Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007824.1 Hibiscus syriacus cultivar Beakdansim tig00110162_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: 895964
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 4 of 4
Found at i:709940 original size:19 final size:18
Alignment explanation
Indices: 709908--709943 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
709898 TGTTGATCAT
*
709908 ATTTTCAATTAATTCTCC
1 ATTTTCAATAAATTCTCC
709926 ATTTATCAATAAATTCTC
1 ATTT-TCAATAAATTCTC
709944 AAATTCCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTTCAATAAATTCTCC
Found at i:716434 original size:21 final size:21
Alignment explanation
Indices: 716409--716461 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
716399 ATTATGACTA
716409 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* *
716430 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
716451 TCGCAATGCGA
1 TCGCATTGCGA
716462 ATACGTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:716476 original size:20 final size:20
Alignment explanation
Indices: 716451--716543 Score: 168
Period size: 20 Copynumber: 4.7 Consensus size: 20
716441 TTTTCCTAAT
716451 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
716471 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
716491 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
716511 TCGCAATACGAATAAGTAAA
1 TCGCAATGCGAATACGTAAA
716531 TCGCAATGCGAAT
1 TCGCAATGCGAAT
716544 CTGACTATCG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:716766 original size:22 final size:22
Alignment explanation
Indices: 716741--716806 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
716731 GGCGACATCC
716741 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* * *
716763 GTCCCCATCGCTGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
716785 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
716807 TTCACGGTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.24, C:0.38, G:0.17, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:717199 original size:20 final size:20
Alignment explanation
Indices: 717174--717223 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
717164 TACGATTCTT
717174 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
717194 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
717214 GTGTTGCGAT
1 GCGTTGCGAT
717224 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:717229 original size:20 final size:20
Alignment explanation
Indices: 717191--717245 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
717181 GATAGTCAAA
* **
717191 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
717211 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
717231 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
717246 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:717253 original size:20 final size:20
Alignment explanation
Indices: 717210--717253 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
717200 CGATAGTCAT
** *
717210 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
717230 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
717250 TTTC
1 TTTC
717254 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:719150 original size:20 final size:20
Alignment explanation
Indices: 719121--719273 Score: 109
Period size: 20 Copynumber: 8.3 Consensus size: 20
719111 AGAATAGTTT
*
719121 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
*
719141 ACTATTGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
*
719161 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAACGCGAAAATG
*
719177 A--ATCGCAATGCG-AAATG
1 ACTATCGCAACGCGAAAATG
**
719194 AAAATCGCAA--C-AACAA--
1 ACTATCGCAACGCGAA-AATG
719210 A--ATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
*
719228 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
* **
719248 ACTATCGCAATGCGAATTTG
1 ACTATCGCAACGCGAAAATG
719268 ACTATC
1 ACTATC
719274 ACAATGCGAT
Statistics
Matches: 111, Mismatches: 8, Indels: 28
0.76 0.05 0.19
Matches are distributed among these distances:
14 14 0.13
16 10 0.09
17 8 0.07
18 5 0.05
19 7 0.06
20 67 0.60
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Found at i:719278 original size:20 final size:20
Alignment explanation
Indices: 719211--719287 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 20
719201 CAACAACAAA
* **
719211 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAATTTGACT
**
719231 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAATTTGACT
719251 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAATTTGACT
* *
719271 ATCACAATGCGATTTTG
1 ATCGCAATGCGAATTTG
719288 TTGTTGCGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATTTGACT
Found at i:719315 original size:33 final size:34
Alignment explanation
Indices: 719278--719353 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 34
719268 ACTATCACAA
* * **
719278 TGCGATTTTGTTGTTGCGATTTTCA-TTTCGCAT
1 TGCGATTTTCTCGTTGCGATAGTCATTTTCGCAT
* *
719311 TGCGATTATCTCGTTGCGATAGTCATTTTCGCGT
1 TGCGATTTTCTCGTTGCGATAGTCATTTTCGCAT
719345 TGCGATTTT
1 TGCGATTTT
719354 AAGTTTTAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
33 20 0.57
34 15 0.43
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.47
Consensus pattern (34 bp):
TGCGATTTTCTCGTTGCGATAGTCATTTTCGCAT
Found at i:719925 original size:21 final size:21
Alignment explanation
Indices: 719834--719937 Score: 75
Period size: 21 Copynumber: 5.0 Consensus size: 21
719824 GACTCACCTG
* **
719834 TCATCATTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTA
*
719856 T-ATCATTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
** * *
719876 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTA
* * *
719897 TCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTA
* *
719918 TCATCGTTGAAGAGGTCCCT
1 TCATCGTTCAAGAGGCCCCT
719938 CCCAACATTC
Statistics
Matches: 65, Mismatches: 16, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 3 0.05
21 61 0.94
22 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTA
Found at i:721345 original size:14 final size:14
Alignment explanation
Indices: 721326--721361 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
721316 ATTGTTTAAT
721326 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
721340 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
721354 TGATTTGT
1 TGATTTGT
721362 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:721498 original size:33 final size:34
Alignment explanation
Indices: 721439--721512 Score: 123
Period size: 33 Copynumber: 2.2 Consensus size: 34
721429 TGATTTCGCA
*
721439 TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
1 TTGCGATTTTCATTTTAGCATTGCGATTCACTCG
*
721473 TTGCGATTTTCA-TTTAGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTTAGCATTGCGATTCACTCG
721506 TTGCGAT
1 TTGCGAT
721513 AGTCATTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 26 0.68
34 12 0.32
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.45
Consensus pattern (34 bp):
TTGCGATTTTCATTTTAGCATTGCGATTCACTCG
Found at i:721519 original size:33 final size:33
Alignment explanation
Indices: 721456--721520 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
721446 TTTCATTTTC
**
721456 GCATTGCGATTCACTCGTTGCGATTTTCATTTA
1 GCATTGCGATTCACTCGTTGCGATAGTCATTTA
*
721489 GCATTGCGATTCTCTCGTTGCGATAGTCATTT
1 GCATTGCGATTCACTCGTTGCGATAGTCATTT
721521 CCGCGTTGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (33 bp):
GCATTGCGATTCACTCGTTGCGATAGTCATTTA
Found at i:721529 original size:20 final size:20
Alignment explanation
Indices: 721504--721634 Score: 203
Period size: 20 Copynumber: 6.5 Consensus size: 20
721494 GCGATTCTCT
721504 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
721524 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
721544 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
721564 CGTTGCGATAGTCAATTT-CG
1 CGTTGCGATAGTC-ATTTCCG
721584 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
721604 TGTTGCGATAGTCATATT-CA
1 CGTTGCGATAGTCAT-TTCCG
721624 CGTTGCGATAG
1 CGTTGCGATAG
721635 CCAAATGAAT
Statistics
Matches: 103, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
19 4 0.04
20 94 0.91
21 5 0.05
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:724073 original size:24 final size:24
Alignment explanation
Indices: 724039--724092 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
724029 CTGAAAAATC
724039 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
724063 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
724087 ATCAAA
1 ATCAAA
724093 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:724106 original size:24 final size:24
Alignment explanation
Indices: 724039--724106 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
724029 CTGAAAAATC
* * *
724039 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
724063 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
724087 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
724107 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:724962 original size:20 final size:20
Alignment explanation
Indices: 724937--724980 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
724927 TTCAGTATTA
*
724937 CGATAGTCAGAATCTCGTTG
1 CGATAGTCAGAATCGCGTTG
*
724957 CGATAGTCAGATTCGCGTTG
1 CGATAGTCAGAATCGCGTTG
724977 CGAT
1 CGAT
724981 TTACGTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (20 bp):
CGATAGTCAGAATCGCGTTG
Found at i:724990 original size:20 final size:20
Alignment explanation
Indices: 724967--725274 Score: 292
Period size: 20 Copynumber: 15.7 Consensus size: 20
724957 CGATAGTCAG
*
724967 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
724987 ATTCGTATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
725007 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* **
725027 ATTCGCATTGCGATATTCCAA
1 ATTCGCATTGCGAT-TTACGT
*
725048 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
725068 ATTCGCATTGCG----A---
1 ATTCGCATTGCGATTTACGT
*
725081 A-T-GCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
* * **
725099 ATTCGCATTACGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
725120 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
725140 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
725160 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
725181 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
725201 ATTCGCATTGCGATGTACGT
1 ATTCGCATTGCGATTTACGT
* * **
725221 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
725242 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
725262 ATTCGCATTGCGA
1 ATTCGCATTGCGA
725275 ATTAGGAAAA
Statistics
Matches: 231, Mismatches: 44, Indels: 26
0.77 0.15 0.09
Matches are distributed among these distances:
11 8 0.03
12 1 0.00
13 1 0.00
15 1 0.00
16 1 0.00
18 1 0.00
19 1 0.00
20 156 0.68
21 61 0.26
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:725064 original size:41 final size:40
Alignment explanation
Indices: 724967--725274 Score: 312
Period size: 41 Copynumber: 7.8 Consensus size: 40
724957 CGATAGTCAG
* * * *
724967 ATTCGCGTTGCGATTTACGTATTCGTATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTCCAA
*
725007 ATTCGTATTGCGATTTACGTATTCGCATTGCGATATTCCAA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGAT-TTCCAA
*
725048 ATTCGCGTTGCGATTTACGTATTCGCATTGCG-------A
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTCCAA
* *
725081 A-T-GCATTGCGATTTACATATTCGCATTACGATTTTCCAA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGA-TTTCCAA
* **
725120 ATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTT-CCAA
* ** * * **
725161 A-TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGA-TTTACGTATTCGCATTGCGATTTCCAA
* *
725201 ATTCGCATTGCGATGTACGTAATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGA-TTTCCAA
*
725242 ATTCGCGTTGCGATTTACGTATTCGCATTGCGA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGA
725275 ATTAGGAAAA
Statistics
Matches: 217, Mismatches: 36, Indels: 29
0.77 0.13 0.10
Matches are distributed among these distances:
31 25 0.12
32 1 0.00
33 2 0.01
39 2 0.01
40 60 0.28
41 127 0.59
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTCCAA
Found at i:725071 original size:61 final size:60
Alignment explanation
Indices: 725014--725274 Score: 290
Period size: 61 Copynumber: 4.4 Consensus size: 60
725004 CATATTCGTA
* * ** *
725014 TTGCGATTTACGTATTCGCATTGCGATATTCCAAATTCGCGTTGCGA-TTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCATTGCGAT-TTCCAAA-TCGCATTGCGATTTTCCAAATTCGCG
* * *
725075 TTGCG----A---A-T-GCATTGCGATTTACATATTCGCATTACGATTTTCCAAATTCGCG
1 TTGCGATTTACGTATTCGCATTGCGATTTCCA-AATCGCATTGCGATTTTCCAAATTCGCG
**
725127 TTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCGCG
1 TTGCGATTTACGTATTCGCATTGCGATTT-CCAAATCGCATTGCGATTTTCCAAATTCGCG
* **
725188 TTGCGATTTACGTATTCGCATTGCGATGTACGTAATCGCATTGCGATTTTCCAAATTCGCG
1 TTGCGATTTACGTATTCGCATTGCGAT-TTCCAAATCGCATTGCGATTTTCCAAATTCGCG
725249 TTGCGATTTACGTATTCGCATTGCGA
1 TTGCGATTTACGTATTCGCATTGCGA
725275 ATTAGGAAAA
Statistics
Matches: 173, Mismatches: 14, Indels: 26
0.81 0.07 0.12
Matches are distributed among these distances:
51 13 0.08
52 26 0.15
53 1 0.01
54 1 0.01
56 1 0.01
57 1 0.01
59 1 0.01
60 1 0.01
61 127 0.73
62 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (60 bp):
TTGCGATTTACGTATTCGCATTGCGATTTCCAAATCGCATTGCGATTTTCCAAATTCGCG
Found at i:725130 original size:72 final size:72
Alignment explanation
Indices: 725013--725152 Score: 253
Period size: 72 Copynumber: 1.9 Consensus size: 72
725003 ACATATTCGT
* *
725013 ATTGCGATTTACGTATTCGCATTGCGATATTCCAAATTCGCGTTGCGATTTACGTATTCGCATTG
1 ATTGCGATTTACATATTCGCATTACGATATTCCAAATTCGCGTTGCGATTTACGTATTCGCATTG
725078 CGAATGC
66 CGAATGC
*
725085 ATTGCGATTTACATATTCGCATTACGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCATTG
1 ATTGCGATTTACATATTCGCATTACGATATTCCAAATTCGCGTTGCGATTTACGTATTCGCATTG
725150 CGA
66 CGA
725153 TTTACGTAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (72 bp):
ATTGCGATTTACATATTCGCATTACGATATTCCAAATTCGCGTTGCGATTTACGTATTCGCATTG
CGAATGC
Found at i:725151 original size:92 final size:92
Alignment explanation
Indices: 724993--725276 Score: 266
Period size: 102 Copynumber: 3.0 Consensus size: 92
724983 ACGTATTCGT
* * ** * *
724993 ATTGCGATTTACATATTCGTATTGCGATTTACGTATTCGCATTGCGATATTCCAAATTCGCGTTG
1 ATTGCGATTTACATATTCGCATTACGATTTACAAATTCGCATTGCGATATTACAAATTCGCATTG
*
725058 CGATTTACGTATTCGCATTGCGAATGC
66 CGATTTACGTAATCGCATTGCGAATGC
* * **
725085 ATTGCGATTTACATATTCGCATTACGATTTTCCAAATTCGCGTTGCGAT-TTACGTATTCGCATT
1 ATTGCGATTTACATATTCGCATTACGA-TTTACAAATTCGCATTGCGATATTACAAATTCGCATT
725149 GCGATTTACGTAATCGCATTGCGATTTTCCAAATTCGC
65 GCGATTTACGTAATCGCATTGCG--------AA-T-GC
* * * * * * * *
725187 GTTGCGATTTACGTATTCGCATTGCGATGTACGTAA-TCGCATTGCGATTTTCCAAATTCGCGTT
1 ATTGCGATTTACATATTCGCATTACGATTTAC-AAATTCGCATTGCGATATTACAAATTCGCATT
*
725251 GCGATTTACGTATTCGCATTGCGAAT
65 GCGATTTACGTAATCGCATTGCGAAT
725277 TAGGAAAAGC
Statistics
Matches: 156, Mismatches: 23, Indels: 25
0.76 0.11 0.12
Matches are distributed among these distances:
92 58 0.37
93 18 0.12
94 2 0.01
100 2 0.01
101 15 0.10
102 61 0.39
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (92 bp):
ATTGCGATTTACATATTCGCATTACGATTTACAAATTCGCATTGCGATATTACAAATTCGCATTG
CGATTTACGTAATCGCATTGCGAATGC
Found at i:725294 original size:21 final size:21
Alignment explanation
Indices: 725265--725337 Score: 119
Period size: 21 Copynumber: 3.5 Consensus size: 21
725255 TTTACGTATT
*
725265 CGCATTGCGAATTAGGAAAAG
1 CGCAATGCGAATTAGGAAAAG
725286 CGCAATGCGAATTAGGAAAAG
1 CGCAATGCGAATTAGGAAAAG
* *
725307 CGCAATGCGAATTTGGAAAAT
1 CGCAATGCGAATTAGGAAAAG
725328 CGCAATGCGA
1 CGCAATGCGA
725338 TAGTCAGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.18
Consensus pattern (21 bp):
CGCAATGCGAATTAGGAAAAG
Found at i:728720 original size:6 final size:6
Alignment explanation
Indices: 728709--728733 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
728699 TTTTTATTAA
728709 TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
728734 GTGAGAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:732515 original size:24 final size:25
Alignment explanation
Indices: 732488--732541 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
732478 GTATATAAAA
732488 TTAAAAACAAG-CATATTAATTTTG
1 TTAAAAACAAGACATATTAATTTTG
**
732512 TTAAAATTAAGAACATATTAATTTTG
1 TTAAAAACAAG-ACATATTAATTTTG
732538 TTAA
1 TTAA
732542 CATAGGACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 9 0.35
26 17 0.65
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (25 bp):
TTAAAAACAAGACATATTAATTTTG
Found at i:743907 original size:54 final size:54
Alignment explanation
Indices: 743773--743951 Score: 216
Period size: 54 Copynumber: 3.3 Consensus size: 54
743763 CAAGACCGGC
* ** *
743773 GGTCCAAGTTCCGGAGGAAAATGTCATGCATTCGTTGACGCTTTC-TCCAAGTCAT
1 GGTCCAAGTTCCGGAGGAAAAGGTCATGCATTCGTTGACGCAGTCAT-CAACTC-T
* * * *
743828 GAGGTCCAAGTTCCGGAGGACAAGGTCATGCATTTGTTGATGCCGTCATCAACTCT
1 --GGTCCAAGTTCCGGAGGAAAAGGTCATGCATTCGTTGACGCAGTCATCAACTCT
* * *
743884 GGTCCAAGTTCCGGAGGAGAAGGTCATGCATTCATTGACGCAGTCACCAACTCT
1 GGTCCAAGTTCCGGAGGAAAAGGTCATGCATTCGTTGACGCAGTCATCAACTCT
743938 GGTCCAAGTTCCGG
1 GGTCCAAGTTCCGG
743952 TGGTGATGGA
Statistics
Matches: 108, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
54 62 0.57
56 1 0.01
57 44 0.41
58 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (54 bp):
GGTCCAAGTTCCGGAGGAAAAGGTCATGCATTCGTTGACGCAGTCATCAACTCT
Found at i:744349 original size:38 final size:38
Alignment explanation
Indices: 744302--744375 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
744292 TTATTTTATA
* *
744302 TTTTGATTATTGGTACTTGCAGTTACAAGTCTAATTTT
1 TTTTGATTATTGGTACTTGCAATTACAAGTATAATTTT
* *
744340 TTTTTATTATTGGTACTTTCAATTACAAGTATAATT
1 TTTTGATTATTGGTACTTGCAATTACAAGTATAATT
744376 ATAAGTACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.51
Consensus pattern (38 bp):
TTTTGATTATTGGTACTTGCAATTACAAGTATAATTTT
Found at i:744953 original size:23 final size:23
Alignment explanation
Indices: 744926--744970 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
744916 TAAGCTACCA
744926 AAAGGCAGAGAAAAATGTGTCAC
1 AAAGGCAGAGAAAAATGTGTCAC
* *
744949 AAAGGCAGAGATAAATTTGTCA
1 AAAGGCAGAGAAAAATGTGTCA
744971 TAAAAACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (23 bp):
AAAGGCAGAGAAAAATGTGTCAC
Found at i:746103 original size:18 final size:17
Alignment explanation
Indices: 746080--746113 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
746070 CGAGATCATA
*
746080 ATATTATTTTTTCATATT
1 ATATTATATTTT-ATATT
746098 ATATTATATTTTATAT
1 ATATTATATTTTATAT
746114 AAATAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:758693 original size:37 final size:36
Alignment explanation
Indices: 758634--758753 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
758624 ATCCCATTAT
* *
758634 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
758670 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
758706 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
758741 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
758754 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:758709 original size:21 final size:21
Alignment explanation
Indices: 758685--758745 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
758675 TTCAAAGAAA
758685 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
758706 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
758720 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
758741 CATTT
1 CATTT
758746 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:758762 original size:35 final size:36
Alignment explanation
Indices: 758636--758780 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 36
758626 CCCATTATCA
*
758636 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
758671 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
758708 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
758744 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
758778 TTT
1 TTT
758781 AATAATTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:763330 original size:35 final size:35
Alignment explanation
Indices: 763248--763392 Score: 229
Period size: 35 Copynumber: 4.1 Consensus size: 35
763238 CCATTATCAT
* * *
763248 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTA
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCA
*
763283 TTTTTCAAAGAAATATTTACCAAACTTTGAAAACCA
1 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
763319 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
763354 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
763389 TTTT
1 TTTT
763393 TTCAAAATTG
Statistics
Matches: 103, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
35 73 0.71
36 11 0.11
37 19 0.18
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (35 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:763408 original size:70 final size:70
Alignment explanation
Indices: 763263--763426 Score: 217
Period size: 70 Copynumber: 2.3 Consensus size: 70
763253 AACAAACATC
* *
763263 TACCAAACTTTGAAAAACTATTTTTCAAAGAAATATTTACCAAACTTTGAAAACCATTTTCAAAG
1 TACCAAACTTTG-AAAACCA-TTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTTTCAAAG
*
763328 AAACATT
64 AAACAGT
763335 TACCAAACTTTGAAAACCATTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTTTTTC-AA-
1 TACCAAACTTTGAAAACCATTTTCAAAGAAACATTTACCAAACTTTGAAAACCA--TTTTCAAAG
***
763398 AATTGGT
64 AAACAGT
763405 TACCAAAC-TTGAAAACCATTTT
1 TACCAAACTTTGAAAACCATTTT
763427 AATAATTTCA
Statistics
Matches: 84, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
69 14 0.17
70 45 0.54
71 8 0.10
72 17 0.20
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.32
Consensus pattern (70 bp):
TACCAAACTTTGAAAACCATTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTTTCAAAGAA
ACAGT
Found at i:768663 original size:13 final size:13
Alignment explanation
Indices: 768647--768676 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
768637 TAATTTAATT
768647 TTTTTTAAAATGA
1 TTTTTTAAAATGA
768660 TTTTTTAAAATGA
1 TTTTTTAAAATGA
768673 TTTT
1 TTTT
768677 ACAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (13 bp):
TTTTTTAAAATGA
Found at i:778998 original size:20 final size:20
Alignment explanation
Indices: 778973--779022 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
778963 AACCAACAAA
778973 TTCGCAACGCAAACTCCAAT
1 TTCGCAACGCAAACTCCAAT
***
778993 TTCGCAAAC-CAGTTTCCAAT
1 TTCGC-AACGCAAACTCCAAT
779013 TTCGCAACGC
1 TTCGCAACGC
779023 GAATATGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 3 0.12
20 19 0.76
21 3 0.12
ACGTcount: A:0.30, C:0.34, G:0.12, T:0.24
Consensus pattern (20 bp):
TTCGCAACGCAAACTCCAAT
Found at i:779060 original size:21 final size:21
Alignment explanation
Indices: 779034--779078 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
779024 AATATGTAAA
779034 TCGCATTGCGATTTTCAAAAT
1 TCGCATTGCGATTTTCAAAAT
*
779055 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCAAAAT
779076 TCG
1 TCG
779079 TAAAGCGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCAAAAT
Found at i:779086 original size:21 final size:21
Alignment explanation
Indices: 779041--779086 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
779031 AAATCGCATT
**
779041 GCGATTTTCAAAATTCGCATT
1 GCGATTTTCAAAATTCGCAAA
* *
779062 GCGATTTTCCAAATTCGTAAA
1 GCGATTTTCAAAATTCGCAAA
779083 GCGA
1 GCGA
779087 ATTTGTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (21 bp):
GCGATTTTCAAAATTCGCAAA
Found at i:779229 original size:20 final size:20
Alignment explanation
Indices: 779107--779222 Score: 133
Period size: 20 Copynumber: 5.8 Consensus size: 20
779097 CGCAATACAG
*
779107 AAGTCAAATTCGCAACACAA
1 AAGTCAAATTCGCAACACGA
* * *
779127 AAGTTAAATTCGTAACGCGA
1 AAGTCAAATTCGCAACACGA
*
779147 TAGTCAAATTCGCAACACTGA
1 AAGTCAAATTCGCAACAC-GA
** *
779168 ATTTCAAATTCGCAACACAA
1 AAGTCAAATTCGCAACACGA
**
779188 AAGTCAAATTCGCAATGCGA
1 AAGTCAAATTCGCAACACGA
779208 AAGTCAAATTCGCAA
1 AAGTCAAATTCGCAA
779223 TGCGAAACAC
Statistics
Matches: 78, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
20 61 0.78
21 17 0.22
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.22
Consensus pattern (20 bp):
AAGTCAAATTCGCAACACGA
Found at i:781088 original size:24 final size:24
Alignment explanation
Indices: 781054--781107 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
781044 CCATCACATC
781054 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
781078 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
781102 ATCAAA
1 ATCAAA
781108 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:781121 original size:24 final size:24
Alignment explanation
Indices: 781054--781121 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
781044 CCATCACATC
* * *
781054 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAGTCTGAATACTGACCAAG
** *
781078 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAGTCTGAATACTGACCAAG
* *
781102 ATCAAATTTTGAATACTGAC
1 ATCAAAGTCTGAATACTGAC
781122 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (24 bp):
ATCAAAGTCTGAATACTGACCAAG
Found at i:781888 original size:14 final size:16
Alignment explanation
Indices: 781853--781889 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
781843 GAAATCTTTG
781853 AAAATTATATAGAAAT
1 AAAATTATATAGAAAT
*
781869 AAAATTATGTA-AAA-
1 AAAATTATATAGAAAT
781883 AAAATTA
1 AAAATTA
781890 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAATTATATAGAAAT
Found at i:782122 original size:20 final size:20
Alignment explanation
Indices: 782038--782151 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
782028 AACTAAAACA
* *
782038 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAATTTGAATTTCG
** **
782057 TGTTGCGAATTCCAAAATC-
1 TGTTGCGAATTTGAATTTCG
*
782076 TAGTTGCGAATTTGAAATTCCG
1 T-GTTGCGAATTTG-AATTTCG
* *
782098 CGTTGCGAATTTGAATTTTG
1 TGTTGCGAATTTGAATTTCG
* *
782118 TGTTGCGAATTTGACTGTCG
1 TGTTGCGAATTTGAATTTCG
782138 TGTTGCGAATTTGA
1 TGTTGCGAATTTGA
782152 CTATCGCGTT
Statistics
Matches: 76, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
19 11 0.14
20 50 0.66
21 15 0.20
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.39
Consensus pattern (20 bp):
TGTTGCGAATTTGAATTTCG
Found at i:782152 original size:20 final size:19
Alignment explanation
Indices: 782078--782275 Score: 141
Period size: 20 Copynumber: 9.9 Consensus size: 19
782068 CCAAAATCTA
*
782078 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTG-ACTT-CGC
* * *
782099 GTTGCGAATTTGAATTTTGT
1 GTTGCGAATTTG-ACTTCGC
*
782119 GTTGCGAATTTGACTGTCGT
1 GTTGCGAATTTGACT-TCGC
782139 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACT-TCGC
** ** *
782159 GTTAAGCTTTTGACTTCTGT
1 GTTGCGAATTTGACTTC-GC
782179 GTTGCG-ATTT-ACAAATTCGC
1 GTTGCGAATTTGAC---TTCGC
*
782199 GTTGCGATTTATAGA-TTCGC
1 GTTGCGAATT-T-GACTTCGC
782219 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACT-TCGC
* *
782239 GTTGCGAATTTGATTATCAC
1 GTTGCGAATTTGACT-TCGC
782259 GTTGCGAATTTGACTTC
1 GTTGCGAATTTGACTTC
782276 TATATTGCGA
Statistics
Matches: 145, Mismatches: 21, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
18 4 0.03
19 11 0.08
20 107 0.74
21 21 0.14
22 1 0.01
24 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (19 bp):
GTTGCGAATTTGACTTCGC
Found at i:782200 original size:100 final size:101
Alignment explanation
Indices: 782119--782326 Score: 303
Period size: 100 Copynumber: 2.1 Consensus size: 101
782109 TGAATTTTGT
* * * ** * *
782119 GTTGCGAATTTGACTGTCGTGTTGCGAATTTGACTATCGCGTTAAGCTTTTGACTTCTGTGTTGC
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCACGTTAAGAATTTGACTTCTATATTGC
782184 GATTTACAAATTCGCGTTGCG-ATTTATAGATTCGC
66 GATTTACAAATTCGCGTTGCGAATTTATAGATTCGC
* **
782219 GTTGCGAATTTGACTATCGCGTTGCGAATTTGATTATCACGTTGCGAATTTGACTTCTATATTGC
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCACGTTAAGAATTTGACTTCTATATTGC
*
782284 GATTTACAAATTCGCGTTGCG-ATTTACAGATTCGC
66 GATTTACAAATTCGCGTTGCGAATTTATAGATTCGC
782319 GTTGCGAA
1 GTTGCGAA
782327 ATTGGAAATT
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (101 bp):
GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCACGTTAAGAATTTGACTTCTATATTGC
GATTTACAAATTCGCGTTGCGAATTTATAGATTCGC
Found at i:782303 original size:20 final size:20
Alignment explanation
Indices: 782280--782325 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
782270 GACTTCTATA
782280 TTGCGATTTACAAATTCGCG
1 TTGCGATTTACAAATTCGCG
*
782300 TTGCGATTTACAGATTCGCG
1 TTGCGATTTACAAATTCGCG
782320 TTGCGA
1 TTGCGA
782326 AATTGGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (20 bp):
TTGCGATTTACAAATTCGCG
Found at i:782324 original size:40 final size:39
Alignment explanation
Indices: 782179--782325 Score: 90
Period size: 40 Copynumber: 3.7 Consensus size: 39
782169 TGACTTCTGT
* *
782179 GTTGCG-ATTTACAAATTCGCGTTGCGATTTATAGATTCGC
1 GTTGCGAATTTAC-GATTCGCGTTGCGATTTA-AAATTCGC
* * * *
782219 GTTGCGAATTTGACTA-TCGCGTTGCGAATTT-GATTATCAC
1 GTTGCGAATTT-ACGATTCGCGTTGCG-ATTTAAAAT-TCGC
***
782259 GTTGCGAATTT--GACTTCTATATTGCGATTTACAAATTCGC
1 GTTGCGAATTTACGA-TTC-GCGTTGCGATTTA-AAATTCGC
782299 GTTGCG-ATTTACAGATTCGCGTTGCGA
1 GTTGCGAATTTAC-GATTCGCGTTGCGA
782326 AATTGGAAAT
Statistics
Matches: 80, Mismatches: 15, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
37 1 0.01
39 11 0.14
40 50 0.62
41 14 0.17
42 4 0.05
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (39 bp):
GTTGCGAATTTACGATTCGCGTTGCGATTTAAAATTCGC
Found at i:782362 original size:20 final size:21
Alignment explanation
Indices: 782313--782363 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
782303 CGATTTACAG
*
782313 ATTCGCGTTGCGAAATTGGAA
1 ATTCGCGTTGCAAAATTGGAA
*
782334 ATT-GTGTTGCAAAATTGG-A
1 ATTCGCGTTGCAAAATTGGAA
*
782353 GTTCGCGTTGC
1 ATTCGCGTTGC
782364 GAACTTGATG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 3 0.12
20 19 0.76
21 3 0.12
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (21 bp):
ATTCGCGTTGCAAAATTGGAA
Found at i:782362 original size:100 final size:100
Alignment explanation
Indices: 782167--782371 Score: 270
Period size: 100 Copynumber: 2.0 Consensus size: 100
782157 GCGTTAAGCT
* * * *
782167 TTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGATTTATAGATTCGCGTTGCGAATTTGA
1 TTTGACTTCTATATTGCGATTTACAAATTCGCGTTGCGATTTACAGATTCGCGTTGCGAATTGGA
* * * *
782232 CTATCGCGTTGCGAATTTGATTATCACGTTGCGAA
66 CAATCGCGTTGCAAATTGGAGTATCACGTTGCGAA
782267 TTTGACTTCTATATTGCGATTTACAAATTCGCGTTGCGATTTACAGATTCGCGTTGCGAAATTGG
1 TTTGACTTCTATATTGCGATTTACAAATTCGCGTTGCGATTTACAGATTCGCGTTGCG-AATTGG
* * *
782332 A-AATTGTGTTGCAAAATTGGAGT-TCGCGTTGCGAA
65 ACAATCGCGTTGC-AAATTGGAGTATCACGTTGCGAA
*
782367 CTTGA
1 TTTGA
782372 TGGTCATTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
100 78 0.86
101 13 0.14
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (100 bp):
TTTGACTTCTATATTGCGATTTACAAATTCGCGTTGCGATTTACAGATTCGCGTTGCGAATTGGA
CAATCGCGTTGCAAATTGGAGTATCACGTTGCGAA
Found at i:786746 original size:12 final size:13
Alignment explanation
Indices: 786729--786757 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
786719 CTTAGGAGCG
786729 AAAATTAAAA-TT
1 AAAATTAAAATTT
786741 AAAATTAAAATTT
1 AAAATTAAAATTT
786754 AAAA
1 AAAA
786758 AACGATTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:786898 original size:21 final size:19
Alignment explanation
Indices: 786858--786942 Score: 57
Period size: 21 Copynumber: 4.2 Consensus size: 19
786848 AAGGGAAGAA
* *
786858 AAAATCAAAAA-AATAAAT
1 AAAATGAAAAAGAAAAAAT
786876 AAAATGAAAATAGATAAAAAT
1 AAAATGAAAA-AGA-AAAAAT
*
786897 -AAATCGAAGAAGAAAAAAGAT
1 AAAAT-GAAAAAG-AAAAA-AT
*
786918 AAAATAAAAAAAGAATAAAAT
1 AAAAT-GAAAAAGAA-AAAAT
786939 AAAA
1 AAAA
786943 AAATATTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
18 9 0.17
19 1 0.02
20 11 0.21
21 20 0.38
22 12 0.23
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.14
Consensus pattern (19 bp):
AAAATGAAAAAGAAAAAAT
Found at i:786911 original size:27 final size:25
Alignment explanation
Indices: 786866--786943 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 25
786856 AAAAAATCAA
*
786866 AAAAATAAATAAAATGAAAATAGAT
1 AAAAATAAATAAAATGAAAAAAGAT
786891 AAAAATAAATCGAAGAA-GAAAAAAGAT
1 AAAAATAAAT--AA-AATGAAAAAAGAT
*
786918 -AAAATAAA-AAAA-GAATAAA-AT
1 AAAAATAAATAAAATGAAAAAAGAT
786939 AAAAA
1 AAAAA
786944 AATATTAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
21 2 0.04
22 12 0.26
23 2 0.04
25 10 0.21
26 8 0.17
27 11 0.23
28 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.09, T:0.14
Consensus pattern (25 bp):
AAAAATAAATAAAATGAAAAAAGAT
Found at i:786953 original size:16 final size:16
Alignment explanation
Indices: 786909--786945 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
786899 ATCGAAGAAG
786909 AAAAAAG-ATAAAATA
1 AAAAAAGAATAAAATA
786924 AAAAAAGAATAAAATA
1 AAAAAAGAATAAAATA
786940 AAAAAA
1 AAAAAA
786946 TATTAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (16 bp):
AAAAAAGAATAAAATA
Found at i:787100 original size:15 final size:14
Alignment explanation
Indices: 787080--787134 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
787070 TAAAAGCAAT
787080 GAAATAAAACAATAA
1 GAAATAAAA-AATAA
787095 GAAATAAAAAATAA
1 GAAATAAAAAATAA
* *
787109 TAATTTTAAAAAAT-A
1 GAA--ATAAAAAATAA
787124 -AAATAAAAAAT
1 GAAATAAAAAAT
787135 TAGAGGATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
12 8 0.23
14 9 0.26
15 10 0.29
16 8 0.23
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.22
Consensus pattern (14 bp):
GAAATAAAAAATAA
Found at i:787121 original size:79 final size:80
Alignment explanation
Indices: 786960--787130 Score: 294
Period size: 80 Copynumber: 2.1 Consensus size: 80
786950 AAAAAATATT
*
786960 AAATAAATTAAAGGTAAAAAAGTTAAATTTTAAAAGCAATGAAATAAAAACAATAAGAAATAAAA
1 AAATAAAATAAAGGTAAAAAAGTTAAATTTTAAAAGCAATGAAATAAAAACAATAAGAAATAAAA
787025 GAAATAATAATTTAA
66 GAAATAATAATTTAA
787040 AAATAAAATAAAGGTAAAAAAGTTAAATTTTAAAAGCAATGAAAT-AAAACAATAAGAAAT-AAA
1 AAATAAAATAAAGGTAAAAAAGTTAAATTTTAAAAGCAATGAAATAAAAACAATAAGAAATAAAA
787103 -AAATAATAATTTTAAA
66 GAAATAATAA-TTT-AA
787119 AAATAAAATAAA
1 AAATAAAATAAA
787131 AAATTAGAGG
Statistics
Matches: 88, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
77 9 0.10
78 6 0.07
79 29 0.33
80 44 0.50
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (80 bp):
AAATAAAATAAAGGTAAAAAAGTTAAATTTTAAAAGCAATGAAATAAAAACAATAAGAAATAAAA
GAAATAATAATTTAA
Found at i:787470 original size:15 final size:13
Alignment explanation
Indices: 787444--787474 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
787434 TCTCTCTAAC
787444 CCTCTCTTTCTCT
1 CCTCTCTTTCTCT
787457 CCTCTCTTTCTCT
1 CCTCTCTTTCTCT
787470 -CTCTC
1 CCTCTC
787475 ATCCGCCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (13 bp):
CCTCTCTTTCTCT
Found at i:787955 original size:18 final size:18
Alignment explanation
Indices: 787932--787966 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
787922 CGGTGCTCAC
*
787932 TGTTCCCGCTATTATCGT
1 TGTTCCCGCTATCATCGT
787950 TGTTCCCGCTATCATCG
1 TGTTCCCGCTATCATCG
787967 GGCCGTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.31, G:0.17, T:0.40
Consensus pattern (18 bp):
TGTTCCCGCTATCATCGT
Found at i:788275 original size:34 final size:33
Alignment explanation
Indices: 788237--788381 Score: 121
Period size: 36 Copynumber: 4.2 Consensus size: 33
788227 AATAATATAT
788237 TATATAT-AAAAATATTTCCAAAAACTATATAATATA
1 TATATATAAAAAATATTT-C-AAAACTATAT-AT-TA
* * **
788273 TATTTATTCAAAAATATTTTTAAACTATATATTA
1 TATATA-TAAAAAATATTTCAAAACTATATATTA
*
788307 TATATTTAAAAAATATTTTCAAAACTATATATTA
1 TATATATAAAAAATA-TTTCAAAACTATATATTA
* * *
788341 TATAGTTTTCAAAAAATGTTTTAAAACTATATATTA
1 TATA--TAT-AAAAAATATTTCAAAACTATATATTA
*
788377 GATAT
1 TATAT
788382 GTTTTCAAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
33 8 0.09
34 27 0.29
35 2 0.02
36 37 0.40
37 8 0.09
38 10 0.11
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.43
Consensus pattern (33 bp):
TATATATAAAAAATATTTCAAAACTATATATTA
Found at i:788318 original size:70 final size:69
Alignment explanation
Indices: 788231--788381 Score: 202
Period size: 70 Copynumber: 2.2 Consensus size: 69
788221 TAATATAATA
*
788231 ATATATTATATA-T-AAAAATATTTCCAAAAACTATATAATATATATTTATTCAAAAATAT-TTT
1 ATATATTATATATTAAAAAATATTTCC-AAAACTATATAATATATAGTT-TTCAAAAA-ATGTTT
788293 T-AAACT
63 TAAAACT
* *
788299 ATATATTATATATTTAAAAAATATTTTCAAAACTATATATTATATAGTTTTCAAAAAATGTTTTA
1 ATATATTATATA-TTAAAAAATATTTCCAAAACTATATAATATATAGTTTTCAAAAAATGTTTTA
788364 AAACT
65 AAACT
*
788369 ATATATTAGATAT
1 ATATATTATATAT
788382 GTTTTCAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
68 14 0.19
69 13 0.18
70 36 0.49
71 11 0.15
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (69 bp):
ATATATTATATATTAAAAAATATTTCCAAAACTATATAATATATAGTTTTCAAAAAATGTTTTAA
AACT
Found at i:788374 original size:38 final size:36
Alignment explanation
Indices: 788257--788599 Score: 220
Period size: 36 Copynumber: 9.8 Consensus size: 36
788247 AATATTTCCA
* *
788257 AAAACTATATAATATATATTTATTCAAAAATAT-TTTT
1 AAAACTATATATTATATAGTT-TTCAAAAA-ATGTTTT
*
788294 -AAACTATATATTATATA--TTT-AAAAAATATTTT
1 AAAACTATATATTATATAGTTTTCAAAAAATGTTTT
788326 CAAAACTATATATTATATAGTTTTCAAAAAATGTTTT
1 -AAAACTATATATTATATAGTTTTCAAAAAATGTTTT
*
788363 AAAACTATATATTAGATATGTTTTCAAAAAATGTTTTT
1 AAAACTATATATTATATA-GTTTTCAAAAAATG-TTTT
* *
788401 AAAACTATATATTATAAAATTTTCAAAATAA---TTT
1 AAAACTATATATTATATAGTTTTCAAAA-AATGTTTT
*
788435 ----C---ATATTATA-AGTTTT--TAAAATGTTTT
1 AAAACTATATATTATATAGTTTTCAAAAAATGTTTT
*
788461 CAAAAACTAAATATTATATATATA-TTTTC--AAAATGTTTC
1 --AAAACT--ATA-TAT-TATATAGTTTTCAAAAAATGTTTT
*
788500 AAAA--ACTATATTATATATTTTTC--AAAATGTTTT
1 AAAACTA-TATATTATATAGTTTTCAAAAAATGTTTT
* * *
788533 AAAAAACCATATATTATATATATTTTC--AAAACGTTTT
1 --AAAACTATATATTATATA-GTTTTCAAAAAATGTTTT
788570 GAAAACTATATATTATATA-TATTTCAAAAA
1 -AAAACTATATATTATATAGT-TTTCAAAAA
788600 CAAGAAAAAA
Statistics
Matches: 255, Mismatches: 14, Indels: 74
0.74 0.04 0.22
Matches are distributed among these distances:
23 2 0.01
24 2 0.01
26 8 0.03
27 8 0.03
30 1 0.00
31 2 0.01
32 16 0.06
33 20 0.08
34 24 0.09
35 8 0.03
36 64 0.25
37 57 0.22
38 25 0.10
39 17 0.07
40 1 0.00
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (36 bp):
AAAACTATATATTATATAGTTTTCAAAAAATGTTTT
Found at i:788476 original size:100 final size:98
Alignment explanation
Indices: 788335--788527 Score: 223
Period size: 98 Copynumber: 1.9 Consensus size: 98
788325 TCAAAACTAT
* *
788335 ATATTATATAGTTTTCAAAAAATGTTTTAAAACTATATA-T-TAGATATGTTTTCAAAAAATGTT
1 ATATTATATAGTTTT-AAAAAATGTTTTAAAACTAAATATTATAGATATATTTTC--AAAATGTT
**
788398 TTTAAAACTATATATTATAAAATTTTCAAAATAATTTC
63 TCAAAAAC--TATATTATAAAATTTTCAAAATAATTTC
* *
788436 ATATTATA-AGTTTT-TAAAATGTTTTCAAAAACTAAATATTATATATATATTTTCAAAATGTTT
1 ATATTATATAGTTTTAAAAAATGTTTT--AAAACTAAATATTATAGATATATTTTCAAAATGTTT
* *
788499 CAAAAACTATATTATATATTTTTCAAAAT
64 CAAAAACTATATTATAAAATTTTCAAAAT
788528 GTTTTAAAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
98 30 0.38
100 30 0.38
101 9 0.11
102 11 0.14
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (98 bp):
ATATTATATAGTTTTAAAAAATGTTTTAAAACTAAATATTATAGATATATTTTCAAAATGTTTCA
AAAACTATATTATAAAATTTTCAAAATAATTTC
Found at i:788515 original size:36 final size:36
Alignment explanation
Indices: 788446--788598 Score: 181
Period size: 34 Copynumber: 4.2 Consensus size: 36
788436 ATATTATAAG
*
788446 TTTTTAAAATGTTTTCAAAAACTAAATATTATATATATA
1 TTTTCAAAATGTTTTCAAAAACT--ATA-TATATATATA
788485 TTTTCAAAATG-TTTCAAAAACTATAT-TATATAT-
1 TTTTCAAAATGTTTTCAAAAACTATATATATATATA
* *
788518 TTTTCAAAATGTTTTAAAAAACCATATATTATATATA
1 TTTTCAAAATGTTTTCAAAAACTATATA-TATATATA
* *
788555 TTTTCAAAACGTTTT-GAAAACTATATAT-TATATA
1 TTTTCAAAATGTTTTCAAAAACTATATATATATATA
788589 TATTTCAAAA
1 T-TTTCAAAA
788599 ACAAGAAAAA
Statistics
Matches: 103, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
33 11 0.11
34 27 0.26
35 10 0.10
36 20 0.19
37 14 0.14
38 11 0.11
39 10 0.10
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (36 bp):
TTTTCAAAATGTTTTCAAAAACTATATATATATATA
Found at i:788608 original size:70 final size:68
Alignment explanation
Indices: 788477--788608 Score: 149
Period size: 70 Copynumber: 1.9 Consensus size: 68
788467 CTAAATATTA
* * ***
788477 TATATATATTTTCAAAATGTTTCAAAAACTATATTATATATTTTTCAAAATGTTTTAAAAAACCA
1 TATATATATTTTCAAAACGTTTCAAAAACTATATTATATATATTTCAAAA--TACAAAAAAACCA
788542 TATAT
64 TATAT
**
788547 TATATATATTTTCAAAACGTTTTGAAAACTATATATTATATATATTTCAAAA-ACAAGAAAAA
1 TATATATATTTTCAAAACGTTTCAAAAAC--TATATTATATATATTTCAAAATACAA-AAAAA
788609 AAATGAAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
69 1 0.02
70 31 0.60
72 20 0.38
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (68 bp):
TATATATATTTTCAAAACGTTTCAAAAACTATATTATATATATTTCAAAATACAAAAAAACCATA
TAT
Found at i:797845 original size:18 final size:18
Alignment explanation
Indices: 797822--797888 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
797812 ACAGTAATAG
*
797822 GTAAAGAAATGATAGGTT
1 GTAAAGAAATGATAGGCT
*
797840 GTAAAGAAAGGATAGGCT
1 GTAAAGAAATGATAGGCT
*
797858 GTAAAGAAATATTGGTAGGCT
1 GTAAAG-AA-A-TGATAGGCT
797879 GTAAAGAAAT
1 GTAAAGAAAT
797889 ATTGGTTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
18 23 0.55
19 3 0.07
20 3 0.07
21 13 0.31
ACGTcount: A:0.45, C:0.03, G:0.28, T:0.24
Consensus pattern (18 bp):
GTAAAGAAATGATAGGCT
Found at i:797878 original size:21 final size:21
Alignment explanation
Indices: 797852--797894 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
797842 AAAGAAAGGA
797852 TAGGCTGTAAAGAAATATTGG
1 TAGGCTGTAAAGAAATATTGG
797873 TAGGCTGTAAAGAAATATTGG
1 TAGGCTGTAAAGAAATATTGG
797894 T
1 T
797895 TTGAACATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.28, T:0.30
Consensus pattern (21 bp):
TAGGCTGTAAAGAAATATTGG
Found at i:803493 original size:32 final size:32
Alignment explanation
Indices: 803455--803515 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
803445 ACAATTATAG
* *
803455 AAAATTTTCAATGATATATCACTTCATTTTAT
1 AAAATTTTCAATGAGATATAACTTCATTTTAT
* *
803487 AAAATTTTCAGTGAGATATAACTTTATTT
1 AAAATTTTCAATGAGATATAACTTCATTT
803516 CAACAACATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (32 bp):
AAAATTTTCAATGAGATATAACTTCATTTTAT
Found at i:815753 original size:23 final size:23
Alignment explanation
Indices: 815726--815784 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
815716 CACGCAATGT
815726 TCTCTCCAGTCTCACGGTAAAAC
1 TCTCTCCAGTCTCACGGTAAAAC
*
815749 TCTCTCCAATCTCACGGTAAAAC
1 TCTCTCCAGTCTCACGGTAAAAC
815772 TCTCTCCAGTCTC
1 TCTCTCCAGTCTC
815785 TCAACTCCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.24, C:0.37, G:0.10, T:0.29
Consensus pattern (23 bp):
TCTCTCCAGTCTCACGGTAAAAC
Found at i:820836 original size:15 final size:16
Alignment explanation
Indices: 820818--820847 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
820808 AAATAAATAT
820818 AAATAAAA-ATATACG
1 AAATAAAACATATACG
820833 AAATAAAACATATAC
1 AAATAAAACATATAC
820848 AACAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.20
Consensus pattern (16 bp):
AAATAAAACATATACG
Found at i:823037 original size:134 final size:134
Alignment explanation
Indices: 822689--823046 Score: 477
Period size: 134 Copynumber: 2.7 Consensus size: 134
822679 GTTTGGGTCG
* * * * *
822689 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAAATCTGGTCAGGAGATGACACTGCTCATATGT
1 TCTAAGGGTGACACGACTCCTACGTGATGAAGAGATCTGGTCAGGGGATGACACTGCTCATACGT
* * * **
822754 GATGAAGAGTTCTGGCCATCTTTAGGAATGGTGATAACTTGGTTCCTACGCGATGAGGACGATTG
66 GATGAAGAGTTCTGGTCATCTTTAGAAAGGGTGATAACACGGTTCCTACGCGATGAGGACGATTG
822819 ATTA
131 ATTA
* *
822823 TCTATGGGTGACACGACTCCTACGTGATGAAGAGATCTGGTCAGGGGATGACACGGCTCATACGT
1 TCTAAGGGTGACACGACTCCTACGTGATGAAGAGATCTGGTCAGGGGATGACACTGCTCATACGT
* *
822888 GATGAAGAGTTCTGGTCATTTTTAGAAAGGGTGATAACACGGTTCCTACGTGATGAGGACG-TCT
66 GATGAAGAGTTCTGGTCATCTTTAGAAAGGGTGATAACACGGTTCCTACGCGATGAGGACGAT-T
*
822952 GGTTA
130 GATTA
* * * * * *
822957 TCTAGGGGTAACACGACTCCTATGCGATGAAGAGATCTGGTCAGGGGATGACACTTCTCCTACGT
1 TCTAAGGGTGACACGACTCCTACGTGATGAAGAGATCTGGTCAGGGGATGACACTGCTCATACGT
* *
823022 GATGAGGACG-GCTGGTCATCTTTAG
66 GATGAAGA-GTTCTGGTCATCTTTAG
823047 TGATTGTGGT
Statistics
Matches: 197, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
133 1 0.01
134 195 0.99
135 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (134 bp):
TCTAAGGGTGACACGACTCCTACGTGATGAAGAGATCTGGTCAGGGGATGACACTGCTCATACGT
GATGAAGAGTTCTGGTCATCTTTAGAAAGGGTGATAACACGGTTCCTACGCGATGAGGACGATTG
ATTA
Found at i:823677 original size:31 final size:30
Alignment explanation
Indices: 823613--823677 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
823603 ACAAAATTCG
* *
823613 TTTCAAGGGAAACGACTCAAAGATAGTTTTA
1 TTTCAAGAGAAACAACTCAAAGATA-TTTTA
823644 TTTCAAGAGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGAGAAAC-AACTCAAAGATATTT-TA
823675 TTT
1 TTT
823678 TTATAGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 3 0.10
31 17 0.57
32 10 0.33
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (30 bp):
TTTCAAGAGAAACAACTCAAAGATATTTTA
Found at i:823981 original size:120 final size:120
Alignment explanation
Indices: 823763--823983 Score: 270
Period size: 120 Copynumber: 1.8 Consensus size: 120
823753 ACTGTCTCGA
*
823763 GAGACAAAAGTTTGTTTCAAAGGAAATAAACTCAAAGATTTTTTCTCAAAAGAAATTGTCATTAA
1 GAGACAAAAGTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAATTGTCATTAA
* * *
823828 GATATAAAATTTTGTTTCAAAATAAACAAACTCAAAGATGGATTACATCTTAAGT
66 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATGGATTACATCTTAAGT
* * * **
823883 GAGACGAAA-TTTGTTTCAAAGGAAACAATCTCAAAGGTTGGTTTT-TCATTAGAAATTGTC-TT
1 GAGACAAAAGTTTGTTTCAAAGGAAACAAACTCAAAGATT--TTTTCTCAAAAGAAATTGTCATT
* * *
823945 GAAAGAGACAAAA-TTTGTTTTAAAAGAAATAGACTCAAA
64 --AAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAA
823984 TATGATTTTG
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
119 29 0.34
120 43 0.51
121 13 0.15
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.31
Consensus pattern (120 bp):
GAGACAAAAGTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAATTGTCATTAA
GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATGGATTACATCTTAAGT
Found at i:824207 original size:66 final size:65
Alignment explanation
Indices: 824130--824252 Score: 176
Period size: 66 Copynumber: 1.9 Consensus size: 65
824120 TAAGAGAAAT
* * *
824130 TGTCTCAAAAGAGACAAACCTTTGTTTTCATAA-AAACAGACTTAAAGATTTTTCTTCAAAAGGA
1 TGTCTCAAAAGAGACAAAACTTTGTTTCCA-AAGAAACAGACTCAAAGATTTTT-TTCAAAAGGA
824194 AC
64 AC
* *
824196 TGTCTCAAAAGAGACAAAATTTTGTTTCCAAAGAAACATACTCAAAGATTTTTTTCA
1 TGTCTCAAAAGAGACAAAACTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTCA
824253 TTTTGCTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
65 6 0.12
66 45 0.88
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (65 bp):
TGTCTCAAAAGAGACAAAACTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTCAAAAGGAAC
Found at i:824369 original size:30 final size:31
Alignment explanation
Indices: 824315--824373 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
824305 GAGAGACAGT
824315 TTTGTTTCAAAAGAAATAGACTCAAAGATCA
1 TTTGTTTCAAAAGAAATAGACTCAAAGATCA
824346 TTTGTTTCAAAAGAAAT-GACTCAAAGAT
1 TTTGTTTCAAAAGAAATAGACTCAAAGAT
824374 GATGTTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAATAGACTCAAAGATCA
Found at i:824452 original size:37 final size:37
Alignment explanation
Indices: 824411--824515 Score: 140
Period size: 36 Copynumber: 2.9 Consensus size: 37
824401 ATAATTTGTA
* **
824411 AAATTGTCTCAAGTGAGACAACCTTTGTTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAAAATTTGTTTTTTAGAG
* * *
824448 AAATTGTCTCAAACGACACAAAAATTG-TTTTTAGAG
1 AAATTGTCTCAAGCGAGACAAAATTTGTTTTTTAGAG
*
824484 AAATTGTCTCAAGCGAGACAATATTTGTTTTT
1 AAATTGTCTCAAGCGAGACAAAATTTGTTTTT
824516 GAGAAAACGA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 32 0.56
37 25 0.44
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (37 bp):
AAATTGTCTCAAGCGAGACAAAATTTGTTTTTTAGAG
Found at i:824822 original size:103 final size:102
Alignment explanation
Indices: 824488--824825 Score: 352
Period size: 104 Copynumber: 3.3 Consensus size: 102
824478 TTAGAGAAAT
* * * *
824488 TGTCTCAAGCGAGAC-AATATTTGTTTT-TGAGAAA-ACGATCTTAAGTGAGATCCACTTTGTTT
1 TGTCTCAAACGAGACGAA-ATTTGTTTTAAGA-AAATACGATCTCAAGTGAGATCAACTTTGTTT
* *
824550 AATATGAAAACAAATTTGAAATTTGTATTCTCAAAGGAAAAA
64 AATGTG-AAACAAA-TTCAAATTTGTA-TCTCAAAGGAAAAA
* *
824592 TGTCTCAAACGAGACGAAATTTGTTTTGAA-AAGAATAAC-AGTCTCAAGTGAGATTAATTTTTG
1 TGTCTCAAACGAGACGAAATTTGTTTT-AAGAA-AAT-ACGA-TCTCAAGTGAGATCAA-CTTTG
*
824655 TTTCAA-GTGAATCAAATTCGAAATTTGTA--T-AAAGGAAAAAA
61 TTT-AATGTGAAACAAATTC-AAATTTGTATCTCAAAGG-AAAAA
* * * *
824696 TGTCTCAAGCAAGACGAAGTTTGTTTTAAGAAAATACGATCTCAAATGAGATCAACTTTGTTTAA
1 TGTCTCAAACGAGACGAAATTTGTTTTAAGAAAATACGATCTCAAGTGAGATCAACTTTGTTTAA
*
824761 TGTGAAACAAATTCAAATTTTCTATCTCAAAGGAAAAA
66 TGTGAAACAAATTCAAA-TTTGTATCTCAAAGGAAAAA
*
824799 TGTCTCAAATGAGACGAAATTTGTTTT
1 TGTCTCAAACGAGACGAAATTTGTTTT
824826 GAAAGAAATT
Statistics
Matches: 195, Mismatches: 21, Indels: 37
0.77 0.08 0.15
Matches are distributed among these distances:
100 5 0.03
101 24 0.12
102 16 0.08
103 40 0.21
104 61 0.31
105 5 0.03
106 3 0.02
107 30 0.15
108 9 0.05
109 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (102 bp):
TGTCTCAAACGAGACGAAATTTGTTTTAAGAAAATACGATCTCAAGTGAGATCAACTTTGTTTAA
TGTGAAACAAATTCAAATTTGTATCTCAAAGGAAAAA
Found at i:827102 original size:20 final size:20
Alignment explanation
Indices: 827079--827119 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
827069 GGATAAATGC
827079 AATGTTTAAAGGTCACAAAG
1 AATGTTTAAAGGTCACAAAG
* *
827099 AATGTTTCAAGGTCTCAAAG
1 AATGTTTAAAGGTCACAAAG
827119 A
1 A
827120 GAGGGAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (20 bp):
AATGTTTAAAGGTCACAAAG
Found at i:827802 original size:20 final size:20
Alignment explanation
Indices: 827779--827817 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
827769 CTTAAAAATA
*
827779 AAATGCAGATACAAAAATGC
1 AAATGCAAATACAAAAATGC
*
827799 AAATGCAAATGCAAAAATG
1 AAATGCAAATACAAAAATG
827818 TTGATCCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.13, G:0.15, T:0.15
Consensus pattern (20 bp):
AAATGCAAATACAAAAATGC
Found at i:830264 original size:15 final size:16
Alignment explanation
Indices: 830246--830275 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
830236 AAATAAATAT
830246 AAATAAAA-ATATACG
1 AAATAAAACATATACG
830261 AAATAAAACATATAC
1 AAATAAAACATATAC
830276 AACAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.20
Consensus pattern (16 bp):
AAATAAAACATATACG
Found at i:831951 original size:14 final size:14
Alignment explanation
Indices: 831934--831994 Score: 70
Period size: 14 Copynumber: 4.2 Consensus size: 14
831924 AATGTAATAT
*
831934 TAATAATAATATAA
1 TAATATTAATATAA
831948 TAATATTAATGA-AA
1 TAATATTAAT-ATAA
831962 TAATATTAATATAA
1 TAATATTAATATAA
*
831976 TAATTATTATTACTAA
1 TAA-TATTAATA-TAA
831992 TAA
1 TAA
831995 AAAAAGACCC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
13 1 0.02
14 26 0.63
15 8 0.20
16 6 0.15
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (14 bp):
TAATATTAATATAA
Found at i:832140 original size:39 final size:39
Alignment explanation
Indices: 832070--832162 Score: 125
Period size: 39 Copynumber: 2.4 Consensus size: 39
832060 TTCCCATTCA
* *
832070 CAGCTAAGCATTTCAATGTAAATAGTGATATTCATAA-CC
1 CAGCTAAACATTTCAATATAAATAGTGATATTCA-AATCC
* * *
832109 CAGTTAAACATTTCAATATAAGTAGTTATATTCAAATCC
1 CAGCTAAACATTTCAATATAAATAGTGATATTCAAATCC
832148 CAGCTAAACATTTCA
1 CAGCTAAACATTTCA
832163 GTAACATTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 2 0.04
39 45 0.96
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (39 bp):
CAGCTAAACATTTCAATATAAATAGTGATATTCAAATCC
Found at i:832422 original size:25 final size:25
Alignment explanation
Indices: 832394--832444 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
832384 AAATAAATTA
832394 AATAAGATTAAAGAATACCTGATTT
1 AATAAGATTAAAGAATACCTGATTT
*
832419 AATAAGATTAAAGAATACCTGGTTT
1 AATAAGATTAAAGAATACCTGATTT
832444 A
1 A
832445 GGGACTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (25 bp):
AATAAGATTAAAGAATACCTGATTT
Found at i:862481 original size:3 final size:3
Alignment explanation
Indices: 862473--862504 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
862463 CAAGAACTTT
862473 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
862505 GATGGCAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:875007 original size:43 final size:42
Alignment explanation
Indices: 874937--875027 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 42
874927 TTTACCCTAA
**
874937 ACCCGACCCGACCCGAACAGTGTATTTTTTAAAAAAAAACCCG
1 ACCCGACCCGACCCGAACAGTAAATTTTTT-AAAAAAAACCCG
* * *
874980 ACCCGACCCGACCCGAACCCG-AAATTTTTTTAAAAAAATCCG
1 ACCCGACCCGACCCGAA-CAGTAAATTTTTTAAAAAAAACCCG
875022 ACCCGA
1 ACCCGA
875028 TCGGGTCGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 16 0.38
43 24 0.57
44 2 0.05
ACGTcount: A:0.36, C:0.33, G:0.13, T:0.18
Consensus pattern (42 bp):
ACCCGACCCGACCCGAACAGTAAATTTTTTAAAAAAAACCCG
Found at i:875523 original size:169 final size:167
Alignment explanation
Indices: 875161--875557 Score: 733
Period size: 167 Copynumber: 2.4 Consensus size: 167
875151 TCGAGGGAGT
875161 TCTGTTTCCTATCATTTTAATTTGAATTCAACATAAAACAAATTAATTCTCAATTATAGGTTAAG
1 TCTGTTTCCTATCATTTTAATTTGAATTCAACATAAAACAAATTAATTCTCAATTATAGGTTAAG
*
875226 GTTTAGGTTTAGATATTTTATAAATTCTATACATATTTTTAATTAATTATTTTTTTATTTTACTC
66 GTTTAGGTTTAGATATTTTATAAATTCTATACATATTTTTAATTAATTATTTTTTTACTTTACTC
875291 AAGTTGTTTACACAATTTAATTAATCATGAAATTAGA
131 AAGTTGTTTACACAATTTAATTAATCATGAAATTAGA
*
875328 TCTGTTTCCTATCATTTTAATTTGAATTCAACATAAAACAAATTAATTATCAATTATAGGTTAAG
1 TCTGTTTCCTATCATTTTAATTTGAATTCAACATAAAACAAATTAATTCTCAATTATAGGTTAAG
875393 GTTTAGGTTTAGATATTTTATATAAATTCTATACATATTTTTAATTAATTATTTTTTTTACTTTA
66 GTTTAGGTTTAGATA-TTT-TATAAATTCTATACATATTTTTAATTAATTA-TTTTTTTACTTTA
875458 CTCAAGTTGTTTACACAATTTAATTAATCATGAAATTAGA
128 CTCAAGTTGTTTACACAATTTAATTAATCATGAAATTAGA
*
875498 TCTGTTTCCTATCA-TTTAATTTGAATTCAACATAAAACAAATTAATTCTCAATTGTAGGT
1 TCTGTTTCCTATCATTTTAATTTGAATTCAACATAAAACAAATTAATTCTCAATTATAGGT
875558 GGTGGATAAG
Statistics
Matches: 223, Mismatches: 4, Indels: 4
0.97 0.02 0.02
Matches are distributed among these distances:
167 79 0.35
168 3 0.01
169 75 0.34
170 66 0.30
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (167 bp):
TCTGTTTCCTATCATTTTAATTTGAATTCAACATAAAACAAATTAATTCTCAATTATAGGTTAAG
GTTTAGGTTTAGATATTTTATAAATTCTATACATATTTTTAATTAATTATTTTTTTACTTTACTC
AAGTTGTTTACACAATTTAATTAATCATGAAATTAGA
Found at i:878157 original size:22 final size:22
Alignment explanation
Indices: 878131--878190 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
878121 CAACTTATCT
*
878131 ATTAGATTTAAATAAAT-AATT
1 ATTAGATTTAAATAAATAAATG
878152 ATTTAGATTTAAATAAATAAATG
1 A-TTAGATTTAAATAAATAAATG
*
878175 ATTATATTTAAATAAA
1 ATTAGATTTAAATAAA
878191 CTTTATAACC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 1 0.03
22 30 0.86
23 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (22 bp):
ATTAGATTTAAATAAATAAATG
Found at i:880902 original size:27 final size:26
Alignment explanation
Indices: 880842--880903 Score: 63
Period size: 27 Copynumber: 2.2 Consensus size: 26
880832 CCAAGCCTTT
*
880842 TACTTTACTCTTTCCTATTTTGCTCAC
1 TACTTTACTC-TTCCTATTTTACTCAC
880869 TAAACTTTACTC-TCCTATTTTACTCATC
1 T--ACTTTACTCTTCCTATTTTACTCA-C
880897 GTACTTT
1 -TACTTT
880904 CAATTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
27 19 0.63
28 1 0.03
29 10 0.33
ACGTcount: A:0.19, C:0.27, G:0.03, T:0.50
Consensus pattern (26 bp):
TACTTTACTCTTCCTATTTTACTCAC
Found at i:888000 original size:111 final size:110
Alignment explanation
Indices: 887804--888039 Score: 357
Period size: 111 Copynumber: 2.1 Consensus size: 110
887794 GATACTTATA
* *
887804 ATAAAGTATCGACACTATCAACATATCTGGTAGTGCTTTACCTGTTTTGTCATTTATAAACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGGT
* * *
887869 TTGTCATTTGTTTACCTGTTATATTGTTATTGATCGATACAGTTTT
66 TTGTCATTTGTTTACATGTTATATTGTTATAGATCAATACA-TTTT
* * * *
887915 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGG-
*
887980 TTTGTCATTT-TTTACATGTTATATTGTTATAGATCAATATATTTT
65 TTTGTCATTTGTTTACATGTTATATTGTTATAGATCAATACATTTT
888025 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
888040 AAACCGACAA
Statistics
Matches: 114, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
110 19 0.17
111 85 0.75
112 10 0.09
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (110 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGGT
TTGTCATTTGTTTACATGTTATATTGTTATAGATCAATACATTTT
Found at i:889247 original size:30 final size:32
Alignment explanation
Indices: 889211--889269 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
889201 AAAACCTGAC
889211 CCGACCCGA-CC-CAATTTTTTTTAAAAAAAT
1 CCGACCCGATCCTCAATTTTTTTTAAAAAAAT
* *
889241 CCGACCCGATCCTGAATTTTTTTTTAAAA
1 CCGACCCGATCCTCAATTTTTTTTAAAAA
889270 TACACGACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.36
31 2 0.08
32 14 0.56
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.34
Consensus pattern (32 bp):
CCGACCCGATCCTCAATTTTTTTTAAAAAAAT
Found at i:889337 original size:100 final size:100
Alignment explanation
Indices: 889180--889372 Score: 214
Period size: 100 Copynumber: 1.9 Consensus size: 100
889170 ACCCGAACAC
* ** ** *
889180 GACCCGAATATCACACTTTAAAAAACCTGACCCGACCCGACCCAATTTTTTTTAAAAA-AATCCG
1 GACCCGAATATCACACTTTAAAAAACCTGACCCGACCCGAACCAA-TACTTAAAAAAATAACCCG
*
889244 ACCCGATCCT-GAATTTTTTTTTAAAATACACGACCA
65 ACCCGA-CCTCGAATTATTTTTTAAAATACACGACCA
* *
889280 GACCCGAATATCACACTTTAAAAAAACC-GACCCGACCCGAATATCAA-ACTTAAAAAAATTCGA
1 GACCCGAATATCACACTTT-AAAAAACCTGACCCGACCCG-A-ACCAATACTTAAAAAAA-T-AA
889343 CCCGACCCGACCTCGAATTATTTTTTAAAA
61 CCCGACCCGACCTCGAATTATTTTTTAAAA
889373 AATCCGACCC
Statistics
Matches: 77, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
100 37 0.48
101 9 0.12
102 6 0.08
103 25 0.32
ACGTcount: A:0.38, C:0.28, G:0.09, T:0.24
Consensus pattern (100 bp):
GACCCGAATATCACACTTTAAAAAACCTGACCCGACCCGAACCAATACTTAAAAAAATAACCCGA
CCCGACCTCGAATTATTTTTTAAAATACACGACCA
Found at i:889354 original size:38 final size:33
Alignment explanation
Indices: 889274--889352 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
889264 TTAAAATACA
* * *
889274 CGACCAGACCCGAATATCACACTTTAAAAAAAC
1 CGACCCGACCCGAATATCAAACTTAAAAAAAAC
**
889307 CGACCCGACCCGAATATCAAACTTAAAAAAATT
1 CGACCCGACCCGAATATCAAACTTAAAAAAAAC
889340 CGACCCGACCCGA
1 CGACCCGACCCGA
889353 CCTCGAATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.33, G:0.11, T:0.14
Consensus pattern (33 bp):
CGACCCGACCCGAATATCAAACTTAAAAAAAAC
Found at i:890319 original size:23 final size:23
Alignment explanation
Indices: 890293--890340 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
890283 ATAAAGTACA
*
890293 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
890316 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
890339 AT
1 AT
890341 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:890742 original size:21 final size:22
Alignment explanation
Indices: 890717--890768 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
890707 ACACTTTACA
*
890717 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
890740 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
890763 ATATAA
1 ATATAA
890769 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:890753 original size:23 final size:23
Alignment explanation
Indices: 890727--890789 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
890717 ATATAACCAC
890727 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
890750 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
890773 TACCTATTACATCATAT
1 TACCTATTACATTATAT
890790 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:891241 original size:39 final size:39
Alignment explanation
Indices: 891183--891271 Score: 142
Period size: 39 Copynumber: 2.3 Consensus size: 39
891173 ACTCAAGTTG
*
891183 TAGATTTTGATTTCCTTTTGCTTGGCATCATATGAGATT
1 TAGATTTTGATTTCCTTTTGCTTGGCACCATATGAGATT
* * *
891222 TGGATTTTGATTTCTTTTTGCTTGGCACCATATGAGCTT
1 TAGATTTTGATTTCCTTTTGCTTGGCACCATATGAGATT
891261 TAGATTTTGAT
1 TAGATTTTGAT
891272 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.49
Consensus pattern (39 bp):
TAGATTTTGATTTCCTTTTGCTTGGCACCATATGAGATT
Found at i:891553 original size:18 final size:18
Alignment explanation
Indices: 891530--891566 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
891520 CGAAATATAT
891530 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
891548 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
891566 A
1 A
891567 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:891911 original size:25 final size:25
Alignment explanation
Indices: 891861--891911 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
891851 TTTTTCCAAA
* *
891861 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATATTCAAT
*
891886 TAATGTACCCACAACAATATTTAAT
1 TAATGTACCCACAACAATATTCAAT
891911 T
1 T
891912 GATTTGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATATTCAAT
Found at i:892203 original size:21 final size:22
Alignment explanation
Indices: 892178--892229 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
892168 ACACTTTACA
*
892178 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
892201 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
892224 ATATAA
1 ATATAA
892230 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:892214 original size:23 final size:23
Alignment explanation
Indices: 892188--892250 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
892178 ATATAACCAC
892188 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
892211 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
892234 TACCTATTACATCATAT
1 TACCTATTACATTATAT
892251 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:892589 original size:25 final size:25
Alignment explanation
Indices: 892532--892597 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
892522 CACTCAAAAG
*
892532 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
892557 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
892582 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
892598 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:894910 original size:91 final size:90
Alignment explanation
Indices: 894755--894936 Score: 355
Period size: 91 Copynumber: 2.0 Consensus size: 90
894745 AAAGTCGATA
894755 CTTTTATGTCAGGTGTCGATACTTTCGAAAGGATAATTACCTATTTCTTTGAAAGTGTCGATAAT
1 CTTTTATGTCAGGTGTCGATACTTTCGAAAGGATAATTACCTATTTCTTTGAAAGTGTCGATAAT
894820 TTATTACACGTACTTACGAAAAGTAT
66 TTATTACACGTACTTACG-AAAGTAT
894846 CTTTTATGTCAGGTGTCGATACTTTCGAAAGGATAATTACCTATTTCTTTGAAAGTGTCGATAAT
1 CTTTTATGTCAGGTGTCGATACTTTCGAAAGGATAATTACCTATTTCTTTGAAAGTGTCGATAAT
894911 TTATTACACGTACTTACGAAAGTAT
66 TTATTACACGTACTTACGAAAGTAT
894936 C
1 C
894937 GACACTTTCA
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
90 8 0.09
91 83 0.91
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.38
Consensus pattern (90 bp):
CTTTTATGTCAGGTGTCGATACTTTCGAAAGGATAATTACCTATTTCTTTGAAAGTGTCGATAAT
TTATTACACGTACTTACGAAAGTAT
Found at i:895004 original size:19 final size:19
Alignment explanation
Indices: 894961--895005 Score: 83
Period size: 18 Copynumber: 2.4 Consensus size: 19
894951 ATCCGGTATC
894961 ATTTTACCGGTTTTATCAT
1 ATTTTACCGGTTTTATCAT
894980 -TTTTACCGGTTTTATCAT
1 ATTTTACCGGTTTTATCAT
894998 ATTTTACC
1 ATTTTACC
895006 TGTATATCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.20, C:0.18, G:0.09, T:0.53
Consensus pattern (19 bp):
ATTTTACCGGTTTTATCAT
Found at i:895151 original size:20 final size:20
Alignment explanation
Indices: 895125--895170 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
895115 CACTTTTAAA
895125 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
895144 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
895165 TTTACC
1 TTTACC
895171 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:895632 original size:226 final size:224
Alignment explanation
Indices: 895234--895676 Score: 739
Period size: 226 Copynumber: 2.0 Consensus size: 224
895224 TTAAAACTGC
895234 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTCATGTTTTCCACCTACAATAT
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTCATGTTTTCCACCTACAATAT
**
895299 TAATTTAATAATTTAATTTACACAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTATTT
66 TAATTTAATAATTTAATTTACACAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTT
*
895364 AGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATAT-GTTTCAACAGTGAAATAAGT
131 AGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATAGTTTC-ACAGTGAAATAAGT
*
895428 ATGGACACTTTTATAAAAATGATATATACTT
195 ATGGACAC-TTTATAAAAAGGATATATACTT
*
895459 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTG-TTCATGTTTTCCACCTACAAT
*
895524 ATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAA-A-TA
64 ATTAATTTAATAATTTAATTTACAC-AAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
* * *
895587 TTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAATAA
128 TTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATAGTTTCACAGTGAAATAA
895652 GTATGGACACTTTATAAAAAGGATA
193 GTATGGACACTTTATAAAAAGGATA
895677 GATAATTTAC
Statistics
Matches: 205, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
225 18 0.09
226 105 0.51
227 50 0.24
228 32 0.16
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (224 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTCATGTTTTCCACCTACAATAT
TAATTTAATAATTTAATTTACACAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTT
AGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATAGTTTCACAGTGAAATAAGTA
TGGACACTTTATAAAAAGGATATATACTT
Done.