Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008893.1 Hibiscus syriacus cultivar Beakdansim tig00112159_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: 2797279
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 13
Found at i:763176 original size:15 final size:15
Alignment explanation
Indices: 763156--763200 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
763146 AAAACTTTAA
763156 AAATAAATAGATTAT
1 AAATAAATAGATTAT
* *
763171 AAATAATTAAATTA-
1 AAATAAATAGATTAT
*
763185 CAATAAATAGATTAT
1 AAATAAATAGATTAT
763200 A
1 A
763201 TTTATAATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (15 bp):
AAATAAATAGATTAT
Found at i:765307 original size:3 final size:3
Alignment explanation
Indices: 765299--765351 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
765289 ATAAAAGATA
765299 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
765347 AAT AA
1 AAT AA
765352 CATGTTATTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:769022 original size:18 final size:18
Alignment explanation
Indices: 768999--769049 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
768989 ATCTTCCAAG
768999 AAGATAGAGTTCTCTAAA
1 AAGATAGAGTTCTCTAAA
* **
769017 AAGATAAAGTTCTCTACG
1 AAGATAGAGTTCTCTAAA
*
769035 AAGATAGAATTCTCT
1 AAGATAGAGTTCTCT
769050 TGAGTCGATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (18 bp):
AAGATAGAGTTCTCTAAA
Found at i:769431 original size:5 final size:4
Alignment explanation
Indices: 769415--769612 Score: 75
Period size: 3 Copynumber: 53.0 Consensus size: 4
769405 GTCCGGGATA
769415 ATAT ATAT -TAT AGTAT ATAGT ATAT ATAT -TAT AT-T ATAT AGTAT ATGAT
1 ATAT ATAT ATAT A-TAT ATA-T ATAT ATAT ATAT ATAT ATAT A-TAT AT-AT
*
769464 -TAT ATAT ATAT -TAT AGCAT -TAT AT-T ATAT AT-T ATAT -TAGT -TAT
1 ATAT ATAT ATAT ATAT A-TAT ATAT ATAT ATAT ATAT ATAT ATA-T ATAT
* * * *
769507 -TTT ATAT AT-T ATAGT ATAT GTAT TTAT AT-T TTAT ATAT -TAT AGTAT
1 ATAT ATAT ATAT ATA-T ATAT ATAT ATAT ATAT ATAT ATAT ATAT A-TAT
*
769553 ATAT -TAT AT-T AGTAT ATGT AT-T AT-T AT-T ATA- ATAT A-AT AT-T
1 ATAT ATAT ATAT A-TAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
769594 AT-T ACAT CATAT AT-T ATAT
1 ATAT ATAT -ATAT ATAT ATAT
769613 TATTATAGAT
Statistics
Matches: 153, Mismatches: 12, Indels: 58
0.69 0.05 0.26
Matches are distributed among these distances:
3 63 0.41
4 61 0.40
5 29 0.19
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.53
Consensus pattern (4 bp):
ATAT
Found at i:769433 original size:7 final size:7
Alignment explanation
Indices: 769423--769573 Score: 65
Period size: 7 Copynumber: 22.1 Consensus size: 7
769413 TAATATATAT
769423 TATAGTA
1 TATAGTA
769430 TATAGTA
1 TATAGTA
769437 TATA-TA
1 TATAGTA
*
769443 TTATATTA
1 -TATAGTA
769451 TATAGTA
1 TATAGTA
769458 TAT-G-A
1 TATAGTA
769463 T-TA-TA
1 TATAGTA
769468 TATA-TA
1 TATAGTA
*
769474 TTATAGCA
1 -TATAGTA
*
769482 TTATATTA
1 -TATAGTA
*
769490 TATATTA
1 TATAGTA
769497 TATTAGT-
1 TA-TAGTA
**
769504 TATTTTA
1 TATAGTA
769511 TATA-T-
1 TATAGTA
769516 TATAGTA
1 TATAGTA
769523 TAT-GTA
1 TATAGTA
* *
769529 TTTATATTT
1 --TATAGTA
769538 TATA-TA
1 TATAGTA
769544 TTATAGTA
1 -TATAGTA
*
769552 TATATTA
1 TATAGTA
769559 TATTAGTA
1 TA-TAGTA
769567 TAT-GTA
1 TATAGTA
769573 T
1 T
769574 TATTATTATA
Statistics
Matches: 114, Mismatches: 13, Indels: 35
0.70 0.08 0.22
Matches are distributed among these distances:
4 1 0.01
5 8 0.07
6 19 0.17
7 62 0.54
8 23 0.20
9 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (7 bp):
TATAGTA
Found at i:769433 original size:12 final size:12
Alignment explanation
Indices: 769416--769595 Score: 94
Period size: 12 Copynumber: 14.8 Consensus size: 12
769406 TCCGGGATAA
769416 TATATATTATAG
1 TATATATTATAG
769428 TATATAGTATATA-
1 TATATA-T-TATAG
769441 TATTATATTATATAG
1 TA-TATA-T-TATAG
769456 TATATGATTATA-
1 TATAT-ATTATAG
769468 TATATATTATAG
1 TATATATTATAG
*
769480 CATTATATTATA-
1 TA-TATATTATAG
769492 TAT-TA-TATTAG
1 TATATATTA-TAG
*
769503 T-TATTTTATA-
1 TATATATTATAG
*
769513 TATTATAGTATATG
1 TA-TATATTATA-G
* **
769527 TATTTA-TATTT
1 TATATATTATAG
769538 TATATATTATAG
1 TATATATTATAG
*
769550 TATATATTATAT
1 TATATATTATAG
769562 TAGTATATGTAT--
1 TA-TATAT-TATAG
*
769574 TAT-TATTATAA
1 TATATATTATAG
769585 TATAATATTAT
1 TAT-ATATTAT
769596 TACATCATAT
Statistics
Matches: 133, Mismatches: 13, Indels: 43
0.70 0.07 0.23
Matches are distributed among these distances:
9 5 0.04
10 9 0.07
11 20 0.15
12 43 0.32
13 30 0.23
14 23 0.17
15 3 0.02
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (12 bp):
TATATATTATAG
Found at i:769613 original size:5 final size:5
Alignment explanation
Indices: 769418--769615 Score: 93
Period size: 5 Copynumber: 36.6 Consensus size: 5
769408 CGGGATAATA
*
769418 TATAT TATAG TATA- TAGTAT ATATAT TATAT TATA- TAGTA- TATGAT
1 TATAT TATAT TATAT TA-TAT -TATAT TATAT TATAT TA-TAT TAT-AT
*
769464 TATAT ATATAT TATAGCAT TATATT ATATAT TATAT TAGTTAT TTTA- TATAT
1 TATAT -TATAT TAT---AT TATA-T -TATAT TATAT TA--TAT TATAT TATAT
* *
769516 TATAG TATAT GTAT-T TATAT TTTA- TATAT TATAGT ATATAT TATAT
1 TATAT TATAT -TATAT TATAT TATAT TATAT TATA-T -TATAT TATAT
* * * *
769562 TAGTAT ATGTAT TATTAT TATAA TATAA TATTAT TACAT CATATAT TATAT
1 TA-TAT -TATAT TA-TAT TATAT TATAT TA-TAT TATAT --TATAT TATAT
769613 TAT
1 TAT
769616 TATAGATGAA
Statistics
Matches: 154, Mismatches: 13, Indels: 52
0.70 0.06 0.24
Matches are distributed among these distances:
4 14 0.09
5 83 0.54
6 33 0.21
7 19 0.12
8 5 0.03
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.54
Consensus pattern (5 bp):
TATAT
Found at i:771921 original size:20 final size:20
Alignment explanation
Indices: 771896--771977 Score: 128
Period size: 20 Copynumber: 4.1 Consensus size: 20
771886 TTGTTGATCG
771896 TTGACTTTTGATAGTTGACT
1 TTGACTTTTGATAGTTGACT
*
771916 TTGACTTTTGATAGATGACT
1 TTGACTTTTGATAGTTGACT
* *
771936 TTGACTTTTGATGGTTGATT
1 TTGACTTTTGATAGTTGACT
*
771956 TTGACTTTTTATAGTTGACT
1 TTGACTTTTGATAGTTGACT
771976 TT
1 TT
771978 TTAAGACATC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.52
Consensus pattern (20 bp):
TTGACTTTTGATAGTTGACT
Found at i:771975 original size:40 final size:40
Alignment explanation
Indices: 771877--771977 Score: 134
Period size: 40 Copynumber: 2.5 Consensus size: 40
771867 TCGTTGATCA
*
771877 TTGACTTTTT-T-GTTGATCGTTGACTTTTGATAGTTGACT
1 TTGACTTTTTATAGTTGA-CTTTGACTTTTGATAGTTGACT
* * * *
771916 TTGACTTTTGATAGATGACTTTGACTTTTGATGGTTGATT
1 TTGACTTTTTATAGTTGACTTTGACTTTTGATAGTTGACT
771956 TTGACTTTTTATAGTTGACTTT
1 TTGACTTTTTATAGTTGACTTT
771978 TTAAGACATC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 9 0.17
40 40 0.75
41 4 0.08
ACGTcount: A:0.18, C:0.09, G:0.20, T:0.53
Consensus pattern (40 bp):
TTGACTTTTTATAGTTGACTTTGACTTTTGATAGTTGACT
Found at i:772995 original size:24 final size:24
Alignment explanation
Indices: 772968--773015 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
772958 TAATATGGAA
*
772968 TACAATTAACCCTAACTATATATC
1 TACAATTAACCCTAACCATATATC
*
772992 TACAATTAGCCCTAACCATATATC
1 TACAATTAACCCTAACCATATATC
773016 AAGTGGAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.27, G:0.02, T:0.31
Consensus pattern (24 bp):
TACAATTAACCCTAACCATATATC
Found at i:774933 original size:25 final size:25
Alignment explanation
Indices: 774905--774958 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
774895 ATCATCTTCA
* *
774905 ATCTATTACATAAAACACTTCTTTC
1 ATCTATTACACAAAACACTCCTTTC
* *
774930 ATCTCTTACACAACACACTCCTTTC
1 ATCTATTACACAAAACACTCCTTTC
774955 ATCT
1 ATCT
774959 TCAATCTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (25 bp):
ATCTATTACACAAAACACTCCTTTC
Found at i:774971 original size:32 final size:32
Alignment explanation
Indices: 774930--774990 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
774920 CACTTCTTTC
774930 ATCTCTTACACAACACA-CTCCTTTCATCTTCA
1 ATCTCTTACACAACA-AGCTCCTTTCATCTTCA
774962 ATCTCTTACACAACAAGCTCCTTTCATCT
1 ATCTCTTACACAACAAGCTCCTTTCATCT
774991 AACCAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.28, C:0.36, G:0.02, T:0.34
Consensus pattern (32 bp):
ATCTCTTACACAACAAGCTCCTTTCATCTTCA
Found at i:782573 original size:28 final size:28
Alignment explanation
Indices: 782533--782588 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
782523 AAAGTAGGAA
*
782533 ACCTAGTTTGATTAAAAGTTGAAAACTT
1 ACCTAGTTTGATTAAAAGTAGAAAACTT
782561 ACCTAGTTTGATTAAAAGTAGAAAACTT
1 ACCTAGTTTGATTAAAAGTAGAAAACTT
782589 TATTAAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (28 bp):
ACCTAGTTTGATTAAAAGTAGAAAACTT
Found at i:787335 original size:28 final size:28
Alignment explanation
Indices: 787284--787358 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
787274 TAAAGTAGAG
787284 AGAATATTTTTTAATTTAATTATAATTTT
1 AGAA-ATTTTTTAATTTAATTATAATTTT
*
787313 AGAAATTTTTTAGTTTTAA-TATAATTTT
1 AGAAATTTTTTA-ATTTAATTATAATTTT
787341 A-AAA--TTTTAATTTAATTA
1 AGAAATTTTTTAATTTAATTA
787359 ATATTATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
24 5 0.12
25 7 0.17
27 3 0.07
28 18 0.43
29 9 0.21
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (28 bp):
AGAAATTTTTTAATTTAATTATAATTTT
Found at i:787359 original size:28 final size:29
Alignment explanation
Indices: 787291--787370 Score: 82
Period size: 28 Copynumber: 2.9 Consensus size: 29
787281 GAGAGAATAT
787291 TTTTTAATTTAA-T--TATAATTTTAGAAA
1 TTTTTAATTTAATTAATATAATTTTA-AAA
* *
787318 TTTTTTAGTT--TTAATATAATTTTAAAA
1 TTTTTAATTTAATTAATATAATTTTAAAA
*
787345 -TTTTAATTTAATTAATATTATTTTAA
1 TTTTTAATTTAATTAATATAATTTTAA
787371 TCATATATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
26 8 0.19
27 11 0.26
28 24 0.56
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (29 bp):
TTTTTAATTTAATTAATATAATTTTAAAA
Found at i:789027 original size:3 final size:3
Alignment explanation
Indices: 789019--789054 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
789009 TTAATTTCAC
789019 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
789055 CCTTTAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:796255 original size:14 final size:14
Alignment explanation
Indices: 796233--796262 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
796223 ATATAATAAT
*
796233 AAAATAACGGAAAA
1 AAAAAAACGGAAAA
796247 AAAAAAACGGAAAA
1 AAAAAAACGGAAAA
796261 AA
1 AA
796263 CGTCTACAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.07, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAAACGGAAAA
Found at i:796603 original size:87 final size:88
Alignment explanation
Indices: 796425--796769 Score: 426
Period size: 87 Copynumber: 4.0 Consensus size: 88
796415 CGTCTAAGGG
* * * * * * *
796425 TGACATGGCTCCTACGTGATGAAGAGATCTGGTCATCTTTAGGGAGGATAACTCGGTT-CTA---
1 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTTAAAGG-TGATAACACGGTTCCTACGT
*
796486 -ATGAGGACGACTGGTTATCAGGT
65 GATGAGGACGGCTGGTTATCAGGT
796509 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATC-TAAAGGTGATAACACGGGTTCCTA-GT
1 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTTAAAGGTGATAACAC-GGTTCCTACGT
796572 GATGAGGACGGCTGGTTATCAGGT
65 GATGAGGACGGCTGGTTATCAGGT
796596 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATC-TAAAGGTGATAACACGGTTCCTACGTG
1 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTTAAAGGTGATAACACGGTTCCTACGTG
796660 ATGAGGACGGCTGGTTATCTATGGT
66 ATGAGGACGGCTGGTTATC-A-GGT
* * *
796685 TGACACGGCTCATACATGATGAAGA-ACTCTGGCCATCGTTAGGAAGGGTGATAACTCGG-TCCT
1 TGACACGGCTCTTACGTGATGAAGAGA-TCTGGCCATC-TTA--AA-GGTGATAACACGGTTCCT
796748 ACGTGATGAGGACGG--GGTTATC
61 ACGTGATGAGGACGGCTGGTTATC
796770 CTAATGTTGA
Statistics
Matches: 236, Mismatches: 11, Indels: 21
0.88 0.04 0.08
Matches are distributed among these distances:
82 7 0.03
83 8 0.03
84 37 0.16
86 8 0.03
87 96 0.41
88 2 0.01
89 36 0.15
91 9 0.04
93 21 0.09
94 12 0.05
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (88 bp):
TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTTAAAGGTGATAACACGGTTCCTACGTG
ATGAGGACGGCTGGTTATCAGGT
Found at i:796680 original size:46 final size:46
Alignment explanation
Indices: 796543--796680 Score: 146
Period size: 46 Copynumber: 3.1 Consensus size: 46
796533 AGATCTGGCC
796543 ATCTAAAGGTGATAACACGGGTTCCTA-GTGATGAGGACGGCTGGTT
1 ATCTAAAGGTGATAACAC-GGTTCCTACGTGATGAGGACGGCTGGTT
* * * * * **
796589 ATC---AGGT--TGACACGGCTCTTACGTGATGAAGA-GATCTGGCC
1 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTT
796630 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
1 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
796676 ATCTA
1 ATCTA
796681 TGGTTGACAC
Statistics
Matches: 70, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
40 7 0.10
41 21 0.30
43 4 0.06
44 4 0.06
46 33 0.47
47 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (46 bp):
ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
Found at i:806071 original size:21 final size:21
Alignment explanation
Indices: 806045--806084 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
806035 TCTCCAGATG
806045 TAAAGGTATCTTATCATTTGT
1 TAAAGGTATCTTATCATTTGT
806066 TAAAGGTATCTTATCATTT
1 TAAAGGTATCTTATCATTT
806085 ACCCTCCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.47
Consensus pattern (21 bp):
TAAAGGTATCTTATCATTTGT
Found at i:806184 original size:39 final size:40
Alignment explanation
Indices: 806141--806221 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
806131 CCGCTCCAAC
806141 TTTAG-CCTAAAAGTCATCCTCCAAGAATCAGCCACATCT
1 TTTAGTCCTAAAAGTCATCCTCCAAGAATCAGCCACATCT
806180 TTTAGTCCTAAAAGTCATCCTCCAAGAATCAGCCACATCT
1 TTTAGTCCTAAAAGTCATCCTCCAAGAATCAGCCACATCT
806220 TT
1 TT
806222 GATTTTCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 5 0.12
40 36 0.88
ACGTcount: A:0.32, C:0.30, G:0.10, T:0.28
Consensus pattern (40 bp):
TTTAGTCCTAAAAGTCATCCTCCAAGAATCAGCCACATCT
Found at i:808539 original size:21 final size:20
Alignment explanation
Indices: 808515--808557 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
808505 AACAAGTAAT
808515 ATTGATAGTATAAAAAACA-AA
1 ATTGAT-GT-TAAAAAACATAA
*
808536 ATTGATGTTAAGAAACATAA
1 ATTGATGTTAAAAAACATAA
808556 AT
1 AT
808558 AGACTAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 6 0.30
21 6 0.30
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.28
Consensus pattern (20 bp):
ATTGATGTTAAAAAACATAA
Found at i:812662 original size:42 final size:42
Alignment explanation
Indices: 812589--813076 Score: 320
Period size: 42 Copynumber: 11.9 Consensus size: 42
812579 AAGACGACCT
** *
812589 TTAGCGGCGTTT-TTTA-AAAATGCCACTAAAGTACATGTAA
1 TTAGCGGCGTTTGTGCATAAAACGCCACTAAAGTACATGTAA
* *
812629 TTAGCGGCGTTTGTGCATAAAATGCCA-TAAAAGTACGTGTAA
1 TTAGCGGCGTTTGTGCATAAAACGCCACT-AAAGTACATGTAA
* * **
812671 TTAGTGGCGTTTGTGCTTGCAACGCCACTAAAGTAC--G-ACCA
1 TTAGCGGCGTTTGTGCATAAAACGCCACTAAAGTACATGTA--A
* * *
812712 TTAGCGGCGTTTGT--ATAAAAACACCACTAAAGTATA-GTAT
1 TTAGCGGCGTTTGTGCAT-AAAACGCCACTAAAGTACATGTAA
** * * * * * **
812752 TTCTCAGCGTTTAT--ATAAAAATGCAACTAGAGTATGTGTAA
1 TTAGCGGCGTTTGTGCAT-AAAACGCCACTAAAGTACATGTAA
* *
812793 TTAGCGGCGTTTGTGTATAAAACGCCACTAAAGAACATGTAA
1 TTAGCGGCGTTTGTGCATAAAACGCCACTAAAGTACATGTAA
* * **
812835 TTAGCGGCGTTTTTGCTTAAAACGCCACTAAAGTACGACCT--
1 TTAGCGGCGTTTGTGCATAAAACGCCACTAAAGTAC-ATGTAA
* *
812876 TTAGCGGCGTTTGT--ATAAAAACGCC-CATTAAGTACA-GTAT
1 TTAGCGGCGTTTGTGCAT-AAAACGCCAC-TAAAGTACATGTAA
* * * * * *
812916 TTATCAGCGTTTAT--ATAAAAACGCCACTATAGTGCGTGTAA
1 TTAGCGGCGTTTGTGCAT-AAAACGCCACTAAAGTACATGTAA
* * *
812957 TTAGCGGCGTTTGTGCATAAAATGCCACTAAAATACGTGTAA
1 TTAGCGGCGTTTGTGCATAAAACGCCACTAAAGTACATGTAA
* * **
812999 TGAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACGACCT--
1 TTAGCGGCGTTTGTGCATAAAACGCCACTAAAGTAC-ATGTAA
* *
813040 TTAACGGCGTTTGT--ATAAAAATGCCACTAAAGTACAT
1 TTAGCGGCGTTTGTGCAT-AAAACGCCACTAAAGTACAT
813077 TATTTTCTGG
Statistics
Matches: 353, Mismatches: 72, Indels: 47
0.75 0.15 0.10
Matches are distributed among these distances:
38 1 0.00
39 7 0.02
40 113 0.32
41 71 0.20
42 153 0.43
43 8 0.02
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (42 bp):
TTAGCGGCGTTTGTGCATAAAACGCCACTAAAGTACATGTAA
Found at i:812874 original size:164 final size:164
Alignment explanation
Indices: 812595--813081 Score: 694
Period size: 164 Copynumber: 3.0 Consensus size: 164
812585 ACCTTTAGCG
* *
812595 GCGTTT-TTTAAAAATGCCACTAAAGTACATGTAATTAGCGGCGTTTGTGCATAAAATGCCA-TA
1 GCGTTTATATAAAAATGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCATAAAATGCCACT-
* * ** *
812658 AAAGTACGTGTAATTAGTGGCGTTTGTGCTTGCAACGCCACTAAAGTACGACCATTAGCGGCGTT
65 AAAGAACGTGTAATTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACGACCTTTAGCGGCGTT
* * *
812723 TGTATAAAAACACCACTAAAGTATAGTATTTCTCA
130 TGTATAAAAACGCCACTAAAGTACAGTATTTATCA
* * * * *
812758 GCGTTTATATAAAAATGCAACTAGAGTATGTGTAATTAGCGGCGTTTGTGTATAAAACGCCACTA
1 GCGTTTATATAAAAATGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCATAAAATGCCACTA
* *
812823 AAGAACATGTAATTAGCGGCGTTTTTGCTTAAAACGCCACTAAAGTACGACCTTTAGCGGCGTTT
66 AAGAACGTGTAATTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACGACCTTTAGCGGCGTTT
*
812888 GTATAAAAACGCC-CATTAAGTACAGTATTTATCA
131 GTATAAAAACGCCAC-TAAAGTACAGTATTTATCA
* * *
812922 GCGTTTATATAAAAACGCCACTATAGTGCGTGTAATTAGCGGCGTTTGTGCATAAAATGCCACTA
1 GCGTTTATATAAAAATGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCATAAAATGCCACTA
* *
812987 AA-ATACGTGTAATGAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACGACCTTTAACGGCGTT
66 AAGA-ACGTGTAATTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACGACCTTTAGCGGCGTT
* *
813051 TGTATAAAAATGCCACTAAAGTACATTATTT
130 TGTATAAAAACGCCACTAAAGTACAGTATTT
813082 TCTGGCGTTT
Statistics
Matches: 287, Mismatches: 32, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
163 8 0.03
164 277 0.97
165 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (164 bp):
GCGTTTATATAAAAATGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCATAAAATGCCACTA
AAGAACGTGTAATTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACGACCTTTAGCGGCGTTT
GTATAAAAACGCCACTAAAGTACAGTATTTATCA
Found at i:813369 original size:20 final size:20
Alignment explanation
Indices: 813344--813415 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
813334 CTTTACACAG
813344 TAGTATCGATACCATGAGCA
1 TAGTATCGATACCATGAGCA
*
813364 TAGTATCGATACCATGAACA
1 TAGTATCGATACCATGAGCA
813384 TAGTATCGATACCATGAGCA
1 TAGTATCGATACCATGAGCA
*
813404 TAGTATCAATAC
1 TAGTATCGATAC
813416 TGGTCAAGCC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (20 bp):
TAGTATCGATACCATGAGCA
Found at i:813497 original size:21 final size:21
Alignment explanation
Indices: 813463--813544 Score: 128
Period size: 21 Copynumber: 3.9 Consensus size: 21
813453 AAATATTATG
813463 AAGGTAGTACCGATACTCATTA
1 AAGG-AGTACCGATACTCATTA
*
813485 AAGGAGTATCGATACTCATTA
1 AAGGAGTACCGATACTCATTA
*
813506 AAGGAGTACCGATACTTATTA
1 AAGGAGTACCGATACTCATTA
*
813527 AAGGAGTATCGATACTCA
1 AAGGAGTACCGATACTCA
813545 CTGTCTTGGG
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
21 51 0.93
22 4 0.07
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (21 bp):
AAGGAGTACCGATACTCATTA
Found at i:813527 original size:42 final size:43
Alignment explanation
Indices: 813463--813544 Score: 148
Period size: 42 Copynumber: 1.9 Consensus size: 43
813453 AAATATTATG
813463 AAGGTAGTACCGATACTCATTAAAGGAGTATCGATACTCATTA
1 AAGGTAGTACCGATACTCATTAAAGGAGTATCGATACTCATTA
*
813506 AAGG-AGTACCGATACTTATTAAAGGAGTATCGATACTCA
1 AAGGTAGTACCGATACTCATTAAAGGAGTATCGATACTCA
813545 CTGTCTTGGG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
42 34 0.89
43 4 0.11
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (43 bp):
AAGGTAGTACCGATACTCATTAAAGGAGTATCGATACTCATTA
Found at i:825294 original size:2 final size:2
Alignment explanation
Indices: 825219--825281 Score: 83
Period size: 2 Copynumber: 30.0 Consensus size: 2
825209 TCTAATCAAG
825219 TA TA TA TA TA TA TA TA TA TA TA TA TA CTCA TA -A TCA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -T-A TA TA T-A -TA TA TA
825262 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
825282 ATTATTGATA
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
1 1 0.02
2 49 0.88
3 4 0.07
4 2 0.04
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:825802 original size:7 final size:7
Alignment explanation
Indices: 825790--825829 Score: 71
Period size: 7 Copynumber: 5.6 Consensus size: 7
825780 TTTAAAATAA
825790 TAAAAAT
1 TAAAAAT
825797 TAAAAAT
1 TAAAAAT
825804 TAAAAAT
1 TAAAAAT
825811 TAAAAAT
1 TAAAAAT
825818 TAAAAAT
1 TAAAAAT
825825 ATAAA
1 -TAAA
825830 TAAATATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 28 0.88
8 4 0.12
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
TAAAAAT
Found at i:826013 original size:2 final size:2
Alignment explanation
Indices: 826006--826043 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
825996 AGGTCTTTAA
826006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
826044 GTGGTTCACG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:826341 original size:19 final size:19
Alignment explanation
Indices: 826275--826341 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
826265 CAAGTTATTA
826275 TATATATTAAATTATCTTT
1 TATATATTAAATTATCTTT
* *
826294 TATCAT-TTATATTTAAT-TTA
1 TAT-ATATTA-AATT-ATCTTT
* *
826314 TACATATTAGATTATCTTT
1 TATATATTAAATTATCTTT
826333 TATATATTA
1 TATATATTA
826342 TATTGATTGT
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
18 2 0.06
19 20 0.56
20 12 0.33
21 2 0.06
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (19 bp):
TATATATTAAATTATCTTT
Found at i:826396 original size:26 final size:25
Alignment explanation
Indices: 826359--826410 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
826349 TGTCTATTTT
*
826359 TATTTTTTAAAATTTTATAAGATCA
1 TATTTTTTAAAATATTATAAGATCA
*
826384 TATTTTCTTAAAATATTATAAGTTCA
1 TATTTT-TTAAAATATTATAAGATCA
826410 T
1 T
826411 CCTCAACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (25 bp):
TATTTTTTAAAATATTATAAGATCA
Found at i:831490 original size:19 final size:19
Alignment explanation
Indices: 831466--831511 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
831456 TTTTGTGTAC
831466 CGATGCACAAGCCATGAAT
1 CGATGCACAAGCCATGAAT
*
831485 CGATGCACAAGCCATGCAT
1 CGATGCACAAGCCATGAAT
831504 CGATGCAC
1 CGATGCAC
831512 TCTTGAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.33, C:0.30, G:0.22, T:0.15
Consensus pattern (19 bp):
CGATGCACAAGCCATGAAT
Found at i:831620 original size:65 final size:65
Alignment explanation
Indices: 831485--831622 Score: 152
Period size: 65 Copynumber: 2.1 Consensus size: 65
831475 AGCCATGAAT
* * * * * **
831485 CGATGCACAAGCCATGCATCGATGCACTCTTGAATATTTTGAAACATCGAATACATTTTGTGTAC
1 CGATGCACAAACCATGCATAGATGCACTCCTGAATATTTTGAAACATCGAATACAATTAGTAAAC
* ** *
831550 CGATGCACAAACTATGCATAGATGCACTCCTGGCT-TGTTTGAAACATCGAATGCAATTAGTAAA
1 CGATGCACAAACCATGCATAGATGCACTCCTGAATAT-TTTGAAACATCGAATACAATTAGTAAA
831614 C
65 C
*
831615 TGATGCAC
1 CGATGCAC
831623 CCCTAGTGTA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
64 1 0.02
65 59 0.98
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (65 bp):
CGATGCACAAACCATGCATAGATGCACTCCTGAATATTTTGAAACATCGAATACAATTAGTAAAC
Found at i:832614 original size:21 final size:21
Alignment explanation
Indices: 832566--832615 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
832556 GTTTCCAGAT
*
832566 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
832587 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
832608 TCGCAATG
1 TCGCAATG
832616 TCAAATTACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:842183 original size:154 final size:154
Alignment explanation
Indices: 842005--842313 Score: 618
Period size: 154 Copynumber: 2.0 Consensus size: 154
841995 GATTAGGGTT
842005 TAGAATTTAAGATTGTGGTAAAAAGAGATTTTTTTATTGCGAGTTAAAATATATTTATTTGTGAG
1 TAGAATTTAAGATTGTGGTAAAAAGAGATTTTTTTATTGCGAGTTAAAATATATTTATTTGTGAG
842070 TTATAAATTTCAATTAAATCTAAGTCATTTATTTATTGAAATATAATGGATATAAATTGGTATAA
66 TTATAAATTTCAATTAAATCTAAGTCATTTATTTATTGAAATATAATGGATATAAATTGGTATAA
842135 GACCTATTAATTTTACATAGTGTA
131 GACCTATTAATTTTACATAGTGTA
842159 TAGAATTTAAGATTGTGGTAAAAAGAGATTTTTTTATTGCGAGTTAAAATATATTTATTTGTGAG
1 TAGAATTTAAGATTGTGGTAAAAAGAGATTTTTTTATTGCGAGTTAAAATATATTTATTTGTGAG
842224 TTATAAATTTCAATTAAATCTAAGTCATTTATTTATTGAAATATAATGGATATAAATTGGTATAA
66 TTATAAATTTCAATTAAATCTAAGTCATTTATTTATTGAAATATAATGGATATAAATTGGTATAA
842289 GACCTATTAATTTTACATAGTGTA
131 GACCTATTAATTTTACATAGTGTA
842313 T
1 T
842314 GCATATTCTG
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
154 155 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (154 bp):
TAGAATTTAAGATTGTGGTAAAAAGAGATTTTTTTATTGCGAGTTAAAATATATTTATTTGTGAG
TTATAAATTTCAATTAAATCTAAGTCATTTATTTATTGAAATATAATGGATATAAATTGGTATAA
GACCTATTAATTTTACATAGTGTA
Found at i:848466 original size:35 final size:35
Alignment explanation
Indices: 848427--848495 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
848417 TAGAGGTGAT
**
848427 ACCCCACTTACT-TAGTCACTGTTCTGACTTTTCTA
1 ACCCCACTTA-TGTAGTCACTAATCTGACTTTTCTA
*
848462 ACCCCACTTATGTAGTCACTAATCTGATTTTTCT
1 ACCCCACTTATGTAGTCACTAATCTGACTTTTCT
848496 GTCAACTGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 1 0.03
35 29 0.97
ACGTcount: A:0.22, C:0.29, G:0.09, T:0.41
Consensus pattern (35 bp):
ACCCCACTTATGTAGTCACTAATCTGACTTTTCTA
Found at i:848813 original size:2 final size:2
Alignment explanation
Indices: 848806--848831 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
848796 AACTTTTTAT
848806 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
848832 AAGATGATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:860176 original size:20 final size:20
Alignment explanation
Indices: 860151--860200 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
860141 CTGGGTTTGG
860151 GTATCGATACTGGAAGAACA
1 GTATCGATACTGGAAGAACA
860171 GTATCGATACTGGAAGAACA
1 GTATCGATACTGGAAGAACA
860191 GTATCGATAC
1 GTATCGATAC
860201 CATAAGGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (20 bp):
GTATCGATACTGGAAGAACA
Found at i:862313 original size:23 final size:23
Alignment explanation
Indices: 862286--862355 Score: 113
Period size: 23 Copynumber: 3.0 Consensus size: 23
862276 ATATTTTCAT
862286 TTATGTTCGTTTACATTCGTTTA
1 TTATGTTCGTTTACATTCGTTTA
** *
862309 TTATGTTCGTTTATGTTCATTTA
1 TTATGTTCGTTTACATTCGTTTA
862332 TTATGTTCGTTTACATTCGTTTA
1 TTATGTTCGTTTACATTCGTTTA
862355 T
1 T
862356 GTTTATTTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.17, C:0.11, G:0.13, T:0.59
Consensus pattern (23 bp):
TTATGTTCGTTTACATTCGTTTA
Found at i:862319 original size:13 final size:13
Alignment explanation
Indices: 862301--862344 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
862291 TTCGTTTACA
862301 TTCGTTTATTATG
1 TTCGTTTATTATG
862314 TTCG--T-TTATG
1 TTCGTTTATTATG
*
862324 TTCATTTATTATG
1 TTCGTTTATTATG
862337 TTCGTTTA
1 TTCGTTTA
862345 CATTCGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 8 0.31
11 1 0.04
12 1 0.04
13 16 0.62
ACGTcount: A:0.16, C:0.09, G:0.14, T:0.61
Consensus pattern (13 bp):
TTCGTTTATTATG
Found at i:867687 original size:20 final size:20
Alignment explanation
Indices: 867662--867719 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
867652 TTCTCATACT
867662 TGTTATCAAGATAATACATA
1 TGTTATCAAGATAATACATA
867682 TGTTAT----AT-A-AC-T-
1 TGTTATCAAGATAATACATA
867694 TGTTATCAAGATAATACATA
1 TGTTATCAAGATAATACATA
867714 TGTTAT
1 TGTTAT
867720 ATAACTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 16
0.65 0.00 0.35
Matches are distributed among these distances:
12 6 0.20
13 1 0.03
14 2 0.07
15 1 0.03
16 4 0.13
17 1 0.03
18 2 0.07
19 1 0.03
20 12 0.40
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (20 bp):
TGTTATCAAGATAATACATA
Found at i:867700 original size:32 final size:32
Alignment explanation
Indices: 867659--867729 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
867649 CAATTCTCAT
867659 ACTTGTTATCAAGATAATACATATGTTATATA
1 ACTTGTTATCAAGATAATACATATGTTATATA
867691 ACTTGTTATCAAGATAATACATATGTTATATA
1 ACTTGTTATCAAGATAATACATATGTTATATA
867723 ACTTGTT
1 ACTTGTT
867730 CAGGTTTAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (32 bp):
ACTTGTTATCAAGATAATACATATGTTATATA
Found at i:870228 original size:21 final size:22
Alignment explanation
Indices: 870187--870228 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
870177 CTTATTTAAC
*
870187 TTAAAATTCCAGCATTCAATAA
1 TTAAAATTCCAACATTCAATAA
*
870209 TTAAAATT-CAACATTGAATA
1 TTAAAATTCCAACATTCAATA
870229 CTCCAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (22 bp):
TTAAAATTCCAACATTCAATAA
Found at i:871020 original size:15 final size:15
Alignment explanation
Indices: 871002--871032 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
870992 AATTACCATT
*
871002 TTCCATTGAAATATC
1 TTCCATTAAAATATC
871017 TTCCATTAAAATATC
1 TTCCATTAAAATATC
871032 T
1 T
871033 CATAGTCAAA
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:0.35, C:0.19, G:0.03, T:0.42
Consensus pattern (15 bp):
TTCCATTAAAATATC
Found at i:874449 original size:19 final size:20
Alignment explanation
Indices: 874406--874453 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
874396 TCTAAATCCT
*
874406 TTTTCAAAATTTCATTTTCG
1 TTTTCAAAATCTCATTTTCG
* *
874426 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTCG
874445 TTTTCAAAA
1 TTTTCAAAA
874454 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.15, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTCG
Found at i:876646 original size:21 final size:22
Alignment explanation
Indices: 876616--876656 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
876606 CATAGCCTTG
*
876616 ATTTCATCTTTTAGTTGTTTCT
1 ATTTCATCTTCTAGTTGTTTCT
876638 ATTTC-TCTTCTAGTTGTTT
1 ATTTCATCTTCTAGTTGTTT
876657 GTTCTGTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.12, C:0.15, G:0.10, T:0.63
Consensus pattern (22 bp):
ATTTCATCTTCTAGTTGTTTCT
Found at i:879539 original size:18 final size:16
Alignment explanation
Indices: 879506--879543 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 16
879496 GTACAATGCA
879506 AAAATAAAAACAAAAT
1 AAAATAAAAACAAAAT
879522 AAAATAAAAAGGCAAAAT
1 AAAATAAAAA--CAAAAT
879540 AAAA
1 AAAA
879544 CTAGTCAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.50
18 10 0.50
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (16 bp):
AAAATAAAAACAAAAT
Found at i:882516 original size:12 final size:12
Alignment explanation
Indices: 882499--882527 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
882489 AATGGTTTTA
882499 TTGGGCTAGGGT
1 TTGGGCTAGGGT
882511 TTGGGCTAGGGT
1 TTGGGCTAGGGT
882523 TTGGG
1 TTGGG
882528 TTAGTTAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.52, T:0.34
Consensus pattern (12 bp):
TTGGGCTAGGGT
Found at i:882931 original size:73 final size:74
Alignment explanation
Indices: 882770--882960 Score: 183
Period size: 73 Copynumber: 2.6 Consensus size: 74
882760 TCAATATAAA
* * * * * *
882770 AAAAGTATCGAA-CCTCATAACATATGTATCGATATTTTAACTATCAATCATATTTATCAACTTG
1 AAAAGTATC-AATCATCATCACATAAGTATCGATATTTTAAATTTTAATCATATTTATCAACTTG
882834 TTCAATATCT
65 TTCAATATCT
* * * * *
882844 AAAAGTCTCTATCATCATCACATAAGTATCGATATTTTAAATTTTGATC-TTTTTATCAA-TATT
1 AAAAGTATCAATCATCATCACATAAGTATCGATATTTTAAATTTTAATCATATTTATCAACT-TG
* *
882907 TTCAATTTTT
65 TTCAATATCT
* * **
882917 AAAAGTATCAATCATTACCGTATAAGTATCGATA-TTTAAATTTT
1 AAAAGTATCAATCATCATCACATAAGTATCGATATTTTAAATTTT
882961 TAAACTATTT
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
72 11 0.11
73 47 0.49
74 38 0.40
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.42
Consensus pattern (74 bp):
AAAAGTATCAATCATCATCACATAAGTATCGATATTTTAAATTTTAATCATATTTATCAACTTGT
TCAATATCT
Found at i:883146 original size:78 final size:77
Alignment explanation
Indices: 882985--883212 Score: 269
Period size: 77 Copynumber: 2.9 Consensus size: 77
882975 GTGCAACCTA
* * * *
882985 TTTATTAATAAAAATATTAACATAACATATCGCAACATATTTCTTAGTG-ACCTATGACATTCTT
1 TTTATTAATAAAAATATTAACATTACATATCGCAACCTATTTCTTAGTGAATC-ATAACATTCTT
** * *
883049 GGGCGCAACCTAT
65 GAACGTAACATAT
*
883062 TTTATTAAAAAAAATATTAACATTACATATCGCAACCTACTTTCTTAGTGAATCATAACATTCTT
1 TTTATTAATAAAAATATTAACATTACATATCGCAACCTA-TTTCTTAGTGAATCATAACATTCTT
*
883127 GAACGTAACATGT
65 GAACGTAACATAT
* * ** * * * *
883140 TTTATTAATAAAAATATTAATATTACAGATCATAACCTATTTATTAGTTAATTATAACATTATTG
1 TTTATTAATAAAAATATTAACATTACATATCGCAACCTATTTCTTAGTGAATCATAACATTCTTG
883205 AACGTAAC
66 AACGTAAC
883213 TGTATTTCTT
Statistics
Matches: 130, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
77 66 0.51
78 62 0.48
79 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (77 bp):
TTTATTAATAAAAATATTAACATTACATATCGCAACCTATTTCTTAGTGAATCATAACATTCTTG
AACGTAACATAT
Found at i:883460 original size:78 final size:80
Alignment explanation
Indices: 883324--883470 Score: 183
Period size: 79 Copynumber: 1.9 Consensus size: 80
883314 GCGCAACTCA
* * * * *
883324 TTTTATTATTAAAAAATATTAAAATTTCATATTGCAACATACTTTTTTAATGAACCATGACATTC
1 TTTTATTAATAAAAAATATTAAAATTACAGATCGCAACATACTTTTTTAATGAACCATGACATTA
883389 TTGGACATAACCTTT
66 TTGGACATAACCTTT
* * * *
883404 TTTTATTAAT-AAAAATATTAACATTACAGATCGCAATATA-TTTATTT-GTGAACCATGATATT
1 TTTTATTAATAAAAAATATTAAAATTACAGATCGCAACATACTTT-TTTAATGAACCATGACATT
883466 ATTGG
65 ATTGG
883471 GTGCAACTGT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
78 20 0.35
79 28 0.49
80 9 0.16
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (80 bp):
TTTTATTAATAAAAAATATTAAAATTACAGATCGCAACATACTTTTTTAATGAACCATGACATTA
TTGGACATAACCTTT
Found at i:883576 original size:263 final size:261
Alignment explanation
Indices: 883041--883583 Score: 617
Period size: 263 Copynumber: 2.1 Consensus size: 261
883031 GTGACCTATG
* * *
883041 ACATTCTTGGGCGCAACCTATTTTATTAAAAAAAATATTAACATTACATATCGCAACCTACTTTC
1 ACATT-TTAGGCGCAACCTATTTTATTAAAAAAAATATTAAAATTACATATCGCAACATACTTTC
* * * *
883106 TTAGTGAATCATAACATTCTTGAACGTAACATGTTTTATTAATAAAAATATTAATATTACAGATC
65 TTAATGAACCATAACATTCTTGAACATAACATGTTTTATTAATAAAAATATTAACATTACAGATC
* * * ** *
883171 ATAACCTATTTATTAGTTAATTATAACATTATTGAACGTAACTGTATTTCTTATATATATTAATA
130 ACAACATATTTATTAGTGAACCATAACATTATTGAACGCAACTGTA--TCTTATATATATTAATA
* * *
883236 ACATTTCAGCTTTTAATTTATTCTTTTATCGTGGGAAAATTCAAAGCTCCATCAGCTTAAACTCT
193 ACATTTCAGCTTTTAACTTATTCTTTTATCATGAGAAAATTCAAAGCTCCATCAGCTTAAACTCT
*
883301 GATA
258 AATA
* * *
883305 ACATTTTAGGCGCAA-CTCATTTTATTATTAAAAAATATTAAAATTTCATATTGCAACATACTTT
1 ACATTTTAGGCGCAACCT-ATTTTATTA-AAAAAAATATTAAAATTACATATCGCAACATACTTT
* * * * *
883369 TTTAATGAACCATGACATTCTTGGACATAACCTTTTTTTATTAATAAAAATATTAACATTACAGA
64 CTTAATGAACCATAACATTCTTGAACATAA-CATGTTTTATTAATAAAAATATTAACATTACAGA
* * * * * ***
883434 TCGCAATATATTTATTTGTGAACCATGATATTATTGGGTGCAACTGTA-CTTATATATA-TACAT
128 TCACAACATATTTATTAGTGAACCATAACATTATTGAACGCAACTGTATCTTATATATATTA-AT
* * * *
883497 AACATTTTCAGCTTTTAACTTATTTTTTTATTATGAGAAAATTCAATA-CTCTATCAGCTTTAAC
192 AACA-TTTCAGCTTTTAACTTATTCTTTTATCATGAGAAAATTCAA-AGCTCCATCAGCTTAAAC
*
883561 TTTAATA
255 TCTAATA
* *
883568 ATATTTTAGGCACAAC
1 ACATTTTAGGCGCAAC
883584 AGAAAATATT
Statistics
Matches: 232, Mismatches: 40, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
261 2 0.01
262 18 0.08
263 86 0.37
264 61 0.26
265 65 0.28
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (261 bp):
ACATTTTAGGCGCAACCTATTTTATTAAAAAAAATATTAAAATTACATATCGCAACATACTTTCT
TAATGAACCATAACATTCTTGAACATAACATGTTTTATTAATAAAAATATTAACATTACAGATCA
CAACATATTTATTAGTGAACCATAACATTATTGAACGCAACTGTATCTTATATATATTAATAACA
TTTCAGCTTTTAACTTATTCTTTTATCATGAGAAAATTCAAAGCTCCATCAGCTTAAACTCTAAT
A
Found at i:892454 original size:6 final size:6
Alignment explanation
Indices: 892443--892469 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
892433 ACCTAAAAAC
892443 TAACAA TAACAA TAACAA TAACAA TAA
1 TAACAA TAACAA TAACAA TAACAA TAA
892470 AAAGATCGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.19
Consensus pattern (6 bp):
TAACAA
Found at i:893403 original size:48 final size:48
Alignment explanation
Indices: 893342--893433 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
893332 TCAGGTCGGA
** *
893342 TCATTTCGGGTTTCGATTTTATTCGAGTCTATAGTAAGTCGGGTTGGG
1 TCATTTCAAGTTTCAATTTTATTCGAGTCTATAGTAAGTCGGGTTGGG
* *
893390 TCATTTCAAGTTTCAATTTTATTTGGGTCTATAGTAAGTCGGGT
1 TCATTTCAAGTTTCAATTTTATTCGAGTCTATAGTAAGTCGGGT
893434 CGTTTCGGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.43
Consensus pattern (48 bp):
TCATTTCAAGTTTCAATTTTATTCGAGTCTATAGTAAGTCGGGTTGGG
Found at i:894071 original size:21 final size:22
Alignment explanation
Indices: 894047--894090 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
894037 ATTAAAATAA
*
894047 TTTGTAAA-TTAATTTAATAGT
1 TTTGGAAAGTTAATTTAATAGT
* *
894068 TTTGGAAAGTTATTTTAGTAGT
1 TTTGGAAAGTTAATTTAATAGT
894090 T
1 T
894091 CCAAAGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (22 bp):
TTTGGAAAGTTAATTTAATAGT
Found at i:894364 original size:46 final size:47
Alignment explanation
Indices: 894277--894399 Score: 153
Period size: 47 Copynumber: 2.7 Consensus size: 47
894267 GATAAAGCAT
* * * * *
894277 TACCTAAAACACTA-TTTGTTCTACCGG-AATGTTAATATTGGACGC
1 TACCTAAAATATTATTTTTTTCAACCGGAAATGTTAATATTGGACAC
*
894322 TACCT-AAATATTATTTTTTTCAACCGGAAATGTTAATATTGGATAC
1 TACCTAAAATATTATTTTTTTCAACCGGAAATGTTAATATTGGACAC
* *
894368 TACTTAAAATATTATTTTTTTCTACCGGAAAT
1 TACCTAAAATATTATTTTTTTCAACCGGAAAT
894400 TAGCTAGTGA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
44 6 0.09
45 16 0.24
46 20 0.30
47 25 0.37
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.40
Consensus pattern (47 bp):
TACCTAAAATATTATTTTTTTCAACCGGAAATGTTAATATTGGACAC
Found at i:894395 original size:47 final size:46
Alignment explanation
Indices: 894295--894399 Score: 158
Period size: 47 Copynumber: 2.3 Consensus size: 46
894285 ACACTATTTG
*
894295 TTCTACCGG-AATGTTAATATTGGACGCTACCTAAATATTATTTTT
1 TTCTACCGGAAATGTTAATATTGGACACTACCTAAATATTATTTTT
* * *
894340 TTCAACCGGAAATGTTAATATTGGATACTACTTAAAATATTATTTTT
1 TTCTACCGGAAATGTTAATATTGGACACTACCT-AAATATTATTTTT
894387 TTCTACCGGAAAT
1 TTCTACCGGAAAT
894400 TAGCTAGTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
45 8 0.15
46 20 0.38
47 25 0.47
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.41
Consensus pattern (46 bp):
TTCTACCGGAAATGTTAATATTGGACACTACCTAAATATTATTTTT
Found at i:897402 original size:17 final size:17
Alignment explanation
Indices: 897380--897413 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
897370 TTTGATACAA
897380 ATTTATATTATATATAC
1 ATTTATATTATATATAC
897397 ATTTATATTATATATAC
1 ATTTATATTATATATAC
897414 GTAATACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATATTATATATAC
Found at i:908299 original size:34 final size:34
Alignment explanation
Indices: 908223--908357 Score: 173
Period size: 34 Copynumber: 3.9 Consensus size: 34
908213 GGGTAAGTCA
* *
908223 ATCTTAAGCCTTCACCAAAGAGGAATGAAGCAAACC
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGC--ACC
* **
908259 ATCTTAAGCCTTCATCGGAGAGTAGTGAAGCACC
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCACC
*
908293 ATCTTAAGCCTTCA-CAGAGAAGTAGTGAAGCACC
1 ATCTTAAGCCTTCACCAAAG-AGTAGTGAAGCACC
*
908327 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGC
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGC
908358 GAATCCATCC
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
33 4 0.04
34 56 0.63
35 3 0.03
36 26 0.29
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (34 bp):
ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCACC
Found at i:908349 original size:68 final size:69
Alignment explanation
Indices: 908223--908357 Score: 193
Period size: 68 Copynumber: 2.0 Consensus size: 69
908213 GGGTAAGTCA
* *
908223 ATCTTAAGCCTTCACCAAAGAGGAATGAAGCAAACCATCTTAAGCCTTCATCGGAGAGTAGTGAA
1 ATCTTAAGCCTTCACCAAAGAGGAATGAAGC-AACCATCTTAAGCCTTCACCGAAGAGTAGTGAA
908288 GCACC
65 GCACC
* * *
908293 ATCTTAAGCCTTCA-CAGAGAAGTAGTGAAGC-ACCATCTTAAGCCTTCACCGAAGAGTAGTGAA
1 ATCTTAAGCCTTCACCAAAG-AGGAATGAAGCAACCATCTTAAGCCTTCACCGAAGAGTAGTGAA
908356 GC
65 GC
908358 GAATCCATCC
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
68 32 0.54
69 4 0.07
70 23 0.39
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (69 bp):
ATCTTAAGCCTTCACCAAAGAGGAATGAAGCAACCATCTTAAGCCTTCACCGAAGAGTAGTGAAG
CACC
Found at i:908826 original size:83 final size:83
Alignment explanation
Indices: 908687--908923 Score: 393
Period size: 83 Copynumber: 2.9 Consensus size: 83
908677 TTCACAATTT
* *
908687 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATATGTCGGGTCATCTGTA
1 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTA
*
908752 AGCCTTTAGAGCAAGATG
66 AGCCTTTAGAGAAAGATG
* *
908770 ATAAGCCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCTTTCGGGTCATCTGTA
1 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTA
908835 AGCCTTTAGAGAAAGATG
66 AGCCTTTAGAGAAAGATG
* * * *
908853 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAATAAATCCTTCGGGTAATTTGTA
1 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTA
908918 AGCCTT
66 AGCCTT
908924 CACCAAAGAT
Statistics
Matches: 143, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 143 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (83 bp):
ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTA
AGCCTTTAGAGAAAGATG
Found at i:908919 original size:42 final size:42
Alignment explanation
Indices: 908687--908919 Score: 220
Period size: 42 Copynumber: 5.6 Consensus size: 42
908677 TTCACAATTT
* * *
908687 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA
1 ATAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGA
* * * * *
908729 TTAAAT-ATGTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG-
1 ATAAATCCT-TCGGGTCATCTGTAAGTCTTTCGAGCATGATGA
** * * *
908770 ATAAGCCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGA
1 ATAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGA
* * * * * *
908812 TTAAATCTTTCGGGTCATCTGTAAGCCTTTAGAGAAAGATG-
1 ATAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGA
* * *
908853 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA
1 ATAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGA
* *
908895 ATAAATCCTTCGGGTAATTTGTAAG
1 ATAAATCCTTCGGGTCATCTGTAAG
908920 CCTTCACCAA
Statistics
Matches: 144, Mismatches: 43, Indels: 8
0.74 0.22 0.04
Matches are distributed among these distances:
41 62 0.43
42 82 0.57
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (42 bp):
ATAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGA
Found at i:918422 original size:20 final size:21
Alignment explanation
Indices: 918397--918448 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
918387 TTTTCCCAAT
*
918397 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
918417 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
918438 TCGCAATGCGA
1 TCGCAATGCGA
918449 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:918462 original size:20 final size:20
Alignment explanation
Indices: 918437--918550 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
918427 AATTGGGAAA
*
918437 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
918457 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
918477 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
918498 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
918518 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
918538 TTCGCAACGCGAT
1 ATCGCAACGCGAT
918551 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:918481 original size:61 final size:61
Alignment explanation
Indices: 918434--918550 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
918424 GCGAATTGGG
* * * * *
918434 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
918495 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
918551 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:919128 original size:19 final size:19
Alignment explanation
Indices: 919104--919167 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
919094 GCAACGAGAT
919104 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
919123 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
**
919142 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATAAA
919161 AATCGCA
1 AATCGCA
919168 TTGCGATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:919190 original size:19 final size:19
Alignment explanation
Indices: 919163--919347 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
919153 GAAACCAAAA
*
919163 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
919182 TTGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
919201 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
919220 TCGCGGTTGAGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
919240 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
919256 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
919273 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
919287 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
919306 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
919326 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
919346 TC
1 TC
919348 AACCAAAAGA
Statistics
Matches: 134, Mismatches: 19, Indels: 26
0.75 0.11 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 57 0.43
20 48 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:919239 original size:39 final size:38
Alignment explanation
Indices: 919163--919252 Score: 135
Period size: 39 Copynumber: 2.3 Consensus size: 38
919153 GAAACCAAAA
* * *
919163 TCGCATTGCGATTTTCATTTTGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGAGATTTTCATT
*
919201 TCGCGTTGCGATTTTTATTTCGCGGTTGAGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGAGATTTTCATT
919240 TCGCGTTGCGATT
1 TCGCGTTGCGATT
919253 GTCTGGTCGC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 20 0.43
39 27 0.57
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGAGATTTTCATT
Found at i:919263 original size:39 final size:39
Alignment explanation
Indices: 919186--919263 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
919176 TTCATTTTGC
* * **
919186 GTTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCG
1 GTTGAGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCG
919225 GTTGAGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 GTTGAGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
919264 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.10, C:0.18, G:0.27, T:0.45
Consensus pattern (39 bp):
GTTGAGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCG
Found at i:919317 original size:34 final size:33
Alignment explanation
Indices: 919235--919322 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
919225 GTTGAGATTT
* *
919235 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
919268 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
919301 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
919323 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:919324 original size:20 final size:20
Alignment explanation
Indices: 919290--919347 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
919280 GCGATTCTCT
**
919290 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
919310 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
919330 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
919348 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:921409 original size:42 final size:42
Alignment explanation
Indices: 921349--921471 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
921339 GCCCGACTCG
* * *
921349 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
921391 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
921433 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
921472 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:921429 original size:21 final size:21
Alignment explanation
Indices: 921405--921471 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
921395 TCATTCCTCG
921405 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
921426 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
921447 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
921468 AGAG
1 AGAG
921472 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:922848 original size:14 final size:14
Alignment explanation
Indices: 922829--922864 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
922819 ATTGTTTAAT
922829 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
922843 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
922857 TGATTTGT
1 TGATTTGT
922865 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:923089 original size:33 final size:32
Alignment explanation
Indices: 923047--923169 Score: 176
Period size: 33 Copynumber: 3.8 Consensus size: 32
923037 ATTAAATTCG
*
923047 CGTTGCGATTTTCATTTCACATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
923080 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
923113 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
923146 CGTTGCGATTTTCATTTCGCATTG
1 CGTTGCGATTTTCATTTCGCATTG
923170 TGATAGTAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
31 3 0.04
33 75 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:923136 original size:66 final size:66
Alignment explanation
Indices: 923040--923169 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
923030 ACGCGAAATT
*
923040 AAATTCGCGTTGCGATTTTCATTTCACATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCACATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
923105 G
66 G
* *
923106 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTG
1 AAATTAGCGTTGCGATTTTCATTTCACATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTG
923170 TGATAGTAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCACATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:925480 original size:12 final size:12
Alignment explanation
Indices: 925463--925487 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
925453 TCTTCGGGAA
925463 CTTTTTCTTCTT
1 CTTTTTCTTCTT
925475 CTTTTTCTTCTT
1 CTTTTTCTTCTT
925487 C
1 C
925488 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:925696 original size:24 final size:24
Alignment explanation
Indices: 925662--925715 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
925652 CTGAAACATC
* *
925662 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
925686 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
925710 ATCAAA
1 ATCAAA
925716 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:926800 original size:20 final size:20
Alignment explanation
Indices: 926775--926832 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
926765 ATTCATTTGA
*
926775 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATAG
926795 CTATCGCAACGCGAAAATAG
1 CTATCGCAACGCGAAAATAG
* *
926815 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
926833 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATAG
Found at i:926892 original size:19 final size:19
Alignment explanation
Indices: 926851--926918 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
926841 GAAATGAAAA
926851 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
926867 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
926884 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
926903 TCGCGTTGCAATTTTC
1 TCGCATTGCGATTTTC
926919 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 28 0.62
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:927054 original size:14 final size:15
Alignment explanation
Indices: 927035--927072 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
927025 CATCAATTAA
927035 ACAAATCAAT-ATTT
1 ACAAATCAATCATTT
*
927049 ACAAATC-ATCTTTT
1 ACAAATCAATCATTT
927063 ACAAATCAAT
1 ACAAATCAAT
927073 TAAACAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (15 bp):
ACAAATCAATCATTT
Found at i:928937 original size:14 final size:14
Alignment explanation
Indices: 928918--928975 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
928908 AATAGTTTCG
928918 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
928932 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
928948 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
928964 CGTTGCGATTTT
1 CGTTGCGATTTT
928976 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:928956 original size:32 final size:33
Alignment explanation
Indices: 928913--928991 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
928903 AGAAGAATAG
*
928913 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
928945 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
928978 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
928992 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 26 0.58
33 19 0.42
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:929010 original size:20 final size:19
Alignment explanation
Indices: 928976--929030 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
928966 TTGCGATTTT
*
928976 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
928995 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
929015 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
929031 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:929556 original size:18 final size:18
Alignment explanation
Indices: 929512--929556 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
929502 GTCGATCAGA
*
929512 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* * *
929530 TAATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
929548 TGATGGCTC
1 TGATGGCTC
929557 CCGAAGTGGA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.40, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:930901 original size:20 final size:20
Alignment explanation
Indices: 930876--930913 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
930866 AATAGTTTTT
930876 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
930896 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
930914 GAGAGAATTG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:931204 original size:22 final size:22
Alignment explanation
Indices: 931177--931220 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
931167 GATGGAGATA
931177 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
931199 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
931221 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:931433 original size:20 final size:20
Alignment explanation
Indices: 931408--931501 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
931398 GATTATGTAT
931408 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
931428 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
931448 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
931469 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
931489 TATCGCATTGCGA
1 TATCGCGTTGCGA
931502 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:931473 original size:41 final size:41
Alignment explanation
Indices: 931428--931505 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
931418 CGAAAGTCAG
* * *
931428 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
931469 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
931506 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:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:931502 original size:20 final size:20
Alignment explanation
Indices: 931388--931502 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
931378 CGCTTTGAAA
*
931388 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
931409 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
931429 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
931449 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
931470 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
931490 ATCGCATTGCGAT
1 ATCGCATTGCGAT
931503 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:931521 original size:41 final size:41
Alignment explanation
Indices: 931428--931523 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
931418 CGAAAGTCAG
* * * ** *
931428 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
* *
931469 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
931511 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
931524 TTACTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:931535 original size:20 final size:19
Alignment explanation
Indices: 931510--931564 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
931500 GATTTTCCCA
* *
931510 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGAATT-CTT
*
931530 ATTCGCATTGCGAATTGTT
1 ATTCGCATTGCGAATTCTT
931549 ATTCGCATTGCGAATT
1 ATTCGCATTGCGAATT
931565 GGGAAAATCG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (19 bp):
ATTCGCATTGCGAATTCTT
Found at i:931552 original size:19 final size:19
Alignment explanation
Indices: 931528--931565 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
931518 TGCGATTTAC
931528 TTATTCGCATTGCGAATTG
1 TTATTCGCATTGCGAATTG
931547 TTATTCGCATTGCGAATTG
1 TTATTCGCATTGCGAATTG
931566 GGAAAATCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (19 bp):
TTATTCGCATTGCGAATTG
Found at i:941584 original size:187 final size:187
Alignment explanation
Indices: 941269--941645 Score: 754
Period size: 187 Copynumber: 2.0 Consensus size: 187
941259 GTCATTTGAC
941269 AAAAATATTTCTAAGTTTTACAAGCAATCCTCGAAATGTTAGGCTCGATCTTGCATCTGATGGAT
1 AAAAATATTTCTAAGTTTTACAAGCAATCCTCGAAATGTTAGGCTCGATCTTGCATCTGATGGAT
941334 TTAATCCTTTTAAAATCAGGAGTACTTCGTACTGTACTTGGCCTGATCTACTTATTCCCTACAAT
66 TTAATCCTTTTAAAATCAGGAGTACTTCGTACTGTACTTGGCCTGATCTACTTATTCCCTACAAT
941399 TTGCCTCCGTAGATTTGCATAAAACAATTGTCGACACTGTTTTTTGCCCAGGCAGGG
131 TTGCCTCCGTAGATTTGCATAAAACAATTGTCGACACTGTTTTTTGCCCAGGCAGGG
941456 AAAAATATTTCTAAGTTTTACAAGCAATCCTCGAAATGTTAGGCTCGATCTTGCATCTGATGGAT
1 AAAAATATTTCTAAGTTTTACAAGCAATCCTCGAAATGTTAGGCTCGATCTTGCATCTGATGGAT
941521 TTAATCCTTTTAAAATCAGGAGTACTTCGTACTGTACTTGGCCTGATCTACTTATTCCCTACAAT
66 TTAATCCTTTTAAAATCAGGAGTACTTCGTACTGTACTTGGCCTGATCTACTTATTCCCTACAAT
941586 TTGCCTCCGTAGATTTGCATAAAACAATTGTCGACACTGTTTTTTGCCCAGGCAGGG
131 TTGCCTCCGTAGATTTGCATAAAACAATTGTCGACACTGTTTTTTGCCCAGGCAGGG
941643 AAA
1 AAA
941646 GACTGATACC
Statistics
Matches: 190, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
187 190 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (187 bp):
AAAAATATTTCTAAGTTTTACAAGCAATCCTCGAAATGTTAGGCTCGATCTTGCATCTGATGGAT
TTAATCCTTTTAAAATCAGGAGTACTTCGTACTGTACTTGGCCTGATCTACTTATTCCCTACAAT
TTGCCTCCGTAGATTTGCATAAAACAATTGTCGACACTGTTTTTTGCCCAGGCAGGG
Found at i:941944 original size:3 final size:3
Alignment explanation
Indices: 941931--942065 Score: 193
Period size: 3 Copynumber: 45.0 Consensus size: 3
941921 TTCATTTAAA
* * *
941931 ATT AGT ATT ATT ATT ATT AGT ATT ATT ATT ATT AGT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
941979 AGT ATT A-T ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
942025 AGT ATTT ATT ATT ATT ATT ATT ATT ATAT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
942066 TAATAAATAA
Statistics
Matches: 118, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
2 4 0.03
3 109 0.92
4 5 0.04
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:944437 original size:13 final size:15
Alignment explanation
Indices: 944406--944442 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
944396 TTATATGTTT
944406 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
944421 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
944434 TA-TTTATTT
1 TATTTTATTT
944443 TTCTGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:951210 original size:83 final size:83
Alignment explanation
Indices: 951114--951300 Score: 338
Period size: 83 Copynumber: 2.3 Consensus size: 83
951104 TTTTGACAGT
*
951114 GTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGAAAGATGAATGTGA
1 GTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGAAAGAGGAATGTGA
*
951179 TCATAACATCTTCTGGAA
66 TAATAACATCTTCTGGAA
* *
951197 GTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGGAAGAGGAATGTGC
1 GTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGAAAGAGGAATGTGA
951262 TAATAACATCTTCTGGAA
66 TAATAACATCTTCTGGAA
951280 GTGTTCTTTGAGTTATCTGAT
1 GTGTTCTTTGAGTTATCTGAT
951301 TTGATTTGAT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 100 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.39
Consensus pattern (83 bp):
GTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGAAAGAGGAATGTGA
TAATAACATCTTCTGGAA
Found at i:953520 original size:54 final size:54
Alignment explanation
Indices: 953456--953610 Score: 229
Period size: 54 Copynumber: 2.9 Consensus size: 54
953446 GAAATCTTGG
* *
953456 CAGAAACCACAGTAAAGGATGAATGTGTTGTCAAATGTTTTACGAACTTCTGAA
1 CAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
* *
953510 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAG
1 CAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
* *** *
953564 CAGAAGCCACAGAAAAGGATGAATGCACTATCAAATGTTTTACGAAC
1 CAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
953611 CTGCTATTCT
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 92 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (54 bp):
CAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
Found at i:953999 original size:22 final size:22
Alignment explanation
Indices: 953971--954025 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
953961 ATCTACACTC
* *
953971 TTCAAAGATGATAGATTATCTT
1 TTCAAAGATGACAAATTATCTT
* *
953993 TTTAAAGATGACAAATTCTCTT
1 TTCAAAGATGACAAATTATCTT
954015 TTCAAAGATGA
1 TTCAAAGATGA
954026 AAACTTTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAAATTATCTT
Found at i:954766 original size:29 final size:29
Alignment explanation
Indices: 954730--954828 Score: 198
Period size: 29 Copynumber: 3.4 Consensus size: 29
954720 ATGTTTCCAA
954730 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
954759 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
954788 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
954817 AAAGCCTTCGGG
1 AAAGCCTTCGGG
954829 TCATCTGTAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (29 bp):
AAAGCCTTCGGGAGCTTTTTGATGTTTTC
Found at i:954916 original size:76 final size:76
Alignment explanation
Indices: 954788--955544 Score: 1441
Period size: 76 Copynumber: 10.0 Consensus size: 76
954778 TGATGTTTTC
*
954788 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
954853 GATGTTTCCAA
66 GATGTTTCCAA
954864 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
954929 GATGTTTCCAA
66 GATGTTTCCAA
954940 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
955005 GATGTTTCCAA
66 GATGTTTCCAA
955016 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
955081 GATGTTTCC-A
66 GATGTTTCCAA
*
955091 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTC-GGTCATCTGTAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
955155 GATGTTTCCAA
66 GATGTTTCCAA
955166 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
955231 GATGTTTCCAA
66 GATGTTTCCAA
*
955242 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
955307 GATGTTTCCAA
66 GATGTTTCCAA
955318 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
955383 GATGTTTCCAA
66 GATGTTTCCAA
955394 AAAGCCTTCGGGAGC-TTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
955458 GATGTTTCC-A
66 GATGTTTCCAA
*
955468 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
*
955533 GATGTTTTCAA
66 GATGTTTCCAA
955544 A
1 A
955545 CATTTCCATC
Statistics
Matches: 670, Mismatches: 7, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
74 50 0.07
75 192 0.29
76 428 0.64
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (76 bp):
AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCAT
GATGTTTCCAA
Found at i:955324 original size:302 final size:303
Alignment explanation
Indices: 954778--955544 Score: 1452
Period size: 302 Copynumber: 2.5 Consensus size: 303
954768 GGGAGCTTTT
*
954778 TGATGTTTTC-AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTC
1 TGATGTTTCCAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTC
954842 CTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTC
66 CTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTC
954907 ATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
131 ATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
954972 GCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
196 GCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
955037 ATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCA
261 ATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCA
955080 TGATGTTTCCAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTC-GGTCATCTGTAAGTC
1 TGATGTTTCCAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTC
955144 CTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTC
66 CTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTC
955209 ATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
131 ATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
*
955274 GCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
196 GCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
955339 ATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCA
261 ATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCA
*
955382 TGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAAAGCCTTCGGGTCATCTATAAGT
1 TGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
955446 CCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
65 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
* *
955510 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAA
130 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAA
955545 CATTTCCATC
Statistics
Matches: 457, Mismatches: 5, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
302 369 0.81
303 88 0.19
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (303 bp):
TGATGTTTCCAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTC
CTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTC
ATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
GCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
ATGTTTTCAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCA
Found at i:955682 original size:3 final size:3
Alignment explanation
Indices: 955669--955784 Score: 160
Period size: 3 Copynumber: 38.0 Consensus size: 3
955659 TTCATTTAAA
* * *
955669 ATT AGT ATT ATT ATT ATT AGT ATT ATT ATT ATT AGT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
955717 AGT ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT ATTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
*
955763 ATT AAT ATT ATAT ATT ATT ATT
1 ATT ATT ATT AT-T ATT ATT ATT
955785 TTAATAAATA
Statistics
Matches: 99, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
3 94 0.95
4 5 0.05
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:955689 original size:15 final size:15
Alignment explanation
Indices: 955669--955784 Score: 178
Period size: 15 Copynumber: 7.6 Consensus size: 15
955659 TTCATTTAAA
955669 ATTAGTATTATTATT
1 ATTAGTATTATTATT
955684 ATTAGTATTATTATT
1 ATTAGTATTATTATT
955699 ATTAGTATTATTATT
1 ATTAGTATTATTATT
955714 ATTAGTATTATTATT
1 ATTAGTATTATTATT
*
955729 ATTATTATTATTATT
1 ATTAGTATTATTATT
955744 ATTAGTATTTATTATT
1 ATTAGTA-TTATTATT
* *
955760 ATTATTAATATTATAT
1 ATTAGTATTATTAT-T
*
955776 ATTATTATT
1 ATTAGTATT
955785 TTAATAAATA
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
15 71 0.76
16 23 0.24
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.61
Consensus pattern (15 bp):
ATTAGTATTATTATT
Found at i:955798 original size:19 final size:22
Alignment explanation
Indices: 955689--955798 Score: 97
Period size: 21 Copynumber: 5.2 Consensus size: 22
955679 TTATTATTAG
* *
955689 TATTATTATTATTAGTATTAT-
1 TATTATTATTATTAATATAATA
* * *
955710 TATTATTAGTATTATTATTAT-
1 TATTATTATTATTAATATAATA
* *
955731 TATTATTATTATTATTAGT-ATT
1 TATTATTATTATTAATA-TAATA
*
955753 TATTATTATTATTAATATTATA
1 TATTATTATTATTAATATAATA
955775 TATTATTATT-TTAATA-AATA
1 TATTATTATTATTAATATAATA
955795 -ATTA
1 TATTA
955799 CAAAATTAGA
Statistics
Matches: 80, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.05
20 3 0.04
21 44 0.55
22 29 0.36
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (22 bp):
TATTATTATTATTAATATAATA
Found at i:959555 original size:14 final size:14
Alignment explanation
Indices: 959536--959564 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
959526 TGGGGTTTAA
959536 GTAAATTTGTTCAT
1 GTAAATTTGTTCAT
959550 GTAAATTTGTTCAT
1 GTAAATTTGTTCAT
959564 G
1 G
959565 GACAAGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (14 bp):
GTAAATTTGTTCAT
Found at i:959600 original size:16 final size:16
Alignment explanation
Indices: 959579--959626 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
959569 AGATATTTTG
959579 TAAATTTTAAAAAAAA
1 TAAATTTTAAAAAAAA
*
959595 TAAATTTT--GAAAAA
1 TAAATTTTAAAAAAAA
* *
959609 TAAGTTTTAATAAAAA
1 TAAATTTTAAAAAAAA
959625 TA
1 TA
959627 TTAATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 12 0.44
16 15 0.56
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (16 bp):
TAAATTTTAAAAAAAA
Found at i:963479 original size:17 final size:18
Alignment explanation
Indices: 963459--963492 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
963449 GAAGAATACT
963459 ATTATTGAAAA-AATATA
1 ATTATTGAAAATAATATA
*
963476 ATTATTTAAAATAATAT
1 ATTATTGAAAATAATAT
963493 CTAACTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTATTGAAAATAATATA
Found at i:964332 original size:19 final size:18
Alignment explanation
Indices: 964305--964340 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
964295 GTTTTTTATA
964305 TTAAAAATATTATTATTAG
1 TTAAAAATATT-TTATTAG
*
964324 TTAATAATATTTTATTA
1 TTAAAAATATTTTATTA
964341 TTTATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TTAAAAATATTTTATTAG
Found at i:964348 original size:21 final size:21
Alignment explanation
Indices: 964305--964353 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
964295 GTTTTTTATA
964305 TTAAAAATA--TTATTATTAG
1 TTAAAAATATTTTATTATTAG
*
964324 TTAATAATATTTTATTATTTA-
1 TTAAAAATATTTTATTA-TTAG
964345 TTAAAAATA
1 TTAAAAATA
964354 ATAGATTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 8 0.32
21 14 0.56
22 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TTAAAAATATTTTATTATTAG
Found at i:965419 original size:82 final size:81
Alignment explanation
Indices: 965322--965503 Score: 292
Period size: 82 Copynumber: 2.2 Consensus size: 81
965312 GTTTTGCATC
*
965322 TATATAACAACCCATTTTAACATTGTTTTTGTATGTTTAAATAATTAAATATATAGAATTTTAAC
1 TATATAACAGCCCATTTTAACATTGTTTTTGTATGTTTAAATAATTAAATATATAGAA-TTTAAC
**
965387 ATGTTAATAATTTATTT
65 ACATTAATAATTTATTT
* * *
965404 TATATAACAGTCCATTTCAGCATTGTTTTTGTATGTTTAAATAATTAAATATATAGAATTTAACA
1 TATATAACAGCCCATTTTAACATTGTTTTTGTATGTTTAAATAATTAAATATATAGAATTTAACA
965469 CATTAATAATTTATTT
66 CATTAATAATTTATTT
*
965485 TATATGACAGCCCATTTTA
1 TATATAACAGCCCATTTTA
965504 TTTTTTTTGA
Statistics
Matches: 91, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
81 37 0.41
82 54 0.59
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (81 bp):
TATATAACAGCCCATTTTAACATTGTTTTTGTATGTTTAAATAATTAAATATATAGAATTTAACA
CATTAATAATTTATTT
Found at i:976414 original size:27 final size:28
Alignment explanation
Indices: 976379--976437 Score: 111
Period size: 27 Copynumber: 2.1 Consensus size: 28
976369 GTTCATCATG
976379 TGTTGGTTCTGCTTCAGAAGAATCTTCT
1 TGTTGGTTCTGCTTCAGAAGAATCTTCT
976407 TGTT-GTTCTGCTTCAGAAGAATCTTCT
1 TGTTGGTTCTGCTTCAGAAGAATCTTCT
976434 TGTT
1 TGTT
976438 CAAACTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (28 bp):
TGTTGGTTCTGCTTCAGAAGAATCTTCT
Found at i:979162 original size:21 final size:21
Alignment explanation
Indices: 979121--979159 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
979111 ATATCTTATC
*
979121 GTCATTTTTGTTAAATCAATA
1 GTCATTTTTGTTAAATAAATA
979142 GTCATTTTT-TTAAATAAA
1 GTCATTTTTGTTAAATAAA
979160 ATATTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (21 bp):
GTCATTTTTGTTAAATAAATA
Found at i:979434 original size:22 final size:21
Alignment explanation
Indices: 979403--979480 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 21
979393 AATAATATAA
*
979403 TTACATATTTAATCCTTAATAT
1 TTACACATTTAAT-CTTAATAT
*
979425 TTACACATTTAATGTGTAATTAT
1 TTACACATTTAATCT-TAA-TAT
979448 ATT--A-ATTTAATCTTCAATAT
1 -TTACACATTTAATCTT-AATAT
979468 TTACACATTTAAT
1 TTACACATTTAAT
979481 GTATAATTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
19 2 0.04
20 4 0.09
21 12 0.26
22 23 0.50
23 3 0.07
24 2 0.04
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.49
Consensus pattern (21 bp):
TTACACATTTAATCTTAATAT
Found at i:979459 original size:43 final size:43
Alignment explanation
Indices: 979409--979495 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
979399 ATAATTACAT
*
979409 ATTTAATCCTT-AATATTTACACATTTAATGTGTAATTATATTA
1 ATTTAAT-CTTCAATATTTACACATTTAATGTATAATTATATTA
979452 ATTTAATCTTCAATATTTACACATTTAATGTATAATTATATTA
1 ATTTAATCTTCAATATTTACACATTTAATGTATAATTATATTA
979495 A
1 A
979496 CTATTTTAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
42 3 0.07
43 39 0.93
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.48
Consensus pattern (43 bp):
ATTTAATCTTCAATATTTACACATTTAATGTATAATTATATTA
Found at i:981141 original size:42 final size:42
Alignment explanation
Indices: 981076--981169 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
981066 AAAAATATTA
*
981076 ATTATTAAA-ATATTCAAAATATA-TTTATTAATATTTTTAAT
1 ATTATAAAATATATTCAAAATATATTTTATTAATA-TTTTAAT
* **
981117 ATTATAATAATATATTC-AATTATATTTTATTCTTATTTTAAT
1 ATTATAA-AATATATTCAAAATATATTTTATTAATATTTTAAT
981159 ATTATAAAATA
1 ATTATAAAATA
981170 AATTATATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
41 10 0.22
42 22 0.48
43 14 0.30
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (42 bp):
ATTATAAAATATATTCAAAATATATTTTATTAATATTTTAAT
Found at i:982821 original size:93 final size:93
Alignment explanation
Indices: 982658--982846 Score: 333
Period size: 93 Copynumber: 2.0 Consensus size: 93
982648 CCGTGTCGAG
*
982658 GTTGCGGACAAGATTTATTTTCTAGAAATAACTATGTTTCTAAATTTGACATTATAGTGTCATGA
1 GTTGCGGACAAGATTTATTTTCTAGAAATAACTATGTTTCTAAATTTGACATCATAGTGTCATGA
982723 CGATCTTGAAAAGTATTACGAAGCTGCC
66 CGATCTTGAAAAGTATTACGAAGCTGCC
* *
982751 GTTGCGGACATGATTTATTTTCTAGAAATAACTATGTTTCTAAATTTGACATCATAGTGTCGTGA
1 GTTGCGGACAAGATTTATTTTCTAGAAATAACTATGTTTCTAAATTTGACATCATAGTGTCATGA
* *
982816 TGATCTTGAAAAGTGTTACGAAGCTGCC
66 CGATCTTGAAAAGTATTACGAAGCTGCC
982844 GTT
1 GTT
982847 ACACTGTGTT
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.37
Consensus pattern (93 bp):
GTTGCGGACAAGATTTATTTTCTAGAAATAACTATGTTTCTAAATTTGACATCATAGTGTCATGA
CGATCTTGAAAAGTATTACGAAGCTGCC
Found at i:993307 original size:25 final size:25
Alignment explanation
Indices: 993256--993315 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
993246 TTATTTATTT
*
993256 ATTTAAAAAATAAAAATTATTTTAA
1 ATTTAAAAAATAAAAATTATTTAAA
* *
993281 ATTTTAAATATAAAAA-TATTTAAA
1 ATTTAAAAAATAAAAATTATTTAAA
*
993305 AATTAAAAAAT
1 ATTTAAAAAAT
993316 TAAATAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
24 15 0.52
25 14 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
ATTTAAAAAATAAAAATTATTTAAA
Found at i:993310 original size:23 final size:25
Alignment explanation
Indices: 993265--993311 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
993255 TATTTAAAAA
**
993265 ATAAAAATTATTTTAAATTTTAAAT
1 ATAAAAATTATTTTAAAAATTAAAT
993290 ATAAAAA-TA-TTTAAAAATTAAA
1 ATAAAAATTATTTTAAAAATTAAA
993312 AAATTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 2 0.10
25 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATAAAAATTATTTTAAAAATTAAAT
Done.