Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009822.1 Corchorus capsularis cultivar CVL-1 contig09843, 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: 160891
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1952 original size:19 final size:19
Alignment explanation
Indices: 1928--1973 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1918 TCTTCAATAG
1928 TCTTCAAGTCTTCAAATTA
1 TCTTCAAGTCTTCAAATTA
1947 TCTTCAAGTCTTCAAATTA
1 TCTTCAAGTCTTCAAATTA
1966 TCTTCAAG
1 TCTTCAAG
1974 AAATCTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (19 bp):
TCTTCAAGTCTTCAAATTA
Found at i:4540 original size:14 final size:14
Alignment explanation
Indices: 4521--4548 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4511 GGCCGATTAG
4521 AGGAGAAGTCGACT
1 AGGAGAAGTCGACT
4535 AGGAGAAGTCGACT
1 AGGAGAAGTCGACT
4549 TTACAAGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.36, T:0.14
Consensus pattern (14 bp):
AGGAGAAGTCGACT
Found at i:5628 original size:24 final size:23
Alignment explanation
Indices: 5601--5647 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
5591 AGTTATTTAG
5601 TTTATGCTT-TATCTTTAATTTTTC
1 TTTAT-CTTATATCTTT-ATTTTTC
*
5625 TTTATCTTATGTCTTTATTTTTC
1 TTTATCTTATATCTTTATTTTTC
5648 AAGTTTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.15, C:0.13, G:0.04, T:0.68
Consensus pattern (23 bp):
TTTATCTTATATCTTTATTTTTC
Found at i:7195 original size:19 final size:18
Alignment explanation
Indices: 7171--7206 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7161 TGAAGATCTC
7171 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
7190 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
7207 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:7868 original size:27 final size:27
Alignment explanation
Indices: 7838--7912 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
7828 AACTGAACTT
* *
7838 AAAATGACCAAAATACCCCTAAATGCA
1 AAAATGACCAAAATGCCCCTAAACGCA
* **
7865 AAAATGACCAAAATGCCCCTGAACGTG
1 AAAATGACCAAAATGCCCCTAAACGCA
7892 AAAATGACCAAAATGCCCCTA
1 AAAATGACCAAAATGCCCCTA
7913 TGTGACCCTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.47, C:0.27, G:0.12, T:0.15
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAAACGCA
Found at i:11427 original size:27 final size:28
Alignment explanation
Indices: 11397--11449 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
11387 GCATTAGGGT
11397 CATCCA-GGGGCATTTTGGTCATTTTCA
1 CATCCAGGGGGCATTTTGGTCATTTTCA
*
11424 CATCTAGGGGGCATTTTGGTCATTTT
1 CATCCAGGGGGCATTTTGGTCATTTT
11450 TGCATTTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.40
Consensus pattern (28 bp):
CATCCAGGGGGCATTTTGGTCATTTTCA
Found at i:11435 original size:28 final size:28
Alignment explanation
Indices: 11403--11475 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
11393 GGGTCATCCA
11403 GGGGCATTTTGGTCATTTTCACATCTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
** *
11431 GGGGCATTTTGGTCATTTTTGCATTTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
**
11459 GGGATATTTTGGTCATT
1 GGGGCATTTTGGTCATT
11476 CTTAATCTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.16, C:0.12, G:0.27, T:0.44
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTCACATCTAG
Found at i:16223 original size:21 final size:21
Alignment explanation
Indices: 16199--16291 Score: 67
Period size: 21 Copynumber: 4.8 Consensus size: 21
16189 AATTCAGTTT
16199 AATTAAGTAAATTGGTGATTA
1 AATTAAGTAAATTGGTGATTA
*
16220 AATTAAGT-AATT--T-AGTA
1 AATTAAGTAAATTGGTGATTA
* * *
16237 AA-CAACTTAATTCGGTG--T-
1 AATTAAGTAAATT-GGTGATTA
16255 AATTAAGTAAATTGGTGATTA
1 AATTAAGTAAATTGGTGATTA
* *
16276 AATTAGGTAATTTGGT
1 AATTAAGTAAATTGGT
16292 AAACAACTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
16 3 0.05
17 9 0.16
18 7 0.13
19 8 0.15
20 6 0.11
21 22 0.40
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.39
Consensus pattern (21 bp):
AATTAAGTAAATTGGTGATTA
Found at i:16258 original size:56 final size:56
Alignment explanation
Indices: 16178--16326 Score: 253
Period size: 56 Copynumber: 2.7 Consensus size: 56
16168 TGGTAATCTG
* *
16178 GTAAACAACTTAATTCAGTTTAATTAAGTAAATTGGTGATTAAATTAAGTAATTTA
1 GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTGATTAAATTAAGTAATTTA
* *
16234 GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTGATTAAATTAGGTAATTTG
1 GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTGATTAAATTAAGTAATTTA
*
16290 GTAAACAACTTAATTCGGTGTAATCAAGTAAATTGGT
1 GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGT
16327 AATTTGGCAA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 88 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (56 bp):
GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTGATTAAATTAAGTAATTTA
Found at i:16329 original size:43 final size:44
Alignment explanation
Indices: 16274--16363 Score: 146
Period size: 43 Copynumber: 2.1 Consensus size: 44
16264 AATTGGTGAT
*
16274 TAAATTAGGTAATTTGGTAAACAACTTAATTCGGTGTAATCAAG
1 TAAATTAGGTAATTTGGCAAACAACTTAATTCGGTGTAATCAAG
* *
16318 TAAATT-GGTAATTTGGCAAACAACTTAGTTCGGTGTAATTAAG
1 TAAATTAGGTAATTTGGCAAACAACTTAATTCGGTGTAATCAAG
16361 TAA
1 TAA
16364 TTCGGTGTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
43 37 0.86
44 6 0.14
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (44 bp):
TAAATTAGGTAATTTGGCAAACAACTTAATTCGGTGTAATCAAG
Found at i:16343 original size:99 final size:100
Alignment explanation
Indices: 16226--16576 Score: 346
Period size: 99 Copynumber: 3.5 Consensus size: 100
16216 ATTAAATTAA
*
16226 GTAATTTAGTAAACAACTTAATTCGGTGTAATTAAGTAAATT-GGTG-ATTAAATTAGGTAATTT
1 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTCGGTGAATTAAATT-GGTAATTT
*
16289 GGTAAACAACTTAATTCGGTGTAATCAAGTAAATTG
65 GGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
* *
16325 GTAATTTGGCAAACAACTTAGTTCGGTGTAATTAAGT-AATTCGGTGTAATTAAGTAACTTGGTA
1 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTCGGTG-AATT-A--AA-TTGGTA
*
16389 ATTTGGTAAGCAACTTAATTCGGTGTAATTAAGTAAATTG
61 ATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
* * * * ** * *** ** * *
16429 GTGA--T--TAAATTAA-GTAATTTGGTAAACAACTTAATTCGGTGT-AATTAAGTAAATTGGTA
1 GTAATTTGGTAAA-CAACTTAATTCGGT--GTAA-TTAAGTAAAT-TCGGTGAATTAAATTGGTA
*
16488 ATCTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
61 ATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
16528 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATT-GGT-AATT
1 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTCGGTGAATT
16577 TGGTAAACAA
Statistics
Matches: 199, Mismatches: 35, Indels: 37
0.73 0.13 0.14
Matches are distributed among these distances:
98 7 0.04
99 87 0.44
100 18 0.09
101 8 0.04
102 7 0.04
103 20 0.10
104 49 0.25
105 3 0.02
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (100 bp):
GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTCGGTGAATTAAATTGGTAATTTG
GTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
Found at i:16369 original size:18 final size:18
Alignment explanation
Indices: 16346--16381 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
16336 AACAACTTAG
16346 TTCGGTGTAATTAAGTAA
1 TTCGGTGTAATTAAGTAA
16364 TTCGGTGTAATTAAGTAA
1 TTCGGTGTAATTAAGTAA
16382 CTTGGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39
Consensus pattern (18 bp):
TTCGGTGTAATTAAGTAA
Found at i:16372 original size:61 final size:61
Alignment explanation
Indices: 16300--16667 Score: 351
Period size: 61 Copynumber: 6.0 Consensus size: 61
16290 GTAAACAACT
* * *
16300 TAATTCGGTGTAATCAAGTAAATTGGTAATTTGGCAAACAACTTAGTTCGGTGTAATTAAG
1 TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
* *
16361 TAATTCGGTGTAATTAAGTAACTTGGTAATTTGGTAAGCAACTTAATTCGGTGTAATTAAG
1 TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
* *
16422 TAAATT-GGTG--ATTAAATTAA---GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
1 T-AATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
** * * ** **** *
16478 TAAATT-GGTAATCTGGTAAACAACTTAATTCGGTGTAATTAAGTAAA-TTGGTAATT-TG-GTA
1 T-AATTCGG-----T-GTAATTAAGTAAATT--G-GTAATTTGGTAAACAACTTAATTCGGTGTA
** *
16539 AACAACT
56 ATTAA-G
16546 TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
1 TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
* *
16607 TAATTCAGTGTAATTAAGTAAATTGGTAATCTGGTAAACAACTTAATTCGGTGTAATTAAG
1 TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
16668 CAAAATAGTA
Statistics
Matches: 249, Mismatches: 38, Indels: 40
0.76 0.12 0.12
Matches are distributed among these distances:
56 43 0.17
59 18 0.07
60 6 0.02
61 122 0.49
62 22 0.09
63 1 0.00
64 7 0.03
67 10 0.04
68 4 0.02
69 5 0.02
70 11 0.04
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.36
Consensus pattern (61 bp):
TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
Found at i:16427 original size:160 final size:160
Alignment explanation
Indices: 16168--16523 Score: 546
Period size: 160 Copynumber: 2.3 Consensus size: 160
16158 TTTAAGAAAA
* * * *
16168 TGGTAATCTGGTAAACAACTTAATTCAGTTTAATTAAGTAAATT-GGTG--ATT-A--AA-TTAA
1 TGGTAATCTGGCAAACAACTTAATTCGGTGTAATTAAGT-AATTCGGTGTAATTAAGTAACTT-G
*
16226 GTAATTTAGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTGATTAAATTAGGTAATTTGG
64 GTAATTTAGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTGATTAAATTAAGTAATTTGG
16291 TAAACAACTTAATTCGGTGTAATCAAGTAAAT
129 TAAACAACTTAATTCGGTGTAATCAAGTAAAT
* *
16323 TGGTAATTTGGCAAACAACTTAGTTCGGTGTAATTAAGTAATTCGGTGTAATTAAGTAACTTGGT
1 TGGTAATCTGGCAAACAACTTAATTCGGTGTAATTAAGTAATTCGGTGTAATTAAGTAACTTGGT
* *
16388 AATTTGGTAAGCAACTTAATTCGGTGTAATTAAGTAAATTGGTGATTAAATTAAGTAATTTGGTA
66 AATTTAGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTGATTAAATTAAGTAATTTGGTA
*
16453 AACAACTTAATTCGGTGTAATTAAGTAAAT
131 AACAACTTAATTCGGTGTAATCAAGTAAAT
*
16483 TGGTAATCTGGTAAACAACTTAATTCGGTGTAATTAAGTAA
1 TGGTAATCTGGCAAACAACTTAATTCGGTGTAATTAAGTAA
16524 ATTGGTAATT
Statistics
Matches: 181, Mismatches: 13, Indels: 9
0.89 0.06 0.04
Matches are distributed among these distances:
154 4 0.02
155 38 0.21
157 3 0.02
158 1 0.01
160 133 0.73
161 2 0.01
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.37
Consensus pattern (160 bp):
TGGTAATCTGGCAAACAACTTAATTCGGTGTAATTAAGTAATTCGGTGTAATTAAGTAACTTGGT
AATTTAGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTGATTAAATTAAGTAATTTGGTA
AACAACTTAATTCGGTGTAATCAAGTAAAT
Found at i:16495 original size:43 final size:43
Alignment explanation
Indices: 16442--16609 Score: 327
Period size: 43 Copynumber: 3.9 Consensus size: 43
16432 ATTAAATTAA
16442 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
1 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
*
16485 GTAATCTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
1 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
16528 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
1 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
16571 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAA
1 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAA
16610 TTCAGTGTAA
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 123 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (43 bp):
GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
Found at i:16612 original size:18 final size:18
Alignment explanation
Indices: 16589--16627 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
16579 GTAAACAACT
*
16589 TAATTCGGTGTAATTAAG
1 TAATTCAGTGTAATTAAG
16607 TAATTCAGTGTAATTAAG
1 TAATTCAGTGTAATTAAG
16625 TAA
1 TAA
16628 ATTGGTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.38
Consensus pattern (18 bp):
TAATTCAGTGTAATTAAG
Found at i:16683 original size:104 final size:104
Alignment explanation
Indices: 16503--16710 Score: 362
Period size: 104 Copynumber: 2.0 Consensus size: 104
16493 GTAAACAACT
* * *
16503 TAATTCGGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAA
1 TAATTCAGTGTAATTAAGTAAATTGGTAATCTGGTAAACAACTTAATTCGGTGTAATTAAGCAAA
* *
16568 TTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
66 ATAGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
16607 TAATTCAGTGTAATTAAGTAAATTGGTAATCTGGTAAACAACTTAATTCGGTGTAATTAAGCAAA
1 TAATTCAGTGTAATTAAGTAAATTGGTAATCTGGTAAACAACTTAATTCGGTGTAATTAAGCAAA
*
16672 ATAGTAATTTGGTAAACAACTTAATTCGGTTTAATTAAG
66 ATAGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
16711 AAAATTGGTA
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
104 98 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.37
Consensus pattern (104 bp):
TAATTCAGTGTAATTAAGTAAATTGGTAATCTGGTAAACAACTTAATTCGGTGTAATTAAGCAAA
ATAGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
Found at i:16723 original size:43 final size:43
Alignment explanation
Indices: 16607--16723 Score: 173
Period size: 43 Copynumber: 2.7 Consensus size: 43
16597 TGTAATTAAG
* * *
16607 TAATTCAGTGTAATTAAGTAAATTGGTAATCTGGTAAACAACT
1 TAATTCGGTGTAATTAAGAAAATTGGTAATTTGGTAAACAACT
*
16650 TAATTCGGTGTAATTAAGCAAAA-TAGTAATTTGGTAAACAACT
1 TAATTCGGTGTAATTAAG-AAAATTGGTAATTTGGTAAACAACT
*
16693 TAATTCGGTTTAATTAAGAAAATTGGTAATT
1 TAATTCGGTGTAATTAAGAAAATTGGTAATT
16724 AAGCTAAGTA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
42 4 0.06
43 59 0.89
44 3 0.05
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (43 bp):
TAATTCGGTGTAATTAAGAAAATTGGTAATTTGGTAAACAACT
Found at i:16731 original size:21 final size:21
Alignment explanation
Indices: 16707--16746 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16697 TCGGTTTAAT
16707 TAAGAAAATTGGTAATTAAGC
1 TAAGAAAATTGGTAATTAAGC
* *
16728 TAAGTAATTTGGTAATTAA
1 TAAGAAAATTGGTAATTAA
16747 ATTAGGTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.17, T:0.35
Consensus pattern (21 bp):
TAAGAAAATTGGTAATTAAGC
Found at i:16755 original size:21 final size:21
Alignment explanation
Indices: 16715--16757 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
16705 ATTAAGAAAA
*
16715 TTGGTAATTAAGCTAAGTAAT
1 TTGGTAATTAAACTAAGTAAT
* *
16736 TTGGTAATTAAATTAGGTAAT
1 TTGGTAATTAAACTAAGTAAT
16757 T
1 T
16758 AACTTAATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (21 bp):
TTGGTAATTAAACTAAGTAAT
Found at i:16776 original size:19 final size:19
Alignment explanation
Indices: 16752--16810 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
16742 ATTAAATTAG
16752 GTAATTAACTTAATTCGGT
1 GTAATTAACTTAATTCGGT
* *
16771 GTAATTAA-GTAAATC-G-
1 GTAATTAACTTAATTCGGT
*
16787 GTAATCAACTTAATTCGGT
1 GTAATTAACTTAATTCGGT
16806 GTAAT
1 GTAAT
16811 CAAGTAAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 7 0.22
17 6 0.19
18 6 0.19
19 13 0.41
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (19 bp):
GTAATTAACTTAATTCGGT
Found at i:16818 original size:35 final size:35
Alignment explanation
Indices: 16751--16854 Score: 136
Period size: 35 Copynumber: 3.0 Consensus size: 35
16741 AATTAAATTA
*
16751 GGTAATTAACTTAATTCGGTGTAATTAAGTAAATC
1 GGTAATCAACTTAATTCGGTGTAATTAAGTAAATC
*
16786 GGTAATCAACTTAATTCGGTGTAATCAAGTAAATC
1 GGTAATCAACTTAATTCGGTGTAATTAAGTAAATC
* * *** *
16821 AGTAGTGGGCTTAATTCGGTATAATTAAGTAAAT
1 GGTAATCAACTTAATTCGGTGTAATTAAGTAAAT
16855 AAAGGGCTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 60 1.00
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.35
Consensus pattern (35 bp):
GGTAATCAACTTAATTCGGTGTAATTAAGTAAATC
Found at i:16865 original size:31 final size:34
Alignment explanation
Indices: 16795--16865 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 34
16785 CGGTAATCAA
* *
16795 CTTAATTCGGTGTAATCAAGTAAATCAGTAGTGGG
1 CTTAATTCGGTATAATCAAGTAAATCAG-AGAGGG
*
16830 CTTAATTCGGTATAATTAAGTAAAT-A-A-AGGG
1 CTTAATTCGGTATAATCAAGTAAATCAGAGAGGG
16861 CTTAA
1 CTTAA
16866 CCTAGTAGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 8 0.24
32 1 0.03
34 1 0.03
35 23 0.70
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (34 bp):
CTTAATTCGGTATAATCAAGTAAATCAGAGAGGG
Found at i:30310 original size:55 final size:55
Alignment explanation
Indices: 30226--30337 Score: 199
Period size: 55 Copynumber: 2.0 Consensus size: 55
30216 TCTTTCTTGG
*
30226 GAGCATCAGGAAATTTGAAAATTCCCCGATCAATCTTCTC-TGACACTATATTTTT
1 GAGCATCAGGAAATTTGAAAATTCCCCGATCAAGCTTCTCTTG-CACTATATTTTT
30281 GAGCATCAGGAAATTTGAAAATTCCCCGATCAAGCTTCTCTTGCACTATATTTTT
1 GAGCATCAGGAAATTTGAAAATTCCCCGATCAAGCTTCTCTTGCACTATATTTTT
30336 GA
1 GA
30338 ATACAGTACA
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
55 53 0.96
56 2 0.04
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.34
Consensus pattern (55 bp):
GAGCATCAGGAAATTTGAAAATTCCCCGATCAAGCTTCTCTTGCACTATATTTTT
Found at i:40516 original size:2 final size:2
Alignment explanation
Indices: 40509--40536 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40499 GAACCGGTAA
40509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40537 CTAACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42014 original size:17 final size:16
Alignment explanation
Indices: 41984--42062 Score: 65
Period size: 17 Copynumber: 4.9 Consensus size: 16
41974 TGTTCCCAAA
*
41984 TTTTTCTTTATTTTCC
1 TTTTTCTTTTTTTTCC
*
42000 TTATTTCTTTTTTTTTTC
1 TT-TTTC-TTTTTTTTCC
*
42018 TTTTTCTTTTCTTT-C
1 TTTTTCTTTTTTTTCC
42033 -TTTTCTTTCTTTCTTCC
1 TTTTTCTTT-TTT-TTCC
*
42050 -TTATCTTTTTTTT
1 TTTTTCTTTTTTTT
42063 TTATAATACT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
14 8 0.15
15 5 0.09
16 14 0.26
17 16 0.30
18 10 0.19
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCTTTTTTTTCC
Found at i:42021 original size:9 final size:9
Alignment explanation
Indices: 41984--42044 Score: 54
Period size: 9 Copynumber: 7.0 Consensus size: 9
41974 TGTTCCCAAA
41984 TTTTTCTTT
1 TTTTTCTTT
* *
41993 ATTTTC-CT
1 TTTTTCTTT
*
42001 TATTTCTTT
1 TTTTTCTTT
*
42010 TTTTT-TTC
1 TTTTTCTTT
42018 TTTTTCTTT
1 TTTTTCTTT
*
42027 TCTTTCTTT
1 TTTTTCTTT
*
42036 TCTTTCTTT
1 TTTTTCTTT
42045 CTTCCTTATC
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
8 12 0.29
9 29 0.71
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:42176 original size:37 final size:34
Alignment explanation
Indices: 42089--42190 Score: 109
Period size: 35 Copynumber: 2.9 Consensus size: 34
42079 AGCCCATTGG
*
42089 CTGGCCTGCCTAGCAGGCCGCCCAGGCCAAGCCCA
1 CTGGCCTGCCTAGCAGGCCGCGCAGGCC-AGCCCA
42124 CTGG-CTAGCCTAGCAGGCCGCGCAGGCCAGCCAGGCA
1 CTGGCCT-GCCTAGCAGGCCGCGCAGGCCAGCC---CA
* *
42161 CTGGCCTG-CTAAGCAGGCCACGCGGGCCAG
1 CTGGCCTGCCT-AGCAGGCCGCGCAGGCCAG
42191 TCCAAACATT
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
34 6 0.10
35 24 0.41
36 2 0.03
37 24 0.41
38 2 0.03
ACGTcount: A:0.18, C:0.40, G:0.33, T:0.09
Consensus pattern (34 bp):
CTGGCCTGCCTAGCAGGCCGCGCAGGCCAGCCCA
Found at i:48355 original size:30 final size:30
Alignment explanation
Indices: 48319--48398 Score: 124
Period size: 30 Copynumber: 2.7 Consensus size: 30
48309 CAAAGGATCA
48319 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGGCATCTTTGGTGCGATTCCTCCATCC
48349 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGGCATCTTTGGTGCGATTCCTCCATCC
* ***
48379 ATTGATGTCTTTGGTGCGAT
1 AATGGCATCTTTGGTGCGAT
48399 CCCATCTCCT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (30 bp):
AATGGCATCTTTGGTGCGATTCCTCCATCC
Found at i:53158 original size:24 final size:23
Alignment explanation
Indices: 53131--53185 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
53121 AAGAAAGGAG
53131 AAGATTAAACGAAATAAAAAATAA
1 AAGATTAAAC-AAATAAAAAATAA
* *
53155 AAGA-TAGAACAAATTAAAAATAG
1 AAGATTA-AACAAATAAAAAATAA
53178 AA-ATTAAA
1 AAGATTAAA
53186 GTGTTCCCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 3 0.11
23 17 0.63
24 7 0.26
ACGTcount: A:0.69, C:0.04, G:0.09, T:0.18
Consensus pattern (23 bp):
AAGATTAAACAAATAAAAAATAA
Found at i:56440 original size:14 final size:14
Alignment explanation
Indices: 56421--56447 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
56411 CATTTTACTT
56421 TTTCTTTTCTTTTC
1 TTTCTTTTCTTTTC
56435 TTTCTTTTCTTTT
1 TTTCTTTTCTTTT
56448 TGGGCTCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTCTTTTCTTTTC
Found at i:62938 original size:21 final size:21
Alignment explanation
Indices: 62885--62944 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
62875 TTTGGAGCAA
*
62885 GAATATTCCAATCGATTCTAT
1 GAATATTCCAATCGATTCTAG
** * *
62906 GTCTACTACAATCGATTCTAG
1 GAATATTCCAATCGATTCTAG
62927 GAATATTCCAATCGATTC
1 GAATATTCCAATCGATTC
62945 CAAGATATGC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (21 bp):
GAATATTCCAATCGATTCTAG
Found at i:69404 original size:21 final size:21
Alignment explanation
Indices: 69351--69410 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
69341 TTTGGAGCAA
*
69351 GAATATTCCAATCGATTCTAT
1 GAATATTCCAATCGATTCTAG
** * *
69372 GTCTACTACAATCGATTCTAG
1 GAATATTCCAATCGATTCTAG
69393 GAATATTCCAATCGATTC
1 GAATATTCCAATCGATTC
69411 AAAGATATGC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (21 bp):
GAATATTCCAATCGATTCTAG
Found at i:71420 original size:2 final size:2
Alignment explanation
Indices: 71413--71446 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
71403 TTCCTCACAA
71413 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
71447 ATACCTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:76709 original size:11 final size:11
Alignment explanation
Indices: 76690--76724 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
76680 TTGACAGCGC
76690 AACAAAAACAA
1 AACAAAAACAA
* *
76701 AATAAAAACGA
1 AACAAAAACAA
76712 AACAAAAACAA
1 AACAAAAACAA
76723 AA
1 AA
76725 ATCAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.80, C:0.14, G:0.03, T:0.03
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:78350 original size:73 final size:70
Alignment explanation
Indices: 78273--78414 Score: 151
Period size: 73 Copynumber: 2.0 Consensus size: 70
78263 CCAAAAATCA
*
78273 AAATT-CAAAAATCAAGAATCAAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCTCATCAAGTCTC
1 AAATTGCAAAAATC--GAATCAAGTTTTCAAAGTTTTC-AATTGGGAAAGTTC-CACCAAGTCTC
78337 CAAAGTTTT
62 CAAAGTTTT
* ** ** * * *
78346 AAATTGGGAAAGTTCTCATTAAGTTTTCAAAGTTTTCAATTGGGAAAGTTCCACCAAGTTTTCAA
1 AAATT-GCAAAAATCGAATCAAGTTTTCAAAGTTTTCAATTGGGAAAGTTCCACCAAGTCTCCAA
78411 AGTT
65 AGTT
78415 ATCAAGTAGG
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
71 15 0.26
72 14 0.24
73 24 0.41
75 5 0.09
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.35
Consensus pattern (70 bp):
AAATTGCAAAAATCGAATCAAGTTTTCAAAGTTTTCAATTGGGAAAGTTCCACCAAGTCTCCAAA
GTTTT
Found at i:78357 original size:36 final size:36
Alignment explanation
Indices: 78290--78432 Score: 189
Period size: 36 Copynumber: 3.9 Consensus size: 36
78280 AAAATCAAGA
78290 ATCAAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCTC
1 ATCAAGTTTTCAAAGTTTT-AAATTGGGAAAGTTCTC
* *
78327 ATCAAGTCTCCAAAGTTTTAAATTGGGAAAGTTCTC
1 ATCAAGTTTTCAAAGTTTTAAATTGGGAAAGTTCTC
* *
78363 ATTAAGTTTTCAAAGTTTTCAATTGGGAAAGTTC-C
1 ATCAAGTTTTCAAAGTTTTAAATTGGGAAAGTTCTC
* * * *
78398 ACCAAGTTTTCAAAGTTATCAAGTAGGGAAAGTTC
1 ATCAAGTTTTCAAAGTT-TTAAATTGGGAAAGTTC
78433 CCATTAGGTT
Statistics
Matches: 93, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
35 16 0.17
36 60 0.65
37 17 0.18
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (36 bp):
ATCAAGTTTTCAAAGTTTTAAATTGGGAAAGTTCTC
Found at i:79939 original size:2 final size:2
Alignment explanation
Indices: 79932--79961 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
79922 AAAGCATGTC
79932 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
79962 TTGAGAATTA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84075 original size:21 final size:21
Alignment explanation
Indices: 84041--84081 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
84031 CCCCTTTTCT
84041 ATATAAAATAAATTATCAAATA
1 ATATAAAATAAATTAT-AAATA
*
84063 ATAT-AAATTAATTATAAAT
1 ATATAAAATAAATTATAAAT
84082 TTGTTATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATAAAATAAATTATAAATA
Found at i:86061 original size:30 final size:30
Alignment explanation
Indices: 86025--86081 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
86015 AAGCAAACTC
*
86025 ATGGGACCTACATATCCATGTCAGATGCTA
1 ATGGGACCCACATATCCATGTCAGATGCTA
*
86055 ATGGGACCCACATGTCCATGTCAGATG
1 ATGGGACCCACATATCCATGTCAGATG
86082 TGTGTTAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGGACCCACATATCCATGTCAGATGCTA
Found at i:91881 original size:17 final size:18
Alignment explanation
Indices: 91859--91898 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
91849 ATACATATAC
91859 ATATTAATAT-TTGTATT
1 ATATTAATATATTGTATT
91876 ATATT-ATATATTGTATT
1 ATATTAATATATTGTATT
*
91893 AGATTA
1 ATATTA
91899 GGAACTCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
ATATTAATATATTGTATT
Found at i:92897 original size:27 final size:28
Alignment explanation
Indices: 92857--92914 Score: 109
Period size: 27 Copynumber: 2.1 Consensus size: 28
92847 TGATTTATAA
92857 TTAATTTTTTACTAGATAAATGTAACAC
1 TTAATTTTTTACTAGATAAATGTAACAC
92885 TTAA-TTTTTACTAGATAAATGTAACAC
1 TTAATTTTTTACTAGATAAATGTAACAC
92912 TTA
1 TTA
92915 CTGTGGGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 26 0.87
28 4 0.13
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (28 bp):
TTAATTTTTTACTAGATAAATGTAACAC
Found at i:96496 original size:161 final size:162
Alignment explanation
Indices: 96070--96513 Score: 495
Period size: 166 Copynumber: 2.7 Consensus size: 162
96060 GGATTAATGA
* * *
96070 GGAGCGAGAGAACTAATTTTTTTCGTTTTTTCCCACTTGACCA-ATTACTTAAATGCCCTAACTT
1 GGAGCTAGAGAACTAATTTTTTTCG-TTTTTCCTACTTGA--AGATTACTTAAATGTCCTAACTT
* * * *
96134 TTGATTCTTGAGGTGATTAAATAACTAGACTTATTGGTCATTTCTCAATTGACTTTAATAGAGTA
63 TTGATTCTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTA
* * * **
96199 ATGGAATTACTAAAAGATCCCTACCAAGGTTTGCTTTT
128 ATGGAATTAATAAAAGA---CTACCAAGGATTGATAAT
* * * * * *
96237 GGAGTTAGAGAACT-TTTTTTTTCGTCTTTTCTTATTTGGCAGATTACTTAAATGTCCTAAGTTT
1 GGAGCTAGAGAACTAATTTTTTTCGT-TTTTCCTACTT-GAAGATTACTTAAATGTCCTAACTTT
* * * *
96301 TGATTATTGAGGGGATTAAATAAGTAATCTTTTTGGTCATTTCTTAA-TGTACTTGAATAGAGTA
64 TGATTCTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATTG-ACTTGAATAGAGTA
* *
96365 GTGGAATTAATAAAAGA-T-CCAATGATTGATAAT
128 ATGGAATTAATAAAAGACTACCAAGGATTGATAAT
* *
96398 -GAGCTAGAGAACTAATCTTTTTCGTTTTTACCTACTTAGAAGATCACTTAAATGTCCTAACTTT
1 GGAGCTAGAGAACTAATTTTTTTCGTTTTT-CCTACTT-GAAGATTACTTAAATGTCCTAACTTT
* *
96462 TGATTCTTAAGGGGATTAAATAACTAAACTTTTTGATCATTTCTCAATTGAC
64 TGATTCTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATTGAC
96514 AAATGACTCA
Statistics
Matches: 231, Mismatches: 39, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
160 16 0.07
161 90 0.39
162 3 0.01
165 4 0.02
166 105 0.45
167 13 0.06
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (162 bp):
GGAGCTAGAGAACTAATTTTTTTCGTTTTTCCTACTTGAAGATTACTTAAATGTCCTAACTTTTG
ATTCTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTAATG
GAATTAATAAAAGACTACCAAGGATTGATAAT
Found at i:104769 original size:1 final size:1
Alignment explanation
Indices: 104763--104790 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
104753 TCCTGGCGGG
104763 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
104791 GTATTTGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:105093 original size:31 final size:31
Alignment explanation
Indices: 105017--105096 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 31
105007 TCTTTTACTC
**
105017 ATGTATAAGTATTTGATGCTTTTTTTTTTGGTT
1 ATGTATAAGTATTTGATG--TTTTTTTGAGGTT
*
105050 A---A-AAATATTTGATGTTTTTTTGAGGTT
1 ATGTATAAGTATTTGATGTTTTTTTGAGGTT
105077 ATGTATAAGTATTTGATGTT
1 ATGTATAAGTATTTGATGTT
105097 ATTAGTTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
27 12 0.31
29 11 0.28
30 2 0.05
31 13 0.33
33 1 0.03
ACGTcount: A:0.25, C:0.01, G:0.19, T:0.55
Consensus pattern (31 bp):
ATGTATAAGTATTTGATGTTTTTTTGAGGTT
Found at i:110846 original size:118 final size:118
Alignment explanation
Indices: 110638--110875 Score: 476
Period size: 118 Copynumber: 2.0 Consensus size: 118
110628 GAAGCATGTC
110638 AAATTAGTTATGGAAAAATAAGGACATCTTCTCTAAGTGGATAAGTTTCTCCACAATGTGCTAGC
1 AAATTAGTTATGGAAAAATAAGGACATCTTCTCTAAGTGGATAAGTTTCTCCACAATGTGCTAGC
110703 AATCTATAAACAATTTTTAATTTTTACTAACTTAACCCATATACGAAAATGAA
66 AATCTATAAACAATTTTTAATTTTTACTAACTTAACCCATATACGAAAATGAA
110756 AAATTAGTTATGGAAAAATAAGGACATCTTCTCTAAGTGGATAAGTTTCTCCACAATGTGCTAGC
1 AAATTAGTTATGGAAAAATAAGGACATCTTCTCTAAGTGGATAAGTTTCTCCACAATGTGCTAGC
110821 AATCTATAAACAATTTTTAATTTTTACTAACTTAACCCATATACGAAAATGAA
66 AATCTATAAACAATTTTTAATTTTTACTAACTTAACCCATATACGAAAATGAA
110874 AA
1 AA
110876 TATATGTACA
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 120 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (118 bp):
AAATTAGTTATGGAAAAATAAGGACATCTTCTCTAAGTGGATAAGTTTCTCCACAATGTGCTAGC
AATCTATAAACAATTTTTAATTTTTACTAACTTAACCCATATACGAAAATGAA
Found at i:122674 original size:5 final size:5
Alignment explanation
Indices: 122664--122706 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
122654 TCAATATGTT
122664 CATCG CATCG CATCG CATCG CATCG CATCG CATCG CATCG CAT
1 CATCG CATCG CATCG CATCG CATCG CATCG CATCG CATCG CAT
122707 GCTAGTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (5 bp):
CATCG
Found at i:124859 original size:3 final size:3
Alignment explanation
Indices: 124851--124877 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
124841 GAGAGAAACC
124851 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
124878 GGGAAGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:125247 original size:3 final size:3
Alignment explanation
Indices: 125241--125270 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
125231 GGTTTTTTTT
125241 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
125271 CAAAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:125543 original size:30 final size:30
Alignment explanation
Indices: 125502--125566 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
125492 ATCTTGAGTT
*
125502 TTATGTTAATTACTATTCATAATCATGATG
1 TTATATTAATTACTATTCATAATCATGATG
*
125532 TTATATTAATTACTTTTCATAATCATGATG
1 TTATATTAATTACTATTCATAATCATGATG
125562 TTATA
1 TTATA
125567 GTATTAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.49
Consensus pattern (30 bp):
TTATATTAATTACTATTCATAATCATGATG
Found at i:141247 original size:24 final size:24
Alignment explanation
Indices: 141200--141247 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
141190 TCCTAAAAAG
* *
141200 AAATTGATGATTTTTTTTGGCCAA
1 AAATTGATGATTTATTTTAGCCAA
*
141224 AAATTGATGATTTATTTTATCCAA
1 AAATTGATGATTTATTTTAGCCAA
141248 TGAAACTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.46
Consensus pattern (24 bp):
AAATTGATGATTTATTTTAGCCAA
Found at i:160875 original size:9 final size:9
Alignment explanation
Indices: 160861--160887 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
160851 TGGAGCAGCA
160861 GCAAAAGAG
1 GCAAAAGAG
160870 GCAAAAGAG
1 GCAAAAGAG
160879 GCAAAAGAG
1 GCAAAAGAG
160888 AAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.33, T:0.00
Consensus pattern (9 bp):
GCAAAAGAG
Done.