Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007110.1 Corchorus capsularis cultivar CVL-1 contig07131, 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: 69359
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:1517 original size:19 final size:19
Alignment explanation
Indices: 1493--1531 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1483 GAGAGATTCA
1493 TTCAAT-GGCTCTCTCACTC
1 TTCAATCGG-TCTCTCACTC
*
1512 TTCAATCGGTCTCTCCCTC
1 TTCAATCGGTCTCTCACTC
1531 T
1 T
1532 CTTAAATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.13, C:0.38, G:0.10, T:0.38
Consensus pattern (19 bp):
TTCAATCGGTCTCTCACTC
Found at i:1533 original size:21 final size:20
Alignment explanation
Indices: 1493--1539 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
1483 GAGAGATTCA
*
1493 TTCAAT-GGCTCTCTCACTC
1 TTCAATCGGCTCTCCCACTC
*
1512 TTCAATCGGTCTCTCCCTCTC
1 TTCAATCGG-CTCTCCCACTC
*
1533 TTAAATC
1 TTCAATC
1540 TTTGAAACAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 6 0.26
20 2 0.09
21 15 0.65
ACGTcount: A:0.17, C:0.36, G:0.09, T:0.38
Consensus pattern (20 bp):
TTCAATCGGCTCTCCCACTC
Found at i:13430 original size:24 final size:24
Alignment explanation
Indices: 13384--13430 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
13374 ACTGAAAAGC
* * *
13384 GTTAAAGACACTATTTCAGAGTAT
1 GTTAAAGACACTAATGCAAAGTAT
*
13408 GTTAAAGTCACTAATGCAAAGTA
1 GTTAAAGACACTAATGCAAAGTA
13431 GGGAAATAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (24 bp):
GTTAAAGACACTAATGCAAAGTAT
Found at i:14709 original size:51 final size:51
Alignment explanation
Indices: 14609--14711 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 51
14599 AAAAGTAAAG
**
14609 TTTATTTGGCTTTCCAAGAATACCCTTTCGGTCAAAGGGTAAGTTTTGTCA
1 TTTATTTGGCTTTCCAAGAATACCCTTTCGGTCAAAGGGTAAGCCTTGTCA
*
14660 TTTACTTT-GCTTTCCAAGAATACCCTTTCGGTCAAAGGGTCAGCCTTGTCA
1 TTTA-TTTGGCTTTCCAAGAATACCCTTTCGGTCAAAGGGTAAGCCTTGTCA
14711 T
1 T
14712 GTTTCTTGCA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
51 45 0.94
52 3 0.06
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.38
Consensus pattern (51 bp):
TTTATTTGGCTTTCCAAGAATACCCTTTCGGTCAAAGGGTAAGCCTTGTCA
Found at i:15072 original size:186 final size:186
Alignment explanation
Indices: 14728--15163 Score: 515
Period size: 186 Copynumber: 2.3 Consensus size: 186
14718 TGCATTTAGA
* * *
14728 TTCAATTTCCCAGAAA-AACCTTTCAAACAAAGGGCCAGTTCTGTCACATTTCGTGCATTTAGAT
1 TTCAATTTCCCA-AAATACCCTTTCAAACAAAGGGTCAGTTTTGTCACATTT--TGCATTTAGAT
* * * * *
14792 TTAGCTTCCCAAGATACCCTTTCGGACAAAGGGTCGGTTGTGTCAGATTTCTCTCATATAGTCTC
63 TTAACTTCCCAAGATACCCTTTCGGACAAAGGGTCAGTTGTGTCACATTTCCCGCATATAGTCTC
* *
14857 TATTTCCCAGAATACCCTTTCGGACAAAGGCTCAATTCTGTCACA-TTCTCTCATATAGT
128 TATTTCCCAAAATACCCTTTCGGACAAAGGCTCAATTCTGTCACACTT-TCACATATAGT
**
14916 TTCAATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACACTTTTGCATTTAG-TTT
1 TTCAATTTCCCAAAATACCCTTTCAAACAAAGGGTCAGTTTTGTCACA-TTTTGCATTTAGATTT
* * * *
14980 CAA-TTTCCTAGAATACCCTTTCGGACAAAGGGTCAGTT-TAGTCACA-TTCCCGCATTTAGTTT
65 -AACTTCCCAAG-ATACCCTTTCGGACAAAGGGTCAGTTGT-GTCACATTTCCCGCATATAGTCT
* * *
15042 CTATTTCCCAAAATACCCTTTCGGACAAAGGCTCAGTTTTGTCACACTTTCACATTTAGT
127 CTATTTCCCAAAATACCCTTTCGGACAAAGGCTCAATTCTGTCACACTTTCACATATAGT
* * * * * *
15102 CTAAATTTCCCAAAATACCATTTCAAACAAAGGGTCGGTTTTGCCATATTTCTTGCATTTAG
1 TTCAATTTCCCAAAATACCCTTTCAAACAAAGGGTCAGTTTTGTCACA-TT-TTGCATTTAG
15164 GGTAAATTTT
Statistics
Matches: 213, Mismatches: 28, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
186 116 0.54
187 55 0.26
188 39 0.18
189 3 0.01
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (186 bp):
TTCAATTTCCCAAAATACCCTTTCAAACAAAGGGTCAGTTTTGTCACATTTTGCATTTAGATTTA
ACTTCCCAAGATACCCTTTCGGACAAAGGGTCAGTTGTGTCACATTTCCCGCATATAGTCTCTAT
TTCCCAAAATACCCTTTCGGACAAAGGCTCAATTCTGTCACACTTTCACATATAGT
Found at i:15143 original size:62 final size:62
Alignment explanation
Indices: 14673--15214 Score: 457
Period size: 62 Copynumber: 8.6 Consensus size: 62
14663 ACTTTGCTTT
* ** ** * *
14673 CCAAGAATACCCTTTCGGTCAAAGGGTCAGCCTTGTCATGTTTCTTGCATTTAGATTCAATTTC
1 CCAA-AATACCCTTTCGGACAAAGGGTCAGTTTTGTCA-CATTCTCGCATTTAGTTTCAATTTC
* ** * * **
14737 CCAGAAA-AACCTTTCAAACAAAGGGCCAGTTCTGTCACATT-TCGTGCATTTAGATTT-AGCTT
1 CCA-AAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACATTCTC--GCATTTAG-TTTCAATTT
14799 C
62 C
* * * * * * * *
14800 CCAAGATACCCTTTCGGACAAAGGGTCGGTTGTGTCAGATTTCTCTCATATAGTCTCTATTTC
1 CCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACA-TTCTCGCATTTAGTTTCAATTTC
* * * * * *
14863 CCAGAATACCCTTTCGGACAAAGGCTCAATTCTGTCACATTCTCTCATATAGTTTCAATTTC
1 CCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACATTCTCGCATTTAGTTTCAATTTC
*
14925 CCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACACTT-TTGCATTTAGTTTCAATTTC
1 CCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACA-TTCTCGCATTTAGTTTCAATTTC
* * * * *
14987 CTAGAATACCCTTTCGGACAAAGGGTCAGTTTAGTCACATTCCCGCATTTAGTTTCTATTTC
1 CCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACATTCTCGCATTTAGTTTCAATTTC
* * * *
15049 CCAAAATACCCTTTCGGACAAAGGCTCAGTTTTGTCACACTT-TCACATTTAGTCTAAATTTC
1 CCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACA-TTCTCGCATTTAGTTTCAATTTC
* ** * * * * ** *
15111 CCAAAATACCATTTCAAACAAAGGGTCGGTTTTGCCATATTTCTTGCATTTAGGGTAAATTTTC
1 CCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACA-TTCTCGCATTTAGTTTCAA-TTTC
* *
15175 TTCCTAAAATTCCCTTTCGGTA-AAAGGGTCAGTTCTGTCA
1 --CC-AAAATACCCTTTCGG-ACAAAGGGTCAGTTTTGTCA
15215 TGTTTCTGGT
Statistics
Matches: 383, Mismatches: 78, Indels: 31
0.78 0.16 0.06
Matches are distributed among these distances:
61 3 0.01
62 216 0.56
63 119 0.31
64 13 0.03
65 3 0.01
66 2 0.01
67 26 0.07
68 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (62 bp):
CCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACATTCTCGCATTTAGTTTCAATTTC
Found at i:15484 original size:64 final size:64
Alignment explanation
Indices: 15400--16157 Score: 665
Period size: 64 Copynumber: 11.5 Consensus size: 64
15390 CACTTAGGTC
* *
15400 CTAGTTTTCACAAAATGCCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATTTAAGTT
1 CTAGTTTTCCCAAAATACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATTTAAGTT
* ** * * *
15464 CTAGTTTTCCTAAAACGCCCTTTCAGACAAAGGCCTAGTTTTATCACATTCCAGCATCTAAGTT
1 CTAGTTTTCCCAAAATACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATTTAAGTT
* *
15528 C-AGCATTTTCGATACCCAAAATACCCTTTAAGA-AAAGGGCTAGTTTCGTCACATTCCAGCATT
1 CTAG---TTT---T-CCCAAAATACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATT
15591 TAAGTT
59 TAAGTT
* * * * *
15597 CGAGTTTTCCCAAAACT-CCATTTCAGATAAAGGGCTAGTTTTATCACATTCCAGCATCTAAGTT
1 CTAGTTTTCCCAAAA-TACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATTTAAGTT
* * * * * * * **
15661 CAGTATTTTCGATTCCCAAAATACCATGTCGGACAAAGTGTTAGTTTTGTCATATTCTTGCATTT
1 C--TA-GTT---TTCCCAAAATACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATTT
*
15726 AGGTT
60 AAGTT
** * * * *
15731 CTAGTTTTCCCAAAATGTCCTTTGAGACAAAGGGCAAGTTTTGTCACATTCCAACATCTAAGTT
1 CTAGTTTTCCCAAAATACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATTTAAGTT
* * * * * * *
15795 CAACATTTTCGATTCCCAAAATAACCTTTCAGACTAACGCCTAGTTTTGTCACATTCCAACATTT
1 C--TA-GTT---TTCCCAAAATACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATTT
15860 AAGTT
60 AAGTT
* * * *
15865 CTAGTTTTCCCAAAATGCCTTTTCAGATAAAGGGCTAGTTTTGTCACATTCCAGCATCTAAGTT
1 CTAGTTTTCCCAAAATACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATTTAAGTT
* * * **
15929 C-AGCATTTTCGATTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTTGTCATATTCTTGCATT
1 CTAG----TT---TTCCCAAAATACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATT
*
15993 TATGTT
59 TAAGTT
* * * * *
15999 CTTGTTTTCCCAAAACACCCTTGCAGACAAAGGGCTAGTTTCGTCACATTCCTA-TATTTAAGTT
1 CTAGTTTTCCCAAAATACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCC-AGCATTTAAGTT
* *
16063 C-AGTATTCCCAAAATACCCTTTCAGACAAAGGG-TCAGTTTTATCACATTCTCA-CATTTATA-
1 CTAGTTTTCCCAAAATACCCTTTCAGACAAAGGGCT-AGTTTTGTCACATTC-CAGCATTTA-AG
16124 TT
63 TT
16126 CTA--TTTCCCAAAATACCCTTTCAGACAAAGGG
1 CTAGTTTTCCCAAAATACCCTTTCAGACAAAGGG
16158 TCAGTTTGGT
Statistics
Matches: 560, Mismatches: 98, Indels: 74
0.77 0.13 0.10
Matches are distributed among these distances:
62 29 0.05
63 69 0.12
64 240 0.43
66 5 0.01
67 15 0.03
68 3 0.01
69 35 0.06
70 163 0.29
71 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (64 bp):
CTAGTTTTCCCAAAATACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATTTAAGTT
Found at i:15789 original size:134 final size:133
Alignment explanation
Indices: 15410--16157 Score: 862
Period size: 134 Copynumber: 5.7 Consensus size: 133
15400 CTAGTTTTCA
* *
15410 CAAAATGCCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATTTAAGTTCTAGTTTTCCT
1 CAAAATACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATTTAAGTTCTAGTTTTCCC
* * *
15475 AAAACGCCCTTTCAGACAAAGGCCTAGTTTTATCACATTCCAGCATCTAAGTTCAGCATTTTCGA
66 AAAA-GTCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATCTAAGTTCAGCATTTTCGA
*
15540 TACC
130 TTCC
* * *
15544 CAAAATACCCTTTAAGA-AAAGGGCTAGTTTCGTCACATTCCAGCATTTAAGTTCGAGTTTTCCC
1 CAAAATACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATTTAAGTTCTAGTTTTCCC
* * * *
15608 AAAACTCCATTTCAGATAAAGGGCTAGTTTTATCACATTCCAGCATCTAAGTTCAGTATTTTCGA
66 AAAAGTCC-TTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATCTAAGTTCAGCATTTTCGA
15673 TTCC
130 TTCC
* * * * * * ** *
15677 CAAAATACCATGTCGGACAAAGTGTTAGTTTTGTCATATTCTTGCATTTAGGTTCTAGTTTTCCC
1 CAAAATACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATTTAAGTTCTAGTTTTCCC
* * * *
15742 AAAATGTCCTTTGAGACAAAGGGCAAGTTTTGTCACATTCCAACATCTAAGTTCAACATTTTCGA
66 AAAA-GTCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATCTAAGTTCAGCATTTTCGA
15807 TTCC
130 TTCC
* * * * *
15811 CAAAATAACCTTTCAGACTAACGCCTAGTTTTGTCACATTCCAACATTTAAGTTCTAGTTTTCCC
1 CAAAATACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATTTAAGTTCTAGTTTTCCC
*
15876 AAAA-TGCCTTTTCAGATAAAGGGCTAGTTTTGTCACATTCCAGCATCTAAGTTCAGCATTTTCG
66 AAAAGT-CC-TTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATCTAAGTTCAGCATTTTCG
15940 ATTCC
129 ATTCC
* * * ** * *
15945 CAAAATACCCTTTCGGACAAAGGGTTAGTTTTGTCATATTCTTGCATTTATGTTCTTGTTTTCCC
1 CAAAATACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATTTAAGTTCTAGTTTTCCC
** * * * *
16010 AAAACACCCTTGCAGACAAAGGGCTAGTTTCGTCACATTCCTA-TATTTAAGTTCAG-----T--
66 AAAA-GTCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCC-AGCATCTAAGTTCAGCATTTTCG
16067 ATTCC
129 ATTCC
*
16072 CAAAATACCCTTTCAGACAAAGGG-TCAGTTTTATCACATTCTCA-CATTTATA-TTCTA--TTT
1 CAAAATACCCTTTCAGACAAAGGGCT-AGTTTTGTCACATTC-CAGCATTTA-AGTTCTAGTTTT
16132 CCCAAAA-TACCCTTTCAGACAAAGGG
63 CCCAAAAGT--CCTTTCAGACAAAGGG
16158 TCAGTTTGGT
Statistics
Matches: 524, Mismatches: 77, Indels: 35
0.82 0.12 0.06
Matches are distributed among these distances:
125 25 0.05
126 1 0.00
127 51 0.10
129 1 0.00
132 3 0.01
133 119 0.23
134 318 0.61
135 6 0.01
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (133 bp):
CAAAATACCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATTTAAGTTCTAGTTTTCCC
AAAAGTCCTTTCAGACAAAGGGCTAGTTTTGTCACATTCCAGCATCTAAGTTCAGCATTTTCGAT
TCC
Found at i:15850 original size:70 final size:69
Alignment explanation
Indices: 15617--15985 Score: 280
Period size: 70 Copynumber: 5.4 Consensus size: 69
15607 CAAAACTCCA
* * *
15617 TTTCAGA-TAAAGGGCTAGTTTTATCACATTCCAGCATCTAAGTTCAGTATTTTCGATTCCCAAA
1 TTTCAGACT-AAGGGCTAGTTTTGTCACATTCCAACATCTAAGTTCA-CATTTTCGATTCCCAAA
15681 AT-ACC
64 ATAACC
* * * * * * *** * * * *
15686 ATGTCGGACAAAGTGTTAGTTTTGTCATATTCTTGCATTTAGGTTC-TA-GTT---TTCCCAAAA
1 -TTTCAGACTAAGGGCTAGTTTTGTCACATTCCAACATCTAAGTTCACATTTTCGATTCCCAAAA
**
15746 TGTCC
65 TAACC
* * *
15751 TTTGAGACAAAGGGCAAGTTTTGTCACATTCCAACATCTAAGTTCAACATTTTCGATTCCCAAAA
1 TTTCAGACTAAGGGCTAGTTTTGTCACATTCCAACATCTAAGTTC-ACATTTTCGATTCCCAAAA
15816 TAACC
65 TAACC
* * * * *
15821 TTTCAGACTAACGCCTAGTTTTGTCACATTCCAACATTTAAGTTC-TA-GTT---TTCCCAAAAT
1 TTTCAGACTAAGGGCTAGTTTTGTCACATTCCAACATCTAAGTTCACATTTTCGATTCCCAAAAT
*
15881 -GCC
66 AACC
*
15884 TTTTCAGA-TAAAGGGCTAGTTTTGTCACATTCCAGCATCTAAGTTCAGCATTTTCGATTCCCAA
1 -TTTCAGACT-AAGGGCTAGTTTTGTCACATTCCAACATCTAAGTTCA-CATTTTCGATTCCCAA
*
15948 AATACCC
63 AATAACC
* * * *
15955 TTTCGGACAAAGGGTTAGTTTTGTCATATTC
1 TTTCAGACTAAGGGCTAGTTTTGTCACATTC
15986 TTGCATTTAT
Statistics
Matches: 232, Mismatches: 49, Indels: 36
0.73 0.15 0.11
Matches are distributed among these distances:
63 3 0.01
64 92 0.40
65 2 0.01
66 2 0.01
67 8 0.03
68 3 0.01
70 120 0.52
71 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (69 bp):
TTTCAGACTAAGGGCTAGTTTTGTCACATTCCAACATCTAAGTTCACATTTTCGATTCCCAAAAT
AACC
Found at i:16109 original size:63 final size:62
Alignment explanation
Indices: 15936--16169 Score: 253
Period size: 63 Copynumber: 3.7 Consensus size: 62
15926 GTTCAGCATT
* * * * * *
15936 TTCG-ATTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTTGTCATATTCTTGCATTTATG
1 TTCGTATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTTGTCACATTCCTACATTTAAG
* * * * *
15997 TTCTTGTTTTCCCAAAACACCCTTGCAGACAAAGGG-CTAGTTTCGTCACATTCCTATATTTAAG
1 TTC--GTATTCCCAAAATACCCTTTCAGACAAAGGGTC-AGTTTTGTCACATTCCTACATTTAAG
*
16061 TTCAGTATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTTATCACATT-CTCACATTTATA-
1 TTC-GTATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTTGTCACATTCCT-ACATTTA-AG
*
16124 TTC-TATTTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTGGTCA
1 TTCGTA-TTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTTGTCA
16170 TATTTCTTGC
Statistics
Matches: 145, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
61 5 0.03
62 40 0.28
63 50 0.34
64 50 0.34
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (62 bp):
TTCGTATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTTGTCACATTCCTACATTTAAG
Found at i:17119 original size:10 final size:10
Alignment explanation
Indices: 17095--17123 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
17085 GCTTATCGAT
17095 ATCTCCATG-
1 ATCTCCATGC
17104 ATCTCCATGC
1 ATCTCCATGC
17114 ATCTCCATGC
1 ATCTCCATGC
17124 TTCCTTGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.21, C:0.38, G:0.10, T:0.31
Consensus pattern (10 bp):
ATCTCCATGC
Found at i:20467 original size:30 final size:30
Alignment explanation
Indices: 20427--20489 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
20417 TGTCTTCAAG
*
20427 TCCATAATAAGTCCTT-GGCGCATCATTCTC
1 TCCATAATAAG-CCTTGGGCGCATCATTCCC
*
20457 TCCATGATAAGCCTTGGGCGCATCATTCCC
1 TCCATAATAAGCCTTGGGCGCATCATTCCC
20487 TCC
1 TCC
20490 CCCTTGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.21, C:0.33, G:0.16, T:0.30
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATCATTCCC
Found at i:20898 original size:33 final size:33
Alignment explanation
Indices: 20861--20934 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
20851 AAAACAGTCC
**
20861 TATTTTCAATGCTATGATCAGGCAAAACAGAAT
1 TATTTTCAATGCTATGATCAACCAAAACAGAAT
*
20894 TATTTTCAATGCTATGATCAACCAAAACAGATT
1 TATTTTCAATGCTATGATCAACCAAAACAGAAT
*
20927 TGTTTTCA
1 TATTTTCA
20935 TCACAATTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (33 bp):
TATTTTCAATGCTATGATCAACCAAAACAGAAT
Found at i:20992 original size:33 final size:33
Alignment explanation
Indices: 20950--21013 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
20940 ATTGGCATCC
* *
20950 AAAAAAGATTTTGTTTCATCACAAACAACACCT
1 AAAAAAGATTTAGTGTCATCACAAACAACACCT
* **
20983 AAAACAGATTTAGTGTCATTGCAAACAACAC
1 AAAAAAGATTTAGTGTCATCACAAACAACAC
21014 TCAAATTAGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.09, T:0.25
Consensus pattern (33 bp):
AAAAAAGATTTAGTGTCATCACAAACAACACCT
Found at i:22458 original size:9 final size:9
Alignment explanation
Indices: 22444--22476 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
22434 CTGGTCGATT
22444 TTTTTTTAA
1 TTTTTTTAA
22453 TTTTTTTAA
1 TTTTTTTAA
22462 TTTTTTTAA
1 TTTTTTTAA
22471 TTTTTT
1 TTTTTT
22477 GGTATAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:24018 original size:33 final size:33
Alignment explanation
Indices: 23976--24091 Score: 187
Period size: 33 Copynumber: 3.5 Consensus size: 33
23966 TTCTTTTCAC
* * *
23976 CCAAAACAGAATTATTTTCAATGTTATGATTAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
24009 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
24042 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
* *
24075 TCAAAATAGAATTATTT
1 CCAAAACAGAATTATTT
24092 TCATCTAACA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:24727 original size:19 final size:18
Alignment explanation
Indices: 24703--24738 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
24693 TGAAGATTTC
24703 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
24722 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
24739 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:26042 original size:15 final size:16
Alignment explanation
Indices: 26022--26055 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
26012 GATTGCTTTC
*
26022 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
26037 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
26053 TTA
1 TTA
26056 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:28902 original size:19 final size:19
Alignment explanation
Indices: 28870--28907 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28860 ATAAGTCTTG
28870 ATAAGCCTTGGGCGCATCA
1 ATAAGCCTTGGGCGCATCA
* *
28889 ATAAGTCTTTGGCGCATCA
1 ATAAGCCTTGGGCGCATCA
28908 TTCCTTCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (19 bp):
ATAAGCCTTGGGCGCATCA
Found at i:57280 original size:18 final size:17
Alignment explanation
Indices: 57257--57291 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
57247 ATTTTTTTCC
57257 TTTTTTTTATGTTTGCA
1 TTTTTTTTATGTTTGCA
57274 TTTTTTTTATGTTTGCA
1 TTTTTTTTATGTTTGCA
57291 T
1 T
57292 GCATTGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.06, G:0.11, T:0.71
Consensus pattern (17 bp):
TTTTTTTTATGTTTGCA
Done.