Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022038.1 Corchorus olitorius cultivar O-4 contig22071, 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: 143708
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:3971 original size:18 final size:18
Alignment explanation
Indices: 3948--3987 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3938 TGCAATTGCT
*
3948 CCTACCATCATTAGCTCC
1 CCTACCATAATTAGCTCC
3966 CCTACCATAATTAGCTCC
1 CCTACCATAATTAGCTCC
3984 CCTA
1 CCTA
3988 ATTATGGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.25, C:0.42, G:0.05, T:0.28
Consensus pattern (18 bp):
CCTACCATAATTAGCTCC
Found at i:8407 original size:2 final size:2
Alignment explanation
Indices: 8400--8471 Score: 50
Period size: 2 Copynumber: 37.0 Consensus size: 2
8390 AACATGCATG
8400 AT AT AT AT A- AT AT AT AT -T AT AT AT AT CAT -T AT CAT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT AT AT
8440 AT AT -T CAT -T AT AT AT AT -T CAT GAT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT -AT -AT AT AT AT AT
8472 TCATTATAAG
Statistics
Matches: 58, Mismatches: 1, Indels: 22
0.72 0.01 0.27
Matches are distributed among these distances:
1 7 0.12
2 43 0.74
3 8 0.14
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8414 original size:9 final size:9
Alignment explanation
Indices: 8400--8454 Score: 58
Period size: 9 Copynumber: 5.9 Consensus size: 9
8390 AACATGCATG
*
8400 ATATATATA
1 ATATATATT
8409 ATATATATT
1 ATATATATT
*
8418 ATATATATC
1 ATATATATT
8427 AT-TATCATT
1 ATATAT-ATT
8436 ATATATATT
1 ATATATATT
8445 CATTATATAT
1 -A-TATATAT
8455 ATTCATGATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
8 3 0.08
9 25 0.64
10 4 0.10
11 7 0.18
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (9 bp):
ATATATATT
Found at i:8425 original size:13 final size:13
Alignment explanation
Indices: 8400--8472 Score: 64
Period size: 13 Copynumber: 5.5 Consensus size: 13
8390 AACATGCATG
8400 ATATA-TATA-AT
1 ATATATTATATAT
8411 ATATATTATATAT
1 ATATATTATATAT
*
8424 AT-CATTATCATTAT
1 ATATATTAT-A-TAT
8438 ATATATTCAT-TAT
1 ATATATT-ATATAT
8451 ATATATTCATGATAT
1 ATATATT-AT-ATAT
8466 ATATATT
1 ATATATT
8473 CATTATAAGT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
11 5 0.10
12 9 0.17
13 18 0.35
14 5 0.10
15 13 0.25
16 2 0.04
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.51
Consensus pattern (13 bp):
ATATATTATATAT
Found at i:8479 original size:13 final size:13
Alignment explanation
Indices: 8409--8479 Score: 83
Period size: 13 Copynumber: 5.2 Consensus size: 13
8399 GATATATATA
8409 ATATATATT-A-T
1 ATATATATTCATT
8420 ATATATCATTATCATT
1 ATATAT-A-T-TCATT
8436 ATATATATTCATT
1 ATATATATTCATT
8449 ATATATATTCATGAT
1 ATATATATTCAT--T
8464 ATATATATTCATT
1 ATATATATTCATT
8477 ATA
1 ATA
8480 AGTCTAAATT
Statistics
Matches: 53, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.11
12 1 0.02
13 22 0.42
14 2 0.04
15 15 0.28
16 7 0.13
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (13 bp):
ATATATATTCATT
Found at i:9316 original size:24 final size:24
Alignment explanation
Indices: 9275--9322 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
9265 TTGTCTTTCT
*
9275 ACTTTTTTATTTCAATTTACTCAA
1 ACTTTTTTACTTCAATTTACTCAA
* * *
9299 ACTTTTTTGCTTCTATTTAGTCAA
1 ACTTTTTTACTTCAATTTACTCAA
9323 TTAAGAGAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.04, T:0.54
Consensus pattern (24 bp):
ACTTTTTTACTTCAATTTACTCAA
Found at i:12411 original size:17 final size:19
Alignment explanation
Indices: 12391--12425 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
12381 TTTGAAGAAG
12391 AAGAAAA-AAA-AAGGAAA
1 AAGAAAAGAAATAAGGAAA
12408 AAGAAAAGAAATAAGGAA
1 AAGAAAAGAAATAAGGAA
12426 TTGAGAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (19 bp):
AAGAAAAGAAATAAGGAAA
Found at i:13234 original size:27 final size:27
Alignment explanation
Indices: 13203--13273 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
13193 TAGTATGCAA
* *
13203 AAATTACCGTTTTGCCCCTGGTCGGCT
1 AAATTACAGTTTTGCCCCTGGCCGGCT
*
13230 TAATTACAGTTTTGCCCCTGGCCGGCT
1 AAATTACAGTTTTGCCCCTGGCCGGCT
13257 AAATTACAGTTTTGCCC
1 AAATTACAGTTTTGCCC
13274 TTAAAGGCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (27 bp):
AAATTACAGTTTTGCCCCTGGCCGGCT
Found at i:22302 original size:32 final size:32
Alignment explanation
Indices: 22261--22323 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
22251 ATTAATGCCC
* *
22261 TCTTCTTTTTATTCTTTCTTTCTTCTTCTCCA
1 TCTTCTTTTTATTCTTTCCTTCTTCTACTCCA
22293 TCTTCTTTTTATTCTTTCCTTCTTCTACTCC
1 TCTTCTTTTTATTCTTTCCTTCTTCTACTCC
22324 TTTGTGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.06, C:0.30, G:0.00, T:0.63
Consensus pattern (32 bp):
TCTTCTTTTTATTCTTTCCTTCTTCTACTCCA
Found at i:22444 original size:24 final size:23
Alignment explanation
Indices: 22417--22471 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 23
22407 GGTAGAAGGT
22417 GGAGATGAAATCAGATCTGGAGGG
1 GGAGATGAAATCAGATCTGGA-GG
*
22441 GGAGATGAGATCAGATCTGGAGG
1 GGAGATGAAATCAGATCTGGAGG
*
22464 AGAGATGA
1 GGAGATGA
22472 GCCGAGGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 9 0.31
24 20 0.69
ACGTcount: A:0.35, C:0.07, G:0.42, T:0.16
Consensus pattern (23 bp):
GGAGATGAAATCAGATCTGGAGG
Found at i:26509 original size:400 final size:400
Alignment explanation
Indices: 25762--26566 Score: 1432
Period size: 400 Copynumber: 2.0 Consensus size: 400
25752 CGTTTGGGTT
* *
25762 ATCCAACGCACCTAGCACTTTCATGAGGCTGATGAATCATGTATTGAAAACTTTTCTTGGCCAGT
1 ATCCAACGCACCTAGCACTTTAATGAGGCTGATGAATCAGGTATTGAAAACTTTTCTTGGCCAGT
*
25827 TTGTTATGGTGTATTTTGATGACATCTTGATTTATAATAATTCTAAAGAAGAACATTTGTCGCAC
66 TTGTTATGGTGTATTTCGATGACATCTTGATTTATAATAATTCTAAAGAAGAACATTTGTCGCAC
* * *
25892 TTAAGGCAAGTGTTAGAGGTTTTGCATCAGAATAAATTGTATGTGAACATGAAGAAGTGTATCTT
131 TTAAGGCAAGTGTTAGAGGTTTTGCATCAAAATAAATTGTATGTCAACATGAAGAAGTGTAACTT
* * *
25957 CTTAACACGTCAGCTATTATTTTTGGGATTTGTGGTTTCTGTGGTTGATGTGTAGGTTGATGAAA
196 CTTAACACGTCAGCTATTATTTTTGGGATTTGTGGTTTCCGTGATTGATGTGCAGGTTGATGAAA
* *
26022 CTAAGATTAAGGCAATTAGGGACTGGCCTGAACTGAAAAAGGTGGCAGAATTGCATAGTTTCCAT
261 CTAAGATTAAGGCAATGAGGGACTGGCCTGAACCGAAAAAGGTGGCAGAATTGCATAGTTTCCAT
*
26087 GGTTTAGTGATGAACTAATTCTGCAAGTGCACAGAGTCAGTTGAAGTAATAATCCTAGAATAAAC
326 GGTTTAGTGATGAACTAATTCTGCAAGTGCACAGAGTCAATTGAAGTAATAATCCTAGAATAAAC
*
26152 CTGGTGTCGA
391 CAGGTGTCGA
* *
26162 ATCCAATGCACCTAGCACTTTAATGATGCTGATGAATCAGGTATTGAAAACTTTTCTTGGCCAGT
1 ATCCAACGCACCTAGCACTTTAATGAGGCTGATGAATCAGGTATTGAAAACTTTTCTTGGCCAGT
26227 TTGTTATGGTGTATTTCGATGACATCTTGATTTATAATAATTCTAAAGAAGAACATTTGTCGCAC
66 TTGTTATGGTGTATTTCGATGACATCTTGATTTATAATAATTCTAAAGAAGAACATTTGTCGCAC
*
26292 TTAAGGCAAGTGTTAGAGGTTTTGCATCAAAATGAATTGTATGTCAACATGAAGAAGTGTAACTT
131 TTAAGGCAAGTGTTAGAGGTTTTGCATCAAAATAAATTGTATGTCAACATGAAGAAGTGTAACTT
26357 CTTAACACGTCAGCTATTATTTTTGGGATTTGTGGTTTCCGCT-ATTGATGTGCAGGTTGATGAA
196 CTTAACACGTCAGCTATTATTTTTGGGATTTGTGGTTTCCG-TGATTGATGTGCAGGTTGATGAA
* *
26421 ACTAAGATTAAGGCAATGAGGGACTGGCCTGAACCGAGAAAGGTGGCAGAATTGCATTGTTTCCA
260 ACTAAGATTAAGGCAATGAGGGACTGGCCTGAACCGAAAAAGGTGGCAGAATTGCATAGTTTCCA
26486 TGGTTTAGTGATGAACTAATTCTGCAAGTGCACAGAGTCAATTGAAGTAATAATCCTAGAATAAA
325 TGGTTTAGTGATGAACTAATTCTGCAAGTGCACAGAGTCAATTGAAGTAATAATCCTAGAATAAA
26551 CCAGGTGTCGA
390 CCAGGTGTCGA
26562 ATCCA
1 ATCCA
26567 CAAAGAACAA
Statistics
Matches: 386, Mismatches: 18, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
400 385 1.00
401 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (400 bp):
ATCCAACGCACCTAGCACTTTAATGAGGCTGATGAATCAGGTATTGAAAACTTTTCTTGGCCAGT
TTGTTATGGTGTATTTCGATGACATCTTGATTTATAATAATTCTAAAGAAGAACATTTGTCGCAC
TTAAGGCAAGTGTTAGAGGTTTTGCATCAAAATAAATTGTATGTCAACATGAAGAAGTGTAACTT
CTTAACACGTCAGCTATTATTTTTGGGATTTGTGGTTTCCGTGATTGATGTGCAGGTTGATGAAA
CTAAGATTAAGGCAATGAGGGACTGGCCTGAACCGAAAAAGGTGGCAGAATTGCATAGTTTCCAT
GGTTTAGTGATGAACTAATTCTGCAAGTGCACAGAGTCAATTGAAGTAATAATCCTAGAATAAAC
CAGGTGTCGA
Found at i:42455 original size:22 final size:22
Alignment explanation
Indices: 42422--42472 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
42412 AGAAAAGTAC
42422 AATGAAAAATAACTTCAAATATA
1 AATG-AAAATAACTTCAAATATA
42445 AATGAAAATAACTTCAAATATA
1 AATGAAAATAACTTCAAATATA
42467 AA-GAAA
1 AATGAAA
42473 GAAACAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 4 0.14
22 20 0.71
23 4 0.14
ACGTcount: A:0.63, C:0.08, G:0.06, T:0.24
Consensus pattern (22 bp):
AATGAAAATAACTTCAAATATA
Found at i:42516 original size:2 final size:2
Alignment explanation
Indices: 42511--42541 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42501 CACCACACAA
42511 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42542 AAATCAAAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46409 original size:76 final size:76
Alignment explanation
Indices: 46283--46434 Score: 200
Period size: 76 Copynumber: 2.0 Consensus size: 76
46273 ACAAGGAACC
* *
46283 CGACTCCACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
46348 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * **
46359 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGTGTTTTGCCTGATCACCCAG
1 CGACTCCACCTGGGTGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTTGCCTGAGAACCCAG
*
46422 ATGGGCTGTGTCA
64 ATGGGCAGTGTCA
46435 TAGCTCATCA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
76 60 0.91
77 6 0.09
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (76 bp):
CGACTCCACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:53543 original size:58 final size:58
Alignment explanation
Indices: 53476--53677 Score: 350
Period size: 58 Copynumber: 3.5 Consensus size: 58
53466 TTGCTCATTA
*
53476 TTCATGTCCAGGGGCATTTTGGTCATTTTGCATGTCCAGGGGATATTTTAGTCACTTT
1 TTCATGTCCAGGGGCATTTTGGTCATTTTGCATGTCCAGGGGACATTTTAGTCACTTT
53534 TTCATGTCCAGGGGCATTTTGGTCATTTTGCATGTCCAGGGGACATTTTAGTCACTTT
1 TTCATGTCCAGGGGCATTTTGGTCATTTTGCATGTCCAGGGGACATTTTAGTCACTTT
* *
53592 TTCATGTCCAGGGGTATTTTGGTCATTTTGCATGTCCAAGGGACATTTTAGTCACTTT
1 TTCATGTCCAGGGGCATTTTGGTCATTTTGCATGTCCAGGGGACATTTTAGTCACTTT
* * *
53650 TGCATATCCAGGGGTATTTTGGTCATTT
1 TTCATGTCCAGGGGCATTTTGGTCATTT
53678 CTAGTGCACT
Statistics
Matches: 139, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 139 1.00
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.41
Consensus pattern (58 bp):
TTCATGTCCAGGGGCATTTTGGTCATTTTGCATGTCCAGGGGACATTTTAGTCACTTT
Found at i:53552 original size:29 final size:28
Alignment explanation
Indices: 53465--53677 Score: 257
Period size: 29 Copynumber: 7.4 Consensus size: 28
53455 ATCAAATCGC
*
53465 TTTGCTCATTATT-CATGTCCAGGGGCAT
1 TTTGGTCATT-TTGCATGTCCAGGGGCAT
*
53493 TTTGGTCATTTTGCATGTCCAGGGGATAT
1 TTTGGTCATTTTGCATGTCCAGGGG-CAT
* *
53522 TTTAGTCACTTTTTCATGTCCAGGGGCAT
1 TTTGGTCA-TTTTGCATGTCCAGGGGCAT
53551 TTTGGTCATTTTGCATGTCCAGGGGACAT
1 TTTGGTCATTTTGCATGTCCAGGGG-CAT
* * *
53580 TTTAGTCACTTTTTCATGTCCAGGGGTAT
1 TTTGGTCA-TTTTGCATGTCCAGGGGCAT
*
53609 TTTGGTCATTTTGCATGTCCAAGGGACAT
1 TTTGGTCATTTTGCATGTCC-AGGGGCAT
* * *
53638 TTTAGTCACTTTTGCATATCCAGGGGTAT
1 TTTGGTCA-TTTTGCATGTCCAGGGGCAT
53667 TTTGGTCATTT
1 TTTGGTCATTT
53678 CTAGTGCACT
Statistics
Matches: 159, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.01
28 51 0.32
29 63 0.40
30 43 0.27
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.42
Consensus pattern (28 bp):
TTTGGTCATTTTGCATGTCCAGGGGCAT
Found at i:58251 original size:10 final size:9
Alignment explanation
Indices: 58234--58284 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 9
58224 TAAAAGTAAC
58234 TAAAAAAAA
1 TAAAAAAAA
58243 TAAACAAAAA
1 TAAA-AAAAA
*
58253 TAAAAGAAA
1 TAAAAAAAA
*
58262 -AAGAAAAA
1 TAAAAAAAA
*
58270 TAACGAAAAA
1 TAA-AAAAAA
58280 TAAAA
1 TAAAA
58285 GGATAAGGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 6 0.17
9 11 0.31
10 18 0.51
ACGTcount: A:0.80, C:0.04, G:0.06, T:0.10
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:64322 original size:17 final size:17
Alignment explanation
Indices: 64300--64342 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
64290 AACCCAAAAG
*
64300 AAACATGATTACTAATT
1 AAACATGATAACTAATT
*
64317 AAACATGGCTAACTAATT
1 AAACAT-GATAACTAATT
64335 AAACATGA
1 AAACATGA
64343 CTATTAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (17 bp):
AAACATGATAACTAATT
Found at i:65150 original size:35 final size:35
Alignment explanation
Indices: 65087--65154 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
65077 CTCAATTAAA
* *
65087 ATCGAGACAATTTATCCCCTAAATTTCCCAAATTC
1 ATCGAGACAATTTATCCCATAAACTTCCCAAATTC
*
65122 ATCGAGACAATTTAAT-CTATAAACTTCCCAAAT
1 ATCGAGACAATTT-ATCCCATAAACTTCCCAAAT
65155 GGATGCTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 27 0.93
36 2 0.07
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (35 bp):
ATCGAGACAATTTATCCCATAAACTTCCCAAATTC
Found at i:90437 original size:27 final size:27
Alignment explanation
Indices: 90407--90473 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
90397 GCACCAGGGC
90407 CAGCCTC-CCTCTCCCTATACATCCGAG
1 CAGCCTCACC-CTCCCTATACATCCGAG
*
90434 CAGCCTCAGCCTCCCTATACATCCGAG
1 CAGCCTCACCCTCCCTATACATCCGAG
*
90461 CAGCCTCAACCTC
1 CAGCCTCACCCTC
90474 TTTATCCCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 36 0.97
28 1 0.03
ACGTcount: A:0.21, C:0.48, G:0.12, T:0.19
Consensus pattern (27 bp):
CAGCCTCACCCTCCCTATACATCCGAG
Found at i:90618 original size:26 final size:26
Alignment explanation
Indices: 90576--90643 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
90566 TCTTCCAGCC
* * **
90576 TAAATAAAAAATAATAATTAATTTTAG
1 TAAAT-AAAAATTATAAGTAATTACAG
90603 TAAATAAAAATTATAAGTAATTACAG
1 TAAATAAAAATTATAAGTAATTACAG
90629 T-AATAAATAATTATA
1 TAAATAAA-AATTATA
90644 GTCAAAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 6 0.17
26 25 0.69
27 5 0.14
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.35
Consensus pattern (26 bp):
TAAATAAAAATTATAAGTAATTACAG
Found at i:90652 original size:16 final size:16
Alignment explanation
Indices: 90620--90673 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
90610 AAATTATAAG
*
90620 TAATTACAGT-AATAAA
1 TAATTATAGTCAA-AAA
90636 TAATTATAGTCAAAAA
1 TAATTATAGTCAAAAA
*
90652 TTAAGTATAGTCAAATAA
1 -TAATTATAGTCAAA-AA
90670 TAAT
1 TAAT
90674 AAAATAACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 12 0.38
17 18 0.56
18 2 0.06
ACGTcount: A:0.54, C:0.06, G:0.07, T:0.33
Consensus pattern (16 bp):
TAATTATAGTCAAAAA
Found at i:91830 original size:2 final size:2
Alignment explanation
Indices: 91823--91851 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
91813 TTTTAGTATC
91823 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 T
91852 TCTTGGCTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:92003 original size:24 final size:23
Alignment explanation
Indices: 91976--92039 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
91966 ATATGATGAC
* * *
91976 ATATTTAATTTTTAATGTTATATT
1 ATATTTAATTCTTAACGTTACA-T
92000 ATATTTAATTCTTAACGTTACAT
1 ATATTTAATTCTTAACGTTACAT
*
92023 ATATTTACGTTCTTAAC
1 ATATTTA-ATTCTTAAC
92040 AAACAAACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 8 0.23
24 27 0.77
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (23 bp):
ATATTTAATTCTTAACGTTACAT
Found at i:99436 original size:21 final size:23
Alignment explanation
Indices: 99407--99450 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
99397 CTTCAGCCCT
99407 GTTTCGACCCAGA-GAAGGTCGA
1 GTTTCGACCCAGATGAAGGTCGA
*
99429 GTTT-GACCCTGATGAAGGTCGA
1 GTTTCGACCCAGATGAAGGTCGA
99451 AACAGGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23
Consensus pattern (23 bp):
GTTTCGACCCAGATGAAGGTCGA
Found at i:113241 original size:31 final size:31
Alignment explanation
Indices: 113206--113296 Score: 74
Period size: 31 Copynumber: 3.2 Consensus size: 31
113196 ACCTAAAGAT
113206 CTATGGCAAAATTCAAGTCCTAGGCCGAAAA
1 CTATGGCAAAATTCAAGTCCTAGGCCGAAAA
* *
113237 CTAT-G-AAAA-T---GTTC-A--CCTAAAGA
1 CTATGGCAAAATTCAAGTCCTAGGCCGAAA-A
*
113260 TCTATGGCAAAATTCAAGTCCTAGGCCGACAA
1 -CTATGGCAAAATTCAAGTCCTAGGCCGAAAA
113292 CTATG
1 CTATG
113297 TAGTTTTTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 22
0.62 0.07 0.31
Matches are distributed among these distances:
22 5 0.11
23 1 0.02
24 5 0.11
25 4 0.09
26 4 0.09
27 1 0.02
28 1 0.02
29 4 0.09
30 4 0.09
31 10 0.23
32 1 0.02
33 4 0.09
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (31 bp):
CTATGGCAAAATTCAAGTCCTAGGCCGAAAA
Found at i:113271 original size:55 final size:55
Alignment explanation
Indices: 113187--113296 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
113177 TTCATGCAGC
113187 AAAATGTTCACCTAAAGATCTATGGCAAAATTCAAGTCCTAGGCCGAAAACTATG
1 AAAATGTTCACCTAAAGATCTATGGCAAAATTCAAGTCCTAGGCCGAAAACTATG
*
113242 AAAATGTTCACCTAAAGATCTATGGCAAAATTCAAGTCCTAGGCCGACAACTATG
1 AAAATGTTCACCTAAAGATCTATGGCAAAATTCAAGTCCTAGGCCGAAAACTATG
113297 TAGTTTTTAC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (55 bp):
AAAATGTTCACCTAAAGATCTATGGCAAAATTCAAGTCCTAGGCCGAAAACTATG
Found at i:113272 original size:26 final size:26
Alignment explanation
Indices: 113185--113272 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
113175 ATTTCATGCA
113185 GCAAAATGTTCACCTAAAGATCTATG
1 GCAAAATGTTCACCTAAAGATCTATG
* *
113211 GCAAAATTCAAGTCCTAGGCCGAAA-A-CTAT-
1 GCAAAA-T---GTTC-A--CCTAAAGATCTATG
113241 G-AAAATGTTCACCTAAAGATCTATG
1 GCAAAATGTTCACCTAAAGATCTATG
113266 GCAAAAT
1 GCAAAAT
113273 TCAAGTCCTA
Statistics
Matches: 47, Mismatches: 4, Indels: 22
0.64 0.05 0.30
Matches are distributed among these distances:
22 5 0.11
23 1 0.02
24 5 0.11
25 4 0.09
26 11 0.23
27 1 0.02
28 1 0.02
29 4 0.09
30 4 0.09
31 5 0.11
32 1 0.02
33 5 0.11
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (26 bp):
GCAAAATGTTCACCTAAAGATCTATG
Found at i:113688 original size:13 final size:13
Alignment explanation
Indices: 113670--113695 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
113660 CTTGGCATGA
113670 GTGATGATTTTTG
1 GTGATGATTTTTG
113683 GTGATGATTTTTG
1 GTGATGATTTTTG
113696 TTGCTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:121115 original size:11 final size:11
Alignment explanation
Indices: 121099--121123 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
121089 ACCTTCTTTA
121099 TCACTCGTTCT
1 TCACTCGTTCT
121110 TCACTCGTTCT
1 TCACTCGTTCT
121121 TCA
1 TCA
121124 TATTTTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.36, G:0.08, T:0.44
Consensus pattern (11 bp):
TCACTCGTTCT
Found at i:124497 original size:21 final size:21
Alignment explanation
Indices: 124454--124498 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
124444 GTGACACTGC
* * *
124454 CCACCTGGGTTCTCAAGTAAA
1 CCACATGGGTGCTCAAGGAAA
*
124475 CCACATGGGTGCTCAAGGCAA
1 CCACATGGGTGCTCAAGGAAA
124496 CCA
1 CCA
124499 TGTGGGCGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.18
Consensus pattern (21 bp):
CCACATGGGTGCTCAAGGAAA
Found at i:127281 original size:21 final size:21
Alignment explanation
Indices: 127242--127290 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
127232 TCAATGCTTT
**
127242 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
127264 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
127285 A-GAAGC
1 AGGAAGC
127291 TACAATTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:142728 original size:26 final size:23
Alignment explanation
Indices: 142698--142744 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
142688 CTTGAAAATT
142698 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
142724 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
142745 AATAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAAAAACTTGATGATAGATGGA
Done.