Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008315.1 Corchorus capsularis cultivar CVL-1 contig08336, 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: 20941
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Found at i:337 original size:194 final size:196
Alignment explanation
Indices: 1--476 Score: 586
Period size: 194 Copynumber: 2.4 Consensus size: 196
*
1 AAATGGGATATGTGTCAACTT-TTAACCCGCTTATAGAA-TCCAAAATTTATACTGACAGTGTAT
1 AAATGGG-TATGTGTCAACTTCTTAACCCGCTTAT-GAAGTCCAAAA-TT-TACAGACAGTGTAT
* * * *
64 TGTATAATAATCGTATAAGAAAATTTATGCAATAAACTGTCAGTGTAGTTTAGCAGACTGCACGC
62 TGTATAATAATCCTATAAGAAAAATTATACAATAAACCGTCAGTGTAGTTTAGCAGACTGCACGC
* * * * **
129 ACGAGGTTTAAGGGTTGACATGTGTCCTCTTAGGGAATATGTATTAATATTTTATA-TTAATTAA
127 ACGAGGCTTAAGGGTTGACATGTGTCCCCTTAAGGAAAATGTATTAATATTAAATATTTAATTAA
193 TTATG
192 TTATG
* * * *
198 AAATGGGTATGCGTCAACTTCTTAACCCGCTCATGAAGTTCAAAATTTACAGACAATGTATTGTA
1 AAATGGGTATGTGTCAACTTCTTAACCCGCTTATGAAGTCCAAAATTTACAGACAGTGTATTGTA
* * * **
263 TAACAATCCTATAA-AAAAATTATACAATACACCGTTAGTAG-AGTTTAGCAGACTGCACGTGC-
66 TAATAATCCTATAAGAAAAATTATACAATAAACCGTCAGT-GTAGTTTAGCAGACTGCACGCACG
325 ATGGCTTAAGGGTTGACATGTGTCCCCTTAAGGAAAATGTATTAATATTAAATATTTAATTAATT
130 A-GGCTTAAGGGTTGACATGTGTCCCCTTAAGGAAAATGTATTAATATTAAATATTTAATTAATT
390 ATG
194 ATG
* ** *
393 AAATTGAGGTATGTATCAACTTCTTAACTAGCTTATGGAGTCCAAAATTTACATTGACAGTGTAT
1 AAA-TG-GGTATGTGTCAACTTCTTAACCCGCTTATGAAGTCCAAAATTTACA--GACAGTGTAT
*
458 TGTACAATAATCCTTATAA
62 TGTATAATAATCC-TATAA
477 TAAACCTTAC
Statistics
Matches: 239, Mismatches: 30, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
193 1 0.00
194 85 0.36
195 45 0.19
196 19 0.08
197 64 0.27
199 20 0.08
200 5 0.02
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (196 bp):
AAATGGGTATGTGTCAACTTCTTAACCCGCTTATGAAGTCCAAAATTTACAGACAGTGTATTGTA
TAATAATCCTATAAGAAAAATTATACAATAAACCGTCAGTGTAGTTTAGCAGACTGCACGCACGA
GGCTTAAGGGTTGACATGTGTCCCCTTAAGGAAAATGTATTAATATTAAATATTTAATTAATTAT
G
Found at i:3043 original size:12 final size:12
Alignment explanation
Indices: 3026--3064 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
3016 TCCACATAAG
*
3026 CATCCGCGTAAT
1 CATCCGGGTAAT
3038 CATCCGGGTAAT
1 CATCCGGGTAAT
*
3050 CATCTGGGTAAT
1 CATCCGGGTAAT
3062 CAT
1 CAT
3065 AGCCTCCGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (12 bp):
CATCCGGGTAAT
Found at i:7039 original size:17 final size:16
Alignment explanation
Indices: 7013--7044 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
7003 TTCTTTTTAT
7013 TATAATATATATAATA
1 TATAATATATATAATA
7029 TATATATATATATAAT
1 TATA-ATATATATAAT
7045 TCAAGAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATATATATAATA
Found at i:7201 original size:16 final size:15
Alignment explanation
Indices: 7182--7226 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 15
7172 ATTTTTTTCC
7182 TAATTTTATCTTTTGA
1 TAATTTT-TCTTTTGA
7198 TAATTATTTCTTTTGA
1 TAATT-TTTCTTTTGA
7214 TAATTTTT-TTTTG
1 TAATTTTTCTTTTG
7227 GTACATATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.18
15 3 0.11
16 18 0.64
17 2 0.07
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (15 bp):
TAATTTTTCTTTTGA
Found at i:7224 original size:13 final size:16
Alignment explanation
Indices: 7190--7249 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 16
7180 CCTAATTTTA
7190 TCTTTTGATAATTATT
1 TCTTTTGATAATTATT
7206 TCTTTTGATAATT-TT
1 TCTTTTGATAATTATT
*
7221 T-TTTTGGTACA-TA--
1 TCTTTTGATA-ATTATT
7234 TCTTTTGATAATTATT
1 TCTTTTGATAATTATT
7250 AGTTTTAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 2 0.06
14 17 0.47
15 4 0.11
16 13 0.36
ACGTcount: A:0.23, C:0.07, G:0.08, T:0.62
Consensus pattern (16 bp):
TCTTTTGATAATTATT
Found at i:7392 original size:22 final size:22
Alignment explanation
Indices: 7366--8012 Score: 209
Period size: 22 Copynumber: 29.9 Consensus size: 22
7356 TTATGTCTAT
7366 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
7388 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * * **
7410 TATGGAATTTCGAGAACATTTT
1 TATGAAATTTTGATAACCTTCC
* * ** *
7432 TATTAATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* * *
7454 TATGAAATTTTGTTAAGCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
7476 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
7498 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
7520 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* * *
7543 TATGAGATGTTAATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
7564 ATATGATATATTGATAACCATGC
1 -TATGAAATTTTGATAACCTTCC
* * *
7587 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
7608 ACATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * * *
7631 TCTAAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
7653 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
* *
7675 TATGAAATTTCGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
7698 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * * *
7721 TATAAAATTTTGATTACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
7743 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
7760 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
7781 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
7803 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * * *
7825 TATTATAA-TTTGATCTA-CATAC
1 TATGA-AATTTTGAT-AACCTTCC
* * *
7847 TATAAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
7869 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
7891 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
*
7913 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
*
7934 T-TGAAATTTTGATTA-C-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
7953 ATAATAAAAGTTTAATAACCTTCC
1 -T-ATGAAATTTTGATAACCTTCC
* * *
7977 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACCTTCC
7994 TATGAAATTTTGATAACCT
1 TATGAAATTTTGATAACCT
8013 CCCCATAAAT
Statistics
Matches: 451, Mismatches: 133, Indels: 82
0.68 0.20 0.12
Matches are distributed among these distances:
16 11 0.02
17 12 0.03
18 2 0.00
19 5 0.01
20 14 0.03
21 25 0.06
22 305 0.68
23 72 0.16
24 5 0.01
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:7705 original size:23 final size:23
Alignment explanation
Indices: 7667--7730 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
7657 AAATTGTGAT
* *
7667 AACCTCGCTATGAAATTTCGATA
1 AACCTCCCTATAAAATTTCGATA
* * *
7690 AATCTTCCTATAAAATTTTGATA
1 AACCTCCCTATAAAATTTCGATA
7713 AACCTCCCTATAAAATTT
1 AACCTCCCTATAAAATTT
7731 TGATTACTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (23 bp):
AACCTCCCTATAAAATTTCGATA
Found at i:7757 original size:45 final size:45
Alignment explanation
Indices: 7652--7758 Score: 110
Period size: 45 Copynumber: 2.4 Consensus size: 45
7642 GATAATCACA
* *
7652 CTATGAAATTGTGAT-AACCTCGCTATGAAATTTCGATAAATCTTC
1 CTATGAAATT-TGATAAACCTCCCTATAAAATTTCGATAAATCTTC
* * * *
7697 CTATAAAATTTTGATAAACCTCCCTATAAAATTTTGATTACT-TTC
1 CTATGAAA-TTTGATAAACCTCCCTATAAAATTTCGATAAATCTTC
*
7742 TTATGAAATCTTGATAA
1 CTATGAAAT-TTGATAA
7759 CTACAAATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
44 1 0.02
45 27 0.53
46 23 0.45
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (45 bp):
CTATGAAATTTGATAAACCTCCCTATAAAATTTCGATAAATCTTC
Found at i:7795 original size:128 final size:126
Alignment explanation
Indices: 7635--7887 Score: 283
Period size: 128 Copynumber: 2.0 Consensus size: 126
7625 TCACACTCTA
* * *
7635 AAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTATGAAATTTCGATAAATCTTCCTA
1 AAATTTTGATAACCACACTATGAAATTGTGATAACCTCACTATGAAATTTCG-TAAATCTCCCTA
* * * ** *
7700 -TAAAATTTTGATAAACCTCCCTATAAAATTTTGATTACTTTCTTATGAAATCTTGATAACTAC
65 TTAAAA-TTTGATAAACAT-ACTATAAAATTTTGATAACCCTCTTATGAAATCTTGAAAACTAC
* * ** * * * *
7763 AAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTAT
1 AAATTTTGATAACCACACTATGAAATTGTGATAACCTCACTATGAAATTTCGTAAATCTCCCTAT
* ** *
7828 TATAATTTGATCTACATACTATAAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTA
66 TAAAATTTGATAAACATACTATAAAATTTTGATAACCCTCTTATGAAATCTTGAAAACTA
7888 AACTATGAAA
Statistics
Matches: 103, Mismatches: 21, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
126 37 0.36
127 19 0.18
128 47 0.46
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (126 bp):
AAATTTTGATAACCACACTATGAAATTGTGATAACCTCACTATGAAATTTCGTAAATCTCCCTAT
TAAAATTTGATAAACATACTATAAAATTTTGATAACCCTCTTATGAAATCTTGAAAACTAC
Found at i:8077 original size:22 final size:22
Alignment explanation
Indices: 8052--8427 Score: 216
Period size: 22 Copynumber: 16.9 Consensus size: 22
8042 AATCACGTTT
8052 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
*
8074 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
8096 TAAAATTTTGTTAACCCCCTTTA
1 TGAAATTTTGATAA-CCTCTCTA
* * *
8119 TGAAATTCTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * *
8141 TGTAATTTTGATAACCTCACTT
1 TGAAATTTTGATAACCTCTCTA
* *
8163 TGAAATTTTGAT-ACCAACACTA
1 TGAAATTTTGATAACC-TCTCTA
* *
8185 TGAAATTTTGATAATCTTTCTA
1 TGAAATTTTGATAACCTCTCTA
*
8207 -CAAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTCTA
* * *
8231 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTCTA
*
8253 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
* *
8273 TCAAATTTTGGT-A-CTC-CTTA
1 TGAAATTTTGATAACCTCTC-TA
*
8293 TGAAATTGAGACTTTTATAACCT-TCATA
1 TGAAA-T-----TTTGATAACCTCTC-TA
* * *
8321 TGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* * *
8343 TAAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTCTCTA
*
8365 TGAAATATT-AGTAACCTC-CTAA
1 TGAAATTTTGA-TAACCTCTCT-A
* * *
8387 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
8409 TGACATTTTGATAATCTCT
1 TGAAATTTTGATAACCTCT
8428 TTGATAACCT
Statistics
Matches: 268, Mismatches: 60, Indels: 52
0.71 0.16 0.14
Matches are distributed among these distances:
19 3 0.01
20 14 0.05
21 31 0.12
22 163 0.61
23 24 0.09
24 6 0.02
25 11 0.04
26 4 0.01
27 2 0.01
28 10 0.04
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:8192 original size:44 final size:44
Alignment explanation
Indices: 8030--8198 Score: 155
Period size: 44 Copynumber: 3.8 Consensus size: 44
8020 AATACCACCA
* * * * *
8030 TGAAATTTTTG-TAATCACGTTTTGAAATTTTGATAACCTCTCTA
1 TGAAA-TTTTGATAACCACATTATGAAATTTTGATAACCTCACTT
* * * * *
8074 TGAAATTTTGATAACCTCTTTATAAAATTTTGTTAACC-CCCTTT
1 TGAAATTTTGATAACCACATTATGAAATTTTGATAACCTCAC-TT
* * *
8118 ATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCACTT
1 -TGAAATTTTGATAACCACATTATGAAATTTTGATAACCTCACTT
*
8163 TGAAATTTTGAT-ACCAACACTATGAAATTTTGATAA
1 TGAAATTTTGATAACC-ACATTATGAAATTTTGATAA
8199 TCTTTCTACA
Statistics
Matches: 100, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
43 9 0.09
44 56 0.56
45 33 0.33
46 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (44 bp):
TGAAATTTTGATAACCACATTATGAAATTTTGATAACCTCACTT
Found at i:8262 original size:111 final size:110
Alignment explanation
Indices: 8050--8268 Score: 261
Period size: 111 Copynumber: 2.0 Consensus size: 110
8040 GTAATCACGT
* * * *
8050 TTTGAAATTTTGATAACCTCTCTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTAACCCCC
1 TTTGAAATTTTGATAACCACACTATGAAATTTTGATAA-CTCTTTATAAAATTTTGATAACCACC
*
8115 TTTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCAC
65 TCTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCAC
*
8161 TTTGAAATTTTGAT-ACCAACACTATGAAATTTTGATAA-TCTTTCTACAAATTTTGATAATCCG
1 TTTGAAATTTTGATAACC-ACACTATGAAATTTTGATAACTCTTTATA-AAATTTTGATAA-CC-
*
8224 ATCTCTATGAAATT-TCGATAATCAC-TCTATG-AGA-TTTGATAACCT
62 ACCTCTATGAAATTCT-GATAATCACAT-TATGTA-ATTTTGATAACCT
8269 TCTATCAAAT
Statistics
Matches: 94, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
109 7 0.07
110 14 0.15
111 48 0.51
112 25 0.27
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.41
Consensus pattern (110 bp):
TTTGAAATTTTGATAACCACACTATGAAATTTTGATAACTCTTTATAAAATTTTGATAACCACCT
CTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCAC
Found at i:8484 original size:21 final size:20
Alignment explanation
Indices: 8458--8520 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 20
8448 TTGTGATAAT
8458 TAACCATCCTATGAAATTCAA
1 TAACCATCCTATGAAATT-AA
* *
8479 TAACCAACCTAAGAGATATTAA
1 TAACCATCCTATGA-A-ATTAA
*
8501 TAACCTGATTCTATGAAATT
1 TAACC--ATCCTATGAAATT
8521 TTGGTAATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
21 12 0.36
22 11 0.33
23 4 0.12
24 6 0.18
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (20 bp):
TAACCATCCTATGAAATTAA
Found at i:8799 original size:20 final size:19
Alignment explanation
Indices: 8762--8799 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
8752 TATTGACATT
8762 TAAAAATTGAAATTAAAAG
1 TAAAAATTGAAATTAAAAG
8781 TAAAATATT-AAATTTAAAA
1 TAAAA-ATTGAAA-TTAAAA
8800 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
TAAAAATTGAAATTAAAAG
Found at i:9453 original size:31 final size:31
Alignment explanation
Indices: 9418--9483 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
9408 TGGTAATTTA
* * *
9418 GAAATATGTTTTTTAAAA-AAGGGTATAATTG
1 GAAATATG-TTTTAAAAATAAGGGTACAATCG
9449 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
9480 GAAA
1 GAAA
9484 ACATAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.32
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Found at i:10129 original size:16 final size:15
Alignment explanation
Indices: 10108--10137 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
10098 TAATTAAAAA
10108 ATAATAAATATAATAT
1 ATAATAAATA-AATAT
10124 ATAATAAATAAATA
1 ATAATAAATAAATA
10138 AAAAGGCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAATAAATAAATAT
Found at i:11143 original size:23 final size:24
Alignment explanation
Indices: 11099--11144 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
11089 CGTTGGTCCC
*
11099 TTTTGTAATTTTTTTATTTTATTA
1 TTTTGTAATTTTTTTATATTATTA
11123 TTTT-TAATATTTTTTA-ATTATT
1 TTTTGTAAT-TTTTTTATATTATT
11145 TAAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (24 bp):
TTTTGTAATTTTTTTATATTATTA
Found at i:11675 original size:81 final size:81
Alignment explanation
Indices: 11542--11787 Score: 431
Period size: 81 Copynumber: 3.0 Consensus size: 81
11532 GAATCATAAC
* * *
11542 CATCAGAGTCCCCGGAATATGCAGAATCTTCGCATCCTTCTCCTTCATCGTCGTCACTCTCCTCA
1 CATCAGAGTCCCCAGAATATGCAGAATCCTCACATCCTTCTCCTTCATCGTCGTCACTCTCCTCA
11607 TATTTGTTGTAATGAT
66 TATTTGTTGTAATGAT
11623 CATCAGAGTCCCCAGAATATGCAGAATCCTCACATCCTTCTCCTTCATCGTCGTCACTCTCCTCA
1 CATCAGAGTCCCCAGAATATGCAGAATCCTCACATCCTTCTCCTTCATCGTCGTCACTCTCCTCA
11688 TATTTGTTGTAATGAT
66 TATTTGTTGTAATGAT
*
11704 CATCAGAGTCCCCAGAATATGCAGAAT-CTGCACATCCTTCTCCTTCATCGTCTTCACTCTCCTC
1 CATCAGAGTCCCCAGAATATGCAGAATCCT-CACATCCTTCTCCTTCATCGTCGTCACTCTCCTC
*
11768 ATATTTGTTGCAATGAT
65 ATATTTGTTGTAATGAT
11785 CAT
1 CAT
11788 TGCTTATGGC
Statistics
Matches: 159, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
80 2 0.01
81 157 0.99
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.34
Consensus pattern (81 bp):
CATCAGAGTCCCCAGAATATGCAGAATCCTCACATCCTTCTCCTTCATCGTCGTCACTCTCCTCA
TATTTGTTGTAATGAT
Found at i:12469 original size:36 final size:36
Alignment explanation
Indices: 12422--12502 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
12412 TATGATCCAG
* * *
12422 CACCATAGTTGCCCATGTTGTAGCTGCTGTTGCTGC
1 CACCATAGTTGCCCATGTTGTAGCCGCTGCTGCAGC
* *
12458 CACCATAGTTGCCCTTGTTGTAGCCGTTGCTGCAGC
1 CACCATAGTTGCCCATGTTGTAGCCGCTGCTGCAGC
12494 CACCATAGT
1 CACCATAGT
12503 CGACCCTGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.16, C:0.30, G:0.23, T:0.31
Consensus pattern (36 bp):
CACCATAGTTGCCCATGTTGTAGCCGCTGCTGCAGC
Found at i:18427 original size:16 final size:15
Alignment explanation
Indices: 18406--18435 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18396 TTGTTTTAAT
18406 AAAAAAGATTTAAAAA
1 AAAAAAGA-TTAAAAA
18422 AAAAAAGATTAAAA
1 AAAAAAGATTAAAA
18436 GAATCTGCCA
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:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAAAAGATTAAAAA
Found at i:18954 original size:6 final size:6
Alignment explanation
Indices: 18943--18971 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
18933 CTTAAAATAA
18943 AATTTT AATTTT AATTTT AATTTT AATTT
1 AATTTT AATTTT AATTTT AATTTT AATTT
18972 GGGCTAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
AATTTT
Found at i:20081 original size:25 final size:25
Alignment explanation
Indices: 20006--20085 Score: 72
Period size: 25 Copynumber: 3.1 Consensus size: 25
19996 GTTCAATCTC
*
20006 TAACAACCTCAAGTATCAAAAATAA
1 TAACAACCTCAAGTACCAAAAATAA
* ** * *
20031 TAATAGTCT-AATTGGAACCAATAATAA
1 TAACAACCTCAA---GTACCAAAAATAA
20058 TAACAACCTCAAGTACCAAAAATAA
1 TAACAACCTCAAGTACCAAAAATAA
20083 TAA
1 TAA
20086 TAACAAGTTA
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
24 2 0.05
25 20 0.50
27 16 0.40
28 2 0.05
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.23
Consensus pattern (25 bp):
TAACAACCTCAAGTACCAAAAATAA
Found at i:20914 original size:2 final size:2
Alignment explanation
Indices: 20907--20941 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
20897 GTTAAAAATA
20907 AT AT 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 AT AT A
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.