Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007906.1 Hibiscus syriacus cultivar Beakdansim tig00110300_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: 551901
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:332 original size:19 final size:19
Alignment explanation
Indices: 310--407 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
300 GGAAATTACT
310 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
329 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
343 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
362 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
376 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
395 ATCGCAACGCGAA
1 ATCGCAATGCGAA
408 TTTAATTTCG
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 18 0.30
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 30 0.50
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:410 original size:33 final size:33
Alignment explanation
Indices: 311--410 Score: 157
Period size: 33 Copynumber: 3.0 Consensus size: 33
301 GAAATTACTA
* *
311 TCGCAATGCGAAATGAAAATCGCAACGAGAGA-A
1 TCGCAATGCGAAATGAAAATCGCAACGCGA-ATT
*
344 TCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
377 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
410 T
1 T
411 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
32 1 0.02
33 61 0.98
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.18
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:425 original size:19 final size:20
Alignment explanation
Indices: 403--445 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
393 AAATCGCAAC
403 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
422 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
442 GCGA
1 GCGA
446 TTCTCTCGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:604 original size:14 final size:14
Alignment explanation
Indices: 585--621 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
575 ACATCAATTA
585 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
599 ACAAATCACCTTTT
1 ACAAATCAACTTTT
613 ACAAATCAA
1 ACAAATCAA
622 TTAACAATAA
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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2028 original size:21 final size:21
Alignment explanation
Indices: 1962--2028 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1952 GTGAATCGGG
*
1962 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1982 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2004 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2025 CTCT
1 CTCT
2029 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2047 original size:42 final size:41
Alignment explanation
Indices: 1962--2084 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1952 GTGAATCGGG
* * * * *
1962 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
2004 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
2046 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
2085 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:4140 original size:33 final size:33
Alignment explanation
Indices: 4083--4182 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
4073 ACGAGATAAT
*
4083 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
4117 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
4150 GATAATCGCAACGCGAAATGAAAATCGCAACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
4183 CGAAATAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 46 0.77
34 14 0.23
ACGTcount: A:0.40, C:0.25, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:4175 original size:19 final size:19
Alignment explanation
Indices: 4058--4242 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
4048 TCTTTTGGTT
*
4058 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
4077 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
4097 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
4115 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
4131 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
4149 ---A-GATAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
4164 GAAATGAAAATCGCAACCAC
1 GAAATGAAAATCGCAA-CGC
*
4184 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
4203 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
4222 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
4241 GA
1 GA
4243 TTTTGGTTCG
Statistics
Matches: 135, Mismatches: 18, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
14 18 0.13
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 61 0.45
20 44 0.33
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:4207 original size:39 final size:38
Alignment explanation
Indices: 4153--4242 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
4143 GCGACCAGAT
4153 AATCGCAACGCGAAATGAAAATCGCAACCACGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CACGAAATAAA
* *
4192 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACACGAAATAAA
*
4230 AATCGCAATGCGA
1 AATCGCAACGCGA
4243 TTTTGGTTCG
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACACGAAATAAA
Found at i:4271 original size:19 final size:19
Alignment explanation
Indices: 4249--4303 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
4239 GCGATTTTGG
4249 TTCGCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTTAT
**
4268 TTCGCGTTGCGATAGTTAT
1 TTCGCGTTGCGATTTTTAT
4287 TTCCGCGTTGCGATTTT
1 TT-CGCGTTGCGATTTT
4304 CATTCTCGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTTAT
Found at i:4846 original size:20 final size:20
Alignment explanation
Indices: 4821--4870 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
4811 CGCTATGTAA
*
4821 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
4841 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
4861 ATCTCGTTGC
1 ATCGCGTTGC
4871 AATTTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:4906 original size:20 final size:20
Alignment explanation
Indices: 4821--4914 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
4811 CGCTATGTAA
* *
4821 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
4841 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* * ** * *
4861 ATCTCGTTGCAATTTTTTATT
1 ATCGCGTTGCGA-TAGTAAGT
*
4882 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
4902 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
4915 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 46 0.79
21 12 0.21
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:4917 original size:41 final size:41
Alignment explanation
Indices: 4840--4917 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
4830 CGAAAGTCAG
* * *
4840 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCAATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTTTTAT
* *
4881 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTT
4918 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTTTTAT
Found at i:6284 original size:20 final size:21
Alignment explanation
Indices: 6242--6286 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
6232 TTACATATTG
* **
6242 ATTTCGTATATTAATAATTTT
1 ATTTAGTATATTAATAAAATT
6263 ATTTAGTATA-TAATAAAATT
1 ATTTAGTATATTAATAAAATT
6283 ATTT
1 ATTT
6287 CATTAAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (21 bp):
ATTTAGTATATTAATAAAATT
Found at i:7399 original size:3 final size:3
Alignment explanation
Indices: 7393--7421 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
7383 ATGATGATGA
7393 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
7422 ATGATGATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:7591 original size:15 final size:14
Alignment explanation
Indices: 7571--7630 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
7561 CTTGTAAATT
*
7571 TTTTTAATTATTTAA
1 TTTTT-ATTACTTAA
7586 TTTTTATTACTTAA
1 TTTTTATTACTTAA
** *
7600 TTTATT-TTGTTTATT
1 TTT-TTATTACTTA-A
7615 TTTTTATTACTTAA
1 TTTTTATTACTTAA
7629 TT
1 TT
7631 CAAGTGAATG
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
14 20 0.57
15 15 0.43
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTTTATTACTTAA
Found at i:11586 original size:152 final size:153
Alignment explanation
Indices: 11304--11587 Score: 543
Period size: 152 Copynumber: 1.9 Consensus size: 153
11294 AAAAGTCTTA
*
11304 AAAAGTCCAGTCTTTGAATAGAATATAAATTATATGTTTTTGATTTTATCATATGGTAAATACAA
1 AAAAGTCCAGTCTTTGAATAGAATATAAATTACATGTTTTTGATTTTATCATATGGTAAATACAA
11369 AAATAATATTTACTGTTAGATCATTAATGAAAAATAACATTATCATATGGTAAATATAAAAATAA
66 AAATAATATTTACTGTTAGATCATTAATGAAAAATAACATTATCATATGGTAAATATAAAAATAA
11434 TTGATCTAACACAATAGATTTTT
131 TTGATCTAACACAATAGATTTTT
11457 AAAAGTCCAGTCTTTGAATAGAATATAAATTACATGTTTTTGATTTTATCATATGGTAAATAC-A
1 AAAAGTCCAGTCTTTGAATAGAATATAAATTACATGTTTTTGATTTTATCATATGGTAAATACAA
*
11521 AAATAATATTTACTGTTAGCTCATTAATGAAAAATAACATTATCATATGGTAAATATAAAAATAA
66 AAATAATATTTACTGTTAGATCATTAATGAAAAATAACATTATCATATGGTAAATATAAAAATAA
11586 TT
131 TT
11588 TTTCTACTGT
Statistics
Matches: 129, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
152 67 0.52
153 62 0.48
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (153 bp):
AAAAGTCCAGTCTTTGAATAGAATATAAATTACATGTTTTTGATTTTATCATATGGTAAATACAA
AAATAATATTTACTGTTAGATCATTAATGAAAAATAACATTATCATATGGTAAATATAAAAATAA
TTGATCTAACACAATAGATTTTT
Found at i:11877 original size:15 final size:15
Alignment explanation
Indices: 11857--11887 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11847 TCATTAATGG
11857 TATAAACAGCAATTT
1 TATAAACAGCAATTT
*
11872 TATAAATAGCAATTT
1 TATAAACAGCAATTT
11887 T
1 T
11888 GAAATTTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (15 bp):
TATAAACAGCAATTT
Found at i:28496 original size:25 final size:23
Alignment explanation
Indices: 28448--28513 Score: 107
Period size: 25 Copynumber: 2.8 Consensus size: 23
28438 CCCATCTGTT
28448 TCTTCACTTTTCTT-TTTCTTTC
1 TCTTCACTTTTCTTCTTTCTTTC
28470 TCTTCACTTTTCTTCACTTTCTTTC
1 TCTTCACTTTTCTT--CTTTCTTTC
28495 TCTTCACTTTTCTTCTTTC
1 TCTTCACTTTTCTTCTTTC
28514 GCATCGAATC
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
22 14 0.34
23 5 0.12
25 22 0.54
ACGTcount: A:0.06, C:0.30, G:0.00, T:0.64
Consensus pattern (23 bp):
TCTTCACTTTTCTTCTTTCTTTC
Found at i:28508 original size:10 final size:10
Alignment explanation
Indices: 28446--28489 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
28436 TCCCCATCTG
28446 TTTCTTCACT
1 TTTCTTCACT
**
28456 TTTCTTTTTCT
1 TTTC-TTCACT
28467 TTCTCTTCACT
1 TT-TCTTCACT
28478 TTTCTTCACT
1 TTTCTTCACT
28488 TT
1 TT
28490 CTTTCTCTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 14 0.50
11 12 0.43
12 2 0.07
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTCTTCACT
Found at i:28510 original size:15 final size:16
Alignment explanation
Indices: 28448--28508 Score: 63
Period size: 15 Copynumber: 3.9 Consensus size: 16
28438 CCCATCTGTT
*
28448 TCTTCACTTTTCTTTT
1 TCTTCACTTTTCTTTC
* **
28464 TCTTTCTCTTCACTTT-
1 TC-TTCACTTTTCTTTC
28480 TCTTCAC-TTTCTTTC
1 TCTTCACTTTTCTTTC
28495 TCTTCACTTTTCTT
1 TCTTCACTTTTCTT
28509 CTTTCGCATC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
14 5 0.14
15 11 0.31
16 10 0.28
17 10 0.28
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.64
Consensus pattern (16 bp):
TCTTCACTTTTCTTTC
Found at i:30324 original size:21 final size:21
Alignment explanation
Indices: 30282--30324 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
30272 TTTCTGGGCT
*
30282 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
30303 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
30324 A
1 A
30325 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:30377 original size:20 final size:20
Alignment explanation
Indices: 30352--30389 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30342 AAACGCTAGA
*
30352 GGGGAATCGATACCCCCAAG
1 GGGGAACCGATACCCCCAAG
*
30372 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
30390 TAAAAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.29, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAAG
Found at i:31053 original size:103 final size:103
Alignment explanation
Indices: 30869--31094 Score: 391
Period size: 103 Copynumber: 2.2 Consensus size: 103
30859 GTAGAGGGTC
* * * *
30869 TATGTGATCCTTCGGGACTTATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACCTAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
*
30934 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
30972 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
31037 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
31075 TATGTGGTCCTT-ATGGACAT
1 TATGTGGTCCTTCA-GGACAT
31095 TATTATATGG
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
102 1 0.01
103 116 0.99
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:31131 original size:23 final size:23
Alignment explanation
Indices: 31101--31188 Score: 101
Period size: 23 Copynumber: 3.8 Consensus size: 23
31091 ACATTATTAT
31101 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
31124 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
** *
31147 GCGGCACT-CTGGTGTAATTCTA-
1 ATGGCACTAC-GGTGCAATTCTAC
31169 AGTGGCACTTA-GGTGCAATT
1 A-TGGCAC-TACGGTGCAATT
31189 ATACGAGCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
22 1 0.02
23 53 0.96
24 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (23 bp):
ATGGCACTACGGTGCAATTCTAC
Found at i:31175 original size:46 final size:46
Alignment explanation
Indices: 31103--31193 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 46
31093 ATTATTATAT
*
31103 GGCACTACGGTGCAATTCTACATGGCAC-TACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACATGGCACTTA-GGTGCAATTATACGC
*
31149 GGCACT-CTGGTGTAATTCTA-AGTGGCACTTAGGTGCAATTATACG
1 GGCACTAC-GGTGCAATTCTACA-TGGCACTTAGGTGCAATTATACG
31194 AGCTATGGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
45 2 0.05
46 36 0.90
47 2 0.05
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.27
Consensus pattern (46 bp):
GGCACTACGGTGCAATTCTACATGGCACTTAGGTGCAATTATACGC
Found at i:37335 original size:20 final size:20
Alignment explanation
Indices: 37310--37347 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
37300 GAACTATAGA
*
37310 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
37330 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
37348 TAAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:38006 original size:103 final size:103
Alignment explanation
Indices: 37822--38039 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
37812 GTAGAGGGTC
* * *
37822 TATGTGATCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTCAGACACCTAC
1 TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACATGTGTGAGGTCTGGTCAGACACATAC
*
37887 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
37925 TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACATGTGTGAGGTCTGGTCAGACACATAC
37990 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
38028 TATGTGGTCCTT
1 TATGTGGTCCTT
38040 ATGGATATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACATGTGTGAGGTCTGGTCAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:38083 original size:23 final size:23
Alignment explanation
Indices: 38056--38123 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
38046 ATTATTATAT
38056 GGCACTATGGTGCAATTCTACGC
1 GGCACTATGGTGCAATTCTACGC
** * *
38079 GGCACTCCGGTGCAATTCTAAGT
1 GGCACTATGGTGCAATTCTACGC
*
38102 GGCACTTAT-GTGCAATTATACG
1 GGCAC-TATGGTGCAATTCTACG
38124 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.28
Consensus pattern (23 bp):
GGCACTATGGTGCAATTCTACGC
Found at i:39082 original size:15 final size:15
Alignment explanation
Indices: 39059--39104 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
39049 ACAATGAAGA
*
39059 AAAGTGAAGAGAAAG
1 AAAGAGAAGAGAAAG
39074 AAAGAGAAGA-AAAG
1 AAAGAGAAGAGAAAG
39088 TAAAGAGAA-AGAAAG
1 -AAAGAGAAGAGAAAG
39103 AA
1 AA
39105 GAAGAAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 7 0.25
15 21 0.75
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.04
Consensus pattern (15 bp):
AAAGAGAAGAGAAAG
Found at i:39087 original size:25 final size:26
Alignment explanation
Indices: 39054--39125 Score: 119
Period size: 25 Copynumber: 2.8 Consensus size: 26
39044 AATGAACAAT
39054 GAAGAAAAGTGAAGAGAAAGAAAG-A
1 GAAGAAAAGTGAAGAGAAAGAAAGAA
*
39079 GAAGAAAAGTAAAGAGAAAGAAAGAA
1 GAAGAAAAGTGAAGAGAAAGAAAGAA
*
39105 GAAGAAAAGTGAAGAAAAAGA
1 GAAGAAAAGTGAAGAGAAAGA
39126 TGGGGAATGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
25 23 0.53
26 20 0.47
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.04
Consensus pattern (26 bp):
GAAGAAAAGTGAAGAGAAAGAAAGAA
Found at i:67215 original size:26 final size:26
Alignment explanation
Indices: 67180--67239 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
67170 AAAACACCGT
67180 CGTTTTGGACCTAAACGAAGTGACGC
1 CGTTTTGGACCTAAACGAAGTGACGC
* *
67206 CGTTTTGGACCTAAACGAAGTGGCGT
1 CGTTTTGGACCTAAACGAAGTGACGC
67232 CGTTTTGG
1 CGTTTTGG
67240 CGTGGCAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (26 bp):
CGTTTTGGACCTAAACGAAGTGACGC
Found at i:69191 original size:54 final size:55
Alignment explanation
Indices: 68787--69423 Score: 522
Period size: 55 Copynumber: 11.6 Consensus size: 55
68777 AATGTCCTAG
* * * * * * * *
68787 AAACGGGTTCGCTCCCTCTTCCTTCAGGAAGTATAAAACTTGAACAATCATCAAT
1 AAACGGGTTCGCTCCCACTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTAC
* * *
68842 AATCGTG-TCTGCTCCCTA-TTTCTTCA-GGAGTATAAGAA-TCGAACAATCTTCAAC
1 AAACGGGTTC-GCTCCC-ACTTTCTTCAGGGAGTAT-AGAACTCGAACAATCTTCTAC
* * * * * * *
68896 AATCGTG-TCTACT-CCATATTTCTTCAGAGAGTATA-AGACTCGAACACTCTTCAAC
1 AAACGGGTTC-GCTCCCA-CTTTCTTCAGGGAGTATAGA-ACTCGAACAATCTTCTAC
* * * *
68951 AATCGTG-TCAGCTCCCTA-TTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAAC
1 AAACGGGTTC-GCTCCC-ACTTTCTTCAGGGAGTATAGA-ACTCGAACAATCTTCTAC
* * * *
69006 AATCGTG-TCTGCTCCCTA-TTTCTTCAGAGAGTATA-AGACTCAAACAATCTTCTGA-
1 AAACGGGTTC-GCTCCC-ACTTTCTTCAGGGAGTATAGA-ACTCGAACAATCTTCT-AC
* * * *
69061 AAATGGGTTCGCTCCCTCTTTCTTCAGGGAGTAT-GAAACTCAAACAATCTTCTAT
1 AAACGGGTTCGCTCCCACTTTCTTCAGGGAGTATAG-AACTCGAACAATCTTCTAC
69116 AAACGGGTTCGCT-CCATCTTTCTTCAGGGAGTATAGAACTCGAAC-ATCTTCTAC
1 AAACGGGTTCGCTCCCA-CTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTAC
* **
69170 AAACGGGTTCGCTCTCACTTTCTTCAGGGAGTATAGAACTCGAACAATC-TCTGT
1 AAACGGGTTCGCTCCCACTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTAC
* * * * *
69224 AAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAAC-ATCTTTTTC
1 AAACGGGTTCGCTCCCACTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTAC
* * * *
69278 AAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACAATCTTCTTC
1 AAACGGGTTCGCTCCCACTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTAC
** * * * * * *
69333 TTACGGGTTCGCTCTCTA-TTCCTTTCAGAGAGTATAAAACTCGAATAATCTTCTGC
1 AAACGGGTTCGCTC-CCACTTTC-TTCAGGGAGTATAGAACTCGAACAATCTTCTAC
*
69389 AAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATA
1 AAACGGGTTCGCTCCCACTTTCTTCAGGGAGTATA
69424 AAATTCAAAC
Statistics
Matches: 500, Mismatches: 57, Indels: 50
0.82 0.09 0.08
Matches are distributed among these distances:
52 1 0.00
53 6 0.01
54 184 0.37
55 258 0.52
56 50 0.10
57 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (55 bp):
AAACGGGTTCGCTCCCACTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTAC
Found at i:69813 original size:37 final size:37
Alignment explanation
Indices: 69767--69875 Score: 114
Period size: 37 Copynumber: 3.0 Consensus size: 37
69757 TAATGATCTG
*
69767 ATGG-TTTGCTCCAAC-ACTCTTTCGAGAAGGCTTAAA
1 ATGGATTTGCTCC-ACTACTCTTTAGAGAAGGCTTAAA
* * *
69803 ATGGATTTGCTTCACTACTCTTTAGTGAAGGCTTAAG
1 ATGGATTTGCTCCACTACTCTTTAGAGAAGGCTTAAA
* * ** *
69840 ATGGATTTACTTCACTACTCTTCGGTGAAGGCTTAA
1 ATGGATTTGCTCCACTACTCTTTAGAGAAGGCTTAA
69876 GATTGACTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
36 6 0.09
37 58 0.91
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (37 bp):
ATGGATTTGCTCCACTACTCTTTAGAGAAGGCTTAAA
Found at i:69876 original size:37 final size:37
Alignment explanation
Indices: 69792--69878 Score: 138
Period size: 37 Copynumber: 2.4 Consensus size: 37
69782 ACTCTTTCGA
* * *
69792 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTAGT
1 GAAGGCTTAAGATGGATTTACTTCACTACTCTTCAGT
*
69829 GAAGGCTTAAGATGGATTTACTTCACTACTCTTCGGT
1 GAAGGCTTAAGATGGATTTACTTCACTACTCTTCAGT
69866 GAAGGCTTAAGAT
1 GAAGGCTTAAGAT
69879 TGACTTTGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (37 bp):
GAAGGCTTAAGATGGATTTACTTCACTACTCTTCAGT
Found at i:78462 original size:24 final size:24
Alignment explanation
Indices: 78423--78474 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
78413 AGTCCAGTGG
78423 CCCTACAAAATCACGGCCACCGTGA
1 CCCTACAAAATCACGGCCACCGT-A
78448 CCCTAC-AAATCACGGCCACCGTA
1 CCCTACAAAATCACGGCCACCGTA
78471 CCCT
1 CCCT
78475 TTCCCTTCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 5 0.19
24 16 0.59
25 6 0.22
ACGTcount: A:0.29, C:0.44, G:0.13, T:0.13
Consensus pattern (24 bp):
CCCTACAAAATCACGGCCACCGTA
Found at i:79714 original size:23 final size:23
Alignment explanation
Indices: 79679--79763 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
79669 TAGCTCATAT
79679 AATGCACCGAAGTGCCACGTAGA
1 AATGCACCGAAGTGCCACGTAGA
** * *
79702 AATGCACTAAAGTGTCGCGTAG-
1 AATGCACCGAAGTGCCACGTAGA
* * *
79724 AATGCACCGAAGTGTCGCGTAAA
1 AATGCACCGAAGTGCCACGTAGA
79747 AATGCACCGAAGTGCCA
1 AATGCACCGAAGTGCCA
79764 TATAAAATGT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 19 0.37
23 33 0.63
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.16
Consensus pattern (23 bp):
AATGCACCGAAGTGCCACGTAGA
Found at i:81073 original size:17 final size:17
Alignment explanation
Indices: 81051--81094 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
81041 ATTTCCATAT
*
81051 ATAATATGCACGTTCTA
1 ATAATATGCACATTCTA
81068 ATAATATGCACATTCTA
1 ATAATATGCACATTCTA
81085 ATAATATGCA
1 ATAATATGCA
81095 TTCACCTGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (17 bp):
ATAATATGCACATTCTA
Found at i:85030 original size:21 final size:21
Alignment explanation
Indices: 84989--85031 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
84979 TTATGGGTCG
* *
84989 TGTGCATCGATGCATATTCAA
1 TGTGCATCGATACATACTCAA
85010 TGTGCATCGATACACT-CTCAA
1 TGTGCATCGATACA-TACTCAA
85031 T
1 T
85032 AAACAAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (21 bp):
TGTGCATCGATACATACTCAA
Found at i:86464 original size:23 final size:21
Alignment explanation
Indices: 86436--86499 Score: 87
Period size: 23 Copynumber: 3.0 Consensus size: 21
86426 GACATTATAT
86436 GGCACTACGGTGCATTTCTAC
1 GGCACTACGGTGCATTTCTAC
*
86457 GCGACACTTCGGTGCATTTCTAC
1 G-G-CACTACGGTGCATTTCTAC
86480 GGCACTAC-GTGCA-TTCTAC
1 GGCACTACGGTGCATTTCTAC
86499 G
1 G
86500 TGGTACTTCG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 7 0.18
20 5 0.13
21 6 0.15
22 2 0.05
23 19 0.49
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.28
Consensus pattern (21 bp):
GGCACTACGGTGCATTTCTAC
Found at i:86508 original size:42 final size:44
Alignment explanation
Indices: 86430--86522 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 44
86420 CTTATGGACA
* *
86430 TTATATGGCACTACGGTGCATTTCTACGCGACACTTCGGTGCAT
1 TTATACGGCACTACGGTGCATTTCTACGCGACACTTCGGTACAT
* * **
86474 TTCTACGGCACTAC-GTGCA-TTCTACGTGGTACTTCGGTACAT
1 TTATACGGCACTACGGTGCATTTCTACGCGACACTTCGGTACAT
86516 TTATACG
1 TTATACG
86523 AGCTGTGGTG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 25 0.60
43 5 0.12
44 12 0.29
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (44 bp):
TTATACGGCACTACGGTGCATTTCTACGCGACACTTCGGTACAT
Found at i:89649 original size:399 final size:398
Alignment explanation
Indices: 88951--89722 Score: 1068
Period size: 399 Copynumber: 1.9 Consensus size: 398
88941 AATTATAAAA
* * *
88951 TTTTTACTATATAATATTTTTGACATAAAAAAATAGAGAGAATTGTTTCTGATAGTATACTTTTT
1 TTTTTACTATATAACATTTTTGACATAAAAAAATAGAGAGAAATGTTTCTGATAGTATAATTTTT
89016 CATAATGATTAAAATATATAACTACAAAAATAATTGATTACAAAAAACTTAAATTTTATTATTTA
66 CATAATGATTAAAATATATAACTACAAAAATAATTGATTACAAAAAACTTAAATTTTATTATTTA
*
89081 TTGTGATAATTTTTCTATAACAATAACTATAAATTATAATTACAAAACTTTCAACATAACTTTTG
131 TTATGATAATTTTTCTATAACAATAAC-ATAAATTATAATTACAAAACTTTCAACATAACTTTTG
* * *
89146 GAAACAAAAAATTGGAGAAAAATATTTATCACAATATGTTAATACAAAATTAAAATTTATAAGTA
195 GAAACAAAAAATGGGAGAAAAATAATTATCACAATATGTTAATACAAAATTAAAATTTATAACTA
* * * *
89211 TAAGTATAATTTGTCACAAAAATATGAATACCATA-TTTTTGTGACAAT-TTTTTGTAATAATTA
260 CAAATATAATTTGTCACAAAAACATGAATAACATATTTTTTGTGACAATATTTTTGTAATAA--A
* *
89274 TAAACAC-TATAGTAACAAAAATTGTTACTATATGATTTTTTGACAAAAAATGGAGGAAAATCTT
323 T-AACACTTATAGTAACAAAAATTGTCACTATATGACTTTTTGACAAAAAATGGAGGAAAATCTT
89338 ATGACATATATC
387 ATGACATATATC
89350 TTTTGTACTATATAACATTTTTGACACTAAAAAAATATGA-AGAAATGATTT-TGATAGTATAAT
1 TTTT-TACTATATAACATTTTTGACA-TAAAAAAATA-GAGAGAAATG-TTTCTGATAGTATAAT
* * *
89413 TTTTCATAATGATT-AAA-ATATAAGTACAAAAAT-ATTTATTACAAAAAACCTTGAATTTTATT
62 TTTTCATAATGATTAAAATATATAACTACAAAAATAATTGATTACAAAAAA-CTTAAATTTTATT
* *
89475 ATTTGA-TATGATAATTTTTCTATAACAATAAC-TAAATTATAATTATAAAA-TTGTCAATATAA
126 ATTT-ATTATGATAATTTTTCTATAACAATAACATAAATTATAATTACAAAACTT-TCAACATAA
* * *
89537 CTTTT-GAAACAAAAAA-GGGAGAAAAATAATTATGACAATATATGTT-ATCACTATAGTTAAAA
189 CTTTTGGAAACAAAAAATGGGAGAAAAATAATTATCAC-A-ATATGTTAAT-AC-AAAATTAAAA
* *
89599 TTTATAACTACAAATATAATTTGTCACGAAAACGTGAATAACATTATTTTTTGTGACAATATTTT
250 TTTATAACTACAAATATAATTTGTCACAAAAACATGAATAACA-TATTTTTTGTGACAATATTTT
* * *
89664 TGTAATAAGTAACACTTATAGTTACAAAATTTGTCACTATATGACTTTTTGACAAAAAA
314 TGTAATAAATAACACTTATAGTAACAAAAATTGTCACTATATGACTTTTTGACAAAAAA
89723 ATATGGAAAG
Statistics
Matches: 332, Mismatches: 26, Indels: 30
0.86 0.07 0.08
Matches are distributed among these distances:
395 17 0.05
396 16 0.05
397 39 0.12
398 63 0.19
399 102 0.31
400 37 0.11
401 53 0.16
402 5 0.02
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (398 bp):
TTTTTACTATATAACATTTTTGACATAAAAAAATAGAGAGAAATGTTTCTGATAGTATAATTTTT
CATAATGATTAAAATATATAACTACAAAAATAATTGATTACAAAAAACTTAAATTTTATTATTTA
TTATGATAATTTTTCTATAACAATAACATAAATTATAATTACAAAACTTTCAACATAACTTTTGG
AAACAAAAAATGGGAGAAAAATAATTATCACAATATGTTAATACAAAATTAAAATTTATAACTAC
AAATATAATTTGTCACAAAAACATGAATAACATATTTTTTGTGACAATATTTTTGTAATAAATAA
CACTTATAGTAACAAAAATTGTCACTATATGACTTTTTGACAAAAAATGGAGGAAAATCTTATGA
CATATATC
Found at i:94052 original size:13 final size:13
Alignment explanation
Indices: 94008--94054 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
93998 CTGTTCTTTG
*
94008 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
94022 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
94034 TTTATTTAAAATAA
1 -ATATTTAAAATAA
94048 ATATTTA
1 ATATTTA
94055 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:95015 original size:18 final size:20
Alignment explanation
Indices: 94992--95028 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
94982 GTTCTTCTTT
94992 CTTTTTT-T-TCTGTCTCTC
1 CTTTTTTGTCTCTGTCTCTC
95010 CTTTTTTGTCTCTGTCTCT
1 CTTTTTTGTCTCTGTCTCT
95029 GTCTTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.00, C:0.27, G:0.08, T:0.65
Consensus pattern (20 bp):
CTTTTTTGTCTCTGTCTCTC
Found at i:95035 original size:20 final size:18
Alignment explanation
Indices: 94990--95039 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
94980 GTGTTCTTCT
*
94990 TTCTTTTTTTTCTGTCTC
1 TTCTTTTTTCTCTGTCTC
*
95008 TCCTTTTTTGTCTCTGTCTC
1 TTC-TTTTT-TCTCTGTCTC
95028 TGTCTTTTTTCT
1 T-TCTTTTTTCT
95040 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.08
19 8 0.31
20 15 0.58
21 1 0.04
ACGTcount: A:0.00, C:0.24, G:0.08, T:0.68
Consensus pattern (18 bp):
TTCTTTTTTCTCTGTCTC
Found at i:95458 original size:9 final size:10
Alignment explanation
Indices: 95425--95463 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
95415 TGGGCTTGTA
95425 ATTTAATATT
1 ATTTAATATT
95435 ATTTATATATGT
1 ATTTA-ATAT-T
95447 ATTTAATA-T
1 ATTTAATATT
95456 ATTTAATA
1 ATTTAATA
95464 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.33
10 5 0.19
11 7 0.26
12 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:95467 original size:3 final size:3
Alignment explanation
Indices: 95459--95528 Score: 108
Period size: 3 Copynumber: 24.0 Consensus size: 3
95449 TTAATATATT
* *
95459 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TGA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
95506 TAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
95529 ATGGGTAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 4 0.07
3 57 0.93
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:96130 original size:113 final size:116
Alignment explanation
Indices: 95836--96496 Score: 981
Period size: 112 Copynumber: 5.9 Consensus size: 116
95826 TGTAGAATTA
*
95836 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAC-AGTTCTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
*
95900 GAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTC-AACAAAAG
66 GAACTCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAG
95949 -TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTT-TTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
96012 GAACTCTTC-CTGGCAATG-TGATCCATCAAATGATGAATTCAAACAAAAG
66 GAACTCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAG
*
96061 TTGAACAAGTTCTTCTCATTATGAACTTCTT-TTCCTTCTTCAGATGACGAGTTTTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
96125 GAACTCTTC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAG
66 GAACTCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC-AAAAG
96176 TTGAACAAGTTCTTCTCATTATGAA-TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
* **
96237 GAACT-TTCTCTGGAAATGTTGATCCATCAAATGATG-ATTCAAGTAAAAGG
66 GAACTCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAA-G
* * *
96287 TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGACAAGTTCTTCTCATT-T
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
** * * *
96351 GAAC-CTTCTCTGGCAA-AATAAT-CATCAAGTGATGAATTCAGACAAAAGG
66 GAACTCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAA-G
*
96400 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
* *
96462 GAACT-TTCTCTGGAAATGATGATCCATCAAATGAT
66 GAACTCTTCTCTGGCAATGTTGATCCATCAAATGAT
96497 AGATTTAAAT
Statistics
Matches: 506, Mismatches: 23, Indels: 38
0.89 0.04 0.07
Matches are distributed among these distances:
110 17 0.03
111 71 0.14
112 184 0.36
113 131 0.26
114 46 0.09
115 57 0.11
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (116 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
GAACTCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAG
Found at i:96233 original size:225 final size:227
Alignment explanation
Indices: 95836--96501 Score: 1016
Period size: 225 Copynumber: 3.0 Consensus size: 227
95826 TGTAGAATTA
*
95836 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACAGTTCTTCTCATTATG
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACAGTTCTTCTCATTATG
*
95901 AACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTC-AAC-AAAAG-TGAACAAGTTCTTC
66 AACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTC
*
95963 TCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTT-TTCTCATTATGAACTCTTC-CTGGC
131 TCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGA
96026 AATG-TGATCCATCAAATGATGAATTCAAACAAAA-G
192 AATGATGATCCATCAAATGATG-ATTCAAACAAAAGG
*
96061 TTGAACAAGTTCTTCTCATTATGAACTTCTT-TTCCTTCTTCAGATGACGAGTTTTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC-AGTTCTTCTCATTAT
96125 GAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTT
65 GAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTT
96190 CTCATTATGAA-TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAT
130 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAT
* **
96254 GTTGATCCATCAAATGATGATTCAAGTAAAAGG
195 GATGATCCATCAAATGATGATTCAAACAAAAGG
* *
96287 TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGACAAGTTCTTCTCATT-T
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC-AGTTCTTCTCATTAT
** * * * * *
96351 GAAC-CTTCTCTGGCAA-AATAAT-CATCAAGTGATGAATTCAGACAAAAGGTTGAACAAATTCT
65 GAACTCTTC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCT
96413 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
129 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
96478 TGATGATCCATCAAATGATAGATT
194 TGATGATCCATCAAATGAT-GATT
96502 TAAATCTTTG
Statistics
Matches: 411, Mismatches: 18, Indels: 23
0.91 0.04 0.05
Matches are distributed among these distances:
224 73 0.18
225 194 0.47
226 66 0.16
227 54 0.13
228 24 0.06
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (227 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACAGTTCTTCTCATTATG
AACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTC
TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATG
ATGATCCATCAAATGATGATTCAAACAAAAGG
Found at i:97409 original size:83 final size:83
Alignment explanation
Indices: 97205--97491 Score: 503
Period size: 83 Copynumber: 3.5 Consensus size: 83
97195 GTTCCTACCA
97205 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC-AATTCATCTTC-AAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
97268 CAATGATT-GTTCTGTCC
66 CAATGATTGGTTCTGTCC
*
97285 AA-CAGATCA-ATAACTTAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
97348 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
* *
97366 AACCAGATCATATAACTCAAAGAATACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
97431 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
*
97449 AACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
97492 GAGCACATTA
Statistics
Matches: 198, Mismatches: 4, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
78 35 0.18
79 18 0.09
80 15 0.08
81 11 0.06
82 7 0.04
83 112 0.57
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.29
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
CAATGATTGGTTCTGTCC
Found at i:98650 original size:19 final size:19
Alignment explanation
Indices: 98628--98677 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
98618 TGACCCCCCC
98628 TTTTTCTTTTTTCTCTTCT
1 TTTTTCTTTTTTCTCTTCT
*
98647 TTTTT-TTTCTTTCTCTTTT
1 TTTTTCTTT-TTTCTCTTCT
98666 TTTTTCTTTTTT
1 TTTTTCTTTTTT
98678 TTTCAAGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 22 0.79
20 3 0.11
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTCTTTTTTCTCTTCT
Found at i:98659 original size:26 final size:26
Alignment explanation
Indices: 98630--98681 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
98620 ACCCCCCCTT
98630 TTTCT-TTTTTCTCTTCTTTTTTTTTC
1 TTTCTCTTTTT-TCTTCTTTTTTTTTC
*
98656 TTTCTCTTTTTTTTTCTTTTTTTTTC
1 TTTCTCTTTTTTCTTCTTTTTTTTTC
98682 AAGCATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (26 bp):
TTTCTCTTTTTTCTTCTTTTTTTTTC
Found at i:98663 original size:16 final size:15
Alignment explanation
Indices: 98634--98680 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
98624 CCCCTTTTTC
*
98634 TTTTTTCTCTTCTTT
1 TTTTTTCTTTTCTTT
98649 TTTTTTCTTTCTCTTT
1 TTTTTTCTTT-TCTTT
98665 TTTTTTCTTTT-TTT
1 TTTTTTCTTTTCTTT
98679 TT
1 TT
98681 CAAGCATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 5 0.17
15 10 0.33
16 15 0.50
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTCTTTTCTTT
Found at i:110483 original size:13 final size:13
Alignment explanation
Indices: 110439--110485 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
110429 ATGTTCTTTG
*
110439 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
110453 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
110465 TTTATTTAAAATAA
1 -ATATTTAAAATAA
110479 ATATTTA
1 ATATTTA
110486 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:111467 original size:20 final size:19
Alignment explanation
Indices: 111442--111492 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
111432 CTTCTTCTTT
111442 TTTTTTTTCTTTGTCTCTCC
1 TTTTTTTTCTTTGTCTCT-C
* * *
111462 TTTTTTGTCTCTGTCTCTG
1 TTTTTTTTCTTTGTCTCTC
*
111481 TCTTTTTTCTTT
1 TTTTTTTTCTTT
111493 TTTTTTTCAG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.00, C:0.22, G:0.08, T:0.71
Consensus pattern (19 bp):
TTTTTTTTCTTTGTCTCTC
Found at i:111911 original size:11 final size:10
Alignment explanation
Indices: 111881--111921 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
111871 GGGCTTTGTA
111881 ATTTAATATT
1 ATTTAATATT
111891 ATTTATATATGT
1 ATTTA-ATAT-T
111903 ATTTAATATAT
1 ATTTAATAT-T
111914 ATTTAATA
1 ATTTAATA
111922 ATAATAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:111925 original size:3 final size:3
Alignment explanation
Indices: 111917--112017 Score: 148
Period size: 3 Copynumber: 33.7 Consensus size: 3
111907 AATATATATT
* * *
111917 TAA TAA TAA TAA TAT TAA TGA TAA TAA TAA TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
111965 TAA TAA TAA TGA TAA TGA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
112013 TAA TA
1 TAA TA
112018 TGGGTAAAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:112316 original size:23 final size:23
Alignment explanation
Indices: 112276--112320 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
112266 TTGGGGGGCG
*
112276 GAAAAAATGAAAACAAAATAGAA
1 GAAAAAAGGAAAACAAAATAGAA
112299 GAAAAAAGGAGAAA-AAAATAGA
1 GAAAAAAGGA-AAACAAAATAGA
112321 CGCTTACCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (23 bp):
GAAAAAAGGAAAACAAAATAGAA
Found at i:119693 original size:14 final size:15
Alignment explanation
Indices: 119674--119708 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
119664 GGTCTGTAAT
119674 TATTTATTT-ATATA
1 TATTTATTTAATATA
119688 TATTTATTTAATATA
1 TATTTATTTAATATA
119703 TATTTA
1 TATTTA
119709 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTTATTTAATATA
Found at i:119715 original size:3 final size:3
Alignment explanation
Indices: 119707--119768 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
119697 AATATATATT
*
119707 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
119755 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
119769 TGGATAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:120144 original size:40 final size:40
Alignment explanation
Indices: 120100--120202 Score: 188
Period size: 40 Copynumber: 2.6 Consensus size: 40
120090 AAGTTGAACA
*
120100 AGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATG
1 AGTTCTTCTTATTATGAACTTCTTATTTCTTCTTCAGATG
*
120140 AGTTCTTCTCATTATGAACTTCTTATTTCTTCTTCAGATG
1 AGTTCTTCTTATTATGAACTTCTTATTTCTTCTTCAGATG
120180 AGTTCTTCTTATTATGAACTTCT
1 AGTTCTTCTTATTATGAACTTCT
120203 CTGGAAAAGA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.51
Consensus pattern (40 bp):
AGTTCTTCTTATTATGAACTTCTTATTTCTTCTTCAGATG
Found at i:120370 original size:113 final size:113
Alignment explanation
Indices: 120142--120572 Score: 731
Period size: 113 Copynumber: 3.8 Consensus size: 113
120132 TTCAGATGAG
* * *
120142 TTCTTCTCATTATGAACTTCTTATTTCTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
120206 GAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATAATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
120254 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
120319 GAAAAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATAATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
*
120367 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
120432 GAAAAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATAATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
120480 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
120545 GCAAAA-ATAATCCATCAAGTGATAGATT
66 G-AAAAGATAATCCATCAAATGATGGATT
120573 TGAATCTTTG
Statistics
Matches: 304, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
112 54 0.18
113 246 0.81
114 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGATAATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
Found at i:121356 original size:83 final size:83
Alignment explanation
Indices: 121217--121425 Score: 400
Period size: 83 Copynumber: 2.5 Consensus size: 83
121207 TAATTCTTAC
*
121217 CAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGAAAATTCATCTTCTAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGAAAATTCATCTTCTAAA
121282 TTCAATGATTGGTTCTGT
66 TTCAATGATTGGTTCTGT
*
121300 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGAAAATTCATCTTCTAAA
121365 TTCAATGATTGGTTCTGT
66 TTCAATGATTGGTTCTGT
121383 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
121426 TGGTTCTGTC
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 124 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGAAAATTCATCTTCTAAA
TTCAATGATTGGTTCTGT
Found at i:121435 original size:52 final size:52
Alignment explanation
Indices: 121373--121475 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
121363 AATTCAATGA
121373 TTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
1 TTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
*
121425 TTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
1 TTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
121476 TTATTGGCAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (52 bp):
TTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
Found at i:121532 original size:135 final size:135
Alignment explanation
Indices: 121290--121560 Score: 488
Period size: 135 Copynumber: 2.0 Consensus size: 135
121280 AATTCAATGA
121290 TTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1 TTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
121355 ATCTTCTAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
66 ATCTTCTAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
121420 GATGC
131 GATGC
* *
121425 TTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGCAAATTC
1 TTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
* * * *
121490 ATCTTCTAAATTTATTGATTGGTTCTGTCTAACCAGATCAGATAACTCAACGAACACTTCCAGAA
66 ATCTTCTAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
121555 GATGC
131 GATGC
121560 T
1 T
121561 ATTGGCAAAT
Statistics
Matches: 130, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
135 130 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.28
Consensus pattern (135 bp):
TTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
ATCTTCTAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
GATGC
Found at i:121564 original size:83 final size:83
Alignment explanation
Indices: 121425--121720 Score: 496
Period size: 83 Copynumber: 3.6 Consensus size: 83
121415 CAGAAGATGC
* *
121425 TTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGCAAATTC
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
121490 ATCTTCTAAATTTATTGA
66 ATCTTCTAAATTTATTGA
*
121508 TTGGTTCTGTCTAACCAGATCAGATAACTCAACGAACACTTCCAGAAGATGCTATTGGCAAATTC
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
121573 ATCTTCTAAATTTATTGA
66 ATCTTCTAAATTTATTGA
*
121591 TTGGTTCTGTCTAACCAGATCAGATAACTCAACGAACACTTCCAGAAGATGC---T---AAATTC
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
121650 ATCTTCTAAATTTATTGA
66 ATCTTCTAAATTTATTGA
* *
121668 TTGGTTCTGTCTAACCAGATCAGATAAATCAAAGAACACTTCTAGAAGATGCT
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
121721 GTTGAGCACA
Statistics
Matches: 206, Mismatches: 6, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
77 73 0.35
80 1 0.00
83 132 0.64
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (83 bp):
TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
ATCTTCTAAATTTATTGA
Found at i:121597 original size:218 final size:218
Alignment explanation
Indices: 121219--121643 Score: 751
Period size: 218 Copynumber: 1.9 Consensus size: 218
121209 ATTCTTACCA
*
121219 AACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGAAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGAAAATTCATCTTCTAAATT
121284 CAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
66 CAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
121349 AAATTCATCTTCTAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTT
131 AAATTCATCTTCTAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTT
121414 CCAGAAGATGCTTGGTTCTGTCC
196 CCAGAAGATGCTTGGTTCTGTCC
* *
121437 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGAAAATTCATCTTCTAAATT
* * * *
121502 TATTGATTGGTTCTGTCTAACCAGATCAGATAACTCAACGAACACTTCCAGAAGATGCTATTGGC
66 CAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
* * * *
121567 AAATTCATCTTCTAAATTTATTGATTGGTTCTGTCTAACCAGATCAGATAACTCAACGAACACTT
131 AAATTCATCTTCTAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTT
121632 CCAGAAGATGCT
196 CCAGAAGATGCT
121644 AAATTCATCT
Statistics
Matches: 196, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
218 196 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.29
Consensus pattern (218 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGAAAATTCATCTTCTAAATT
CAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
AAATTCATCTTCTAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTT
CCAGAAGATGCTTGGTTCTGTCC
Found at i:121707 original size:160 final size:162
Alignment explanation
Indices: 121425--121720 Score: 488
Period size: 160 Copynumber: 1.8 Consensus size: 162
121415 CAGAAGATGC
*
121425 TTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGCAAATTC
1 TTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG-T-CT-G-AAATTC
* *
121490 ATCTTCTAAATTTATTGATTGGTTCTGTCTAACCAGATCAGATAACTCAACGAACACTTCCAGAA
62 ATCTTCTAAATTTATTGATTGGTTCTGTCTAACCAGATCAGATAAATCAAAGAACACTTCCAGAA
121555 GATGCTATTGGCAAATTCATCTTCTAAATTTATTGA
127 GATGCTATTGGCAAATTCATCTTCTAAATTTATTGA
* *
121591 TTGGTTCTGTCTAACCAGATCAGATAACTCAACGAACACTTCCAGAAGATG-CT-AAATTCATCT
1 TTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTCTGAAATTCATCT
*
121654 TCTAAATTTATTGATTGGTTCTGTCTAACCAGATCAGATAAATCAAAGAACACTTCTAGAAGATG
66 TCTAAATTTATTGATTGGTTCTGTCTAACCAGATCAGATAAATCAAAGAACACTTCCAGAAGATG
121719 CT
131 CT
121721 GTTGAGCACA
Statistics
Matches: 124, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
160 74 0.60
163 1 0.01
166 49 0.40
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (162 bp):
TTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTCTGAAATTCATCT
TCTAAATTTATTGATTGGTTCTGTCTAACCAGATCAGATAAATCAAAGAACACTTCCAGAAGATG
CTATTGGCAAATTCATCTTCTAAATTTATTGA
Found at i:122898 original size:10 final size:9
Alignment explanation
Indices: 122878--122951 Score: 60
Period size: 10 Copynumber: 7.6 Consensus size: 9
122868 TGACCCCCCC
122878 CTTTCTTTTT
1 CTTT-TTTTT
122888 CTTCTTTTTT
1 CTT-TTTTTT
122898 CTTTCTTTTT
1 CTTT-TTTTT
*
122908 -TCCTTTTTT
1 CT-TTTTTTT
122917 CTATTTTTTT
1 CT-TTTTTTT
122927 CTATTTTCTTT
1 CT-TTTT-TTT
*
122938 CTTTTCTTT
1 CTTTTTTTT
122947 CTTTT
1 CTTTT
122952 CTCTTAAGCA
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
9 15 0.27
10 34 0.62
11 6 0.11
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:122941 original size:36 final size:36
Alignment explanation
Indices: 122879--122956 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
122869 GACCCCCCCC
*
122879 TTTCTTTTTCTTCTTTTTTCTTTCTTTT-TTCCTTT
1 TTTCTTTTTCTTCTATTTTCTTTCTTTTCTTCCTTT
* *
122914 TTTCTATTTTTTTCTATTTTCTTTCTTTTCTTTCTTT
1 TTTCT-TTTTCTTCTATTTTCTTTCTTTTCTTCCTTT
*
122951 TCTCTT
1 TTTCTT
122957 AAGCATAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 5 0.14
36 22 0.59
37 10 0.27
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (36 bp):
TTTCTTTTTCTTCTATTTTCTTTCTTTTCTTCCTTT
Found at i:122946 original size:9 final size:9
Alignment explanation
Indices: 122878--122953 Score: 59
Period size: 9 Copynumber: 8.2 Consensus size: 9
122868 TGACCCCCCC
122878 CTTTCTTTTT
1 CTTTC-TTTT
*
122888 CTTCTTTTTT
1 CTT-TCTTTT
122898 CTTTC-TTT
1 CTTTCTTTT
*
122906 -TTTCCTTT
1 CTTTCTTTT
122914 -TTTCTATTT
1 CTTTCT-TTT
*
122923 TTTTCTATTTT
1 CTTTC--TTTT
122934 CTTTCTTTT
1 CTTTCTTTT
122943 CTTTCTTTT
1 CTTTCTTTT
122952 CT
1 CT
122954 CTTAAGCATA
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
7 4 0.07
8 10 0.18
9 19 0.34
10 14 0.25
11 8 0.14
12 1 0.02
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (9 bp):
CTTTCTTTT
Found at i:133605 original size:18 final size:19
Alignment explanation
Indices: 133575--133619 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
133565 TGCAAATAAA
133575 ATAAAACAT-ATAAATAT-T
1 ATAAAA-ATAATAAATATAT
*
133593 ATGAAAATAATAAATATAT
1 ATAAAAATAATAAATATAT
133612 ATAAAAAT
1 ATAAAAAT
133620 TTTAAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 13 0.57
19 8 0.35
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
ATAAAAATAATAAATATAT
Found at i:135726 original size:14 final size:15
Alignment explanation
Indices: 135707--135741 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
135697 GGTCTGTAAT
135707 TATTTATTT-ATATA
1 TATTTATTTAATATA
135721 TATTTATTTAATATA
1 TATTTATTTAATATA
135736 TATTTA
1 TATTTA
135742 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTTATTTAATATA
Found at i:135748 original size:3 final size:3
Alignment explanation
Indices: 135740--135798 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
135730 AATATATATT
*
135740 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
135788 TAA TAA TAA TA
1 TAA TAA TAA TA
135799 TGGATAAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:137283 original size:27 final size:27
Alignment explanation
Indices: 137231--137287 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
137221 AATCTCGAGC
*
137231 ATATATTTTAATTATACATATAATTAA
1 ATATATTTTAATTAGACATATAATTAA
* *
137258 ATATA-TTTAATTAGACCTATTTATTAA
1 ATATATTTTAATTAGACATA-TAATTAA
137285 ATA
1 ATA
137288 AACTATTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (27 bp):
ATATATTTTAATTAGACATATAATTAA
Found at i:143766 original size:21 final size:21
Alignment explanation
Indices: 143736--143790 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
143726 TGTAACCTGG
143736 AAAT-CTTTTTTTCCAATCAA
1 AAATCCTTTTTTTCCAATCAA
143756 AAATCCTTTTTTTCCAATCAA
1 AAATCCTTTTTTTCCAATCAA
143777 AAATCCTTTTTTTC
1 AAATCCTTTTTTTC
143791 TTCCAATTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.12
21 30 0.88
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATCCTTTTTTTCCAATCAA
Found at i:148004 original size:17 final size:17
Alignment explanation
Indices: 147970--148004 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
147960 AATAAATAAT
*
147970 AATGTATATATTTAAAA
1 AATGTATATATGTAAAA
147987 AATGTATATATAGTAAAA
1 AATGTATATAT-GTAAAA
148005 TAAAATGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (17 bp):
AATGTATATATGTAAAA
Found at i:151189 original size:45 final size:45
Alignment explanation
Indices: 151132--151247 Score: 180
Period size: 45 Copynumber: 2.6 Consensus size: 45
151122 ATCCAAATCT
*
151132 CCCTTT-CGGGTTTTCAACTTGGACCCATCCTTGGTTGCAAGACG
1 CCCTTTGCGGGTTTTCAACTTGGACCCATCCTTAGTTGCAAGACG
* *
151176 CCCTTTGTGGGTTTTCAACTTGGACCCATCCTTAGTTGTAAGACG
1 CCCTTTGCGGGTTTTCAACTTGGACCCATCCTTAGTTGCAAGACG
* *
151221 CCCTTTGCGGGTTTTCATCTTGAACCC
1 CCCTTTGCGGGTTTTCAACTTGGACCC
151248 GCCTTATTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
44 6 0.09
45 59 0.91
ACGTcount: A:0.16, C:0.28, G:0.22, T:0.34
Consensus pattern (45 bp):
CCCTTTGCGGGTTTTCAACTTGGACCCATCCTTAGTTGCAAGACG
Found at i:151384 original size:10 final size:10
Alignment explanation
Indices: 151335--151385 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
151325 ACCCTAAACA
*
151335 TTTTTTTCTC
1 TTTTTTTTTC
*
151345 TTTTTTGTTC
1 TTTTTTTTTC
* *
151355 TTTTTTATTG
1 TTTTTTTTTC
151365 TTTTCTTTTTC
1 TTTT-TTTTTC
151376 TTTTTTTTTC
1 TTTTTTTTTC
151386 AATCTTCGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 26 0.76
11 8 0.24
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.82
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:161595 original size:7 final size:6
Alignment explanation
Indices: 161567--161596 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
161557 TTTAATTGCG
161567 AAAATT AAAATT AAAATT AAAATTT AAAAT
1 AAAATT AAAATT AAAATT AAAA-TT AAAAT
161597 ATTTGATTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAAATT
Found at i:161761 original size:24 final size:25
Alignment explanation
Indices: 161708--161766 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
161698 AAAAATGTAG
161708 AAATAATAAAAAAGAAAAATAATCATT
1 AAATAA-AAAAAAGAAAAATAA-CATT
*
161735 AAATAAAAAAAGGAAAAAGTAA-A-T
1 AAATAAAAAAAAGAAAAA-TAACATT
161759 AAATAAAA
1 AAATAAAA
161767 TAGATAGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 9 0.30
25 1 0.03
26 11 0.37
27 9 0.30
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.17
Consensus pattern (25 bp):
AAATAAAAAAAAGAAAAATAACATT
Found at i:163115 original size:15 final size:15
Alignment explanation
Indices: 163080--163121 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
163070 AAAAAACAAA
* *
163080 AAAATAATAAATAAT
1 AAAATAATATATTAT
163095 AAAATAATATATTAT
1 AAAATAATATATTAT
*
163110 ATAAT-ATATATT
1 AAAATAATATATT
163122 TTTAGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATAATATATTAT
Found at i:163240 original size:98 final size:98
Alignment explanation
Indices: 163113--163292 Score: 249
Period size: 98 Copynumber: 1.8 Consensus size: 98
163103 ATATTATATA
* *
163113 ATATATATTTTTAGAAAATTGTTTTAAAACTATA-TATA-ATATTCAAATATTTAAAAAACAATA
1 ATATATATTTTCAGAAAAATGTTTTAAAACTATATTATATATATTCAAATATTTAAAAAACAATA
*
163176 TATTATATAATTTTTAAAAAATGTTTTCAAATTCT
66 TA-TATAT-ATTTTCAAAAAATGTTTTCAAATTCT
* * * *
163211 ATATATAGTTTTCA-AAAAATGTTTTAAAACTATATTATATGTTTTCAAATGTTTAAAAAACCAT
1 ATATATA-TTTTCAGAAAAATGTTTTAAAACTATATTATATATATTCAAATATTTAAAAAACAAT
163275 ATATATATATTTTCAAAA
65 ATATATATATTTTCAAAA
163293 TGTTTTAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
98 35 0.49
99 14 0.19
100 23 0.32
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (98 bp):
ATATATATTTTCAGAAAAATGTTTTAAAACTATATTATATATATTCAAATATTTAAAAAACAATA
TATATATATTTTCAAAAAATGTTTTCAAATTCT
Found at i:163288 original size:32 final size:34
Alignment explanation
Indices: 163107--163496 Score: 207
Period size: 33 Copynumber: 11.4 Consensus size: 34
163097 AATAATATAT
*
163107 TATATAATATATATTTTTAGAAAATTGTTTT--AAAAC
1 TATAT-ATATATA-TTTT-CAAAA-TGTTTTAAAAAAC
*
163143 TATATATA-ATA--TTC-AAAT-ATTTAAAAAAC
1 TATATATATATATTTTCAAAATGTTTTAAAAAAC
* * *
163172 AATATATTATATAATTTTTAAAAAATGTTTT--CAAA-
1 TATATA-TATAT-A-TTTT-CAAAATGTTTTAAAAAAC
*
163207 T-TCTATATATAGTTTTCAAAAAATGTTTT--AAAAC
1 TATATATATATA-TTTTC--AAAATGTTTTAAAAAAC
*
163241 TATAT-TATATGTTTTC-AAATG-TTTAAAAAAC
1 TATATATATATATTTTCAAAATGTTTTAAAAAAC
* *
163272 CATATATATATATTTTCAAAATGTTTTAAAAAAA
1 TATATATATATATTTTCAAAATGTTTTAAAAAAC
* *
163306 TAT-TATGTATATATTTC-AAATGATTT-AAAAA-
1 TATATATATATAT-TTTCAAAATGTTTTAAAAAAC
* *
163337 TATATATATA-ATTTTTCAAAATGTTTTAGAAACC
1 TATATATATATA-TTTTCAAAATGTTTTAAAAAAC
* *
163371 ATATTATATATATATATTCAAAACGCTTTTAAAAAAC
1 -TA-TATATATATATTTTCAAAATG-TTTTAAAAAAC
163408 TATAT-TATATAAGTTTTCTAAAAT-TATTTAAAAAAAAC
1 TATATATATAT-A-TTTTC-AAAATGT-TTT--AAAAAAC
* * *
163446 TATATATTCTACAAGTTGTCAAAAT-TATTTAAAAAAC
1 TATATA-TATA-TA-TTTTCAAAATGT-TTTAAAAAAC
163483 TATATAATATATAT
1 TATAT-ATATATAT
163497 ATGTATATGT
Statistics
Matches: 280, Mismatches: 34, Indels: 81
0.71 0.09 0.21
Matches are distributed among these distances:
27 3 0.01
28 1 0.00
29 16 0.06
30 7 0.03
31 21 0.08
32 35 0.12
33 47 0.17
34 32 0.11
35 15 0.05
36 35 0.12
37 33 0.12
38 16 0.06
39 10 0.04
40 9 0.03
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (34 bp):
TATATATATATATTTTCAAAATGTTTTAAAAAAC
Found at i:163470 original size:39 final size:38
Alignment explanation
Indices: 163398--163493 Score: 117
Period size: 37 Copynumber: 2.6 Consensus size: 38
163388 TCAAAACGCT
* *
163398 TTTAAAAAAC--TATATTATATAAGTTTTCTAAAATTA
1 TTTAAAAAACTATATATTATACAAGTTGTCTAAAATTA
*
163434 TTTAAAAAAAACTATATATTCTACAAGTTGTC-AAAATTA
1 TTT--AAAAAACTATATATTATACAAGTTGTCTAAAATTA
*
163473 TTTAAAAAACTATATAATATA
1 TTTAAAAAACTATATATTATA
163494 TATATGTATA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
36 3 0.06
37 16 0.31
38 7 0.14
39 10 0.20
40 15 0.29
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (38 bp):
TTTAAAAAACTATATATTATACAAGTTGTCTAAAATTA
Found at i:163481 original size:40 final size:38
Alignment explanation
Indices: 163401--163481 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 38
163391 AAACGCTTTT
* *
163401 AAAAAACTATATTATATAAGTTTTCTAAAATTATTTAA
1 AAAAAACTATATTATACAAGTTGTCTAAAATTATTTAA
*
163439 AAAAAACTATATATTCTACAAGTTGTC-AAAATTATTTAA
1 AAAAAAC--TATATTATACAAGTTGTCTAAAATTATTTAA
163478 AAAA
1 AAAA
163482 CTATATAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 7 0.18
39 16 0.42
40 15 0.39
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (38 bp):
AAAAAACTATATTATACAAGTTGTCTAAAATTATTTAA
Found at i:163910 original size:18 final size:18
Alignment explanation
Indices: 163884--163930 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
163874 ATTAAACATC
*
163884 TTTTT-AAAATCAAATTA
1 TTTTTAAAAATCAAATGA
* *
163901 TTTTTAAAAATTATATGA
1 TTTTTAAAAATCAAATGA
163919 TTTTATAAAAAT
1 TTTT-TAAAAAT
163931 ATCATGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 5 0.20
18 13 0.52
19 7 0.28
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TTTTTAAAAATCAAATGA
Found at i:163929 original size:19 final size:18
Alignment explanation
Indices: 163900--163940 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
163890 AAATCAAATT
163900 ATTTTTAAAAATTAT-ATG
1 ATTTTTAAAAA-TATCATG
163918 ATTTTATAAAAATATCATG
1 ATTTT-TAAAAATATCATG
163937 ATTT
1 ATTT
163941 AATTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (18 bp):
ATTTTTAAAAATATCATG
Found at i:189509 original size:5 final size:5
Alignment explanation
Indices: 189499--189525 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
189489 TATAAGTTTG
189499 AATTT AATTT AATTT AATTT AATTT AA
1 AATTT AATTT AATTT AATTT AATTT AA
189526 GATCCCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
AATTT
Found at i:189963 original size:131 final size:131
Alignment explanation
Indices: 189718--190086 Score: 535
Period size: 131 Copynumber: 2.8 Consensus size: 131
189708 ATAATTTTAG
** * *
189718 GAGAGAAAAAAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTTATACTTTAAAACA
1 GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTTATACCTTAAAGCA
* * *
189783 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAATTCAATATCAATT
66 GTCATTTATTACTCCAATCAAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATCAATT
189848 C
131 C
* * * *
189849 GAGTGAAATTGATAATATCTAATTATTTCTAATTGAGAATAAATGACCTCTTATACCTTAAAGC-
1 GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTTATACCTTAAAGCA
* * *
189913 GTTCATTTATTGCTCCAATCAAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATTAGT
66 G-TCATTTATTACTCCAATCAAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATCAAT
189978 TC
130 TC
* *
189980 GAGAGAAAATGATAATAT-TGAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
1 GAGAGAAAATGATAATATCT-AATTATTTCCAATCGAGAATAAATGACCTCTTATACCTTAAAGC
* * *
190044 AGTCATTTATTACTCCAACCAAAATGAAAAGATATTACTATTC
65 AGTCATTTATTACTCCAATCAAAATGAAGAGATATCACTATTC
190087 TCAATATCGA
Statistics
Matches: 211, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
130 2 0.01
131 208 0.99
132 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (131 bp):
GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTTATACCTTAAAGCA
GTCATTTATTACTCCAATCAAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATCAATT
C
Found at i:192140 original size:3 final size:3
Alignment explanation
Indices: 192132--192199 Score: 64
Period size: 3 Copynumber: 21.7 Consensus size: 3
192122 TATATTTTTT
* * * *
192132 ATA ATA ATA ATA ATTA ATA ATTA ATG CTA ATA ATA ATA ACTA TTG ATA
1 ATA ATA ATA ATA A-TA ATA A-TA ATA ATA ATA ATA ATA A-TA ATA ATA
*
192180 ATA GTA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
192200 GGTAATAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
3 44 0.85
4 8 0.15
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:192151 original size:13 final size:13
Alignment explanation
Indices: 192133--192196 Score: 53
Period size: 13 Copynumber: 5.0 Consensus size: 13
192123 ATATTTTTTA
192133 TAATAATAATAAT
1 TAATAATAATAAT
192146 TAATAAT--TAAT
1 TAATAATAATAAT
*
192157 GCTAATAATAATAAC
1 --TAATAATAATAAT
* * *
192172 TATTGATAAT-AG
1 TAATAATAATAAT
192184 TAATAATAATAAT
1 TAATAATAATAAT
192197 AATGGTAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
11 4 0.10
12 9 0.23
13 23 0.59
15 3 0.08
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (13 bp):
TAATAATAATAAT
Found at i:192170 original size:19 final size:19
Alignment explanation
Indices: 192133--192199 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
192123 ATATTTTTTA
*
192133 TAATAATAATAATTAATAAT
1 TAATGATAATAA-TAATAAT
* *
192153 TAATGCTAATAATAATAAC
1 TAATGATAATAATAATAAT
* *
192172 TATTGATAATAGTAATAA-
1 TAATGATAATAATAATAAT
*
192190 TAATAATAAT
1 TAATGATAAT
192200 GGTAATAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
18 8 0.21
19 21 0.54
20 10 0.26
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.37
Consensus pattern (19 bp):
TAATGATAATAATAATAAT
Found at i:192557 original size:20 final size:19
Alignment explanation
Indices: 192528--192599 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 19
192518 CATCTTGCCT
*
192528 GAAGGTCTTATGGATGGCCC
1 GAAGGACTTAT-GATGGCCC
* * *
192548 GAAGGACTTATCATCTTGCTC
1 GAAGGACTTATGA--TGGCCC
192569 G-AGAGACTTATAGATGGCCC
1 GAAG-GACTTAT-GATGGCCC
192589 GAAGGACTTAT
1 GAAGGACTTAT
192600 CAATTTTGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
19 1 0.03
20 24 0.60
21 14 0.35
22 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (19 bp):
GAAGGACTTATGATGGCCC
Found at i:192635 original size:191 final size:193
Alignment explanation
Indices: 192362--192770 Score: 574
Period size: 191 Copynumber: 2.1 Consensus size: 193
192352 CCCGCAGGGT
* * *
192362 TTAATCATCATGCTCGAAAGACTTAGTGATGGTCCGAAGGACTTACTCAGTTTTATAAATAGTTT
1 TTAATCATCATGCTCGAAAGACTTAGTGATGGCCCGAAGGACTTACTCAATTTTAGAAATAGTTT
* * *
192427 ACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTTAGAATCAAACGAGAATA-TTT
66 ACTAAGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAAATTTCAGAATCAAACGAGAA-ACTTT
* ** *
192491 TCTCATTTTTCAAAAGACACGTGAAAACATCTTGCCTGAAGGTCTTATGGATGGCCCGAAGGAC
130 TCTCATTTTTCAAAAGACACGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCAAAGGAC
* * *
192555 TT-ATCATCTTGCTCGAGAGACTTA-TAGATGGCCCGAAGGACTTA-TCAATTTTGGAAATAGTT
1 TTAATCATCATGCTCGAAAGACTTAGT-GATGGCCCGAAGGACTTACTCAATTTTAGAAATAGTT
* * * *
192617 TACTAAGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAAATTTCATATTTAAATGAGAAACTTT
65 TACTAAGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAAATTTCAGAATCAAACGAGAAACTTT
* * * *
192682 TCTCATTTTTCGAGAGACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCAAAGGAT
130 TCTCATTTTTCAAAAGACACGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCAAAGGAC
*
192746 TTAATCATCATGCTTGAAAGACTTA
1 TTAATCATCATGCTCGAAAGACTTA
192771 CATATGAGCC
Statistics
Matches: 189, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
190 1 0.01
191 130 0.69
192 56 0.30
193 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (193 bp):
TTAATCATCATGCTCGAAAGACTTAGTGATGGCCCGAAGGACTTACTCAATTTTAGAAATAGTTT
ACTAAGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAAATTTCAGAATCAAACGAGAAACTTTT
CTCATTTTTCAAAAGACACGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCAAAGGAC
Found at i:198674 original size:20 final size:20
Alignment explanation
Indices: 198643--198697 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
198633 AGTTTACTTG
198643 ATCATG-AAACCTTTTGTCC
1 ATCATGAAAACCTTTTGTCC
198662 ATCATGAAAACCTTTTGTCC
1 ATCATGAAAACCTTTTGTCC
198682 ATCATGAAAACCTTTT
1 ATCATGAAAACCTTTT
198698 ATTCTGATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 6 0.17
20 29 0.83
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (20 bp):
ATCATGAAAACCTTTTGTCC
Found at i:198887 original size:12 final size:12
Alignment explanation
Indices: 198870--198899 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
198860 GAAAAACGAT
198870 AATACAAATGCA
1 AATACAAATGCA
198882 AATACAAATGCA
1 AATACAAATGCA
198894 AATACA
1 AATACA
198900 CAAGGTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.60, C:0.17, G:0.07, T:0.17
Consensus pattern (12 bp):
AATACAAATGCA
Found at i:204021 original size:15 final size:15
Alignment explanation
Indices: 203982--204064 Score: 80
Period size: 15 Copynumber: 5.5 Consensus size: 15
203972 TATTGGTTTG
203982 TGAAAATGTT-TATA
1 TGAAAATGTTCTATA
*
203996 GGTGAATATGTTCTATA
1 --TGAAAATGTTCTATA
* *
204013 TGAAAATGTTTTATG
1 TGAAAATGTTCTATA
*
204028 TGAAAATGTGCTA-A
1 TGAAAATGTTCTATA
*
204042 GTGAAAATGTTCTACA
1 -TGAAAATGTTCTATA
204058 TGAAAAT
1 TGAAAAT
204065 ACCATATATG
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
15 42 0.75
16 10 0.18
17 4 0.07
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (15 bp):
TGAAAATGTTCTATA
Found at i:204047 original size:30 final size:32
Alignment explanation
Indices: 203981--204052 Score: 96
Period size: 30 Copynumber: 2.3 Consensus size: 32
203971 TTATTGGTTT
* *
203981 GTGAAAATGTTTATAGGTGAATATGTTCTATA
1 GTGAAAATGTTTATAGGTGAAAATGTGCTATA
*
204013 -TGAAAATGTTT-TATGTGAAAATGTGCTA-A
1 GTGAAAATGTTTATAGGTGAAAATGTGCTATA
204042 GTGAAAATGTT
1 GTGAAAATGTT
204053 CTACATGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 1 0.03
30 24 0.67
31 11 0.31
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (32 bp):
GTGAAAATGTTTATAGGTGAAAATGTGCTATA
Found at i:204227 original size:23 final size:23
Alignment explanation
Indices: 204196--204265 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
204186 AGTCGAGGGT
*
204196 TCTACGTGGTTCTTCGGGATAAA
1 TCTACGTGGTCCTTCGGGATAAA
* *
204219 TCTATGTGGTCCTTCGGGATAAT
1 TCTACGTGGTCCTTCGGGATAAA
* * *
204242 TCTACGTTGTCCTTTGGGACAAA
1 TCTACGTGGTCCTTCGGGATAAA
204265 T
1 T
204266 TCTATGCGGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGGGATAAA
Found at i:204880 original size:16 final size:16
Alignment explanation
Indices: 204838--204881 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
204828 TGAATATAAG
204838 TAAAAGTTCAAAATTTT
1 TAAAAGTT-AAAATTTT
* *
204855 CAACAAGTTAAAGTTTT
1 TAA-AAGTTAAAATTTT
204872 TAAAAGTTAA
1 TAAAAGTTAA
204882 TGTAACACCT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 7 0.30
17 11 0.48
18 5 0.22
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (16 bp):
TAAAAGTTAAAATTTT
Found at i:211017 original size:15 final size:15
Alignment explanation
Indices: 210981--211059 Score: 56
Period size: 15 Copynumber: 5.3 Consensus size: 15
210971 TGGTATGAGG
210981 AAATGTT-TATTAGTGA
1 AAATGTTCTA-TA-TGA
*
210997 ATATGTTCTATATGA
1 AAATGTTCTATATGA
* *
211012 AAATGTTTTATGTGA
1 AAATGTTCTATATGA
* *
211027 AAATATGCTA-A-GTA
1 AAATGTTCTATATG-A
*
211041 AAATGTTCTACATGA
1 AAATGTTCTATATGA
211056 AAAT
1 AAAT
211060 ACCCTATGTC
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
13 1 0.02
14 9 0.18
15 28 0.57
16 9 0.18
17 2 0.04
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (15 bp):
AAATGTTCTATATGA
Found at i:211269 original size:24 final size:23
Alignment explanation
Indices: 211198--211289 Score: 96
Period size: 24 Copynumber: 3.9 Consensus size: 23
211188 GGTTCTACGC
*
211198 GGTCCTTCGGGACAAA-TCTATGT
1 GGTCCTTCAGGA-AAATTCTATGT
* * *
211221 GGTCCTTCTGGACAATTCTACGT
1 GGTCCTTCAGGAAAATTCTATGT
*
211244 GGTCCTTCAAGATAAATTCTATGT
1 GGTCCTTCAGGA-AAATTCTATGT
*
211268 GGTCCTTCGGGACAAATTCTAT
1 GGTCCTTCAGGA-AAATTCTAT
211290 ATGGCACTTC
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
22 2 0.04
23 27 0.47
24 28 0.49
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (23 bp):
GGTCCTTCAGGAAAATTCTATGT
Found at i:211299 original size:24 final size:24
Alignment explanation
Indices: 211198--211289 Score: 125
Period size: 23 Copynumber: 3.9 Consensus size: 24
211188 GGTTCTACGC
211198 GGTCCTTCGGGACAAA-TCTATGT
1 GGTCCTTCGGGACAAATTCTATGT
* *
211221 GGTCCTTCTGGAC-AATTCTACGT
1 GGTCCTTCGGGACAAATTCTATGT
** *
211244 GGTCCTTCAAGATAAATTCTATGT
1 GGTCCTTCGGGACAAATTCTATGT
211268 GGTCCTTCGGGACAAATTCTAT
1 GGTCCTTCGGGACAAATTCTAT
211290 ATGGCACTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
22 2 0.03
23 28 0.48
24 28 0.48
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (24 bp):
GGTCCTTCGGGACAAATTCTATGT
Found at i:211806 original size:19 final size:19
Alignment explanation
Indices: 211765--211803 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
211755 TTAAGTATTT
* *
211765 ATTTTCAATGTGAGTTTGA
1 ATTTTCAATGTAACTTTGA
211784 ATTTTCAATAGTAACTTTGA
1 ATTTTCAAT-GTAACTTTGA
211804 TTTAAGGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (19 bp):
ATTTTCAATGTAACTTTGA
Found at i:212399 original size:3 final size:3
Alignment explanation
Indices: 212391--212449 Score: 55
Period size: 3 Copynumber: 18.7 Consensus size: 3
212381 TATTTTATAG
* * * *
212391 TAA TAA TAA TAAA TAA TCAA TAA TAC TAA TAA GCAC TGA TAA TAA TAA
1 TAA TAA TAA T-AA TAA T-AA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
212439 TAA TAA TAA TA
1 TAA TAA TAA TA
212450 GGAATAAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
3 38 0.84
4 7 0.16
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:212992 original size:189 final size:189
Alignment explanation
Indices: 212606--213027 Score: 521
Period size: 187 Copynumber: 2.2 Consensus size: 189
212596 CGATGACCCA
* * * * * * * *
212606 AAGGGTTTAATCATCATGCTTGAAGGACTTACTGATGGCTCGAAGGACTTACTCAGTTTTAGAAA
1 AAGGATTTAATCATCATGCTCGAAAGACTTACAGATGACCCGAAAGACTTACTCAATTTTAGAAA
* * *
212671 TAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAATTTTCAATTTTAAGAATCAAATGAGAA
66 TAGTTTACTAGGTAAGAAACTTTTATTACTTTTCAAAAATTTCAAATTTAAGAATCAAATGAGAA
* * *
212736 ATTTTTCATTTTCGAAAGACACTTGAAATATCATGCCCGAAGGTCTTATGAATGGCCCG
131 ATTTTTCATTTTCGAAAGACACTTGAAACATCAGGCCCAAAGGTCTTATGAATGGCCCG
* * * * *
212795 AAGGATTT-ATCATCTTGCTCGATAGACTTACAGATGTCCCGAAAGACTTAC-CAATTTTGGGAA
1 AAGGATTTAATCATCATGCTCGAAAGACTTACAGATGACCCGAAAGACTTACTCAATTTTAGAAA
* * * * * *
212858 TAGTTTACTAGGTAAGAAACTTTTATTATTTTTCAAAAATTTCAAATTTCATATTTAAATGATAA
66 TAGTTTACTAGGTAAGAAACTTTTATTACTTTTCAAAAATTTCAAATTTAAGAATCAAATGAGAA
* *
212923 ACTTTCTT-ATTTTTCGAGAGACA-TGTGAAACATTC-GGCCCAAAGGTCTTATGGATGGCCCG
131 A-TTT-TTCA-TTTTCGAAAGACACT-TGAAACA-TCAGGCCCAAAGGTCTTATGAATGGCCCG
212984 AAGGATTTAATCATCATGCTCGAAAGACTTACAGATGACCCGAA
1 AAGGATTTAATCATCATGCTCGAAAGACTTACAGATGACCCGAA
213028 GGATTTAAGC
Statistics
Matches: 198, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
187 66 0.33
188 40 0.20
189 58 0.29
190 34 0.17
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (189 bp):
AAGGATTTAATCATCATGCTCGAAAGACTTACAGATGACCCGAAAGACTTACTCAATTTTAGAAA
TAGTTTACTAGGTAAGAAACTTTTATTACTTTTCAAAAATTTCAAATTTAAGAATCAAATGAGAA
ATTTTTCATTTTCGAAAGACACTTGAAACATCAGGCCCAAAGGTCTTATGAATGGCCCG
Found at i:213711 original size:3 final size:3
Alignment explanation
Indices: 213703--213755 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
213693 GTATATTTTT
* *
213703 ATA ATA ATA ATA ATA ATTA ATA CTA ATA ATA GTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
213749 GTA ATA A
1 ATA ATA A
213756 ATAAAATGTC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:214527 original size:17 final size:17
Alignment explanation
Indices: 214501--214567 Score: 68
Period size: 17 Copynumber: 4.1 Consensus size: 17
214491 ACAATTATTT
214501 TCTTTCTATTATATTAG
1 TCTTTCTATTATATTAG
*
214518 TCTTTGTATTATATTAG
1 TCTTTCTATTATATTAG
* *
214535 TATTTTCTATTCTATT--
1 T-CTTTCTATTATATTAG
*
214551 T-TTTCTATTCTATTAG
1 TCTTTCTATTATATTAG
214567 T
1 T
214568 ATTAGATTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
14 13 0.30
16 2 0.05
17 17 0.40
18 11 0.26
ACGTcount: A:0.21, C:0.10, G:0.06, T:0.63
Consensus pattern (17 bp):
TCTTTCTATTATATTAG
Found at i:214556 original size:14 final size:14
Alignment explanation
Indices: 214537--214564 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
214527 TATATTAGTA
214537 TTTTCTATTCTATT
1 TTTTCTATTCTATT
214551 TTTTCTATTCTATT
1 TTTTCTATTCTATT
214565 AGTATTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:219142 original size:3 final size:3
Alignment explanation
Indices: 219134--219158 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
219124 AACAAAACAG
219134 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
219159 ATTAGATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:237172 original size:26 final size:27
Alignment explanation
Indices: 237143--237193 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
237133 GATTGTATTA
*
237143 AATAACTAGACTTTAA-TTAATAAAAC
1 AATAACTAGACTTTAAGTAAATAAAAC
*
237169 AATAACTATACTTTAAGTAAATAAA
1 AATAACTAGACTTTAAGTAAATAAA
237194 TTTAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (27 bp):
AATAACTAGACTTTAAGTAAATAAAAC
Found at i:240058 original size:13 final size:14
Alignment explanation
Indices: 240040--240068 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
240030 TGTTGTGGAC
240040 ATCACGGT-TTAAA
1 ATCACGGTCTTAAA
240053 ATCACGGTCTTAAA
1 ATCACGGTCTTAAA
240067 AT
1 AT
240069 ATGATAGCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (14 bp):
ATCACGGTCTTAAA
Found at i:252324 original size:23 final size:23
Alignment explanation
Indices: 252294--252345 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
252284 TCATATAAAC
252294 GCACCGAAGTGCCACGTAGAATT
1 GCACCGAAGTGCCACGTAGAATT
* *
252317 GCACCGAAGTGTCGCGTAGAATT
1 GCACCGAAGTGCCACGTAGAATT
252340 GCACCG
1 GCACCG
252346 TAATGACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (23 bp):
GCACCGAAGTGCCACGTAGAATT
Found at i:253599 original size:327 final size:327
Alignment explanation
Indices: 253005--253637 Score: 1203
Period size: 327 Copynumber: 1.9 Consensus size: 327
252995 CCATGTATAC
253005 ACTTACTTAAACTAATTATTATCCATTCGATACCTTTAAAACTTAGAAATCCAATTCTCCATATA
1 ACTTACTTAAACTAATTATTATCCATTCGATACCTTTAAAACTTAGAAATCCAATTCTCCATATA
253070 AAATTTAAGAATTTCACTCAATTTCCAACATATTCTAAATCGAATTCTGACACTTCATATCCTTT
66 AAATTTAAGAATTTCACTCAATTTCCAACATATTCTAAATCGAATTCTGACACTTCATATCCTTT
253135 AATTTGCTTGATGACAAGTCAAATCCCACTTATAATTCTTATTATGAACTCTATTCCAAGATTTC
131 AATTTGCTTGATGACAAGTCAAATCCCACTTATAATTCTTATTATGAACTCTATTCCAAGATTTC
253200 ACTTTTCTACTTCCTTTCTTTAATCCTTCATGTACTCATCATCTTATTGTTTTAAGATAACCTAA
196 ACTTTTCTACTTCCTTTCTTTAATCCTTCATGTACTCATCATCTTATTGTTTTAAGATAACCTAA
253265 GCTTTCCTTAAGCTTAGTTATAATCTAATGATCAATAAGCAACCTTTTATATCCCTAACTTGCAT
261 GCTTTCCTTAAGCTTAGTTATAATCTAATGATCAATAAGCAACCTTTTATATCCCTAACTTGCAT
253330 AT
326 AT
253332 ACTTACTTAAACTAATTATTATCCATTCGATACCTTTAAAACTTAGAAATCCAATTCTCCATATA
1 ACTTACTTAAACTAATTATTATCCATTCGATACCTTTAAAACTTAGAAATCCAATTCTCCATATA
* *
253397 AAATTTAAGAATTTCACTCAATTTTCAACATGTTCTAAATCGAATTCTGACACTTCATATCCTTT
66 AAATTTAAGAATTTCACTCAATTTCCAACATATTCTAAATCGAATTCTGACACTTCATATCCTTT
* *
253462 AATTTGCTTGATGACAAGTCAAATCCCACTTCTAATTCTTATTATGAACTCTATTCTAAGATTTC
131 AATTTGCTTGATGACAAGTCAAATCCCACTTATAATTCTTATTATGAACTCTATTCCAAGATTTC
*
253527 ACTTTTCTACTTCCTTTCTTTAATCCTTCATGTACTCCTCATCTTATTGTTTTAAGATAACCTAA
196 ACTTTTCTACTTCCTTTCTTTAATCCTTCATGTACTCATCATCTTATTGTTTTAAGATAACCTAA
* *
253592 GCTTTCCTTAAGCTTAGTTATCATCTAATGATTAATAAGCAACCTT
261 GCTTTCCTTAAGCTTAGTTATAATCTAATGATCAATAAGCAACCTT
253638 AAATTCATCA
Statistics
Matches: 299, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
327 299 1.00
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (327 bp):
ACTTACTTAAACTAATTATTATCCATTCGATACCTTTAAAACTTAGAAATCCAATTCTCCATATA
AAATTTAAGAATTTCACTCAATTTCCAACATATTCTAAATCGAATTCTGACACTTCATATCCTTT
AATTTGCTTGATGACAAGTCAAATCCCACTTATAATTCTTATTATGAACTCTATTCCAAGATTTC
ACTTTTCTACTTCCTTTCTTTAATCCTTCATGTACTCATCATCTTATTGTTTTAAGATAACCTAA
GCTTTCCTTAAGCTTAGTTATAATCTAATGATCAATAAGCAACCTTTTATATCCCTAACTTGCAT
AT
Found at i:259584 original size:31 final size:30
Alignment explanation
Indices: 259540--259599 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
259530 TATTGTATAG
259540 ACATATAATTTCCAT-ACCTTTATCACATAA
1 ACATATAATTTCCATCA-CTTTATCACATAA
*
259570 ACATATCATGTTCCATCACTTTATCACATA
1 ACATATAAT-TTCCATCACTTTATCACATA
259600 GCTTATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 18 0.67
32 1 0.04
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTTATCACATAA
Found at i:260751 original size:33 final size:33
Alignment explanation
Indices: 260709--260781 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
260699 CTAAGATTTA
260709 TAATTTCCTTGTTAAAAGACTTATTTACCCCTT
1 TAATTTCCTTGTTAAAAGACTTATTTACCCCTT
260742 TAATTTCCTTGTTAAAAGACTTATTTACCCCTT
1 TAATTTCCTTGTTAAAAGACTTATTTACCCCTT
260775 TAATTTC
1 TAATTTC
260782 TCTTCTTTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.47
Consensus pattern (33 bp):
TAATTTCCTTGTTAAAAGACTTATTTACCCCTT
Found at i:261084 original size:33 final size:33
Alignment explanation
Indices: 261047--261112 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
261037 TTTCTGAAGA
261047 AGAAATTAGAAGTCTTTGATACATTCAGAAAAT
1 AGAAATTAGAAGTCTTTGATACATTCAGAAAAT
261080 AGAAATTAGAAGTCTTTGATACATTCAGAAAAT
1 AGAAATTAGAAGTCTTTGATACATTCAGAAAAT
261113 GGAAGGCCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.30
Consensus pattern (33 bp):
AGAAATTAGAAGTCTTTGATACATTCAGAAAAT
Found at i:272229 original size:30 final size:31
Alignment explanation
Indices: 272170--272270 Score: 114
Period size: 31 Copynumber: 3.3 Consensus size: 31
272160 AAAAATGATT
* * * *
272170 AAATTTTAATTTAATATCTATATTTTAGATA
1 AAATATTAATTTAATATCTAAACTCTAGATA
** *
272201 AAATATTGTTTTAA-CTCTAAACTCTAGATA
1 AAATATTAATTTAATATCTAAACTCTAGATA
* *
272231 AAATAATAATTTAATATCTAAACTTTAGATA
1 AAATATTAATTTAATATCTAAACTCTAGATA
272262 AAATATTAA
1 AAATATTAA
272271 ATTGACTCAT
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
30 23 0.41
31 33 0.59
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.43
Consensus pattern (31 bp):
AAATATTAATTTAATATCTAAACTCTAGATA
Found at i:273820 original size:18 final size:18
Alignment explanation
Indices: 273799--273891 Score: 50
Period size: 18 Copynumber: 5.0 Consensus size: 18
273789 AAAAAAATAT
273799 ATAAAATATAAAATAAAA
1 ATAAAATATAAAATAAAA
* *
273817 AT-AAATCA-ATCAATCAAA
1 ATAAAAT-ATA-AAATAAAA
273835 AT-AAATCAATAAAAT-AAA
1 ATAAAAT--ATAAAATAAAA
*
273853 ATAAAAATATTAAATAAACCA
1 AT-AAAATATAAAATAAA--A
* *
273874 AAAAAATATAAGATAAAA
1 ATAAAATATAAAATAAAA
273892 GAAAAGAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
17 5 0.09
18 27 0.47
19 6 0.10
20 18 0.31
21 2 0.03
ACGTcount: A:0.71, C:0.06, G:0.01, T:0.22
Consensus pattern (18 bp):
ATAAAATATAAAATAAAA
Done.