Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005493.1 Hibiscus syriacus cultivar Beakdansim tig00012637_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: 62945
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2772 original size:33 final size:34
Alignment explanation
Indices: 2735--2805 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 34
2725 AACCCTAAAT
2735 ATTAAAATACTTT-AATTTAGGGTTTAGAATGTA
1 ATTAAAATACTTTAAATTTAGGGTTTAGAATGTA
* * *
2768 ATTAAAGTATTTTAAAATTTGGGGTTTAGAATGTA
1 ATTAAAATACTTT-AAATTTAGGGTTTAGAATGTA
2803 ATT
1 ATT
2806 GAAGTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 11 0.33
35 22 0.67
ACGTcount: A:0.38, C:0.01, G:0.17, T:0.44
Consensus pattern (34 bp):
ATTAAAATACTTTAAATTTAGGGTTTAGAATGTA
Found at i:6437 original size:31 final size:31
Alignment explanation
Indices: 6399--6567 Score: 250
Period size: 31 Copynumber: 5.5 Consensus size: 31
6389 GGGTCGAGGG
*
6399 TTACCTATGTTCTTCAGGACATATGGAATGT
1 TTACCTATGTTCTTCGGGACATATGGAATGT
6430 TTACCTATGTTCTTCGGGACATAT-GAACTGT
1 TTACCTATGTTCTTCGGGACATATGGAA-TGT
* *
6461 TTACCTATGTTCTTCGGGACATATGGACTAT
1 TTACCTATGTTCTTCGGGACATATGGAATGT
*
6492 TTACCTATGTTCTTCGGGACATATGGATTGT
1 TTACCTATGTTCTTCGGGACATATGGAATGT
* **
6523 TTACCTATGTTCTTCGAGACATATGGCCTGT
1 TTACCTATGTTCTTCGGGACATATGGAATGT
*
6554 TTACCTAGGTTCTT
1 TTACCTATGTTCTT
6568 TGGAATCTAT
Statistics
Matches: 127, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
30 3 0.02
31 122 0.96
32 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGAATGT
Found at i:6516 original size:93 final size:93
Alignment explanation
Indices: 6399--6567 Score: 284
Period size: 93 Copynumber: 1.8 Consensus size: 93
6389 GGGTCGAGGG
*
6399 TTACCTATGTTCTTCAGGACATATGGAATGTTTACCTATGTTCTTCGGGACATATGAACTGTTTA
1 TTACCTATGTTCTTCAGGACATATGGAATGTTTACCTATGTTCTTCGAGACATATGAACTGTTTA
*
6464 CCTATGTTCTTCGGGACATATGGACTAT
66 CCTAGGTTCTTCGGGACATATGGACTAT
* * **
6492 TTACCTATGTTCTTCGGGACATATGGATTGTTTACCTATGTTCTTCGAGACATATGGCCTGTTTA
1 TTACCTATGTTCTTCAGGACATATGGAATGTTTACCTATGTTCTTCGAGACATATGAACTGTTTA
6557 CCTAGGTTCTT
66 CCTAGGTTCTT
6568 TGGAATCTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (93 bp):
TTACCTATGTTCTTCAGGACATATGGAATGTTTACCTATGTTCTTCGAGACATATGAACTGTTTA
CCTAGGTTCTTCGGGACATATGGACTAT
Found at i:7301 original size:21 final size:21
Alignment explanation
Indices: 7275--7354 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
7265 AAAGTTACTG
7275 TAGCAGTGCATCGATACGCTA
1 TAGCAGTGCATCGATACGCTA
* *
7296 TAGCAGTGCATTGGTACGCTA
1 TAGCAGTGCATCGATACGCTA
* * *
7317 TAGCAGTGCATCGGTACACTG
1 TAGCAGTGCATCGATACGCTA
*
7338 TAACAGTGCATCGATAC
1 TAGCAGTGCATCGATAC
7355 ACAATTTATA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
TAGCAGTGCATCGATACGCTA
Found at i:7403 original size:21 final size:21
Alignment explanation
Indices: 7377--7427 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
7367 CGATGTTTTT
* *
7377 GTGCATCGGTATACTGTAGCA
1 GTGCATCGGTACAATGTAGCA
*
7398 GTGCATTGGTACAATGTAGCA
1 GTGCATCGGTACAATGTAGCA
*
7419 CTGTCATCG
1 GTG-CATCG
7428 ATTGTTCATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (21 bp):
GTGCATCGGTACAATGTAGCA
Found at i:9448 original size:21 final size:21
Alignment explanation
Indices: 9422--9462 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
9412 AACTATCGAA
9422 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTCCAAATTCGCG
*
9443 TTGCGATTTTCCTAATTCGC
1 TTGCGATTTTCCAAATTCGC
9463 AATGCGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCG
Found at i:9468 original size:21 final size:21
Alignment explanation
Indices: 9423--9469 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
9413 ACTATCGAAT
**
9423 TGCGATTTTCCAAATTCGCGT
1 TGCGATTTTCCAAATTCGCAA
*
9444 TGCGATTTTCCTAATTCGCAA
1 TGCGATTTTCCAAATTCGCAA
9465 TGCGA
1 TGCGA
9470 ATACGTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (21 bp):
TGCGATTTTCCAAATTCGCAA
Found at i:9484 original size:20 final size:20
Alignment explanation
Indices: 9459--9583 Score: 216
Period size: 20 Copynumber: 6.3 Consensus size: 20
9449 TTTTCCTAAT
9459 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
9479 TCGCAAT-CGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
9498 TCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
9518 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
9538 TCGCAATACGAATACATAAA
1 TCGCAATGCGAATACGTAAA
9558 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
9578 TCGCAA
1 TCGCAA
9584 AGTGAATCTA
Statistics
Matches: 98, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
19 18 0.18
20 80 0.82
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:9814 original size:22 final size:22
Alignment explanation
Indices: 9788--9853 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
9778 GGCGACATCC
*
9788 GTCCCCATCTCCGACAAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
9810 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
*
9832 GTCTCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
9854 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:0.27, C:0.39, G:0.12, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:10266 original size:20 final size:20
Alignment explanation
Indices: 10223--10286 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
10213 CAATTCTTGC
* ** *
10223 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTTATTTTCGT
10243 GTTGCGATAGTTATTTTCGT
1 GTTGCGATAGTTATTTTCGT
*
10263 GTTGCGAT-TTTCATTTTCGT
1 GTTGCGATAGTT-ATTTTCGT
10283 GTTG
1 GTTG
10287 TGATTTAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 2 0.05
20 36 0.95
ACGTcount: A:0.16, C:0.14, G:0.25, T:0.45
Consensus pattern (20 bp):
GTTGCGATAGTTATTTTCGT
Found at i:10291 original size:20 final size:20
Alignment explanation
Indices: 10255--10292 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
10245 TGCGATAGTT
10255 ATTTTCGTGTTGCGATTTTC
1 ATTTTCGTGTTGCGATTTTC
*
10275 ATTTTCGTGTTGTGATTT
1 ATTTTCGTGTTGCGATTT
10293 AAAGTTTCAG
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:0.11, C:0.11, G:0.21, T:0.58
Consensus pattern (20 bp):
ATTTTCGTGTTGCGATTTTC
Found at i:10300 original size:20 final size:20
Alignment explanation
Indices: 10257--10300 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
10247 CGATAGTTAT
** *
10257 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
*
10277 TTTCGTGTTGTGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
10297 TTTC
1 TTTC
10301 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.11, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:12207 original size:20 final size:20
Alignment explanation
Indices: 12182--12339 Score: 137
Period size: 20 Copynumber: 8.6 Consensus size: 20
12172 AGAATAGTTT
12182 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
12202 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
12222 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
12242 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
12258 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
12275 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
* *
12291 A--ATCTCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
12309 ACTATCGCAACGTGAAAATG
1 ACTATCGCAATGCGAAAATG
12329 ACTATCGCAAT
1 ACTATCGCAAT
12340 TCGCGTTGCG
Statistics
Matches: 117, Mismatches: 7, Indels: 28
0.77 0.05 0.18
Matches are distributed among these distances:
14 13 0.11
16 10 0.09
17 8 0.07
18 5 0.04
19 7 0.06
20 74 0.63
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.17
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:12304 original size:33 final size:34
Alignment explanation
Indices: 12185--12319 Score: 121
Period size: 33 Copynumber: 3.8 Consensus size: 34
12175 ATAGTTTACT
*
12185 ATCGCAATGCGAAAATGACTATCGCAATGCGAA-AATGA
1 ATCGCAACGCGAAAATGACTATCGCAA--C-AACAA--A
* * *
12223 CTATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 --ATCGCAACGCGAAAATGACTATCGCAACAACAAA
* **
12259 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAAATGACTATCGCAACAACAAA
*
12292 ATCTCAACGCGAAAATGACTATCGCAAC
1 ATCGCAACGCGAAAATGACTATCGCAAC
12320 GTGAAAATGA
Statistics
Matches: 80, Mismatches: 13, Indels: 10
0.78 0.13 0.10
Matches are distributed among these distances:
33 26 0.32
34 24 0.30
36 1 0.01
37 1 0.01
38 2 0.03
40 26 0.32
ACGTcount: A:0.43, C:0.23, G:0.19, T:0.16
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGACTATCGCAACAACAAA
Found at i:12932 original size:42 final size:42
Alignment explanation
Indices: 12832--12953 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 42
12822 CCCGACTCAC
* * * * *
12832 CTGTCATCGTTCAAGAGACCTCC-CCTATCATTCAAGATGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCAACATTCAAGAGGCCA
* ** *
12874 CTATCATCCCTCAAGAGTCCCCTCCCACCATTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCAACATTCAAGAGGCCA
* *
12916 CTGTCATCGTTGAAGAGGT-CCCTCCCAACATTCTAGAG
1 CTGTCATCGTTCAAGA-GTCCCCTCCCAACATTCAAGAG
12954 CCTGATTCAC
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
41 2 0.03
42 60 0.94
43 2 0.03
ACGTcount: A:0.25, C:0.36, G:0.16, T:0.24
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCAACATTCAAGAGGCCA
Found at i:14533 original size:33 final size:34
Alignment explanation
Indices: 14472--14567 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
14462 AAAACAGACT
* * **
14472 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
* *
14506 ATCGTAATGCG-AAATGAAAATCTCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
14539 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
14568 CGAAACTAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 29 0.54
34 25 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:14621 original size:19 final size:20
Alignment explanation
Indices: 14578--14630 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
14568 CGAAACTAAA
*
14578 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
14598 TTCGCATTGCGATTTTCA-T
1 TTCGCATTGCGATTTTCATT
14617 TTCGCATTGCGATT
1 TTCGCATTGCGATT
14631 CTCTTGTTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Found at i:14661 original size:20 final size:20
Alignment explanation
Indices: 14636--14723 Score: 133
Period size: 20 Copynumber: 4.4 Consensus size: 20
14626 CGATTCTCTT
14636 GTTGCGATAGTCATTTCCGC
1 GTTGCGATAGTCATTTCCGC
*
14656 GTTGCGATAGTCAATTCCGC
1 GTTGCGATAGTCATTTCCGC
* *
14676 GTTGCGATAGTCATTTCTGT
1 GTTGCGATAGTCATTTCCGC
14696 GTTGCGATAGTCATATT-CGC
1 GTTGCGATAGTCAT-TTCCGC
14716 GTTGCGAT
1 GTTGCGAT
14724 TTCCACGTTG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 59 0.97
21 2 0.03
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGC
Found at i:17118 original size:24 final size:24
Alignment explanation
Indices: 17067--17121 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
17057 AAAATCCTAG
**
17067 TATTGACCAAGATCAAAGTCCGGG
1 TATTGACCAAGATCAAAGTCCGAA
* *
17091 TATTGACCAAGATCAAATTTCGAA
1 TATTGACCAAGATCAAAGTCCGAA
17115 TATTGAC
1 TATTGAC
17122 TAGTACTCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (24 bp):
TATTGACCAAGATCAAAGTCCGAA
Found at i:18013 original size:20 final size:20
Alignment explanation
Indices: 17951--18004 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
17941 AAATTTAGTA
17951 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
17971 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
17991 TTGCGATAGTCAGA
1 TTGCGATAGTCAGA
18005 TTCGCGTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:18027 original size:20 final size:20
Alignment explanation
Indices: 18004--18109 Score: 121
Period size: 20 Copynumber: 5.5 Consensus size: 20
17994 CGATAGTCAG
*
18004 ATTCGCGTTGTGATTTACGT
1 ATTCGCATTGTGATTTACGT
*
18024 ATTCGTATTGTGATTTACGT
1 ATTCGCATTGTGATTTACGT
*
18044 ATTCACA-T-T-A-TTACGT
1 ATTCGCATTGTGATTTACGT
* *
18060 ATTCACATTATGATTTACGT
1 ATTCGCATTGTGATTTACGT
*
18080 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGTGATTTACGT
*
18100 ATTCTCATTG
1 ATTCGCATTG
18110 CGAATTAGGA
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
16 13 0.18
17 2 0.03
18 2 0.03
19 2 0.03
20 55 0.74
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (20 bp):
ATTCGCATTGTGATTTACGT
Found at i:18059 original size:16 final size:16
Alignment explanation
Indices: 18038--18070 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
18028 GTATTGTGAT
18038 TTACGTATTCACATTA
1 TTACGTATTCACATTA
18054 TTACGTATTCACATTA
1 TTACGTATTCACATTA
18070 T
1 T
18071 GATTTACGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (16 bp):
TTACGTATTCACATTA
Found at i:18074 original size:36 final size:36
Alignment explanation
Indices: 18018--18088 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
18008 GCGTTGTGAT
** *
18018 TTACGTATTCGTATTGTGATTTACGTATTCACATTA
1 TTACGTATTCACATTATGATTTACGTATTCACATTA
*
18054 TTACGTATTCACATTATGATTTACGTATTCGCATT
1 TTACGTATTCACATTATGATTTACGTATTCACATT
18089 GCGATTTACG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.46
Consensus pattern (36 bp):
TTACGTATTCACATTATGATTTACGTATTCACATTA
Found at i:18135 original size:21 final size:21
Alignment explanation
Indices: 18109--18154 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
18099 TATTCTCATT
18109 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
18130 GCGAATTTGGAAAATTGCAAT
1 GCGAATTAGGAAAATCGCAAC
18151 GCGA
1 GCGA
18155 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.15, G:0.26, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:19524 original size:48 final size:48
Alignment explanation
Indices: 19438--19530 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
19428 TTCTAATTAT
*
19438 TTCAATACTTCCCGATTAAAGCTTTGTTAAGCAGAATTCAATATTTAC
1 TTCAATACTTCCCGATTAAAGCTTTATTAAGCAGAATTCAATATTTAC
* * * *
19486 TTCAATACTTCTCGATTGAAGCTTTATT-CGACATAATTCAATATT
1 TTCAATACTTCCCGATTAAAGCTTTATTAAG-CAGAATTCAATATT
19531 AAGGTTGGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 1 0.03
48 38 0.97
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (48 bp):
TTCAATACTTCCCGATTAAAGCTTTATTAAGCAGAATTCAATATTTAC
Found at i:23739 original size:30 final size:30
Alignment explanation
Indices: 23699--23755 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
23689 AAATGTTATT
*
23699 AAAAAAATATT-GTTTGGATAAATAATTGAG
1 AAAAAAATATTGGGTT-GATAAATAATTGAG
*
23729 AAAAACATATTGGGTTGATAAATAATT
1 AAAAAAATATTGGGTTGATAAATAATT
23756 TGAAGGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (30 bp):
AAAAAAATATTGGGTTGATAAATAATTGAG
Found at i:27952 original size:20 final size:18
Alignment explanation
Indices: 27927--27972 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
27917 CATTCCCAAT
27927 CTCTTCTCTCCTCGCCGTTC
1 CTCTTCTCT--TCGCCGTTC
*
27947 CTCTTCTCTTTGCCGTTC
1 CTCTTCTCTTCGCCGTTC
*
27965 TTCTTCTC
1 CTCTTCTC
27973 CTCCGACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 15 0.62
20 9 0.38
ACGTcount: A:0.00, C:0.43, G:0.09, T:0.48
Consensus pattern (18 bp):
CTCTTCTCTTCGCCGTTC
Found at i:32947 original size:18 final size:18
Alignment explanation
Indices: 32914--32964 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
32904 CATTCCCAAT
32914 CTCTTCTCTCCTCGCCGTTC
1 CTCTTCTCT-C-CGCCGTTC
32934 CTCTTCTCTCCGCCGTTC
1 CTCTTCTCTCCGCCGTTC
*
32952 TTCTTCTCCTCCG
1 CTCTTCT-CTCCG
32965 ACTATAACAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 14 0.48
19 6 0.21
20 9 0.31
ACGTcount: A:0.00, C:0.49, G:0.10, T:0.41
Consensus pattern (18 bp):
CTCTTCTCTCCGCCGTTC
Found at i:35253 original size:3 final size:3
Alignment explanation
Indices: 35245--35270 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35235 ATATAAAAAT
35245 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
35271 TACCCTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:35634 original size:23 final size:23
Alignment explanation
Indices: 35608--35655 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
35598 ATAAAGTACA
* *
35608 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
**
35631 ATAATGTAATAGATAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
35654 AT
1 AT
35656 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGATAGCGCTTAT
Found at i:36063 original size:21 final size:22
Alignment explanation
Indices: 36038--36089 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
36028 ACACTTTACA
*
36038 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
36061 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
36084 ATATAA
1 ATATAA
36090 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:36074 original size:23 final size:23
Alignment explanation
Indices: 36048--36110 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
36038 ATATAACCAC
36048 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
36071 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
36094 TACCTATTACATCATAT
1 TACCTATTACATTATAT
36111 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:36489 original size:39 final size:39
Alignment explanation
Indices: 36435--36517 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
36425 TCAAGTTGTA
*
36435 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
36474 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
36513 GATTT
1 GATTT
36518 GATGAGCATC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.17, C:0.14, G:0.20, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:36801 original size:18 final size:18
Alignment explanation
Indices: 36778--36814 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
36768 CCGAATATAT
36778 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
36796 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
36814 A
1 A
36815 CTCCAATTAC
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:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:37091 original size:25 final size:25
Alignment explanation
Indices: 37063--37113 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
37053 TTAATCCAAA
*
37063 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
37088 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
37113 T
1 T
37114 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:37407 original size:21 final size:22
Alignment explanation
Indices: 37382--37433 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
37372 AAACTTTACA
*
37382 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
37405 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
37428 ATATAA
1 ATATAA
37434 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:37418 original size:23 final size:23
Alignment explanation
Indices: 37392--37454 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
37382 ATATAACCAC
37392 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
37415 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
37438 TACCTATTACATCATAT
1 TACCTATTACATTATAT
37455 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:37838 original size:21 final size:21
Alignment explanation
Indices: 37813--37863 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
37803 ATAACCACTA
37813 CTATTACATTATAAACGATAC
1 CTATTACATTATAAACGATAC
** *
37834 CTATTACATTATAAGGGCTAC
1 CTATTACATTATAAACGATAC
37855 CTATTACAT
1 CTATTACAT
37864 CATATGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (21 bp):
CTATTACATTATAAACGATAC
Found at i:38040 original size:27 final size:27
Alignment explanation
Indices: 38010--38067 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
38000 ATTTGCAGAA
*
38010 AAAATTATTT-G-ATGTTTTATATTTTAT
1 AAAATTATTTAGAAT-TTTTA-ATTTAAT
38037 AAAATTATTTAGAATTTTTAATTTAAT
1 AAAATTATTTAGAATTTTTAATTTAAT
38064 AAAA
1 AAAA
38068 AGGATCGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 20 0.71
28 6 0.21
29 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (27 bp):
AAAATTATTTAGAATTTTTAATTTAAT
Found at i:38211 original size:162 final size:160
Alignment explanation
Indices: 37902--38227 Score: 618
Period size: 162 Copynumber: 2.0 Consensus size: 160
37892 CCATACTTTT
37902 ATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTAACAGTGTTT
1 ATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTAACAGTGTTT
37967 CATGTTTTCCACCTACAATTGATTTAATATTTCATTTGCAGAAAAAATTATTTGATGTTTTATAT
66 CATGTTTTCCACCTACAATTGATTTAATATTTCATTTGCAGAAAAAATTATTTGATGTTTTATAT
38032 TTTATAAAATTATTTAGAATTTTTAATTTA
131 TTTATAAAATTATTTAGAATTTTTAATTTA
38062 ATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTT
1 ATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAA-TTTTTTAACAGTGTT
38127 TCATGTTTTCCACCTACAATATTGATTTAA-ATTTCATTTGCAGAAAAAATTATTTGATGTTTTA
65 TCATGTTTTCCACCTAC-A-ATTGATTTAATATTTCATTTGCAGAAAAAATTATTTGATGTTTTA
38191 TATTTTATAAAATTATTTAGAATTTTTAATTTA
128 TATTTTATAAAATTATTTAGAATTTTTAATTTA
38224 ATAA
1 ATAA
38228 TAATATACCG
Statistics
Matches: 163, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
160 49 0.30
161 32 0.20
162 72 0.44
163 10 0.06
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (160 bp):
ATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTAACAGTGTTT
CATGTTTTCCACCTACAATTGATTTAATATTTCATTTGCAGAAAAAATTATTTGATGTTTTATAT
TTTATAAAATTATTTAGAATTTTTAATTTA
Found at i:38222 original size:27 final size:27
Alignment explanation
Indices: 38172--38227 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
38162 ATTTGCAGAA
*
38172 AAAATTATTTGATGTTTTATATTTTAT
1 AAAATTATTTGATGTTTTATATTTAAT
38199 AAAATTATTTAGAAT-TTTTA-ATTTAAT
1 AAAATTATTT-G-ATGTTTTATATTTAAT
38226 AA
1 AA
38228 TAATATACCG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 18 0.69
28 6 0.23
29 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (27 bp):
AAAATTATTTGATGTTTTATATTTAAT
Found at i:38438 original size:21 final size:22
Alignment explanation
Indices: 38368--38443 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 22
38358 GATAGAAACT
* *
38368 TTACA-ATATAACCACTACCTA
1 TTACATATATAAACGCTACCTA
*
38389 TTACATTATATAAACGATACCTA
1 TTACA-TATATAAACGCTACCTA
**
38412 TTACAT-TATAAGGGCTACCTA
1 TTACATATATAAACGCTACCTA
38433 TTACATCATAT
1 TTACAT-ATAT
38444 GTTTACCTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
21 23 0.51
22 1 0.02
23 21 0.47
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACATATATAAACGCTACCTA
Found at i:38633 original size:29 final size:29
Alignment explanation
Indices: 38585--38649 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
38575 TCATTTGCAG
* * *
38585 AAAA-ATTATTTGATTGTTTTTATTTTAT
1 AAAATATTATTTGAATGTTTTAATTTAAT
38613 AAAATATTATTTAGAAT-TTTTAATTTAAT
1 AAAATATTATTT-GAATGTTTTAATTTAAT
38642 AATAATAT
1 AA-AATAT
38650 ATACCGTACG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 4 0.13
29 19 0.61
30 8 0.26
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.54
Consensus pattern (29 bp):
AAAATATTATTTGAATGTTTTAATTTAAT
Found at i:38767 original size:989 final size:1008
Alignment explanation
Indices: 37155--38962 Score: 3289
Period size: 989 Copynumber: 1.8 Consensus size: 1008
37145 TTAATTTAAT
37155 AATTTCATTTGCAGAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTT
1 AATTTCATTTGCAGAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTT
37220 TAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
66 TAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
37285 TAATATCTTAAAACTCACTCAAAAATTAATATTAAATTAATGTTTTCCACAGTGAAAAAAGTATG
131 TAATATCTTAAAACTCACTCAAAAA-TAATATTAAATTAATGTTTTCCACAGTGAAAAAAGTATG
37350 GACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATATAAACGA
195 GACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATATAAACGA
37415 TACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTC
260 TACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACC-ATTATATTGAAAGTGTC
37480 CATACTTTTATAAAAAGGATCGATACTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTA
324 CATACTTTTATAAAAAGGATCGATACTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTA
37545 ACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCAGAAAAAATTATTT
389 ACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCAGAAAAAATTATTT
37610 GATTGTTTTTATATTTTAATATTATTTAGAATTTTTAATTTAATAATAATATACCGTAACGTAAA
454 GATTGTTTTTATATTTTAATATTATTTAGAATTTTTAATTTAATAATAATATACCGTAACGTAAA
37675 AAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAATTAATAT
519 AAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAATTAATAT
37740 TAAATTATGTTTTCCACAGTGAAAAAGTATGGACACTTTTAT-AAAAGGATAGAAACTTTACAA-
584 TAAATTATGTTTTCCACAGTGAAAAAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAAT
37803 ATAACCACTA-CTATTACATTATA-AACGATACCTATTACA-T-TATAAGGGCTACCTATTACAT
649 ATAACCAC-ACCTATTACATTATATAACGATACCTATTACATTATATAAGGGCTACCTATTAC-T
37864 CATATGTTTACCTATTATA-TG-AAAGTGTCCATAC-TTTTATAAAAAGGATCGATAC-TTTTTT
712 CATATGTTTACCTATTATATTGAAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTT
37925 TAAAACTTATGTAATTTATGTTTCAA-TTTTTTAACAGTGTTTCATGTTTTCCACCTACAATTGA
777 TAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATTGA
37989 TTTAATATTTCATTTGCAGAAAAAATTATTTGATGTTTTATATTTTATAAAATTATTTAGAATTT
842 TTTAATATTTCATTTGCAGAAAAAATTATTTGATGTTTTATATTTTATAAAATTATTTAGAATTT
38054 TTAATTTAATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTA
907 TTAATTTAATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTA
38119 ACAGTGTTTCATGTTTTCCACCTACAATATTGATTTA
972 ACAGTGTTTCATGTTTTCCACCTACAATATTGATTTA
38156 AATTTCATTTGCAGAAAAAATTATTTGA-TG-TTTTATATTTTAT-AAA-ATTATTTAGAATTTT
1 AATTTCATTTGCAGAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTT
38217 TAATTTAATAAT-A-ATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
66 TAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
38280 TAATATCTTAAAACTCACTC-AAAA-AATATTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
131 TAATATCTTAAAACTCACTCAAAAATAATATTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
38343 ACACTTTTAT-AAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATATAAACGAT
196 ACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATATAAACGAT
38407 ACCTATTACA-T-TATAAGGGCTACCTATTACATCATATGTTTACC-TTATATTGAAAGTGTCCA
261 ACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCATTATATTGAAAGTGTCCA
38469 TACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTA
326 TAC-TTTTATAAAAAGGATCGATAC-TTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTA
38534 ACAGTGTTTCATGTTTTCCACCTAC-ATATTGA-TTAATAATTTCATTTGCAG-AAAAATTATTT
389 ACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCAGAAAAAATTATTT
38596 GATTGTTTTTAT-TTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACCGT-AC
454 GATTGTTTTTATATTT-T--AATATTATTTAGAATTTTTAATTTAATAAT-A-ATATACCGTAAC
38659 GTAAAAAATAAATCATTAGACG-CTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAATT
514 GTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAATT
38723 AATATT-AATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGAAACT
579 AATATTAAATT-ATGTTTTCCACAGTG-AAAAAGTATGGACACTTTTATAAAAAGGATAGAAACT
38787 TTACAATATAACCACACCTATTACATTATATAACGATACCTATTACATTATATAAGGGCTACCTA
642 TTACAATATAACCACACCTATTACATTATATAACGATACCTATTACATTATATAAGGGCTACCTA
38852 TTACTCATATGTTTACCTATTATATTGAAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTT
707 TTACTCATATGTTTACCTATTATATTGAAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTT
38917 TTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGT
772 TTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGT
38963 ACTTGCGAAT
Statistics
Matches: 787, Mismatches: 0, Indels: 43
0.95 0.00 0.05
Matches are distributed among these distances:
985 3 0.00
986 24 0.03
987 44 0.06
988 121 0.15
989 143 0.18
990 32 0.04
991 85 0.11
992 65 0.08
993 21 0.03
994 25 0.03
995 83 0.11
996 22 0.03
997 59 0.07
998 17 0.02
999 13 0.02
1000 2 0.00
1001 28 0.04
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (1008 bp):
AATTTCATTTGCAGAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTT
TAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAAT
TAATATCTTAAAACTCACTCAAAAATAATATTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
ACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATATAAACGAT
ACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCATTATATTGAAAGTGTCCA
TACTTTTATAAAAAGGATCGATACTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAAC
AGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCAGAAAAAATTATTTGA
TTGTTTTTATATTTTAATATTATTTAGAATTTTTAATTTAATAATAATATACCGTAACGTAAAAA
ATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAATTAATATTA
AATTATGTTTTCCACAGTGAAAAAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATAT
AACCACACCTATTACATTATATAACGATACCTATTACATTATATAAGGGCTACCTATTACTCATA
TGTTTACCTATTATATTGAAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTTAAA
ACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATTGATTTA
ATATTTCATTTGCAGAAAAAATTATTTGATGTTTTATATTTTATAAAATTATTTAGAATTTTTAA
TTTAATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAG
TGTTTCATGTTTTCCACCTACAATATTGATTTA
Found at i:38774 original size:572 final size:564
Alignment explanation
Indices: 37630--38693 Score: 1601
Period size: 575 Copynumber: 1.9 Consensus size: 564
37620 ATATTTTAAT
37630 ATTATTTAGAATTTTTAATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCT
1 ATTATTTAGAATTTTTAATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCT
37695 ATAATTACTAAATTAATATCTTAAAACTCACTCAAAAATTAATATTAAATTATGTTTTCCACAGT
66 ATAATTACTAAATTAATATCTTAAAACTCACTCAAAAA-TAATATTAAATTATGTTTTCCACAGT
37760 GAAAAAGTATGGACACTTTTATAAAAGGATAGAAACTTTACAAATAACCACTACTATTACATTAT
130 GAAAAAGTATGGACACTTTTATAAAAGGATAGAAACTTTACAAATAACCACTACTATTACATTAT
37825 AAACGATACCTATTACATTATAAGGGCTACCTATTACATCATATGTTTACCTATTATATGAAAGT
195 AAACGATACCTATTACATTATAAGGGCTACCTATTACATCATATGTTTACCTATTATATGAAAGT
37890 GTCCATACTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
260 GTCCATACTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
37955 TTAACAGTGTTTCATGTTTTCCACCTACAATTGATTTAATATTTCATTTGCAGAAAAAATTATTT
325 TTAACAGTGTTTCATGTTTTCCACCTACAATTGATTTAATATTTCATTTGCAGAAAAAATTATTT
** ***
38020 GATGTTTTATATTTTATAAAATTATTTAGAATTTTTAATTTAATAAAAAGGATCGATACTTTTTT
390 GATGTTTTATATTTTATAAAATTATTTAGAATTTTTAATTTAATAAAAAGGATC-ATACCGTACG
** ** * * * ** * * ** *
38085 TAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATT
454 TAAAAAATAAATAATTGACGTATCAA-TTTACTAACAGTGTATCATCTTAACCACCTACAAAATT
* * * *
38150 GATTTAAATTTCATTTGCAGAAAAAATTATTTGATGTTTTATATTTTATAAA
518 AATTTAAATTTCATTTACAGAAAAAAGTA-TTGA-G---TACATTTTATAAA
38202 ATTATTTAGAATTTTTAATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCT
1 ATTATTTAGAATTTTTAATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCT
38267 ATAATTACTAAATTAATATCTTAAAACTCACTC-AAAA-AATATTAAATTAATGTTTTCCACAGT
66 ATAATTACTAAATTAATATCTTAAAACTCACTCAAAAATAATATTAAATT-ATGTTTTCCACAGT
38330 GAAAAAAGTATGGACACTTTTATAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACAT
130 G-AAAAAGTATGGACACTTTTATAAAAGGATAGAAACTTTACAA-ATAACCACTA-CTATTACA-
38395 TATATAAACGATACCTATTACATTATAAGGGCTACCTATTACATCATATGTTTACC--TTATATT
191 T-TATAAACGATACCTATTACATTATAAGGGCTACCTATTACATCATATGTTTACCTATTATA-T
38458 GAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTT
254 GAAAGTGTCCATAC-TTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTT
38523 CAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACATATTGA-TTAATAATTTCATTTGCAG-A
318 CAA-TTTTTTAACAGTGTTTCATGTTTTCCACCTACA-ATTGATTTAAT-ATTTCATTTGCAGAA
* *
38586 AAAATTATTTGATTGTTTT-TATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAA-TA
380 AAAATTATTTGA-TGTTTTATATTTTAT-AAA-ATTATTTAGAATTTTTAATTTAATAAAAAGGA
*
38649 T-ATACCGTACGTAAAAAATAAATCATTAGACGCTAT-AA-TTACTAA
442 TCATACCGTACGTAAAAAATAAATAATT-GACG-TATCAATTTACTAA
38694 ATTAATATCT
Statistics
Matches: 459, Mismatches: 17, Indels: 30
0.91 0.03 0.06
Matches are distributed among these distances:
569 11 0.02
570 15 0.03
571 46 0.10
572 108 0.24
573 13 0.03
574 21 0.05
575 123 0.27
576 63 0.14
577 31 0.07
578 28 0.06
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (564 bp):
ATTATTTAGAATTTTTAATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCT
ATAATTACTAAATTAATATCTTAAAACTCACTCAAAAATAATATTAAATTATGTTTTCCACAGTG
AAAAAGTATGGACACTTTTATAAAAGGATAGAAACTTTACAAATAACCACTACTATTACATTATA
AACGATACCTATTACATTATAAGGGCTACCTATTACATCATATGTTTACCTATTATATGAAAGTG
TCCATACTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTT
TAACAGTGTTTCATGTTTTCCACCTACAATTGATTTAATATTTCATTTGCAGAAAAAATTATTTG
ATGTTTTATATTTTATAAAATTATTTAGAATTTTTAATTTAATAAAAAGGATCATACCGTACGTA
AAAAATAAATAATTGACGTATCAATTTACTAACAGTGTATCATCTTAACCACCTACAAAATTAAT
TTAAATTTCATTTACAGAAAAAAGTATTGAGTACATTTTATAAA
Found at i:38853 original size:23 final size:22
Alignment explanation
Indices: 38792--38855 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
38782 AAACTTTACA
* *
38792 ATATAACCACACCTATTACATT
1 ATATAACGATACCTATTACATT
38814 ATATAACGATACCTATTACATT
1 ATATAACGATACCTATTACATT
* *
38836 ATATAAGGGCTACCTATTAC
1 ATATAA-CGATACCTATTAC
38856 TCATATGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 26 0.70
23 11 0.30
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (22 bp):
ATATAACGATACCTATTACATT
Found at i:41231 original size:48 final size:46
Alignment explanation
Indices: 41175--41270 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 46
41165 AAGAAGTGCC
41175 GAAGAACAAGGTCGAGAAGAAATTAGGCGATGTGGGTACTGCAACGGT
1 GAAGAACAAGGTCGAGAAGAAATTAGGCGAT-TGGGTACTGC-ACGGT
41223 GAAGAACAAGGTCGAGAAGAAATTAGGCGATTGGGTACTGCACGGT
1 GAAGAACAAGGTCGAGAAGAAATTAGGCGATTGGGTACTGCACGGT
41269 GA
1 GA
41271 GGGCATAACA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 7 0.15
47 10 0.21
48 31 0.65
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.17
Consensus pattern (46 bp):
GAAGAACAAGGTCGAGAAGAAATTAGGCGATTGGGTACTGCACGGT
Found at i:41941 original size:181 final size:183
Alignment explanation
Indices: 41465--41959 Score: 826
Period size: 183 Copynumber: 2.7 Consensus size: 183
41455 TTCAAATTAC
* **
41465 CGACACTTTTTT-AATGGTATCGACAC-TTTTTATTCCAATGGGGACATAAAGTACCGACACATA
1 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACATA
41528 TTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTA
66 TTA-AAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTA
41593 TATTACAAAATTATCTATTACATTATAATTATGGGTTGCGATGTGTTAAAATGT
130 TATTACAAAATTATCTATTACATTATAATTATGGGTTGCGATGTGTTAAAATGT
*
41647 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACAC-AT
41712 ATT-AAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTA
65 ATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTA
41776 TATTACAAAATTA-CTATTACATTATAATTAT-GGTTGCGATGTG-TAAAATGT
130 TATTACAAAATTATCTATTACATTATAATTATGGGTTGCGATGTGTTAAAATGT
* *
41827 CGACACTTTTTTAAATCGTATCGACACATTTTTCTT-CAATATGTACATAAAGTACCGACACACT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACA-T
* *
41891 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATA-TTATACCGGTT
65 ATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
41955 ATATT
129 ATATT
41960 GCAATTTACC
Statistics
Matches: 299, Mismatches: 8, Indels: 14
0.93 0.02 0.04
Matches are distributed among these distances:
178 1 0.00
179 27 0.09
180 59 0.20
181 58 0.19
182 30 0.10
183 87 0.29
184 32 0.11
185 5 0.02
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACATA
TTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTAT
ATTACAAAATTATCTATTACATTATAATTATGGGTTGCGATGTGTTAAAATGT
Found at i:43419 original size:3 final size:3
Alignment explanation
Indices: 43411--43497 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
43401 ACTTGTTTGG
* * * **
43411 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
43459 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
43498 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:43434 original size:18 final size:18
Alignment explanation
Indices: 43411--43512 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
43401 ACTTGTTTGG
43411 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
43429 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
43447 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
43465 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
43483 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
43501 AGCTTCATCTTC
1 ATCATCATCTTC
43513 TGCGACCGCT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:43478 original size:42 final size:42
Alignment explanation
Indices: 43419--43509 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
43409 GGATCATCAT
*
43419 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
43461 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
43503 CTTCATC
1 CTTCATC
43510 TTCTGCGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:45307 original size:196 final size:197
Alignment explanation
Indices: 44956--46412 Score: 2517
Period size: 195 Copynumber: 7.5 Consensus size: 197
44946 ATTAGTATCG
44956 ACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACC-GTATAATTGTAC
1 ACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTAC
45020 CGGTTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC
66 CGG-TTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC
45084 TTTTTATATATGGATCGACAC-TTATGGGTGCA-CCTG-TTTCCATTCATTCTGGAAAAAAAATA
130 TTTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAATA
45146 TCGAC
193 TCGAC
45151 ACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCCGGTATAATTGTA
1 ACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAA-CCGGTATAATTGTA
45216 CCGGTTAGATTGAAAAA-TACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC
65 CCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC
*
45280 TTTTTTATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCA-TAATTCTGG-AAAAAATATC
130 TTTTTTATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATC
45343 GAC
195 GAC
45346 ACAAACTATATTAGTGTCG--ACATTATTTAGAC--ATCCTCTCATAAAACCGGTATAATTGTAC
1 ACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTAC
45407 CGGTTAGATTGAAAAATTACAT-TTACATTATACTTTTGGGTTC---GATTTTGGGATCGACAC-
66 CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACT
45467 TTTTTATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAAATAT
131 TTTTTATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG--AAAAAAATAT
45532 CGAC
194 CGAC
* *
45536 A-AAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA-CTGTATAATTGTAC
1 ACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTAC
45599 CGGTTTAGATTG-AAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGATCGACAC
66 CGG-TTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC
*
45662 TTTTATATATGGATCGACACTTTATGGGTGCACCCT-TTTTCCATTCATTCTGGAAAAAAATATC
130 TTTTTTATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATC
45726 GAC
195 GAC
*
45729 ACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG--TAATTGTA-
1 ACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTAC
45791 CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACT
66 CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACT
45856 TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATAT
131 TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAATAT
45921 CGAC
194 CGAC
45925 ACAAACTATATTAGTGTCGACACATTATTTAGACATAT-C-CTC-TAAAACCGGTA-AATTGTAC
1 ACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTAC
45986 CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACT
66 CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACT
* *
46051 TTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTCCATTCATTCTGGAAAAAAATATCG
131 TTTTTATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCG
46115 AC
196 AC
*
46117 ACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAACCGGTATAATTGTAC
1 ACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTAC
46181 CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACT
66 CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACT
*
46246 TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTAATTCTGGAAAAAAATATC
131 TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATC
46311 GAC
195 GAC
46314 ACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAAACCGGTATAATTGTA
1 ACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCAT-AAAACCGGTATAATTGTA
46379 CCGGTTAGATTGAAAAATTACATATTACATTATA
65 CCGGTTAGATTGAAAAATTACATATTACATTATA
46413 TGGATCGACA
Statistics
Matches: 1210, Mismatches: 13, Indels: 74
0.93 0.01 0.06
Matches are distributed among these distances:
186 43 0.04
187 25 0.02
189 17 0.01
190 66 0.05
191 40 0.03
192 112 0.09
193 127 0.10
194 132 0.11
195 296 0.24
196 190 0.16
197 105 0.09
198 6 0.00
199 51 0.04
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (197 bp):
ACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATAATTGTAC
CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACT
TTTTTATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATATCG
AC
Found at i:46606 original size:18 final size:19
Alignment explanation
Indices: 46561--46603 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
46551 TTATATTCAC
46561 ATACAAAA--ATAAATCGT
1 ATACAAAATTATAAATCGT
*
46578 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
46597 ATACAAA
1 ATACAAA
46604 TTAACTCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.35
19 15 0.65
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:48423 original size:33 final size:33
Alignment explanation
Indices: 48386--48451 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
48376 CATCTTAATA
*
48386 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
48419 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
48452 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:50785 original size:19 final size:19
Alignment explanation
Indices: 50740--50785 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
50730 TCCGGTATCA
50740 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
50759 TTGATACCGG-TTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
50779 TTTTACC
1 TTTTACC
50786 TGTTATATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.20, C:0.17, G:0.11, T:0.52
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:50933 original size:20 final size:20
Alignment explanation
Indices: 50907--50952 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
50897 CACTTTTAAA
*
50907 TTTACCGGTTTTATCAT-TT
1 TTTACCGGGTTTATCATATT
50926 TGTTACCGGGTTTATCATATT
1 T-TTACCGGGTTTATCATATT
50947 TTTACC
1 TTTACC
50953 TGGTATATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.52
Consensus pattern (20 bp):
TTTACCGGGTTTATCATATT
Found at i:50961 original size:20 final size:20
Alignment explanation
Indices: 50908--50961 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
50898 ACTTTTAAAT
* *
50908 TTACCGGTTTTATCATTTTG
1 TTACCGGGTATATCATTTTG
*
50928 TTACCGGGTTTATCATATTT-
1 TTACCGGGTATATCAT-TTTG
*
50948 TTACCTGGTATATC
1 TTACCGGGTATATC
50962 GTTTGGATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 27 0.90
21 3 0.10
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.50
Consensus pattern (20 bp):
TTACCGGGTATATCATTTTG
Found at i:60686 original size:20 final size:20
Alignment explanation
Indices: 60661--60776 Score: 90
Period size: 21 Copynumber: 5.7 Consensus size: 20
60651 GCGAAATAAA
60661 AATCGCAACGCGATTTCCAG
1 AATCGCAACGCGATTTCCAG
** * *
60681 AATCGCAAATCAATTCCCAG
1 AATCGCAACGCGATTTCCAG
**
60701 AATCGCAACGCGATTATGAAG
1 AATCGCAACGCGATT-TCCAG
* * *
60722 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGAT-TTCCAG
**
60742 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGA-TTTCCAG
60764 AATCGCAACGCGA
1 AATCGCAACGCGA
60777 ATATGAAAAT
Statistics
Matches: 72, Mismatches: 19, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
20 30 0.42
21 39 0.54
22 3 0.04
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (20 bp):
AATCGCAACGCGATTTCCAG
Found at i:60725 original size:21 final size:20
Alignment explanation
Indices: 60701--60833 Score: 83
Period size: 20 Copynumber: 6.5 Consensus size: 20
60691 CAATTCCCAG
60701 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
60721 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
60742 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
*
60764 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
60784 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
* *
60804 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
*
60824 TATCGCAACG
1 AATCGCAACG
60834 AGTATCCGTA
Statistics
Matches: 87, Mismatches: 17, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
19 2 0.02
20 46 0.53
21 35 0.40
22 3 0.03
23 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:60789 original size:20 final size:20
Alignment explanation
Indices: 60764--60978 Score: 132
Period size: 20 Copynumber: 10.7 Consensus size: 20
60754 GATTTTCCAG
*
60764 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
60784 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
60804 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
60824 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * *
60845 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
60865 AATCGCAAC-CACAATACGTAA
1 AATCGCAACGC-GAATACG-AA
* * *
60886 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * *
60906 AATCGCAATGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
60926 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* *
60946 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
*
60966 AATCGCAATGCGA
1 AATCGCAACGCGA
60979 TTTTGGTTTC
Statistics
Matches: 153, Mismatches: 32, Indels: 20
0.75 0.16 0.10
Matches are distributed among these distances:
19 4 0.03
20 112 0.73
21 36 0.24
22 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:60854 original size:81 final size:80
Alignment explanation
Indices: 60764--60980 Score: 215
Period size: 81 Copynumber: 2.7 Consensus size: 80
60754 GATTTTCCAG
* * * * *
60764 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCGATTCTG-ACTATC
1 AATCGCAACGCGTATCTGTAAATCGCAACGCGAACATATAAATCGCAACGCGATTCCGTA-AATC
* *
60828 GCAACGAGTATCCGTAA
65 GCAACGAGAATACGT-A
* * * *
60845 AATCGCAACGCGTATCCGTAAATCGCAACCACAATACGTA-AAATCGCAACGCG-TATCCGTAAA
1 AATCGCAACGCGTATCTGTAAATCGCAA-CGCGA-ACATATAAATCGCAACGCGAT-TCCGTAAA
*
60908 TCGCAATGAGAATACGTA
63 TCGCAACGAGAATACGTA
* * ** *
60926 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGATT
1 AATCGCAACGCGTATCTGTAAATCGCAACGCGAACATATAAATCGCAACGCGATT
60981 TTGGTTTCGC
Statistics
Matches: 109, Mismatches: 21, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
79 1 0.01
80 15 0.14
81 54 0.50
82 34 0.31
83 5 0.05
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (80 bp):
AATCGCAACGCGTATCTGTAAATCGCAACGCGAACATATAAATCGCAACGCGATTCCGTAAATCG
CAACGAGAATACGTA
Found at i:60856 original size:41 final size:40
Alignment explanation
Indices: 60764--60973 Score: 226
Period size: 40 Copynumber: 5.2 Consensus size: 40
60754 GATTTTCCAG
* ** * * * **
60764 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * * *
60804 AATCGCAACGCG-ATTC-TGACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGTATCCGT-A-AATCGCAACGAGAATACGT-A
* *
60845 AATCGCAACGCGTATCCGTAAATCGCAACCACAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-A
*
60886 AATCGCAACGCGTATCCGTAAATCGCAATGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
*
60926 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
60966 AATCGCAA
1 AATCGCAA
60974 TGCGATTTTG
Statistics
Matches: 144, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
39 3 0.02
40 71 0.49
41 65 0.45
42 4 0.03
43 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
Found at i:60940 original size:40 final size:41
Alignment explanation
Indices: 60825--60973 Score: 230
Period size: 41 Copynumber: 3.7 Consensus size: 41
60815 GATTCTGACT
* *
60825 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
60866 ATCGCAACCACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
60907 ATCGCAATGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
60947 ATCGCAACGAGAATACGT-AAATCGCAA
1 ATCGCAACGAGAATACGTAAAATCGCAA
60974 TGCGATTTTG
Statistics
Matches: 99, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 47 0.47
41 52 0.53
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:62564 original size:19 final size:18
Alignment explanation
Indices: 62540--62607 Score: 72
Period size: 19 Copynumber: 3.9 Consensus size: 18
62530 GCAACGAGAG
62540 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATG-A
*
62559 AATCGCAA--CG-AGTG-
1 AATCGCAATGCGAAATGA
62573 AATCGCAATGCGAAAATGA
1 AATCGCAATGCG-AAATGA
*
62592 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
62608 TAGTTTCGCG
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 7 0.17
19 19 0.46
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (18 bp):
AATCGCAATGCGAAATGA
Found at i:62566 original size:33 final size:34
Alignment explanation
Indices: 62524--62601 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 34
62514 TTAACTGTAT
62524 AAAATCGCAACGAGAGAATCGCAATGCG-AAATG
1 AAAATCGCAACGAGAGAATCGCAATGCGAAAATG
*
62557 AAAATCGCAACGAGTGAATCGCAATGCGAAAATG
1 AAAATCGCAACGAGAGAATCGCAATGCGAAAATG
62591 -AAATCGCAACG
1 AAAATCGCAACG
62602 CGAAATTAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
33 38 0.88
34 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (34 bp):
AAAATCGCAACGAGAGAATCGCAATGCGAAAATG
Found at i:62674 original size:33 final size:33
Alignment explanation
Indices: 62616--62712 Score: 131
Period size: 33 Copynumber: 2.8 Consensus size: 33
62606 ATTAGTTTCG
*
62616 CGTTGCGATTTTTTATTTTCGCATTGCGATTCACT
1 CGTTGCGA-TTTTCA-TTTCGCATTGCGATTCACT
*
62651 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
* *
62684 CGTTGCGATATTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
62713 ATATGTTTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
33 34 0.60
34 15 0.26
35 8 0.14
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:62829 original size:14 final size:14
Alignment explanation
Indices: 62810--62846 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
62800 CATCAATTAA
62810 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
62824 ACAAATCATCTTTT
1 ACAAATCAACATTT
62838 ACAAATCAA
1 ACAAATCAA
62847 TTAAACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Done.