Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017274.1 Corchorus olitorius cultivar O-4 contig17307, 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: 78808
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1253 original size:17 final size:17
Alignment explanation
Indices: 1218--1253 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1208 TAAATTATCA
*
1218 TTTAACAAGTGTTTAGT
1 TTTAACAAGTGGTTAGT
*
1235 TTTAACAAGTGGTTGGT
1 TTTAACAAGTGGTTAGT
1252 TT
1 TT
1254 AAATGATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (17 bp):
TTTAACAAGTGGTTAGT
Found at i:2425 original size:179 final size:180
Alignment explanation
Indices: 2172--2504 Score: 483
Period size: 179 Copynumber: 1.9 Consensus size: 180
2162 CTTTTAACAT
* * * *
2172 ACACTTGAATCAACTCAATCAGACATCTGGAGCAAAAATTATGTATTAATAAGTGGACCGTTCAT
1 ACACTTGAATCAACTCAATAAAACATCTGGAGCAAAAATAATGTATTAATAAGTGGACCGTCCAT
* * * *
2237 TCTCGTTAACCGAAAAAATTAATTTTTTGGAAGCTTTTTTT-ATAC-TAAAACATTAAATTTAGC
66 TCCCGTTAACCGAAAAAACTAATTATTCGGAAG-TTTTTTTGATACTTAAAACATTAAATTTAGC
2300 TTTCGAGTCTTGCATGAAAGTTGTAAATCATATAAAATAACTTTTTATATC
130 TTTCGAGTCTTGCATGAAAGTTGTAAATCATATAAAATAACTTTTTATATC
* * * *
2351 ACACTTGAATCAACTCAATAAAACATTTGGAGCAAAAGTAATGT-TATATTAAGTGGATCGTCCA
1 ACACTTGAATCAACTCAATAAAACATCTGGAGCAAAAATAATGTAT-TAATAAGTGGACCGTCCA
* * *
2415 TTCCCGTTAACCGAAACAACTAATTATTCGGAAGTTTTTTTGATACTTGAAACATTAAATTTAGT
65 TTCCCGTTAACCGAAAAAACTAATTATTCGGAAGTTTTTTTGATACTTAAAACATTAAATTTAGC
*
2480 TTTCGAGTCTTTCATGAAAGTTGTA
130 TTTCGAGTCTTGCATGAAAGTTGTA
2505 GATTATGGAA
Statistics
Matches: 135, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
178 8 0.06
179 87 0.64
180 40 0.30
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (180 bp):
ACACTTGAATCAACTCAATAAAACATCTGGAGCAAAAATAATGTATTAATAAGTGGACCGTCCAT
TCCCGTTAACCGAAAAAACTAATTATTCGGAAGTTTTTTTGATACTTAAAACATTAAATTTAGCT
TTCGAGTCTTGCATGAAAGTTGTAAATCATATAAAATAACTTTTTATATC
Found at i:2624 original size:5 final size:5
Alignment explanation
Indices: 2614--2638 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2604 TATAAATATG
2614 TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA
2639 ATTTAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:2887 original size:80 final size:79
Alignment explanation
Indices: 2728--2889 Score: 263
Period size: 80 Copynumber: 2.0 Consensus size: 79
2718 AACCAAATTC
2728 AATATTAACCAAATTAATAATGTAACAACTTTAGACCATATCTTTTGTAATTTCACTTCTACCTA
1 AATATTAACCAAATTAATAATGTAACAACTTTAGACCATATCTTTTGTAATTTCACTTCTACCTA
2793 TTATGATTCTTTAT
66 TTATGATTCTTTAT
* * * *
2807 AATATTAACCAAATTAATAATGTAACATCTTTAGACCGTTTTTTTTTGTAATTTCACTTCTACCT
1 AATATTAACCAAATTAATAATGTAACAACTTTAGACC-ATATCTTTTGTAATTTCACTTCTACCT
2872 ATTAT-ACTTCTTTAT
65 ATTATGA-TTCTTTAT
2887 AAT
1 AAT
2890 TTGTCTTCAT
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
79 37 0.48
80 40 0.52
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (79 bp):
AATATTAACCAAATTAATAATGTAACAACTTTAGACCATATCTTTTGTAATTTCACTTCTACCTA
TTATGATTCTTTAT
Found at i:4945 original size:27 final size:28
Alignment explanation
Indices: 4915--4971 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
4905 AATTATTTTC
*
4915 CTATTACATATA-AAAAATATT-ATATAT
1 CTATTA-ATATATAAAAATATTCAAATAT
*
4942 CTATTAATCTATAAAAATATTCAAATAT
1 CTATTAATATATAAAAATATTCAAATAT
4970 CT
1 CT
4972 TGTTAGTCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 15 0.58
28 7 0.27
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (28 bp):
CTATTAATATATAAAAATATTCAAATAT
Found at i:5169 original size:46 final size:46
Alignment explanation
Indices: 5108--5196 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
5098 AGGCGATTTC
* *
5108 AACTACACCTAAAAAGAAGAAACAAGTGTCATCTTTCAACAATTGA
1 AACTACACCTAAAAAGAAGAAACAAGAGTCATCCTTCAACAATTGA
* * *
5154 AACTTCACCTTAAAAGAAGAAACTAGAGTCATCCTTCAACAAT
1 AACTACACCTAAAAAGAAGAAACAAGAGTCATCCTTCAACAAT
5197 CTAAATTCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.22
Consensus pattern (46 bp):
AACTACACCTAAAAAGAAGAAACAAGAGTCATCCTTCAACAATTGA
Found at i:6367 original size:21 final size:21
Alignment explanation
Indices: 6341--6387 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
6331 GAGGATGATT
6341 AAATCGATTTCCATAAGGG-TG
1 AAATCGATTTCCAT-AGGGTTG
6362 AAATCGATTTCCATAGGGTTG
1 AAATCGATTTCCATAGGGTTG
6383 AAATC
1 AAATC
6388 CTTCATTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (21 bp):
AAATCGATTTCCATAGGGTTG
Found at i:16756 original size:26 final size:26
Alignment explanation
Indices: 16719--16768 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
16709 AAAAGTTTGT
*
16719 GGTTTTGGAGGTTATTTGGGGATTAG
1 GGTTTTGCAGGTTATTTGGGGATTAG
*
16745 GGTTTTGCAGGTTTTTTGGGGATT
1 GGTTTTGCAGGTTATTTGGGGATT
16769 TCTTGATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.12, C:0.02, G:0.40, T:0.46
Consensus pattern (26 bp):
GGTTTTGCAGGTTATTTGGGGATTAG
Found at i:26716 original size:43 final size:43
Alignment explanation
Indices: 26668--26753 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
26658 TCCTTTGATA
*
26668 TCAGCATGATCAAAATAGATTATCACCTTATATCCCAAGATGT
1 TCAGCATGATCAAAATAGATTATCACCTTAGATCCCAAGATGT
26711 TCAGCATGATCAAAATAGATTATCACCTTAGATCCCAAGATGT
1 TCAGCATGATCAAAATAGATTATCACCTTAGATCCCAAGATGT
26754 GTAGCCGAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (43 bp):
TCAGCATGATCAAAATAGATTATCACCTTAGATCCCAAGATGT
Found at i:29487 original size:401 final size:401
Alignment explanation
Indices: 28744--29546 Score: 1543
Period size: 401 Copynumber: 2.0 Consensus size: 401
28734 ATAGGTCTTC
28744 ACAGGGTAATGCTTCATTGATTGCAGTCTCTTCATCCTTGCCTTCAATTCTGCTTAGATGATCAG
1 ACAGGGTAATGCTTCATTGATTGCAGTCTCTTCATCCTTGCCTTCAATTCTGCTTAGATGATCAG
28809 CAACAACATTTTCTACTCCCTTCTTGTCCTTTATTTCAATATCGAATTCTTGAAAAAACAATAGT
66 CAACAACATTTTCTACTCCCTTCTTGTCCTTTATTTCAATATCGAATTCTTGAAAAAACAATAGT
28874 CAGCGCATAAACCTAGCTTTTGCTTCTCTTTTCGGCGTCAATTAACGGAGTGCAGCATGATCAGA
131 CAGCGCATAAACCTAGCTTTTGCTTCTCTTTTCGGCGTCAATTAACGGAGTGCAGCATGATCAGA
28939 ATAGATTATCACCTTAGATTCCAAGATGTGTGGCCGAAATTTCTCCAAAGCAAAGACTACGGCAA
196 ATAGATTATCACCTTAGATTCCAAGATGTGTGGCCGAAATTTCTCCAAAGCAAAGACTACGGCAA
29004 GCATCTTTTTTTCTGTGGTGTAGTTCTTCTGAGCAGCATCAAGGGTTCTTGAAGCATAGAAGATA
261 GCATCTTTTTTTCTGTGGTGTAGTTCTTCTGAGCAGCATCAAGGGTTCTTGAAGCATAGAAGATA
29069 ACATGAGGTACCTTGTCTACTCTCTAACCTAGAACAACTCCAATAGCTACATCACTTGCATCACA
326 ACATGAGGTACCTTGTCTACTCTCTAACCTAGAACAACTCCAATAGCTACATCACTTGCATCACA
29134 CATGATCTCGA
391 CATGATCTCGA
*
29145 ACAGGGTAATGCTTCATTGATTGCAGTCTCTTCTTCCTTGCCTTCAATTCTGCTTAGATGATCAG
1 ACAGGGTAATGCTTCATTGATTGCAGTCTCTTCATCCTTGCCTTCAATTCTGCTTAGATGATCAG
* * *
29210 CAACAACATTTTCTGCTCCCTTCTTGTCCTTTATTTTAATATCGAGTTCTTGAAAAAACAATAGT
66 CAACAACATTTTCTACTCCCTTCTTGTCCTTTATTTCAATATCGAATTCTTGAAAAAACAATAGT
29275 CAGCGCATAAACCTAGCTTTTGCTTCTCTTTTCGGCGTCAATTAACGGAGTGCAGCATGATCAGA
131 CAGCGCATAAACCTAGCTTTTGCTTCTCTTTTCGGCGTCAATTAACGGAGTGCAGCATGATCAGA
29340 ATAGATTATCACCTTAGATTCCAAGATGTGTGGCCGAAATTTCTCCAAAGCAAAGACTACGGCAA
196 ATAGATTATCACCTTAGATTCCAAGATGTGTGGCCGAAATTTCTCCAAAGCAAAGACTACGGCAA
29405 GCATCTTTTTTTCTGTGGTGTAGTTCTTCTGAGCAGCATCAAGGGTTCTTGAAGCATAGAAGATA
261 GCATCTTTTTTTCTGTGGTGTAGTTCTTCTGAGCAGCATCAAGGGTTCTTGAAGCATAGAAGATA
* * *
29470 ACATGAGGTACCTTGTCTACTCTCTCACCTAGAACAGCTCCAATAGCTATATCACTTGCATCACA
326 ACATGAGGTACCTTGTCTACTCTCTAACCTAGAACAACTCCAATAGCTACATCACTTGCATCACA
29535 CATGATCTCGA
391 CATGATCTCGA
29546 A
1 A
29547 TGGTAGATCC
Statistics
Matches: 395, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
401 395 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (401 bp):
ACAGGGTAATGCTTCATTGATTGCAGTCTCTTCATCCTTGCCTTCAATTCTGCTTAGATGATCAG
CAACAACATTTTCTACTCCCTTCTTGTCCTTTATTTCAATATCGAATTCTTGAAAAAACAATAGT
CAGCGCATAAACCTAGCTTTTGCTTCTCTTTTCGGCGTCAATTAACGGAGTGCAGCATGATCAGA
ATAGATTATCACCTTAGATTCCAAGATGTGTGGCCGAAATTTCTCCAAAGCAAAGACTACGGCAA
GCATCTTTTTTTCTGTGGTGTAGTTCTTCTGAGCAGCATCAAGGGTTCTTGAAGCATAGAAGATA
ACATGAGGTACCTTGTCTACTCTCTAACCTAGAACAACTCCAATAGCTACATCACTTGCATCACA
CATGATCTCGA
Found at i:37097 original size:32 final size:32
Alignment explanation
Indices: 36970--37093 Score: 153
Period size: 32 Copynumber: 3.9 Consensus size: 32
36960 CAAAATTAGC
*
36970 GGCGTTTCTGTACT-GAAACGCCGCT-AATAGT
1 GGCGTTTCAGTA-TGGAAACGCCGCTAAATAGT
* ** *
37001 GGCGTTTCAATGCGGAAAAGCCGCTAAATAGT
1 GGCGTTTCAGTATGGAAACGCCGCTAAATAGT
* *
37033 GGCGTTACAGTATGGAAACGCCGCTAAATTGT
1 GGCGTTTCAGTATGGAAACGCCGCTAAATAGT
*
37065 GGCGTTTCAGTTTGGAAACGCCGCTAAAT
1 GGCGTTTCAGTATGGAAACGCCGCTAAAT
37094 TGTGACTATT
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
31 19 0.24
32 59 0.76
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (32 bp):
GGCGTTTCAGTATGGAAACGCCGCTAAATAGT
Found at i:39480 original size:32 final size:32
Alignment explanation
Indices: 39300--39467 Score: 214
Period size: 32 Copynumber: 5.3 Consensus size: 32
39290 CAAAATTAGC
* *
39300 GGCGTTTCTGTACT-GAAACGCCGCT-ATTAGT
1 GGCGTTTCAGTA-TGGAAACGCCGCTAAATAGT
* *
39331 GGCGTTTCAATACGGAAACGCCGCTAAATAGT
1 GGCGTTTCAGTATGGAAACGCCGCTAAATAGT
* * * *
39363 GGTGTTACAGTATGGAAATGCCGCTAAATTGT
1 GGCGTTTCAGTATGGAAACGCCGCTAAATAGT
* *
39395 GGCGTTTCAGTTTGGAAACGCCGCTAAATTGT
1 GGCGTTTCAGTATGGAAACGCCGCTAAATAGT
*
39427 GGCGTTTCAGTATGGAAACGCCGCCAAATAGT
1 GGCGTTTCAGTATGGAAACGCCGCTAAATAGT
39459 GGCGTTTCA
1 GGCGTTTCA
39468 ATGCGGAAAC
Statistics
Matches: 118, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
31 21 0.18
32 97 0.82
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (32 bp):
GGCGTTTCAGTATGGAAACGCCGCTAAATAGT
Found at i:39495 original size:64 final size:64
Alignment explanation
Indices: 39293--39498 Score: 220
Period size: 64 Copynumber: 3.2 Consensus size: 64
39283 TTTATTTCAA
* * *
39293 AATTAGCGGCGTTTCTGTACT-GAAACGCCG-CTATTAGTGGCGTTTCAATACGGAAACGCCGCT
1 AATTAGCGGCGTTTCAGTA-TGGAAACGCCGCCAAATAGTGGCGTTTCAATACGGAAACGCCGCT
* * * * * * * * **
39356 AAATAGTGGTGTTACAGTATGGAAATGCCGCTAAATTGTGGCGTTTCAGTTTGGAAACGCCGCT
1 AATTAGCGGCGTTTCAGTATGGAAACGCCGCCAAATAGTGGCGTTTCAATACGGAAACGCCGCT
* * *
39420 AAATT-GTGGCGTTTCAGTATGGAAACGCCGCCAAATAGTGGCGTTTCAATGCGGAAACGCCACT
1 -AATTAGCGGCGTTTCAGTATGGAAACGCCGCCAAATAGTGGCGTTTCAATACGGAAACGCCGCT
*
39484 ATTTAGCGGCGTTTC
1 AATTAGCGGCGTTTC
39499 CATACTGAAA
Statistics
Matches: 114, Mismatches: 25, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
62 1 0.01
63 25 0.22
64 85 0.75
65 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (64 bp):
AATTAGCGGCGTTTCAGTATGGAAACGCCGCCAAATAGTGGCGTTTCAATACGGAAACGCCGCT
Found at i:39495 original size:96 final size:96
Alignment explanation
Indices: 39292--39517 Score: 246
Period size: 96 Copynumber: 2.4 Consensus size: 96
39282 TTTTATTTCA
* *
39292 AAATTAGCGGCGTTTCTGTACTGAAACGCCGCTATTAGTGGCGTTTCAATACGGAAACGCCGCTA
1 AAATTAGCGGCGTTTCAGTACTGAAACGCCGCTATTAGTGGCGTTTCAATACGGAAACGCCGCCA
* * * * *
39357 AATAGTGGTGTTACAGTATGGAAATGCCGCT
66 AATAGTGGCGTTACAATACGGAAACGCCACT
* * * *
39388 AAATT-GTGGCGTTTCAGT-TTGGAAACGCCGCTAAATT-GTGGCGTTTCAGTATGGAAACGCCG
1 AAATTAGCGGCGTTTCAGTACT-GAAACGCCGCT--ATTAGTGGCGTTTCAATACGGAAACGCCG
* *
39450 CCAAATAGTGGCGTTTCAATGCGGAAACGCCACT
63 CCAAATAGTGGCGTTACAATACGGAAACGCCACT
* *
39484 -ATTTAGCGGCGTTTCCA-TACTGAAACGCAGCTAT
1 AAATTAGCGGCGTTT-CAGTACTGAAACGCCGCTAT
39518 ATTTGCTTCT
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
94 3 0.03
95 25 0.23
96 73 0.68
97 6 0.06
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (96 bp):
AAATTAGCGGCGTTTCAGTACTGAAACGCCGCTATTAGTGGCGTTTCAATACGGAAACGCCGCCA
AATAGTGGCGTTACAATACGGAAACGCCACT
Found at i:39593 original size:2 final size:2
Alignment explanation
Indices: 39586--39617 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39576 TTAAAATTGA
39586 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
39618 TACTTTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39752 original size:104 final size:104
Alignment explanation
Indices: 39592--39781 Score: 353
Period size: 104 Copynumber: 1.8 Consensus size: 104
39582 TTGAATATAT
* *
39592 ATATATATATATATATATATATATATTACTTTTAAGTAGTATAATAAGATATCCAAATACATGAT
1 ATATATATATATATATATATATATATTACATTTAAGTAGTATAATAAGATATCCAAATACACGAT
39657 GTAATCAGGAAGTTGATTCATTCAAATAATTTAAATTGA
66 GTAATCAGGAAGTTGATTCATTCAAATAATTTAAATTGA
*
39696 ATATATATATATATATATATATGTATTACATTTAAGTAGTATAATAAGATATCCAAATACACGAT
1 ATATATATATATATATATATATATATTACATTTAAGTAGTATAATAAGATATCCAAATACACGAT
39761 GTAATCAGGAAGTTGATTCAT
66 GTAATCAGGAAGTTGATTCAT
39782 GTTACATGGT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 83 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (104 bp):
ATATATATATATATATATATATATATTACATTTAAGTAGTATAATAAGATATCCAAATACACGAT
GTAATCAGGAAGTTGATTCATTCAAATAATTTAAATTGA
Found at i:40950 original size:22 final size:20
Alignment explanation
Indices: 40914--40965 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
40904 GGTCCTCATG
*
40914 GGTTTGT-GTATGTGATTGTTT
1 GGTTTGTAG-ATGTGA-TGATT
40935 GGTTTGGTAGATGTGATGATT
1 GGTTT-GTAGATGTGATGATT
40956 GGTTTGTAGA
1 GGTTTGTAGA
40966 GACCGAGCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.18
21 14 0.50
22 8 0.29
23 1 0.04
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (20 bp):
GGTTTGTAGATGTGATGATT
Found at i:42035 original size:15 final size:15
Alignment explanation
Indices: 42013--42048 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
42003 AGCCGCAAGT
42013 TATATATGAGATAGA
1 TATATATGAGATAGA
*
42028 TTTATATGAGATAGA
1 TATATATGAGATAGA
42043 TATATA
1 TATATA
42049 CCTCGAGGTA
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:0.44, C:0.00, G:0.17, T:0.39
Consensus pattern (15 bp):
TATATATGAGATAGA
Found at i:43900 original size:38 final size:38
Alignment explanation
Indices: 43804--43951 Score: 226
Period size: 38 Copynumber: 3.9 Consensus size: 38
43794 GGCTGTGCAT
*
43804 AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGT-AAG
* * *
43843 AGTGGACTCATACCACAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
43881 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
43919 AGTGGACCCGTGCCTCAGGGGGTT-AACTGTTGG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGG
43952 CTAGACTCGA
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
37 9 0.09
38 61 0.60
39 31 0.31
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (38 bp):
AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
Found at i:43992 original size:6 final size:6
Alignment explanation
Indices: 43981--44018 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
43971 CGTTAACGGA
43981 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TG
1 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TG
44019 GTGCAGCCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (6 bp):
TGATTG
Found at i:47466 original size:38 final size:38
Alignment explanation
Indices: 47370--47517 Score: 226
Period size: 38 Copynumber: 3.9 Consensus size: 38
47360 GGCTGTGCAT
*
47370 AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGT-AAG
* * *
47409 AGTGGACTCATACCACAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
47447 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
47485 AGTGGACCCGTGCCTCAGGGGGTT-AACTGTTGG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGG
47518 CTAGACTCGA
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
37 9 0.09
38 61 0.60
39 31 0.31
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (38 bp):
AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
Found at i:47558 original size:6 final size:6
Alignment explanation
Indices: 47547--47578 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
47537 CGTTAACGGA
47547 TGATTG TGATTG TGATTG TGATTG TGATTG TG
1 TGATTG TGATTG TGATTG TGATTG TGATTG TG
47579 GTGCAGCCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (6 bp):
TGATTG
Found at i:48590 original size:30 final size:30
Alignment explanation
Indices: 48556--48614 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
48546 TTTTATCTTG
*
48556 ACTTTCCTCTTATACCCTCTAATTTTAATC
1 ACTTTCCTCTTATACCCTCAAATTTTAATC
*
48586 ACTTTTCTCTTATACCCTCAAATTTTAAT
1 ACTTTCCTCTTATACCCTCAAATTTTAAT
48615 GGCTTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.27, G:0.00, T:0.47
Consensus pattern (30 bp):
ACTTTCCTCTTATACCCTCAAATTTTAATC
Found at i:50847 original size:282 final size:283
Alignment explanation
Indices: 50339--50895 Score: 969
Period size: 282 Copynumber: 2.0 Consensus size: 283
50329 TGCTACATAT
* *
50339 AATCAATATTTTCTAGGGAAAAATATATGATTATTATTATAATTATTGGGGGAGGGAATTTTTCC
1 AATCAATATTTTCTAGGAAAAAATATACGATTATTATTATAATTATTGGGGGAGGGAATTTTTCC
* *
50404 CTTAAAAAAAAAAATTTCTCCCTCCATATATGGCGGCGTTTAAATCCAAAACGCCACTAATTATT
66 CTTAAAAAAAAAAATTTCTCCCTCCATATATGGCGACGTTTAAATCCAAAACGCCACTAATTAGT
*
50469 GGCATTTCTAGTTAGAAACGCCGCCAATTGAATAATTCTTTGAATATAAATGTGGAAAAAAATTT
131 GGCATTTCTAGTTAGAAACGCCGCCAATTGAATAATTCCTTGAATATAAATGTGGAAAAAAATTT
* *
50534 CCCGTATATTTTGCTTAAAGATAGTGGCGTTTGTG-AATAGAAACGCCGCTAATTAGCGGTGTTT
196 CCCGTATATTTTGCTTAAAGATAGCGGCGTTTGTGTAA-AGAAACGCCGCTAATTAGCGGCGTTT
50598 CAAAAGTTAAACGCCGTTATATAA
260 CAAAAGTTAAACGCCGTTATATAA
50622 AATCAATATTTTCTAGGAAAAAATATACGATTATTATTATAATTATTGGGGGAGGGAATTTTTCC
1 AATCAATATTTTCTAGGAAAAAATATACGATTATTATTATAATTATTGGGGGAGGGAATTTTTCC
* * *
50687 C-TGAAAAAAAAAATTTCTCCCTCCATATATGGCGATGTTTAAGTCCAAAACGCCACTAATTAGT
66 CTTAAAAAAAAAAATTTCTCCCTCCATATATGGCGACGTTTAAATCCAAAACGCCACTAATTAGT
50751 GG-AGTTTCTAGTTAGAAACGCCGCCAATTGAATAATTCCTTGAATATAAATGTGGGAAAAAAAT
131 GGCA-TTTCTAGTTAGAAACGCCGCCAATTGAATAATTCCTTGAATATAAATGT-GGAAAAAAAT
50815 TTCCCGTAT-TTTTGCTTAAAGATAGCGGCGTTTGTGTAAAGAAACGCCGCTAATTAGCGGCGTT
194 TTCCCGTATATTTTGCTTAAAGATAGCGGCGTTTGTGTAAAGAAACGCCGCTAATTAGCGGCGTT
50879 TCAAAAGTTAAACGCCG
259 TCAAAAGTTAAACGCCG
50896 CTATCTTCAA
Statistics
Matches: 261, Mismatches: 10, Indels: 7
0.94 0.04 0.03
Matches are distributed among these distances:
281 1 0.00
282 175 0.67
283 85 0.33
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (283 bp):
AATCAATATTTTCTAGGAAAAAATATACGATTATTATTATAATTATTGGGGGAGGGAATTTTTCC
CTTAAAAAAAAAAATTTCTCCCTCCATATATGGCGACGTTTAAATCCAAAACGCCACTAATTAGT
GGCATTTCTAGTTAGAAACGCCGCCAATTGAATAATTCCTTGAATATAAATGTGGAAAAAAATTT
CCCGTATATTTTGCTTAAAGATAGCGGCGTTTGTGTAAAGAAACGCCGCTAATTAGCGGCGTTTC
AAAAGTTAAACGCCGTTATATAA
Found at i:51062 original size:18 final size:18
Alignment explanation
Indices: 51039--51074 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
51029 AGGTGTAGAC
51039 ACATTACTTTTAGGTTCT
1 ACATTACTTTTAGGTTCT
*
51057 ACATTATTTTTAGGTTCT
1 ACATTACTTTTAGGTTCT
51075 GTTTGGATTA
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:0.22, C:0.14, G:0.11, T:0.53
Consensus pattern (18 bp):
ACATTACTTTTAGGTTCT
Found at i:54789 original size:35 final size:35
Alignment explanation
Indices: 54743--55134 Score: 595
Period size: 35 Copynumber: 11.2 Consensus size: 35
54733 CAAGAAATAA
*
54743 AATTAAGGAAATTGGTATTCAACTTAATTCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
54778 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
54813 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
*
54848 AATTAAGGAAATTGGTATTCAACTTAATTCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
*
54883 AATTAAGGAAATTGGTAATCAACTTAATTCGGTAT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
*
54918 AATTAAGGAAATTGGTAATCAACTTAAATCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
**
54953 AATTAAGGAAATCAGTAATCAACTTAATTCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
* *
54988 AATTAAGGAAATTGGTATTCAACTTAATTTGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
* **
55023 AATTAAGGAAATTAGTAATCAACTTAATTCATTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
* * * *
55058 AATTAAGGAATTTGGTAGTTAACTTAATTCTGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
* ** * * *
55093 AATTAAGTAAATCAGCAATCAACGTAATTCGATGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
55128 AATTAAG
1 AATTAAG
55135 AATCAAAGAA
Statistics
Matches: 323, Mismatches: 34, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 323 1.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (35 bp):
AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
Found at i:58455 original size:13 final size:14
Alignment explanation
Indices: 58434--58464 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
58424 ACTACTAATA
58434 TTTTCTTTTGAGTT
1 TTTTCTTTTGAGTT
*
58448 TTTTTTTTTGAGTT
1 TTTTCTTTTGAGTT
58462 TTT
1 TTT
58465 CTAGGAAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.03, G:0.13, T:0.77
Consensus pattern (14 bp):
TTTTCTTTTGAGTT
Found at i:61487 original size:22 final size:22
Alignment explanation
Indices: 61462--61507 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
61452 GTCGTGCCAC
*
61462 CACCAAGCCACTACCGGCCATT
1 CACCAAGCCACCACCGGCCATT
* *
61484 CACCGAGCCACCACCGGTCATT
1 CACCAAGCCACCACCGGCCATT
61506 CA
1 CA
61508 TCCTAAGCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.46, G:0.15, T:0.13
Consensus pattern (22 bp):
CACCAAGCCACCACCGGCCATT
Found at i:64009 original size:12 final size:12
Alignment explanation
Indices: 63992--64017 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
63982 TTTAGATTTA
63992 TTCTTCTAGTTT
1 TTCTTCTAGTTT
64004 TTCTTCTAGTTT
1 TTCTTCTAGTTT
64016 TT
1 TT
64018 AGGTAAGGGT
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:0.08, T:0.69
Consensus pattern (12 bp):
TTCTTCTAGTTT
Found at i:72360 original size:17 final size:17
Alignment explanation
Indices: 72334--72371 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
72324 ACACCGTAGG
*
72334 ATCAAGAGTCAACAAAA
1 ATCAAAAGTCAACAAAA
*
72351 ATCAAAAGTCAACAAAG
1 ATCAAAAGTCAACAAAA
72368 ATCA
1 ATCA
72372 TCATCGTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.18, G:0.11, T:0.13
Consensus pattern (17 bp):
ATCAAAAGTCAACAAAA
Found at i:76914 original size:14 final size:14
Alignment explanation
Indices: 76889--76923 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
76879 TAAATGGTTG
76889 CTTGGTTTTGTTTGT
1 CTTGG-TTTGTTTGT
*
76904 TTTGGTTTGTTTGT
1 CTTGGTTTGTTTGT
76918 CTTGGT
1 CTTGGT
76924 GTTTTATTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.00, C:0.06, G:0.29, T:0.66
Consensus pattern (14 bp):
CTTGGTTTGTTTGT
Done.