Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016284.1 Corchorus olitorius cultivar O-4 contig16317, 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: 126183
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:143 original size:19 final size:20
Alignment explanation
Indices: 121--163 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
111 TTTTGTTTCC
*
121 AATAAGCATTTTTTGGATA-
1 AATAAGCATTTTTTGAATAT
140 AAT-AGCATTTTTTGAATAT
1 AATAAGCATTTTTTGAATAT
159 AATAA
1 AATAA
164 ACTGTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 14 0.67
19 6 0.29
20 1 0.05
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (20 bp):
AATAAGCATTTTTTGAATAT
Found at i:4130 original size:29 final size:29
Alignment explanation
Indices: 4075--4133 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
4065 CATTATTATT
*
4075 TTCTTTTCCTTTTCTCTTTATGTAACTTG
1 TTCTTTTCCTTTTCTCTTTATGCAACTTG
*
4104 TTCTTTTCCTTTTCTTTTTCA-GCAACTTG
1 TTCTTTTCCTTTTCTCTTT-ATGCAACTTG
4133 T
1 T
4134 CAGGCAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.10, C:0.22, G:0.07, T:0.61
Consensus pattern (29 bp):
TTCTTTTCCTTTTCTCTTTATGCAACTTG
Found at i:11821 original size:22 final size:22
Alignment explanation
Indices: 11796--11842 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
11786 TTTTTAGTTG
*
11796 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
11818 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
11840 AGT
1 AGT
11843 TATAAGTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:11828 original size:93 final size:93
Alignment explanation
Indices: 11719--11897 Score: 286
Period size: 93 Copynumber: 1.9 Consensus size: 93
11709 GCTTTTTAAT
* * * *
11719 TAAATTAGTAATATGGTAAAAATAAAATAGGTATATGGATATTAAATTTGATTAAATAAAAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAAATTTGATTAAAGAAAAATAG
*
11784 AGTTTTTAGTTGAGTAAAACTATAAAAG
66 AGTTTTTAGTTGACTAAAACTATAAAAG
* * *
11812 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGTATATTAGATTTGATTAAAGAAAAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAAATTTGATTAAAGAAAAATAG
11877 AGTTTTTAGTTGACTAAAACT
66 AGTTTTTAGTTGACTAAAACT
11898 GTATAAGTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 78 1.00
ACGTcount: A:0.50, C:0.02, G:0.15, T:0.34
Consensus pattern (93 bp):
TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAAATTTGATTAAAGAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAG
Found at i:12989 original size:89 final size:82
Alignment explanation
Indices: 12880--13043 Score: 238
Period size: 85 Copynumber: 1.9 Consensus size: 82
12870 AAATTATAAT
12880 ATATATCTAAGTTATGTAATTAAAATACAAGTAAAAATGGTAAAAATAAAATAGTTATAAAGAGA
1 ATATATCTAAGTTATGTAATTAAAAT---AGT-AAAATGGTAAAAATAAAATAGTTATAAAGA-A
12945 TTAGATTTAATTAAAAATTCTA
61 TTAGATTTAATTAAAAATTCTA
* * *
12967 ATATATCTAAGTTTTTTTTAATTAAAATAGTAAAATGGTAAAAATGAAATAGTTATAAAGAATTA
1 ATATATCTAAG--TTATGTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGAATTA
13032 GATTTAATTAAA
64 GATTTAATTAAA
13044 TAAAAATAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
84 16 0.22
85 29 0.40
86 3 0.04
87 11 0.15
89 13 0.18
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.36
Consensus pattern (82 bp):
ATATATCTAAGTTATGTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGAATTAGA
TTTAATTAAAAATTCTA
Found at i:30001 original size:2 final size:2
Alignment explanation
Indices: 29994--30026 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29984 GATAAGAAGA
29994 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30027 CGTTCACCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30311 original size:14 final size:14
Alignment explanation
Indices: 30292--30325 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
30282 TTTTATAATT
30292 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
30306 ATTTTATTTTTACT
1 ATTTTATTTTTACC
30320 ATTTTA
1 ATTTTA
30326 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:31323 original size:4 final size:4
Alignment explanation
Indices: 31316--31344 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
31306 TATATATATA
31316 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
31345 AAATAAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:42152 original size:80 final size:80
Alignment explanation
Indices: 42019--42265 Score: 390
Period size: 80 Copynumber: 3.0 Consensus size: 80
42009 AAAGCCCCAA
*
42019 ATCAAATAAATGATAGAACTTTATTAAACTCAAACAGGTATATATATAATTCTACACACTGGCCA
1 ATCAAATAAATGATAGAACTATATTAAACTCAAACAGGTATATATATAATTCTACACACTGGCCA
42084 ATAGGGCAATATTCT
66 ATAGGGCAATATTCT
*
42099 ATCAAATAAATGATAGAACTATATTAAACTCAAACAGGTATATATATAATTCTACACAGTACACG
1 ATCAAATAAATGATAGAACTATATTAAACTCAAACAGGTATATATATAATTCTACAC---AC-TG
42164 CTGCCAATAGGGCAATATTCT
62 --GCCAATAGGGCAATATTCT
*
42185 ATCAAATAAATGACAGAACTATATTAAACTCAAACAGGTATATATATAAATTCTACACACT-GCC
1 ATCAAATAAATGATAGAACTATATTAAACTCAAACAGGTATATATAT-AATTCTACACACTGGCC
42249 AATAGGGCAATA-TCT
65 AATAGGGCAATATTCT
42264 AT
1 AT
42266 AGTAAGAACA
Statistics
Matches: 156, Mismatches: 4, Indels: 15
0.89 0.02 0.09
Matches are distributed among these distances:
79 5 0.03
80 71 0.46
83 2 0.01
84 3 0.02
86 65 0.42
87 10 0.06
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (80 bp):
ATCAAATAAATGATAGAACTATATTAAACTCAAACAGGTATATATATAATTCTACACACTGGCCA
ATAGGGCAATATTCT
Found at i:42203 original size:86 final size:88
Alignment explanation
Indices: 42071--42243 Score: 314
Period size: 86 Copynumber: 2.0 Consensus size: 88
42061 TATATAATTC
*
42071 TACACACTGGCCAATAGGGCAATATTCTATCAAATAAATGATAGAACTATATTAAACTCAAACAG
1 TACACACTGGCCAATAGGGCAATATTCTATCAAATAAATGACAGAACTATATTAAACTCAAACAG
42136 GTATATATAT-AATTCTACACAG
66 GTATATATATAAATTCTACACAG
*
42158 TACACGCT-GCCAATAGGGCAATATTCTATCAAATAAATGACAGAACTATATTAAACTCAAACAG
1 TACACACTGGCCAATAGGGCAATATTCTATCAAATAAATGACAGAACTATATTAAACTCAAACAG
42222 GTATATATATAAATTCTACACA
66 GTATATATATAAATTCTACACA
42244 CTGCCAATAG
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
86 65 0.78
87 18 0.22
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (88 bp):
TACACACTGGCCAATAGGGCAATATTCTATCAAATAAATGACAGAACTATATTAAACTCAAACAG
GTATATATATAAATTCTACACAG
Found at i:46913 original size:32 final size:32
Alignment explanation
Indices: 46872--46944 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
46862 ATATAATATA
46872 TAGCGGCGTTTTTCTCAGC-AGACGCCGCTAAT
1 TAGCGGCGTTTTTCTCA-CAAGACGCCGCTAAT
*
46904 TAGCAGCGTTTTTCTCACAAGACGCCGCTAAT
1 TAGCGGCGTTTTTCTCACAAGACGCCGCTAAT
46936 TAGCGGCGT
1 TAGCGGCGT
46945 CTGAAGAAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 1 0.03
32 37 0.97
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (32 bp):
TAGCGGCGTTTTTCTCACAAGACGCCGCTAAT
Found at i:49191 original size:30 final size:30
Alignment explanation
Indices: 49131--49222 Score: 115
Period size: 27 Copynumber: 3.3 Consensus size: 30
49121 GTCGTCTTAA
* * *
49131 TTCGACCCCAGCAGTGGAGGCT-CT-CC-C
1 TTCGACCCCAGCAGTAGTGGATCCTCCCAC
49158 TTCGACCCCAGCAGTAGTGGATCCTCCCAC
1 TTCGACCCCAGCAGTAGTGGATCCTCCCAC
49188 TTCGACCCCAGC---AGTGGATCCTCCCAC
1 TTCGACCCCAGCAGTAGTGGATCCTCCCAC
49215 TTCGACCC
1 TTCGACCC
49223 GGGTCGGTTC
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
27 42 0.71
28 2 0.03
29 2 0.03
30 13 0.22
ACGTcount: A:0.17, C:0.42, G:0.21, T:0.20
Consensus pattern (30 bp):
TTCGACCCCAGCAGTAGTGGATCCTCCCAC
Found at i:51629 original size:32 final size:32
Alignment explanation
Indices: 51593--51834 Score: 403
Period size: 32 Copynumber: 7.5 Consensus size: 32
51583 GTGTGGAAAG
*
51593 AAAACGCCCTTATTTAGCGGCGTTTAAAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
51625 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
51657 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
51689 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
*
51721 AAAACGCCCTTATTTAGCGGCGTCTAGAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
* *
51753 AAAACGCCCTTATTTAGCGGCGTCTAGACAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
* **
51785 AAAACGCCCTTATTTAGCGGTGTCTTTAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
51817 AAAACGCCGCTATATTTA
1 AAAACGCC-CT-TATTTA
51835 ACTGCTTTTA
Statistics
Matches: 201, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
32 193 0.96
33 2 0.01
34 6 0.03
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (32 bp):
AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
Found at i:60227 original size:2 final size:2
Alignment explanation
Indices: 60220--60254 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
60210 TTTCTAAACT
60220 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 T
60255 GCTTAAATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:63667 original size:35 final size:35
Alignment explanation
Indices: 63628--63700 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
63618 GCTTTTTTTC
* * *
63628 TGTATGGTTTTTGTGGCAGATTGGTCTTTGCTGTT
1 TGTATGGTTTTTGTGGAAGATTGGTCTATGCTGCT
*
63663 TGTATGGTTTTTGTGGAAGATTTGTCTATGCTGCT
1 TGTATGGTTTTTGTGGAAGATTGGTCTATGCTGCT
63698 TGT
1 TGT
63701 GTTTGGACTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.11, C:0.08, G:0.30, T:0.51
Consensus pattern (35 bp):
TGTATGGTTTTTGTGGAAGATTGGTCTATGCTGCT
Found at i:64377 original size:159 final size:155
Alignment explanation
Indices: 64156--64451 Score: 434
Period size: 159 Copynumber: 1.9 Consensus size: 155
64146 AAATCTAGTC
* * *
64156 TACCAATACAAAAAAATACCTCAATGATTATGTTAGCACTAAAATCCTTCCTCCACTTAAGCATA
1 TACCAATACAAAAAAATACCTCAATGATTATGTCAGAACCAAAATCCTTCCTCCACTTAAGCATA
* *
64221 TCAACCCACATTTGCTAAAGACTATC-TTCAG-ATATTAAACAACAACCATATATGTAAACTAAA
66 TCAACCCACATTTGCTAAAGACTATCATT-AGAATAGTAAACAACAAACATATATGTAAACTAAA
64284 GACTAGAGGTTAGGGAAAATCCAATT
130 GACTAGAGGTTAGGGAAAATCCAATT
* *
64310 TACCAATACAAAAAAATGCCTCCATGATTGTGTCATGTCAGAACCAAAATCCTTCCTCCACTTAA
1 TACCAATACAAAAAAATACCTCAATGA---T-T-ATGTCAGAACCAAAATCCTTCCTCCACTTAA
* * *
64375 GCATATCAGCCCACATTTGCTAAAGATTATCATTTGAATAGTAAACAACAAACATATATGTAAAC
61 GCATATCAACCCACATTTGCTAAAGACTATCATTAGAATAGTAAACAACAAACATATATGTAAAC
64440 TAAAGACTAGAG
126 TAAAGACTAGAG
64452 TCTACAGAGG
Statistics
Matches: 125, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
154 25 0.20
157 1 0.01
158 1 0.01
159 58 0.46
160 40 0.32
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.26
Consensus pattern (155 bp):
TACCAATACAAAAAAATACCTCAATGATTATGTCAGAACCAAAATCCTTCCTCCACTTAAGCATA
TCAACCCACATTTGCTAAAGACTATCATTAGAATAGTAAACAACAAACATATATGTAAACTAAAG
ACTAGAGGTTAGGGAAAATCCAATT
Found at i:65241 original size:14 final size:14
Alignment explanation
Indices: 65222--65248 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
65212 GAGATATGGA
65222 GCCAAGAGATTAGC
1 GCCAAGAGATTAGC
65236 GCCAAGAGATTAG
1 GCCAAGAGATTAG
65249 TGGAGCCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.19, G:0.30, T:0.15
Consensus pattern (14 bp):
GCCAAGAGATTAGC
Found at i:67344 original size:2 final size:2
Alignment explanation
Indices: 67337--67410 Score: 94
Period size: 2 Copynumber: 34.0 Consensus size: 2
67327 CAAGAGATTG
67337 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
67381 TA TA CTA TA TA CTA TA TA CTA TA TA CTA TA
1 TA TA -TA TA TA -TA TA TA -TA TA TA -TA TA
67411 ATAATAATAA
Statistics
Matches: 66, Mismatches: 0, Indels: 12
0.85 0.00 0.15
Matches are distributed among these distances:
2 54 0.82
3 12 0.18
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:67377 original size:7 final size:7
Alignment explanation
Indices: 67337--67410 Score: 113
Period size: 7 Copynumber: 11.3 Consensus size: 7
67327 CAAGAGATTG
67337 TATA-TA
1 TATACTA
67343 TATA-TA
1 TATACTA
67349 TATA-TA
1 TATACTA
67355 TATA-TA
1 TATACTA
67361 TATA-TA
1 TATACTA
67367 TATACTA
1 TATACTA
67374 TATACTA
1 TATACTA
67381 TATACTA
1 TATACTA
67388 TATACTA
1 TATACTA
67395 TATACTA
1 TATACTA
67402 TATACTA
1 TATACTA
67409 TA
1 TA
67411 ATAATAATAA
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
6 28 0.42
7 39 0.58
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (7 bp):
TATACTA
Found at i:67416 original size:3 final size:3
Alignment explanation
Indices: 67408--67441 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
67398 ACTATATACT
67408 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
67442 ATATTATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:69397 original size:17 final size:17
Alignment explanation
Indices: 69360--69409 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 17
69350 GAAAATTTTC
69360 ATTTTCAATGATTTAAAA
1 ATTTTCAATG-TTTAAAA
*
69378 ATTTTCAATGTTTGAAA
1 ATTTTCAATGTTTAAAA
69395 ATTTTCAATAGTTTA
1 ATTTTCAAT-GTTTA
69410 TCAAACAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (17 bp):
ATTTTCAATGTTTAAAA
Found at i:70077 original size:3 final size:3
Alignment explanation
Indices: 70069--70106 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
70059 ATATATATAT
70069 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
70107 TGTATTAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:71902 original size:105 final size:104
Alignment explanation
Indices: 71777--72086 Score: 346
Period size: 103 Copynumber: 3.0 Consensus size: 104
71767 TTGTTATTAA
* *
71777 TTTTATTTTTAAGAGTAAATT-AGGAAATTAA-AGGTTTTTTATTATAGAGTTTTAGAAATAAAA
1 TTTTA-TTTTAAGGGTAAATTCA--AAATTAATA-GTTTATTATTATAGAGTTTTAGAAATAAAA
71840 TGTAAAACTAATTTCACTAAGTTTAGGCCCAAATTAAAA-TTT-T
62 T-TAAAACTAATTTCACTAAGTTTA-GCCCAAATTAAAATTTTAT
* *
71883 TTTTATTTTAAGGGTAAATTTCAAAATTAATAATTTATTATTATAGAGTTTTAGAGATAAAA-TA
1 TTTTATTTTAAGGGTAAA-TTCAAAATTAATAGTTTATTATTATAGAGTTTTAGAAATAAAATTA
* * *
71947 CAACCAATTTCACTAAG-TTAGTCCAAATTAAAATTTTAT
65 AAACTAATTTCACTAAGTTTAGCCCAAATTAAAATTTTAT
* * * * *
71986 TTTTATTTTAAGGGTAAATTTCATAATTAATAGCTTATTGTTATAGGGTTTTAAAAATAAAATAT
1 TTTTATTTTAAGGGTAAA-TTCAAAATTAATAGTTTATTATTATAGAGTTTTAGAAATAAAAT-T
* * * *
72051 ATAACTAA-TTCACTAAGTTTATCCTAAAATAAAATT
64 AAAACTAATTTCACTAAGTTTAGCCCAAATTAAAATT
72087 ATTTTAAAGG
Statistics
Matches: 176, Mismatches: 20, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
101 12 0.07
102 6 0.03
103 73 0.41
104 9 0.05
105 67 0.38
106 8 0.05
107 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (104 bp):
TTTTATTTTAAGGGTAAATTCAAAATTAATAGTTTATTATTATAGAGTTTTAGAAATAAAATTAA
AACTAATTTCACTAAGTTTAGCCCAAATTAAAATTTTAT
Found at i:72089 original size:103 final size:104
Alignment explanation
Indices: 71815--72091 Score: 357
Period size: 103 Copynumber: 2.7 Consensus size: 104
71805 TAAAGGTTTT
* *
71815 TTATTATAGAGTTTTAGAAATAAAATGTAAAACTAATTTCACTAAGTTTAGGCCCAAATTAAAAT
1 TTATTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTA-GTCCAAATTAAAAT
* *
71880 TTTTTTTATTTTAAGGGTAAATTTCAAAATTAATAATTTA
65 TATTTTTATTTTAAGGGTAAATTTCAAAATTAATAACTTA
* * *
71920 TTATTATAGAGTTTTAGAGAT-AAA-ATACAACCAATTTCACTAAG-TTAGTCCAAATTAAAATT
1 TTATTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGTCCAAATTAAAA--
* *
71982 TTATTTTTATTTTAAGGGTAAATTTCATAATTAATAGCTTA
64 TTATTTTTATTTTAAGGGTAAATTTCAAAATTAATAACTTA
* * * * *
72023 TTGTTATAGGGTTTTAAAAATAAAATATATAACTAA-TTCACTAAGTTTA-TCCTAAAATAAAAT
1 TTATTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGTCC-AAATTAAAAT
72086 TATTTT
65 TATTTT
72092 AAAGGTTAGA
Statistics
Matches: 150, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
101 12 0.08
102 3 0.02
103 78 0.52
104 18 0.12
105 39 0.26
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.42
Consensus pattern (104 bp):
TTATTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGTCCAAATTAAAATT
ATTTTTATTTTAAGGGTAAATTTCAAAATTAATAACTTA
Found at i:73452 original size:35 final size:35
Alignment explanation
Indices: 73413--73481 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
73403 TTTTTCTGTA
*
73413 TGGTTTTTGTGGC-GTATTTGTCTTTGCTGCTTGTT
1 TGGTTTTTGTGGCAG-ATTTGTCTCTGCTGCTTGTT
73448 TGGTTTTTGTGGCAGATTTGTCTCTGCTGCTTGT
1 TGGTTTTTGTGGCAGATTTGTCTCTGCTGCTTGT
73482 GTTTGGATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 31 0.97
36 1 0.03
ACGTcount: A:0.04, C:0.13, G:0.29, T:0.54
Consensus pattern (35 bp):
TGGTTTTTGTGGCAGATTTGTCTCTGCTGCTTGTT
Found at i:77630 original size:94 final size:93
Alignment explanation
Indices: 77544--77729 Score: 273
Period size: 93 Copynumber: 2.0 Consensus size: 93
77534 ACTTTTTAAT
* * *
77544 TAAATTAGCAATATCGTAAAAATAAAAAAAGGTATAAGGATATTAAATTTAATTAAATAAAAATA
1 TAAAATAGCAAAATCGTAAAAAT-AAAAAAGGTATAAGGATATTAAACTTAATTAAATAAAAATA
*
77609 GAGTTTTTAGTTGAGTAAAACTATAAAAG
65 GAGTTTTTAGTTGACTAAAACTATAAAAG
* * * * * *
77638 TAAAATAGTAAAATGGTTAAAATAAAATAGTTATAAGGATATTAGACTTAATTAAATAAAAATAG
1 TAAAATAGCAAAATCGTAAAAATAAAAAAGGTATAAGGATATTAAACTTAATTAAATAAAAATAG
77703 AGTTTTTAGTTGACTAAAACTATAAAA
66 AGTTTTTAGTTGACTAAAACTATAAAA
77730 ATTTAAACAA
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
93 64 0.78
94 18 0.22
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (93 bp):
TAAAATAGCAAAATCGTAAAAATAAAAAAGGTATAAGGATATTAAACTTAATTAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAG
Found at i:81006 original size:43 final size:43
Alignment explanation
Indices: 80945--81033 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
80935 TAATCTTTTA
80945 TTATACTATTTTTCAAATTATTCAGAGACACAACATTTGATCG
1 TTATACTATTTTTCAAATTATTCAGAGACACAACATTTGATCG
80988 TTATACTATTTTTCAAATTATTCAGAGACACAACATTTGATCG
1 TTATACTATTTTTCAAATTATTCAGAGACACAACATTTGATCG
81031 TTA
1 TTA
81034 GTTTCGCAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (43 bp):
TTATACTATTTTTCAAATTATTCAGAGACACAACATTTGATCG
Found at i:81697 original size:60 final size:61
Alignment explanation
Indices: 81633--81749 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 61
81623 GTTAGGGCCG
* * * *
81633 TATTTGACCAAATTAAAAGCA-TG-GGCTCTTATTTGAGTA-TTTCTGCATACGTTAAGACTC
1 TATTTAACCAAATTAAAAGCATTGAGGC-CTAAATTGAGCATTTTC-GCATACGTTAAGACTC
81693 TATTTAACCAAATTAAAAGCATTGAGGCCTAAATTGAGCATTTTCGCATACGTTAAG
1 TATTTAACCAAATTAAAAGCATTGAGGCCTAAATTGAGCATTTTCGCATACGTTAAG
81750 GGCCTATTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
60 20 0.40
61 23 0.46
62 7 0.14
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (61 bp):
TATTTAACCAAATTAAAAGCATTGAGGCCTAAATTGAGCATTTTCGCATACGTTAAGACTC
Found at i:81767 original size:60 final size:60
Alignment explanation
Indices: 81605--81760 Score: 176
Period size: 60 Copynumber: 2.6 Consensus size: 60
81595 ATGACCTTAT
* * * *
81605 TTGAGTATTTTCGCAGATGTT-AGGGCCGTATTTGACCAAATTAAAAGCATGGGCTCTTAT
1 TTGAGTATTTTCGCATACGTTAAGGGCC-TATTTGACCAAATTAAAAGCATGGGCTCTAAA
* *
81665 TTGAGTA-TTTCTGCATACGTTAA-GACTCTATTTAACCAAATTAAAAGCATTGAGGC-CTAAA
1 TTGAGTATTTTC-GCATACGTTAAGGGC-CTATTTGACCAAATTAAAAGCA-TG-GGCTCTAAA
*
81726 TTGAGCATTTTCGCATACGTTAAGGGCCTATTTGA
1 TTGAGTATTTTCGCATACGTTAAGGGCCTATTTGA
81761 GCAATTAGCC
Statistics
Matches: 80, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
59 4 0.05
60 36 0.45
61 31 0.39
62 9 0.11
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (60 bp):
TTGAGTATTTTCGCATACGTTAAGGGCCTATTTGACCAAATTAAAAGCATGGGCTCTAAA
Found at i:84523 original size:2 final size:2
Alignment explanation
Indices: 84516--84556 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
84506 GACTATTTTA
84516 AT AT AT AT AT AT AT ACT -T AT -T AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
84556 A
1 A
84557 ATTTGCATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 3 0.09
2 31 0.89
3 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:84569 original size:26 final size:26
Alignment explanation
Indices: 84512--84571 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
84502 TAGGGACTAT
* *
84512 TTTAATATATATATATATACTTATTA
1 TTTAATATATATATATATAATTATCA
*
84538 TATAATATATATATATATAATT-TGCA
1 TTTAATATATATATATATAATTAT-CA
84564 TTTAATAT
1 TTTAATAT
84572 CAAGTTGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 1 0.03
26 28 0.97
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTAATATATATATATATAATTATCA
Found at i:92518 original size:2 final size:2
Alignment explanation
Indices: 92496--92541 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
92486 GACTATTTTA
92496 AT AT AT A- AT AT ACT -T AT -T AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
92535 AT AT AT A
1 AT AT AT A
92542 AAAATTTGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.10
2 34 0.87
3 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:92527 original size:11 final size:10
Alignment explanation
Indices: 92496--92541 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 10
92486 GACTATTTTA
92496 ATATATA-AT
1 ATATATATAT
92505 ATACT-TAT-T
1 ATA-TATATAT
92514 ATATATATA-
1 ATATATATAT
92523 ATATATATAT
1 ATATATATAT
92533 ATATATATA
1 ATATATATA
92542 AAAATTTGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 1 0.03
9 21 0.66
10 10 0.31
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (10 bp):
ATATATATAT
Found at i:99889 original size:2 final size:2
Alignment explanation
Indices: 99866--99914 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
99856 GAATTAACCC
* *
99866 AT AT -T AT AT CT AT AT AT CT 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
99907 AT AT AT AT
1 AT AT AT AT
99915 TCAAAGTTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:102521 original size:4 final size:4
Alignment explanation
Indices: 102512--102542 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
102502 GAAACTATTG
102512 CTTT CTTT CTTT CTTT CTTT CTTT -TTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
102543 TTCTCTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
CTTT
Found at i:107259 original size:18 final size:18
Alignment explanation
Indices: 107236--107271 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
107226 ATCGTGTCTT
*
107236 GACACGATTATGACACGA
1 GACACGATTACGACACGA
107254 GACACGATTACGACACGA
1 GACACGATTACGACACGA
107272 TTTGGACACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.25, G:0.22, T:0.14
Consensus pattern (18 bp):
GACACGATTACGACACGA
Found at i:109183 original size:2 final size:2
Alignment explanation
Indices: 109176--109203 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
109166 AAAATTTATC
109176 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
109204 TATTTTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118399 original size:17 final size:18
Alignment explanation
Indices: 118377--118416 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
118367 TGGAATTAAC
*
118377 GATGATAGTCA-TATGAA
1 GATGATAGTCACAATGAA
*
118394 GATGATATTCACAATGAA
1 GATGATAGTCACAATGAA
118412 GATGA
1 GATGA
118417 GAGTGATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.28
Consensus pattern (18 bp):
GATGATAGTCACAATGAA
Found at i:119574 original size:60 final size:60
Alignment explanation
Indices: 119501--119620 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
119491 TGATTAATCC
*
119501 GGATCTGATCCACCTCGCGCACCTGGTTATGGTGGGTGAGTCTCCCAATAGGGATAGTTG
1 GGATCTGATCCACCTCGCGCACCTGGTTATGGTGGGTGAGTCTCCCAACAGGGATAGTTG
*
119561 GGATCTGATCCACCTCGCGCACCTTGTTATGGTGGGTGAGTCTCCCAACAGGGATAGTTG
1 GGATCTGATCCACCTCGCGCACCTGGTTATGGTGGGTGAGTCTCCCAACAGGGATAGTTG
119621 CGTACGCAAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (60 bp):
GGATCTGATCCACCTCGCGCACCTGGTTATGGTGGGTGAGTCTCCCAACAGGGATAGTTG
Done.