Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014231.1 Corchorus olitorius cultivar O-4 contig14264, 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: 77292
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:546 original size:19 final size:19
Alignment explanation
Indices: 522--558 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
512 TTATACTGCA
*
522 AAATAATGGTTAAATGTTC
1 AAATAAGGGTTAAATGTTC
*
541 AAATAAGGGTTTAATGTT
1 AAATAAGGGTTAAATGTT
559 TGTGAAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.38
Consensus pattern (19 bp):
AAATAAGGGTTAAATGTTC
Found at i:17295 original size:251 final size:251
Alignment explanation
Indices: 16847--17348 Score: 900
Period size: 251 Copynumber: 2.0 Consensus size: 251
16837 GAATATATGA
*
16847 GGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATATTGATTTTGGTCCCTGTACTTTTTTT
1 GGTAAAAGTACCCGGGAGGTCCCTGTACTATACAAAATATTGATTTTGGTCCCTGTACTTTTTTT
*
16912 TTCTACAAATTTGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGT
66 TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGT
*
16977 GACAGACCCGTCAAATATGTTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGATGAC
131 GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGATGAC
17042 ACGTGGAATAAAAATTAAAT-TTTTTT-AATATATTTTATTTTATTGAAATTTATTTT
196 ACGTGGAATAAAAATTAAATATTTTTTAAATATATTTTATTTTATTG-AATTT-TTTT
** *
17098 GGTAAAAGTATTCGGGAGGTCCCTGTACTATACAAAATGTTGATTTTGGTCCCTGTACTTTTTTT
1 GGTAAAAGTACCCGGGAGGTCCCTGTACTATACAAAATATTGATTTTGGTCCCTGTACTTTTTTT
17163 TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGT
66 TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGT
* *
17228 GACAGACCCGTCAAATATGCTGACGTGGCACTAACATCGTCTTTTTTGCTGACGTGGCAGGTGAC
131 GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGATGAC
17293 ACGTGGAATAAAAATTAAATATTTTTTAAATATATTTTATTTTATTGAATTTTTTT
196 ACGTGGAATAAAAATTAAATATTTTTTAAATATATTTTATTTTATTGAATTTTTTT
17349 AAAAAAAAGA
Statistics
Matches: 241, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
251 211 0.88
252 11 0.05
253 19 0.08
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (251 bp):
GGTAAAAGTACCCGGGAGGTCCCTGTACTATACAAAATATTGATTTTGGTCCCTGTACTTTTTTT
TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGT
GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGATGAC
ACGTGGAATAAAAATTAAATATTTTTTAAATATATTTTATTTTATTGAATTTTTTT
Found at i:18346 original size:249 final size:249
Alignment explanation
Indices: 17902--18399 Score: 874
Period size: 249 Copynumber: 2.0 Consensus size: 249
17892 TATTTTTTTA
*
17902 AAAATAAATTTCAATAAAATATATTTAAAAAATATTTAATTTTTATTCCACGTGTCACCTGCCAC
1 AAAATAAATTTCAATAAAAAATATTTAAAAAATATTTAATTTTTATTCCACGTGTCACCTGCCAC
* * * **
17967 GTCAGCAAAAAAAGACGGTGTTAGTGTCACGTCAGCATATTTGACGGGTCTGTCACGGCATGCTA
66 GTCAGCAAAAAAAGACGGTGCTAGTGCCACGTCAGCATATTTGACAGGTCTGTCACGGCACACTA
18032 ACGTGAGGGACCTCGGGTGATAGGTTCTGATAGTAGAGCGACGAATTTGTAGAAAAAAAAAGTAC
131 ACGTGAGGGACCTCGGGTGATAGGTTCTGATAGTAGAGCGACGAATTTGTAGAAAAAAAAAGTAC
*
18097 AGGGACCAAAATCAACATTTCGTATAGTAGAGGGACCTCCCGGGTACTTTTACC
196 AGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCCCGGGTACTTTTACC
18151 AAAATAAATTTCAATAAATAAATATATT-AAAAATATTTAATTTTTATTCCACGTGTCACCTGCC
1 AAAATAAATTTCAATAAA-AAATAT-TTAAAAAATATTTAATTTTTATTCCACGTGTCACCTGCC
18215 ACGTCAGC-AAAAAAGACGGTGCTAGTGCCACGTCAGCATATTTGACAGGTCTGTCACGGCACAC
64 ACGTCAGCAAAAAAAGACGGTGCTAGTGCCACGTCAGCATATTTGACAGGTCTGTCACGGCACAC
* * *
18279 TAACGTGAGGGACCTCGGGTGATAGGTTCTGATAGTAGAGGGATGAATTTGTAGAAAAAATAAGT
129 TAACGTGAGGGACCTCGGGTGATAGGTTCTGATAGTAGAGCGACGAATTTGTAGAAAAAAAAAGT
18344 ACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCCCGGGTACTTTTACC
194 ACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCCCGGGTACTTTTACC
18400 GAATATATGA
Statistics
Matches: 237, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
249 186 0.78
250 49 0.21
251 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (249 bp):
AAAATAAATTTCAATAAAAAATATTTAAAAAATATTTAATTTTTATTCCACGTGTCACCTGCCAC
GTCAGCAAAAAAAGACGGTGCTAGTGCCACGTCAGCATATTTGACAGGTCTGTCACGGCACACTA
ACGTGAGGGACCTCGGGTGATAGGTTCTGATAGTAGAGCGACGAATTTGTAGAAAAAAAAAGTAC
AGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCCCGGGTACTTTTACC
Found at i:27258 original size:57 final size:57
Alignment explanation
Indices: 27170--27283 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
27160 CCAAACTAAC
27170 TTTTTTTTTGTATATTTACAAGTTAACCTTGTTCGAGCCGGGTTGGCCCACTATGGG
1 TTTTTTTTTGTATATTTACAAGTTAACCTTGTTCGAGCCGGGTTGGCCCACTATGGG
27227 TTTTTTTTTGTATATTTACAAGTTAACCTTGTTCGAGCCGGGTTGGCCCACTATGGG
1 TTTTTTTTTGTATATTTACAAGTTAACCTTGTTCGAGCCGGGTTGGCCCACTATGGG
27284 GGTAAAGCTC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.42
Consensus pattern (57 bp):
TTTTTTTTTGTATATTTACAAGTTAACCTTGTTCGAGCCGGGTTGGCCCACTATGGG
Found at i:27435 original size:16 final size:16
Alignment explanation
Indices: 27397--27435 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
27387 GTCCAATCCA
*
27397 AACTAACTAAACAAAC
1 AACTAAATAAACAAAC
*
27413 AAATAAATAAACAAAC
1 AACTAAATAAACAAAC
*
27429 TACTAAA
1 AACTAAA
27436 CCCACATTCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.67, C:0.18, G:0.00, T:0.15
Consensus pattern (16 bp):
AACTAAATAAACAAAC
Found at i:27825 original size:17 final size:17
Alignment explanation
Indices: 27803--27837 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
27793 TTGGTACATG
27803 AGAAAATGTTGAGGAAA
1 AGAAAATGTTGAGGAAA
* *
27820 AGAAAATTTTTAGGAAA
1 AGAAAATGTTGAGGAAA
27837 A
1 A
27838 TTAAAAAGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (17 bp):
AGAAAATGTTGAGGAAA
Found at i:28708 original size:16 final size:17
Alignment explanation
Indices: 28687--28720 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28677 GTATGTATAA
*
28687 ATTATAT-TTAATAAAT
1 ATTATATATCAATAAAT
28703 ATTATATATCAATAAAT
1 ATTATATATCAATAAAT
28720 A
1 A
28721 AAAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTATATATCAATAAAT
Found at i:30321 original size:21 final size:21
Alignment explanation
Indices: 30293--30350 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
30283 TGAATATTTT
30293 TATAAAATTTTGATAACTACC
1 TATAAAATTTTGATAACTACC
* *
30314 TATTAAATTTTGATAATTACC
1 TATAAAATTTTGATAACTACC
*
30335 TATAAAATTGTGATAA
1 TATAAAATTTTGATAA
30351 ACTCGATAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (21 bp):
TATAAAATTTTGATAACTACC
Found at i:33216 original size:26 final size:27
Alignment explanation
Indices: 33157--33217 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
33147 CTAAATTTCC
33157 ATTATTTTAATAATGGAATAATTAAAAT
1 ATTA-TTTAATAATGGAATAATTAAAAT
* *
33185 ATTATTTAGTAATGGTA-AATTAGAAAT
1 ATTATTTAATAATGGAATAATTA-AAAT
33212 A-TATTT
1 ATTATTT
33218 GAAAAAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 10 0.33
27 16 0.53
28 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (27 bp):
ATTATTTAATAATGGAATAATTAAAAT
Found at i:34462 original size:28 final size:27
Alignment explanation
Indices: 34395--34473 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
34385 ACTTGTCTCA
* *
34395 AATTTGACGTTTTGCCCCTTAAACTTT
1 AATTTGACATTTTGCCCCCTAAACTTT
34422 AATTTGACATTTTGCCCCCTAAACTTT
1 AATTTGACATTTTGCCCCCTAAACTTT
* *
34449 AATTTGGAACTTTTTGCCCTCTAAA
1 AATTT-G-ACATTTTGCCCCCTAAA
34474 TTTGCCCCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 30 0.65
28 1 0.02
29 15 0.33
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (27 bp):
AATTTGACATTTTGCCCCCTAAACTTT
Found at i:35630 original size:27 final size:28
Alignment explanation
Indices: 35592--35651 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 28
35582 CAAATTCCAC
35592 TTTCCTGGGAA-TTCTGACAGAGGATTT
1 TTTCCTGGGAATTTCTGACAGAGGATTT
35619 TTTCCTGGGAATTCTTTCTGACAGAGGATTT
1 TTTCCTGGGAA---TTTCTGACAGAGGATTT
35650 TT
1 TT
35652 CTCCCTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 11 0.38
31 18 0.62
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (28 bp):
TTTCCTGGGAATTTCTGACAGAGGATTT
Found at i:36976 original size:29 final size:28
Alignment explanation
Indices: 36935--36989 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
36925 AATTTGTACG
* *
36935 ATTTTGACATTTTGTCTCATAAACTTTA
1 ATTTTGACATTTTGCCCCATAAACTTTA
36963 ATTTTGGACATTTTGCCCCATAAACTT
1 ATTTT-GACATTTTGCCCCATAAACTT
36990 GCAATTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.45
Consensus pattern (28 bp):
ATTTTGACATTTTGCCCCATAAACTTTA
Found at i:36997 original size:29 final size:28
Alignment explanation
Indices: 36935--36997 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
36925 AATTTGTACG
* * * *
36935 ATTTTGACATTTTGTCTCATAAACTTTA
1 ATTTGGACATTTTGCCCCATAAACTTCA
36963 ATTTTGGACATTTTGCCCCATAAACTTGCA
1 A-TTTGGACATTTTGCCCCATAAACTT-CA
36993 ATTTG
1 ATTTG
36998 AAACCATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.03
29 26 0.90
30 2 0.07
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.44
Consensus pattern (28 bp):
ATTTGGACATTTTGCCCCATAAACTTCA
Found at i:38173 original size:22 final size:23
Alignment explanation
Indices: 38140--38200 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
38130 CTTATTTGTC
* *
38140 AATCGTGTAAATTTGCTTTTAAT
1 AATCATGTAAATTTGCTTATAAT
*
38163 AA-CATGTAAATATG-TTATAAT
1 AATCATGTAAATTTGCTTATAAT
**
38184 AATTGTGTAAATTTGCT
1 AATCATGTAAATTTGCT
38201 GGTGGATTGC
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
21 8 0.27
22 19 0.63
23 3 0.10
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (23 bp):
AATCATGTAAATTTGCTTATAAT
Found at i:40355 original size:19 final size:19
Alignment explanation
Indices: 40317--40367 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
40307 TAATAATTTC
*
40317 ATATGTACAGTACCTAATCTA
1 ATATGTACAGT--GTAATCTA
* *
40338 ATTTGTACAGTGTAATCTC
1 ATATGTACAGTGTAATCTA
40357 ATATGTACAGT
1 ATATGTACAGT
40368 TGCTAAACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 16 0.62
21 10 0.38
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (19 bp):
ATATGTACAGTGTAATCTA
Found at i:42060 original size:6 final size:6
Alignment explanation
Indices: 42044--42077 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
42034 AAGCACACAG
42044 TGAATGA TGAAGA TGAAGA TGAAGA TGAAGA TGA
1 TGAA-GA TGAAGA TGAAGA TGAAGA TGAAGA TGA
42078 TGAAGAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.32, T:0.21
Consensus pattern (6 bp):
TGAAGA
Found at i:42085 original size:18 final size:18
Alignment explanation
Indices: 42049--42097 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
42039 CACAGTGAAT
* *
42049 GATGAAGATGAAGATGAA
1 GATGAAGATGATGAAGAA
42067 GATGAAGATGATGAAGAA
1 GATGAAGATGATGAAGAA
* *
42085 GAGGACGATGATG
1 GATGAAGATGATG
42098 GTGATTTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.45, C:0.02, G:0.37, T:0.16
Consensus pattern (18 bp):
GATGAAGATGATGAAGAA
Found at i:54197 original size:12 final size:12
Alignment explanation
Indices: 54176--54217 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
54166 CTCGATCTGC
*
54176 TCTTCCTCTTCT
1 TCTTCATCTTCT
*
54188 TCTTCGTCTTCT
1 TCTTCATCTTCT
*
54200 TCTTCATCATCT
1 TCTTCATCTTCT
54212 TCTTCA
1 TCTTCA
54218 ACAGCTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.07, C:0.36, G:0.02, T:0.55
Consensus pattern (12 bp):
TCTTCATCTTCT
Found at i:54202 original size:15 final size:15
Alignment explanation
Indices: 54182--54216 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
54172 CTGCTCTTCC
* *
54182 TCTTCTTCTTCGTCT
1 TCTTCTTCATCATCT
54197 TCTTCTTCATCATCT
1 TCTTCTTCATCATCT
54212 TCTTC
1 TCTTC
54217 AACAGCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.34, G:0.03, T:0.57
Consensus pattern (15 bp):
TCTTCTTCATCATCT
Found at i:56862 original size:26 final size:26
Alignment explanation
Indices: 56826--56878 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
56816 CCTCATTAAT
*
56826 GCCATGTTTTACATTTTTCTTGGTGA
1 GCCATGTTTTACATATTTCTTGGTGA
56852 GCCATGTTTTACATATTTCTTGGTGA
1 GCCATGTTTTACATATTTCTTGGTGA
56878 G
1 G
56879 TAACACCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (26 bp):
GCCATGTTTTACATATTTCTTGGTGA
Found at i:58283 original size:12 final size:12
Alignment explanation
Indices: 58266--58291 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58256 GAGCACAAGA
58266 TTTTACCTGGGT
1 TTTTACCTGGGT
58278 TTTTACCTGGGT
1 TTTTACCTGGGT
58290 TT
1 TT
58292 AGAGCGCCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.23, T:0.54
Consensus pattern (12 bp):
TTTTACCTGGGT
Found at i:59355 original size:9 final size:9
Alignment explanation
Indices: 59341--59376 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
59331 CCCTCTTATT
59341 GATATTTTA
1 GATATTTTA
59350 GATATTCTTA
1 GATATT-TTA
*
59360 GATGTTTTA
1 GATATTTTA
59369 GATATTTT
1 GATATTTT
59377 TTCTTTCGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.28, C:0.03, G:0.14, T:0.56
Consensus pattern (9 bp):
GATATTTTA
Found at i:60263 original size:50 final size:50
Alignment explanation
Indices: 60198--60297 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 50
60188 ATATTGTTGT
*
60198 TACCATATATTCACTTTCCAAACCGCAAATCCTAGTCCTAATTGTACTTG
1 TACCATATATTCACTTTCAAAACCGCAAATCCTAGTCCTAATTGTACTTG
**
60248 TACCATATATTCACTTTCAAAAGGGCAAATCCTAGTCCTAATTGTACTTG
1 TACCATATATTCACTTTCAAAACCGCAAATCCTAGTCCTAATTGTACTTG
60298 GATTTGCTCT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (50 bp):
TACCATATATTCACTTTCAAAACCGCAAATCCTAGTCCTAATTGTACTTG
Found at i:63965 original size:180 final size:180
Alignment explanation
Indices: 63652--64012 Score: 704
Period size: 180 Copynumber: 2.0 Consensus size: 180
63642 TTCAGAGTCA
63652 GTTAATTTGAGTCTGAGTTTGGCTTTTGTCCAGTTTTTAGTTTGCAATAGATTGAAAACAGTTTG
1 GTTAATTTGAGTCTGAGTTTGGCTTTTGTCCAGTTTTTAGTTTGCAATAGATTGAAAACAGTTTG
63717 TTTTGTCGGAATGGTTTTTCTTTCTGATCAAAGGGTGGGTGCTGATGATCCTCGAATCAGCCACT
66 TTTTGTCGGAATGGTTTTTCTTTCTGATCAAAGGGTGGGTGCTGATGATCCTCGAATCAGCCACT
63782 TTTTTATCGCTGTTGAAAGCTTTTTCTTGGATTCACCGAGAAGCAAAAGC
131 TTTTTATCGCTGTTGAAAGCTTTTTCTTGGATTCACCGAGAAGCAAAAGC
*
63832 GTTAGTTTGAGTCTGAGTTTGGCTTTTGTCCAGTTTTTAGTTTGCAATAGATTGAAAACAGTTTG
1 GTTAATTTGAGTCTGAGTTTGGCTTTTGTCCAGTTTTTAGTTTGCAATAGATTGAAAACAGTTTG
*
63897 TTTTGTCGGAATGGTTTTTCTTTCTGATCAAAGGGTGGGTGCTGATGATCCTCGAATCAGCTACT
66 TTTTGTCGGAATGGTTTTTCTTTCTGATCAAAGGGTGGGTGCTGATGATCCTCGAATCAGCCACT
63962 TTTTTATCGCTGTTGAAAGCTTTTTCTTGGATTCACCGAGAAGCAAAAGC
131 TTTTTATCGCTGTTGAAAGCTTTTTCTTGGATTCACCGAGAAGCAAAAGC
64012 G
1 G
64013 ATGGAGTGGT
Statistics
Matches: 179, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 179 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.40
Consensus pattern (180 bp):
GTTAATTTGAGTCTGAGTTTGGCTTTTGTCCAGTTTTTAGTTTGCAATAGATTGAAAACAGTTTG
TTTTGTCGGAATGGTTTTTCTTTCTGATCAAAGGGTGGGTGCTGATGATCCTCGAATCAGCCACT
TTTTTATCGCTGTTGAAAGCTTTTTCTTGGATTCACCGAGAAGCAAAAGC
Found at i:66191 original size:23 final size:23
Alignment explanation
Indices: 66165--66209 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
66155 CAAGAAGCAG
66165 TGCCGCGGCGGGGAGAGAGTCAC
1 TGCCGCGGCGGGGAGAGAGTCAC
66188 TGCCGCGGCGGGGAGAGAGTCA
1 TGCCGCGGCGGGGAGAGAGTCA
66210 TCAGTGACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.49, T:0.09
Consensus pattern (23 bp):
TGCCGCGGCGGGGAGAGAGTCAC
Found at i:66334 original size:51 final size:48
Alignment explanation
Indices: 66262--66457 Score: 158
Period size: 51 Copynumber: 4.1 Consensus size: 48
66252 GAAGAGGTCC
* *
66262 CATCTTCAGTGATGGAAGACGAGCTTCTTCCATTTGATCTAACTAATCCAT
1 CATCATCAGTGATGGAAGACGAG---CTTCCATCTGATCTAACTAATCCAT
*
66313 CATCATCAGTTATGGAAGACGAGCTTCCATCTGATCTAACTAATCCAT
1 CATCATCAGTGATGGAAGACGAGCTTCCATCTGATCTAACTAATCCAT
* * * *
66361 CATCAGTTCCA-TCATCGGAAGAGGAGC-TCTCATTTGATCTAA-TGGAT-C--
1 CATCA--T-CAGTGAT-GGAAGACGAGCTTC-CATCTGATCTAACT-AATCCAT
* * *
66409 CATCATCAGTGA-CG--GACGAGCTTCCATTTGATCTAAATAATCCAT
1 CATCATCAGTGATGGAAGACGAGCTTCCATCTGATCTAACTAATCCAT
66454 CATC
1 CATC
66458 GGAAGATGAG
Statistics
Matches: 122, Mismatches: 11, Indels: 30
0.75 0.07 0.18
Matches are distributed among these distances:
42 20 0.16
43 4 0.03
44 1 0.01
45 6 0.05
46 3 0.02
48 34 0.28
50 8 0.07
51 46 0.38
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30
Consensus pattern (48 bp):
CATCATCAGTGATGGAAGACGAGCTTCCATCTGATCTAACTAATCCAT
Found at i:66348 original size:48 final size:49
Alignment explanation
Indices: 66262--66365 Score: 156
Period size: 48 Copynumber: 2.1 Consensus size: 49
66252 GAAGAGGTCC
* *
66262 CATCTTCAGTGATGGAAGACGAGCTTCTTCCATTTGATCTAACTAATCCAT
1 CATCATCAGTGATGGAAGACGAG--TCTTCCATCTGATCTAACTAATCCAT
*
66313 CATCATCAGTTATGGAAGACGAG-CTTCCATCTGATCTAACTAATCCAT
1 CATCATCAGTGATGGAAGACGAGTCTTCCATCTGATCTAACTAATCCAT
66361 CATCA
1 CATCA
66366 GTTCCATCAT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
48 29 0.58
51 21 0.42
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (49 bp):
CATCATCAGTGATGGAAGACGAGTCTTCCATCTGATCTAACTAATCCAT
Found at i:66469 original size:39 final size:39
Alignment explanation
Indices: 66368--66474 Score: 110
Period size: 42 Copynumber: 2.7 Consensus size: 39
66358 CATCATCAGT
* *
66368 TCCATCATCGGAAGAGGAGC-TCTCATTTGATCTAATGGA
1 TCCATCATCGGAAGACGAGCTTC-CATTTGATCTAATGAA
*
66407 TCCATCATCAGTGACGGACGAGCTTCCATTTGATCTAAAT-AA
1 TCCATCATC-G-GA-AGACGAGCTTCCATTTGATCT-AATGAA
* *
66449 TCCATCATCGGAAGATGAGCTACCAT
1 TCCATCATCGGAAGACGAGCTTCCAT
66475 CCTCGGATGA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
39 20 0.35
40 3 0.05
41 3 0.05
42 26 0.46
43 5 0.09
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (39 bp):
TCCATCATCGGAAGACGAGCTTCCATTTGATCTAATGAA
Found at i:66542 original size:27 final size:28
Alignment explanation
Indices: 66512--66573 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 28
66502 ATCTAATGGA
* *
66512 TCCATCTTCAGTAACG-GAAGATGAGGT
1 TCCATCATCAGTAACGCGAAGATGAGAT
*
66539 TCCATCATCAGTGACGTCCGAAGATGAGAT
1 TCCATCATCAGTAACG--CGAAGATGAGAT
66569 TCCAT
1 TCCAT
66574 TCGATCTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 14 0.48
30 15 0.52
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (28 bp):
TCCATCATCAGTAACGCGAAGATGAGAT
Found at i:72212 original size:13 final size:13
Alignment explanation
Indices: 72194--72246 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
72184 TATCAGATCT
72194 TTATACAAAATAA
1 TTATACAAAATAA
72207 TTATACAAAATCAAA
1 TTATACAAAAT--AA
* **
72222 TCTCTTTAAAATAA
1 T-TATACAAAATAA
72236 TTATACAAAAT
1 TTATACAAAAT
72247 CAAAATCCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
13 18 0.58
14 3 0.10
15 3 0.10
16 7 0.23
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (13 bp):
TTATACAAAATAA
Found at i:72752 original size:16 final size:16
Alignment explanation
Indices: 72733--72780 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
72723 GTCTTTCCCT
72733 ATTTTCATAGTTTAAA
1 ATTTTCATAGTTTAAA
* * *
72749 ATTTTCTTTTGTTTAAC
1 ATTTTC-ATAGTTTAAA
72766 ATTTTCATAGTTTAA
1 ATTTTCATAGTTTAA
72781 TTTGTTTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.56
Consensus pattern (16 bp):
ATTTTCATAGTTTAAA
Done.