Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016374.1 Corchorus olitorius cultivar O-4 contig16407, 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: 148203
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2420 original size:3 final size:3
Alignment explanation
Indices: 2412--2438 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2402 GTAATTTGCT
2412 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
2439 ACTAGTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2823 original size:60 final size:59
Alignment explanation
Indices: 2750--2865 Score: 214
Period size: 60 Copynumber: 1.9 Consensus size: 59
2740 GCAAAACTTA
2750 AACCCGAAACAGTGACTTAGCCAAATCTTTTAAGACTATATTATTTGTTTGAGCTTCACC
1 AACCCGAAACAGTGACTTAGCCAAATCTTTT-AGACTATATTATTTGTTTGAGCTTCACC
*
2810 AACCCGAAACAGTGACTTAGCCAAATCTTTTAGGCTATATTATTTGTTTGAGCTTC
1 AACCCGAAACAGTGACTTAGCCAAATCTTTTAGACTATATTATTTGTTTGAGCTTC
2866 TGGCACGTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
59 24 0.44
60 31 0.56
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (59 bp):
AACCCGAAACAGTGACTTAGCCAAATCTTTTAGACTATATTATTTGTTTGAGCTTCACC
Found at i:3613 original size:2 final size:2
Alignment explanation
Indices: 3608--3638 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3598 CTTTTCAGTT
3608 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 T
3639 CTCCACTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12531 original size:10 final size:11
Alignment explanation
Indices: 12516--12559 Score: 65
Period size: 10 Copynumber: 4.1 Consensus size: 11
12506 CGTAGCGTCT
12516 TATAATA-ATA
1 TATAATATATA
12526 TATAATATATAA
1 TATAATATAT-A
12538 TATAATATA-A
1 TATAATATATA
12548 TATAATATATA
1 TATAATATATA
12559 T
1 T
12560 TCACCCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 17 0.55
11 4 0.13
12 10 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATAATATATA
Found at i:12532 original size:7 final size:7
Alignment explanation
Indices: 12520--12558 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
12510 GCGTCTTATA
12520 ATAATAT
1 ATAATAT
12527 ATAATAT
1 ATAATAT
12534 ATAATAT
1 ATAATAT
12541 A-ATATAAT
1 ATA-AT-AT
12549 ATAATAT
1 ATAATAT
12556 ATA
1 ATA
12559 TTCACCCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 1 0.03
7 22 0.76
8 5 0.17
9 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
ATAATAT
Found at i:12540 original size:5 final size:5
Alignment explanation
Indices: 12520--12556 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
12510 GCGTCTTATA
12520 ATAAT AT-AT A-ATAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT ATA
12557 TATTCACCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 3 0.10
5 25 0.86
6 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:12558 original size:17 final size:17
Alignment explanation
Indices: 12516--12551 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
12506 CGTAGCGTCT
12516 TATAATAATATATAATA
1 TATAATAATATATAATA
12533 TATAAT-ATAATATAATA
1 TATAATAAT-ATATAATA
12550 TA
1 TA
12552 ATATATATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 16 0.89
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATAATAATATATAATA
Found at i:15862 original size:27 final size:27
Alignment explanation
Indices: 15825--15891 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
15815 AGACACGGTA
*
15825 AAATGAAGGAGCTATAGATTTGGCGCT
1 AAATGAGGGAGCTATAGATTTGGCGCT
15852 AAATGAGGGAGCTATAGATTTGGCGCT
1 AAATGAGGGAGCTATAGATTTGGCGCT
*
15879 AAATGAGGAAGCT
1 AAATGAGGGAGCT
15892 TAGCTACATG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.34, C:0.10, G:0.31, T:0.24
Consensus pattern (27 bp):
AAATGAGGGAGCTATAGATTTGGCGCT
Found at i:24394 original size:38 final size:38
Alignment explanation
Indices: 24343--24419 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
24333 GCTTTTTAAT
24343 AAATCCAGATTACTCATATCTTTGGTATTTCAATTTGA
1 AAATCCAGATTACTCATATCTTTGGTATTTCAATTTGA
24381 AAATCCAGATTACTCATATCTTTGGTATTTCAATTTGA
1 AAATCCAGATTACTCATATCTTTGGTATTTCAATTTGA
24419 A
1 A
24420 TTTTGAGGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (38 bp):
AAATCCAGATTACTCATATCTTTGGTATTTCAATTTGA
Found at i:50505 original size:12 final size:12
Alignment explanation
Indices: 50488--50512 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50478 ACCAGATCCA
50488 ACTTATTTAATC
1 ACTTATTTAATC
50500 ACTTATTTAATC
1 ACTTATTTAATC
50512 A
1 A
50513 AATCAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (12 bp):
ACTTATTTAATC
Found at i:55415 original size:17 final size:17
Alignment explanation
Indices: 55389--55422 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
55379 ATCTTGGAGG
* *
55389 AAAAGTGGGAATAAAGA
1 AAAAGGGGGAACAAAGA
55406 AAAAGGGGGAACAAAGA
1 AAAAGGGGGAACAAAGA
55423 TGGTAGTGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.03, G:0.32, T:0.06
Consensus pattern (17 bp):
AAAAGGGGGAACAAAGA
Found at i:63690 original size:26 final size:28
Alignment explanation
Indices: 63633--63690 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
63623 AATTACAACT
**
63633 AGATTAGCTAATAAGTTTTTTCTAGGGA
1 AGATTAGCTAATAAGTTAATTCTAGGGA
*
63661 AGATTAG-TAATAAGTTAATT-TAGGTA
1 AGATTAGCTAATAAGTTAATTCTAGGGA
63687 AGAT
1 AGAT
63691 CTTAAGTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
27 11 0.41
28 7 0.26
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (28 bp):
AGATTAGCTAATAAGTTAATTCTAGGGA
Found at i:71559 original size:51 final size:51
Alignment explanation
Indices: 71504--71609 Score: 203
Period size: 51 Copynumber: 2.1 Consensus size: 51
71494 TGGTTCCTTT
71504 GTTTTCATGTCTGATATTTTCTACTATCACTATATTTAGAAGGTCTTTTAA
1 GTTTTCATGTCTGATATTTTCTACTATCACTATATTTAGAAGGTCTTTTAA
*
71555 GTTTTCATGTCTGATATTTTCTACTATCACTATATTTAGAAGGTCTTTTAT
1 GTTTTCATGTCTGATATTTTCTACTATCACTATATTTAGAAGGTCTTTTAA
71606 GTTT
1 GTTT
71610 GGTCTTTTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.24, C:0.13, G:0.12, T:0.51
Consensus pattern (51 bp):
GTTTTCATGTCTGATATTTTCTACTATCACTATATTTAGAAGGTCTTTTAA
Found at i:73242 original size:873 final size:875
Alignment explanation
Indices: 71555--73276 Score: 3214
Period size: 873 Copynumber: 2.0 Consensus size: 875
71545 GGTCTTTTAA
*
71555 GTTTTCATGTCTGATATTTTCTACTATCACTATATTTAGAAGGTCTTTTATGTTTGGTCTTTTAT
1 GTTTTCATGTCTGATATTTTCTACTATCACTATATTTAGAAGATCTTTTATGTTTGGTCTTTTAT
*
71620 TAGTTACACACTATAGGAAATACTAGGTACAAGGAAAATAAATTTGACATTCATGATTGCCATTG
66 TAGTTACACACTATAGGAAATACTAGGTACAAGGAAAATAAATTCGACATTCATGATTGCCATTG
71685 AGACTAACAACTTTATACTTCTGAGTATTCTCCTAATATATCAACTAGCTAAAGACCAGGCAGTT
131 AGACTAACAACTTTATACTTCTGAGTATTCTCCTAATATATCAACTAGCTAAAGACCAGGCAGTT
71750 AAATTATCATGCAACCACAATTTTAAAGAAATAGTAATTCTATAAAACTTCCATTCAGGAATGAC
196 AAATTATCATGCAACCACAATTTTAAAGAAATAGTAATTCTATAAAACTTCCATTCAGGAATGAC
*
71815 AACAATTTCTCTATGTTCCAAGTGCCACTGGTACTATTGACAGTAAGATTCTTTTTCTAGGAGAG
261 AACAATTTCTCTATGTTCCAAGTGCCACTGGTACTATTGACAGTAAAATTCTTTTTCTAGGAGAG
*
71880 TTTTAAACAATTTTCTTCATTTTTTTTCTAATGGTGGATGGCGTTTTCATTTTATATGGTGGCTC
326 TTTTAAACAATTTTCTTCATTATTTTTCTAATGGTGGATGGCGTTTTCATTTTATATGGTGGCTC
71945 TACCAAGTTAAGTGGTTTTCCCTTTTCCTTACCATCGTTTTCCCAATGGGTATGGGGGGTCAATA
391 TACCAAGTTAAGTGGTTTTCCCTTTTCCTTACCATCGTTTTCCCAATGGGTATGGGGGGTCAATA
* *
72010 AATTGACCCAGAATTGGACTCTTTAAATATTCTGAACAACTGTTACATAGAAAATCATCCTCACT
456 AATTGACCCAGAATTGGACTCTTTAAATATTCTGAACAACTGTTACATAAAAAATCATCATCACT
*
72075 TATTTAACAGAATTGTCCAGTTGCTGATTTGATCATTTGGGGTGTTACCAAAATAAGTCATTGTC
521 TATTTAACAGAATTGTCCAGTTCCTGATTTGATCATTTGGGGTGTTACCAAAATAAGTCATTGTC
72140 ATCCTATTTGACAGATAATTAAAGAAGGTTCTTCTTTTGTGTTAGGTTTCAAATCGAAGTTTTAA
586 ATCCTATTTGACAGATAATTAAAGAAGGTTCTTCTTTTGTGTTAGGTTTCAAATCGAAGTTTTAA
*
72205 TATGTTTTGTCCTCAGCATAAGCAGGGGAAGGGTTTTCGAGCAGAGTAGTTGAAACAAATTACTA
651 TATGTTTTGTCCTCAGCATAAGCAGGGGAAGGGTTTTCAAGCAGAGTAGTTGAAACAAATTACTA
72270 TCTTCTAACAATTGTCTGCGACAAATTATGGATCAACATTGCCATTGTAAATAGTATTAACACTG
716 TCTTCTAACAATTGTCTGCGACAAATTATGGATCAACATTGCCATTGTAAATAGTATTAACACTG
72335 GAATATGTTGAATTCTTATATTTGCATCTTTTTGTATAGGAGCAAAGCATGTTCCTACTGATTTT
781 GAATATGTTGAATTCTTATATTTGCATCTTTTTGTATAGGAGCAAAGCATGTTCCTACTGATTTT
72400 TGTCATGAGTCTGAAACTAATGGTTCCTCT
846 TGTCATGAGTCTGAAACTAATGGTTCCTCT
72430 GTTTTCATGTCTGATATTTTCTACTATCACTATATTTAGAAGATCTTTTATGTTTGGTCTTTTAT
1 GTTTTCATGTCTGATATTTTCTACTATCACTATATTTAGAAGATCTTTTATGTTTGGTCTTTTAT
72495 TAGTTACACACTATAGGAAATACTAGGTACAAGGAAAATAAATTCGACATTCATGATTGCCATTG
66 TAGTTACACACTATAGGAAATACTAGGTACAAGGAAAATAAATTCGACATTCATGATTGCCATTG
* *
72560 AGACTAACAACTTTATACTTCTGAGTATTCTCCTAATATATCAACTAGCTAAAGATCATGCAGTT
131 AGACTAACAACTTTATACTTCTGAGTATTCTCCTAATATATCAACTAGCTAAAGACCAGGCAGTT
72625 AAATTATCATGCAACCACAATTTTAAAGAAATAGTAATTCTATAAAACTTCCATTCAGGAATGAC
196 AAATTATCATGCAACCACAATTTTAAAGAAATAGTAATTCTATAAAACTTCCATTCAGGAATGAC
* *
72690 AACAATTTCTCTATGTTCCAAGTGCCACTGGTACTATTGACAGTAAAATTCTTTTTTTAGGGGAG
261 AACAATTTCTCTATGTTCCAAGTGCCACTGGTACTATTGACAGTAAAATTCTTTTTCTAGGAGAG
* * *
72755 TTTTAAGCAATTTTCTTCA-TATTTTT-TAATGGTGGATGGTGTTTTCATTTTATCTGGTGGCTC
326 TTTTAAACAATTTTCTTCATTATTTTTCTAATGGTGGATGGCGTTTTCATTTTATATGGTGGCTC
*
72818 TACCAAGTTAAGTGGTTTTCCCTTTTCCTTACCATCGTTTTCTCAATGGGTATGGGGGGTCAATA
391 TACCAAGTTAAGTGGTTTTCCCTTTTCCTTACCATCGTTTTCCCAATGGGTATGGGGGGTCAATA
* * * * *
72883 AATTGACTCATAATTGGACTCTTTAGATATTCTGAACAAGTGTTACATAAAAAATCTTCATCACT
456 AATTGACCCAGAATTGGACTCTTTAAATATTCTGAACAACTGTTACATAAAAAATCATCATCACT
72948 TATTTAACAGAATTGTCCAGTTCCTGATTTGATCATTTGGGGTGTTACCAAAATAAGTCATTGTC
521 TATTTAACAGAATTGTCCAGTTCCTGATTTGATCATTTGGGGTGTTACCAAAATAAGTCATTGTC
73013 ATCCTATTTGACAGATAATTAAAGAAGGTTCTTCTTTTGTGTTAGGTTTCAAATCGAAGTTTTAA
586 ATCCTATTTGACAGATAATTAAAGAAGGTTCTTCTTTTGTGTTAGGTTTCAAATCGAAGTTTTAA
73078 TATGTTTTGTCCTCAGCATAAGCAGGGGAAGGGTTTTCAAGCAGAGTAGTTGAAACAAATTACTA
651 TATGTTTTGTCCTCAGCATAAGCAGGGGAAGGGTTTTCAAGCAGAGTAGTTGAAACAAATTACTA
* *
73143 TCTTCTAACAATTGTCTGCGACAAATTATTGATTAACATTGCCATTGTAAATAGTATTAACACTG
716 TCTTCTAACAATTGTCTGCGACAAATTATGGATCAACATTGCCATTGTAAATAGTATTAACACTG
*
73208 GAATATGTTGAATTCTTATATTTGCATCTTTTTGTATAGGAGCAAAGCATGTTCCTATTGATTTT
781 GAATATGTTGAATTCTTATATTTGCATCTTTTTGTATAGGAGCAAAGCATGTTCCTACTGATTTT
73273 TGTC
846 TGTC
73277 GTAACTCTTT
Statistics
Matches: 823, Mismatches: 24, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
873 481 0.58
874 6 0.01
875 336 0.41
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (875 bp):
GTTTTCATGTCTGATATTTTCTACTATCACTATATTTAGAAGATCTTTTATGTTTGGTCTTTTAT
TAGTTACACACTATAGGAAATACTAGGTACAAGGAAAATAAATTCGACATTCATGATTGCCATTG
AGACTAACAACTTTATACTTCTGAGTATTCTCCTAATATATCAACTAGCTAAAGACCAGGCAGTT
AAATTATCATGCAACCACAATTTTAAAGAAATAGTAATTCTATAAAACTTCCATTCAGGAATGAC
AACAATTTCTCTATGTTCCAAGTGCCACTGGTACTATTGACAGTAAAATTCTTTTTCTAGGAGAG
TTTTAAACAATTTTCTTCATTATTTTTCTAATGGTGGATGGCGTTTTCATTTTATATGGTGGCTC
TACCAAGTTAAGTGGTTTTCCCTTTTCCTTACCATCGTTTTCCCAATGGGTATGGGGGGTCAATA
AATTGACCCAGAATTGGACTCTTTAAATATTCTGAACAACTGTTACATAAAAAATCATCATCACT
TATTTAACAGAATTGTCCAGTTCCTGATTTGATCATTTGGGGTGTTACCAAAATAAGTCATTGTC
ATCCTATTTGACAGATAATTAAAGAAGGTTCTTCTTTTGTGTTAGGTTTCAAATCGAAGTTTTAA
TATGTTTTGTCCTCAGCATAAGCAGGGGAAGGGTTTTCAAGCAGAGTAGTTGAAACAAATTACTA
TCTTCTAACAATTGTCTGCGACAAATTATGGATCAACATTGCCATTGTAAATAGTATTAACACTG
GAATATGTTGAATTCTTATATTTGCATCTTTTTGTATAGGAGCAAAGCATGTTCCTACTGATTTT
TGTCATGAGTCTGAAACTAATGGTTCCTCT
Found at i:73824 original size:90 final size:86
Alignment explanation
Indices: 73675--73850 Score: 298
Period size: 90 Copynumber: 2.0 Consensus size: 86
73665 TATGAGCCAA
*
73675 CAAACTACCTACCTACTAAAATAAACTCACATTAAGAGTTGAACTCAAGACCTCACGCTGCATGA
1 CAAACTACCTACCTACTAAAATAAACTCACATTAAGAGTTGAACCCAAGACCTCACGCTGCATGA
73740 TTAGCTACATTTTCGAAACGC
66 TTAGCTACATTTTCGAAACGC
*
73761 CAAACTACCTACCTACTAAAATAAACTCACATTCCGTGAGAGTTGAACCCAAGACCTCACGCTGC
1 CAAACTACCTACCTACTAAAATAAACTCACA-T---TAAGAGTTGAACCCAAGACCTCACGCTGC
73826 ATGATTAGCTACATTTTCGAAACGC
62 ATGATTAGCTACATTTTCGAAACGC
73851 TAATCTATGA
Statistics
Matches: 84, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
86 31 0.37
87 1 0.01
90 52 0.62
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.24
Consensus pattern (86 bp):
CAAACTACCTACCTACTAAAATAAACTCACATTAAGAGTTGAACCCAAGACCTCACGCTGCATGA
TTAGCTACATTTTCGAAACGC
Found at i:87920 original size:12 final size:12
Alignment explanation
Indices: 87905--87929 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
87895 ATAAATAGGA
87905 ATTTTTTATTTT
1 ATTTTTTATTTT
87917 ATTTTTTATTTT
1 ATTTTTTATTTT
87929 A
1 A
87930 AATTTTGACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
ATTTTTTATTTT
Found at i:90054 original size:4 final size:4
Alignment explanation
Indices: 90045--90081 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
90035 ATTTTAACTT
90045 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
90082 GGGCAATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:105229 original size:24 final size:24
Alignment explanation
Indices: 105202--105273 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
105192 TGGATATGGC
105202 GTAAAATGGGACACAAAATTTGGG
1 GTAAAATGGGACACAAAATTTGGG
*
105226 GTAAAATGGGACTCAAAATTTGGG
1 GTAAAATGGGACACAAAATTTGGG
* *
105250 GTAAAATGGGACACCAAACTTGGG
1 GTAAAATGGGACACAAAATTTGGG
105274 TAGGGGATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.39, C:0.11, G:0.29, T:0.21
Consensus pattern (24 bp):
GTAAAATGGGACACAAAATTTGGG
Found at i:113289 original size:68 final size:68
Alignment explanation
Indices: 113180--113314 Score: 180
Period size: 68 Copynumber: 2.0 Consensus size: 68
113170 AGATCGTTGG
* *** *
113180 AAGACTCACCCATTAAAATCAGGTAAACGACGCGGATCGAATTTGGATTAGTCAGAGTAAAGTTC
1 AAGACTCACCCATTAAAATCAGGTAAACGACGCAGATCGAATCCAGATTAGTCAGAGCAAAGTTC
113245 TGA
66 TGA
* * ***
113248 AAGACTCACCCATTAAAATTATGTGTGCGACGCAGATCGAATCCAGATTAGTCAGAGCAAAGTTC
1 AAGACTCACCCATTAAAATCAGGTAAACGACGCAGATCGAATCCAGATTAGTCAGAGCAAAGTTC
113313 TG
66 TG
113315 GATACCGAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
68 57 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (68 bp):
AAGACTCACCCATTAAAATCAGGTAAACGACGCAGATCGAATCCAGATTAGTCAGAGCAAAGTTC
TGA
Found at i:124631 original size:18 final size:18
Alignment explanation
Indices: 124608--124643 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
124598 GTTGTTTCCC
124608 ATTCGCTTTCAGTCCCGG
1 ATTCGCTTTCAGTCCCGG
*
124626 ATTCGCTTTCAGTTCCGG
1 ATTCGCTTTCAGTCCCGG
124644 TTTCTGTTCC
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:0.11, C:0.31, G:0.22, T:0.36
Consensus pattern (18 bp):
ATTCGCTTTCAGTCCCGG
Found at i:127553 original size:5 final size:5
Alignment explanation
Indices: 127517--127550 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
127507 GTCCAGTACT
*
127517 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAA GAAA
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAA
127551 AGAGGTATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:143238 original size:84 final size:87
Alignment explanation
Indices: 143089--143263 Score: 257
Period size: 84 Copynumber: 2.0 Consensus size: 87
143079 GCTTCGAATA
* * *
143089 TGATTAGTCATAATTATAAATAAATCAGTAAAGGAAGGATAATTATTTGATATATTGTCAATATA
1 TGATTAGTCATAATTAT-AATAAACCAGTAAAGGAAGGATAATTATTTGATATACTATCAATATA
*
143154 AAATTTGGACTCCATAAGTGGGG
65 AAATTTGGACTCCATAAGTGAGG
* **
143177 TGATTAGTCATAA-T-T-ATAAACCAGTAAAGGAAGGCTAATTATTTGATATACTATCTGTATAA
1 TGATTAGTCATAATTATAATAAACCAGTAAAGGAAGGATAATTATTTGATATACTATCAATATAA
143239 AATTTGGACTCCATAAGTGAGG
66 AATTTGGACTCCATAAGTGAGG
143261 TGA
1 TGA
143264 GGAGTTGACA
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
84 65 0.81
86 1 0.01
87 1 0.01
88 13 0.16
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (87 bp):
TGATTAGTCATAATTATAATAAACCAGTAAAGGAAGGATAATTATTTGATATACTATCAATATAA
AATTTGGACTCCATAAGTGAGG
Found at i:145362 original size:16 final size:16
Alignment explanation
Indices: 145343--145375 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
145333 TCAATGTGGG
145343 GACTTTAATTTGTGAT
1 GACTTTAATTTGTGAT
145359 GACTTTAATTTGTGAT
1 GACTTTAATTTGTGAT
145375 G
1 G
145376 CTAAAGTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.48
Consensus pattern (16 bp):
GACTTTAATTTGTGAT
Done.