAA
1 AAAGAAAAAAAAA
*
77055 AAAGGAAAAAAAA
1 AAAGAAAAAAAAA
77068 AAAGAAGAAAAA
1 AAAGAA-AAAAA
77080 GATAGATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAA
Found at i:79069 original size:19 final size:19
Alignment explanation
Indices: 79047--79105 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
79037 TTGTTCATAA
79047 CTCTGATCATTATTCAACG
1 CTCTGATCATTATTCAACG
* *
79066 CTCT-AT-ATTGTTCATA-A
1 CTCTGATCATTATTCA-ACG
79083 CTCTGATCATTATTCAACG
1 CTCTGATCATTATTCAACG
79102 CTCT
1 CTCT
79106 ATATTGTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 11 0.34
18 6 0.19
19 15 0.47
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.41
Consensus pattern (19 bp):
CTCTGATCATTATTCAACG
Found at i:79081 original size:36 final size:36
Alignment explanation
Indices: 79034--79113 Score: 160
Period size: 36 Copynumber: 2.2 Consensus size: 36
79024 TTTCTTTATA
79034 ATATTGTTCATAACTCTGATCATTATTCAACGCTCT
1 ATATTGTTCATAACTCTGATCATTATTCAACGCTCT
79070 ATATTGTTCATAACTCTGATCATTATTCAACGCTCT
1 ATATTGTTCATAACTCTGATCATTATTCAACGCTCT
79106 ATATTGTT
1 ATATTGTT
79114 GTACTGCAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.44
Consensus pattern (36 bp):
ATATTGTTCATAACTCTGATCATTATTCAACGCTCT
Found at i:79086 original size:17 final size:18
Alignment explanation
Indices: 79034--79113 Score: 60
Period size: 19 Copynumber: 4.4 Consensus size: 18
79024 TTTCTTTATA
79034 ATATTGTTCATA-ACTCTG
1 ATATTGTTCA-ACACTCTG
* *
79052 ATCATTATTCAACGCTCT-
1 AT-ATTGTTCAACACTCTG
79070 ATATTGTTCATA-ACTCTG
1 ATATTGTTCA-ACACTCTG
* *
79088 ATCATTATTCAACGCTCT-
1 AT-ATTGTTCAACACTCTG
79106 ATATTGTT
1 ATATTGTT
79114 GTACTGCAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
17 16 0.33
18 11 0.22
19 22 0.45
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.44
Consensus pattern (18 bp):
ATATTGTTCAACACTCTG
Found at i:82226 original size:3 final size:3
Alignment explanation
Indices: 82212--82243 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
82202 TCTCCATCTC
*
82212 CAT CAC CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
82244 AAGTCACTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.38, G:0.00, T:0.28
Consensus pattern (3 bp):
CAT
Found at i:88742 original size:4 final size:4
Alignment explanation
Indices: 88733--88788 Score: 112
Period size: 4 Copynumber: 14.0 Consensus size: 4
88723 ACAAAAGTGG
88733 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
88781 TTCT TTCT
1 TTCT TTCT
88789 CGGTTTGCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTCT
Found at i:90901 original size:18 final size:18
Alignment explanation
Indices: 90878--90924 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
90868 AAGATGCTGC
*
90878 TGCTGCTGGTGTTGTTGA
1 TGCTGCTGGTGCTGTTGA
*
90896 TGCTGCTGGTGCTGTTGC
1 TGCTGCTGGTGCTGTTGA
*
90914 TGCTGATGGTG
1 TGCTGCTGGTG
90925 AAAACCCAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.04, C:0.15, G:0.40, T:0.40
Consensus pattern (18 bp):
TGCTGCTGGTGCTGTTGA
Found at i:91581 original size:21 final size:20
Alignment explanation
Indices: 91557--91598 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
91547 AGAAGATGAT
91557 GGTGATGATGAGGATGGAGAG
1 GGTGATGATGAGGATGG-GAG
* *
91578 GGTGATGGTGGGGATGGGAG
1 GGTGATGATGAGGATGGGAG
91598 G
1 G
91599 AAGAGAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.21, C:0.00, G:0.60, T:0.19
Consensus pattern (20 bp):
GGTGATGATGAGGATGGGAG
Found at i:91784 original size:3 final size:3
Alignment explanation
Indices: 91778--91813 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
91768 AGTAGACGAA
* *
91778 TTG TTG TTG TTG TTG TTG TTG TTA TTG TTG GTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
91814 GTATTGTTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.33, T:0.64
Consensus pattern (3 bp):
TTG
Found at i:91818 original size:15 final size:15
Alignment explanation
Indices: 91787--91822 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
91777 ATTGTTGTTG
* *
91787 TTGTTGTTGTTGTTA
1 TTGTTGGTGTTGGTA
91802 TTGTTGGTGTTGGTA
1 TTGTTGGTGTTGGTA
91817 TTGTTG
1 TTGTTG
91823 CTACTTTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.00, G:0.33, T:0.61
Consensus pattern (15 bp):
TTGTTGGTGTTGGTA
Found at i:95862 original size:25 final size:25
Alignment explanation
Indices: 95834--95882 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
95824 ACGTACACCC
*
95834 AATTTGTTACCTTAATTGATAGGTG
1 AATTTGTTAACTTAATTGATAGGTG
95859 AATTTGTTAACTTAATTGATAGGT
1 AATTTGTTAACTTAATTGATAGGT
95883 ATACGCGTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.45
Consensus pattern (25 bp):
AATTTGTTAACTTAATTGATAGGTG
Found at i:96607 original size:8 final size:8
Alignment explanation
Indices: 96587--96650 Score: 56
Period size: 8 Copynumber: 7.8 Consensus size: 8
96577 ATTAATGTAT
*
96587 CATATATT
1 CATATATA
96595 CATATATA
1 CATATATA
*
96603 TATATATA
1 CATATATA
* * *
96611 TATGTACA
1 CATATATA
96619 CATATATA
1 CATATATA
96627 CATATACATA
1 CATAT--ATA
*
96637 CACATATA
1 CATATATA
96645 CATATA
1 CATATA
96651 CATTAATAGT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
8 38 0.84
10 7 0.16
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.38
Consensus pattern (8 bp):
CATATATA
Found at i:96623 original size:18 final size:18
Alignment explanation
Indices: 96588--96653 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
96578 TTAATGTATC
* * *
96588 ATATATTCATATATATAT
1 ATATATACATACACATAT
**
96606 ATATATATGTACACATAT
1 ATATATACATACACATAT
96624 ATACATATACATACACATAT
1 AT--ATATACATACACATAT
*
96644 ACATATACAT
1 ATATATACAT
96654 TAATAGTCTC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
18 23 0.61
20 15 0.39
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.38
Consensus pattern (18 bp):
ATATATACATACACATAT
Found at i:96633 original size:6 final size:6
Alignment explanation
Indices: 96622--96653 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
96612 ATGTACACAT
*
96622 ATATAC ATATAC ATACAC ATATAC ATATAC AT
1 ATATAC ATATAC ATATAC ATATAC ATATAC AT
96654 TAATAGTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (6 bp):
ATATAC
Found at i:96638 original size:20 final size:20
Alignment explanation
Indices: 96600--96653 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
96590 ATATTCATAT
* **
96600 ATATATATATATATGTACAC
1 ATATATACATATACATACAC
96620 ATATATACATATACATACAC
1 ATATATACATATACATACAC
96640 --ATATACATATACAT
1 ATATATACATATACAT
96654 TAATAGTCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 14 0.45
20 17 0.55
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (20 bp):
ATATATACATATACATACAC
Found at i:99511 original size:2 final size:2
Alignment explanation
Indices: 99504--99528 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
99494 CTTATACAGT
99504 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 T
99529 CTCTAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:102510 original size:22 final size:22
Alignment explanation
Indices: 102484--102530 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
102474 TTCACCAACA
102484 TCTCCTTTCCTTCATGCTAAAC
1 TCTCCTTTCCTTCATGCTAAAC
102506 TCTCCTTTCCTTCATGCTAAAC
1 TCTCCTTTCCTTCATGCTAAAC
102528 TCT
1 TCT
102531 AAAGCAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.17, C:0.36, G:0.04, T:0.43
Consensus pattern (22 bp):
TCTCCTTTCCTTCATGCTAAAC
Found at i:110293 original size:44 final size:46
Alignment explanation
Indices: 110225--110324 Score: 143
Period size: 44 Copynumber: 2.2 Consensus size: 46
110215 TAGCTATCTC
** *
110225 AGTTTCAGTTTCAGTCTCTCTTTGTGTTTCAGTGAGTCTCAGTTT-T
1 AGTTTCAG-TTCAGTCTCTCTTTGTGAATCAGTAAGTCTCAGTTTCT
110271 AGTTTCA-TTCAGTCTCTCTTTGTGAATCAGTAAGTCTCAGTTTCT
1 AGTTTCAGTTCAGTCTCTCTTTGTGAATCAGTAAGTCTCAGTTTCT
110316 -GTTTCAGTT
1 AGTTTCAGTT
110325 TCATTCTCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
44 39 0.80
45 3 0.06
46 7 0.14
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.48
Consensus pattern (46 bp):
AGTTTCAGTTCAGTCTCTCTTTGTGAATCAGTAAGTCTCAGTTTCT
Found at i:110322 original size:22 final size:21
Alignment explanation
Indices: 110221--110323 Score: 61
Period size: 22 Copynumber: 4.9 Consensus size: 21
110211 TAGCTAGCTA
* *
110221 TCTCAGTTTCAGTTTCAGT-C
1 TCTCAGTTTCTGTTTCAGTAG
*
110241 TCTC--TTTGTGTTTCAGTGAG
1 TCTCAGTTTCTGTTTCAGT-AG
*
110261 TCTCAGTTT-TAGTTTCATTCAG
1 TCTCAGTTTCT-GTTTCAGT-AG
** * **
110283 TCTCTCTTTGTGAATCAGTAAG
1 TCTCAGTTTCTGTTTCAGT-AG
110305 TCTCAGTTTCTGTTTCAGT
1 TCTCAGTTTCTGTTTCAGT
110324 TTCATTCTCA
Statistics
Matches: 61, Mismatches: 16, Indels: 10
0.70 0.18 0.11
Matches are distributed among these distances:
18 11 0.18
20 8 0.13
21 1 0.02
22 40 0.66
23 1 0.02
ACGTcount: A:0.16, C:0.19, G:0.17, T:0.48
Consensus pattern (21 bp):
TCTCAGTTTCTGTTTCAGTAG
Found at i:112134 original size:21 final size:20
Alignment explanation
Indices: 112100--112140 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
112090 CCTTCTTTCC
*
112100 TTTTTTGGACATCATCACCT
1 TTTTTTGGAAATCATCACCT
112120 TTTTTTGGTAAATCATCACCT
1 TTTTTTGG-AAATCATCACCT
112141 GATTATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (20 bp):
TTTTTTGGAAATCATCACCT
Found at i:112852 original size:65 final size:65
Alignment explanation
Indices: 112672--112863 Score: 269
Period size: 67 Copynumber: 2.9 Consensus size: 65
112662 TATGTGCAAG
* *
112672 GATTAATAATAATATGTGTGACGACAAAACGAAGATACACATACGAAATCGACAAGAAAATTAAT
1 GATTAATAATGATATGTGTGACGACAAAAAGAAGATACACATACGAAATCGACAAGAAAATTAAT
* * * *
112737 GATTAAGAGAATGATATGTGTTACGACAAAAGGAAGATACACATATGAAATCGACAAGAAAATTA
1 GATT-A-ATAATGATATGTGTGACGACAAAAAGAAGATACACATACGAAATCGACAAGAAAATTA
112802 AT
64 AT
* ** *
112804 GATTAATAATGATATGTGTGATGACAAAAAGAAGATATGCACACGAAATCGACAA-AAAAT
1 GATTAATAATGATATGTGTGACGACAAAAAGAAGATACACATACGAAATCGACAAGAAAAT
112864 GAATTTTACC
Statistics
Matches: 112, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
64 5 0.04
65 46 0.41
66 2 0.02
67 59 0.53
ACGTcount: A:0.50, C:0.10, G:0.18, T:0.22
Consensus pattern (65 bp):
GATTAATAATGATATGTGTGACGACAAAAAGAAGATACACATACGAAATCGACAAGAAAATTAAT
Found at i:113035 original size:74 final size:74
Alignment explanation
Indices: 112795--113137 Score: 490
Period size: 74 Copynumber: 4.5 Consensus size: 74
112785 AATCGACAAG
* *
112795 AAAATTAATGATTAATAATGATATGTGTGATGACAAAA-AGAAGATATGCACACGAAATCGACAA
1 AAAATTAATGA--AA-AATGATATGTGTGACGACAAAAGA-AAGATA--CACA-TAAATCGAC-A
*
112859 AAAATGAATTTTACCTC
58 AAAATGAACTTTACCTC
112876 AAAATTAATGAAAAATGATATGTGTGACGACAAAAGAAAGATATATACACATAAATCGACAAAAA
1 AAAATTAATGAAAAATGATATGTGTGACGACAAAAGAAAG----ATACACATAAATCGACAAAAA
112941 TGAACTTTACCTC
62 TGAACTTTACCTC
112954 AAAATTAATGAAAAATGATATGTGTGACGACAAAAGAAAGATACACATAAATCGACAAAAATGAA
1 AAAATTAATGAAAAATGATATGTGTGACGACAAAAGAAAGATACACATAAATCGACAAAAATGAA
113019 CTTTACCTC
66 CTTTACCTC
* * *
113028 AAGATTAATGAAAAATAATATGTATGACGACAAAAGAAAGATACACATAAATCGACAAAAATGAA
1 AAAATTAATGAAAAATGATATGTGTGACGACAAAAGAAAGATACACATAAATCGACAAAAATGAA
*
113093 TTTTACCTC
66 CTTTACCTC
* *
113102 AAAATTAATGAATAATGATATATGTGACGACAAAAG
1 AAAATTAATGAAAAATGATATGTGTGACGACAAAAG
113138 GAGGTACATA
Statistics
Matches: 245, Mismatches: 12, Indels: 17
0.89 0.04 0.06
Matches are distributed among these distances:
74 135 0.55
78 81 0.33
79 11 0.04
80 4 0.02
81 11 0.04
82 3 0.01
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.24
Consensus pattern (74 bp):
AAAATTAATGAAAAATGATATGTGTGACGACAAAAGAAAGATACACATAAATCGACAAAAATGAA
CTTTACCTC
Found at i:117630 original size:2 final size:2
Alignment explanation
Indices: 117625--117668 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
117615 ACACACACAC
117625 AT AT AT AT 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 AT AT AT AT
117667 AT
1 AT
117669 GCTGATTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.