Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010992.1 Corchorus capsularis cultivar CVL-1 contig11013, 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: 55839
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:5348 original size:6 final size:6
Alignment explanation
Indices: 5337--5363 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5327 AAAGCAAAAC
5337 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
5364 GCAGATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:9378 original size:70 final size:70
Alignment explanation
Indices: 9290--9665 Score: 527
Period size: 70 Copynumber: 5.4 Consensus size: 70
9280 TTCATACATT
* * *
9290 AGAGTCAAGGTAATAGTAATCAGTAAATCACTAATTGAGTAAAAGAAATTAATCAGCAAATTGAT
1 AGAGTCAAGGTAATAGTAATCAGTAAATCACTAATTAAGTAAAAGAGATTAATCAGTAAATTGAT
9355 AATTA
66 AATTA
* * * * *
9360 AGAGTCAAGGTAACAGTAATCAGTAAGTCAATAATTAAGTGAAAGAGATTAATCAGTAAAGTGAT
1 AGAGTCAAGGTAATAGTAATCAGTAAATCACTAATTAAGTAAAAGAGATTAATCAGTAAATTGAT
*
9425 AATCA
66 AATTA
* * * * * **
9430 AGAATCAAGGTAATAGTAATCAGTAAGTCAGTAATTAAGTGAAAGAGACTAATCAGTAAAGCGAT
1 AGAGTCAAGGTAATAGTAATCAGTAAATCACTAATTAAGTAAAAGAGATTAATCAGTAAATTGAT
*
9495 AATCA
66 AATTA
* * * *
9500 AGAATCAAGGTAATAGTAATCAGTAAATCAGTAAATCAGTAAAAAGAGATTAATCAGTAAATTGA
1 AGAGTCAAGGTAATAGTAATCAGTAAATCACTAATTAAGT-AAAAGAGATTAATCAGTAAATTGA
9565 TAATTA
65 TAATTA
* *
9571 AGAGCCAAGGCAATAGTAATCAGTAAATCACTAATTAAGTAAAAGAGATTAATCAGTAAATTGAT
1 AGAGTCAAGGTAATAGTAATCAGTAAATCACTAATTAAGTAAAAGAGATTAATCAGTAAATTGAT
9636 AATTA
66 AATTA
*
9641 AGAGTCAAGGTAATAGTGATCAGTA
1 AGAGTCAAGGTAATAGTAATCAGTA
9666 TAGTCAGTAA
Statistics
Matches: 274, Mismatches: 31, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
70 215 0.78
71 59 0.22
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (70 bp):
AGAGTCAAGGTAATAGTAATCAGTAAATCACTAATTAAGTAAAAGAGATTAATCAGTAAATTGAT
AATTA
Found at i:9530 original size:8 final size:8
Alignment explanation
Indices: 9517--9542 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
9507 AGGTAATAGT
9517 AATCAGTA
1 AATCAGTA
9525 AATCAGTA
1 AATCAGTA
9533 AATCAGTA
1 AATCAGTA
9541 AA
1 AA
9543 AAGAGATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.23
Consensus pattern (8 bp):
AATCAGTA
Found at i:9595 original size:141 final size:140
Alignment explanation
Indices: 9290--9675 Score: 547
Period size: 141 Copynumber: 2.7 Consensus size: 140
9280 TTCATACATT
* * *
9290 AGAGTCAAGGTAATAGTAATCAGTAAATCACTAATTGAGTAAAAGAAATTAATCAGCAAATTGAT
1 AGAGTCAAGGTAATAGTAATCAGTAAATCACTAATTAAGTAAAAGAGATTAATCAGTAAATTGAT
* * * *
9355 AATTAAGAGTCAAGGTAACAGTAATCAGTAAGTCAATAATTAAGTGAAAGAGATTAATCAGTAAA
66 AATTAAGAGTCAAGGTAATAGTAATCAGTAAGTCAGTAAATAAGTAAAAGAGATTAATCAGTAAA
9420 GTGATAATCA
131 GTGATAATCA
* * * * * **
9430 AGAATCAAGGTAATAGTAATCAGTAAGTCAGTAATTAAGTGAAAGAGACTAATCAGTAAAGCGAT
1 AGAGTCAAGGTAATAGTAATCAGTAAATCACTAATTAAGTAAAAGAGATTAATCAGTAAATTGAT
* * * *
9495 AATCAAGAATCAAGGTAATAGTAATCAGTAAATCAGTAAATCAGTAAAAAGAGATTAATCAGTAA
66 AATTAAGAGTCAAGGTAATAGTAATCAGTAAGTCAGTAAATAAGT-AAAAGAGATTAATCAGTAA
* *
9560 ATTGATAATTA
130 AGTGATAATCA
* *
9571 AGAGCCAAGGCAATAGTAATCAGTAAATCACTAATTAAGTAAAAGAGATTAATCAGTAAATTGAT
1 AGAGTCAAGGTAATAGTAATCAGTAAATCACTAATTAAGTAAAAGAGATTAATCAGTAAATTGAT
*
9636 AATTAAGAGTCAAGGTAATAGTGATCAGTATAGTCAGTAA
66 AATTAAGAGTCAAGGTAATAGTAATCAGTA-AGTCAGTAA
9676 TCAAGAGTCA
Statistics
Matches: 211, Mismatches: 33, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
140 93 0.44
141 110 0.52
142 8 0.04
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (140 bp):
AGAGTCAAGGTAATAGTAATCAGTAAATCACTAATTAAGTAAAAGAGATTAATCAGTAAATTGAT
AATTAAGAGTCAAGGTAATAGTAATCAGTAAGTCAGTAAATAAGTAAAAGAGATTAATCAGTAAA
GTGATAATCA
Found at i:9657 original size:211 final size:211
Alignment explanation
Indices: 9294--9676 Score: 615
Period size: 211 Copynumber: 1.8 Consensus size: 211
9284 TACATTAGAG
* *
9294 TCAAGGTAATAGTAATCAGTAAATCACTAATTGAGTAAAAGAAATTAATCAGCAAATTGATAATT
1 TCAAGGTAATAGTAATCAGTAAATCACTAAATCAGTAAAAGAAATTAATCAGCAAATTGATAATT
* * * *
9359 AAGAGTCAAGGTAACAGTAATCAGTAAGTCAATAATTAAGTGAAAGAGATTAATCAGTAAAGTGA
66 AAGAGCCAAGGCAACAGTAATCAGTAAATCAATAATTAAGTAAAAGAGATTAATCAGTAAAGTGA
9424 TAATCAAGAATCAAGGTAATAGTAATCAGTA-AGTCAGTAATTAAGTGAAAGAGACTAATCAGTA
131 TAATCAAGAATCAAGGTAATAGTAATCAGTATAGTCAGTAATTAAGTGAAAGAGACTAATCAGTA
9488 AAGCGATAATCAAGAA
196 AAGCGATAATCAAGAA
* * *
9504 TCAAGGTAATAGTAATCAGTAAATCAGTAAATCAGTAAAAAGAGATTAATCAGTAAATTGATAAT
1 TCAAGGTAATAGTAATCAGTAAATCACTAAATCAGT-AAAAGAAATTAATCAGCAAATTGATAAT
* * *
9569 TAAGAGCCAAGGCAATAGTAATCAGTAAATCACTAATTAAGTAAAAGAGATTAATCAGTAAATTG
65 TAAGAGCCAAGGCAACAGTAATCAGTAAATCAATAATTAAGTAAAAGAGATTAATCAGTAAAGTG
* * *
9634 ATAATTAAGAGTCAAGGTAATAGTGATCAGTATAGTCAGTAAT
130 ATAATCAAGAATCAAGGTAATAGTAATCAGTATAGTCAGTAAT
9677 CAAGAGTCAA
Statistics
Matches: 156, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
210 33 0.21
211 113 0.72
212 10 0.06
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.26
Consensus pattern (211 bp):
TCAAGGTAATAGTAATCAGTAAATCACTAAATCAGTAAAAGAAATTAATCAGCAAATTGATAATT
AAGAGCCAAGGCAACAGTAATCAGTAAATCAATAATTAAGTAAAAGAGATTAATCAGTAAAGTGA
TAATCAAGAATCAAGGTAATAGTAATCAGTATAGTCAGTAATTAAGTGAAAGAGACTAATCAGTA
AAGCGATAATCAAGAA
Found at i:10274 original size:16 final size:16
Alignment explanation
Indices: 10253--10444 Score: 106
Period size: 16 Copynumber: 12.4 Consensus size: 16
10243 TAAACAAAAG
*
10253 AGTAAAAATGATATTA
1 AGTAAAAATGGTATTA
*
10269 AGTAAAAATGGTATTG
1 AGTAAAAATGGTATTA
* *
10285 AGTAAAAAAGGCATTA
1 AGTAAAAATGGTATTA
*
10301 AGTAAAAATGGTATTG
1 AGTAAAAATGGTATTA
10317 AGTAAAAA-GG---T-
1 AGTAAAAATGGTATTA
* * *
10328 --CAACAATGGTATCA
1 AGTAAAAATGGTATTA
10342 AGTAAAATATGGTATTA
1 AGTAAAA-ATGGTATTA
* *
10359 AGTAAGAA-GG--TCA
1 AGTAAAAATGGTATTA
*
10372 AG----AATGGTATCA
1 AGTAAAAATGGTATTA
*
10384 AGTGAAATATGGTATTAA
1 AGT-AAAAATGGTATT-A
10402 GAGTAAAGAATGGTATTA
1 -AGTAAA-AATGGTATTA
*
10420 AGTAAAAAAATGGAATTA
1 AGT--AAAAATGGTATTA
10438 AGTAAAA
1 AGTAAAA
10445 GAGTAAGAAA
Statistics
Matches: 135, Mismatches: 20, Indels: 42
0.69 0.10 0.21
Matches are distributed among these distances:
9 6 0.04
10 4 0.03
12 6 0.04
13 4 0.03
15 4 0.03
16 56 0.41
17 24 0.18
18 17 0.13
19 14 0.10
ACGTcount: A:0.49, C:0.03, G:0.21, T:0.26
Consensus pattern (16 bp):
AGTAAAAATGGTATTA
Found at i:10288 original size:32 final size:32
Alignment explanation
Indices: 10252--10324 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
10242 TTAAACAAAA
* *
10252 GAGTAAAAATGATATTAAGTAAAAATGGTATT
1 GAGTAAAAAAGACATTAAGTAAAAATGGTATT
*
10284 GAGTAAAAAAGGCATTAAGTAAAAATGGTATT
1 GAGTAAAAAAGACATTAAGTAAAAATGGTATT
10316 GAGTAAAAA
1 GAGTAAAAA
10325 GGTCAACAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.52, C:0.01, G:0.21, T:0.26
Consensus pattern (32 bp):
GAGTAAAAAAGACATTAAGTAAAAATGGTATT
Found at i:10363 original size:42 final size:42
Alignment explanation
Indices: 10300--10402 Score: 163
Period size: 42 Copynumber: 2.5 Consensus size: 42
10290 AAAAGGCATT
*
10300 AAGTAAAA-ATGGTATTGAGTAAAAAGGTCAACAATGGTATC
1 AAGTAAAATATGGTATTAAGTAAAAAGGTCAACAATGGTATC
* *
10341 AAGTAAAATATGGTATTAAGTAAGAAGGTCAAGAATGGTATC
1 AAGTAAAATATGGTATTAAGTAAAAAGGTCAACAATGGTATC
*
10383 AAGTGAAATATGGTATTAAG
1 AAGTAAAATATGGTATTAAG
10403 AGTAAAGAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 8 0.14
42 49 0.86
ACGTcount: A:0.46, C:0.05, G:0.23, T:0.26
Consensus pattern (42 bp):
AAGTAAAATATGGTATTAAGTAAAAAGGTCAACAATGGTATC
Found at i:10425 original size:17 final size:18
Alignment explanation
Indices: 10371--10446 Score: 75
Period size: 18 Copynumber: 4.2 Consensus size: 18
10361 TAAGAAGGTC
* *
10371 AAGAATGGTATCAAGTGA
1 AAGAATGGTATTAAGTAA
*
10389 AA-TATGGTATTAAG-AGTA
1 AAGAATGGTATTAAGTA--A
10407 AAGAATGGTATTAAGTAA
1 AAGAATGGTATTAAGTAA
* *
10425 AAAAATGGAATTAAGTAA
1 AAGAATGGTATTAAGTAA
10443 AAGA
1 AAGA
10447 GTAAGAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
17 10 0.21
18 25 0.53
19 11 0.23
20 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.22, T:0.25
Consensus pattern (18 bp):
AAGAATGGTATTAAGTAA
Found at i:10446 original size:36 final size:35
Alignment explanation
Indices: 10371--10439 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
10361 TAAGAAGGTC
* * *
10371 AAGAATGGTATCAAGTGAAATATGGTATTAAGAGTA
1 AAGAATGGTATCAAGTAAAAAATGGAATTAAGAG-A
*
10407 AAGAATGGTATTAAGTAAAAAAATGGAATTAAG
1 AAGAATGGTATCAAGT-AAAAAATGGAATTAAG
10440 TAAAAGAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 15 0.54
37 13 0.46
ACGTcount: A:0.49, C:0.01, G:0.23, T:0.26
Consensus pattern (35 bp):
AAGAATGGTATCAAGTAAAAAATGGAATTAAGAGA
Found at i:10466 original size:26 final size:25
Alignment explanation
Indices: 10420--10470 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
10410 AATGGTATTA
10420 AGTAAAAAAATGGAATTAAGTAAAAG
1 AGTAAAAAAATGGAA-TAAGTAAAAG
10446 AGTAAGAAAAATGGTAA-AAGTAAAA
1 AGTAA-AAAAATGG-AATAAGTAAAA
10471 ATGATAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 13 0.57
27 8 0.35
28 2 0.09
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.18
Consensus pattern (25 bp):
AGTAAAAAAATGGAATAAGTAAAAG
Found at i:10472 original size:15 final size:15
Alignment explanation
Indices: 10452--10482 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10442 AAAGAGTAAG
*
10452 AAAAATGGTAAAAGT
1 AAAAATGATAAAAGT
10467 AAAAATGATAAAAGT
1 AAAAATGATAAAAGT
10482 A
1 A
10483 GCAAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (15 bp):
AAAAATGATAAAAGT
Found at i:10488 original size:24 final size:25
Alignment explanation
Indices: 10461--10507 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
10451 GAAAAATGGT
10461 AAAAGTAAAAATGATAA-AAGTAGC
1 AAAAGTAAAAATGATAATAAGTAGC
*
10485 AAAAGTAAAAATGGTAATAAGTA
1 AAAAGTAAAAATGATAATAAGTA
10508 AGGAGAGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.62, C:0.02, G:0.17, T:0.19
Consensus pattern (25 bp):
AAAAGTAAAAATGATAATAAGTAGC
Found at i:11698 original size:12 final size:12
Alignment explanation
Indices: 11678--11707 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
11668 GTCTTTCATC
*
11678 TTCAAGTTTTTG
1 TTCATGTTTTTG
11690 TTCATGTTTTTG
1 TTCATGTTTTTG
11702 TTCATG
1 TTCATG
11708 ATCCTAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.10, G:0.17, T:0.60
Consensus pattern (12 bp):
TTCATGTTTTTG
Found at i:12070 original size:42 final size:38
Alignment explanation
Indices: 11952--12091 Score: 106
Period size: 42 Copynumber: 3.4 Consensus size: 38
11942 CATTTGTACA
* *
11952 TATGC-TCATACATGCATTAGTCAATCACTTGTATATATG
1 TATGCATCAT-CATGCATTAGCCATTCA-TTGTATATATG
* *
11991 -ATGCATTCATCATGCATT-GTCCATTTCTTTGTGTATATG
1 TATGCA-TCATCATGCATTAG-CCA-TTCATTGTATATATG
12030 TTTATGCATCAATCATGCATTAGCCATTCATTAGTATATATG
1 --TATGCATC-ATCATGCATTAGCCATTCATT-GTATATATG
*
12072 CTCATGCATCCATCAGGCAT
1 -T-ATGCAT-CATCATGCAT
12092 CACTTGTATA
Statistics
Matches: 81, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
38 5 0.06
39 20 0.25
40 6 0.07
41 8 0.10
42 40 0.49
43 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (38 bp):
TATGCATCATCATGCATTAGCCATTCATTGTATATATG
Found at i:13752 original size:19 final size:18
Alignment explanation
Indices: 13728--13763 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
13718 TGAAGATTTC
13728 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
13747 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
13764 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:15654 original size:17 final size:17
Alignment explanation
Indices: 15624--15664 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
15614 ACTCAAAGAA
15624 AAGAAAAAGAAAAAAAG
1 AAGAAAAAGAAAAAAAG
15641 AAGAAGAAAG-AAAAAAG
1 AAGAA-AAAGAAAAAAAG
15658 AA-AAAAA
1 AAGAAAAA
15665 CTCAGCCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.13
16 2 0.09
17 14 0.61
18 4 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAAAAAAG
Found at i:15658 original size:14 final size:15
Alignment explanation
Indices: 15618--15659 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
15608 CATTCAACTC
*
15618 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAGAAG
15633 AAA-AAAAGAAGAAG
1 AAAGAAAAGAAGAAG
15647 AAAGAAAA-AAGAA
1 AAAGAAAAGAAGAA
15660 AAAAACTCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAGAAG
Found at i:25888 original size:9 final size:8
Alignment explanation
Indices: 25853--25955 Score: 65
Period size: 9 Copynumber: 12.8 Consensus size: 8
25843 GAACCGAACA
25853 ACCCG-TG
1 ACCCGATG
25860 ACCCGAATG
1 ACCCG-ATG
**
25869 ACCC-ACA
1 ACCCGATG
25876 ACCCAGATG
1 ACCC-GATG
25885 ACCCCGA-G
1 A-CCCGATG
25893 ACCCGAATG
1 ACCCG-ATG
*
25902 ACCCG-TA
1 ACCCGATG
25909 ACCCAGATG
1 ACCC-GATG
*
25918 ACCCGA-A
1 ACCCGATG
25925 ACCCGAATG
1 ACCCG-ATG
25934 ACCCGA-G
1 ACCCGATG
25941 ACCCGTATG
1 ACCCG-ATG
25950 ACCCGA
1 ACCCGA
25956 AACCCGTATA
Statistics
Matches: 75, Mismatches: 8, Indels: 25
0.69 0.07 0.23
Matches are distributed among these distances:
7 30 0.40
8 10 0.13
9 32 0.43
10 3 0.04
ACGTcount: A:0.31, C:0.40, G:0.20, T:0.09
Consensus pattern (8 bp):
ACCCGATG
Found at i:25896 original size:33 final size:32
Alignment explanation
Indices: 25853--25937 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 32
25843 GAACCGAACA
*
25853 ACCCGTGACCCGAATGACCCACAACCCAGATG
1 ACCCGAGACCCGAATGACCCACAACCCAGATG
**
25885 ACCCCGAGACCCGAATGACCCGTAACCCAGATG
1 A-CCCGAGACCCGAATGACCCACAACCCAGATG
*
25918 ACCCGAAACCCGAATGACCC
1 ACCCGAGACCCGAATGACCC
25938 GAGACCCGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 19 0.40
33 29 0.60
ACGTcount: A:0.32, C:0.41, G:0.19, T:0.08
Consensus pattern (32 bp):
ACCCGAGACCCGAATGACCCACAACCCAGATG
Found at i:25899 original size:49 final size:48
Alignment explanation
Indices: 25836--25945 Score: 127
Period size: 49 Copynumber: 2.3 Consensus size: 48
25826 GAACCCACCC
* *
25836 GACCCGAGAACCGAACAACCCGTGACCC-GAATGACCC-ACAACCC-AGAT
1 GACCCGAGACCCGAACAACCCGTAACCCAG-ATGACCCGA-AACCCGA-AT
**
25884 GACCCCGAGACCCGAATGACCCGTAACCCAGATGACCCGAAACCCGAAT
1 GA-CCCGAGACCCGAACAACCCGTAACCCAGATGACCCGAAACCCGAAT
25933 GACCCGAGACCCG
1 GACCCGAGACCCG
25946 TATGACCCGA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
48 13 0.24
49 38 0.70
50 3 0.06
ACGTcount: A:0.33, C:0.40, G:0.21, T:0.06
Consensus pattern (48 bp):
GACCCGAGACCCGAACAACCCGTAACCCAGATGACCCGAAACCCGAAT
Found at i:25929 original size:32 final size:31
Alignment explanation
Indices: 25860--25961 Score: 134
Period size: 32 Copynumber: 3.2 Consensus size: 31
25850 ACAACCCGTG
* *
25860 ACCCGAATGACCCACAACCCAGATGACCCCGAG
1 ACCCGAATGACCC-GAACCCAGATGA-CCCGAA
25893 ACCCGAATGACCCGTAACCCAGATGACCCGAA
1 ACCCGAATGACCCG-AACCCAGATGACCCGAA
25925 ACCCGAATGACCCGAGACCC-GTATGACCCGAA
1 ACCCGAATGACCCGA-ACCCAG-ATGACCCGAA
25957 ACCCG
1 ACCCG
25962 TATACCCCGA
Statistics
Matches: 64, Mismatches: 2, Indels: 7
0.88 0.03 0.10
Matches are distributed among these distances:
31 2 0.03
32 38 0.59
33 24 0.38
ACGTcount: A:0.32, C:0.40, G:0.20, T:0.08
Consensus pattern (31 bp):
ACCCGAATGACCCGAACCCAGATGACCCGAA
Found at i:25960 original size:48 final size:49
Alignment explanation
Indices: 25866--25960 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 49
25856 CGTGACCCGA
*
25866 ATGACCCACAACCCAGATGACCCCGAGACCCGAATGACCCGTAACCCAG
1 ATGACCCACAACCCAGATGACCCCGAGACCCGAATGACCCGAAACCCAG
*
25915 ATGACCCGA-AACCC-GAATGA-CCCGAGACCCGTATGACCCGAAACCC
1 ATGACCC-ACAACCCAG-ATGACCCCGAGACCCGAATGACCCGAAACCC
25961 GTATACCCCG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
48 25 0.60
49 16 0.38
50 1 0.02
ACGTcount: A:0.33, C:0.40, G:0.19, T:0.08
Consensus pattern (49 bp):
ATGACCCACAACCCAGATGACCCCGAGACCCGAATGACCCGAAACCCAG
Found at i:25964 original size:16 final size:16
Alignment explanation
Indices: 25860--25961 Score: 111
Period size: 16 Copynumber: 6.3 Consensus size: 16
25850 ACAACCCGTG
25860 ACCCGAATGACCC-ACA
1 ACCCGAATGACCCGA-A
*
25876 ACCC-AGATGACCCCGAG
1 ACCCGA-ATGA-CCCGAA
*
25893 ACCCGAATGACCCGTA
1 ACCCGAATGACCCGAA
25909 ACCC-AGATGACCCGAA
1 ACCCGA-ATGACCCGAA
*
25925 ACCCGAATGACCCGAG
1 ACCCGAATGACCCGAA
*
25941 ACCCGTATGACCCGAA
1 ACCCGAATGACCCGAA
25957 ACCCG
1 ACCCG
25962 TATACCCCGA
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
15 2 0.03
16 57 0.78
17 12 0.16
18 2 0.03
ACGTcount: A:0.32, C:0.40, G:0.20, T:0.08
Consensus pattern (16 bp):
ACCCGAATGACCCGAA
Found at i:26105 original size:21 final size:21
Alignment explanation
Indices: 26080--26126 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
26070 TACAATTTAT
26080 ATTATTGTTATAATTTTACCA
1 ATTATTGTTATAATTTTACCA
* *
26101 ATTATTGTTATGATTTTACCT
1 ATTATTGTTATAATTTTACCA
26122 ATTAT
1 ATTAT
26127 AAATCGACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (21 bp):
ATTATTGTTATAATTTTACCA
Found at i:32158 original size:16 final size:16
Alignment explanation
Indices: 32139--32241 Score: 102
Period size: 16 Copynumber: 6.5 Consensus size: 16
32129 AACCCGCCCA
*
32139 ACCCGAGACCCAAATG
1 ACCCGAGACCCGAATG
*
32155 ACCCGAGACCTGAATG
1 ACCCGAGACCCGAATG
* *
32171 ACCCGAAACCCGTATG
1 ACCCGAGACCCGAATG
** *
32187 ACCTAAGACCCGAACG
1 ACCCGAGACCCGAATG
*
32203 ACCCGAGACCCGAATA
1 ACCCGAGACCCGAATG
*
32219 ACCCGA-A-CCTAGATG
1 ACCCGAGACCCGA-ATG
32234 ACCCGAGA
1 ACCCGAGA
32242 AAACTGCATA
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
14 3 0.04
15 9 0.13
16 57 0.83
ACGTcount: A:0.35, C:0.36, G:0.20, T:0.09
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:39926 original size:21 final size:21
Alignment explanation
Indices: 39900--39948 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
39890 GCACTGGAGT
* * *
39900 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
*
39921 ACATGGGGCGCCAAGCATACC
1 ACATGGGGCGCCAAGCAAACC
39942 ACATGGG
1 ACATGGG
39949 CTCCCAGCGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.33, T:0.10
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:42184 original size:30 final size:30
Alignment explanation
Indices: 42140--42196 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
42130 CAAGTCTATA
42140 ATAAGTCCTTGGCGCATCATTCCCTCCATG
1 ATAAGTCCTTGGCGCATCATTCCCTCCATG
42170 ATAAG-CCTTGGGCGCATCATTCCCTCC
1 ATAAGTCCTT-GGCGCATCATTCCCTCC
42197 CCCTTGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.19, C:0.35, G:0.18, T:0.28
Consensus pattern (30 bp):
ATAAGTCCTTGGCGCATCATTCCCTCCATG
Found at i:42577 original size:33 final size:33
Alignment explanation
Indices: 42535--42653 Score: 157
Period size: 33 Copynumber: 3.6 Consensus size: 33
42525 TTCTTTTCAC
* * * *
42535 CCAAAACAGAATTTTTTTTAATGTTATAATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
*
42568 CCAAAACAGAATTATTTTCAATGCTATGGTCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
* *
42601 CCAAAATAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
* *
42634 CCAAAACAGATTTGTTTTCA
1 CCAAAACAGAATTATTTTCA
42654 TCACAAACAA
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (33 bp):
CCAAAACAGAATTATTTTCAATGCTATGATCAA
Found at i:46865 original size:17 final size:17
Alignment explanation
Indices: 46833--46865 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
46823 CCCAGTCAAT
*
46833 TTTTGTATAATAAAAAC
1 TTTTGTATAAAAAAAAC
46850 TTTTGTATAAAAAAAA
1 TTTTGTATAAAAAAAA
46866 TGTTACGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (17 bp):
TTTTGTATAAAAAAAAC
Done.