Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002254.1 Hibiscus syriacus cultivar Beakdansim tig00004584_pilon, 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: 151455
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1628 original size:258 final size:260
Alignment explanation
Indices: 1183--1709 Score: 775
Period size: 258 Copynumber: 2.0 Consensus size: 260
1173 AATATATATC
1183 TATCTTTA-TTTATTTTTCTGTTCTCATTCTTAAACATTTTTATTAAATTGAGTCAACTGACAAA
1 TATCTTTATTTTATTTTTCTGTTCTCATTCTTAAACATTTTTATTAAATTGAGTCAACTGAC-AA
* ** *
1247 AAAATTAACAAAACTATTAAATTGATGTTAACTATTTTATATTGTTATCAATGTTTATGTCAGCT
65 AAAATTAACAAAACTATTAAACTGATGTTAACTATTTTATATTACTATAAATGTTTATGTCAGCT
1312 GTAACATGCCAAAATTCGGGTTAATAGTTTCAGGTTTATCGAGAGGGTAAGTGTATCCCGCAAAA
130 GTAACATGCCAAAATTCGGGTTAATAGTTTCAGGTTTATCGAGAGGGTAAGTGTATCCCGCAAAA
* *
1377 ATTCTAATTTAAGT-GTTGGGCTTAATTGGGTTTGAAATCGGGCCCAATTAGCAATAAAAATGAG
195 ATTCTAATTTAAGTCGTTGGGCTTAATTAGATTTGAAATCGGGCCCAATTAGCAAT-AAAATGAG
1441 AT
259 AT
* *
1443 TATCTTTATTTTATTTTTTCTGTTTTCATTCTTAAACA-TTTTATTAAATTGAGTCAATTGAC-A
1 TATCTTTATTTTA-TTTTTCTGTTCTCATTCTTAAACATTTTTATTAAATTGAGTCAACTGACAA
* * **
1506 AAAA-TAACAAAATTATTAAACTGATGTTAACTATTTT-TATTACTATAAATGTTTTTGTCATTT
65 AAAATTAACAAAACTATTAAACTGATGTTAACTATTTTATATTACTATAAATGTTTATGTCAGCT
* * * *
1569 GTAACATGTC-AAATTTGAGGTTAGTAGTTTC-GAGTTTATCCGAGAGGGTAAGTGTATCCCGCG
130 GTAACATGCCAAAATTCG-GGTTAATAGTTTCAG-GTTTAT-CGAGAGGGTAAGTGTATCCCGCA
*
1632 AAAATTCTAATTTAAGTCGTTGGGCTTAATTAGATTTGGAATCGGGCCCAATTAGCAATAAAATG
192 AAAATTCTAATTTAAGTCGTTGGGCTTAATTAGATTTGAAATCGGGCCCAATTAGCAATAAAATG
1697 AGAT
257 AGAT
*
1701 T-TTTTTATT
1 TATCTTTATT
1710 GTAGAAAAAC
Statistics
Matches: 243, Mismatches: 18, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
256 7 0.03
257 54 0.22
258 81 0.33
259 43 0.18
260 8 0.03
261 27 0.11
262 23 0.09
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (260 bp):
TATCTTTATTTTATTTTTCTGTTCTCATTCTTAAACATTTTTATTAAATTGAGTCAACTGACAAA
AAATTAACAAAACTATTAAACTGATGTTAACTATTTTATATTACTATAAATGTTTATGTCAGCTG
TAACATGCCAAAATTCGGGTTAATAGTTTCAGGTTTATCGAGAGGGTAAGTGTATCCCGCAAAAA
TTCTAATTTAAGTCGTTGGGCTTAATTAGATTTGAAATCGGGCCCAATTAGCAATAAAATGAGAT
Found at i:3740 original size:21 final size:22
Alignment explanation
Indices: 3692--3743 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
3682 GCATGTGAAA
*
3692 ATGT-CCGAAGGACCTGCGAGT
1 ATGTCCCGAAGGACCTACGAGT
*
3713 ATGTCCCGAAGGA-CTATGAGT
1 ATGTCCCGAAGGACCTACGAGT
3734 ATGTCCCGAA
1 ATGTCCCGAA
3744 AGAATGCGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (22 bp):
ATGTCCCGAAGGACCTACGAGT
Found at i:7644 original size:18 final size:18
Alignment explanation
Indices: 7617--7653 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7607 AAAAAAATAT
*
7617 TATTTCAAAATAATAAAA
1 TATTTAAAAATAATAAAA
*
7635 TATTTAAAAATTATAAAA
1 TATTTAAAAATAATAAAA
7653 T
1 T
7654 TTAAAAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TATTTAAAAATAATAAAA
Found at i:8336 original size:16 final size:16
Alignment explanation
Indices: 8315--8346 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
8305 AGCATCCTCG
8315 TTTATTTTATAACTGT
1 TTTATTTTATAACTGT
8331 TTTATTTTATAACTGT
1 TTTATTTTATAACTGT
8347 GGGTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTATTTTATAACTGT
Found at i:16256 original size:31 final size:31
Alignment explanation
Indices: 16221--16298 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
16211 TTCAATATCC
* *
16221 AAGTGACCAAAACTTAATAAAA-ATATATCGT
1 AAGTGACCAAAACTTAAGAAAACA-ATAACGT
16252 AAGTGACCAAAACTTAAGAAAACAATAACGT
1 AAGTGACCAAAACTTAAGAAAACAATAACGT
*
16283 AAGTGACTAAAACTTA
1 AAGTGACCAAAACTTA
16299 TGTTTTTTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 42 0.98
32 1 0.02
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.22
Consensus pattern (31 bp):
AAGTGACCAAAACTTAAGAAAACAATAACGT
Found at i:24568 original size:21 final size:21
Alignment explanation
Indices: 24539--24612 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
24529 ATTCTGATTA
*
24539 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCTAAT
* *
24560 TCGCGTTGCGATTTTTCTAAT
1 TCGCATTGCGATTTTCCTAAT
*
24581 TCGCAATGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* *
24602 TCACAATGCGA
1 TCGCATTGCGA
24613 ATACGTAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:24627 original size:20 final size:20
Alignment explanation
Indices: 24602--24674 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
24592 TTTTCCTAAT
24602 TCACAATGCGAATACGTAAA
1 TCACAATGCGAATACGTAAA
24622 TCACAATGCGAATACGTAAA
1 TCACAATGCGAATACGTAAA
*
24642 TCGCAATGCGAATACGTAAA
1 TCACAATGCGAATACGTAAA
* *
24662 TCGCAACGCGAAT
1 TCACAATGCGAAT
24675 CTGACTATCG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (20 bp):
TCACAATGCGAATACGTAAA
Found at i:24896 original size:22 final size:22
Alignment explanation
Indices: 24871--24936 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
24861 GGCGACATCT
24871 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
24893 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
24915 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
24937 TTCACGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:25349 original size:20 final size:20
Alignment explanation
Indices: 25273--25342 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
25263 CGATTCTTTC
*
25273 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
** *
25292 GTTGCGATACTCATTTTCTT
1 GTTGCGATTTTCATTTTCGT
25312 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
25332 GTTGCGATTTT
1 GTTGCGATTTT
25343 AAGTTTCAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 11 0.26
20 32 0.74
ACGTcount: A:0.11, C:0.17, G:0.20, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:27237 original size:20 final size:20
Alignment explanation
Indices: 27212--27348 Score: 77
Period size: 20 Copynumber: 7.5 Consensus size: 20
27202 ATAATAGTTT
27212 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* * *
27232 ACTATCGTAACGGGAAAATG
1 ACTATCGCAATGCGAAAATG
*
27252 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
* *
27268 A--ATCGTAATGTG-AAATG
1 ACTATCGCAATGCGAAAATG
**
27285 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
27301 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
27319 ACTATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATG
27339 ACTATCGCAA
1 ACTATCGCAA
27349 CGAAAGAATC
Statistics
Matches: 90, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
14 13 0.14
16 9 0.10
17 7 0.08
18 4 0.04
19 6 0.07
20 51 0.57
ACGTcount: A:0.44, C:0.20, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:27370 original size:87 final size:87
Alignment explanation
Indices: 27215--27380 Score: 260
Period size: 87 Copynumber: 1.9 Consensus size: 87
27205 ATAGTTTACT
* * ** * * *
27215 ATCGCAATGCGAAAATGACTATCGTAACGGGAAAATGACTATCGCAACGAGAGAATCGTAATGTG
1 ATCGCAACGCGAAAATGACTATCGCAACGCAAAAATGACTATCGCAACGAAAGAATCGCAATGAG
27280 AAATGAAAATCGCAACAACAAA
66 AAATGAAAATCGCAACAACAAA
*
27302 ATCGCAACGCGAAAATGACTATCGCAATGCAAAAATGACTATCGCAACGAAAGAATCGCAATGAG
1 ATCGCAACGCGAAAATGACTATCGCAACGCAAAAATGACTATCGCAACGAAAGAATCGCAATGAG
27367 AAATGAAAATCGCA
66 AAATGAAAATCGCA
27381 TTGCGATTCT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (87 bp):
ATCGCAACGCGAAAATGACTATCGCAACGCAAAAATGACTATCGCAACGAAAGAATCGCAATGAG
AAATGAAAATCGCAACAACAAA
Found at i:27420 original size:20 final size:20
Alignment explanation
Indices: 27393--27461 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
27383 GCGATTCTCT
**
27393 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
27413 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
27433 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
27453 CGTTGCGAT
1 CGTTGCGAT
27462 TTTAAGTTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:27471 original size:20 final size:20
Alignment explanation
Indices: 27393--27471 Score: 70
Period size: 20 Copynumber: 4.0 Consensus size: 20
27383 GCGATTCTCT
*
27393 CGTTGCGATAGTCAA-ATTCG
1 CGTTGCGATAGT-AAGTTTCG
* * *
27413 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
* *
27433 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
**
27453 CGTTGCGATTTTAAGTTTC
1 CGTTGCGATAGTAAGTTTC
27472 AGATTCTATT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
19 1 0.02
20 49 0.98
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTAAGTTTCG
Found at i:28036 original size:21 final size:21
Alignment explanation
Indices: 27945--28036 Score: 62
Period size: 21 Copynumber: 4.4 Consensus size: 21
27935 GACTCACCTG
27945 TCATCGTTCAAGAGGCCTCAC-C
1 TCATCGTTCAAGAGG-C-CACTC
* * *
27967 T-ATCGTTCAATAGGCCCCTA
1 TCATCGTTCAAGAGGCCACTC
** * *
27987 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCACTC
* * *
28008 CCACCGTTCAAGAGGCCACTT
1 TCATCGTTCAAGAGGCCACTC
28029 TCATCGTT
1 TCATCGTT
28037 GAAGGGGTCA
Statistics
Matches: 51, Mismatches: 17, Indels: 5
0.70 0.23 0.07
Matches are distributed among these distances:
19 2 0.04
20 2 0.04
21 46 0.90
22 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCACTC
Found at i:29450 original size:14 final size:14
Alignment explanation
Indices: 29431--29466 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
29421 ATTGTTTAAT
29431 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
29445 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
29459 TGATTTGT
1 TGATTTGT
29467 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:29665 original size:33 final size:33
Alignment explanation
Indices: 29608--29703 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
29598 ACGAATTTCG
*
29608 CGTTGCGAATTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
29642 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
* ** *
29675 CATTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
29704 AGTCAATTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 32 0.58
34 23 0.42
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.41
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:29763 original size:20 final size:20
Alignment explanation
Indices: 29677--29749 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
29667 GATTCTCTCA
29677 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
*
29697 TTGCGATAGTCAATTCCGCG
1 TTGCGATAGTCATTTCCGCG
* *
29717 TTGCGATAGTCATTTCTGTG
1 TTGCGATAGTCATTTCCGCG
29737 TTGCGATAGTCAT
1 TTGCGATAGTCAT
29750 ATTCGTGTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCG
Found at i:29779 original size:14 final size:14
Alignment explanation
Indices: 29760--29791 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
29750 ATTCGTGTTA
29760 CGATTTCCGCGTTG
1 CGATTTCCGCGTTG
29774 CGATTTCCGCGTTG
1 CGATTTCCGCGTTG
29788 CGAT
1 CGAT
29792 AGTCAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.28, G:0.28, T:0.34
Consensus pattern (14 bp):
CGATTTCCGCGTTG
Found at i:31566 original size:17 final size:17
Alignment explanation
Indices: 31544--31585 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
31534 GAACCGAGCA
31544 TTCATGTCAGTCATAAT
1 TTCATGTCAGTCATAAT
31561 TTCATGTCAGTCATAAT
1 TTCATGTCAGTCATAAT
31578 TTCATGTC
1 TTCATGTC
31586 CCCGATATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (17 bp):
TTCATGTCAGTCATAAT
Found at i:32270 original size:24 final size:24
Alignment explanation
Indices: 32236--32289 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
32226 TGAAAAAATC
32236 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
32260 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
32284 ATCAAA
1 ATCAAA
32290 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:33157 original size:20 final size:20
Alignment explanation
Indices: 33132--33178 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
33122 AAATTCAGTA
*
33132 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
33152 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
33172 TTGCGAT
1 TTGCGAT
33179 TTACGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:33188 original size:20 final size:20
Alignment explanation
Indices: 33165--33238 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
33155 CGATAGTCAG
*
33165 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
33185 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
33205 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
33225 AATCGCAATGCGAT
1 ATTCGCATTGCGAT
33239 AGTCAGAATC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:33196 original size:40 final size:40
Alignment explanation
Indices: 33152--33257 Score: 135
Period size: 40 Copynumber: 2.6 Consensus size: 40
33142 CAGAATCTCG
*
33152 TTGCGATAGTCAGATTCGCGTTGCGATTTACGTATTCGCA
1 TTGCGATAGTCAGATTCGCGTTGCGATTTACGTAATCGCA
* *
33192 TTGCGAT--TTACGTATTCGCATTGCGATTTACGTAATCGCA
1 TTGCGATAGTCA-G-ATTCGCGTTGCGATTTACGTAATCGCA
* *
33232 ATGCGATAGTCAGAATCGCGTTGCGA
1 TTGCGATAGTCAGATTCGCGTTGCGA
33258 ATCTGGAAAC
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
38 2 0.04
39 1 0.02
40 49 0.89
41 1 0.02
42 2 0.04
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (40 bp):
TTGCGATAGTCAGATTCGCGTTGCGATTTACGTAATCGCA
Found at i:33520 original size:37 final size:37
Alignment explanation
Indices: 33444--33520 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
33434 TTTTTATATT
* *
33444 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAACATTATCAA
* * *
33481 TTTAATTTTTTAAAGAAAA-TATATAAACATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAACATTAT-CAA
33518 TTT
1 TTT
33521 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 12 0.35
37 22 0.65
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAACATTATCAA
Found at i:38259 original size:14 final size:14
Alignment explanation
Indices: 38226--38252 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38216 AACTACGAAC
38226 ATATCGAGGAGAAT
1 ATATCGAGGAGAAT
38240 ATATCGAGGAGAA
1 ATATCGAGGAGAA
38253 GTTATCGGGA
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:0.44, C:0.07, G:0.30, T:0.19
Consensus pattern (14 bp):
ATATCGAGGAGAAT
Found at i:40587 original size:53 final size:52
Alignment explanation
Indices: 40512--40611 Score: 173
Period size: 53 Copynumber: 1.9 Consensus size: 52
40502 TCATTGATCT
*
40512 ATTAATTTCTAATATAACTTCTAAACTTTACATCAAATATCAAATTTTCATTA
1 ATTAATTTATAATATAACTTCTAAACTTTACATCAAATATC-AATTTTCATTA
*
40565 ATTAATTTATAATATAATTTCTAAACTTTACATCAAATATCAATTTT
1 ATTAATTTATAATATAACTTCTAAACTTTACATCAAATATCAATTTT
40612 ATCCTTAAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 6 0.13
53 39 0.87
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (52 bp):
ATTAATTTATAATATAACTTCTAAACTTTACATCAAATATCAATTTTCATTA
Found at i:52180 original size:3 final size:3
Alignment explanation
Indices: 52172--52239 Score: 91
Period size: 3 Copynumber: 22.0 Consensus size: 3
52162 GATTCATTTG
* *
52172 ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATTT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
*
52218 AAT ATT ATAT ATT ATT ATT ATT
1 ATT ATT AT-T ATT ATT ATT ATT
52240 TAATAAATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
3 51 0.89
4 6 0.11
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:53808 original size:95 final size:92
Alignment explanation
Indices: 53660--53831 Score: 209
Period size: 95 Copynumber: 1.8 Consensus size: 92
53650 ATTATTTTAA
* * * * * *
53660 TATTTATTTTTCAATATCGAAGAAAAGGGCAGTCTTAATACAACTGGATGTCCTATTCTGGTATT
1 TATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTCTGATATT
53725 TTAAAATTAAATATTAATAAAAAAATAT
66 TTAAAA-TAAATATTAATAAAAAAATAT
* * * * *
53753 TATTTAATTTTATTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTGATA
1 TATTT-ATTTT-TCAATATCAAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTCTGATA
*
53818 TTTTTAAATAAATA
64 TTTTAAAATAAATA
53832 AATATATTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
93 5 0.08
94 11 0.17
95 49 0.75
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (92 bp):
TATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTCTGATATT
TTAAAATAAATATTAATAAAAAAATAT
Found at i:55894 original size:15 final size:14
Alignment explanation
Indices: 55832--55895 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 14
55822 TTTGTACATT
55832 TTTACATTTG--TA
1 TTTACATTTGCATA
* *
55844 TTTACATTTACATT
1 TTTACATTTGCATA
55858 TTTACATTTGCATA
1 TTTACATTTGCATA
*
55872 TTTACATTTGGCATC
1 TTTACATTT-GCATA
*
55887 TTTGCATTT
1 TTTACATTT
55896 TTTATGTCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
12 9 0.21
14 22 0.51
15 12 0.28
ACGTcount: A:0.23, C:0.14, G:0.08, T:0.55
Consensus pattern (14 bp):
TTTACATTTGCATA
Found at i:61565 original size:94 final size:94
Alignment explanation
Indices: 61404--61595 Score: 339
Period size: 94 Copynumber: 2.0 Consensus size: 94
61394 AGAAGACTCA
* *
61404 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGAAAAATCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGAAAAACCA
61469 ATCATTAAATTTGAAAGATGAATGTGCTC
66 ATCATTAAATTTGAAAGATGAATGTGCTC
61498 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGAAAAACCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGAAAAACCA
** *
61563 ATCATTGGATTTGAAAGATGAATTTGCTC
66 ATCATTAAATTTGAAAGATGAATGTGCTC
61592 ATAG
1 ATAG
61596 TAGAAATAAG
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (94 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGAAAAACCA
ATCATTAAATTTGAAAGATGAATGTGCTC
Found at i:63842 original size:54 final size:54
Alignment explanation
Indices: 63760--63915 Score: 258
Period size: 54 Copynumber: 2.9 Consensus size: 54
63750 AGAAATCTTG
*
63760 GCAGAAAACATAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAAACACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
*
63814 GCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAAACACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
** * *
63868 GCAGAAGTCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTACGAAC
1 GCAGAAAACACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
63916 CTGTTATTCT
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (54 bp):
GCAGAAAACACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
Found at i:64299 original size:22 final size:22
Alignment explanation
Indices: 64273--64357 Score: 125
Period size: 22 Copynumber: 3.9 Consensus size: 22
64263 ACATCTACAT
64273 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
64295 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* * *
64317 TTTTTAAAGATGACAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
64339 TTTTCAAAGATGAAAGATT
1 TCTTCAAAGATGATAGATT
64358 TATCGGATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:64956 original size:113 final size:113
Alignment explanation
Indices: 64753--65305 Score: 779
Period size: 113 Copynumber: 4.9 Consensus size: 113
64743 GCAAAGATTT
* * * * * * *
64753 AAATCCATCATTCAATGGATCAACAGTACCAGTTAAAGTTCATAATGAAAAGAACTCATCTGAAA
1 AAATCCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
64818 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
64866 TAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAAC
1 AAATCCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * *
64931 AAGGAAGGAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
64979 AAA-CTCATCATTCGATGGATCAGTATTACCAGGTCAAGTTCATAATGAGAAGAACTCATTTGAA
1 AAATC-CATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAA
65043 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * * *
65092 AAATCCATCACTT-GATGAATCAGCTTTTCTAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCA-TTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAA
65156 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * ***
65205 AAATCCATCACTT-GATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCA-TTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAA
* *
65269 GAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
65306 GACTTTAGTT
Statistics
Matches: 399, Mismatches: 38, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
113 396 0.99
114 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (113 bp):
AAATCCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:65327 original size:113 final size:114
Alignment explanation
Indices: 64781--65655 Score: 768
Period size: 113 Copynumber: 7.7 Consensus size: 114
64771 ATCAACAGTA
* *
64781 CCAGTTAAAGTTCATAATGAAAAGAACTCATCTGAA-AAAGGAAGAAGAAGTTCATAATGAGAAG
1 CCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAA-GAAGAAGAAGTTCATAATGAGAAG
* * * *
64845 AATTTGTTCAACTTTTTGCTTTAAT-TCATCA-TTCGATGGATCAGCATTA
65 AATTTGTTCAACCTTTTGCTTTAATCACATCACTT-GATGGATCAGCTTTT
* * * * * *
64894 CCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAACAAGGAAGGAGAAATTCATAATGAGAAGA
1 CCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGA
* * *
64959 ATTTGTTCAACCTTTTG-TTTAAACTCATCA-TTCGATGGATCAG-TATTA
66 ATTTGTTCAACCTTTTGCTTTAATCACATCACTT-GATGGATCAGCT-TTT
* * * *
65007 CCAGGTCAAGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGA
** *
65072 ATTTGTTCAACCTTTTGCTCAAATC-CATCACTTGATGAATCAGCTTTT
66 ATTTGTTCAACCTTTTGCTTTAATCACATCACTTGATGGATCAGCTTTT
* * ** *
65120 CTAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGA
**
65185 ATTTGTTCAACCTTTTGCTCAAATC-CATCACTTGATGGATCAGCTTTT
66 ATTTGTTCAACCTTTTGCTTTAATCACATCACTTGATGGATCAGCTTTT
*
65233 CCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGA
* * * *
65298 ACTTGTTCGA-CTTTAG-TTTAAT--CA--AC-------ATCAACTTTT
66 ATTTGTTCAACCTTTTGCTTTAATCACATCACTTGATGGATCAGCTTTT
* * * *
65334 CCAGAGAAAGTTCATAATGAGAAGAACTTATATGAATAAA-AAGAAGAAGTTCATAATGAGAAGA
1 CCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGA
** ** * ** *
65398 GCTTGTTCAACCTTTTGCATGACTCT-ATCACAGAAGTAGATAGATCAACATCAACTTTT
66 ATTTGTTCAACCTTTTGC-T---T-TAATCACATCACT---T-GAT--GGATCAGCTTTT
* * * *
65457 CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAA-CAAGAAGAAGAAATTCATAATGAGAAGA
1 CCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGA
* * * * * *
65521 ACTTGTTTAACCTTTTG-TTTAACTCTATCA-CAGAAGTAGATGGATCAATATCAACATTT
66 ATTTGTTCAACCTTTTGCTTTAA-TC-A-CATC---ACTTGATGG------ATCAGCTTTT
*
65580 CCAGA-AATGTTCATAATGAGAAGAACTCATCT---GAAA-AAGAAGAAGTTCATAATGAGAAGA
1 CCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGA
*
65640 ATTTGTTCAACTTTTT
66 ATTTGTTCAACCTTTT
65656 TCTAGATCAC
Statistics
Matches: 657, Mismatches: 60, Indels: 84
0.82 0.07 0.10
Matches are distributed among these distances:
100 32 0.05
101 50 0.08
103 1 0.00
106 3 0.00
107 1 0.00
108 4 0.01
110 3 0.00
111 4 0.01
112 10 0.02
113 363 0.55
114 9 0.01
117 1 0.00
118 2 0.00
119 41 0.06
120 3 0.00
121 3 0.00
122 27 0.04
123 100 0.15
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (114 bp):
CCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGA
ATTTGTTCAACCTTTTGCTTTAATCACATCACTTGATGGATCAGCTTTT
Found at i:65338 original size:101 final size:100
Alignment explanation
Indices: 65223--65405 Score: 303
Period size: 101 Copynumber: 1.8 Consensus size: 100
65213 CACTTGATGG
* *
65223 ATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATATGAAGAAA-AAGAAGAAGTTCAT
65288 AATGAGAAGAACTTGTTCGACTTTAGTTTAATCAAC
65 AATGAGAAGAACTTGTTCGACTTTAGTTTAATCAAC
* * *
65324 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATATGAATAAAAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATATGAAGAAAAAGAAGAAGTTCATA
*
65389 ATGAGAAGAGCTTGTTC
66 ATGAGAAGAACTTGTTC
65406 AACCTTTTGC
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
100 31 0.41
101 45 0.59
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.27
Consensus pattern (100 bp):
ATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATATGAAGAAAAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCGACTTTAGTTTAATCAAC
Found at i:65470 original size:123 final size:122
Alignment explanation
Indices: 65318--65655 Score: 502
Period size: 123 Copynumber: 2.8 Consensus size: 122
65308 CTTTAGTTTA
*
65318 ATCAACATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATATGAATAAAAAGAAGAAG
1 ATCAACATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAA-AAAAAGAAGAAG
* *
65383 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGTAGATAG
65 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAGAAGTAGATAG
* *
65441 ATCAACATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAACAAGAAGAAGAAA
1 ATCAACATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAA-AAAAAGAAGAAG
* ** *
65506 TTCATAATGAGAAGAACTTGTTTAACCTTTTGTTTAACTCTATCACAGAAGTAGATGG
65 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAGAAGTAGATAG
* * * *
65564 ATCAATATCAACATTTCCAGA-AATGTTCATAATGAGAAGAACTCATCTG--AAAAAGAAGAAGT
1 ATCAACATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAAAAAAGAAGAAGT
* *
65626 TCATAATGAGAAGAATTTGTTCAACTTTTT
66 TCATAATGAGAAGAACTTGTTCAACCTTTT
65656 TCTAGATCAC
Statistics
Matches: 196, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
119 38 0.19
122 26 0.13
123 132 0.67
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (122 bp):
ATCAACATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAAAAAAGAAGAAGT
TCATAATGAGAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAGAAGTAGATAG
Found at i:65887 original size:3 final size:3
Alignment explanation
Indices: 65879--65948 Score: 104
Period size: 3 Copynumber: 22.7 Consensus size: 3
65869 CATTTGATTC
*
65879 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
65925 TTA ATA TTA TATA TTA TTA TTA TT
1 TTA TTA TTA T-TA TTA TTA TTA TT
65949 TAATAAATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
3 55 0.90
4 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:67354 original size:27 final size:27
Alignment explanation
Indices: 67324--67381 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
67314 ATATATATAG
67324 AATAAATAATAATTT-ATATTT-TTTTTC
1 AATAAAT--TAATTTAATATTTATTTTTC
*
67351 AATAAATTATTTTAATATTTATTTTTC
1 AATAAATTAATTTAATATTTATTTTTC
67378 AATA
1 AATA
67382 TCGAAGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 5 0.18
26 6 0.21
27 17 0.61
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (27 bp):
AATAAATTAATTTAATATTTATTTTTC
Found at i:68336 original size:15 final size:14
Alignment explanation
Indices: 68316--68355 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
68306 AGCGTCACCC
68316 AAAATCCCTAAATCT
1 AAAATCCCTAAAT-T
68331 AAAATCCCTAAAATT
1 AAAATCCCT-AAATT
*
68346 CAAATCCCTA
1 AAAATCCCTA
68356 TTTCCCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 1 0.04
15 18 0.78
16 4 0.17
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAATCCCTAAATT
Found at i:68967 original size:14 final size:16
Alignment explanation
Indices: 68948--68980 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
68938 ATTCAATGTG
68948 AGATTCTTG-A-TTTA
1 AGATTCTTGTACTTTA
68962 AGATTCTTGTACTTTA
1 AGATTCTTGTACTTTA
68978 AGA
1 AGA
68981 ATGAACTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 1 0.06
16 7 0.41
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.45
Consensus pattern (16 bp):
AGATTCTTGTACTTTA
Found at i:70045 original size:14 final size:15
Alignment explanation
Indices: 70026--70059 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
70016 TGCTAGAAAT
70026 TTAAAGGACA-AAAA
1 TTAAAGGACATAAAA
*
70040 TTAAAGTACATAAAA
1 TTAAAGGACATAAAA
70055 TTAAA
1 TTAAA
70060 TTATAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.62, C:0.06, G:0.09, T:0.24
Consensus pattern (15 bp):
TTAAAGGACATAAAA
Found at i:70381 original size:15 final size:15
Alignment explanation
Indices: 70361--70407 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
70351 AATAAATAAA
70361 GTTAGTAAGTTAGGG
1 GTTAGTAAGTTAGGG
**
70376 GTTAGTAAGTTAGAA
1 GTTAGTAAGTTAGGG
70391 GTTAG-AAGTTAGGG
1 GTTAGTAAGTTAGGG
70405 GTT
1 GTT
70408 TAATAATGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.34
Consensus pattern (15 bp):
GTTAGTAAGTTAGGG
Found at i:70392 original size:7 final size:7
Alignment explanation
Indices: 70359--70402 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
70349 TAAATAAATA
70359 AAGTTAG
1 AAGTTAG
70366 TAAGTTAG
1 -AAGTTAG
**
70374 GGGTTAG
1 AAGTTAG
70381 TAAGTTAG
1 -AAGTTAG
70389 AAGTTAG
1 AAGTTAG
70396 AAGTTAG
1 AAGTTAG
70403 GGGTTTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
7 19 0.61
8 12 0.39
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (7 bp):
AAGTTAG
Found at i:70401 original size:22 final size:23
Alignment explanation
Indices: 70359--70402 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
70349 TAAATAAATA
**
70359 AAGTTAGTAAGTTAGGGGTTAGT
1 AAGTTAGTAAGTTAGAAGTTAGT
70382 AAGTTAG-AAGTTAGAAGTTAG
1 AAGTTAGTAAGTTAGAAGTTAG
70403 GGGTTTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (23 bp):
AAGTTAGTAAGTTAGAAGTTAGT
Found at i:70858 original size:20 final size:21
Alignment explanation
Indices: 70819--70864 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
70809 AATCTAAGTC
*
70819 TTTTCTTAAAATTTCATTTTG
1 TTTTCTTAAAATTTCATTTTA
70840 TTTT-TTAAAA-TTCACTTTTA
1 TTTTCTTAAAATTTCA-TTTTA
70860 TTTTC
1 TTTTC
70865 AAATGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 4 0.18
20 14 0.64
21 4 0.18
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTCTTAAAATTTCATTTTA
Found at i:72138 original size:20 final size:19
Alignment explanation
Indices: 72088--72142 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
72078 CATGCACATG
*
72088 CAGTTTCAAAACTTTTGAGA
1 CAGTTTCGAAAC-TTTGAGA
* * *
72108 AAATTTTGAAACTTTGATGA
1 CAGTTTCGAAACTTTGA-GA
72128 CAGTTTCGAAACTTT
1 CAGTTTCGAAACTTT
72143 TACTTAAAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
CAGTTTCGAAACTTTGAGA
Found at i:72341 original size:20 final size:20
Alignment explanation
Indices: 72318--72367 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
72308 TAGTATTTTT
72318 CATA-TTTAAAAATCTTTAAA
1 CATATTTTAAAAA-CTTTAAA
*
72338 CATATTTTAAACACTTTAAA
1 CATATTTTAAAAACTTTAAA
*
72358 CATGTTTTAA
1 CATATTTTAA
72368 TTAACTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (20 bp):
CATATTTTAAAAACTTTAAA
Found at i:75576 original size:31 final size:32
Alignment explanation
Indices: 75515--75580 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
75505 TAAAAATATA
* *
75515 TGTCTAATATTTTTTTTTATTATCAGTTTAGG
1 TGTCTAATATTTTTCTCTATTATCAGTTTAGG
* *
75547 TGTCTAATA-TTTTCTCTATTATTATTTTAGG
1 TGTCTAATATTTTTCTCTATTATCAGTTTAGG
75578 TGT
1 TGT
75581 TCGGACATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 21 0.70
32 9 0.30
ACGTcount: A:0.21, C:0.08, G:0.12, T:0.59
Consensus pattern (32 bp):
TGTCTAATATTTTTCTCTATTATCAGTTTAGG
Found at i:75795 original size:21 final size:20
Alignment explanation
Indices: 75753--75797 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
75743 TTAATAATAA
* *
75753 ATTTGGGATTATGGTTAGGG
1 ATTTGGGATTAAGGTTAAGG
*
75773 ATTTGGGTATTAAGTTTAAGG
1 ATTTGGG-ATTAAGGTTAAGG
75794 ATTT
1 ATTT
75798 ATGTTTTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.44
Consensus pattern (20 bp):
ATTTGGGATTAAGGTTAAGG
Found at i:76327 original size:2 final size:2
Alignment explanation
Indices: 76320--76354 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
76310 ATCATAAAAT
76320 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
76355 AATAGAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:77431 original size:31 final size:31
Alignment explanation
Indices: 77395--77484 Score: 162
Period size: 31 Copynumber: 2.9 Consensus size: 31
77385 AACTTAAAAG
77395 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTGCAATACTGAGATTTAAATAATTTT
77426 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTGCAATACTGAGATTTAAATAATTTT
* *
77457 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTGCAATACTGAGATTTAAATAAT
77485 CCATACAACT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (31 bp):
AGTTTTGCAATACTGAGATTTAAATAATTTT
Found at i:77535 original size:22 final size:22
Alignment explanation
Indices: 77509--77551 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
77499 TAATAAATTA
77509 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
77531 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
77552 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:77560 original size:22 final size:22
Alignment explanation
Indices: 77511--77559 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
77501 ATAAATTATT
**
77511 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
77533 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
77556 TAAA
1 TAAA
77560 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:77563 original size:54 final size:54
Alignment explanation
Indices: 77499--77945 Score: 359
Period size: 54 Copynumber: 8.4 Consensus size: 54
77489 ACAACTACAA
77499 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* ** *
77553 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATA--C
* ** * ** * *
77613 TAAAATAAATCAATCAAAAAAAAATCAAT-CA-ATCCATACAAATAAAT-TAT--TTA-
1 T--AATAAAT-TATTTAAAATAAATCAATCCATAT-TTTA-AAATAAATCAATCCATAC
* * ** * * *
77666 AAATAAATCAATCCATACT-AATAAAT---TA-TTTAAAATAAATCAATCC--A-
1 TAATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
77713 T-A-AAACTA--CAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAA-AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
77764 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
77818 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
77872 TAATAAATTATTTAAAAT--A--AAT---TATTTTAAAATAAATCAATCCATATTTTA
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA----C
77923 TAATAAATTATTTTAAAATAAAT
1 TAATAAATTA-TTTAAAATAAAT
77946 TATTTTAATA
Statistics
Matches: 326, Mismatches: 31, Indels: 71
0.76 0.07 0.17
Matches are distributed among these distances:
42 2 0.01
43 2 0.01
44 7 0.02
45 3 0.01
46 9 0.03
47 31 0.10
48 18 0.06
49 1 0.00
50 10 0.03
51 25 0.08
52 10 0.03
53 5 0.02
54 142 0.44
55 2 0.01
56 2 0.01
57 4 0.01
58 19 0.06
59 9 0.03
60 2 0.01
62 9 0.03
63 14 0.04
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:77569 original size:32 final size:32
Alignment explanation
Indices: 77531--77893 Score: 238
Period size: 32 Copynumber: 12.4 Consensus size: 32
77521 CAATCCATAT
77531 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
77563 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
*
77593 --T--AATAAATCAATCCATATTTTAAAATAAATCAATCAA
1 TTTAAAATAAATCAATCCATA--CT--AATAAAT---T--A
*** * *
77630 AAAAAAATCAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
77662 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
77694 TTTAAAATAAATCAATCC--A-T-A-AAACTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
77721 --CAATAATAAATCAATCC--A-T-AT------
1 TTTAA-AATAAATCAATCCATACTAATAAATTA
77742 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
77774 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
77796 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
77828 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
77850 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
77882 TTTAAAATAAAT
1 TTTAAAATAAAT
77894 TATTTTAAAA
Statistics
Matches: 265, Mismatches: 15, Indels: 102
0.69 0.04 0.27
Matches are distributed among these distances:
22 45 0.17
23 6 0.02
24 3 0.01
25 3 0.01
26 40 0.15
27 5 0.02
28 8 0.03
29 1 0.00
30 7 0.03
31 8 0.03
32 115 0.43
34 1 0.00
37 8 0.03
41 15 0.06
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:77637 original size:15 final size:15
Alignment explanation
Indices: 77614--77644 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
77604 TCCATATTTT
*
77614 AAAATAAATCAATCA
1 AAAAAAAATCAATCA
77629 AAAAAAAATCAATCA
1 AAAAAAAATCAATCA
77644 A
1 A
77645 TCCATACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAAAAATCAATCA
Found at i:77685 original size:131 final size:132
Alignment explanation
Indices: 77528--77848 Score: 484
Period size: 131 Copynumber: 2.4 Consensus size: 132
77518 AATCAATCCA
*
77528 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAA
1 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAAAACTACAA
* * *
77593 TAATAAATCAATCCATATTTTAAAATAAATCAATCAAAAAAAAATCAATCAATCCATACAAATAA
66 TAATAAATCAATCCATATTTTAAAATAAATCAATC-AAAAAAAATAAATCAATCAAAACAAATAA
77658 AT-
130 ATC
77660 TA-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAAAACTACAA
1 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAAAACTACAA
* * ** * * * * *
77724 TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
66 TAATAAATCAATCCATATTTTAAAATAAATCAATCAAAAAAAATAAATCAATCAAAACAAATAAA
77789 TCC
131 T-C
77792 ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1 -TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
77849 TTTTAAAATA
Statistics
Matches: 172, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
130 19 0.11
131 96 0.56
132 2 0.01
133 2 0.01
134 53 0.31
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (132 bp):
TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAAAACTACAA
TAATAAATCAATCCATATTTTAAAATAAATCAATCAAAAAAAATAAATCAATCAAAACAAATAAA
TC
Found at i:77771 original size:22 final size:22
Alignment explanation
Indices: 77698--77771 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
77688 AAATTATTTA
77698 AAATAAATCAATCCATAAAACTACA-
1 AAATAAATCAATCCAT---ACTA-AT
**
77723 ATAATAAATCAATCCATA-TTTT
1 A-AATAAATCAATCCATACTAAT
77745 AAAATAAATCAATCCATACTAAT
1 -AAATAAATCAATCCATACTAAT
77768 AAAT
1 AAAT
77772 TATTTAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
22 21 0.51
23 4 0.10
25 1 0.02
26 15 0.37
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATAAATCAATCCATACTAAT
Found at i:77800 original size:22 final size:22
Alignment explanation
Indices: 77774--77816 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
77764 TAATAAATTA
77774 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
77796 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
77817 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:77825 original size:22 final size:22
Alignment explanation
Indices: 77776--77824 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
77766 ATAAATTATT
**
77776 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
77798 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
77821 TAAA
1 TAAA
77825 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:77854 original size:22 final size:22
Alignment explanation
Indices: 77828--77930 Score: 98
Period size: 22 Copynumber: 4.5 Consensus size: 22
77818 TAATAAATTA
77828 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
77850 TTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
77873 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
77897 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
77919 TTTATAATAAAT
1 TTTAAAATAAAT
77931 TATTTTAAAA
Statistics
Matches: 61, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
22 35 0.57
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:77902 original size:15 final size:15
Alignment explanation
Indices: 77873--78018 Score: 181
Period size: 15 Copynumber: 9.5 Consensus size: 15
77863 AATCCATACT
77873 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
77887 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
77902 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
77924 AATAAATTATTTTAA
1 AATAAATTATTTTAA
77939 AATAAATTATTTT--
1 AATAAATTATTTTAA
*
77952 AATAAATTATTTTAT
1 AATAAATTATTTTAA
77967 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
77982 AATAAATTATTTTAT
1 AATAAATTATTTTAA
77997 AATAAATTATTTTAA
1 AATAAATTATTTTAA
78012 AATAAAT
1 AATAAAT
78019 AACCTTATTA
Statistics
Matches: 117, Mismatches: 5, Indels: 19
0.83 0.04 0.13
Matches are distributed among these distances:
13 13 0.11
14 9 0.08
15 77 0.66
17 1 0.01
18 3 0.03
19 3 0.03
20 1 0.01
22 10 0.09
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:77908 original size:69 final size:65
Alignment explanation
Indices: 77819--77973 Score: 204
Period size: 69 Copynumber: 2.3 Consensus size: 65
77809 AATCCATACT
*
77819 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAAT-AAT-CATA-AAATAAATTAT
77883 TTAA
63 TT-A
* * ** *
77887 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAATAATCATAAAATAAATTATTTA
*
77952 AATAAATTATTTTATAATAAAT
1 AATAAATTATTTTAAAATAAAT
77974 TATTTTAAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
65 21 0.27
66 12 0.15
67 2 0.03
68 11 0.14
69 33 0.42
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (65 bp):
AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAATAATCATAAAATAAATTATTTA
Found at i:77977 original size:43 final size:43
Alignment explanation
Indices: 77872--78018 Score: 182
Period size: 43 Copynumber: 3.5 Consensus size: 43
77862 CAATCCATAC
77872 TAATAAATTA-TTTAAAATAAATTATTTTAAAAT-AA--A--T
1 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAATTATTT
* ** *
77909 CAATCCA-TATTTTATAATAAATTATTTTAAAATAAATTATTT
1 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAATTATTT
*
77951 TAATAAATTATTTTATAATAAATTATTTTAAAATAAATTATTTT
1 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAATTA-TTT
77995 ATAATAAATTATTTTAAAATAAAT
1 -TAATAAATTATTTTAAAATAAAT
78019 AACCTTATTA
Statistics
Matches: 93, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
36 2 0.02
37 26 0.28
38 2 0.02
40 1 0.01
42 5 0.05
43 32 0.34
44 3 0.03
45 22 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (43 bp):
TAATAAATTATTTTAAAATAAATTATTTTAAAATAAATTATTT
Found at i:78031 original size:58 final size:56
Alignment explanation
Indices: 77873--78041 Score: 174
Period size: 58 Copynumber: 3.1 Consensus size: 56
77863 AATCCATACT
* ** *
77873 AATAAATTA-TTTAAAATAAATTATTTTAAAATAAAT-C--AATCCA-TATTTTAT
1 AATAAATTATTTTAAAATAAATTATTTTAAAATAAATACTTATTAAATTATTTTAA
*
77924 AATAAATTATTTTAAAATAAATTATTTT--AATAAATTATTTTATAATAAATTATTTTAA
1 AATAAATTATTTTAAAATAAATTATTTTAAAATAAA-TA-CTTAT--TAAATTATTTTAA
*
77982 AATAAATTATTTTATAATAAATTATTTTAAAATAAATAACCTTATTAAATTA-TTTAA
1 AATAAATTATTTTAAAATAAATTATTTTAAAATAAAT-A-CTTATTAAATTATTTTAA
78039 AAT
1 AAT
78042 TATTTTAATA
Statistics
Matches: 98, Mismatches: 8, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
50 6 0.06
51 10 0.10
52 18 0.18
55 1 0.01
57 10 0.10
58 41 0.42
59 1 0.01
60 11 0.11
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (56 bp):
AATAAATTATTTTAAAATAAATTATTTTAAAATAAATACTTATTAAATTATTTTAA
Found at i:78536 original size:21 final size:21
Alignment explanation
Indices: 78526--78580 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
78516 TAAGATAATA
78526 TATCTTAATATATAAATATAT
1 TATCTTAATATATAAATATAT
78547 TATCTTAATATATAAATATAT
1 TATCTTAATATATAAATATAT
78568 TATCTTAATATAT
1 TATCTTAATATAT
78581 CAAAACATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
TATCTTAATATATAAATATAT
Found at i:82265 original size:15 final size:15
Alignment explanation
Indices: 82247--82278 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
82237 ATTTTTTTGC
82247 TTTATTTTTTCTTTT
1 TTTATTTTTTCTTTT
82262 TTTATTTTTTCTTTT
1 TTTATTTTTTCTTTT
82277 TT
1 TT
82279 CCCATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTATTTTTTCTTTT
Found at i:84310 original size:88 final size:88
Alignment explanation
Indices: 84191--84368 Score: 338
Period size: 88 Copynumber: 2.0 Consensus size: 88
84181 ATTCATAGTC
84191 TAGATGTTAGATTTTAATGTTTAAGGATTAAGGTTATCCAAATATGTCACATCGCAACAATATAA
1 TAGATGTTAGATTTTAATGTTTAAGGATTAAGGTTATCCAAATATGTCACATCGCAACAATATAA
*
84256 TCGCATTTGTGGAGCAATTATTT
66 TCGCATTAGTGGAGCAATTATTT
84279 TAGATGTTAGATTTTAATGTTTAAGGATTAAGGTTATCCAAATATGTCACATCGCAACAATATAA
1 TAGATGTTAGATTTTAATGTTTAAGGATTAAGGTTATCCAAATATGTCACATCGCAACAATATAA
*
84344 TCGCATTAGTGGAGCAATTCTTT
66 TCGCATTAGTGGAGCAATTATTT
84367 TA
1 TA
84369 TACTATCGAT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (88 bp):
TAGATGTTAGATTTTAATGTTTAAGGATTAAGGTTATCCAAATATGTCACATCGCAACAATATAA
TCGCATTAGTGGAGCAATTATTT
Found at i:88966 original size:28 final size:27
Alignment explanation
Indices: 88926--89025 Score: 76
Period size: 27 Copynumber: 3.6 Consensus size: 27
88916 CACAATTTGG
*
88926 GGATGAAA-TTAAAATGTTCAAAAGTTGA
1 GGAT-AAATTTAAAATGTT-AAAAGTTAA
* * **
88954 GGATTAATTTAAAATGATAGTAGTTAA
1 GGATAAATTTAAAATGTTAAAAGTTAA
* * *
88981 GGATAAAATTAAAATATTTAAAAGTTTA
1 GGATAAATTTAAAAT-GTTAAAAGTTAA
*
89009 GAGATCAATTTAAAATG
1 G-GATAAATTTAAAATG
89026 AAGATCATAC
Statistics
Matches: 54, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
27 21 0.39
28 21 0.39
29 12 0.22
ACGTcount: A:0.48, C:0.02, G:0.17, T:0.33
Consensus pattern (27 bp):
GGATAAATTTAAAATGTTAAAAGTTAA
Found at i:91457 original size:72 final size:72
Alignment explanation
Indices: 91367--91512 Score: 292
Period size: 72 Copynumber: 2.0 Consensus size: 72
91357 ATTCAAAGCT
91367 GTGTTTTCAAAAATCATCAAGCAAAACCAAGCTAGTTTCATAGCTGGAAGGAGTATCAATGATAA
1 GTGTTTTCAAAAATCATCAAGCAAAACCAAGCTAGTTTCATAGCTGGAAGGAGTATCAATGATAA
91432 CATCCTG
66 CATCCTG
91439 GTGTTTTCAAAAATCATCAAGCAAAACCAAGCTAGTTTCATAGCTGGAAGGAGTATCAATGATAA
1 GTGTTTTCAAAAATCATCAAGCAAAACCAAGCTAGTTTCATAGCTGGAAGGAGTATCAATGATAA
91504 CATCCTG
66 CATCCTG
91511 GT
1 GT
91513 TGATCAAGAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (72 bp):
GTGTTTTCAAAAATCATCAAGCAAAACCAAGCTAGTTTCATAGCTGGAAGGAGTATCAATGATAA
CATCCTG
Found at i:94106 original size:31 final size:30
Alignment explanation
Indices: 94043--94108 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 30
94033 AAAATTTTTA
*
94043 AAAAAAATACAAAGAAAAATAGTTAAAGTTT
1 AAAAAAATACAAAGAAAAATA-TTAAAATTT
94074 AAAAAAATACAAAGAAAAAT-TTAAAAAATTT
1 AAAAAAATACAAAGAAAAATATT--AAAATTT
94105 AAAA
1 AAAA
94109 TATAAGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 2 0.06
31 30 0.94
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (30 bp):
AAAAAAATACAAAGAAAAATATTAAAATTT
Found at i:94118 original size:17 final size:16
Alignment explanation
Indices: 94089--94125 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
94079 AATACAAAGA
*
94089 AAAATTTAAAAAATTT
1 AAAATATAAAAAATTT
94105 AAAATATAAGAAAATTT
1 AAAATATAA-AAAATTT
94122 AAAA
1 AAAA
94126 ATTTTAGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAATATAAAAAATTT
Found at i:100455 original size:24 final size:21
Alignment explanation
Indices: 100408--100455 Score: 51
Period size: 24 Copynumber: 2.1 Consensus size: 21
100398 TATAAGTGGT
* *
100408 CCTTCGGGACATCTACGTGGC
1 CCTTCGGGACATCTACGCGCC
100429 CCTTCGGGACAAATTCTACGCGCC
1 CCTTCGGGAC--A-TCTACGCGCC
100453 CCT
1 CCT
100456 AGTGGGAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 10 0.45
23 1 0.05
24 11 0.50
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.23
Consensus pattern (21 bp):
CCTTCGGGACATCTACGCGCC
Found at i:108454 original size:45 final size:46
Alignment explanation
Indices: 108367--108471 Score: 149
Period size: 45 Copynumber: 2.3 Consensus size: 46
108357 TGCACTCTCC
** * *
108367 ATGCATCGATGCACTCAGATTTTAATGAAAACATCGATTGCATTTT
1 ATGCATCGATGCACTCAGAGCTTAATCAAAACATCGAATGCATTTT
* *
108413 ATGCATCGATGCACTTAG-GCTTATTCAAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGAGCTTAATCAAAACATCGAATGCATTTT
108458 ATGCATCGATGCAC
1 ATGCATCGATGCAC
108472 ACTTAGTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 36 0.68
46 17 0.32
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (46 bp):
ATGCATCGATGCACTCAGAGCTTAATCAAAACATCGAATGCATTTT
Found at i:114318 original size:44 final size:44
Alignment explanation
Indices: 114263--114359 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
114253 TTGTTCTTAA
* *
114263 TGCATCGATACA-C-TGAACAGTGCATCGATGCA-TCCCTTTGTATG
1 TGCATCGATACATCATGAACA-TGCACCGATGCACT-CC-TTGAATG
*
114307 TGCATCGATACATCATGAATATGCACCGATGCACTCCTTGAATG
1 TGCATCGATACATCATGAACATGCACCGATGCACTCCTTGAATG
114351 TGCATCGAT
1 TGCATCGAT
114360 GCACAAAGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 27 0.57
45 14 0.30
46 6 0.13
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (44 bp):
TGCATCGATACATCATGAACATGCACCGATGCACTCCTTGAATG
Found at i:114380 original size:20 final size:20
Alignment explanation
Indices: 114351--114402 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
114341 TCCTTGAATG
114351 TGCATCGATGCACAAAGCCA
1 TGCATCGATGCACAAAGCCA
*
114371 TGCGTCGATGCACAAAGCCA
1 TGCATCGATGCACAAAGCCA
114391 TGCATCGATGCA
1 TGCATCGATGCA
114403 TCCGTCGGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.29, G:0.23, T:0.17
Consensus pattern (20 bp):
TGCATCGATGCACAAAGCCA
Found at i:117025 original size:20 final size:20
Alignment explanation
Indices: 116996--117033 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
116986 TTTCAAAGGA
116996 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
117016 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
117034 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:117171 original size:45 final size:46
Alignment explanation
Indices: 117080--117184 Score: 149
Period size: 45 Copynumber: 2.3 Consensus size: 46
117070 TGCACTCTCC
* * * *
117080 ATGCATCGATGCACTTAGGTTTTAATGAAAACATCGATTGCATTTT
1 ATGCATCGATGCACTTAGGTCTTAATCAAAACATCGAATACATTTT
* *
117126 ATGCATCGATGCACTTAGG-CTTATTCAAAACATTGAATACATTTT
1 ATGCATCGATGCACTTAGGTCTTAATCAAAACATCGAATACATTTT
117171 ATGCATCGATGCAC
1 ATGCATCGATGCAC
117185 ACTTAATGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 34 0.64
46 19 0.36
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (46 bp):
ATGCATCGATGCACTTAGGTCTTAATCAAAACATCGAATACATTTT
Found at i:118208 original size:49 final size:51
Alignment explanation
Indices: 118139--118241 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 51
118129 TTTTTAAAAG
*
118139 TTAAGATAAT-AAAAATATATA-TTTTAATTGAAATTAAGAATAAAATATA
1 TTAAGATAATAAAAAATATATATTTTTAATTGAAAATAAGAATAAAATATA
* *
118188 TTAAGATAATAATAAAATATATATTTTTTATTTAAAATAAGAATAAAATATA
1 TTAAGATAATAA-AAAATATATATTTTTAATTGAAAATAAGAATAAAATATA
118240 TT
1 TT
118242 TTTAAGTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
49 10 0.21
50 1 0.02
51 10 0.21
52 27 0.56
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (51 bp):
TTAAGATAATAAAAAATATATATTTTTAATTGAAAATAAGAATAAAATATA
Found at i:118256 original size:29 final size:30
Alignment explanation
Indices: 118190--118267 Score: 97
Period size: 29 Copynumber: 2.6 Consensus size: 30
118180 AAAATATATT
* **
118190 AAGATAATAATAAAATATATATTTTTTATTTA
1 AAGATAAGAAT-AAA-ATATATTTTTTAAGTA
118222 AA-ATAAGAATAAAATATA-TTTTTAAGTA
1 AAGATAAGAATAAAATATATTTTTTAAGTA
118250 AAGATAAGAATAAAATAT
1 AAGATAAGAATAAAATAT
118268 TATATATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 10 0.24
29 20 0.48
30 3 0.07
31 7 0.17
32 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.37
Consensus pattern (30 bp):
AAGATAAGAATAAAATATATTTTTTAAGTA
Found at i:118300 original size:64 final size:61
Alignment explanation
Indices: 118190--118310 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 61
118180 AAAATATATT
*
118190 AAGATAATAATAAAATATATATTTTTTATTTAAAATAAGAATAAAATATAT-TTTTAAGTA
1 AAGATAAGAATAAAATATATATTTTTTATTTAAAATAAGAATAAAATATATATTTTAAGTA
*
118250 AAGATAAGAATAAAATATTATATATATTTTAATTTAAAATAATG-GTAAAATATATATTTTA
1 AAGATAAGAATAAAATA-TATAT-T-TTTT-ATTTAAAATAA-GAATAAAATATATATTTTA
118311 TATTATTTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
60 16 0.30
61 5 0.09
62 1 0.02
63 4 0.08
64 21 0.40
65 6 0.11
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (61 bp):
AAGATAAGAATAAAATATATATTTTTTATTTAAAATAAGAATAAAATATATATTTTAAGTA
Found at i:118473 original size:25 final size:27
Alignment explanation
Indices: 118416--118473 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
118406 ACATTAAAAT
118416 AAAAATAAAATATATTTAATAAATTAAGAA
1 AAAAATAAAATATATTTAATAAATT---AA
*
118446 AAAAATAAAA-ATATTTAATAAGTTAA
1 AAAAATAAAATATATTTAATAAATTAA
118472 AA
1 AA
118474 CAAAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 4 0.15
29 13 0.48
30 10 0.37
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.29
Consensus pattern (27 bp):
AAAAATAAAATATATTTAATAAATTAA
Found at i:118483 original size:29 final size:29
Alignment explanation
Indices: 118389--118479 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 29
118379 GACGATAAAG
** *
118389 ATAAAATATATATTTTTACATTAAAATAAAA
1 ATAAAATATAT-TTAATAAATTAAAA-AAAA
118420 ATAAAATATATTTAATAAATTAAGAAAAAA
1 ATAAAATATATTTAATAAATTAA-AAAAAA
* *
118450 ATAAAA-ATATTTAATAAGTTAAAACAAA
1 ATAAAATATATTTAATAAATTAAAAAAAA
118478 AT
1 AT
118480 TAAAGAGATA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
28 7 0.13
29 15 0.28
30 19 0.35
31 13 0.24
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (29 bp):
ATAAAATATATTTAATAAATTAAAAAAAA
Found at i:121048 original size:30 final size:28
Alignment explanation
Indices: 121014--121083 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 28
121004 TAAACATCTT
*
121014 TATTAAAATATTATTAAATTAATATATTAA
1 TATTAAAATATTATTAAATT-AT-TAATAA
121044 TATT-AAATA-TA-TAAATTATTAATAA
1 TATTAAAATATTATTAAATTATTAATAA
121069 T-TTAATAATATTATT
1 TATTAA-AATATTATT
121084 TCTATGAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
24 2 0.06
25 7 0.20
26 6 0.17
27 8 0.23
28 3 0.09
29 5 0.14
30 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TATTAAAATATTATTAAATTATTAATAA
Found at i:121061 original size:19 final size:19
Alignment explanation
Indices: 121025--121081 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
121015 ATTAAAATAT
*
121025 TATTAAATTAATATATTAA
1 TATTAAATTAATAAATTAA
*
121044 TATTAAA-TATATAAATTAT
1 TATTAAATTA-ATAAATTAA
* *
121063 TAATAATTTAATAATATTA
1 TATTAAATTAATAA-ATTA
121082 TTTCTATGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 2 0.06
19 23 0.74
20 6 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTAAATTAATAAATTAA
Found at i:121213 original size:23 final size:24
Alignment explanation
Indices: 121187--121263 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 24
121177 AGTATTTTAT
121187 TATAATATTACAAAATA-TAAT-AA
1 TATAATATTA-AAAATATTAATAAA
* *
121210 TATATTATTATAAATATTAATAAA
1 TATAATATTAAAAATATTAATAAA
* * *
121234 TAT-ATTTTAAATATTTTAAT-AA
1 TATAATATTAAAAATATTAATAAA
121256 T-TAATATT
1 TATAATATT
121264 TTGATTAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
21 1 0.02
22 12 0.28
23 25 0.58
24 5 0.12
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (24 bp):
TATAATATTAAAAATATTAATAAA
Found at i:121244 original size:21 final size:23
Alignment explanation
Indices: 121199--121248 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
121189 TAATATTACA
121199 AAATA-TAATAATATATTATTAT
1 AAATATTAATAATATATTATTAT
*
121221 AAATATTAATAA-ATA-TATTTT
1 AAATATTAATAATATATTATTAT
121242 AAATATT
1 AAATATT
121249 TTAATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
22 8 0.31
23 6 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATATTAATAATATATTATTAT
Found at i:121277 original size:24 final size:23
Alignment explanation
Indices: 121250--121295 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
121240 TTAAATATTT
121250 TAATAATT-AATATTTTGATTAAAA
1 TAAT-ATTAAATATTTT-ATTAAAA
121274 TAATATTAAAATATTTTATTAA
1 TAATATT-AAATATTTTATTAA
121296 TATTAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 3 0.15
24 9 0.45
25 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TAATATTAAATATTTTATTAAAA
Found at i:121873 original size:35 final size:35
Alignment explanation
Indices: 121800--121885 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 35
121790 AAAACAGTCA
* * **
121800 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAACAAT
* * * *
121835 TCAATTTTATTCTAAACCCTAAATTCTAAAACACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAACAAT
*
121870 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
121886 ATACTTCAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.41, C:0.22, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAACAAT
Found at i:121879 original size:21 final size:21
Alignment explanation
Indices: 121854--121896 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
121844 TTCTAAACCC
121854 TAAATTCTAAAACACTTCAAT
1 TAAATTCTAAAACACTTCAAT
*
121875 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAACACTTCAAT
121896 T
1 T
121897 TAAGGTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATTCTAAAACACTTCAAT
Found at i:122051 original size:16 final size:18
Alignment explanation
Indices: 122019--122052 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
122009 TATTAATGTA
122019 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
122037 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
122053 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:134527 original size:28 final size:29
Alignment explanation
Indices: 134461--134527 Score: 66
Period size: 28 Copynumber: 2.3 Consensus size: 29
134451 AAAAAATATT
*
134461 AAAAATATTATTATATTTATTAAAAAACCC
1 AAAAAT-TTCTTATATTTATTAAAAAACCC
* **
134491 TAACTTTTCTTATA-TTA-TAAAACAACCC
1 AAAAATTTCTTATATTTATTAAAA-AACCC
134519 AAAAATTTC
1 AAAAATTTC
134528 AAATCCAAAC
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
27 5 0.17
28 14 0.48
29 7 0.24
30 3 0.10
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (29 bp):
AAAAATTTCTTATATTTATTAAAAAACCC
Found at i:136334 original size:9 final size:9
Alignment explanation
Indices: 136320--136346 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
136310 CTCCAGCAAC
136320 GAGAAGAAG
1 GAGAAGAAG
136329 GAGAAGAAG
1 GAGAAGAAG
136338 GAGAAGAAG
1 GAGAAGAAG
136347 AGGAGAGCAG
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:0.00, G:0.44, T:0.00
Consensus pattern (9 bp):
GAGAAGAAG
Found at i:136973 original size:30 final size:29
Alignment explanation
Indices: 136934--136998 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
136924 TTTCCCCCTA
* * *
136934 AATTTTTAAATTTTATTTTATTTAATTAAT
1 AATTATTAAATATAATTTTATTT-ATTAAT
136964 AATTATTAAATATAATTTTATTTATTAAT
1 AATTATTAAATATAATTTTATTTATTAAT
*
136993 TATTAT
1 AATTAT
136999 ATTATAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
AATTATTAAATATAATTTTATTTATTAAT
Found at i:138036 original size:60 final size:60
Alignment explanation
Indices: 137942--138064 Score: 167
Period size: 60 Copynumber: 2.0 Consensus size: 60
137932 TACAATCTTT
** * * * * *
137942 ATTTTAAATTGGTCCTTAAACTTTTAAATGTTTCAGTTTCATCCCTAAACTATGACTA-TC
1 ATTTTAAATCAGTCCTCAAACTTTTAAATATTTCAATTCCATCCCCAAACTATGA-TATTC
138002 ATTTTAAATCAGTCCTCAAACTTTTAAATATTTCAATTCCATCCCCAAACTATGATATTC
1 ATTTTAAATCAGTCCTCAAACTTTTAAATATTTCAATTCCATCCCCAAACTATGATATTC
138062 ATT
1 ATT
138065 CCAAATTAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 2 0.04
60 53 0.96
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (60 bp):
ATTTTAAATCAGTCCTCAAACTTTTAAATATTTCAATTCCATCCCCAAACTATGATATTC
Found at i:138085 original size:60 final size:60
Alignment explanation
Indices: 137959--138114 Score: 163
Period size: 60 Copynumber: 2.6 Consensus size: 60
137949 ATTGGTCCTT
* * * ** * *
137959 AAACTTTTAAATGTTTCAGTTTCATCCCTAAACTATGACTATCATTTTAAATCAGTCCTC
1 AAACTTTTAAATATTTCAATTTCATCCCCAAACTATGACTATCATTCCAAATCAATCCCC
* *
138019 AAACTTTTAAATATTTCAATTCCATCCCCAAACTATGA-TATTCATTCCAAATTAATCCCC
1 AAACTTTTAAATATTTCAATTTCATCCCCAAACTATGACTA-TCATTCCAAATCAATCCCC
* * * *
138079 ATACTTTTTGAACATTCCAATTTCAT-CCCAAACTAT
1 AAAC-TTTTAAATATTTCAATTTCATCCCCAAACTAT
138115 ACGTATAGAC
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
59 2 0.03
60 61 0.76
61 17 0.21
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (60 bp):
AAACTTTTAAATATTTCAATTTCATCCCCAAACTATGACTATCATTCCAAATCAATCCCC
Found at i:138321 original size:60 final size:60
Alignment explanation
Indices: 138246--138364 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
138236 GATGAATTTT
* ** * *
138246 GGGATGAAATCAGAAT-TTTCAAAAGTTTAAGGACTGATTTAGAATGAGAGTCATAGTTTA
1 GGGATGAAATCAGAATAATT-AAAAGTTTAAGGACCAACTTAAAATGAGAGTCATAGTTTA
* *
138306 GGGATGAAATTAGAATAATTAAAAGTTTAAGGACCAACTTAAAATGAGAGTTATAGTTT
1 GGGATGAAATCAGAATAATTAAAAGTTTAAGGACCAACTTAAAATGAGAGTCATAGTTT
138365 TGTGACATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 49 0.96
61 2 0.04
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (60 bp):
GGGATGAAATCAGAATAATTAAAAGTTTAAGGACCAACTTAAAATGAGAGTCATAGTTTA
Found at i:139916 original size:17 final size:17
Alignment explanation
Indices: 139894--139929 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
139884 TAAGTGGTAT
139894 TGTAATTATTATAAGTA
1 TGTAATTATTATAAGTA
139911 TGTAATTATTATAAGTA
1 TGTAATTATTATAAGTA
139928 TG
1 TG
139930 CAATCATGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (17 bp):
TGTAATTATTATAAGTA
Found at i:150946 original size:31 final size:31
Alignment explanation
Indices: 150911--150969 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
150901 TAAATGATTA
* *
150911 TTTAATTATTTATTTTGATTAAAAATATAAT
1 TTTAAATATTTATTTTAATTAAAAATATAAT
150942 TTTAAATATTTATTTTAATTAAAAATAT
1 TTTAAATATTTATTTTAATTAAAAATAT
150970 TTTAAATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (31 bp):
TTTAAATATTTATTTTAATTAAAAATATAAT
Done.