Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013141.1 Corchorus capsularis cultivar CVL-1 contig13162, 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: 47677
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:386 original size:33 final size:34
Alignment explanation
Indices: 325--389 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
315 ATGCTGGATT
* * *
325 TTGAGTTTTGAACATGAGATGCAGATTTTGAACA
1 TTGAATTTTGAACATGAAATGCAAATTTTGAACA
359 TTGAATTTTGAA-ATGAAATGCAAATTTTGAA
1 TTGAATTTTGAACATGAAATGCAAATTTTGAA
390 TTTTGATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 17 0.61
34 11 0.39
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (34 bp):
TTGAATTTTGAACATGAAATGCAAATTTTGAACA
Found at i:511 original size:35 final size:35
Alignment explanation
Indices: 466--840 Score: 128
Period size: 35 Copynumber: 10.3 Consensus size: 35
456 AAATACAGGT
* * * *
466 TTTGAATTTTGAACCATGAGATGCTAATTTTGAAC
1 TTTGATTTTTGAACAATGAAATGCAAATTTTGAAC
* *
501 TTTGGTTTTTGAATAATGAAATGCAAATTTTGAAC
1 TTTGATTTTTGAACAATGAAATGCAAATTTTGAAC
* * * *
536 TTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAAT
1 TTTGATTTT---TG-A-ACAA---TGAAATGCAAATTTTGAAC
* * ** *** **
579 TTTGACTTTTT-AAGAATGAACTGTGTAATGCAG-GT
1 TTTGA-TTTTTGAACAATGAAATG-CAAATTTTGAAC
* * * ** *
614 TTTGAATTTTGAACCATGAGATGCTGATTTTGAAG
1 TTTGATTTTTGAACAATGAAATGCAAATTTTGAAC
*
649 TTTGATTTTTGAATAATGAAATGCAAATTTTGAAC
1 TTTGATTTTTGAACAATGAAATGCAAATTTTGAAC
* * * * *
684 TTTGATTTTCGAAGGATAGAATGCTGAAATGCAAGTTTTTAAT
1 TTTGATTTT----TGA-ACAA---TGAAATGCAAATTTTGAAC
* * * *** **
727 TTTGACTTTTGAAGAATGAACCGTG-AAATGCAG-GT
1 TTTGATTTTTGAACAATGAA--ATGCAAATTTTGAAC
* * * **
762 TTTGAATTTTGAACCATGAGATGCTGATTTTGAAC
1 TTTGATTTTTGAACAATGAAATGCAAATTTTGAAC
*
797 TTTGATTTTTGAATAATGAAATGCAAATTTTGAAC
1 TTTGATTTTTGAACAATGAAATGCAAATTTTGAAC
*
832 ATTGATTTT
1 TTTGATTTT
841 CGAAGAATAG
Statistics
Matches: 244, Mismatches: 72, Indels: 48
0.67 0.20 0.13
Matches are distributed among these distances:
33 2 0.01
34 11 0.05
35 152 0.62
36 6 0.02
37 2 0.01
38 9 0.04
39 6 0.02
40 6 0.02
43 46 0.19
44 4 0.02
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.40
Consensus pattern (35 bp):
TTTGATTTTTGAACAATGAAATGCAAATTTTGAAC
Found at i:586 original size:148 final size:148
Alignment explanation
Indices: 314--886 Score: 899
Period size: 148 Copynumber: 3.9 Consensus size: 148
304 AAGAAAAGTT
* * * *
314 AATGCTGGATTTTGAGTTTTGAA-CATGAGATGC-AGATTTTGAACATTGAATTTTG-A-AATGA
1 AATGCAGG-TTTTGAATTTTGAACCATGAGATGCTA-ATTTTGAACTTTGATTTTTGAATAATGA
* *
375 AATGCAAATTTTGAATTTTGATTTTCG-A-AA-GGAATGCTGAAATGCAAGTTTTGAATTTTGAC
64 AATGCAAATTTTGAACTTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGAC
437 TTTTGAAGAATGAACCGTGA
129 TTTTGAAGAATGAACCGTGA
* *
457 AATACAGGTTTTGAATTTTGAACCATGAGATGCTAATTTTGAACTTTGGTTTTTGAATAATGAAA
1 AATGCAGGTTTTGAATTTTGAACCATGAGATGCTAATTTTGAACTTTGATTTTTGAATAATGAAA
522 TGCAAATTTTGAACTTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTT
66 TGCAAATTTTGAACTTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTT
* * *
587 TTTAAGAATGAACTGTGT
131 TTGAAGAATGAACCGTGA
* *
605 AATGCAGGTTTTGAATTTTGAACCATGAGATGCTGATTTTGAAGTTTGATTTTTGAATAATGAAA
1 AATGCAGGTTTTGAATTTTGAACCATGAGATGCTAATTTTGAACTTTGATTTTTGAATAATGAAA
* *
670 TGCAAATTTTGAACTTTGATTTTCGAAGGATAGAATGCTGAAATGCAAGTTTTTAATTTTGACTT
66 TGCAAATTTTGAACTTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTT
735 TTGAAGAATGAACCGTGA
131 TTGAAGAATGAACCGTGA
*
753 AATGCAGGTTTTGAATTTTGAACCATGAGATGCTGATTTTGAACTTTGATTTTTGAATAATGAAA
1 AATGCAGGTTTTGAATTTTGAACCATGAGATGCTAATTTTGAACTTTGATTTTTGAATAATGAAA
* * * *
818 TGCAAATTTTGAACATTGATTTTCGAAGAATAGAATGCTGAAATGCAGGTTTTGAAATTTGATTT
66 TGCAAATTTTGAACTTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTT
883 TTGA
131 TTGA
887 GGCAAGAAAT
Statistics
Matches: 396, Mismatches: 27, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
142 13 0.03
143 33 0.08
144 2 0.01
145 31 0.08
146 1 0.00
147 2 0.01
148 314 0.79
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (148 bp):
AATGCAGGTTTTGAATTTTGAACCATGAGATGCTAATTTTGAACTTTGATTTTTGAATAATGAAA
TGCAAATTTTGAACTTTGATTTTCGAAGAATAGAATGCTGAAATGCAAGTTTTGAATTTTGACTT
TTGAAGAATGAACCGTGA
Found at i:620 original size:42 final size:43
Alignment explanation
Indices: 517--625 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 43
507 TTTTGAATAA
* *
517 TGAAATGCAAATTTTGAACTTTGATTTTCGAAGAATAGAATGC
1 TGAAATGCAAGTTTTGAATTTTGATTTTCGAAGAATAGAATGC
*
560 TGAAATGCAAGTTTTGAATTTTGACTTTT-TAAGAAT-GAACTG-
1 TGAAATGCAAGTTTTGAATTTTGA-TTTTCGAAGAATAGAA-TGC
* *
602 TGTAATGCAGGTTTTGAATTTTGA
1 TGAAATGCAAGTTTTGAATTTTGA
626 ACCATGAGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
42 25 0.42
43 30 0.51
44 4 0.07
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.39
Consensus pattern (43 bp):
TGAAATGCAAGTTTTGAATTTTGATTTTCGAAGAATAGAATGC
Found at i:774 original size:28 final size:28
Alignment explanation
Indices: 743--801 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
733 TTTTGAAGAA
* * *
743 TGAACCGTGAAATGCAGGTTTTGAATTT
1 TGAACCATGAAATGCAGATTTTGAACTT
* *
771 TGAACCATGAGATGCTGATTTTGAACTT
1 TGAACCATGAAATGCAGATTTTGAACTT
799 TGA
1 TGA
802 TTTTTGAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (28 bp):
TGAACCATGAAATGCAGATTTTGAACTT
Found at i:1057 original size:37 final size:37
Alignment explanation
Indices: 1016--1286 Score: 260
Period size: 37 Copynumber: 7.3 Consensus size: 37
1006 TGGTGTTTGA
* *
1016 ACACCTAAACAGGCATCTTGAACAAGGTTTTGATGAG
1 ACACCTAAACAGGAATCTTAAACAAGGTTTTGATGAG
* * * *
1053 ACACCTAAACAGGTACCTTAAATAAGGATTTTGATAAG
1 ACACCTAAACAGGAATCTTAAACAAGG-TTTTGATGAG
* * *
1091 AAACCTAAATAGGAATAC-TAAACAAGATTTTGATGAG
1 ACACCTAAACAGGAAT-CTTAAACAAGGTTTTGATGAG
* * * *
1128 ACACCTAAACAAGG-ACCTTAAACAAGGATTTAATAAG
1 ACACCTAAAC-AGGAATCTTAAACAAGGTTTTGATGAG
* * *
1165 AAACCTAAACATGAATCTTAAACAAGATTTTGATGAG
1 ACACCTAAACAGGAATCTTAAACAAGGTTTTGATGAG
* * * *
1202 ACACCTAAACAGGGA-CTTTAAATAAGGATTTGATAAG
1 ACACCTAAACAGGAATC-TTAAACAAGGTTTTGATGAG
* * * * *
1239 AAACCTGAACAGGCATCTTGAACAAGGTTTTGATGAC
1 ACACCTAAACAGGAATCTTAAACAAGGTTTTGATGAG
1276 ACACCTAAACA
1 ACACCTAAACA
1287 AGGATTTGAC
Statistics
Matches: 184, Mismatches: 43, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
36 4 0.02
37 147 0.80
38 32 0.17
39 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (37 bp):
ACACCTAAACAGGAATCTTAAACAAGGTTTTGATGAG
Found at i:1205 original size:74 final size:74
Alignment explanation
Indices: 1018--1290 Score: 379
Period size: 74 Copynumber: 3.7 Consensus size: 74
1008 GTGTTTGAAC
* * *
1018 ACCTAAACAGGCATCTTGAACAAGGTTTTGATGAGACACCTAAAC-AGGTACCTTAAATAAGGAT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAAGG-ACCTTAAATAAGGA-
1082 TTTGATAAGAA
64 TTTGATAAGAA
* *
1093 ACCTAAATAGGAATAC-TAAACAAGATTTTGATGAGACACCTAAACAAGGACCTTAAACAAGGAT
1 ACCTAAACAGGAAT-CTTAAACAAGATTTTGATGAGACACCTAAACAAGGACCTTAAATAAGGAT
*
1157 TTAATAAGAA
65 TTGATAAGAA
* * *
1167 ACCTAAACATGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACTTTAAATAAGGATT
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAAGGACCTTAAATAAGGATT
1232 TGATAAGAA
66 TGATAAGAA
* * * * *
1241 ACCTGAACAGGCATCTTGAACAAGGTTTTGATGACACACCTAAACAAGGA
1 ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAAGGA
1291 TTTGACGAGA
Statistics
Matches: 176, Mismatches: 19, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
73 1 0.01
74 119 0.68
75 52 0.30
76 4 0.02
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.23
Consensus pattern (74 bp):
ACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAAGGACCTTAAATAAGGATT
TGATAAGAA
Found at i:2075 original size:87 final size:87
Alignment explanation
Indices: 1919--2084 Score: 260
Period size: 87 Copynumber: 1.9 Consensus size: 87
1909 ATTGATGCCC
* * * *
1919 CAAACCTTCTTCCAATTTGGTCATGTATTGATATTCCCAACTCAATTGATGTTTCTGGATCAGCT
1 CAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAGCT
1984 TCTCACCTCAAGAATTATTTCT
66 TCTCACCTCAAGAATTATTTCT
* *
2006 CAAATCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAGTT
1 CAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAGCT
* *
2071 TCTCATCTTAAGAA
66 TCTCACCTCAAGAA
2085 ACTTTCAAAC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (87 bp):
CAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAGCT
TCTCACCTCAAGAATTATTTCT
Found at i:2626 original size:15 final size:14
Alignment explanation
Indices: 2602--2631 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2592 TCAAGAACAA
2602 TCTTTTTTTCTTTT
1 TCTTTTTTTCTTTT
2616 TCTTATTTTTCTTTT
1 TCTT-TTTTTCTTTT
2631 T
1 T
2632 TTGTTCCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (14 bp):
TCTTTTTTTCTTTT
Found at i:2920 original size:14 final size:14
Alignment explanation
Indices: 2888--2952 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
2878 ATTCAAAACC
*
2888 TTTTTGAAAACTCA-
1 TTTTTG-AAAGTCAT
2902 TTTTTGAAAGTCATT
1 TTTTTGAAAGTCA-T
2917 TTTTTGAAAG-CAT
1 TTTTTGAAAGTCAT
*
2930 TTTCTTGAAAATC-T
1 TTT-TTGAAAGTCAT
*
2944 TTTTCGAAA
1 TTTTTGAAA
2953 ACATCTTTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
13 15 0.34
14 18 0.41
15 11 0.25
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (14 bp):
TTTTTGAAAGTCAT
Found at i:2920 original size:15 final size:14
Alignment explanation
Indices: 2902--2939 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
2892 TGAAAACTCA
2902 TTTTTGAAAGTCATT
1 TTTTTGAAAG-CATT
2917 TTTTTGAAAGCATT
1 TTTTTGAAAGCATT
*
2931 TTCTTGAAA
1 TTTTTGAAA
2940 ATCTTTTTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (14 bp):
TTTTTGAAAGCATT
Found at i:3036 original size:16 final size:15
Alignment explanation
Indices: 3015--3044 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3005 GATGTCACAA
3015 TTCTTTTTCTTTTTTT
1 TTCTTTTT-TTTTTTT
3031 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
3045 ACTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTCTTTTTTTTTTTT
Found at i:3037 original size:9 final size:10
Alignment explanation
Indices: 3018--3042 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3008 GTCACAATTC
3018 TTTTTCTTTT
1 TTTTTCTTTT
3028 TTTTTCTTTT
1 TTTTTCTTTT
3038 TTTTT
1 TTTTT
3043 TTACTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:3042 original size:13 final size:13
Alignment explanation
Indices: 3024--3055 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3014 ATTCTTTTTC
3024 TTTTTTTTT-CTT
1 TTTTTTTTTACTT
3036 TTTTTTTTTACTT
1 TTTTTTTTTACTT
3049 TTTTTTT
1 TTTTTTT
3056 GGGCAACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.03, C:0.06, G:0.00, T:0.91
Consensus pattern (13 bp):
TTTTTTTTTACTT
Found at i:6406 original size:16 final size:15
Alignment explanation
Indices: 6383--6426 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
6373 ATTTTAAATT
6383 ATTACTTTTATTTTG
1 ATTACTTTTATTTTG
6398 ATATAC-TTTA--TT-
1 AT-TACTTTTATTTTG
6410 ATTACTTTTATTTTG
1 ATTACTTTTATTTTG
6425 AT
1 AT
6427 GTATAATCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
11 3 0.12
12 6 0.25
13 2 0.08
14 2 0.08
15 8 0.33
16 3 0.12
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (15 bp):
ATTACTTTTATTTTG
Found at i:8815 original size:3 final size:3
Alignment explanation
Indices: 8807--8844 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
8797 TATATATAAA
8807 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT A
8845 AACCTACTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:9334 original size:59 final size:59
Alignment explanation
Indices: 9237--9364 Score: 204
Period size: 59 Copynumber: 2.2 Consensus size: 59
9227 TTCTCTCATT
* * * *
9237 CTTCGTATTTTCTTCTTCTTCATATTCTATTGTCTCTCTATTCTCTTGTCTTTTACATA
1 CTTCATATTTTCTTCTTCTCCATATTCTATTGTCTCTCTATTCTCTTATCTTTAACATA
*
9296 CTTCATATTTTCTTTTTCTCCATATTCTATTGTCTCTCTATTCTCTTATCTTTAACATA
1 CTTCATATTTTCTTCTTCTCCATATTCTATTGTCTCTCTATTCTCTTATCTTTAACATA
9355 CTTCA-ATTTT
1 CTTCATATTTT
9365 ACTCCATTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
58 5 0.08
59 59 0.92
ACGTcount: A:0.16, C:0.23, G:0.03, T:0.57
Consensus pattern (59 bp):
CTTCATATTTTCTTCTTCTCCATATTCTATTGTCTCTCTATTCTCTTATCTTTAACATA
Found at i:9466 original size:46 final size:46
Alignment explanation
Indices: 9399--9494 Score: 192
Period size: 46 Copynumber: 2.1 Consensus size: 46
9389 ATTTCACAAC
9399 AAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAAT
1 AAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAAT
9445 AAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAAT
1 AAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAAT
9491 AAAA
1 AAAA
9495 CAGCCGCACG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (46 bp):
AAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAAT
Found at i:9973 original size:22 final size:21
Alignment explanation
Indices: 9948--9996 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
9938 TTTTTCTCAA
*
9948 AAAATAATAAACTTAATTAAC
1 AAAATAACAAACTTAATTAAC
*
9969 TAAAATAACATACTTAATTAAC
1 -AAAATAACAAACTTAATTAAC
9991 AAAATA
1 AAAATA
9997 TATACTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAATAACAAACTTAATTAAC
Found at i:14590 original size:2 final size:2
Alignment explanation
Indices: 14585--14615 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
14575 TGTTTTTTTC
*
14585 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14616 AATAATAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:14616 original size:10 final size:10
Alignment explanation
Indices: 14587--14619 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
14577 TTTTTTTCAT
*
14587 ATATATATAT
1 ATATATATAA
14597 ATATATATAA
1 ATATATATAA
14607 ATATATATAA
1 ATATATATAA
14617 ATA
1 ATA
14620 ATAAGTACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATATAA
Found at i:15000 original size:91 final size:90
Alignment explanation
Indices: 14849--15029 Score: 344
Period size: 91 Copynumber: 2.0 Consensus size: 90
14839 CCACTTCCCA
*
14849 AAAACACGGAGTAGTTTATTAAGGTGCTTTGCATACTCATAATTTTGGATTGTGACTAACACAAA
1 AAAACACGGAGTAGTTTATTAAGGTGCTTTGCATACTCATAATTTTGGATCGTGACTAACACAAA
14914 GGTTGATATTTGTGATAGCGAACCC
66 GGTTGATATTTGTGATAGCGAACCC
14939 AAAACAACGGAGTAGTTTATTAAGGTGCTTTGCATACTCATAATTTTGGATCGTGACTAACACAA
1 AAAAC-ACGGAGTAGTTTATTAAGGTGCTTTGCATACTCATAATTTTGGATCGTGACTAACACAA
15004 AGGTTGATATTTGTGATAGCGAACCC
65 AGGTTGATATTTGTGATAGCGAACCC
15030 CGTGTACTCC
Statistics
Matches: 89, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
90 5 0.06
91 84 0.94
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (90 bp):
AAAACACGGAGTAGTTTATTAAGGTGCTTTGCATACTCATAATTTTGGATCGTGACTAACACAAA
GGTTGATATTTGTGATAGCGAACCC
Found at i:15501 original size:2 final size:2
Alignment explanation
Indices: 15496--15525 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15486 CCCCCCCGCA
15496 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
15526 TTAAGATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:15858 original size:13 final size:14
Alignment explanation
Indices: 15840--15871 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
15830 AAAGCAAAGT
15840 AAACTAAACT-AGA
1 AAACTAAACTAAGA
15853 AAACT-AACTAAGA
1 AAACTAAACTAAGA
15866 AAACTA
1 AAACTA
15872 TTAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.62, C:0.16, G:0.06, T:0.16
Consensus pattern (14 bp):
AAACTAAACTAAGA
Found at i:38631 original size:15 final size:16
Alignment explanation
Indices: 38613--38642 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
38603 ATATAAGGGA
38613 AAGAAAA-ATAAAAAG
1 AAGAAAACATAAAAAG
38628 AAGAAAACATAAAAA
1 AAGAAAACATAAAAA
38643 CGATGCGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (16 bp):
AAGAAAACATAAAAAG
Found at i:42688 original size:16 final size:16
Alignment explanation
Indices: 42663--42694 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42653 TACCCAGTGG
*
42663 TATTTGTTTTTCTTTT
1 TATTTATTTTTCTTTT
42679 TATTTATTTTTCTTTT
1 TATTTATTTTTCTTTT
42695 CTGGGTACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.81
Consensus pattern (16 bp):
TATTTATTTTTCTTTT
Found at i:46728 original size:4 final size:4
Alignment explanation
Indices: 46721--46748 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
46711 AAAAAAAAAA
46721 AAAC AAAC AAAC AAAC AAAC AAAC AAAC
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC
46749 TACTGAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.25, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Done.