Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012435.1 Corchorus olitorius cultivar O-4 contig12468, 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: 38317
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:2128 original size:36 final size:36
Alignment explanation
Indices: 2081--2150 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
2071 TTCAATAACC
* *
2081 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
2117 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
2151 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:3035 original size:210 final size:202
Alignment explanation
Indices: 2636--3053 Score: 694
Period size: 210 Copynumber: 2.0 Consensus size: 202
2626 GCTTAATAAC
2636 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
2701 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAAAGTAGTTGAACATTAGTAGT
66 GATACAACACATTATTATTATATATAAAACTATACC-AAAAAAAAAGTAGTTGAACATTAATAGT
2766 TGATTTATTAAATCAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
130 TGATTTATTAAATCAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGA
2831 TCCGACTTA
194 TCCGACTTA
2840 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
2905 GATACAACACATTACTATTATATATATATATATATAACTATACC-AAAAAAAATTAGTTGAACAT
66 GATACAACACA-T--TA-T-TAT-TATATATA-A-AACTATACCAAAAAAAAAGTAGTTGAACAT
* *
2969 TAATGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATA
123 TAATAGTTGATTTATTAAATCAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATA
*
3034 TTAAGATCCGATTTA
188 TTAAGATCCGACTTA
3049 TTTAT
1 TTTAT
3054 TATTAAGGAA
Statistics
Matches: 201, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
204 76 0.38
205 1 0.00
207 2 0.01
208 1 0.00
209 20 0.10
210 91 0.45
211 1 0.00
212 9 0.04
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (202 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAAGTAGTTGAACATTAATAGTT
GATTTATTAAATCAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATC
CGACTTA
Found at i:3843 original size:4 final size:4
Alignment explanation
Indices: 3834--3858 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3824 ATAAGATTTT
3834 TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC T
3859 ATTTCATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:4203 original size:70 final size:70
Alignment explanation
Indices: 4090--4231 Score: 275
Period size: 70 Copynumber: 2.0 Consensus size: 70
4080 TTGCAACGCA
4090 GGGATTAATCAAGGTCCGAAGAAGCCATCGCTGTTTATGTTAGAATCTCAAGACAGGCTCCTATA
1 GGGATTAATCAAGGTCCGAAGAAGCCATCGCTGTTTATGTTAGAATCTCAAGACAGGCTCCTATA
4155 ACTTG
66 ACTTG
*
4160 GGGATTAATCAAGGTCCGAAGAAGCGATCGCTGTTTATGTTAGAATCTCAAGACAGGCTCCTATA
1 GGGATTAATCAAGGTCCGAAGAAGCCATCGCTGTTTATGTTAGAATCTCAAGACAGGCTCCTATA
4225 ACTTG
66 ACTTG
4230 GG
1 GG
4232 AATCAAATCA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (70 bp):
GGGATTAATCAAGGTCCGAAGAAGCCATCGCTGTTTATGTTAGAATCTCAAGACAGGCTCCTATA
ACTTG
Found at i:8984 original size:59 final size:59
Alignment explanation
Indices: 8944--9082 Score: 269
Period size: 59 Copynumber: 2.4 Consensus size: 59
8934 AAGGGACTGA
*
8944 TCTTTTAATTTGATCAAATAAGGGTCTAATATATCGAAAATGCTCAAATAAGGGCCCAG
1 TCTTTTAATTTGACCAAATAAGGGTCTAATATATCGAAAATGCTCAAATAAGGGCCCAG
9003 TCTTTTAATTTGACCAAATAAGGGTCTAATATATCGAAAATGCTCAAATAAGGGCCCAG
1 TCTTTTAATTTGACCAAATAAGGGTCTAATATATCGAAAATGCTCAAATAAGGGCCCAG
9062 TCTTTTAATTTGACCAAATAA
1 TCTTTTAATTTGACCAAATAA
9083 ATAAGGGTTT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 79 1.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (59 bp):
TCTTTTAATTTGACCAAATAAGGGTCTAATATATCGAAAATGCTCAAATAAGGGCCCAG
Found at i:8993 original size:30 final size:30
Alignment explanation
Indices: 8957--9056 Score: 105
Period size: 30 Copynumber: 3.4 Consensus size: 30
8947 TTTAATTTGA
8957 TCAAATAAGGGTCTAATATATCGAAAATGC
1 TCAAATAAGGGTCTAATATATCGAAAATGC
* * * * ** **
8987 TCAAATAAGGGCCCAGTCT-TTTAATTTGAC
1 TCAAATAAGGGTCTAATATATCGAAAATG-C
9017 -CAAATAAGGGTCTAATATATCGAAAATGC
1 TCAAATAAGGGTCTAATATATCGAAAATGC
9046 TCAAATAAGGG
1 TCAAATAAGGG
9057 CCCAGTCTTT
Statistics
Matches: 51, Mismatches: 16, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
29 20 0.39
30 31 0.61
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (30 bp):
TCAAATAAGGGTCTAATATATCGAAAATGC
Found at i:9107 original size:27 final size:26
Alignment explanation
Indices: 9077--9133 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
9067 TAATTTGACC
9077 AAATAAATAAGGGTTTAACGTTTGTCA
1 AAAT-AATAAGGGTTTAACGTTTGTCA
** *
9104 AAATGCTTAGGGTTTAACGTTTGTCA
1 AAATAATAAGGGTTTAACGTTTGTCA
9130 AAAT
1 AAAT
9134 GCTCAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (26 bp):
AAATAATAAGGGTTTAACGTTTGTCA
Found at i:9115 original size:26 final size:26
Alignment explanation
Indices: 9086--9136 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
9076 CAAATAAATA
9086 AGGGTTTAACGTTTGTCAAAATGCTT
1 AGGGTTTAACGTTTGTCAAAATGCTT
9112 AGGGTTTAACGTTTGTCAAAATGCT
1 AGGGTTTAACGTTTGTCAAAATGCT
9137 CAAATAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (26 bp):
AGGGTTTAACGTTTGTCAAAATGCTT
Found at i:9196 original size:59 final size:59
Alignment explanation
Indices: 9129--9325 Score: 315
Period size: 59 Copynumber: 3.3 Consensus size: 59
9119 AACGTTTGTC
* * *
9129 AAAATGCTCAAATAAGGGGCC-GATCTTTTAATTTGATCAAATAAGGGCCTAACATATCG
1 AAAATGCTCAAATAAGGGCCCAG-TCTTTTAATTTGACCAAATAAGGGTCTAACATATCG
*
9188 AAAATGCTCAAATAAGGGCCTAGTCTTTTAATTTGACCAAATAAGGGTCTAACATATCG
1 AAAATGCTCAAATAAGGGCCCAGTCTTTTAATTTGACCAAATAAGGGTCTAACATATCG
* *
9247 AAAATGCTCAAATAAGCGCCCAGTCTTTTAATTTGACCAAATAAGGGTCTAACGTTATCG
1 AAAATGCTCAAATAAGGGCCCAGTCTTTTAATTTGACCAAATAAGGGTCTAAC-ATATCG
9307 AAAATGCTCAAATAAGGGC
1 AAAATGCTCAAATAAGGGC
9326 ATGGCGTCAG
Statistics
Matches: 128, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
59 104 0.81
60 24 0.19
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (59 bp):
AAAATGCTCAAATAAGGGCCCAGTCTTTTAATTTGACCAAATAAGGGTCTAACATATCG
Found at i:9201 original size:30 final size:30
Alignment explanation
Indices: 9165--9262 Score: 103
Period size: 30 Copynumber: 3.3 Consensus size: 30
9155 TTTAATTTGA
9165 TCAAATAAGGGCCTAACATATCGAAAATGC
1 TCAAATAAGGGCCTAACATATCGAAAATGC
* ** **
9195 TCAAATAAGGGCCTAGTC-T-TTTAATTTGAC
1 TCAAATAAGGGCCTA-ACATATCGAAAATG-C
*
9225 -CAAATAAGGGTCTAACATATCGAAAATGC
1 TCAAATAAGGGCCTAACATATCGAAAATGC
9254 TCAAATAAG
1 TCAAATAAG
9263 CGCCCAGTCT
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
28 1 0.02
29 20 0.38
30 30 0.58
31 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (30 bp):
TCAAATAAGGGCCTAACATATCGAAAATGC
Found at i:9262 original size:208 final size:208
Alignment explanation
Indices: 8904--9290 Score: 693
Period size: 208 Copynumber: 1.9 Consensus size: 208
8894 TGCTTAAATA
* * * *
8904 AGGGTTTAACGTTTGTCAAAATGTTTAAATAAGGGACTGATCTTTTAATTTGATCAAATAAGGGT
1 AGGGTTTAACGTTTGTCAAAATGCTCAAATAAGGGACCGATCTTTTAATTTGATCAAATAAGGGC
* *
8969 CTAATATATCGAAAATGCTCAAATAAGGGCCCAGTCTTTTAATTTGACCAAATAAGGGTCTAATA
66 CTAACATATCGAAAATGCTCAAATAAGGGCCCAGTCTTTTAATTTGACCAAATAAGGGTCTAACA
*
9034 TATCGAAAATGCTCAAATAAGGGCCCAGTCTTTTAATTTGACCAAATAAATAAGGGTTTAACGTT
131 TATCGAAAATGCTCAAATAAGCGCCCAGTCTTTTAATTTGACCAAATAAATAAGGGTTTAACGTT
9099 TGTCAAAATGCTT
196 TGTCAAAATGCTT
*
9112 AGGGTTTAACGTTTGTCAAAATGCTCAAATAAGGGGCCGATCTTTTAATTTGATCAAATAAGGGC
1 AGGGTTTAACGTTTGTCAAAATGCTCAAATAAGGGACCGATCTTTTAATTTGATCAAATAAGGGC
*
9177 CTAACATATCGAAAATGCTCAAATAAGGGCCTAGTCTTTTAATTTGACCAAATAAGGGTCTAACA
66 CTAACATATCGAAAATGCTCAAATAAGGGCCCAGTCTTTTAATTTGACCAAATAAGGGTCTAACA
9242 TATCGAAAATGCTCAAATAAGCGCCCAGTCTTTTAATTTGACCAAATAA
131 TATCGAAAATGCTCAAATAAGCGCCCAGTCTTTTAATTTGACCAAATAA
9291 GGGTCTAACG
Statistics
Matches: 170, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
208 170 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (208 bp):
AGGGTTTAACGTTTGTCAAAATGCTCAAATAAGGGACCGATCTTTTAATTTGATCAAATAAGGGC
CTAACATATCGAAAATGCTCAAATAAGGGCCCAGTCTTTTAATTTGACCAAATAAGGGTCTAACA
TATCGAAAATGCTCAAATAAGCGCCCAGTCTTTTAATTTGACCAAATAAATAAGGGTTTAACGTT
TGTCAAAATGCTT
Found at i:9503 original size:59 final size:59
Alignment explanation
Indices: 9365--9527 Score: 222
Period size: 59 Copynumber: 2.7 Consensus size: 59
9355 TTTTGACGCC
*
9365 AGGCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 AGGCCCTTATTTGAGCATTTTGACAAACGTTAAGCCCTTATTTGGCCAAATTAAAAGAT
* * * *
9424 CGAACCCTTATTTGAGCATTTTGACAAATGTTAAGCTCTTATTT-GCCAAATTAAAAGATT
1 AG-GCCCTTATTTGAGCATTTTGACAAACGTTAAGCCCTTATTTGGCCAAATTAAAAGA-T
* *
9484 AGGCCCTTATTTGAACATTTTGACAAACATT-AGACCCTTATTTG
1 AGGCCCTTATTTGAGCATTTTGACAAACGTTAAG-CCCTTATTTG
9528 AGCAATTAGC
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
58 2 0.02
59 48 0.54
60 39 0.44
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (59 bp):
AGGCCCTTATTTGAGCATTTTGACAAACGTTAAGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:10890 original size:166 final size:165
Alignment explanation
Indices: 10616--10937 Score: 509
Period size: 166 Copynumber: 1.9 Consensus size: 165
10606 GCTACATGTT
* * *
10616 TGAAACCATGTAATCTGAGCCTAATAACTTTTGCAATCACTTGAAACAAATGATGCACATCATAT
1 TGAAACCATGTAACCTGAGCCTAATAACTTTTGCAATCACTTGAAACAAACGATCCACATCATAT
* * *
10681 TGCTTCCCCTTTTAGATTCTGATATTCCGTTCCTTCCACAACAGGTAACAATATGCATTACAGTC
66 TGCTTCCCCTTGTAGATTCTGACATTCCGTTCCTTCCACAACAGGTAACAATATACATTACAGT-
10746 AAGCTTCAAGATCAAAGTGAGAAAGAAGCCCAATTA
130 AAGCTTCAAGATCAAAGTGAGAAAGAAGCCCAATTA
* ** *
10782 TGAAACCATGTAACCTGGGCCTAATAACTTTTGCAATTGCTTGAAACAAACGATCCACATCCTAT
1 TGAAACCATGTAACCTGAGCCTAATAACTTTTGCAATCACTTGAAACAAACGATCCACATCATAT
** *
10847 TGCTTCCCCTTGTAGATTCTGACATTGTGTTCCTTCCACAACAGGTAACAATATACATTACAGTG
66 TGCTTCCCCTTGTAGATTCTGACATTCCGTTCCTTCCACAACAGGTAACAATATACATTACAGTA
*
10912 GGCTTCAAGATCAAAGTGAGAAAGAA
131 AGCTTCAAGATCAAAGTGAGAAAGAA
10938 TTTCCCCTTG
Statistics
Matches: 142, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
165 25 0.18
166 117 0.82
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (165 bp):
TGAAACCATGTAACCTGAGCCTAATAACTTTTGCAATCACTTGAAACAAACGATCCACATCATAT
TGCTTCCCCTTGTAGATTCTGACATTCCGTTCCTTCCACAACAGGTAACAATATACATTACAGTA
AGCTTCAAGATCAAAGTGAGAAAGAAGCCCAATTA
Found at i:20566 original size:24 final size:24
Alignment explanation
Indices: 20534--20581 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
20524 AGATATGAAA
20534 GTTATTGCATCCTGCAGCAACTTT
1 GTTATTGCATCCTGCAGCAACTTT
20558 GTTATTGCATCCTGCAGCAACTTT
1 GTTATTGCATCCTGCAGCAACTTT
20582 TACCACAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (24 bp):
GTTATTGCATCCTGCAGCAACTTT
Found at i:24054 original size:13 final size:13
Alignment explanation
Indices: 24036--24060 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24026 ACCATTATTG
24036 TATTATTATTATA
1 TATTATTATTATA
24049 TATTATTATTAT
1 TATTATTATTAT
24061 GCTATAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTATTATTATA
Found at i:26882 original size:25 final size:24
Alignment explanation
Indices: 26854--26915 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
26844 GTGGATTGTA
* *
26854 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATCAA-ACATT
*
26879 AAATAAATTTAAGAATCAAACATT
1 AAATAAATTGAAGAATCAAACATT
*
26903 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
26916 CTGACTCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 9 0.27
24 8 0.24
25 16 0.48
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.27
Consensus pattern (24 bp):
AAATAAATTGAAGAATCAAACATT
Found at i:29269 original size:7 final size:7
Alignment explanation
Indices: 29257--29285 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
29247 TTACACCAGA
29257 AAATAAT
1 AAATAAT
29264 AAATAAT
1 AAATAAT
29271 AAATAAT
1 AAATAAT
29278 -AATAAT
1 AAATAAT
29284 AA
1 AA
29286 TATTAAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATAAT
Found at i:29502 original size:6 final size:6
Alignment explanation
Indices: 29491--29531 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
29481 GAACTCCCCC
* *
29491 CTGAGT CTGAGT CTGAGG CTGAGG CTGAGG CTGAGG CTGAG
1 CTGAGG CTGAGG CTGAGG CTGAGG CTGAGG CTGAGG CTGAG
29532 AGCAAGTACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.44, T:0.22
Consensus pattern (6 bp):
CTGAGG
Found at i:31431 original size:54 final size:54
Alignment explanation
Indices: 31373--31539 Score: 183
Period size: 54 Copynumber: 3.1 Consensus size: 54
31363 TGGCATTGTC
* *
31373 TTTTCTCACGGAATTTTGAACGGCTCTCAAATTGTCATGCTGTTTGGCACGAGA
1 TTTTCTCACGGAATTTGGAACGGCTCTCAAATTGTCATGCTATTTGGCACGAGA
* * * * * * * * * ** *
31427 TTTTCTGACTGTATTTGGCACAGCTCTCAAATTGGCACGGTATTTCGCA-TTGT
1 TTTTCTCACGGAATTTGGAACGGCTCTCAAATTGTCATGCTATTTGGCACGAGA
*
31480 TTTTCTCACGGAATTTGGAATGGCTCTCAAATTTGTCATGCTATTTGGCACGAGA
1 TTTTCTCACGGAATTTGGAACGGCTCTCAAA-TTGTCATGCTATTTGGCACGAGA
31535 TTTTC
1 TTTTC
31540 AAACAGTATT
Statistics
Matches: 84, Mismatches: 27, Indels: 3
0.74 0.24 0.03
Matches are distributed among these distances:
53 26 0.31
54 52 0.62
55 6 0.07
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (54 bp):
TTTTCTCACGGAATTTGGAACGGCTCTCAAATTGTCATGCTATTTGGCACGAGA
Found at i:31539 original size:108 final size:109
Alignment explanation
Indices: 31345--31555 Score: 327
Period size: 108 Copynumber: 1.9 Consensus size: 109
31335 GTGTTTGTGC
* *
31345 CAAATTTGGCACGGTACTTGGCATTGTCTTTTCTCACGGAATTTTGAACGGCTCTCAAATTGTCA
1 CAAATTTGGCACGGTACTTCGCATTGTCTTTTCTCACGGAATTTGGAACGGCTCTCAAATTGTCA
* ** *
31410 TGCTGTTTGGCACGAGATTTTCTGACTGTATTTGGCACAGCTCT
66 TGCTATTTGGCACGAGATTTTCAAACAGTATTTGGCACAGCTCT
* *
31454 CAAA-TTGGCACGGTATTTCGCATTGT-TTTTCTCACGGAATTTGGAATGGCTCTCAAATTTGTC
1 CAAATTTGGCACGGTACTTCGCATTGTCTTTTCTCACGGAATTTGGAACGGCTCTCAAA-TTGTC
31517 ATGCTATTTGGCACGAGATTTTCAAACAGTATTTGGCAC
65 ATGCTATTTGGCACGAGATTTTCAAACAGTATTTGGCAC
31556 GGTTATTTTT
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
107 29 0.31
108 60 0.65
109 4 0.04
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.36
Consensus pattern (109 bp):
CAAATTTGGCACGGTACTTCGCATTGTCTTTTCTCACGGAATTTGGAACGGCTCTCAAATTGTCA
TGCTATTTGGCACGAGATTTTCAAACAGTATTTGGCACAGCTCT
Found at i:35162 original size:24 final size:24
Alignment explanation
Indices: 35135--35180 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
35125 TTAATCAATA
*
35135 ATTAGTTTAATTAATCATAGTTTT
1 ATTACTTTAATTAATCATAGTTTT
35159 ATTACTTTAATTAATCATAGTT
1 ATTACTTTAATTAATCATAGTT
35181 AATTAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.52
Consensus pattern (24 bp):
ATTACTTTAATTAATCATAGTTTT
Found at i:37210 original size:2 final size:2
Alignment explanation
Indices: 37203--37245 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
37193 TACAGTTTTA
37203 AT AT AT AT AT AT AT AT AT AT AT GAT A- 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
37245 A
1 A
37246 CACTTTTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:37305 original size:38 final size:39
Alignment explanation
Indices: 37232--37320 Score: 153
Period size: 38 Copynumber: 2.3 Consensus size: 39
37222 TATGATAATA
37232 TATATATATATATACACTTTTATAGGTACAGATTTATAC
1 TATATATATATATACACTTTTATAGGTACAGATTTATAC
* *
37271 TATATATATATATAC-TTTTTATAGGTACATATTTATAC
1 TATATATATATATACACTTTTATAGGTACAGATTTATAC
37309 TATATATATATA
1 TATATATATATA
37321 CACGTGTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 33 0.69
39 15 0.31
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (39 bp):
TATATATATATATACACTTTTATAGGTACAGATTTATAC
Done.