Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007923.1 Hibiscus syriacus cultivar Beakdansim tig00110328_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: 8415618
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 40
Found at i:238439 original size:20 final size:20
Alignment explanation
Indices: 238416--238471 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
238406 TGAAATGAAA
238416 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
238436 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
238456 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
238472 CGCAACGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:238475 original size:14 final size:14
Alignment explanation
Indices: 238456--238511 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
238446 GGAAATGACT
238456 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
238470 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
238489 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
238503 ATCGCAACG
1 ATCGCAACG
238512 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:238493 original size:19 final size:19
Alignment explanation
Indices: 238407--238566 Score: 98
Period size: 19 Copynumber: 9.1 Consensus size: 19
238397 TCTTTTGGTT
*
238407 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
238426 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
238446 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
238464 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
238480 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
238497 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
238513 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
238530 G--A-GAGAATCGTAACGC
1 GAAATGAAAATCGCAACGC
*
238546 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
238565 GA
1 GA
238567 TTCTCTCGTT
Statistics
Matches: 109, Mismatches: 15, Indels: 34
0.69 0.09 0.22
Matches are distributed among these distances:
14 27 0.25
15 3 0.03
16 6 0.06
17 5 0.05
18 4 0.04
19 34 0.31
20 28 0.26
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:238493 original size:33 final size:33
Alignment explanation
Indices: 238407--238561 Score: 211
Period size: 33 Copynumber: 4.5 Consensus size: 33
238397 TCTTTTGGTT
238407 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-GA--ATCGCAACGC
**
238446 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
238480 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
238513 GAAATTAAAATCGCAACGAGAGAATCGTAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
238546 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
238562 TGCGATTCTC
Statistics
Matches: 108, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
33 77 0.71
34 10 0.09
36 2 0.02
37 1 0.01
38 3 0.03
40 15 0.14
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:238593 original size:21 final size:20
Alignment explanation
Indices: 238574--238645 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
238564 CGATTCTCTC
238574 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
238594 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
238615 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
238635 GTTGCGATTTT
1 GTTGCGATTTT
238646 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:239210 original size:20 final size:20
Alignment explanation
Indices: 239178--239390 Score: 146
Period size: 20 Copynumber: 10.7 Consensus size: 20
239168 CGCTTTAAAA
*
239178 ATCG-CGTTACGATTTACGT
1 ATCGTCGTTGCGATTTACGT
*
239197 ATTGTCGTTGCGATTTACAG-
1 ATCGTCGTTGCGATTTAC-GT
* *
239217 ATACG-CATTACGA-TTACGT
1 AT-CGTCGTTGCGATTTACGT
239236 ATTC-TCGTTGCGATTTACAG-
1 A-TCGTCGTTGCGATTTAC-GT
*
239256 ATAC-ACGTTGCGATTTACAG-
1 AT-CGTCGTTGCGATTTAC-GT
239276 ATACG-CGTTGCGATTTACGT
1 AT-CGTCGTTGCGATTTACGT
*
239296 ATTC-TCGTTGCGATTTACGG
1 A-TCGTCGTTGCGATTTACGT
239316 ATACG-CGTTGCGATTTTACGT
1 AT-CGTCGTTGCGA-TTTACGT
* *
239337 ATTGTCGTTGCGATTTACGG
1 ATCGTCGTTGCGATTTACGT
*
239357 ATACG-CGTTGCGATTTACGG
1 AT-CGTCGTTGCGATTTACGT
239377 ATAC-TCGTTGCGAT
1 AT-CGTCGTTGCGAT
239391 AGTCAGAATC
Statistics
Matches: 162, Mismatches: 13, Indels: 37
0.76 0.06 0.17
Matches are distributed among these distances:
18 1 0.01
19 18 0.11
20 122 0.75
21 21 0.13
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGTCGTTGCGATTTACGT
Found at i:239237 original size:39 final size:40
Alignment explanation
Indices: 239184--239293 Score: 143
Period size: 39 Copynumber: 2.8 Consensus size: 40
239174 AAAAATCGCG
*
239184 TTACGATTTACGTATTGTCGTTGCGATTTACAGATACGCA
1 TTACGATTTACGTATTCTCGTTGCGATTTACAGATACGCA
* *
239224 TTACGA-TTACGTATTCTCGTTGCGATTTACAGATACACG
1 TTACGATTTACGTATTCTCGTTGCGATTTACAGATACGCA
* * *
239263 TTGCGATTTACAG-ATACGCGTTGCGATTTAC
1 TTACGATTTAC-GTATTCTCGTTGCGATTTAC
239294 GTATTCTCGT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
39 35 0.56
40 26 0.42
41 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (40 bp):
TTACGATTTACGTATTCTCGTTGCGATTTACAGATACGCA
Found at i:239305 original size:40 final size:40
Alignment explanation
Indices: 239241--239451 Score: 221
Period size: 40 Copynumber: 5.2 Consensus size: 40
239231 TACGTATTCT
* *
239241 CGTTGCGATTTACAG-ATACACGTTGCGATTTACAGATACG
1 CGTTGCGATTTAC-GTATTCTCGTTGCGATTTACAGATACG
*
239281 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
* *
239321 CGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCTCGTTGCGATTTACAGATACG
* * *
239362 CGTTGCGATTTACGGATACTCGTTGCGATAGT-CAGA-ATCG
1 CGTTGCGATTTACGTATTCTCGTTGCGAT-TTACAGATA-CG
** * * * * **
239402 CGTTGCGATTTATATGTTCGCGTTGCGATTTTCATATTTG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
239442 CGTTGCGATT
1 CGTTGCGATT
239452 CTGGAAAATC
Statistics
Matches: 146, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
39 3 0.02
40 103 0.71
41 40 0.27
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
Found at i:239380 original size:101 final size:99
Alignment explanation
Indices: 239180--239390 Score: 314
Period size: 101 Copynumber: 2.1 Consensus size: 99
239170 CTTTAAAAAT
* *
239180 CGCGTTACGATTTACGTATTGTCGTTGCGATTTACAGATACGCATTACGATTACGTATTCTCGTT
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCATTACGATTACGTATTCTCGTT
239245 GCGATTTACAGATACACGTTGCGATTTACAGATA
66 GCGATTTACAGATACACGTTGCGATTTACAGATA
* * * *
239279 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCG
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCATTACGA--TTACGTATTCTCG
* * *
239344 TTGCGATTTACGGATACGCGTTGCGATTTACGGATA
64 TTGCGATTTACAGATACACGTTGCGATTTACAGATA
*
239380 CTCGTTGCGAT
1 CGCGTTGCGAT
239391 AGTCAGAATC
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
99 45 0.45
101 55 0.55
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (99 bp):
CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCATTACGATTACGTATTCTCGTT
GCGATTTACAGATACACGTTGCGATTTACAGATA
Found at i:239404 original size:81 final size:81
Alignment explanation
Indices: 239261--239451 Score: 228
Period size: 81 Copynumber: 2.4 Consensus size: 81
239251 TACAGATACA
* * * *
239261 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTG
1 CGTTGCGATTTACAGATACGCGTTGCGATTTACGGATACTCGTTGCGATTCACGAATACGCGTTG
239326 CGATTTTACGTATTGT
66 CGATTTTACGTATTGT
*
239342 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACTCGTTGCGATAGTCA-GAAT-CGCGT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTACGGATACTCGTTGCGAT--TCACGAATACGCGT
* *
239405 TGCGATTTATATGT-TCG-
64 TGCGATTT-TACGTATTGT
* * **
239422 CGTTGCGATTTTCATATTTGCGTTGCGATT
1 CGTTGCGATTTACAGATACGCGTTGCGATT
239452 CTGGAAAATC
Statistics
Matches: 95, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
80 25 0.26
81 61 0.64
82 7 0.07
83 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (81 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTACGGATACTCGTTGCGATTCACGAATACGCGTTG
CGATTTTACGTATTGT
Found at i:239406 original size:101 final size:100
Alignment explanation
Indices: 239180--239451 Score: 288
Period size: 101 Copynumber: 2.7 Consensus size: 100
239170 CTTTAAAAAT
* * * * *
239180 CGCGTTACGATTTACGT-ATTGTCGTTGCGATTTACAGATACGCATTACGA--TTACGTATTCTC
1 CGCGTTGCGATTCACGTAATCG-CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATT-TC
239242 GTTGCGATTTACAGATACACGTTGCGATTTACAGATA
64 GTTGCGATTTACAGATACACGTTGCGATTTACAGATA
* * * *
239279 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCG
1 CGCGTTGCGATTCACGTAATCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATT-TCG
* * *
239344 TTGCGATTTACGGATACGCGTTGCGATTTACGGATA
65 TTGCGATTTACAGATACACGTTGCGATTTACAGATA
* * * *
239380 CTCGTTGCGATAGTCA-G-AATCGCGTTGCGATTTATATG-TTCGCGTTGCGATTTT-CATATTT
1 CGCGTTGCGAT--TCACGTAATCGCGTTGCGATTTACA-GATACGCGTTGCGATTTTACGTATTT
239441 GCGTTGCGATT
63 -CGTTGCGATT
239452 CTGGAAAATC
Statistics
Matches: 147, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
99 42 0.29
100 16 0.11
101 85 0.58
102 2 0.01
103 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (100 bp):
CGCGTTGCGATTCACGTAATCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTTCGT
TGCGATTTACAGATACACGTTGCGATTTACAGATA
Found at i:239422 original size:20 final size:20
Alignment explanation
Indices: 239399--239451 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
239389 ATAGTCAGAA
239399 TCGCGTTGCGATTT-ATATGT
1 TCGCGTTGCGATTTCATAT-T
239419 TCGCGTTGCGATTTTCATATT
1 TCGCGTTGCGA-TTTCATATT
239440 T-GCGTTGCGATT
1 TCGCGTTGCGATT
239452 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.06
20 20 0.65
21 5 0.16
22 4 0.13
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTCATATT
Found at i:242688 original size:29 final size:31
Alignment explanation
Indices: 242654--242711 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
242644 TGACCACATC
242654 TTAATTAAAT-AAAAC-AAAGTAACCATATT
1 TTAATTAAATAAAAACAAAAGTAACCATATT
*
242683 TTAATTAAATAAAAACAAAAGTGACCATA
1 TTAATTAAATAAAAACAAAAGTAACCATA
242712 ATTTGTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.38
30 5 0.19
31 11 0.42
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (31 bp):
TTAATTAAATAAAAACAAAAGTAACCATATT
Found at i:245315 original size:12 final size:13
Alignment explanation
Indices: 245293--245333 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
245283 GTATGTATAC
245293 TTGATTATATGA-A
1 TTGA-TATATGATA
245306 TTGATATATGATA
1 TTGATATATGATA
245319 TATGATATATGATA
1 T-TGATATATGATA
245333 T
1 T
245334 ATGTGATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.27
13 6 0.23
14 13 0.50
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TTGATATATGATA
Found at i:245319 original size:7 final size:7
Alignment explanation
Indices: 245298--245336 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
245288 TATACTTGAT
245298 TATATGA
1 TATATGA
245305 -AT-TGA
1 TATATGA
245310 TATATGA
1 TATATGA
245317 TATATGA
1 TATATGA
245324 TATATGA
1 TATATGA
245331 TATATG
1 TATATG
245337 TGATGCATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 3 0.10
6 4 0.13
7 23 0.77
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (7 bp):
TATATGA
Found at i:256418 original size:9 final size:9
Alignment explanation
Indices: 256394--256434 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
256384 TAAAAACAGT
256394 AAATAAA-A
1 AAATAAATA
*
256402 AGATAAATA
1 AAATAAATA
256411 AAATAAATA
1 AAATAAATA
256420 AAATAAATA
1 AAATAAATA
256429 AAATAA
1 AAATAA
256435 GAAGAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 6 0.20
9 24 0.80
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (9 bp):
AAATAAATA
Found at i:257920 original size:2 final size:2
Alignment explanation
Indices: 257908--257943 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
257898 AAGAGATTAA
257908 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
257944 ATGTATATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:258582 original size:11 final size:11
Alignment explanation
Indices: 258562--258601 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
258552 AAAGTTACTA
*
258562 TAGCAATATTG
1 TAGCAGTATTG
258573 TAGCAGTATTG
1 TAGCAGTATTG
258584 TAGCAGTATTG
1 TAGCAGTATTG
258595 TAGCAGT
1 TAGCAGT
258602 GCATCGATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (11 bp):
TAGCAGTATTG
Found at i:261271 original size:36 final size:36
Alignment explanation
Indices: 261216--261295 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
261206 CCCATTCTTA
* *
261216 TTTTC-AACAAACATCTACCAAACTTTGAAAAATAT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
*
261251 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
261287 TTTTCAAAG
1 TTTTCAAAG
261296 TTGGTTGCCG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 5 0.12
36 36 0.88
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (36 bp):
TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
Found at i:261294 original size:21 final size:21
Alignment explanation
Indices: 261234--261294 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
261224 AAACATCTAC
*
261234 CAAACTTTGAAAAATATTTTT
1 CAAACTTTGAAAAACATTTTT
**
261255 CAAA----G--AAACATTTAC
1 CAAACTTTGAAAAACATTTTT
261270 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
261291 CAAA
1 CAAA
261295 GTTGGTTGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 12
0.63 0.11 0.26
Matches are distributed among these distances:
15 11 0.38
17 1 0.03
19 1 0.03
21 16 0.55
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.33
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:265819 original size:21 final size:20
Alignment explanation
Indices: 265795--265855 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
265785 CAAACTTTAC
265795 CAAACTTTGAAAAACATTTTT
1 CAAA-TTTGAAAAACATTTTT
**
265816 CAAA---G--AAACATTTAC
1 CAAATTTGAAAAACATTTTT
265831 CAAAATTTGAAAAACATTTTT
1 C-AAATTTGAAAAACATTTTT
265852 CAAA
1 CAAA
265856 GTTGGTTGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 13
0.64 0.09 0.28
Matches are distributed among these distances:
15 9 0.30
16 3 0.10
17 1 0.03
19 1 0.03
20 3 0.10
21 13 0.43
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (20 bp):
CAAATTTGAAAAACATTTTT
Found at i:265831 original size:36 final size:35
Alignment explanation
Indices: 265786--265856 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
265776 AACATCTACC
*
265786 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAACTTTACCAAAATTTGAAAAACATTTTTCAAAG
265821 AAACATTTACCAAAATTTGAAAAACATTTTTCAAAG
1 AAAC-TTTACCAAAATTTGAAAAACATTTTTCAAAG
265857 TTGGTTGTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (35 bp):
AAACTTTACCAAAATTTGAAAAACATTTTTCAAAG
Found at i:267341 original size:22 final size:22
Alignment explanation
Indices: 267310--267366 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
267300 CGAGTCAAGT
*
267310 TTTTTTGAGTCGAAAAATTCAG
1 TTTTTCGAGTCGAAAAATTCAG
267332 TTTTTCGAGTCGAAAAATTCAG
1 TTTTTCGAGTCGAAAAATTCAG
267354 TTTTTCGAGTCGA
1 TTTTTCGAGTCGA
267367 GTCGAGTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40
Consensus pattern (22 bp):
TTTTTCGAGTCGAAAAATTCAG
Found at i:277506 original size:2 final size:2
Alignment explanation
Indices: 277499--277528 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
277489 TAAACAAAGT
277499 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
277529 ACCTTATCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:278243 original size:10 final size:10
Alignment explanation
Indices: 278228--278253 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
278218 TTCTATAAAG
278228 TATATATAGT
1 TATATATAGT
278238 TATATATAGT
1 TATATATAGT
278248 TATATA
1 TATATA
278254 ATTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (10 bp):
TATATATAGT
Found at i:278426 original size:2 final size:2
Alignment explanation
Indices: 278419--278445 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
278409 TAGAAAAATA
278419 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
278446 GTTTTTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:295115 original size:22 final size:22
Alignment explanation
Indices: 295090--295138 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
295080 TGTAATTGTA
295090 ATTTTTTATTATAATTTGAGAT
1 ATTTTTTATTATAATTTGAGAT
295112 ATTTTTTATTATAATTTGAGAT
1 ATTTTTTATTATAATTTGAGAT
295134 ATTTT
1 ATTTT
295139 AATTGCTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (22 bp):
ATTTTTTATTATAATTTGAGAT
Found at i:302449 original size:4 final size:4
Alignment explanation
Indices: 302440--302494 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
302430 TTCAACTATG
302440 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
302488 TATT TAT
1 TATT TAT
302495 ACATGCATTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:303803 original size:64 final size:63
Alignment explanation
Indices: 303735--303913 Score: 209
Period size: 64 Copynumber: 2.8 Consensus size: 63
303725 TGGAACACTT
* * * *
303735 AGTGCATCGGTGCACCAAGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAGCCA
1 AGTGCATCGGTGCA-TAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
* * * *
303798 GAGTGCATCAGTGCAT-TGCTTGTGCATCGATGCATGAAATGCATTCGAGGTTTTAATAAAACCC
1 -AGTGCATCGGTGCATAAG--TGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCC
303862 A
63 A
* *
303863 AGTGCATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGGTGCATA-AGTGTGCATCGATGCATGAAATGCATTCGATGTT
303914 CAATTTATTC
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
62 1 0.01
64 89 0.92
65 6 0.06
66 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (63 bp):
AGTGCATCGGTGCATAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
Found at i:303932 original size:64 final size:65
Alignment explanation
Indices: 303755--303962 Score: 187
Period size: 64 Copynumber: 3.2 Consensus size: 65
303745 TGCACCAAGT
* * * * * * *
303755 GTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAGCCAGAGTGCATC-AGTGCATTGCT
1 GTGCATCGATGCATGAAATGCATTCGAGGTTTCAATAAAACCCA-AGTGCATCGA-TGCATAGAT
*
303818 -T
64 GA
*
303819 GTGCATCGATGCATGAAATGCATTCGAGGTTTTAATAAAACCCAAGTGCATCGATGCATAGA-GA
1 GTGCATCGATGCATGAAATGCATTCGAGGTTTCAATAAAACCCAAGTGCATCGATGCATAGATGA
* ** ** *
303883 GTGCATCGATGCATGAAATGCATTCGATG-TTCAAT-TTATTCAATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGAGGTTTCAATAAAACCCAA--GTGCATCGATGCATAGA-
303946 TGA
63 TGA
303949 -TGCATCGATGCATG
1 GTGCATCGATGCATG
303963 CCTTTGAAAA
Statistics
Matches: 122, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
62 4 0.03
63 5 0.04
64 90 0.74
65 21 0.17
66 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGAGGTTTCAATAAAACCCAAGTGCATCGATGCATAGATGA
Found at i:304333 original size:19 final size:20
Alignment explanation
Indices: 304295--304334 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
304285 CTTGAAATTA
*
304295 CTCCCCCTTACTATAACATTT
1 CTCCCCCTTA-TAAAACATTT
304316 CTCCCCCTT-TAAAACATTT
1 CTCCCCCTTATAAAACATTT
304335 TACACTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (20 bp):
CTCCCCCTTATAAAACATTT
Found at i:309985 original size:3 final size:3
Alignment explanation
Indices: 309979--310020 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
309969 TTTTTTTATT
*
309979 TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
310021 ATTAATGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:310288 original size:76 final size:76
Alignment explanation
Indices: 310175--311316 Score: 1933
Period size: 76 Copynumber: 14.9 Consensus size: 76
310165 ACTCTGAGGG
* *
310175 TTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAGCATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
* *
310240 GACCCTGAGGA
66 GACCCTAAGGC
* *
310251 TTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTTGGAAGCATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
* *
310316 GACCTTAAGGT
66 GACCCTAAGGC
310327 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
310392 GACCCTAAGGC
66 GACCCTAAGGC
310403 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
310468 GACCCTAAGGC
66 GACCCTAAGGC
**
310479 TTTGAAAACATCAAAAAAATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
* *
310544 GACTCTAAGGT
66 GACCCTAAGGC
*
310555 TTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
310620 GACCCTAAGGC
66 GACCCTAAGGC
*
310631 TTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTTTTTTGGAAACATCATGCACTGAAGGACTTA
1 TTTGAAAACATCAAAAAGCTCCCGAAGGC-----TTTTTGGAAACATCATGCACTGAAGGACTTA
*
310696 CAGATGACCCTAAGGT
61 CAGATGACCCTAAGGC
*
310712 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTAGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
310777 GACCCTAAGGC
66 GACCCTAAGGC
*
310788 TTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTTTTTTTTGGAAACATCATGCACTGAAGGACT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGC-------TTTTTGGAAACATCATGCACTGAAGGACT
*
310853 TACAGATGACCCTAAGGT
59 TACAGATGACCCTAAGGC
*
310871 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTAGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
310936 GACCCTAAGGC
66 GACCCTAAGGC
**
310947 TTTGAAAACATCAAAAAAATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
*
311012 GACCCTAAGGT
66 GACCCTAAGGC
311023 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
311088 GACCCTAAGGC
66 GACCCTAAGGC
* *
311099 TTTGAAAACATCAAAAAACTCCCGAAAGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
311164 GACCCTAAGGC
66 GACCCTAAGGC
**
311175 TTTGAAAACATCAAAAAAATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
311240 GACCCTAAGGC
66 GACCCTAAGGC
*
311251 TTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
311316 G
66 G
311317 TGGGAAATAG
Statistics
Matches: 1014, Mismatches: 40, Indels: 24
0.94 0.04 0.02
Matches are distributed among these distances:
76 867 0.86
81 74 0.07
83 73 0.07
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (76 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
GACCCTAAGGC
Found at i:312017 original size:22 final size:22
Alignment explanation
Indices: 311992--312046 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
311982 CATAAAGTTT
*
311992 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
312014 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
312036 TCATCTTTGAA
1 TCATCTTTGAA
312047 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:315034 original size:83 final size:83
Alignment explanation
Indices: 314889--315239 Score: 589
Period size: 83 Copynumber: 4.2 Consensus size: 83
314879 CTTATTTCTA
*
314889 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
314954 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
314972 CTATTG-GCAAATTCATCTTTTAAATTCAATGATTGGTTCAGCCAAACCAGATCAGATAACTCAA
1 CTA-TGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAA
315036 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* * *
315055 CTATGAACACATTCATCTTCTAAATTCAATGATTTGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
315120 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * *
315138 CTATGAACACATTCATCTTCTAAATTCAATGATTTGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
315203 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
315221 CTATTG-GCAAATTCATCTT
1 CTA-TGAGCAAATTCATCTT
315240 TCAGTTAATG
Statistics
Matches: 255, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
82 2 0.01
83 249 0.98
84 4 0.02
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:317518 original size:15 final size:14
Alignment explanation
Indices: 317494--317559 Score: 71
Period size: 14 Copynumber: 4.6 Consensus size: 14
317484 CTTGATTCAA
* *
317494 TTTTCCTTTTTCTT
1 TTTTTCTTTTTTTT
317508 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
*
317522 TATTCTCTTTTTTTT
1 T-TTTTCTTTTTTTT
*
317537 CTTTTT-TTTTTATT
1 -TTTTTCTTTTTTTT
317551 TTTTTCTTT
1 TTTTTCTTT
317560 GCTGGATGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
13 5 0.11
14 23 0.52
15 15 0.34
16 1 0.02
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:317522 original size:11 final size:11
Alignment explanation
Indices: 317500--317555 Score: 69
Period size: 11 Copynumber: 5.2 Consensus size: 11
317490 TCAATTTTCC
317500 TTTTTCTTTTT
1 TTTTTCTTTTT
*
317511 TTCTT-TTTTT
1 TTTTTCTTTTT
* *
317521 TTATTCTCTTT
1 TTTTTCTTTTT
317532 TTTTTCTTTTT
1 TTTTTCTTTTT
*
317543 TTTTTATTTTT
1 TTTTTCTTTTT
317554 TT
1 TT
317556 CTTTGCTGGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
10 9 0.24
11 29 0.76
ACGTcount: A:0.04, C:0.09, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:324301 original size:3 final size:3
Alignment explanation
Indices: 324295--324330 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
324285 TTTTTTTATT
* *
324295 TAA TAA TAA TAC TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
324331 AAAAATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:327984 original size:64 final size:64
Alignment explanation
Indices: 327852--328014 Score: 177
Period size: 64 Copynumber: 2.5 Consensus size: 64
327842 TGGAACACTT
* * * ** **
327852 AGTGCATCGGTGCACCA-AGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAGTCTG
1 AGTGCATCGATGCA-TAGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAACCCA
* * ** *
327916 AGTGCATCGGTGCATTGCTTGTGCATCGATGCATGAAATGCATTCGATGTTTTAATAA-AACCCA
1 AGTGCATCGATGCATAGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA-AATAACCCA
*
327980 AGTGCATCGATGCATAGAGGGTGCATCGATGCATG
1 AGTGCATCGATGCATAGAGTGTGCATCGATGCATG
328015 CCTTTGAAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
64 80 0.98
65 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (64 bp):
AGTGCATCGATGCATAGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAACCCA
Found at i:334090 original size:28 final size:28
Alignment explanation
Indices: 334018--334111 Score: 84
Period size: 28 Copynumber: 3.3 Consensus size: 28
334008 TTAAATAGTT
* * *
334018 ATTATATTTTATCTTAATATAATTATATA
1 ATTAT-TTTTATATTAAAATATTTATATA
* *
334047 AATATTTTTTTATTAAAATATTTATATA
1 ATTATTTTTATATTAAAATATTTATATA
* *
334075 ATTATTATTTAT-TTAAATTTATTAAT-TA
1 ATTATT-TTTATATTAAA-ATATTTATATA
334103 ATTATTTTT
1 ATTATTTTT
334112 TGTGCTAATT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
27 3 0.06
28 37 0.69
29 14 0.26
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTATTTTTATATTAAAATATTTATATA
Found at i:335912 original size:21 final size:21
Alignment explanation
Indices: 335888--335960 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
335878 TATGTCATCT
* *
335888 CCGCAGGGTTATATTCCAAGC
1 CCGCAGGGTTACATTCCTAGC
335909 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
335930 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
*
335951 CTGCAGGGTT
1 CCGCAGGGTT
335961 TTATACCATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.04
21 42 0.91
22 2 0.04
ACGTcount: A:0.19, C:0.32, G:0.26, T:0.23
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:336545 original size:34 final size:34
Alignment explanation
Indices: 336472--336538 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
336462 AATAAATGTT
336472 TTTAAAACACAAATTATAGTATTCGAAATTTAAA
1 TTTAAAACACAAATTATAGTATTCGAAATTTAAA
* *
336506 TTTAAAATATAAATTATAGTATTCGAAATTTAA
1 TTTAAAACACAAATTATAGTATTCGAAATTTAA
336539 CATTAAATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (34 bp):
TTTAAAACACAAATTATAGTATTCGAAATTTAAA
Found at i:337194 original size:127 final size:127
Alignment explanation
Indices: 336968--337545 Score: 998
Period size: 127 Copynumber: 4.6 Consensus size: 127
336958 GCGCTTTAAA
*
336968 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
* * *
337033 TAATGATAACATATTATCTGACAAAATAATGGAAGGCGCGCACCCGGGAACGCGTCTTCACG
66 TAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
*
337095 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
*
337160 TAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGTCTTCACG
66 TAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
* *
337222 GTCCCCTAAGGAATAATATGTATTGACATGAATAGTTTTCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
*
337287 TAATGATAACATATTCTCTGACAAAATAATGGAA-G-GCGCCCCCGGGAACACGCCTTCACG
66 TAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
* * *
337347 GTCCCCTAGGGAATAATATGTATTGACATGAATAGTTATCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
* * *
337412 TAATGATAACATATTCTCTGACTAAATAATGGAAGGCACGCCCCCGGGAACGCGCCGTCACG
66 TAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
*
337474 GTCCCCTAAGGAATAATAGGTATTGATATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
337539 TAATGAT
66 TAATGAT
337546 GTAACATCCC
Statistics
Matches: 432, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
125 119 0.28
126 2 0.00
127 311 0.72
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (127 bp):
GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
TAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
Found at i:337441 original size:252 final size:254
Alignment explanation
Indices: 336968--337545 Score: 1007
Period size: 252 Copynumber: 2.3 Consensus size: 254
336958 GCGCTTTAAA
*
336968 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
* *
337033 TAATGATAACATATTATCTGACAAAATAATGGAAGGCGCGCACCCGGGAACGCGTCTTCACGGTC
66 TAATGATAACATATTATCTGACAAAATAATGGAAGGCGCGCACCCGGGAACACGCCTTCACGGTC
*
337098 CCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGGTAA
131 CCCTAAGGAATAATAGGTATTGACATGAATAGTTACCGGGGGACATAAGTGACATAATAGGGTAA
* * *
337163 TGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGTCTTCACG
196 TGATAACATATTCTCTGACAAAATAATGGAAGGCACGCCCCCGGGAACGCGCCGTCACG
* *
337222 GTCCCCTAAGGAATAATATGTATTGACATGAATAGTTTTCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
*
337287 TAATGATAACATATTCTCTGACAAAATAATGGAAGGCGC-C-CCCGGGAACACGCCTTCACGGTC
66 TAATGATAACATATTATCTGACAAAATAATGGAAGGCGCGCACCCGGGAACACGCCTTCACGGTC
* * *
337350 CCCTAGGGAATAATATGTATTGACATGAATAGTTATCGGGGGACATAAGTGACATAATAGGGTAA
131 CCCTAAGGAATAATAGGTATTGACATGAATAGTTACCGGGGGACATAAGTGACATAATAGGGTAA
*
337415 TGATAACATATTCTCTGACTAAATAATGGAAGGCACGCCCCCGGGAACGCGCCGTCACG
196 TGATAACATATTCTCTGACAAAATAATGGAAGGCACGCCCCCGGGAACGCGCCGTCACG
*
337474 GTCCCCTAAGGAATAATAGGTATTGATATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
337539 TAATGAT
66 TAATGAT
337546 GTAACATCCC
Statistics
Matches: 307, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
252 206 0.67
253 1 0.00
254 100 0.33
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (254 bp):
GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
TAATGATAACATATTATCTGACAAAATAATGGAAGGCGCGCACCCGGGAACACGCCTTCACGGTC
CCCTAAGGAATAATAGGTATTGACATGAATAGTTACCGGGGGACATAAGTGACATAATAGGGTAA
TGATAACATATTCTCTGACAAAATAATGGAAGGCACGCCCCCGGGAACGCGCCGTCACG
Found at i:339189 original size:31 final size:31
Alignment explanation
Indices: 339151--339275 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
339141 AGGGTCGAGG
339151 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
339182 GTTTACCTATGTTCTTCGGGACATATTGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
339213 GTTTACCTACGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
339244 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
339275 G
1 G
339276 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:343743 original size:16 final size:16
Alignment explanation
Indices: 343722--343754 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
343712 GGTCAAATCG
343722 CCCAAAATGTGTGCAA
1 CCCAAAATGTGTGCAA
343738 CCCAAAATGTGTGCAA
1 CCCAAAATGTGTGCAA
343754 C
1 C
343755 TGAAGGGTTT
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:0.36, C:0.27, G:0.18, T:0.18
Consensus pattern (16 bp):
CCCAAAATGTGTGCAA
Found at i:344628 original size:32 final size:31
Alignment explanation
Indices: 344564--344636 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 31
344554 CATATTAAGA
** *
344564 TTATTAAATTATTATAAAACGATTGTTTAATT
1 TTATTAAATTATTATAAAACGA-TCATTAAAT
344596 TTATTAAATTATTATAAAAC-AGTCATTAAAT
1 TTATTAAATTATTATAAAACGA-TCATTAAAT
*
344627 TTAATAAATT
1 TTATTAAATT
344637 CCACATTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 16 0.44
32 20 0.56
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (31 bp):
TTATTAAATTATTATAAAACGATCATTAAAT
Found at i:349849 original size:23 final size:23
Alignment explanation
Indices: 349819--349870 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
349809 AACCCTAATT
349819 AAGCTTGTAAACATTTTTTCTCA
1 AAGCTTGTAAACATTTTTTCTCA
349842 AAGCTTGTAAACATTTTTTCTCA
1 AAGCTTGTAAACATTTTTTCTCA
349865 AAGCTT
1 AAGCTT
349871 TTGAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (23 bp):
AAGCTTGTAAACATTTTTTCTCA
Found at i:353929 original size:17 final size:17
Alignment explanation
Indices: 353896--353937 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
353886 AAATTTGAGA
353896 ATTTAAAAATGTGAATT
1 ATTTAAAAATGTGAATT
353913 ATTGTAAAAATGT-AATT
1 ATT-TAAAAATGTGAATT
353930 ATTTAAAA
1 ATTTAAAA
353938 TAATATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.21
17 10 0.42
18 9 0.38
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (17 bp):
ATTTAAAAATGTGAATT
Found at i:354033 original size:17 final size:17
Alignment explanation
Indices: 354011--354043 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
354001 CACTACCATA
*
354011 ATATTATTTTTTATATT
1 ATATTATATTTTATATT
354028 ATATTATATTTTATAT
1 ATATTATATTTTATAT
354044 AAATAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:357357 original size:14 final size:14
Alignment explanation
Indices: 357338--357369 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
357328 AAAACAACGC
357338 ACATCAATGATTCA
1 ACATCAATGATTCA
357352 ACATCAATGATTCA
1 ACATCAATGATTCA
357366 ACAT
1 ACAT
357370 GATTTTATCC
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:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (14 bp):
ACATCAATGATTCA
Found at i:367677 original size:39 final size:38
Alignment explanation
Indices: 367623--367708 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 38
367613 TCAAGTTGTA
*
367623 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGA-ATTTG
*
367662 GATTTTGATTTCCTTTTGCTTGGCACCATATGACTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAATTTG
367700 GATTTTGAT
1 GATTTTGAT
367709 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 13 0.29
39 32 0.71
ACGTcount: A:0.17, C:0.14, G:0.20, T:0.49
Consensus pattern (38 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAATTTG
Found at i:368430 original size:21 final size:22
Alignment explanation
Indices: 368382--368443 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
368372 ACAATAACCA
368382 CTACCTATTACATTATATAAACG
1 CTACCTATTACA-TATATAAACG
* **
368405 ATACCTATTACAT-TATAAGGG
1 CTACCTATTACATATATAAACG
368426 CTACCTATTACATCATAT
1 CTACCTATTACAT-ATAT
368444 GTTTACCTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 18 0.55
22 1 0.03
23 14 0.42
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35
Consensus pattern (22 bp):
CTACCTATTACATATATAAACG
Found at i:368837 original size:23 final size:23
Alignment explanation
Indices: 368778--368849 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
368768 ACACTTTACA
* *
368778 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
368801 ATATAAACGATACCTATTACATT
1 ATATAAACGCTACCTATTACATT
** *
368824 ATATAAGGGCTACCTA-TACATC
1 ATATAAACGCTACCTATTACATT
368846 ATAT
1 ATAT
368850 TTTACCTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 9 0.21
23 33 0.79
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:369163 original size:415 final size:411
Alignment explanation
Indices: 368283--369323 Score: 1745
Period size: 415 Copynumber: 2.6 Consensus size: 411
368273 AACAATGTTC
368283 TATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGGACA
1 TATCTTAAAACTCACTC-AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGGACA
368348 CTTTTAT-AAAAGGATAGACACTTTAC-A-ATAACCACTACCTATTACATTATATAAACGATACC
65 CTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACC
368410 TATTACA-T-TATAAGGGCTACCTATTACATCATATGTTTACCTATATATTGAAGTGTCCATACT
130 TATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATATATTGAAGTGTCCATACT
368473 TTTT-T-AAAAGGATCGATA-TTTTTTT-AAACTTATGTAATTTGTTTCAATTTTTTTAACAGTT
195 TTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTGTTTCAATTTTTTTAACAGTT
368534 TCATGTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTT
260 TCATGTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTT
368599 TATATTTTAAAATATTATTTAGAATTTTTTTTAATAATAATATACCGTACGTAAAAAATAAATCA
325 TATATTTTAAAATATTATTTAGAATTTTTTTTAATAATAATATACCGTACGTAAAAAATAAATCA
368664 TTAGACGCCTATAATTACTAAA
390 TTAGACGCCTATAATTACTAAA
368686 TATCTTAAAACTCACTCAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGGACAC
1 TATCTTAAAACTCACTCAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGGACAC
368751 TTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCT
66 TTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCT
368816 ATTACATTATATAAGGGCTACCTA-TACATCATAT-TTTACCTATTATATTGAAGTGTCCATACT
131 ATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTA-TATATTGAAGTGTCCATACT
*
368879 TTTTATAAAAATGATCGATACTTTTTTTAAAACTTAT-TAATTTATGTTTCAATTTTTTTAACAG
195 TTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAA-TT-TGTTTCAATTTTTTTAACA-
368943 TGTTTCATGTTTTCCACCTACAATA-TGATTT-ATAATTTCATTTGCACAAAAAATTATTTGATT
257 -GTTTCATG-TTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
369006 GTTTTTATATTTTATAAATATTA-TTAGAATTTTTAATTTAATAATAATAATACCGTAACGT-AA
320 GTTTTTATATTTTA-AAATATTATTTAGAATTTTT--TTTAATAATAAT-ATACCGT-ACGTAAA
369069 AAATAAATCATTAGACGCCTAT-A-TACTAAATAA
380 AAATAAATCATTAGACGCCTATAATTACT--A-AA
369102 TATCTTAAAACTCACTCAAAGATAA-CTTAAATTAAT-TTTTCCACAGTGAAAAAAGTATGGACA
1 TATCTTAAAACTCACTCAAAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAGTATGGACA
369165 CTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACA-T-TATAAACGATACC
65 CTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACC
369228 TATTACATTATATAAGGGCTACCTATTACAT-ATATGTTTACCTAT-TATTGAAAGTGTCCATAC
130 TATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATATATTG-AAGTGTCCATAC
369291 TTTTTATAAAAAGGATC-ATACTTTTTTTAAAAC
194 TTTTTATAAAAAGGATCGATACTTTTTTTAAAAC
369324 ATCATTTGCA
Statistics
Matches: 609, Mismatches: 2, Indels: 45
0.93 0.00 0.07
Matches are distributed among these distances:
402 54 0.09
403 36 0.06
404 1 0.00
405 50 0.08
406 35 0.06
407 16 0.03
408 12 0.02
409 10 0.02
410 10 0.02
411 19 0.03
412 78 0.13
413 97 0.16
414 54 0.09
415 106 0.17
416 31 0.05
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (411 bp):
TATCTTAAAACTCACTCAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGGACAC
TTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCT
ATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATATATTGAAGTGTCCATACTT
TTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTGTTTCAATTTTTTTAACAGTTT
CATGTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTT
ATATTTTAAAATATTATTTAGAATTTTTTTTAATAATAATATACCGTACGTAAAAAATAAATCAT
TAGACGCCTATAATTACTAAA
Found at i:369250 original size:23 final size:22
Alignment explanation
Indices: 369193--369262 Score: 81
Period size: 21 Copynumber: 3.2 Consensus size: 22
369183 ACACTTTACA
*
369193 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
369216 ATA-AACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
*
369237 ATATAAGGGCTACCTATTACA-T
1 ATATAA-CGCTACCTATTACATT
369259 ATAT
1 ATAT
369263 GTTTACCTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 17 0.41
22 9 0.22
23 15 0.37
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:370408 original size:21 final size:22
Alignment explanation
Indices: 370384--370424 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
370374 TTATGCCTCG
370384 AGTTTCTCTACGA-CTTGATCA
1 AGTTTCTCTACGACCTTGATCA
*
370405 AGTTTCTCTTCGACCTTGAT
1 AGTTTCTCTACGACCTTGAT
370425 TGTCTTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (22 bp):
AGTTTCTCTACGACCTTGATCA
Found at i:372761 original size:18 final size:16
Alignment explanation
Indices: 372722--372761 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 16
372712 ACACTTTTAA
372722 TTTACCGGTTTTCATT
1 TTTACCGGTTTTCATT
372738 TGTTACCGGTTTATCATAT
1 T-TTACCGGTTT-TCAT-T
372757 TTTAC
1 TTTAC
372762 ATGGTATTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 1 0.05
17 10 0.48
18 8 0.38
19 2 0.10
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.53
Consensus pattern (16 bp):
TTTACCGGTTTTCATT
Found at i:373243 original size:217 final size:214
Alignment explanation
Indices: 372836--373243 Score: 632
Period size: 217 Copynumber: 1.9 Consensus size: 214
372826 CTTTTAAAGT
372836 TGTAATTTATGTTTCATTATTTAATAGTGTTTCATGTTTTCCACCTACATATAATTTAAATTTAA
1 TGTAATTTATGTTTCATTATTTAATAGTGTTTCATGTTTTCCACCTACATATAATTTAAATTTAA
*
372901 TTTACACAAAATTTTATTTGATTGTTTTGATATTTATAAAATATTTTTAGCATTTAAATTAACAA
66 TTTACACAAAATATTATTTGATTGTTTTGATATTTATAAAATATTTTTAGCATTTAAATTAACAA
372966 TATTAACCAAATATAATAATAATAGTTTCAACAGTGAAATAGTATGGACACTTTTATAAAAATGA
131 TATTAACCAAATATAATAATAATAGTTTCAACAGTGAAATAGTATGGACACTTTTATAAAAATGA
373031 TATACTTTTTTGAAAGTTA
196 TATACTTTTTTGAAAGTTA
*
373050 TGTAATTTATGTTTCAATT-TTTTATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAA
1 TGTAATTTATGTTTC-ATTATTTAATAGTGTTTCATGTTTTCCACCTAC-ATA-TAATTT-A-AA
*
373114 TTTCATTTACACAAAA-ATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAG-ATTTAAA
61 TTTAATTTACACAAAATATTATTTGATTGTTTTGATA-TTTATAAAATATT-TTTAGCATTTAAA
* *
373177 TTTAACAATATTAA-CTAA-ATAATAA-ATATATTTTC-ACAGTGAAATAAGTATGGACACTTTT
124 -TTAACAATATTAACCAAATATAATAATA-ATAGTTTCAACAGTGAAAT-AGTATGGACACTTTT
373238 ATAAAA
186 ATAAAA
373244 GGATAGATAA
Statistics
Matches: 179, Mismatches: 5, Indels: 17
0.89 0.02 0.08
Matches are distributed among these distances:
214 43 0.24
215 6 0.03
216 17 0.09
217 55 0.31
218 40 0.22
219 18 0.10
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.45
Consensus pattern (214 bp):
TGTAATTTATGTTTCATTATTTAATAGTGTTTCATGTTTTCCACCTACATATAATTTAAATTTAA
TTTACACAAAATATTATTTGATTGTTTTGATATTTATAAAATATTTTTAGCATTTAAATTAACAA
TATTAACCAAATATAATAATAATAGTTTCAACAGTGAAATAGTATGGACACTTTTATAAAAATGA
TATACTTTTTTGAAAGTTA
Found at i:373672 original size:12 final size:12
Alignment explanation
Indices: 373655--373681 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
373645 GCATTATTTG
373655 CTTCTCCTTCTT
1 CTTCTCCTTCTT
373667 CTTCTCCTTCTT
1 CTTCTCCTTCTT
373679 CTT
1 CTT
373682 AATGCCGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (12 bp):
CTTCTCCTTCTT
Found at i:379591 original size:10 final size:10
Alignment explanation
Indices: 379584--379628 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 10
379574 GAACGTTCAG
379584 TTATGTTCGT
1 TTATGTTCGT
379594 TTATGTTCGTT
1 TTATGTTCG-T
379605 CGGTTATGTTCGT
1 ---TTATGTTCGT
379618 TTATGTTCGT
1 TTATGTTCGT
379628 T
1 T
379629 CGGTTATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 20 0.65
11 1 0.03
13 1 0.03
14 9 0.29
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.58
Consensus pattern (10 bp):
TTATGTTCGT
Found at i:379594 original size:24 final size:24
Alignment explanation
Indices: 379567--379637 Score: 61
Period size: 24 Copynumber: 3.0 Consensus size: 24
379557 CGTTCATTTA
*
379567 CGTTCGTGAACGTTCAGTTATGTT
1 CGTTCATGAACGTTCAGTTATGTT
* ** *
379591 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCATGAACGTTCAGTTATGTT
* ** *
379615 CGTTTATGTTCGTTCGGTTATGT
1 CGTTCATGAACGTTCAGTTATGT
379638 ATGTTTATGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.11, C:0.14, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCATGAACGTTCAGTTATGTT
Found at i:379605 original size:14 final size:14
Alignment explanation
Indices: 379588--379637 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
379578 GTTCAGTTAT
*
379588 GTTCGTTTATGTTC
1 GTTCGGTTATGTTC
379602 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
379616 G-T---TTATGTTC
1 GTTCGGTTATGTTC
379626 GTTCGGTTATGT
1 GTTCGGTTATGT
379638 ATGTTTATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
10 9 0.29
11 1 0.03
13 1 0.03
14 20 0.65
ACGTcount: A:0.08, C:0.12, G:0.26, T:0.54
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:379643 original size:24 final size:24
Alignment explanation
Indices: 379577--379649 Score: 121
Period size: 24 Copynumber: 3.0 Consensus size: 24
379567 CGTTCGTGAA
*
379577 CGTTCAGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
379601 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
379625 CGTTCGGTTATGTAT-GTTTATGTT
1 CGTTCGGTTATGT-TCGTTTATGTT
379649 C
1 C
379650 ATTCATTTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
24 46 0.98
25 1 0.02
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.53
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:379659 original size:24 final size:24
Alignment explanation
Indices: 379577--379662 Score: 120
Period size: 24 Copynumber: 3.6 Consensus size: 24
379567 CGTTCGTGAA
379577 CGTTCAGTTATGTTCGTTTATGTT
1 CGTTCAGTTATGTTCGTTTATGTT
*
379601 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCAGTTATGTTCGTTTATGTT
*
379625 CGTTCGGTTATGTAT-GTTTATGTT
1 CGTTCAGTTATGT-TCGTTTATGTT
* *
379649 CATTCATTTATGTT
1 CGTTCAGTTATGTT
379663 TAACCCAATC
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
23 1 0.02
24 55 0.96
25 1 0.02
ACGTcount: A:0.13, C:0.12, G:0.21, T:0.55
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATGTT
Found at i:380749 original size:10 final size:10
Alignment explanation
Indices: 380734--380807 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
380724 GGTCTCTAAT
380734 GTTTATGTTC
1 GTTTATGTTC
380744 GTTTATGTTC
1 GTTTATGTTC
*
380754 GTGTTCAT-TTAT
1 GT-TT-ATGTT-C
**
380766 GTTCGTGTTC
1 GTTTATGTTC
380776 GTTTATGTTC
1 GTTTATGTTC
*
380786 G----TGTTT
1 GTTTATGTTC
380792 GTTTATGTTC
1 GTTTATGTTC
380802 GTTTAT
1 GTTTAT
380808 TTATTAAATG
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
10 32 0.67
11 7 0.15
12 4 0.08
ACGTcount: A:0.09, C:0.09, G:0.22, T:0.59
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:380758 original size:16 final size:16
Alignment explanation
Indices: 380739--380803 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
380729 CTAATGTTTA
380739 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
380755 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
380771 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
380787 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
380803 T
1 T
380804 TTATTTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:384024 original size:17 final size:17
Alignment explanation
Indices: 383982--384024 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
383972 TTTTATTAGT
*
383982 ATTTTATTTAATTATTTA
1 ATTTT-TTTAATTAATTA
* *
384000 AATATTTTAATTAATTA
1 ATTTTTTTAATTAATTA
384017 ATTTTTTT
1 ATTTTTTT
384025 GCAGTTATAA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTTTTAATTAATTA
Found at i:386381 original size:35 final size:33
Alignment explanation
Indices: 386332--386406 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 33
386322 AATTAATTTG
386332 TTTA-TTACAATTTAATATCAGTTATTGTAA-TTTT
1 TTTATTTACAATTTAATA-C--TTATTGTAAGTTTT
* *
386366 TTTTTTTACCATTTAATACTTATTGTAAGTTTT
1 TTTATTTACAATTTAATACTTATTGTAAGTTTT
386399 TTTATTTA
1 TTTATTTA
386407 AAATATATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 9 0.25
33 11 0.31
34 4 0.11
35 12 0.33
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (33 bp):
TTTATTTACAATTTAATACTTATTGTAAGTTTT
Found at i:390785 original size:14 final size:13
Alignment explanation
Indices: 390750--390783 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
390740 AATTCCGTTA
*
390750 TATTTTTAT-TTT
1 TATTTTTTTCTTT
390762 TATTTTTTTCTTT
1 TATTTTTTTCTTT
390775 TATTTTTTT
1 TATTTTTTT
390784 TCGATTAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (13 bp):
TATTTTTTTCTTT
Found at i:400302 original size:41 final size:41
Alignment explanation
Indices: 400256--400371 Score: 110
Period size: 41 Copynumber: 2.8 Consensus size: 41
400246 ATACAGATAA
* * *
400256 GTACTTTAGTGGCGTTTTTAAACAAACACCGCCACAGAATCC
1 GTACTTTAGTGGCGTTTTTGAACAAACACCGCAAAAGAA-CC
* * ** * *
400298 -TACTTCAGTGACGTTTCGGAATAAACGCCGCAAAAGAACC
1 GTACTTTAGTGGCGTTTTTGAACAAACACCGCAAAAGAACC
*
400338 GTTCTTTAGTGGCGTTTTTGAACAAA-AGCCGCAA
1 GTACTTTAGTGGCGTTTTTGAACAAACA-CCGCAA
400372 TAGGTTAGTG
Statistics
Matches: 56, Mismatches: 16, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
40 2 0.04
41 54 0.96
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (41 bp):
GTACTTTAGTGGCGTTTTTGAACAAACACCGCAAAAGAACC
Found at i:404520 original size:42 final size:42
Alignment explanation
Indices: 404448--404586 Score: 138
Period size: 51 Copynumber: 3.1 Consensus size: 42
404438 TACAACATGG
404448 AGAAAGCAGGAGAAAT-GCAAGAGCT-CCACATGATGCAGAAGC
1 AGAAA-CAGGAGAAATAG-AAGAGCTCCCACATGATGCAGAAGC
*
404490 AGAAACAAGAGAAATAGAAGAGCTCCCACATGATGCAGCAACAACAGAAGC
1 AGAAACAGGAGAAATAGAAGAGCTCCCACATGAT---G------CAGAAGC
* *
404541 AGAAAGAGGAGAAATAGAAGAGCTCCAACATGATGCAGAAGC
1 AGAAACAGGAGAAATAGAAGAGCTCCCACATGATGCAGAAGC
404583 AGAA
1 AGAA
404587 GGGAATTTGG
Statistics
Matches: 82, Mismatches: 4, Indels: 22
0.76 0.04 0.20
Matches are distributed among these distances:
41 16 0.20
42 26 0.32
45 1 0.01
48 1 0.01
51 38 0.46
ACGTcount: A:0.47, C:0.18, G:0.26, T:0.09
Consensus pattern (42 bp):
AGAAACAGGAGAAATAGAAGAGCTCCCACATGATGCAGAAGC
Found at i:407471 original size:24 final size:23
Alignment explanation
Indices: 407444--407490 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
407434 ATTTTTATTT
*
407444 ATTAATGATAACAAATAATATGAA
1 ATTAATCATAACAAA-AATATGAA
* *
407468 ATTAATCCTAATAAAAATATGAA
1 ATTAATCATAACAAAAATATGAA
407491 TAAATAAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (23 bp):
ATTAATCATAACAAAAATATGAA
Found at i:408858 original size:20 final size:21
Alignment explanation
Indices: 408822--408865 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
408812 TAAATTTAAA
408822 AAAAATTATTCAAAATTTT-T
1 AAAAATTATTCAAAATTTTCT
*
408842 AAAAA-TATTCACTAATTTTCT
1 AAAAATTATTCA-AAATTTTCT
408863 AAA
1 AAA
408866 GGAATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAATTATTCAAAATTTTCT
Found at i:409069 original size:26 final size:26
Alignment explanation
Indices: 409040--409093 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
409030 TATAAACAGT
* *
409040 TAATCAAATCAGTTTCTCAAATCAAC
1 TAATCAAATCAATTGCTCAAATCAAC
* *
409066 TAATTAAATCAATTGGTCAAATCAAC
1 TAATCAAATCAATTGCTCAAATCAAC
409092 TA
1 TA
409094 CTGGAACCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (26 bp):
TAATCAAATCAATTGCTCAAATCAAC
Found at i:432827 original size:39 final size:39
Alignment explanation
Indices: 432767--432850 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
432757 TCTTTTACCA
* *
432767 TTTAAAATTATGGATTTTGTGTTCATAGACTAGTATTAT
1 TTTAGAATTATGGATTATGTGTTCATAGACTAGTATTAT
*
432806 TTTAGAATTATGGATTATGTGTTCATAGACTAGTATTGT
1 TTTAGAATTATGGATTATGTGTTCATAGACTAGTATTAT
432845 TTTAGA
1 TTTAGA
432851 TTCCCATTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.30, C:0.05, G:0.18, T:0.48
Consensus pattern (39 bp):
TTTAGAATTATGGATTATGTGTTCATAGACTAGTATTAT
Found at i:433944 original size:64 final size:63
Alignment explanation
Indices: 433871--434050 Score: 209
Period size: 64 Copynumber: 2.8 Consensus size: 63
433861 ACTCTTTTAA
* * **
433871 AATAA-AAACATCAAATGTAATTCATGCATCGATGCATAAGTAGTGCATCGATACATCCCATT
1 AATAATAAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATACATCCCAGC
** * *
433933 AATAATGAAACATCGAATGCAATTGGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGC
1 AATAAT-AAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATACATCCCAGC
* ** * * *
433997 AATAATAATACATCGAATACCTTTTATGCACCGATGCATCAGTAGTGCATCGAT
1 AATAATAA-ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGAT
434051 GCATACGTTC
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
62 5 0.05
63 2 0.02
64 92 0.93
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (63 bp):
AATAATAAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATACATCCCAGC
Found at i:434380 original size:12 final size:12
Alignment explanation
Indices: 434362--434397 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
434352 TATATATGTT
434362 CATGTGATATGA
1 CATGTGATATGA
*
434374 TATGTGATATGA
1 CATGTGATATGA
434386 CATGTGATATGA
1 CATGTGATATGA
434398 GATACATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:434563 original size:15 final size:15
Alignment explanation
Indices: 434519--434566 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
434509 GAGGGTATAA
* *
434519 TAGTCTTTCGGGATA
1 TAGTCCTTCGGGATG
434534 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
434549 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
434564 TAG
1 TAG
434567 GGGTCCTACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.35
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:440773 original size:64 final size:64
Alignment explanation
Indices: 440704--440924 Score: 216
Period size: 64 Copynumber: 3.5 Consensus size: 64
440694 TTGAAGGTGT
* **
440704 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATG
440767 C
64 C
* * * **
440768 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATTGAATGCAATTGGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
** * * * ** *
440832 ATCGATGCATAAGG-AGTGCATCGATGCATCCCAGCAATAATAATACATTGAATACCTTTTATGC
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* *
440896 ACCGATGCATCA-GTAGTGTATCGATGCAT
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT
440925 ACCTTCATTA
Statistics
Matches: 132, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
63 1 0.01
64 125 0.95
65 6 0.05
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
Found at i:441250 original size:12 final size:12
Alignment explanation
Indices: 441232--441267 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
441222 TATATATGTT
441232 CATGTGATATGA
1 CATGTGATATGA
*
441244 TATGTGATATGA
1 CATGTGATATGA
*
441256 CATGTTATATGA
1 CATGTGATATGA
441268 AAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:441430 original size:15 final size:15
Alignment explanation
Indices: 441412--441443 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
441402 GAGGGTATAA
*
441412 TAGTCCTTCGGGATG
1 TAGTCCTTCGGAATG
441427 TAGTCCTTCGGAATG
1 TAGTCCTTCGGAATG
441442 TA
1 TA
441444 AGGGTCCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (15 bp):
TAGTCCTTCGGAATG
Found at i:442365 original size:30 final size:30
Alignment explanation
Indices: 442267--442348 Score: 130
Period size: 30 Copynumber: 2.7 Consensus size: 30
442257 CATCGTTACT
* *
442267 CGTTCTGA-AGTCTGTATGGGATAAACTCCC
1 CGTTCTGACA-TCTGCATGGGATAAATTCCC
442297 CGTTCTGACATCTGCATGGGATAAATTCCC
1 CGTTCTGACATCTGCATGGGATAAATTCCC
442327 CGTTCTGACATCTGCATGGGAT
1 CGTTCTGACATCTGCATGGGAT
442349 TATATCTCCG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 48 0.98
31 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.30
Consensus pattern (30 bp):
CGTTCTGACATCTGCATGGGATAAATTCCC
Found at i:442665 original size:36 final size:36
Alignment explanation
Indices: 442615--442818 Score: 300
Period size: 36 Copynumber: 5.7 Consensus size: 36
442605 CACACATCCT
** * *
442615 TCCGTTCGACTTGAATCGGAAGTGTTGATGCTTTCT
1 TCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCC
* *
442651 TCCGTTTGAATTGAATCGGAAGTGCCGATGCTTCCC
1 TCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCC
442687 TCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCC
1 TCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCC
* * *
442723 TCCGTTTGACTTGAATCGGAAGTGCTGATGTTTCCC
1 TCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCC
* *
442759 TCCGTTCGACTTGAATCGGAAGTGTCGATGCTTCCT
1 TCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCC
*
442795 TTCGTTCGACTTGAATCGGAAGTG
1 TCCGTTCGACTTGAATCGGAAGTG
442819 AACTTTTGAT
Statistics
Matches: 151, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 151 1.00
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (36 bp):
TCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCC
Found at i:447823 original size:20 final size:20
Alignment explanation
Indices: 447794--447848 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
447784 CAGTTTTCAA
447794 ATTCGCAACGCGATTGTAAG
1 ATTCGCAACGCGATTGTAAG
*
447814 ATTCGTAACGCGATTGTAAG
1 ATTCGCAACGCGATTGTAAG
447834 ATTCGCAACGCGATT
1 ATTCGCAACGCGATT
447849 TTGAAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (20 bp):
ATTCGCAACGCGATTGTAAG
Found at i:447877 original size:19 final size:19
Alignment explanation
Indices: 447853--447938 Score: 82
Period size: 19 Copynumber: 4.2 Consensus size: 19
447843 GCGATTTTGA
*
447853 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
*
447872 AAAATGTGTTGCGAGAGTTTG
1 AAAATGTGTTGCGATAG--TG
447893 AAAAACGTGTTGTTGCGATAGTG
1 -AAAA--TG-TGTTGCGATAGTG
* *
447916 AAAAAGTGTTGCAATAGTG
1 AAAATGTGTTGCGATAGTG
447935 AAAA
1 AAAA
447939 ATCCAAAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
19 32 0.57
20 1 0.02
21 1 0.02
22 8 0.14
23 2 0.04
24 2 0.04
25 10 0.18
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:448358 original size:19 final size:20
Alignment explanation
Indices: 448313--448360 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
448303 AATTCTTAAG
448313 AAATCGCAACGTGAACTTGGA
1 AAATCGCAACG-GAACTTGGA
** *
448334 CTATCGCAAC-GAATTTGGA
1 AAATCGCAACGGAACTTGGA
448353 AAATCGCA
1 AAATCGCA
448361 TTGCGATAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 14 0.64
21 8 0.36
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGGAACTTGGA
Found at i:448578 original size:19 final size:19
Alignment explanation
Indices: 448554--448628 Score: 132
Period size: 19 Copynumber: 3.9 Consensus size: 19
448544 TGCGATACTG
448554 GAGATCGCGTTGCGATTTA
1 GAGATCGCGTTGCGATTTA
448573 GAGATCGCGTTGCGATTTA
1 GAGATCGCGTTGCGATTTA
448592 GAGATCGCGTTGCGATTTA
1 GAGATCGCGTTGCGATTTA
* *
448611 GAGATCGCATTACGATTT
1 GAGATCGCGTTGCGATTT
448629 TGTTGGTCAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 54 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (19 bp):
GAGATCGCGTTGCGATTTA
Found at i:454980 original size:2 final size:2
Alignment explanation
Indices: 454973--455000 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
454963 CTACTGCAAC
454973 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
455001 TTATTGATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:458820 original size:15 final size:16
Alignment explanation
Indices: 458782--458824 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
458772 CTTATATGTA
*
458782 CATGAATACATGATATG
1 CATGAA-ACATAATATG
458799 CAT-AAACATAATA-G
1 CATGAAACATAATATG
458813 CATGAAACATAA
1 CATGAAACATAA
458825 GATATATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.17
15 15 0.62
16 2 0.08
17 3 0.12
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (16 bp):
CATGAAACATAATATG
Found at i:475531 original size:2 final size:2
Alignment explanation
Indices: 475524--475586 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
475514 CGTTATTTAA
475524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
475566 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
475587 ATAGTCTCAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:489152 original size:31 final size:31
Alignment explanation
Indices: 489094--489162 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
489084 GAGTATTGCT
* *
489094 GAGCTTGACTCGACTCGAAAATTCTGAAATG
1 GAGCTCGACTCGACTCGAAAATCCTGAAATG
*
489125 GAGCTCGACTCGAACTCG-AAATCCTGAACTG
1 GAGCTCGACTCG-ACTCGAAAATCCTGAAATG
*
489156 AAGCTCG
1 GAGCTCG
489163 TAAGCAGCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (31 bp):
GAGCTCGACTCGACTCGAAAATCCTGAAATG
Found at i:494700 original size:2 final size:2
Alignment explanation
Indices: 494693--494725 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
494683 AGAAAACCCG
494693 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
494726 AATCTTCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:502412 original size:11 final size:11
Alignment explanation
Indices: 502396--502423 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
502386 AACCACCTTC
502396 TATTTTTATTT
1 TATTTTTATTT
502407 TATTTTTATTT
1 TATTTTTATTT
502418 TATTTT
1 TATTTT
502424 AAATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:503048 original size:21 final size:21
Alignment explanation
Indices: 502997--503049 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
502987 ATTATTACTA
502997 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* **
503018 TTGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
503039 TCGCAATGCGA
1 TCGCAATGCGA
503050 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:503082 original size:21 final size:21
Alignment explanation
Indices: 503039--503152 Score: 74
Period size: 21 Copynumber: 5.5 Consensus size: 21
503029 TTTTCCCAAT
* *
503039 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTAGAAAA
*
503059 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
* * **
503080 TCGTAATGCG-ATACT-GACTA
1 TCGCAATGCGAAT-TTAGAAAA
* * *
503100 TCGCAACGCG-ATAATACAAAA
1 TCGCAATGCGAAT-TTAGAAAA
*
503121 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
*
503142 TCGTAATGCGA
1 TCGCAATGCGA
503153 TACTGACTAT
Statistics
Matches: 72, Mismatches: 18, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
20 29 0.40
21 41 0.57
22 2 0.03
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTTAGAAAA
Found at i:503090 original size:62 final size:60
Alignment explanation
Indices: 503039--503193 Score: 204
Period size: 62 Copynumber: 2.5 Consensus size: 60
503029 TTTTCCCAAT
* * *
503039 TCGCAATGCGAATAAGT-AAATCGCAATGCGAATTTGGAAAATCGTAATGCGATACTGACTA
1 TCGCAACGCG-ATAA-TAAAATCGCAATGCGAATTTGGAAAATCGTAATGCGATACTCACAA
* *
503100 TCGCAACGCGATAATACAAAATCGCAATGCGAATTTGGAAAATCGTAATGCGATACTGACTA
1 TCGCAACGCGATAAT--AAAATCGCAATGCGAATTTGGAAAATCGTAATGCGATACTCACAA
503162 TCGCAACGCGATAATACAAAATCGCAATGCGA
1 TCGCAACGCGATAAT--AAAATCGCAATGCGA
503194 TACTAACTAT
Statistics
Matches: 90, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
59 1 0.01
60 4 0.04
61 9 0.10
62 76 0.84
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (60 bp):
TCGCAACGCGATAATAAAATCGCAATGCGAATTTGGAAAATCGTAATGCGATACTCACAA
Found at i:503110 original size:20 final size:20
Alignment explanation
Indices: 503087--503316 Score: 171
Period size: 20 Copynumber: 11.3 Consensus size: 20
503077 AAATCGTAAT
503087 GCGATACTGACTATCGCAAC
1 GCGATACTGACTATCGCAAC
* * *
503107 GCGATAAT-ACAAAATCGCAAT
1 GCGATACTGAC--TATCGCAAC
* ** * *
503128 GCGA-ATTTGGAAAATCGTAAT
1 GCGATA-CT-GACTATCGCAAC
503149 GCGATACTGACTATCGCAAC
1 GCGATACTGACTATCGCAAC
* * *
503169 GCGATAAT-ACAAAATCGCAAT
1 GCGATACTGAC--TATCGCAAC
*
503190 GCGATACTAACTATCGCAAC
1 GCGATACTGACTATCGCAAC
* *
503210 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TATCGCAAC
*
503231 GCGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
*
503251 GCGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
* *
503271 GCGATTCTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
* *
503291 GAGATTCTGACTATCGCAAC
1 GCGATACTGACTATCGCAAC
*
503311 GAGATA
1 GCGATA
503317 ATACAGAATC
Statistics
Matches: 172, Mismatches: 26, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
19 6 0.03
20 106 0.62
21 54 0.31
22 5 0.03
23 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:503165 original size:41 final size:41
Alignment explanation
Indices: 503138--503256 Score: 202
Period size: 41 Copynumber: 2.9 Consensus size: 41
503128 GCGAATTTGG
*
503138 AAAATCGTAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
*
503179 AAAATCGCAATGCGATACTAACTATCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
* *
503220 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATA
503257 CTGACTTTCG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (41 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
Found at i:503187 original size:21 final size:21
Alignment explanation
Indices: 503099--503236 Score: 122
Period size: 21 Copynumber: 6.7 Consensus size: 21
503089 GATACTGACT
503099 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
* * **
503120 ATCGCAATGCGA-ATTTGGAAA
1 ATCGCAACGCGATA-ATACAAA
* * * *
503141 ATCGTAATGCGATACTGAC--T
1 ATCGCAACGCGATAAT-ACAAA
503161 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
* * **
503182 ATCGCAATGCGATACTA-ACT
1 ATCGCAACGCGATAATACAAA
503202 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
503223 ATCGCAACGCGATA
1 ATCGCAACGCGATA
503237 CTGACTTTCG
Statistics
Matches: 90, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
19 2 0.02
20 30 0.33
21 57 0.63
22 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:503227 original size:62 final size:61
Alignment explanation
Indices: 503087--503275 Score: 163
Period size: 62 Copynumber: 3.1 Consensus size: 61
503077 AAATCGTAAT
* * * * * *
503087 GCGATACTGACTATCGCAACGCGATAATACAAAATCGCAATGCGA-ATTTGGAA-AATCGTAAT
1 GCGATAATGACAATCGCAACGCGATAATACAAAATCGCAATGCGATA-CT--AACTATCGCAAC
* *
503149 GCGATACTGACTATCGCAACGCGATAATACAAAATCGCAATGCGATACTAACTATCGCAAC
1 GCGATAATGACAATCGCAACGCGATAATACAAAATCGCAATGCGATACTAACTATCGCAAC
* ** * * *
503210 GCGATAAT-ACAAAATCGCAACGCGATACTGAC--TTTCGCAACGCGATACTGACTTTCGCAAC
1 GCGATAATGAC--AATCGCAACGCGATAAT-ACAAAATCGCAATGCGATACTAACTATCGCAAC
503271 GCGAT
1 GCGAT
503276 TCTGACTTTC
Statistics
Matches: 110, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
60 4 0.04
61 42 0.38
62 61 0.55
63 3 0.03
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (61 bp):
GCGATAATGACAATCGCAACGCGATAATACAAAATCGCAATGCGATACTAACTATCGCAAC
Found at i:503281 original size:40 final size:40
Alignment explanation
Indices: 503149--503316 Score: 151
Period size: 41 Copynumber: 4.2 Consensus size: 40
503139 AAATCGTAAT
* * * * *
503149 GCGATACTGACTATCGCAACGCGATAAT-ACAAAATCGCAAT
1 GCGATACTGACTTTCGCAACGAGATACTGAC--TATCGCAAC
* * * * *
503190 GCGATACTAACTATCGCAACGCGATAAT-ACAAAATCGCAAC
1 GCGATACTGACTTTCGCAACGAGATACTGAC--TATCGCAAC
* *
503231 GCGATACTGACTTTCGCAACGCGATACTGACTTTCGCAAC
1 GCGATACTGACTTTCGCAACGAGATACTGACTATCGCAAC
* *
503271 GCGATTCTGACTTTCGCAACGAGATTCTGACTATCGCAAC
1 GCGATACTGACTTTCGCAACGAGATACTGACTATCGCAAC
*
503311 GAGATA
1 GCGATA
503317 ATACAGAATC
Statistics
Matches: 113, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
40 47 0.42
41 64 0.57
42 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (40 bp):
GCGATACTGACTTTCGCAACGAGATACTGACTATCGCAAC
Found at i:504063 original size:24 final size:24
Alignment explanation
Indices: 504036--504089 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
504026 GTATTCGAAA
*
504036 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
504060 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
504084 TTTGAT
1 TTTGAT
504090 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:506582 original size:20 final size:20
Alignment explanation
Indices: 506515--506587 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
506505 GGCAATCATT
*
506515 TGACTATCGCAACA-AGAAAA
1 TGACTATCGCAACATTG-AAA
*
506535 TGACGT-TCGCAATCATCT-TAA
1 TGAC-TATCGCAA-CAT-TGAAA
*
506556 TGTCTATCGCAACATTGAAA
1 TGACTATCGCAACATTGAAA
506576 TGACTATCGCAA
1 TGACTATCGCAA
506588 TGCGAAAAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
19 1 0.02
20 27 0.64
21 14 0.33
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (20 bp):
TGACTATCGCAACATTGAAA
Found at i:506603 original size:19 final size:19
Alignment explanation
Indices: 506581--506672 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
506571 TGAAATGACT
506581 ATCGCAATGCGAAAAGAAA
1 ATCGCAATGCGAAAAGAAA
*
506600 ATCGCAA--CG---AGAGA
1 ATCGCAATGCGAAAAGAAA
*
506614 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAAAGAAA
*
506633 ATCGCAA--CG---AGAGA
1 ATCGCAATGCGAAAAGAAA
*
506647 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAAAGAAA
506666 ATCGCAA
1 ATCGCAA
506673 CGAGGGAATC
Statistics
Matches: 56, Mismatches: 7, Indels: 20
0.67 0.08 0.24
Matches are distributed among these distances:
14 21 0.38
16 4 0.07
17 4 0.07
19 27 0.48
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAAAGAAA
Found at i:506618 original size:14 final size:14
Alignment explanation
Indices: 506599--506686 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
506589 GCGAAAAGAA
506599 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
506613 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
506632 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
506646 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
506665 AATCGCAACGAGGG
1 AATCGCAACGAGAG
506679 AATCGCAA
1 AATCGCAA
506687 AGCGAAATGA
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 27 0.46
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.34
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:506623 original size:33 final size:33
Alignment explanation
Indices: 506581--506707 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
506571 TGAAATGACT
*
506581 ATCGCAATGCGAAAAGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
506614 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
506647 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
506680 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
506708 CGAATTTAGT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 91 1.00
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:506703 original size:19 final size:18
Alignment explanation
Indices: 506581--506711 Score: 70
Period size: 19 Copynumber: 7.7 Consensus size: 18
506571 TGAAATGACT
*
506581 ATCGCAATGCGAAAAGAAA
1 ATCGCAAAGCG-AAAGAAA
*
506600 ATCGC-AA-CG--AGAGA
1 ATCGCAAAGCGAAAGAAA
*
506614 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAA-GAAA
*
506633 ATCGC-AA-CG--AGAGA
1 ATCGCAAAGCGAAAGAAA
*
506647 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAA-GAAA
**
506666 ATCGC-AA-CG--AGGGA
1 ATCGCAAAGCGAAAGAAA
506680 ATCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAA-GAAA
*
506699 ATCGCAACGCGAA
1 ATCGCAAAGCGAA
506712 TTTAGTTTCG
Statistics
Matches: 83, Mismatches: 14, Indels: 30
0.65 0.11 0.24
Matches are distributed among these distances:
14 24 0.29
15 6 0.07
16 6 0.07
17 6 0.07
18 6 0.07
19 35 0.42
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (18 bp):
ATCGCAAAGCGAAAGAAA
Found at i:506884 original size:13 final size:14
Alignment explanation
Indices: 506868--506903 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
506858 CATCAATTAA
506868 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
506881 ACAAATCATCTTTT
1 ACAAATCAACTTTT
506895 ACAAATCAA
1 ACAAATCAA
506904 TTAAACAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:508911 original size:93 final size:91
Alignment explanation
Indices: 508740--509038 Score: 425
Period size: 93 Copynumber: 3.3 Consensus size: 91
508730 GAATAGTTTC
*
508740 AATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAATACTAACTTCA
1 AATTGGCAGC-AACGAACAAATTTACTTTCAACCAAAAGAAAAACAAAGACAAATACTAACTTCA
508805 CAGTGTTAAAGAATACACGTTTAGCAG
65 CAGTGTTAAAGAATACACGTTTAGCAG
508832 AATTGGCAGCAACTGAACAAATTTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAAC-GAACAAATTTACTTTCAACCAAAAGA-AAAACAAAGACAAATACTAACTTC
508897 ACAGTGTTAAAGAATACACAGTTTTAGCAG
64 ACAGTGTTAAAGAATACAC-G-TTTAGCAG
*
508927 AATTGGCAG---CGAATAAATTTAC-TTCAACC-AAAGACAAAACAAAAGACAAATACTAACTTC
1 AATTGGCAGCAACGAACAAATTTACTTTCAACCAAAAGA-AAAAC-AAAGACAAATACTAACTTC
*
508987 ACAGTGTT-AATAA-ACA-GTTTAGCAG
64 ACAGTGTTAAAGAATACACGTTTAGCAG
* *
509012 TATTGGCAGCAACCGAATAAATTTACT
1 AATTGGCAGCAA-CGAACAAATTTACT
509039 AAGCAATCTA
Statistics
Matches: 192, Mismatches: 5, Indels: 22
0.88 0.02 0.10
Matches are distributed among these distances:
85 16 0.08
86 1 0.01
88 3 0.02
89 27 0.14
90 34 0.18
91 14 0.07
92 37 0.19
93 42 0.22
94 1 0.01
95 17 0.09
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (91 bp):
AATTGGCAGCAACGAACAAATTTACTTTCAACCAAAAGAAAAACAAAGACAAATACTAACTTCAC
AGTGTTAAAGAATACACGTTTAGCAG
Found at i:510748 original size:20 final size:20
Alignment explanation
Indices: 510723--510804 Score: 89
Period size: 20 Copynumber: 4.2 Consensus size: 20
510713 TTTTGGTTGA
510723 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
510743 AATGAAAATCGCAAC-ACG-G
1 AATGAAAATCGCAACGA-GAG
** * *
510762 AAATGACTATCACAACGCGA-
1 -AATGAAAATCGCAACGAGAG
510782 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
510802 AAT
1 AAT
510805 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
19 17 0.35
20 32 0.65
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:510765 original size:40 final size:39
Alignment explanation
Indices: 510721--510796 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 39
510711 TCTTTTGGTT
*
510721 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACACG
1 GAAATGAAAATCACAACGAGA-AATGAAAATCGCAACACG
** *
510761 GAAATGACTATCACAACGCGAAATGAAAATCGCAAC
1 GAAATGAAAATCACAACGAGAAATGAAAATCGCAAC
510797 GAGAGAATCG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 15 0.47
40 17 0.53
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.12
Consensus pattern (39 bp):
GAAATGAAAATCACAACGAGAAATGAAAATCGCAACACG
Found at i:510850 original size:19 final size:19
Alignment explanation
Indices: 510828--510905 Score: 85
Period size: 19 Copynumber: 4.4 Consensus size: 19
510818 AAAATCGCAA
**
510828 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
510847 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
510866 TGCGA--TT-A--TCTCGT
1 TGCGATTTTCATTTCGCGT
510880 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
510899 TTCGATT
1 TGCGATT
510906 CTCTCGTTGC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 33 0.67
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:510886 original size:33 final size:33
Alignment explanation
Indices: 510844--510939 Score: 138
Period size: 33 Copynumber: 2.9 Consensus size: 33
510834 TTTGGTTTCG
510844 CGTTGCGATTTTCATTTCGCGTTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTATCT
* *
510877 CGTTGCGATTTTCATTTCGCGTTTCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTATCT
** *
510910 CGTTGCGATAGTCATTTCCGCGTTGTGATT
1 CGTTGCGATTTTCATTT-CGCGTTGCGATT
510940 TTCATTCTCG
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
33 46 0.82
34 10 0.18
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTATCT
Found at i:511508 original size:20 final size:20
Alignment explanation
Indices: 511485--511618 Score: 207
Period size: 20 Copynumber: 6.7 Consensus size: 20
511475 CGATAGTCAG
511485 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
511505 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
511525 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
511545 ATTCGCATTGCGATTTTTC-T
1 ATTCGCATTGCGA-TTTACGT
*
511565 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
511586 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
511606 ATTCGCATTGCGA
1 ATTCGCATTGCGA
511619 ATTATGAAAA
Statistics
Matches: 104, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
20 86 0.83
21 18 0.17
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:511631 original size:41 final size:41
Alignment explanation
Indices: 511459--511756 Score: 168
Period size: 41 Copynumber: 7.3 Consensus size: 41
511449 CGAATGACGC
* * *
511459 TATGTAAATCGCATTGCGATAGT-CAG-ATTCGCATTGCGATT
1 TATGAAAATCGCATTGCGAT-TTAC-GTATTCGCATTGCGAAT
* * * *
511500 TACG-TATTCGCATTGCGATTTACGTATTCGCATTGCGATT
1 TATGAAAATCGCATTGCGATTTACGTATTCGCATTGCGAAT
* * * * *
511540 TACG-TATTCGCATTGCGATTTTTC-TAATTCGCATTGCGATT
1 TATGAAAATCGCATTGCGA-TTTACGT-ATTCGCATTGCGAAT
* *
511581 TACT--TAATCGCGTTGCGATTTACGTATTCGCATTGCGAAT
1 TA-TGAAAATCGCATTGCGATTTACGTATTCGCATTGCGAAT
** * * *
511621 TATGAAAATCGCAACGCGA-ATACGTAAATCGCAATGCGAAT
1 TATGAAAATCGCATTGCGATTTACGT-ATTCGCATTGCGAAT
* * * *
511662 TAGGAAAATTGCATCGCGATAGT-CAGTA-TCGCATTGCG-AT
1 TATGAAAATCGCATTGCGAT-TTAC-GTATTCGCATTGCGAAT
* * * * *
511702 TTTCCAAATTCGTATTGCGATTTACTTATTCGCATTGCGAAT
1 TAT-GAAAATCGCATTGCGATTTACGTATTCGCATTGCGAAT
**
511744 TGGGAAAATCGCA
1 TATGAAAATCGCA
511757 ACGCGGAATT
Statistics
Matches: 205, Mismatches: 36, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
39 3 0.01
40 79 0.39
41 115 0.56
42 5 0.02
43 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (41 bp):
TATGAAAATCGCATTGCGATTTACGTATTCGCATTGCGAAT
Found at i:511633 original size:61 final size:60
Alignment explanation
Indices: 511485--511626 Score: 203
Period size: 61 Copynumber: 2.4 Consensus size: 60
511475 CGATAGTCAG
* * *
511485 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTATGAATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
* * * *
511545 ATTCGCATTGCGATTTTTCTAATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTAT-GAATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
*
511606 ATTCGCATTGCGAATTATGAA
1 ATTCGCATTGCGATTTATGAA
511627 AATCGCAACG
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 18 0.25
61 53 0.75
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (60 bp):
ATTCGCATTGCGATTTATGAATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
Found at i:511639 original size:21 final size:21
Alignment explanation
Indices: 511615--511680 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
511605 TATTCGCATT
*
511615 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
511636 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
* * *
511656 GCGAATTAGGAAAATTGCATC
1 GCGAATTACGAAAATCGCAAC
511677 GCGA
1 GCGA
511681 TAGTCAGTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:511651 original size:61 final size:61
Alignment explanation
Indices: 511527--511761 Score: 154
Period size: 61 Copynumber: 3.8 Consensus size: 61
511517 ATTTACGTAT
* * * * ** * *
511527 TCGCATTGCGATTTACGTATTCGCATTGCGATTTTTCTAATTCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGAATTATCAAAATCGCAACGCGATATACTAAA
* *
511588 TCGCGTTGCGATTTACGTATTCGCATTGCGAATTATGAAAATCGCAACGCGA-ATACGTAAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGAATTATCAAAATCGCAACGCGATATAC-TAAA
* * * * * ** ** * * *
511649 TCGCAATGCGAATTAGGAAAATT-GCATCGCG-A-TAGTCAGTATCGCATTGCGATTTTCCAAA
1 TCGCATTGCGATTTACG--TATTCGCATTGCGAATTA-TCAAAATCGCAACGCGATATACTAAA
* * ***
511710 TTCGTATTGCGATTTACTTATTCGCATTGCGAATTGGGAAAATCGCAACGCG
1 -TCGCATTGCGATTTACGTATTCGCATTGCGAATTATCAAAATCGCAACGCG
511762 GAATTGGAAA
Statistics
Matches: 127, Mismatches: 38, Indels: 17
0.70 0.21 0.09
Matches are distributed among these distances:
60 8 0.06
61 83 0.65
62 32 0.25
63 4 0.03
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (61 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGAATTATCAAAATCGCAACGCGATATACTAAA
Found at i:511653 original size:81 final size:80
Alignment explanation
Indices: 511487--511659 Score: 195
Period size: 81 Copynumber: 2.1 Consensus size: 80
511477 ATAGTCAGAT
* * * *
511487 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGAATTACGAAATCGCA
** * * *
511552 TTGCGATTTTTCTAAT
66 ACGCGA-TATACTAAA
* * *
511568 TCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTATGAAAATCGC
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGAATTACG-AAATCGC
511633 AACGCGA-ATACGTAAA
65 AACGCGATATAC-TAAA
*
511649 TCGCAATGCGA
1 TCGCATTGCGA
511660 ATTAGGAAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
80 2 0.03
81 65 0.84
82 10 0.13
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (80 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGAATTACGAAATCGCA
ACGCGATATACTAAA
Done.