Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012544.1 Corchorus capsularis cultivar CVL-1 contig12565, 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: 53738
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:19265 original size:32 final size:32
Alignment explanation
Indices: 19156--19458 Score: 394
Period size: 32 Copynumber: 9.0 Consensus size: 32
19146 TTGAGGGCCA
19156 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
19188 ATGTG-ATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
19219 ATGTG-ATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
*
19250 ATGTGAATTAAGGCAAGTTCAATGTCATTTTG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
*
19282 ATGTGAATTAAGGCAAGTTCAATGTTATTTGGGAAAGTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCA--T-------TTGG
19323 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
* *
19355 ATGTGAATCAAGGCAAGTTCAATGTTATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
*
19387 ATGTGAATTAAGGCAAGTTCAATGTTATTTGGAAAGTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCA--T------TTGG
19427 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
19459 GAAAGTTGGT
Statistics
Matches: 245, Mismatches: 8, Indels: 36
0.85 0.03 0.12
Matches are distributed among these distances:
31 62 0.25
32 120 0.49
34 2 0.01
38 1 0.00
39 1 0.00
40 30 0.12
41 29 0.12
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (32 bp):
ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
Found at i:19340 original size:21 final size:21
Alignment explanation
Indices: 19281--19347 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
19271 ATGTCATTTT
19281 GATGTGAATTAAGGCAAGTTC
1 GATGTGAATTAAGGCAAGTTC
* * ** * *
19302 AATGT-TATTTGGGAAAGTTG
1 GATGTGAATTAAGGCAAGTTC
19322 GATGTGAATTAAGGCAAGTTC
1 GATGTGAATTAAGGCAAGTTC
*
19343 AATGT
1 GATGT
19348 CATTTGGATG
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (21 bp):
GATGTGAATTAAGGCAAGTTC
Found at i:19368 original size:73 final size:73
Alignment explanation
Indices: 19246--19503 Score: 309
Period size: 73 Copynumber: 3.5 Consensus size: 73
19236 TCAATGTCAT
*
19246 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTTGATGTGAATTAAGGCAAGTTCAATGTTATT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTTATT
19311 TGGGAAAG
66 TGGGAAAG
*
19319 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATCAAGGCAAGTTCAATGTTA--
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTTATT
19382 T-------
66 TGGGAAAG
*
19383 TTGGATGTGAATTAAGGCAAGTTCAATGTTATTTGGAAAGTTGGATGTGAATTAAGGCAAGTTCA
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCA--T------TTGGATGTGAATTAAGGCAAGTTCA
*
19448 ATGTCATTTGGGAAAGTTGG
58 ATGTTATTTGGGAAA----G
19468 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
19504 GAATGTTAAA
Statistics
Matches: 158, Mismatches: 6, Indels: 38
0.78 0.03 0.19
Matches are distributed among these distances:
64 30 0.19
66 1 0.01
71 1 0.01
72 29 0.18
73 61 0.39
74 1 0.01
77 4 0.03
83 1 0.01
85 30 0.19
ACGTcount: A:0.31, C:0.07, G:0.27, T:0.35
Consensus pattern (73 bp):
TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTTATT
TGGGAAAG
Found at i:19406 original size:105 final size:104
Alignment explanation
Indices: 19215--19458 Score: 445
Period size: 105 Copynumber: 2.3 Consensus size: 104
19205 TCAATGTCAT
*
19215 TTGGATGTG-ATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTCATT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATCAAGGCAAGTTCAATGTCATT
*
19279 TTGATGTGAATTAAGGCAAGTTCAATGTTATTTGGGAAAG
66 TGGATGTGAATTAAGGCAAGTTCAATGTTATTT-GGAAAG
*
19319 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATCAAGGCAAGTTCAATGTTATT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATCAAGGCAAGTTCAATGTCATT
19384 TGGATGTGAATTAAGGCAAGTTCAATGTTATTTGGAAAG
66 TGGATGTGAATTAAGGCAAGTTCAATGTTATTTGGAAAG
19423 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
19459 GAAAGTTGGT
Statistics
Matches: 136, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
104 51 0.38
105 85 0.62
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (104 bp):
TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATCAAGGCAAGTTCAATGTCATT
TGGATGTGAATTAAGGCAAGTTCAATGTTATTTGGAAAG
Found at i:19451 original size:21 final size:21
Alignment explanation
Indices: 19387--19451 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
19377 TGTTATTTGG
19387 ATGTGAATTAAGGCAAGTTCA
1 ATGTGAATTAAGGCAAGTTCA
* * * **
19408 ATGT-TATT-TGGAAAGTTGG
1 ATGTGAATTAAGGCAAGTTCA
19427 ATGTGAATTAAGGCAAGTTCA
1 ATGTGAATTAAGGCAAGTTCA
19448 ATGT
1 ATGT
19452 CATTTGGGAA
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
19 11 0.34
20 6 0.19
21 15 0.47
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (21 bp):
ATGTGAATTAAGGCAAGTTCA
Found at i:19486 original size:45 final size:41
Alignment explanation
Indices: 19383--19520 Score: 197
Period size: 45 Copynumber: 3.3 Consensus size: 41
19373 TCAATGTTAT
*
19383 TTGGATGTGAATTAAGGCAAGTTCAATGTTATTT-GGAAAG
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAG
19423 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAA----G
*
19468 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAATG
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAG
**
19509 TTAAATGTGAAT
1 TTGGATGTGAAT
19521 GTGCCGCGTG
Statistics
Matches: 89, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
40 33 0.37
41 16 0.18
45 40 0.45
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.35
Consensus pattern (41 bp):
TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAG
Found at i:23167 original size:331 final size:330
Alignment explanation
Indices: 21751--23861 Score: 1843
Period size: 331 Copynumber: 6.4 Consensus size: 330
21741 TCAGTTAGGT
* * ** * *
21751 AACATGATTCAGATG-TCCGTAAAAATAAATTATTAAATCTAACGTGGCTGAAATTTGGTTAGAT
1 AACAAGATTCAGATGCT-CGTAAAAAGAAATCCTTAAATCCAACGTGGCTGAGATTTGGTTAGAT
** * * *
21815 GAATATAGATATTTCAAGGAGTCTCAGTGCCAAAAATTAAGCAAAACTGAGTTGGGGCCTCAGAA
65 GAATATAGATATTTCAAGGAGTCTGGGTGCCAAAAATCAAGCAAAACTGAGTTGGGGCCCCGGAA
* * * * *
21880 CACG-TTTTAGTC-AAAATCCATGATGGTTGGAACACGATTTCAGCTAAAATTTTAC-AAAAATG
130 CACGTTTTTAGCCAAAAAT-CGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAATG
** *** * * * *
21942 ATTC-ATTTGTTTT-TTCAATTTTT-AGCCACGATACTCAGAAAAAATATATAATTCAACGCCAA
194 ACCCGAAAAGTTTTCCTCAATTTTTGA-CCACAATACTCAAAAAAAATATATAATTCAA-TCCAA
* * * * *
22004 AAAAATTGAAGGGCTTTTCAAGCATCTAATATTGTTTTACCTATTTTTTCTGAATTAATTTTTGA
257 AAAGATTGAAGGGCTTTTCAAGCATCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAA
*
22069 TTAAATCTA
322 TTAAATCAA
* * * * ** * *
22078 AACATGATTCAGATGCTCATAAAAATAAATCTTTAAATCCAATTTGGTTGAGATTTGATTAGATG
1 AACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAACGTGGCTGAGATTTGGTTAGATG
* * * * **
22143 AATATAAATATTTC---GAGTCTGGATGCTAAAAATCAAGCAAAATTGAGTTGGGGCCCTAGAAC
66 AATATAGATATTTCAAGGAGTCTGGGTGCCAAAAATCAAGCAAAACTGAGTTGGGGCCCCGGAAC
** * ** * *
22205 GTGTTTTTAGCCAAAAAATCGTGATGGTTAGTACACAATTTTGGCTAAATTTTTGCAAAAAATAA
131 ACGTTTTTAGCC-AAAAATCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAATGA
* * *
22270 CCTGAATAGTTTTACCTCAATTTTTGACCACAAAACTCATAAAAAAA-ATTATAATTCAATGCCA
195 CCCGAAAAGTTTT-CCTCAATTTTTGACCACAATACTCA-AAAAAAATA-TATAATTCAAT-CCA
* * ** * *
22334 AAATTGATTGAAGGGCTTTACGCGCATCTAGTATCGTTTTTCC-ATTTCTTT-TACGAATTAGTT
256 AAA-AGATTGAAGGGCTTTTCAAGCATCTAATATCGTTTTTCCTATTT-TTTCT--GAATTAATT
*
22397 TCTAATAAAAT-ACA
317 TCTAATTAAATCA-A
* * * * ** * * *
22411 AACAATATTTACATGCTCGTAAAAACAAGA-CCTTAAATGTAATGTGGTTGAGATTTGATTAGAT
1 AACAAGATTCAGATGCTCGTAAAAAGAA-ATCCTTAAATCCAACGTGGCTGAGATTTGGTTAGAT
*** * * * * * * **
22475 TCCTAT-GTATGTTTCAATGAGTCTGGGCGCTAAAAATCAAACAAAACTGAGTTAGGGCCCCAAA
65 GAATATAG-ATATTTCAAGGAGTCTGGGTGCCAAAAATCAAGCAAAACTGAGTTGGGGCCCCGGA
* * *
22539 ACACGTTTTTGGCC----ACCGTGATGATTAGTACACGATTTCAG-TAAAAATTTTGCAAAAAAA
129 ACACGTTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCAGCT-AAAATTTTGC-AAAAAA
* ** * * * *
22599 TGATTCAAAAAATTTTTCCTTAATTTTTTG-CAACAATACT--AAAAAAA-A-ATAATTTAATGC
192 TGA-CCCGAAAAGTTTTCCTCAA-TTTTTGACCACAATACTCAAAAAAAATATATAATTCAAT-C
* * *** *
22659 AAAAAAGATGGAATTTCTTTTCAAGCATCTAATATCGTTTTTCCTATTTTTTCTGATTTAATTTC
254 CAAAAAGATTGAAGGGCTTTTCAAGCATCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTC
* *
22724 TGATTAAATCGA
319 TAATTAAATCAA
* * * * * * *
22736 AAC---A-T---ATGCTTGTAAAAACAAATCTTTAAATCCAATGTGACCGAGATTTCGTTAGATT
1 AACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAACGTGGCTGAGATTTGGTTAGA-T
* * * * * *
22794 G-ATATAGATATTTCAAGGACTCTCGGCGCCAAAAATCAAGCAAAACCGAGTCGGGGCTCCGGAA
65 GAATATAGATATTTCAAGGAGTCTGGGTGCCAAAAATCAAGCAAAACTGAGTTGGGGCCCCGGAA
* * * * *
22858 CACGTTTTTAGCCAAAAATTGTGATGATTAATACATGATTTCAGCTAGAATTTTGCAAAAAATGA
130 CACGTTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAATGA
22923 CCCGAAAATGTTTTCCTCAA-TTTTGACCACAATTA-TCAAAAAAAGATATATAATTCAACTCCA
195 CCCGAAAA-GTTTTCCTCAATTTTTGACCACAA-TACTCAAAAAAA-ATATATAATTCAA-TCCA
* ** *
22986 AAAATATTGAAGGGCTTTTCAATTATATAATATCGTTTTTCC-ATTTTATTCTGAATTAATTTCT
256 AAAAGATTGAAGGGCTTTTCAAGCATCTAATATCGTTTTTCCTATTTT-TTCTGAATTAATTTCT
23050 AATTAAATCAA
320 AATTAAATCAA
* * * * *
23061 AACAAGACTCAAATGCTCGT-TAAAGAAATCCTTATATCCAACGTGCCTGAGATTTGGTTAGATG
1 AACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAACGTGGCTGAGATTTGGTTAGATG
* * * * * * * ** **
23125 AATATAAATGTTTCAAGGAGACTGGGCGCCAAAAACCAAGCAAAATTGAGCTGGGATCTTGGAAC
66 AATATAGATATTTCAAGGAGTCTGGGTGCCAAAAATCAAGCAAAACTGAGTTGGGGCCCCGGAAC
* *
23190 ACGTTTTTAGCCAAAAATCGTGA-CG-T-GTACATGATTTCAGCTAAAATTTTTGCAAAAAATGA
131 ACGTTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCAGCTAAAA-TTTTGCAAAAAATGA
* ** * * **
23252 TCCGAAAAGTTTTTCCTCAATACTTGACCACAATACTCATAAAATATATATAATTCCAAGACAAA
195 CCCGAAAAG-TTTTCCTCAATTTTTGACCACAATACTCAAAAAAAATATATAATT-CAATCCAAA
* ** *
23317 AAGATT-AGAGGTCTTTTCGCGCATCTAATATCGTTTTTCCATATTTTTTTCCGAATTAATTTCT
258 AAGATTGA-AGGGCTTTTCAAGCATCTAATATCGTTTTTCC-TA-TTTTTTCTGAATTAATTTCT
23381 AATTAAAT-AGA
320 AATTAAATCA-A
* * * * *
23392 AACAAGATTTAGATGCTCATAAAAAGAAATCCTTAAATCCAACATGGTTTAGATTTGGTTAGATG
1 AACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAACGTGGCTGAGATTTGGTTAGATG
* * ** * * * *
23457 TATATATACGTATCAAGGAGTCTGGATGCCAAAAATCAAGCATAACTGAGTTGGGACCCCGGAAC
66 AATATAGATATTTCAAGGAGTCTGGGTGCCAAAAATCAAGCAAAACTGAGTTGGGGCCCCGGAAC
* *
23522 ACGTTTTTAGCCAAAAA-CTGTGATGGTTAGTACACGATTTTCGGCTAAAATTTTACAAAAAAAA
131 ACGTTTTTAGCCAAAAATC-GTGATGGTTAGTACACGA-TTTCAGCTAAAATTTTGC--AAAAAA
* * *
23586 TGACCCGAAAAGTTTTTCCTTAATTTTTTG-CCACAATACTCAGAAAAAATATATAACTCAACTC
192 TGACCCGAAAAG-TTTTCCTCAA-TTTTTGACCACAATACTCAAAAAAAATATATAATTCAA-TC
* * * *
23650 CAAAAAGATTGAAGGGATTTTCAAGCACCTAATATTGCTTTTCCTATTTTTT-TGAATTAATTTC
254 CAAAAAGATTGAAGGGCTTTTCAAGCATCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTC
** **
23714 GGATTAAATTGA
319 TAATTAAATCAA
* * ** *
23726 GACATGATTCAGATGCTCGTAAAAAGAAATTATTAAATCCAACGT-GATCGAGATTTGGTTAGAT
1 AACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAACGTGGCT-GAGATTTGGTTAGAT
*
23790 GAATATAGATATTTCAAGGAGTCCT-GGTGCCAAAAATCAAGCAAAACTGAGTTGGGGCCCCGAA
65 GAATATAGATATTTCAAGGAGT-CTGGGTGCCAAAAATCAAGCAAAACTGAGTTGGGGCCCCGGA
*
23854 ACATGTTT
129 ACACGTTT
23862 ATTAAATCCA
Statistics
Matches: 1437, Mismatches: 268, Indels: 151
0.77 0.14 0.08
Matches are distributed among these distances:
317 1 0.00
318 100 0.07
319 7 0.00
320 11 0.01
321 21 0.01
322 39 0.03
323 2 0.00
324 47 0.03
325 98 0.07
326 63 0.04
327 99 0.07
328 29 0.02
329 89 0.06
330 44 0.03
331 206 0.14
332 176 0.12
333 95 0.07
334 132 0.09
335 20 0.01
336 66 0.05
337 87 0.06
338 5 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (330 bp):
AACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAACGTGGCTGAGATTTGGTTAGATG
AATATAGATATTTCAAGGAGTCTGGGTGCCAAAAATCAAGCAAAACTGAGTTGGGGCCCCGGAAC
ACGTTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAATGAC
CCGAAAAGTTTTCCTCAATTTTTGACCACAATACTCAAAAAAAATATATAATTCAATCCAAAAAG
ATTGAAGGGCTTTTCAAGCATCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAA
ATCAA
Found at i:23887 original size:105 final size:105
Alignment explanation
Indices: 23755--23966 Score: 397
Period size: 105 Copynumber: 2.0 Consensus size: 105
23745 TAAAAAGAAA
* *
23755 TTATTAAATCCAACGTGATCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCCTGGTGC
1 TTATTAAATCCAACGTGACCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCCCGGTGC
23820 CAAAAATCAAGCAAAACTGAGTTGGGGCCCCGAAACATGT
66 CAAAAATCAAGCAAAACTGAGTTGGGGCCCCGAAACATGT
*
23860 TTATTAAATCCAACGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCCCGGTGC
1 TTATTAAATCCAACGTGACCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCCCGGTGC
23925 CAAAAATCAAGCAAAACTGAGTTGGGGCCCCGAAACATGT
66 CAAAAATCAAGCAAAACTGAGTTGGGGCCCCGAAACATGT
23965 TT
1 TT
23967 TTAGCCAAAA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.26
Consensus pattern (105 bp):
TTATTAAATCCAACGTGACCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCCCGGTGC
CAAAAATCAAGCAAAACTGAGTTGGGGCCCCGAAACATGT
Found at i:24424 original size:41 final size:40
Alignment explanation
Indices: 24334--24424 Score: 94
Period size: 42 Copynumber: 2.2 Consensus size: 40
24324 AGGGCTATCA
* * *
24334 TGGGCCTTCAAGCTTATTGTTAAAAACCATAGGCTTATAT
1 TGGGCCTTCAAGCATATTGTTAAAAACCATAGGATTACAT
* **
24374 TGGACCCTTCAAAGCATATTGTTAAAAGTCAT-GAGATTACAT
1 TGG-GCCTTC-AAGCATATTGTTAAAAACCATAG-GATTACAT
24416 TGGGCCTTC
1 TGGGCCTTC
24425 CAAGTAATGA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
40 3 0.07
41 11 0.27
42 27 0.66
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (40 bp):
TGGGCCTTCAAGCATATTGTTAAAAACCATAGGATTACAT
Found at i:26008 original size:53 final size:53
Alignment explanation
Indices: 25922--26052 Score: 217
Period size: 53 Copynumber: 2.5 Consensus size: 53
25912 CAACACGCGA
* *
25922 AGACACGAAGCTACACGAGAAGACAGAGGCCTCCGGAGTGAGGCGAGGCCAGT
1 AGACACGAAGCTACACGAGAAGACAGAGGCCTCCGAAGTGAGGCGAGGCCAGC
* *
25975 GGACATGAAGCTACACGAGAAGACAGAGGCCTCCGAAGTGAGGCGAGGCCAGC
1 AGACACGAAGCTACACGAGAAGACAGAGGCCTCCGAAGTGAGGCGAGGCCAGC
*
26028 AGACACGAAGGTACACGAGAAGACA
1 AGACACGAAGCTACACGAGAAGACA
26053 CACACAAGGT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 71 1.00
ACGTcount: A:0.35, C:0.24, G:0.34, T:0.07
Consensus pattern (53 bp):
AGACACGAAGCTACACGAGAAGACAGAGGCCTCCGAAGTGAGGCGAGGCCAGC
Found at i:26063 original size:23 final size:24
Alignment explanation
Indices: 26030--26077 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
26020 AGGCCAGCAG
*
26030 ACACGAAGGTACACGAGAAGACAC
1 ACACGAAGGTACACAAGAAGACAC
26054 ACAC-AAGGTACACAAGAAGACAC
1 ACACGAAGGTACACAAGAAGACAC
26077 A
1 A
26078 TGAAACACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.50, C:0.25, G:0.21, T:0.04
Consensus pattern (24 bp):
ACACGAAGGTACACAAGAAGACAC
Found at i:26087 original size:21 final size:21
Alignment explanation
Indices: 26063--26129 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
26053 CACACAAGGT
* *
26063 ACACAAGAAGACACATGAAAC
1 ACACAAGAAGACACACGACAC
*
26084 ACACGAGAAGACACACGACAC
1 ACACAAGAAGACACACGACAC
*
26105 ACACAAAAAGACACACGACAC
1 ACACAAGAAGACACACGACAC
26126 ACAC
1 ACAC
26130 GAAGGTACAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.54, C:0.31, G:0.13, T:0.01
Consensus pattern (21 bp):
ACACAAGAAGACACACGACAC
Found at i:26116 original size:42 final size:43
Alignment explanation
Indices: 26040--26131 Score: 116
Period size: 42 Copynumber: 2.1 Consensus size: 43
26030 ACACGAAGGT
* * *
26040 ACACGAGAAGACACACACAAGGTACACAAGAAGACACATGAAAC
1 ACACGAGAAGACACACACAA-GCACACAAAAAGACACACGAAAC
*
26084 ACACGAGAAGACACACGAC-A-CACACAAAAAGACACACGACAC
1 ACACGAGAAGACACAC-ACAAGCACACAAAAAGACACACGAAAC
26126 ACACGA
1 ACACGA
26132 AGGTACACGG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 24 0.56
44 17 0.40
45 2 0.05
ACGTcount: A:0.52, C:0.29, G:0.16, T:0.02
Consensus pattern (43 bp):
ACACGAGAAGACACACACAAGCACACAAAAAGACACACGAAAC
Found at i:34891 original size:12 final size:12
Alignment explanation
Indices: 34866--34900 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
34856 AAGGACTAGC
*
34866 TTCTGCTTCGGT
1 TTCTGCTTCTGT
*
34878 TTCTGTTTCTGT
1 TTCTGCTTCTGT
34890 TTCTGCTTCTG
1 TTCTGCTTCTG
34901 CTTCGTTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.23, G:0.20, T:0.57
Consensus pattern (12 bp):
TTCTGCTTCTGT
Found at i:37609 original size:7 final size:7
Alignment explanation
Indices: 37597--37621 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
37587 ATTTGTACTT
37597 GACAGTA
1 GACAGTA
37604 GACAGTA
1 GACAGTA
37611 GACAGTA
1 GACAGTA
37618 GACA
1 GACA
37622 CAGTAGAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.16, G:0.28, T:0.12
Consensus pattern (7 bp):
GACAGTA
Found at i:38876 original size:30 final size:29
Alignment explanation
Indices: 38842--38910 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
38832 ATAGCAAAAA
*
38842 GGCTTATTTGGCCAAAATTCATAGTTTAGG
1 GGCTTATTTGGCCAAAATTCA-AGTTAAGG
** * *
38872 GGCTTATAAGGCCAAAATTGAAGTTAAGT
1 GGCTTATTTGGCCAAAATTCAAGTTAAGG
38901 GGCTTATTTG
1 GGCTTATTTG
38911 ACTATATATT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.35
Consensus pattern (29 bp):
GGCTTATTTGGCCAAAATTCAAGTTAAGG
Found at i:41719 original size:14 final size:14
Alignment explanation
Indices: 41700--41727 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41690 GGAGTATTCG
41700 GTTTAGTATGAATA
1 GTTTAGTATGAATA
41714 GTTTAGTATGAATA
1 GTTTAGTATGAATA
41728 ATTGGAGAAG
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:0.00, G:0.21, T:0.43
Consensus pattern (14 bp):
GTTTAGTATGAATA
Found at i:44244 original size:30 final size:29
Alignment explanation
Indices: 44177--44246 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
44167 ACACCGAACC
***
44177 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTATAAAA
* *
44206 GCCAAATAAGCCCCTGAACTCTTATAAAAA
1 GTCAAATAAGCCCCTGAACTATTAT-AAAA
44236 GTCAAATAAGC
1 GTCAAATAAGC
44247 TCTGTTGCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 23 0.68
30 11 0.32
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.24
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTATAAAA
Found at i:47975 original size:2 final size:2
Alignment explanation
Indices: 47968--48011 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
47958 CAATATAAAG
* *
47968 AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T CT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48008 AT AT
1 AT AT
48012 TCAAGGCCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50698 original size:16 final size:16
Alignment explanation
Indices: 50677--50710 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
50667 ACTTTACTTT
50677 AAATTACTCGAGATTC
1 AAATTACTCGAGATTC
50693 AAATTACTCGAGATTC
1 AAATTACTCGAGATTC
50709 AA
1 AA
50711 TATGATTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (16 bp):
AAATTACTCGAGATTC
Found at i:51505 original size:2 final size:2
Alignment explanation
Indices: 51500--51525 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
51490 CATGATTTTC
51500 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
51526 TTTCATGATT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53011 original size:13 final size:13
Alignment explanation
Indices: 52993--53026 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
52983 TCCTAAATTT
52993 AAACAAAAATAAG
1 AAACAAAAATAAG
53006 AAAC-AAAATAAG
1 AAACAAAAATAAG
53018 AAACAAAAA
1 AAACAAAAA
53027 AGAAGAAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.79, C:0.09, G:0.06, T:0.06
Consensus pattern (13 bp):
AAACAAAAATAAG
Found at i:53013 original size:12 final size:12
Alignment explanation
Indices: 52993--53030 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
52983 TCCTAAATTT
52993 AAACAAAAATAAG
1 AAAC-AAAATAAG
53006 AAACAAAATAAG
1 AAACAAAATAAG
53018 AAACAAAA-AAG
1 AAACAAAATAAG
53029 AA
1 AA
53031 GAAAGCCTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 5 0.20
12 16 0.64
13 4 0.16
ACGTcount: A:0.79, C:0.08, G:0.08, T:0.05
Consensus pattern (12 bp):
AAACAAAATAAG
Done.