Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002144.1 Hibiscus syriacus cultivar Beakdansim tig00004383_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: 293050
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 1 of 2
Found at i:1176 original size:41 final size:39
Alignment explanation
Indices: 1126--1306 Score: 184
Period size: 42 Copynumber: 4.4 Consensus size: 39
1116 ACTTCGACTA
* *
1126 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATTTACAAATTCG--TTGCGATAGTCGAAGT
* * * *
1167 TTGCGTTGCGAATCTAGAAACT-GATTTGCGATAGTCGAAGT
1 TCGCGTTGCG-ATTTACAAATTCG--TTGCGATAGTCGAAGT
1208 TCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGA--T-TTACAAATTCGTTGCGATAGTCGAAGT
*
1250 TCGCGTTGCGATTTATACCAAGTTCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGA-TT-TA-CAAATTCGTTGCGATAGTCGAAGT
*
1292 TCGTGTTGCGATTTA
1 TCGCGTTGCGATTTA
1307 TTCCAAATTC
Statistics
Matches: 119, Mismatches: 14, Indels: 15
0.80 0.09 0.10
Matches are distributed among these distances:
40 4 0.03
41 40 0.34
42 68 0.57
43 6 0.05
44 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (39 bp):
TCGCGTTGCGATTTACAAATTCGTTGCGATAGTCGAAGT
Found at i:1177 original size:21 final size:21
Alignment explanation
Indices: 1151--1303 Score: 72
Period size: 21 Copynumber: 7.3 Consensus size: 21
1141 CATATTCGCA
1151 TTGCGATAGTCGAAGTTTGCG
1 TTGCGATAGTCGAAGTTTGCG
** **
1172 TTGCGA-A-TCTAGAA-ACTGAT
1 TTGCGATAGTC--GAAGTTTGCG
*
1192 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTTGCG
* *
1213 TTGCGATTTATTAC-AA-ATT-CG
1 TTGCGA--TAGT-CGAAGTTTGCG
*
1234 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTTGCG
*
1255 TTGCGATTTA-TACCAAG-TT-CG
1 TTGCGA--TAGT-CGAAGTTTGCG
* *
1276 TTGCGATAGTCGAAGTTCGTG
1 TTGCGATAGTCGAAGTTTGCG
1297 TTGCGAT
1 TTGCGAT
1304 TTATTCCAAA
Statistics
Matches: 95, Mismatches: 20, Indels: 34
0.64 0.13 0.23
Matches are distributed among these distances:
18 1 0.01
19 13 0.14
20 15 0.16
21 49 0.52
22 5 0.05
23 11 0.12
24 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (21 bp):
TTGCGATAGTCGAAGTTTGCG
Found at i:1249 original size:42 final size:42
Alignment explanation
Indices: 1151--1317 Score: 209
Period size: 42 Copynumber: 4.0 Consensus size: 42
1141 CATATTCGCA
* * *
1151 TTGCGATAGTCGAAGTTTGCGTTGCGA---ATCTAGAAACT-G
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTAT-TACAAATTCG
1190 ATTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCG
1 --TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCG
*
1234 TTGCGATAGTCGAAGTTCGCGTTGCGATTTA-TACCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTA-CAAATTCG
* *
1276 TTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCG
1318 CAACGACTGG
Statistics
Matches: 113, Mismatches: 7, Indels: 11
0.86 0.05 0.08
Matches are distributed among these distances:
41 28 0.25
42 75 0.66
43 7 0.06
44 3 0.03
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCG
Found at i:2207 original size:42 final size:42
Alignment explanation
Indices: 2148--2334 Score: 301
Period size: 42 Copynumber: 4.5 Consensus size: 42
2138 TGCGATTTTG
2148 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
2190 GACTATCGCAATGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
2232 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
2274 GACTATCGCAACGAACTTCGACT--ATCGCAA--CGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
2312 GACTATCGCAACGCGAACTTGGA
1 GACTATCGCAA--CGAACTTGGA
2335 CTATCGCAAC
Statistics
Matches: 138, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
38 19 0.14
40 16 0.12
42 103 0.75
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:2360 original size:40 final size:38
Alignment explanation
Indices: 2152--2361 Score: 132
Period size: 42 Copynumber: 5.2 Consensus size: 38
2142 ATTTTGGACT
* * **
2152 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTCGACT--ATCGCAA--CGAACTTCGAAA
* * * **
2194 ATCGCAATGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTCGACT--ATCGCAA--CGAACTTCGAAA
* * **
2236 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTCGACT--ATCGCAA--CGAACTTCGAAA
**
2278 ATCGCAACGAACTTCGACTATCGCAACGAACTTCGACT
1 ATCGCAACGAACTTCGACTATCGCAACGAACTTCGAAA
* * *
2316 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAA
1 ATCGCAA--CGAACTTCGACTATCGCAACGAACTTCGAAA
2356 ATCGCA
1 ATCGCA
2362 TTGCGATAGT
Statistics
Matches: 157, Mismatches: 9, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
38 19 0.12
40 39 0.25
42 99 0.63
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (38 bp):
ATCGCAACGAACTTCGACTATCGCAACGAACTTCGAAA
Found at i:2361 original size:19 final size:19
Alignment explanation
Indices: 2148--2347 Score: 202
Period size: 19 Copynumber: 9.8 Consensus size: 19
2138 TGCGATTTTG
*
2148 GACTATCGCAACGAACTTG
1 GACTATCGCAACGAACTTC
*
2167 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAA--CGAACTTC
* *
2190 GACTATCGCAATGAACTTG
1 GACTATCGCAACGAACTTC
*
2209 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAA--CGAACTTC
*
2232 GACTATCGCAACGAACTTG
1 GACTATCGCAACGAACTTC
*
2251 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAA--CGAACTTC
2274 GACTATCGCAACGAACTTC
1 GACTATCGCAACGAACTTC
2293 GACTATCGCAACGAACTTC
1 GACTATCGCAACGAACTTC
*
2312 GACTATCGCAACGCGAACTTG
1 GACTATCGCAA--CGAACTTC
2333 GACTATCGCAACGAA
1 GACTATCGCAACGAA
2348 TTTGGAAAAT
Statistics
Matches: 153, Mismatches: 14, Indels: 28
0.78 0.07 0.14
Matches are distributed among these distances:
19 64 0.42
21 60 0.39
23 29 0.19
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (19 bp):
GACTATCGCAACGAACTTC
Found at i:2386 original size:21 final size:21
Alignment explanation
Indices: 2357--2409 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2347 ATTTGGAAAA
*
2357 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
2378 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
2399 TCGCGTTGCGA
1 TCGCGTTGCGA
2410 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:2625 original size:14 final size:14
Alignment explanation
Indices: 2606--2642 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2596 GATTATGTTA
2606 AACATAAATGAACG
1 AACATAAATGAACG
*
2620 AACATAAACGAACG
1 AACATAAATGAACG
*
2634 AAAATAAAT
1 AACATAAAT
2643 AAATATAAAC
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:0.62, C:0.14, G:0.11, T:0.14
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:3440 original size:27 final size:26
Alignment explanation
Indices: 3405--3509 Score: 77
Period size: 27 Copynumber: 3.8 Consensus size: 26
3395 AATTCATATA
3405 TTAACATTAAAAATATATATTTTTTATT
1 TTAA-ATTAAAAATATAT-TTTTTTATT
* * *
3433 TTAAATTATGAAATCTATTTTATTATTGT
1 TTAAATTA-AAAATATATTTTTTTA-T-T
**
3462 CTTAACCTAAAAATATATTTATTTTTATT
1 -TTAAATTAAAAATATA-TT-TTTTTATT
*
3491 TTAACTT-AAAATATATTTT
1 TTAAATTAAAAATATATTTT
3510 AATATTAGCA
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
25 2 0.03
26 2 0.03
27 18 0.29
28 18 0.29
29 8 0.13
30 9 0.15
31 5 0.08
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (26 bp):
TTAAATTAAAAATATATTTTTTTATT
Found at i:3530 original size:55 final size:57
Alignment explanation
Indices: 3412--3552 Score: 164
Period size: 55 Copynumber: 2.5 Consensus size: 57
3402 ATATTAACAT
* * * * *
3412 TAAAAATATATAT-TTTTTATTTTAAATTATGAAATCTATTTTATTATTGTCTTAACC
1 TAAAAATATATTTATTTTTATTTTAACTTA-GAAATATATTTTAATATTGTCATAACC
3469 TAAAAATATATTTATTTTTATTTTAACTTA-AAATATATTTTAATATTAG-CATAA-C
1 TAAAAATATATTTATTTTTATTTTAACTTAGAAATATATTTTAATATT-GTCATAACC
* * *
3524 TTAAAATATTTTTATTTTTATCTTAACTT
1 TAAAAATATATTTATTTTTATTTTAACTT
3553 TTAAAAATAT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
55 27 0.36
56 19 0.26
57 13 0.18
58 15 0.20
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (57 bp):
TAAAAATATATTTATTTTTATTTTAACTTAGAAATATATTTTAATATTGTCATAACC
Found at i:3550 original size:27 final size:27
Alignment explanation
Indices: 3450--3552 Score: 107
Period size: 28 Copynumber: 3.7 Consensus size: 27
3440 ATGAAATCTA
* *
3450 TTTTATTATTGTCTTAACCTAAAAATAT
1 TTTTATTATTATCTTAA-CTTAAAATAT
* * *
3478 ATTTATTTTTATTTTAACTTAAAATAT
1 TTTTATTATTATCTTAACTTAAAATAT
* * *
3505 ATTTTAATATTAGCATAACTTAAAATAT
1 -TTTTATTATTATCTTAACTTAAAATAT
*
3533 TTTTATTTTTATCTTAACTT
1 TTTTATTATTATCTTAACTT
3553 TTAAAAATAT
Statistics
Matches: 59, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
27 25 0.42
28 34 0.58
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (27 bp):
TTTTATTATTATCTTAACTTAAAATAT
Found at i:3655 original size:25 final size:27
Alignment explanation
Indices: 3593--3651 Score: 73
Period size: 30 Copynumber: 2.1 Consensus size: 27
3583 TTACATATGT
*
3593 TATATTTTTAACTTAAATTATTAAATA
1 TATAATTTTAACTTAAATTATTAAATA
*
3620 TATTCTAATTTTACCTTAAATTATTAAATA
1 TA---TAATTTTAACTTAAATTATTAAATA
3650 TA
1 TA
3652 ATTTATCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 2 0.07
30 25 0.93
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (27 bp):
TATAATTTTAACTTAAATTATTAAATA
Found at i:3710 original size:26 final size:28
Alignment explanation
Indices: 3667--3721 Score: 80
Period size: 26 Copynumber: 2.0 Consensus size: 28
3657 TCCTTATTTT
3667 AATATATTATTCTTATTTTTAA-TTAAA
1 AATATATTATTCTTATTTTTAAGTTAAA
3694 AATATA-TATT-TTAATTTTTAAGTTAAA
1 AATATATTATTCTT-ATTTTTAAGTTAAA
3721 A
1 A
3722 TATGAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 2 0.08
26 12 0.46
27 12 0.46
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
AATATATTATTCTTATTTTTAAGTTAAA
Found at i:3742 original size:29 final size:28
Alignment explanation
Indices: 3707--3783 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 28
3697 ATATATTTTA
*
3707 ATTTTTAAGTTAAAATATGAATAAAATAT
1 ATTTTTAAGTTAAGATAT-AATAAAATAT
3736 ATTTTTAAGTTAAGATAATAATAAAATAT
1 ATTTTTAAGTTAAGAT-ATAATAAAATAT
*
3765 AATTTTAATGTTAAGATAT
1 ATTTTTAA-GTTAAGATAT
3784 TAATTTAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 34 0.77
30 10 0.23
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (28 bp):
ATTTTTAAGTTAAGATATAATAAAATAT
Found at i:3779 original size:35 final size:34
Alignment explanation
Indices: 3692--3779 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 34
3682 TTTTTAATTA
3692 AAAATATATATTTTAATTTTTAAGTTAAAATATGAAT
1 AAAATATA-ATTTTAA--TTTAAGTTAAAATATGAAT
*
3729 AAAATAT-A--TT--TTTAAGTTAAGATAAT-AAT
1 AAAATATAATTTTAATTTAAGTTAAAAT-ATGAAT
3758 AAAATATAATTTTAATGTTAAG
1 AAAATATAATTTTAAT-TTAAG
3780 ATATTAATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 16
0.72 0.02 0.27
Matches are distributed among these distances:
29 22 0.51
30 3 0.07
32 2 0.05
33 2 0.05
34 1 0.02
35 6 0.14
37 7 0.16
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (34 bp):
AAAATATAATTTTAATTTAAGTTAAAATATGAAT
Found at i:4021 original size:7 final size:7
Alignment explanation
Indices: 4009--4036 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3999 AAAGATTAAA
4009 AATTGTT
1 AATTGTT
4016 AATTGTT
1 AATTGTT
4023 AATTGTT
1 AATTGTT
4030 AATTGTT
1 AATTGTT
4037 TACCCAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (7 bp):
AATTGTT
Found at i:6428 original size:14 final size:14
Alignment explanation
Indices: 6405--6460 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
6395 TGTTTGTGAA
6405 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
6419 CGTTCTGTTATGTT
1 CGTTCGGTTATGTT
6433 CG-T---TTATGTT
1 CGTTCGGTTATGTT
6443 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
6457 CGTT
1 CGTT
6461 TATGTTCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.07, C:0.14, G:0.25, T:0.54
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:6433 original size:24 final size:24
Alignment explanation
Indices: 6406--6480 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
6396 GTTTGTGAAC
*
6406 GTTCGGTTATGTTCGTTCTGTTAT
1 GTTCGTTTATGTTCGTTCTGTTAT
*
6430 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCTGTTAT
*
6454 GTTCGTTTATGTTCATTCAT-TTAT
1 GTTCGTTTATGTTCGTTC-TGTTAT
6478 GTT
1 GTT
6481 ATCCCAATCT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.11, C:0.12, G:0.21, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCTGTTAT
Found at i:7304 original size:12 final size:11
Alignment explanation
Indices: 7276--7327 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
7266 TGGGGCAATG
7276 TCGAGCTTGAA
1 TCGAGCTTGAA
7287 TCGAGCTTAGAA
1 TCGAGCTT-GAA
*
7299 TTGAGCTTGAA
1 TCGAGCTTGAA
*
7310 TCGAGCTTCAA
1 TCGAGCTTGAA
7321 TCGAGCT
1 TCGAGCT
7328 CAAGTCTCGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
11 27 0.73
12 10 0.27
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:7586 original size:16 final size:16
Alignment explanation
Indices: 7561--7632 Score: 78
Period size: 16 Copynumber: 4.7 Consensus size: 16
7551 CCAACGTTTA
*
7561 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
7577 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
7593 TGTTC-GTTATGTTCG
1 TGTTCATTTATGTTCG
** *
7608 TGCGCGTTTATGTTCG
1 TGTTCATTTATGTTCG
7624 T-TT-ATTTAT
1 TGTTCATTTAT
7633 TAAATGAACG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
14 5 0.11
15 12 0.26
16 30 0.64
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.56
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:7606 original size:31 final size:32
Alignment explanation
Indices: 7561--7624 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
7551 CCAACGTTTA
**
7561 TGTTCGTTTATGTTCGTGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCGTGCGCATTTATGTTCG
*
7593 TGTTCG-TTATGTTCGTGCGCGTTTATGTTCG
1 TGTTCGTTTATGTTCGTGCGCATTTATGTTCG
7624 T
1 T
7625 TTATTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 23 0.79
32 6 0.21
ACGTcount: A:0.08, C:0.14, G:0.25, T:0.53
Consensus pattern (32 bp):
TGTTCGTTTATGTTCGTGCGCATTTATGTTCG
Found at i:7712 original size:16 final size:16
Alignment explanation
Indices: 7691--7722 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
7681 AAAAAAAAAT
7691 GTGTTCGCTTATGTTC
1 GTGTTCGCTTATGTTC
*
7707 GTGTTCGTTTATGTTC
1 GTGTTCGCTTATGTTC
7723 ATTTATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.16, G:0.25, T:0.53
Consensus pattern (16 bp):
GTGTTCGCTTATGTTC
Found at i:8726 original size:34 final size:35
Alignment explanation
Indices: 8670--8739 Score: 124
Period size: 34 Copynumber: 2.0 Consensus size: 35
8660 AAGAAAAATA
*
8670 AAGATTTTTTTGCCATATAAGTATAGTCATAGAAT
1 AAGAATTTTTTGCCATATAAGTATAGTCATAGAAT
8705 AAGAATTTTTTGCCATA-AAGTATAGTCATAGAAT
1 AAGAATTTTTTGCCATATAAGTATAGTCATAGAAT
8739 A
1 A
8740 CCTTTTTTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.53
35 16 0.47
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (35 bp):
AAGAATTTTTTGCCATATAAGTATAGTCATAGAAT
Found at i:11155 original size:125 final size:124
Alignment explanation
Indices: 10998--11246 Score: 464
Period size: 125 Copynumber: 2.0 Consensus size: 124
10988 CCACTCCCAA
*
10998 ATATATAGAATAAGCACAATAAAAGGGTAAATTTTGTGTTTAGTACGTAAACTATCAATTTTAGT
1 ATATATAGAATAAGCACAATAAAAGGGTAAATTTCGTGTTTAGTACGTAAACTATCAATTTTAGT
11063 CTAGTTTAATACTTAAACTTTCATTTTTTTTAAATCATATCTAACGTTTAGTATTTATTT
66 CTAGTTTAATACTTAAACTTTCA-TTTTTTTAAATCATATCTAACGTTTAGTATTTATTT
11123 ATATATAGAATAA-CACAATAAAAAGGGTAAATTTCGTGTTTAGTACGTAAACTATCAATTTTAG
1 ATATATAGAATAAGCACAAT-AAAAGGGTAAATTTCGTGTTTAGTACGTAAACTATCAATTTTAG
11187 TCTAGTTTAATACTTAAACTTTCATTTTTTTAAATCATATCTAACGTTTAGTATTTATTT
65 TCTAGTTTAATACTTAAACTTTCATTTTTTTAAATCATATCTAACGTTTAGTATTTATTT
11247 CATTTTAGTA
Statistics
Matches: 122, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
124 42 0.34
125 80 0.66
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (124 bp):
ATATATAGAATAAGCACAATAAAAGGGTAAATTTCGTGTTTAGTACGTAAACTATCAATTTTAGT
CTAGTTTAATACTTAAACTTTCATTTTTTTAAATCATATCTAACGTTTAGTATTTATTT
Found at i:11920 original size:3 final size:3
Alignment explanation
Indices: 11912--11950 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
11902 AAGCCTGCAA
11912 AAT AAT AAT -AT AAT AAT AAT AAT AA- AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11951 CCTGCAACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.18
3 27 0.82
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11926 original size:8 final size:8
Alignment explanation
Indices: 11913--11950 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
11903 AGCCTGCAAA
11913 ATAATAAT
1 ATAATAAT
11921 ATAATAAT
1 ATAATAAT
*
11929 AATAATAAA
1 -ATAATAAT
11938 ATAATAAT
1 ATAATAAT
11946 ATAAT
1 ATAAT
11951 CCTGCAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
ATAATAAT
Found at i:11928 original size:11 final size:11
Alignment explanation
Indices: 11913--11950 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
11903 AGCCTGCAAA
11913 ATAATAAT-AT
1 ATAATAATAAT
11923 AATAATAATAAT
1 -ATAATAATAAT
*
11935 AAAATAATAAT
1 ATAATAATAAT
11946 ATAAT
1 ATAAT
11951 CCTGCAACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 22 0.92
12 2 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:11931 original size:14 final size:14
Alignment explanation
Indices: 11912--11946 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
11902 AAGCCTGCAA
*
11912 AATAATAATATAAT
1 AATAATAATAAAAT
11926 AATAATAATAAAAT
1 AATAATAATAAAAT
11940 AATAATA
1 AATAATA
11947 TAATCCTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AATAATAATAAAAT
Found at i:18745 original size:21 final size:22
Alignment explanation
Indices: 18701--18745 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
18691 AAAAACGTTG
*
18701 ATAATATTTAATTATTATACTT
1 ATAATATTTAATTATTATAATT
18723 ATAA-ATTTAA-TATTATCAATT
1 ATAATATTTAATTATTAT-AATT
18744 AT
1 AT
18746 TGAAGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 11 0.52
22 4 0.19
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAATATTTAATTATTATAATT
Found at i:22553 original size:20 final size:21
Alignment explanation
Indices: 22530--22578 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
22520 AAATAGAATT
22530 TAAAAATGT-AAATGT-TTTCA
1 TAAAAATGTAAAAT-TATTTCA
22550 TAAAAAT-TAAAATTAATTTCA
1 TAAAAATGTAAAATT-ATTTCA
22571 TAAAAATG
1 TAAAAATG
22579 AGGAAAATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 2 0.08
20 11 0.44
21 12 0.48
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (21 bp):
TAAAAATGTAAAATTATTTCA
Found at i:23611 original size:42 final size:40
Alignment explanation
Indices: 23563--23660 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 40
23553 TATTTTAATA
*
23563 AAAAATTAAAATTATTATTTATATCAGAAATACTT-AATTTCT
1 AAAAATTAAAATTATTAATTATATCAGAAATA-TTCAA-TT-T
* *
23605 TAAAATTAAACTTATTAATTATATCAGAAATATTCAATTT
1 AAAAATTAAAATTATTAATTATATCAGAAATATTCAATTT
23645 AAGAAATTAAAATTAT
1 AA-AAATTAAAATTAT
23661 ATGTATGAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
40 2 0.04
41 16 0.33
42 31 0.63
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (40 bp):
AAAAATTAAAATTATTAATTATATCAGAAATATTCAATTT
Found at i:25130 original size:11 final size:10
Alignment explanation
Indices: 25114--25169 Score: 58
Period size: 11 Copynumber: 5.2 Consensus size: 10
25104 TAAAATAAAG
*
25114 TAATTAAACAT
1 TAATTAAA-AA
25125 TAATTATAAAA
1 TAATTA-AAAA
*
25136 TAATTAAACAT
1 TAATTAAA-AA
25147 TAATTATAAAA
1 TAATTA-AAAA
25158 TAATTAAAAA
1 TAATTAAAAA
25168 TA
1 TA
25170 TTTAGAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 8 0.21
11 27 0.69
12 4 0.10
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (10 bp):
TAATTAAAAA
Found at i:25139 original size:22 final size:22
Alignment explanation
Indices: 25108--25165 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
25098 AGCGGTTAAA
*
25108 ATAAAGTAATTAAACATTAATT
1 ATAAAATAATTAAACATTAATT
25130 ATAAAATAATTAAACATTAATT
1 ATAAAATAATTAAACATTAATT
25152 ATAAAATAATTAAA
1 ATAAAATAATTAAA
25166 AATATTTAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (22 bp):
ATAAAATAATTAAACATTAATT
Found at i:25378 original size:23 final size:23
Alignment explanation
Indices: 25352--25397 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
25342 ATAATTATCT
25352 TATTAAATATTAAAAGAATAAAA
1 TATTAAATATTAAAAGAATAAAA
* * *
25375 TATTTAATTTTAAAATAATAAAA
1 TATTAAATATTAAAAGAATAAAA
25398 ACTTATTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
TATTAAATATTAAAAGAATAAAA
Found at i:25489 original size:24 final size:23
Alignment explanation
Indices: 25434--25489 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
25424 TTGATAATGA
*
25434 TAAAAATTTAATTTTACTTAAAT
1 TAAAAATTTAATATTACTTAAAT
* *
25457 TTAAGATTTAAAATATTA-TTAAAT
1 TAAAAATTT--AATATTACTTAAAT
25481 TAAAAATTT
1 TAAAAATTT
25490 TAAGAGAGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 7 0.27
24 13 0.50
25 6 0.23
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
TAAAAATTTAATATTACTTAAAT
Found at i:26515 original size:328 final size:332
Alignment explanation
Indices: 26137--26799 Score: 1000
Period size: 328 Copynumber: 2.0 Consensus size: 332
26127 AAATTAATTT
* *
26137 TATTAAAAATAAATAAACATTATCAAATGTTGTTAAAAAATAATAATTAATGAATAATAATTCAT
1 TATTAAAAATAAATAAACATTATCAAACGTTGTTAAAAAATAATAATTAATAAATAATAATTCAT
*
26202 TTAAT-CTCTCAATTGTAATTAAAAGTTTATTTTAATTT-TTTTATATTTTTAAACAATTAATTT
66 TTAATCCT-TCAATTGTAATTAAAAATTTATTTTAATTTATTTTATATTTTTAAACAATTAATTT
26265 TAAAAGTCAA-TAAAATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTA
130 T-AAAGTCAATTAAAATTTT-AAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTA
* *
26329 TTATCA-T-T-A-TCATCATTTTGTAAAA-AAATACTAGTTATAAAACTTTTATAAAATTATTCA
193 TCATCATTATCACTCATCATTTTATAAAAGAAATACTAGTTATAAAACTTTTATAAAATTATTCA
* * * * *
26389 TATTTTAAAATATTTACCCTCAAAATTTTCCTATACTATATTATACGTATTATATAATTTTATGC
258 TATTTTAAAATACTTACCCTCAAAATTTT-CTATACCAGATTATACATATTATATAATTTCATGC
26454 AAAAATCAAAA
322 AAAAATCAAAA
* * *
26465 TATTAAAAATGAATAAATATTATCAACCGTTGTTAAAAAATAATAATTAATAAATAATAATTCAT
1 TATTAAAAATAAATAAACATTATCAAACGTTGTTAAAAAATAATAATTAATAAATAATAATTCAT
* *
26530 TTGATCCTTCAATTGTAATTAAAAATTTATTTTGATTTATTTTATATTTTTAAACAATTAATTTT
66 TTAATCCTTCAATTGTAATTAAAAATTTATTTTAATTTATTTTATATTTTTAAACAATTAATTTT
*
26595 AAAGTCAATTAATATTTTAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATCA
131 AAAGTCAATTAAAATTTTAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATCA
* *
26660 TCATTATCATCGTCATCATTTTATAAAAGAAATATTAGTTATAAAATTTTTATAAAATTATTCAT
196 TCATTATCA-C-TCATCATTTTATAAAAGAAATACTAGTTATAAAACTTTTATAAAATTATTCAT
* * * *
26725 ATTTTAAAATACTTACCCTCAAAGTTTTTTATACCAGATTATACATATTGTGTAATTTCATGCAA
259 ATTTTAAAATACTTACCCTCAAAATTTTCTATACCAGATTATACATATTATATAATTTCATGCAA
* *
26790 ATATTAAAA
324 AAATCAAAA
26799 T
1 T
26800 TTATCGAGTT
Statistics
Matches: 301, Mismatches: 24, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
328 149 0.50
329 37 0.12
330 1 0.00
331 1 0.00
334 53 0.18
335 60 0.20
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (332 bp):
TATTAAAAATAAATAAACATTATCAAACGTTGTTAAAAAATAATAATTAATAAATAATAATTCAT
TTAATCCTTCAATTGTAATTAAAAATTTATTTTAATTTATTTTATATTTTTAAACAATTAATTTT
AAAGTCAATTAAAATTTTAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATCA
TCATTATCACTCATCATTTTATAAAAGAAATACTAGTTATAAAACTTTTATAAAATTATTCATAT
TTTAAAATACTTACCCTCAAAATTTTCTATACCAGATTATACATATTATATAATTTCATGCAAAA
ATCAAAA
Found at i:26519 original size:14 final size:14
Alignment explanation
Indices: 26497--26526 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
26487 TCAACCGTTG
26497 TTAAAAAATAATAA
1 TTAAAAAATAATAA
*
26511 TTAATAAATAATAA
1 TTAAAAAATAATAA
26525 TT
1 TT
26527 CATTTGATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAAAAATAATAA
Found at i:32985 original size:17 final size:18
Alignment explanation
Indices: 32965--33002 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
32955 TTTTAATTAA
32965 AAAATATATA-AAAATTT
1 AAAATATATAGAAAATTT
*
32982 AAAATATATAGTAAATTT
1 AAAATATATAGAAAATTT
33000 AAA
1 AAA
33003 TTTTCAGGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
AAAATATATAGAAAATTT
Found at i:39830 original size:19 final size:20
Alignment explanation
Indices: 39793--39841 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
39783 AAATACTATT
39793 TAAAATATTATTATTTTACC
1 TAAAATATTATTATTTTACC
39813 TAAAATATTATT-TTTTACC
1 TAAAATATTATTATTTTACC
**
39832 GGAAATATTA
1 TAAAATATTA
39842 ATTTCGCTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (20 bp):
TAAAATATTATTATTTTACC
Found at i:52065 original size:87 final size:87
Alignment explanation
Indices: 51913--52084 Score: 265
Period size: 87 Copynumber: 2.0 Consensus size: 87
51903 TCTAATATTC
* * *
51913 TGTTCAGAAAGGAGCGTCCCTTGCACCGTTAAGATATTAAATCAAAAAATATAATCTAAATGATA
1 TGTTCAGAAAGGAGCGTCCCCTACACCGTTAAGATATTAAATCAAAAAATATAATCTAAACGATA
*
51978 TCTGATAAGAAAATAAAAGGAT
66 TCTAATAAGAAAATAAAAGGAT
* *
52000 TGTTTAGAAAGGAGCGTCCCCTACACCGTTAA-AGTATTAAATCAAAAAATATAGTCTAAACGAT
1 TGTTCAGAAAGGAGCGTCCCCTACACCGTTAAGA-TATTAAATCAAAAAATATAATCTAAACGAT
*
52064 ATTTAATAAGAAAATAAAAGG
65 ATCTAATAAGAAAATAAAAGG
52085 GTTAGGGTGA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
86 1 0.01
87 76 0.99
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (87 bp):
TGTTCAGAAAGGAGCGTCCCCTACACCGTTAAGATATTAAATCAAAAAATATAATCTAAACGATA
TCTAATAAGAAAATAAAAGGAT
Found at i:54299 original size:37 final size:38
Alignment explanation
Indices: 54220--54317 Score: 103
Period size: 37 Copynumber: 2.6 Consensus size: 38
54210 TAACCAATTT
* *
54220 ATATTCAATTAAAATAAAAATATCTTATTTATACATTA
1 ATATTCAATTGAAATAAAAATATATTATTTATACATTA
** *
54258 ATATTTGATT-AAATACAAATATATTATTTATGA-A-TA
1 ATATTCAATTGAAATAAAAATATATTATTTAT-ACATTA
*
54294 TATATTCAATTGAAATATAAATAT
1 -ATATTCAATTGAAATAAAAATAT
54318 TTTAGTACAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
36 2 0.04
37 28 0.56
38 20 0.40
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (38 bp):
ATATTCAATTGAAATAAAAATATATTATTTATACATTA
Found at i:56346 original size:67 final size:67
Alignment explanation
Indices: 56245--56441 Score: 245
Period size: 67 Copynumber: 2.9 Consensus size: 67
56235 TGAGCAAGAG
* * * * * * *
56245 TTTAATGACCTTAATAAGCAATGAGTCGAACAACAAAATTTCTTAATGAGCATGAGTCGATCAAA
1 TTTAACGAGCTTAATCAGCAATGAGTCGAGCAACAAAATTTCTTAACGAGCACGAGTCGAACAAA
56310 AT
66 AT
* *
56312 TTTAACGAGCTTAA-CATGCAATGAGCCGAGCAACAAATTTTCTTAACGAGCACGAGTCGAACAA
1 TTTAACGAGCTTAATCA-GCAATGAGTCGAGCAACAAAATTTCTTAACGAGCACGAGTCGAACAA
56376 AAT
65 AAT
* * * *
56379 TTTAATGAGCTTAATGAGCAATGAGTCGAGCAACAAAAGTTT-TTAACGAGCACAAGTCAAACA
1 TTTAACGAGCTTAATCAGCAATGAGTCGAGCAACAAAA-TTTCTTAACGAGCACGAGTCGAACA
56442 TTGCCCAACT
Statistics
Matches: 112, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
66 1 0.01
67 107 0.96
68 4 0.04
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (67 bp):
TTTAACGAGCTTAATCAGCAATGAGTCGAGCAACAAAATTTCTTAACGAGCACGAGTCGAACAAA
AT
Found at i:73702 original size:22 final size:22
Alignment explanation
Indices: 73677--73724 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
73667 AATTATTGGA
73677 TATTTTATTATT-ATCTTATATT
1 TATTTT-TTATTAATCTTATATT
* *
73699 TATTTTTTATTAATTTTTTATT
1 TATTTTTTATTAATCTTATATT
73721 TATT
1 TATT
73725 CTTCTTTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (22 bp):
TATTTTTTATTAATCTTATATT
Found at i:73709 original size:11 final size:11
Alignment explanation
Indices: 73677--73724 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
73667 AATTATTGGA
73677 TATTTTATTA-T
1 TATTTT-TTATT
* *
73688 TATCTTATATT
1 TATTTTTTATT
73699 TATTTTTTATT
1 TATTTTTTATT
*
73710 AATTTTTTATT
1 TATTTTTTATT
73721 TATT
1 TATT
73725 CTTCTTTCCT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
10 2 0.07
11 28 0.93
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTTTTTATT
Found at i:78274 original size:42 final size:43
Alignment explanation
Indices: 78228--78314 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
78218 ATGAAAAGTA
78228 GGTTAAATTCAAGGAATAAAC-AAGAAATACCTCGAGAAGCTT
1 GGTTAAATTCAAGGAATAAACAAAGAAATACCTCGAGAAGCTT
*
78270 GGTTAAATTCAAGGAATAAACAAAGAAATACCTTGAGAAGCTT
1 GGTTAAATTCAAGGAATAAACAAAGAAATACCTCGAGAAGCTT
78313 GG
1 GG
78315 CCTCATGGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 21 0.49
43 22 0.51
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.22
Consensus pattern (43 bp):
GGTTAAATTCAAGGAATAAACAAAGAAATACCTCGAGAAGCTT
Found at i:80197 original size:30 final size:31
Alignment explanation
Indices: 80163--80233 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
80153 AATTTAGGAG
80163 TTTTTTGAAATTTT-ATGGAATTT-A-AGGTTT
1 TTTTTTGAAATTTTAAT--AATTTCATAGGTTT
*
80193 TTTTTTGGAATTTTAATAATTTCATAGGTTT
1 TTTTTTGAAATTTTAATAATTTCATAGGTTT
*
80224 TTTTATGAAA
1 TTTTTTGAAA
80234 ATAACTTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 5 0.14
30 14 0.40
31 16 0.46
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.56
Consensus pattern (31 bp):
TTTTTTGAAATTTTAATAATTTCATAGGTTT
Found at i:82424 original size:20 final size:20
Alignment explanation
Indices: 82330--82698 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
82320 GATTTTCCAT
* ** *
82330 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
82350 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
82370 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
82390 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
82410 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
82430 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
82450 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
82470 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
82490 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
82510 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
82530 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
82550 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
82570 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
82590 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
82610 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
82630 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
82650 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
82670 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
82690 AATCACAAC
1 AATCGCAAC
82699 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:83408 original size:24 final size:24
Alignment explanation
Indices: 83369--83415 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
83359 AAATTTGGTC
83369 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
83393 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
83416 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:83607 original size:12 final size:12
Alignment explanation
Indices: 83590--83614 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
83580 ATATAATCCT
83590 GAAGAAGAAAAA
1 GAAGAAGAAAAA
83602 GAAGAAGAAAAA
1 GAAGAAGAAAAA
83614 G
1 G
83615 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:85941 original size:19 final size:19
Alignment explanation
Indices: 85919--86206 Score: 320
Period size: 19 Copynumber: 16.4 Consensus size: 19
85909 CGGAAAATAC
*
85919 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
85938 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
85952 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
85972 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
85986 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
86005 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
86024 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
86038 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
86057 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
86076 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
86090 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
86109 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
86128 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
86147 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
86161 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
86180 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
86199 AATCGCAA
1 AATCGCAA
86207 CGAGATAATC
Statistics
Matches: 230, Mismatches: 13, Indels: 52
0.78 0.04 0.18
Matches are distributed among these distances:
14 45 0.20
15 4 0.02
16 16 0.07
17 15 0.07
18 5 0.02
19 132 0.57
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:86006 original size:33 final size:33
Alignment explanation
Indices: 85919--86187 Score: 248
Period size: 33 Copynumber: 7.8 Consensus size: 33
85909 CGGAAAATAC
* *
85919 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
85952 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
85986 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
86024 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
86057 AATCGCAATGCGAAATGAAAATCG-AACCGACAT
1 AATCGCAATGCGAAATGAAAATCGCAA-CGAGAA
*
86090 AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAA
86128 AATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
86160 GAATCGCAATGCGAAATGAAAATCGCAA
1 -AATCGCAATGCGAAATGAAAATCGCAA
86188 TGCGAAATGA
Statistics
Matches: 204, Mismatches: 13, Indels: 38
0.80 0.05 0.15
Matches are distributed among these distances:
32 2 0.01
33 106 0.52
34 32 0.16
35 8 0.04
36 8 0.04
37 6 0.03
38 42 0.21
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:86034 original size:52 final size:53
Alignment explanation
Indices: 85947--86187 Score: 327
Period size: 52 Copynumber: 4.6 Consensus size: 53
85937 AAATCCCAAC
85947 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACCGAGAGAATCGCAATGCGAA
86000 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACCGAGAGAATCGCAATGCGAA
* *
86052 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACCGAGAGAATCGCAATGCGAA
* * * *
86104 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CCG--A-GAGAATCGCAATGCGAA
86159 A-G--AATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
86188 TGCGAAATGA
Statistics
Matches: 173, Mismatches: 9, Indels: 13
0.89 0.05 0.07
Matches are distributed among these distances:
51 2 0.01
52 136 0.79
53 18 0.10
54 2 0.01
55 5 0.03
56 1 0.01
57 9 0.05
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACCGAGAGAATCGCAATGCGAA
Found at i:86131 original size:123 final size:124
Alignment explanation
Indices: 85986--86238 Score: 449
Period size: 123 Copynumber: 2.1 Consensus size: 124
85976 GCAACGAGAG
* *
85986 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
86051 AATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAAATTA-A
66 AATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACATAATCGCAATGCGAAATTATA
86109 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
*
86174 AATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTATA
66 AATGAAAATCGCAATGCGAAATGAAAATCGCAACGACATAATCGCAATGCGAAATTATA
86233 AA-CGCA
1 AATCGCA
86239 TTGCGATTTT
Statistics
Matches: 125, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
123 120 0.96
124 5 0.04
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (124 bp):
AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAAAATCGCAATGCGAAATGAAAATCGCAACGACATAATCGCAATGCGAAATTATA
Found at i:86188 original size:52 final size:52
Alignment explanation
Indices: 85919--86228 Score: 258
Period size: 52 Copynumber: 5.9 Consensus size: 52
85909 CGGAAAATAC
*
85919 AATCGCAACGCGAAATGAAAATCCCAA-C-ATGAA-AATCGCAATGCGGAAATGAA
1 AATCGCAA-GCGAAATGAAAATCGCAAGCGA--AAGAATCGCAATGC-GAAATGAA
*
85972 AATCGCAA-CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAAGCGAAATGAAAATCGCAA-GCGAAA-G--AATCGCAATGCGAAATGAA
*
86024 AATCGCAA-CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAAGCGAAATGAAAATCGCAA-GCGAAA-G--AATCGCAATGCGAAATGAA
* * * *
86076 AATCG-AACCGACAT---AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAAGCGAAATGAAAATCGCAA-GCG-AA--AGAATCGCAATGCGAAATGAA
86128 AATCGCAATGCGAAATGAAAATCGCAA-CGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAA-GCGAAATGAAAATCGCAAGCGAAAGAATCGCAATGCGAAATGAA
* *
86180 AATCGCAATGCGAAATGAAAATCGCAA-CGAGATAATCGCAATGCGAAAT
1 AATCGCAA-GCGAAATGAAAATCGCAAGCGAAAGAATCGCAATGCGAAAT
86229 TATAAACGCA
Statistics
Matches: 228, Mismatches: 10, Indels: 39
0.82 0.04 0.14
Matches are distributed among these distances:
48 9 0.04
49 3 0.01
50 1 0.00
51 5 0.02
52 168 0.74
53 23 0.10
54 8 0.04
55 3 0.01
57 8 0.04
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (52 bp):
AATCGCAAGCGAAATGAAAATCGCAAGCGAAAGAATCGCAATGCGAAATGAA
Found at i:86244 original size:71 final size:67
Alignment explanation
Indices: 86038--86227 Score: 188
Period size: 71 Copynumber: 2.7 Consensus size: 67
86028 GCAACGAGAG
* * *
86038 AATCGCAATGCGAAATGAAAATCGCAATGCGAAAT-GAAAATCGAACCGACATAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAATCG-CAATCGAA---A-ATAATCGCAATGCG
*
86102 AAATTAA
61 AAATGAA
* *
86109 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CG-AAAGAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-G-AAATCGCAATCGAAAATAATCGCAATGC
86172 GAAATGAA
60 GAAATGAA
86180 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGA-AATCGCAAT-CGAAA
86228 TTATAAACGC
Statistics
Matches: 101, Mismatches: 7, Indels: 24
0.77 0.05 0.18
Matches are distributed among these distances:
65 1 0.01
66 9 0.09
67 1 0.01
68 2 0.02
69 4 0.04
71 71 0.70
72 1 0.01
73 1 0.01
75 1 0.01
76 3 0.03
77 6 0.06
78 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.19, T:0.15
Consensus pattern (67 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAAATCGCAATCGAAAATAATCGCAATGCGAAATG
AA
Found at i:86344 original size:19 final size:19
Alignment explanation
Indices: 86235--86336 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
86225 AAATTATAAA
86235 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
86254 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
86274 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
86290 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
86307 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
86326 CGCATTGCGAT
1 CGCATTGCGAT
86337 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:86462 original size:14 final size:14
Alignment explanation
Indices: 86443--86479 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
86433 CATCAATTAC
86443 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
86457 ACAAATCATCTTTT
1 ACAAATCAACTTTT
86471 ACAAATCAA
1 ACAAATCAA
86480 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:86491 original size:12 final size:12
Alignment explanation
Indices: 86474--86546 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
86464 ATCTTTTACA
86474 AATCAATTAAAC
1 AATCAATTAAAC
*
86486 AATCAA--AAATTG
1 AATCAATTAAA--C
**
86498 AATCAACTTTTAC
1 AATCAA-TTAAAC
86511 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
86524 AATCAA-AAAAC
1 AATCAATTAAAC
86535 AATCAATTAAAC
1 AATCAATTAAAC
86547 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:86508 original size:38 final size:38
Alignment explanation
Indices: 86460--86532 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
86450 AACTTTTACA
*
86460 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
86498 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
86533 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:88422 original size:14 final size:14
Alignment explanation
Indices: 88403--88459 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
88393 GCGAAATGAA
*
88403 AATCGCAACGACAG
1 AATCGCAACGAAAG
88417 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
88434 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
88450 AATCGCAACG
1 AATCGCAACG
88460 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:88430 original size:33 final size:33
Alignment explanation
Indices: 88384--88476 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
88374 GCGAAACCAA
*
88384 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
88417 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
88450 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
88477 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:88441 original size:19 final size:19
Alignment explanation
Indices: 88347--88481 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
88337 TAGTTTACTT
* *
88347 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
88367 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
88386 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
88405 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
88419 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
88438 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
88452 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
88471 TCGCAATGCGA
1 TCGCAACGCGA
88482 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:88499 original size:19 final size:19
Alignment explanation
Indices: 88477--88605 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
88467 AAAATCGCAA
88477 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
88496 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
88510 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
88529 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
88543 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
88562 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
88581 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
88601 TGCGA
1 TGCGA
88606 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:88519 original size:33 final size:33
Alignment explanation
Indices: 88477--88568 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
88467 AAAATCGCAA
88477 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
88510 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
88543 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
88569 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:88968 original size:92 final size:93
Alignment explanation
Indices: 88648--89025 Score: 735
Period size: 92 Copynumber: 4.1 Consensus size: 93
88638 TTGAATGGAT
88648 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
88712 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
88740 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
88805 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
88833 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
88897 AGTTTAGCAGAATTGGCAGCAACCG-AC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
88924 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
88989 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
89017 AAATTTACT
1 AAATTTACT
89026 AAGCAATCTA
Statistics
Matches: 283, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
91 41 0.14
92 142 0.50
93 100 0.35
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:90744 original size:14 final size:14
Alignment explanation
Indices: 90725--90814 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
90715 TTGAAATGAA
90725 AATCGCAACGAGAG
1 AATCGCAACGAGAG
90739 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
*
90756 ACAATCGCAACGATAG
1 --AATCGCAACGAGAG
*
90772 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
90791 AATCGCAACGAGAG
1 AATCGCAACGAGAG
90805 AATCGCAACG
1 AATCGCAACG
90815 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 28 0.45
15 1 0.02
16 8 0.13
17 7 0.11
18 1 0.02
19 17 0.27
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:90762 original size:33 final size:33
Alignment explanation
Indices: 90717--90831 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
90707 TCTTTTGGTT
90717 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * *
90750 GAGATGACAATCGCAACGATAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
90783 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
90816 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
90832 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:90763 original size:19 final size:19
Alignment explanation
Indices: 90720--90836 Score: 84
Period size: 19 Copynumber: 6.9 Consensus size: 19
90710 TTTGGTTGAA
90720 ATGAAAATCGCAA--CGAG
1 ATGAAAATCGCAACGCGAG
90737 A-G--AATCGCAACGCGAG
1 ATGAAAATCGCAACGCGAG
*
90753 ATGACAATCGCAA--C--G
1 ATGAAAATCGCAACGCGAG
* *
90768 AT-AGAATCGCAACGCGAA
1 ATGAAAATCGCAACGCGAG
90786 ATGAAAATCGCAA--CGAG
1 ATGAAAATCGCAACGCGAG
*
90803 A-G--AATCGCAACGCGAA
1 ATGAAAATCGCAACGCGAG
*
90819 ATGAAAATCGCAATGCGA
1 ATGAAAATCGCAACGCGA
90837 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
14 25 0.32
15 3 0.04
16 12 0.15
17 8 0.10
18 2 0.03
19 29 0.37
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (19 bp):
ATGAAAATCGCAACGCGAG
Found at i:91051 original size:33 final size:33
Alignment explanation
Indices: 91009--91079 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
90999 AATACTAACT
*
91009 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
91042 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
91075 TGAAA
1 TGAAA
91080 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:91312 original size:22 final size:22
Alignment explanation
Indices: 91260--91314 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
91250 ATGGTTGTGA
**
91260 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
91282 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
91304 GGATTTCTTCG
1 GGATTTCTTCG
91315 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:91485 original size:20 final size:20
Alignment explanation
Indices: 91460--91653 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
91450 CTTTAAATAT
91460 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
91480 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
91502 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
91521 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
91541 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
91561 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
91581 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
91601 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
91621 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
91641 CGCGTTGCGATTT
1 CGCGTTGCGATTT
91654 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:91647 original size:60 final size:60
Alignment explanation
Indices: 91460--91653 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
91450 CTTTAAATAT
**
91460 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
91521 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
91581 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
91641 CGCGTTGCGATTT
1 CGCGTTGCGATTT
91654 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:91670 original size:21 final size:20
Alignment explanation
Indices: 91646--91722 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
91636 ATATTCGCGT
91646 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
91667 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
91687 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
91709 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
91723 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:91733 original size:20 final size:20
Alignment explanation
Indices: 91708--91759 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
91698 AAGAATCGCG
*
91708 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
91728 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
91748 TTGCGATTCTGG
1 TTGCGATTCTGG
91760 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:92992 original size:20 final size:20
Alignment explanation
Indices: 92961--93011 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
92951 TTTTATTGAG
92961 GTGTTGGAAATTAAAGTTAGA
1 GTGTT-GAAATTAAAGTTAGA
* *
92982 GTGTTGAAATTTATGTTAGA
1 GTGTTGAAATTAAAGTTAGA
*
93002 ATG-TGAAATT
1 GTGTTGAAATT
93012 GGATCCTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.39
Consensus pattern (20 bp):
GTGTTGAAATTAAAGTTAGA
Found at i:93314 original size:19 final size:19
Alignment explanation
Indices: 93290--93339 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
93280 AGACTTGAAT
93290 GGTCAACTTGAAGTATTAA
1 GGTCAACTTGAAGTATTAA
93309 GGTCAACTTGAAGTATTAA
1 GGTCAACTTGAAGTATTAA
93328 GGTCAACTTGAA
1 GGTCAACTTGAA
93340 ATAGAAGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (19 bp):
GGTCAACTTGAAGTATTAA
Found at i:101459 original size:3 final size:3
Alignment explanation
Indices: 101451--101497 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
101441 TTGAAAATCC
101451 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
101498 ATTTGTCCTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:101534 original size:13 final size:13
Alignment explanation
Indices: 101518--101544 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
101508 CATGTTTGAT
101518 CTATTGAGTAGAG
1 CTATTGAGTAGAG
101531 CTATTGAGTAGAG
1 CTATTGAGTAGAG
101544 C
1 C
101545 AAGTGTGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (13 bp):
CTATTGAGTAGAG
Found at i:107565 original size:44 final size:46
Alignment explanation
Indices: 107499--107585 Score: 133
Period size: 44 Copynumber: 1.9 Consensus size: 46
107489 TTATTTTCGT
*
107499 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGTTTA
1 TTTTTCGAATAAA-GCATGCGAACTAGATATCATGCAGTTAGGTTTA
*
107546 TTTTT-GAATAAA-CATGCGAATTAGATATCATGCAGTTAGG
1 TTTTTCGAATAAAGCATGCGAACTAGATATCATGCAGTTAGG
107586 ATTTTCTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
44 26 0.68
46 7 0.18
47 5 0.13
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (46 bp):
TTTTTCGAATAAAGCATGCGAACTAGATATCATGCAGTTAGGTTTA
Found at i:117288 original size:18 final size:18
Alignment explanation
Indices: 117257--117328 Score: 58
Period size: 18 Copynumber: 3.9 Consensus size: 18
117247 GAAATAAAAG
**
117257 AGAAAAAATGAAAAAATA
1 AGAAAAAAACAAAAAATA
117275 AGAAAAAAAC-AAAAATGA
1 AGAAAAAAACAAAAAAT-A
* *
117293 TGGAAAAAACAAAAAGA-A
1 AGAAAAAAACAAAAA-ATA
*
117311 AGAAAAAGAAGAAAAAAT
1 AGAAAAA-AACAAAAAAT
117329 GAAAAAGGGA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
17 6 0.14
18 24 0.57
19 11 0.26
20 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.14, T:0.07
Consensus pattern (18 bp):
AGAAAAAAACAAAAAATA
Found at i:117354 original size:22 final size:20
Alignment explanation
Indices: 117320--117366 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
117310 AAGAAAAAGA
117320 AGAAAAAATGAAAAAGGGAAG
1 AGAAAAAATGAAAAA-GGAAG
*
117341 AGAACAAATGGAAAAAGGAAG
1 AGAAAAAAT-GAAAAAGGAAG
117362 A-AAAA
1 AGAAAA
117367 GAGAAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 3 0.13
21 14 0.61
22 6 0.26
ACGTcount: A:0.68, C:0.02, G:0.26, T:0.04
Consensus pattern (20 bp):
AGAAAAAATGAAAAAGGAAG
Found at i:117385 original size:14 final size:15
Alignment explanation
Indices: 117361--117393 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
117351 GAAAAAGGAA
117361 GAAAAAGAGAAAAAT
1 GAAAAAGAGAAAAAT
117376 GAAAAA-AGAAAAAT
1 GAAAAAGAGAAAAAT
117390 -AAAA
1 GAAAA
117394 GGAGGGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 8 0.44
15 6 0.33
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (15 bp):
GAAAAAGAGAAAAAT
Found at i:118770 original size:51 final size:51
Alignment explanation
Indices: 118709--119171 Score: 647
Period size: 51 Copynumber: 8.9 Consensus size: 51
118699 AAATTCGTTT
118709 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
*
118760 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
118811 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
118862 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
118913 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* * * *
118964 ATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGTGGACTAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* * ** *
119015 ATTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* * * * * ** *
119066 ATTGAAGATTTTTCGAGTTCTATACTCTCTTAAGGAATAGAGAGCGGACCCGTTTT
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTC
* * * *
119122 ATTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACA
1 GTTGAAGATTG----AGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
119172 CATTTTATGA
Statistics
Matches: 381, Mismatches: 22, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
51 303 0.80
52 1 0.00
53 2 0.01
54 2 0.01
55 33 0.09
56 40 0.10
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
Found at i:122243 original size:15 final size:16
Alignment explanation
Indices: 122225--122261 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
122215 CATATTTCCT
122225 AAAAATATA-TTTAAA
1 AAAAATATACTTTAAA
122240 AAAAATATACTTTAAA
1 AAAAATATACTTTAAA
*
122256 ACAAAT
1 AAAAAT
122262 TTTAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAATATACTTTAAA
Found at i:123823 original size:21 final size:21
Alignment explanation
Indices: 123797--123840 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
123787 ACAAAAGCTT
*
123797 GCTGGAATCTAAGTGATGCTA
1 GCTGGAATCTAAATGATGCTA
123818 GCTGGAATCTAAATGATGCTA
1 GCTGGAATCTAAATGATGCTA
123839 GC
1 GC
123841 AGCAAACAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (21 bp):
GCTGGAATCTAAATGATGCTA
Found at i:127424 original size:18 final size:20
Alignment explanation
Indices: 127403--127442 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
127393 AAAATGAAGG
127403 TTTTCAAAATT-T-TGAATT
1 TTTTCAAAATTCTATGAATT
*
127421 TTTTGAAAATTCTATGAATT
1 TTTTCAAAATTCTATGAATT
127441 TT
1 TT
127443 AAAAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 1 0.05
20 8 0.42
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTTCAAAATTCTATGAATT
Found at i:138557 original size:26 final size:26
Alignment explanation
Indices: 138527--138640 Score: 210
Period size: 26 Copynumber: 4.4 Consensus size: 26
138517 GTTCAAGCCT
*
138527 TTTCGAGTTCAAGTTTCAATATTACA
1 TTTCGAGTTCAAGTTTCAATATTATA
138553 TTTCGAGTTCAAGTTTCAATATTATA
1 TTTCGAGTTCAAGTTTCAATATTATA
138579 TTTCGAGTTCAAGTTTCAATATTATA
1 TTTCGAGTTCAAGTTTCAATATTATA
*
138605 TTCCGAGTTCAAGTTTCAATATTATA
1 TTTCGAGTTCAAGTTTCAATATTATA
138631 TTTCGAGTTC
1 TTTCGAGTTC
138641 GGGTTGAATT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 85 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (26 bp):
TTTCGAGTTCAAGTTTCAATATTATA
Found at i:140650 original size:17 final size:16
Alignment explanation
Indices: 140628--140662 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
140618 AACGATTCTA
*
140628 TCAGATCGATTCAGAGG
1 TCAGATCGACTCAG-GG
140645 TCAGATCGACTCAGGG
1 TCAGATCGACTCAGGG
140661 TC
1 TC
140663 GCCAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.23
Consensus pattern (16 bp):
TCAGATCGACTCAGGG
Found at i:141278 original size:20 final size:19
Alignment explanation
Indices: 141253--141295 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
141243 GTATACATGG
141253 ATTATCCATA-CTGATAAAT
1 ATTATCCATATC-GATAAAT
141272 CATTATCCATATCGATAAAT
1 -ATTATCCATATCGATAAAT
141292 ATTA
1 ATTA
141296 GGCAATTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.18
20 17 0.77
21 1 0.05
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTATCCATATCGATAAAT
Found at i:153719 original size:18 final size:18
Alignment explanation
Indices: 153696--153732 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
153686 ATATTTCCAC
153696 TTGTCACAGATAGTGACA
1 TTGTCACAGATAGTGACA
153714 TTGTCACAGATAGTGACA
1 TTGTCACAGATAGTGACA
153732 T
1 T
153733 GTGACACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (18 bp):
TTGTCACAGATAGTGACA
Found at i:166130 original size:19 final size:19
Alignment explanation
Indices: 166106--166142 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
166096 ATATCACATC
166106 ATAAAAATTAA-TAAAATAA
1 ATAAAAA-TAAGTAAAATAA
166125 ATAAAAATAAGTAAAATA
1 ATAAAAATAAGTAAAATA
166143 TTAATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (19 bp):
ATAAAAATAAGTAAAATAA
Found at i:168108 original size:25 final size:27
Alignment explanation
Indices: 168080--168131 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
168070 TCAGTTATTT
*
168080 AATTAATTA-AATAAT-ATATTATAAA
1 AATTAATTATAAAAATGATATTATAAA
*
168105 AATTAATTATAAAAATGATGTTATAAA
1 AATTAATTATAAAAATGATATTATAAA
168132 TTTAATTTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
26 5 0.22
27 9 0.39
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
AATTAATTATAAAAATGATATTATAAA
Found at i:168115 original size:13 final size:13
Alignment explanation
Indices: 168080--168120 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
168070 TCAGTTATTT
*
168080 AATTAATTA-AAT
1 AATTAATTATAAA
168092 AA-TATATTATAAA
1 AATTA-ATTATAAA
168105 AATTAATTATAAA
1 AATTAATTATAAA
168118 AAT
1 AAT
168121 GATGTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 2 0.08
12 6 0.24
13 15 0.60
14 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AATTAATTATAAA
Found at i:168640 original size:30 final size:30
Alignment explanation
Indices: 168605--168662 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
168595 AACTTAAAAG
* *
168605 AGTTTTGCAATACTGAGATTTAAATAATTT
1 AGTTTTACAATACTGAAATTTAAATAATTT
168635 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
168663 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (30 bp):
AGTTTTACAATACTGAAATTTAAATAATTT
Found at i:168713 original size:22 final size:22
Alignment explanation
Indices: 168687--168729 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
168677 TAATAAATTA
168687 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
168709 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
168730 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:168738 original size:22 final size:22
Alignment explanation
Indices: 168689--168737 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
168679 ATAAATTATT
**
168689 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
168711 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
168734 TAAA
1 TAAA
168738 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:168741 original size:54 final size:54
Alignment explanation
Indices: 168677--169694 Score: 1070
Period size: 54 Copynumber: 18.8 Consensus size: 54
168667 ACAACTACAA
168677 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *** * * *
168731 TAATAAATTATTTAAAATAAATCAATACATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATAC
*
168784 -CAT--A-T-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
168833 TAATAAATTATTTAAAATAAATAAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
168887 TAATAAATTATTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAA-TC---C--AT--A-T-TTTAAAATAAATCAATCCATAC
* * **
168951 TAATAAATTATTTAAAATAAATCAATCAATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** **
169008 TTTTAAAATAAAT-CAATCCATGCTAATAAAT-TATTTAAAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
** * * * *
169062 TTTTAAA--A--T-AAATCAATCCATACTAATATTATTTAAAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAAT-C-CATA-T-TTTAAAATAAATCAATCCATA--C
* * * * * *
169117 TAAAATAAATCAATTCATACT-AATAAAT---TA-TTTAAAATAAATCAATTCATAC
1 T--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * *
169169 -AACTACA--A--T--AATAAATCAATCTATATTTTAAAATAAATTAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
169217 TAATAAATTATTTAAAATAAATAAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
169271 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
169325 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
169379 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
169433 TAATAAATTATTTAAAATAAATCAATCCATA--TTAAAATAAATCAATACATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
169485 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
169539 GAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * *
169593 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATAAATCAAATTATT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATC-CA-TA-C
* *
169650 TAAAATAAATTATTTAAAAATAAATCAATCTATATTTTATAATAA
1 T--AATAAATTATTT-AAAATAAATCAATCCATATTTTAAAATAA
169695 TTTATTCTAA
Statistics
Matches: 832, Mismatches: 73, Indels: 112
0.82 0.07 0.11
Matches are distributed among these distances:
43 2 0.00
44 6 0.01
47 8 0.01
48 54 0.06
49 7 0.01
50 17 0.02
52 79 0.09
53 2 0.00
54 493 0.59
55 13 0.02
56 7 0.01
57 19 0.02
58 24 0.03
59 14 0.02
60 30 0.04
62 6 0.01
63 5 0.01
64 46 0.06
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:168747 original size:32 final size:32
Alignment explanation
Indices: 168709--169623 Score: 406
Period size: 32 Copynumber: 31.7 Consensus size: 32
168699 CAATCCATAT
168709 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
168741 TTTAAAATAAATCAATACATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
168771 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
168789 TTTAAAATAAATCAATCCATA-T--T---TTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
168815 ---AAA-TAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
168843 TTTAAAATAAAT-AA---AT-C-CAT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
168865 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
168897 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
168929 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
168961 TTTAAAATAAATCAATCAATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
168991 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
169009 TTTAAAATAAATCAATCCATGCTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
169041 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
169063 TTTAAAATAAATCAATCCATACTAAT--ATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
169093 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
169115 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
169147 TTTAAAATAAATCAATTCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* *
169177 --T--AATAAATCAATCTATATTTTAAAATAAATTAA
1 TTTAAAATAAATCAATCCATA--CT--AATAAATT-A
* * * ** * *
169210 TCCATACTAATAAAT-TATTTAAAATAAATAAATCCATA
1 T--TTA-AAATAAATCAATCCATACT-AATAAAT---TA
*
169248 TTTTAAAATAAATCAATTCATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
169281 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
169303 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
169335 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
169357 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
169389 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
169411 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
169443 TTTAAAATAAATCAATCCATATTAAAATAAATCAATA
1 TTTAAAATAAATCAATCCATACT--AATAAAT---TA
** * * ** * * *
169480 CATACTAATAAAT-TATTTAAAATAAATCAATCCATA
1 TTTA-AAATAAATCAATCCATACT-AATAAAT---TA
* *
169516 TTTTAAAATAAATCAATTCATACGAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
169549 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
169571 TTTAAAATAAATCAATCAATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
169603 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
169624 TTTTAAAATA
Statistics
Matches: 701, Mismatches: 48, Indels: 268
0.69 0.05 0.26
Matches are distributed among these distances:
20 2 0.00
22 150 0.21
23 21 0.03
24 13 0.02
25 2 0.00
26 61 0.09
27 2 0.00
28 28 0.04
29 2 0.00
30 28 0.04
31 24 0.03
32 262 0.37
33 5 0.01
34 7 0.01
36 46 0.07
37 26 0.04
38 8 0.01
39 7 0.01
40 7 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:168840 original size:22 final size:22
Alignment explanation
Indices: 168772--168831 Score: 120
Period size: 22 Copynumber: 2.7 Consensus size: 22
168762 CAACTACAAT
168772 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
168794 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
168816 AATAAATCAATCCATA
1 AATAAATCAATCCATA
168832 CTAATAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:168869 original size:22 final size:22
Alignment explanation
Indices: 168843--168885 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
168833 TAATAAATTA
168843 TTTAAAATAAATAAATCCATAT
1 TTTAAAATAAATAAATCCATAT
*
168865 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATAAATCCATA
168886 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATAAATCCATAT
Found at i:168894 original size:22 final size:22
Alignment explanation
Indices: 168845--168893 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
168835 ATAAATTATT
**
168845 TAAAATAAATAAATCCATATTT
1 TAAAATAAATAAATCCATATAA
*
168867 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATAAATCCATA-TAA
168890 TAAA
1 TAAA
168894 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATAAATCCATATAA
Found at i:168907 original size:14 final size:14
Alignment explanation
Indices: 168888--168972 Score: 62
Period size: 14 Copynumber: 5.5 Consensus size: 14
168878 AATCCATACT
168888 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
168902 AATAAATCAATTCATACT
1 AATAAAT-TATT--TA-A
168920 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
168934 AATAAATCAATTCATACT
1 AATAAAT-TATT--TA-A
168952 AATAAATTATTTAA
1 AATAAATTATTTAA
168966 AATAAAT
1 AATAAAT
168973 CAATCAATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
14 21 0.38
15 10 0.18
17 10 0.18
18 14 0.25
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:168955 original size:18 final size:18
Alignment explanation
Indices: 168870--168958 Score: 77
Period size: 18 Copynumber: 5.4 Consensus size: 18
168860 CATATTTTAA
*
168870 AATAAATCAATCCATACT
1 AATAAATCAATTCATACT
* *
168888 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
168902 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
* *
168920 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
168934 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
168952 AATAAAT
1 AATAAAT
168959 TATTTAAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
14 14 0.26
15 10 0.19
17 9 0.17
18 21 0.39
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:169135 original size:22 final size:22
Alignment explanation
Indices: 169041--169083 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
169031 TAATAAATTA
169041 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
169063 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
169084 CTAATATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:169141 original size:18 final size:18
Alignment explanation
Indices: 169119--169170 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
169109 CCATATTTTA
169119 AAATAAATCAATTCATAC
1 AAATAAATCAATTCATAC
* *
169137 TAATAAAT-TATT--TA-
1 AAATAAATCAATTCATAC
169151 AAATAAATCAATTCATAC
1 AAATAAATCAATTCATAC
169169 AA
1 AA
169171 CTACAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
14 7 0.27
15 5 0.19
17 5 0.19
18 9 0.35
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAAATCAATTCATAC
Found at i:169142 original size:186 final size:186
Alignment explanation
Indices: 168794--169694 Score: 939
Period size: 186 Copynumber: 4.7 Consensus size: 186
168784 CATATTTTAA
168794 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAAAT
168859 CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACTAATA
66 CCATATTTTAAAATAAATCAATCCATACTAAT-AATTATTTAAAATAAATCAA-TC---C--AT-
168924 AATTATTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCAATACAACTAC
123 -A-T-TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATC-ATACAACTAC
168989 AAT
184 AAT
* *
168992 AATAAATCAATCCATATTTTAAAATAAATCAATCCATGCTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAAAT
169057 CCATATTTTAAAATAAATCAATCCATACTAAT-ATTATTTAAAATAAATCAATCCATATTTTAAA
66 CCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAAAATAAATCAATCCATATTTTAAA
169121 ATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAAT
131 ATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAA-TCATACAACTACAAT
* *
169178 AATAAATCAATCTATATTTTAAAATAAATTAATCCATACTAATAAATTATTTAAAATAAATAAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAAAT
*
169243 CCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAA
66 CCATATTTTAAAATAAATCAATCCATACTAAT-AATTATTTAAAATAAATCAATCCATATTTTAA
* *** *
169308 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAAT
130 AATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT-CATACAACTACAAT
* * * ** * * * *
169365 AAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCC
1 -AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAAT-AAATTATTTAA--A
* * * *
169429 ATACTAATAAAT---TA-TTTAAAATAAATCAATCCATATTAA-AATAAATCAATACATACTAAT
56 ATA--AATAAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAA-A-ATA--AAT
*
169489 AAAT---TA-TTTAAAATAAATCAA-TC---C--AT--A-T-TTTAAAATAAATCAATTCATACG
115 CAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAA-TCATAC-
*
169540 AA-TAAATTATTT
178 AACTACA--A--T
* *
169552 AAAATAAATCAATCCATATTTTAAAATAAATCAATCAATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAA
* * * *
169617 ATCCATATTTTAAAATAAATAAATCAAATTATTTAAAATAAATTATTTAAAAATAAATCAATCTA
64 ATCCATATTTTAAAATAAATCAATC-CA-TA-CT--AAT-AATTATTT-AAAATAAATCAATCCA
*
169682 TATTTTATAATAA
122 TATTTTAAAATAA
169695 TTTATTCTAA
Statistics
Matches: 609, Mismatches: 49, Indels: 98
0.81 0.06 0.13
Matches are distributed among these distances:
178 6 0.01
180 3 0.00
181 2 0.00
182 63 0.10
183 10 0.02
184 4 0.01
185 3 0.00
186 162 0.27
187 13 0.02
188 100 0.16
189 9 0.01
190 15 0.02
191 1 0.00
192 24 0.04
193 6 0.01
194 54 0.09
195 4 0.01
196 28 0.05
198 102 0.17
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (186 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAAAT
CCATATTTTAAAATAAATCAATCCATACTAATAATTATTTAAAATAAATCAATCCATATTTTAAA
ATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCATACAACTACAAT
Found at i:169144 original size:22 final size:22
Alignment explanation
Indices: 169095--169143 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
169085 TAATATTATT
**
169095 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
169117 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
169140 TAAA
1 TAAA
169144 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:169239 original size:18 final size:18
Alignment explanation
Indices: 169218--169292 Score: 52
Period size: 22 Copynumber: 4.2 Consensus size: 18
169208 AATCCATACT
169218 AATAAATTATTTAAAATA
1 AATAAATTATTTAAAATA
169236 AATAAATCCATATTTTAAAATA
1 AATAAAT---TA-TTTAAAATA
* *
169258 AATCAATTCA--T--ACT-
1 AATAAATT-ATTTAAAATA
169272 AATAAATTATTTAAAATA
1 AATAAATTATTTAAAATA
169290 AAT
1 AAT
169293 CAATCCATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 20
0.64 0.06 0.30
Matches are distributed among these distances:
13 1 0.02
14 7 0.16
15 3 0.07
17 3 0.07
18 10 0.23
19 1 0.02
20 1 0.02
21 2 0.05
22 15 0.35
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAATTATTTAAAATA
Found at i:169252 original size:22 final size:22
Alignment explanation
Indices: 169227--169269 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
169217 TAATAAATTA
169227 TTTAAAATAAATAAATCCATAT
1 TTTAAAATAAATAAATCCATAT
* *
169249 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATAAATCCATA
169270 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATAAATCCATAT
Found at i:169307 original size:22 final size:22
Alignment explanation
Indices: 169281--169323 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
169271 TAATAAATTA
169281 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
169303 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
169324 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:169332 original size:22 final size:22
Alignment explanation
Indices: 169283--169331 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
169273 ATAAATTATT
**
169283 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
169305 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
169328 TAAA
1 TAAA
169332 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:169361 original size:22 final size:22
Alignment explanation
Indices: 169335--169377 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
169325 TAATAAATTA
169335 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
169357 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
169378 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:169386 original size:22 final size:22
Alignment explanation
Indices: 169337--169385 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
169327 ATAAATTATT
**
169337 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
169359 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
169382 TAAA
1 TAAA
169386 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:169415 original size:22 final size:22
Alignment explanation
Indices: 169389--169431 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
169379 TAATAAATTA
169389 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
169411 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
169432 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:169440 original size:22 final size:22
Alignment explanation
Indices: 169391--169439 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
169381 ATAAATTATT
**
169391 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
169413 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
169436 TAAA
1 TAAA
169440 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:169521 original size:22 final size:22
Alignment explanation
Indices: 169495--169537 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
169485 TAATAAATTA
169495 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
169517 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
169538 CGAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:169600 original size:22 final size:22
Alignment explanation
Indices: 169551--169599 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
169541 ATAAATTATT
* **
169551 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCAATATAA
169573 TAAAATAAATCAATCAATACTAA
1 TAAAATAAATCAATCAATA-TAA
169596 TAAA
1 TAAA
169600 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCAATATAA
Found at i:169641 original size:22 final size:23
Alignment explanation
Indices: 169597--169659 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 23
169587 CAATACTAAT
*
169597 AAATTATTTAAAATAAATCAATC
1 AAATTATTTAAAATAAATAAATC
*
169620 -CA-TATTTTAAAATAAATAAATC
1 AAATTA-TTTAAAATAAATAAATC
169642 AAATTATTTAAAATAAAT
1 AAATTATTTAAAATAAAT
169660 TATTTAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 2 0.06
22 17 0.50
23 13 0.38
24 2 0.06
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (23 bp):
AAATTATTTAAAATAAATAAATC
Found at i:169668 original size:37 final size:36
Alignment explanation
Indices: 169625--169711 Score: 95
Period size: 37 Copynumber: 2.3 Consensus size: 36
169615 CAATCCATAT
169625 TTTAAAATAAATAAATCAA-ATTATTTAAAATAAATTA
1 TTTAAAATAAATAAATCAATA-T-TTTAAAATAAATTA
* * * *
169662 TTTAAAAATAAATCAATCTATATTTTATAATAATTTA
1 TTT-AAAATAAATAAATCAATATTTTAAAATAAATTA
169699 TTCTAAAATAAAT
1 TT-TAAAATAAAT
169712 TATTTTATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
37 26 0.60
38 16 0.37
39 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (36 bp):
TTTAAAATAAATAAATCAATATTTTAAAATAAATTA
Found at i:169669 original size:15 final size:15
Alignment explanation
Indices: 169637--169741 Score: 86
Period size: 15 Copynumber: 6.5 Consensus size: 15
169627 TAAAATAAAT
169637 AAATCAAATTA-TTTA
1 AAAT-AAATTATTTTA
*
169652 AAATAAATTATTTAA
1 AAATAAATTATTTTA
169667 AAATAAATCAATCTATATTTTA
1 AAAT--A--AA--T-TATTTTA
* * *
169689 TAATAATTTATTCTA
1 AAATAAATTATTTTA
169704 AAATAAATTATTTTA
1 AAATAAATTATTTTA
*
169719 TAATAAATTATTTTA
1 AAATAAATTATTTTA
169734 AAATAAAT
1 AAATAAAT
169742 AATCTTATTA
Statistics
Matches: 72, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
14 6 0.08
15 50 0.69
16 1 0.01
17 1 0.01
18 1 0.01
19 2 0.03
20 1 0.01
21 1 0.01
22 9 0.12
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATAAATTATTTTA
Done.