Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008826.1 Hibiscus syriacus cultivar Beakdansim tig00112000_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: 3884024
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 18
Found at i:214188 original size:20 final size:20
Alignment explanation
Indices: 214163--214234 Score: 135
Period size: 20 Copynumber: 3.6 Consensus size: 20
214153 ATTGTGAAGG
214163 GAGTATCGATACCAAGGGTT
1 GAGTATCGATACCAAGGGTT
*
214183 GAGTATCGATACCAAGGATT
1 GAGTATCGATACCAAGGGTT
214203 GAGTATCGATACCAAGGGTT
1 GAGTATCGATACCAAGGGTT
214223 GAGTATCGATAC
1 GAGTATCGATAC
214235 TCCCCATAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (20 bp):
GAGTATCGATACCAAGGGTT
Found at i:214261 original size:40 final size:40
Alignment explanation
Indices: 214163--214261 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 40
214153 ATTGTGAAGG
** *
214163 GAGTATCGATACCAAGGGTTGAGTATCGATACCAAGGATT
1 GAGTATCGATACCAAGGGTTGAGTATCGATACCAACCATA
*
214203 GAGTATCGATACCAAGGGTTGAGTATCGATACTC-CCCATA
1 GAGTATCGATACCAAGGGTTGAGTATCGATAC-CAACCATA
*
214243 GTAGTATCAATACC-AGGGT
1 G-AGTATCGATACCAAGGGT
214262 ATTTTTCAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 40 0.77
41 12 0.23
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (40 bp):
GAGTATCGATACCAAGGGTTGAGTATCGATACCAACCATA
Found at i:215029 original size:22 final size:22
Alignment explanation
Indices: 214988--215054 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
214978 CTCGTATAAA
214988 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
215011 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
215033 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
215055 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:219814 original size:22 final size:22
Alignment explanation
Indices: 219773--219839 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
219763 CTCGTATAAA
219773 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
219796 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
219818 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
219840 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:234450 original size:10 final size:10
Alignment explanation
Indices: 234435--234472 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
234425 TTTTTTGTGT
234435 TGTTCGTTTA
1 TGTTCGTTTA
**
234445 TGTTCGTTCG
1 TGTTCGTTTA
234455 TGTTCGTTTA
1 TGTTCGTTTA
234465 TGTTCGTT
1 TGTTCGTT
234473 CGTTCGTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.05, C:0.13, G:0.24, T:0.58
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:234460 original size:20 final size:20
Alignment explanation
Indices: 234435--234475 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
234425 TTTTTTGTGT
234435 TGTTCGTTTATGTTCGTTCG
1 TGTTCGTTTATGTTCGTTCG
234455 TGTTCGTTTATGTTCGTTCG
1 TGTTCGTTTATGTTCGTTCG
234475 T
1 T
234476 TCGTGTTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.05, C:0.15, G:0.24, T:0.56
Consensus pattern (20 bp):
TGTTCGTTTATGTTCGTTCG
Found at i:236647 original size:14 final size:14
Alignment explanation
Indices: 236572--236680 Score: 58
Period size: 14 Copynumber: 7.6 Consensus size: 14
236562 AAACTGAACC
*
236572 TTTAATTTCTATTA
1 TTTAATTTCTAGTA
* ***
236586 TTTACATTTATACCC
1 TTTA-ATTTCTAGTA
*
236601 TTTAATTTTTAGTA
1 TTTAATTTCTAGTA
*
236615 TTTCAATTTC-AGTTC
1 TTT-AATTTCTAG-TA
236630 TTTAATTTCTAGTA
1 TTTAATTTCTAGTA
* * *
236644 TTTACTTTTTAGTCC
1 TTTAATTTCTAGT-A
* **
236659 TTTAAATTCTAACA
1 TTTAATTTCTAGTA
236673 TTTAATTT
1 TTTAATTT
236681 TATTCATTTT
Statistics
Matches: 69, Mismatches: 21, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
14 40 0.58
15 29 0.42
ACGTcount: A:0.27, C:0.13, G:0.04, T:0.57
Consensus pattern (14 bp):
TTTAATTTCTAGTA
Found at i:236661 original size:29 final size:30
Alignment explanation
Indices: 236570--236669 Score: 107
Period size: 29 Copynumber: 3.4 Consensus size: 30
236560 AAAAACTGAA
* * *
236570 CCTTTAATTTCTATTATTTACATTTATA-C
1 CCTTTAATTTCTAGTATTTACATTTTTAGT
* * *
236599 CCTTTAATTTTTAGTATTT-CAATTTCAGT
1 CCTTTAATTTCTAGTATTTACATTTTTAGT
*
236628 TCTTTAATTTCTAGTATTTAC-TTTTTAGT
1 CCTTTAATTTCTAGTATTTACATTTTTAGT
*
236657 CCTTTAAATTCTA
1 CCTTTAATTTCTA
236670 ACATTTAATT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
28 5 0.09
29 51 0.89
30 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.04, T:0.56
Consensus pattern (30 bp):
CCTTTAATTTCTAGTATTTACATTTTTAGT
Found at i:238847 original size:2 final size:2
Alignment explanation
Indices: 238840--238866 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
238830 TAAGTAAATC
238840 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
238867 ATGATGGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:251063 original size:22 final size:22
Alignment explanation
Indices: 251022--251063 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
251012 CCGCAATAAC
* *
251022 ATTCATGATAAATATCATATAT
1 ATTCATGACAAACATCATATAT
*
251044 ATTCATGACAAACATTATAT
1 ATTCATGACAAACATCATAT
251064 GTAATAACCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (22 bp):
ATTCATGACAAACATCATATAT
Found at i:255084 original size:22 final size:22
Alignment explanation
Indices: 255059--255137 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
255049 AACTTTATAG
*
255059 TTAATACTTATATTCATATACT
1 TTAATACTTATATTCATACACT
* * *
255081 TTAATACTAATATCCAAACACT
1 TTAATACTTATATTCATACACT
* * *
255103 TTATTATTTTATATT-ATAGACT
1 TTAATA-CTTATATTCATACACT
255125 TT-ATACTTTATAT
1 TTAATAC-TTATAT
255138 ATATATAAAG
Statistics
Matches: 43, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
21 8 0.19
22 30 0.70
23 5 0.12
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49
Consensus pattern (22 bp):
TTAATACTTATATTCATACACT
Found at i:255142 original size:22 final size:22
Alignment explanation
Indices: 255100--255142 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
255090 ATATCCAAAC
*
255100 ACTTTATTATTTTATATTATAG
1 ACTTTATTACTTTATATTATAG
255122 ACTTTA-TACTTTATATATATA
1 ACTTTATTACTTTATAT-TATA
255143 TAAAGTACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
ACTTTATTACTTTATATTATAG
Found at i:255265 original size:25 final size:24
Alignment explanation
Indices: 255219--255264 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
255209 TGATGAGGGA
*
255219 TGAAATTGAATTAATTATAAAATG
1 TGAAACTGAATTAATTATAAAATG
255243 TGAAACTGATATTAA-TATAAAA
1 TGAAACTGA-ATTAATTATAAAA
255265 AATGGACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (24 bp):
TGAAACTGAATTAATTATAAAATG
Found at i:255644 original size:6 final size:6
Alignment explanation
Indices: 255636--256456 Score: 1238
Period size: 6 Copynumber: 138.2 Consensus size: 6
255626 TGTATGTTAT
* * * *
255636 ACATAT ACATAG ACATAT ACATAT ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * *
255684 ACATAC ACATAT ACAT-- ACATAT ACATAC ACA-AC ACATAT ACAT--
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * *
255727 ACATAT ACATAT ACATAT ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * * *
255775 ATACAT ACATAC ACATAC ACATAC ACATAC ACATAT ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * * * *
255823 ACATAC ATATAC ATATAC ACATAC ATATAC ACATAC ATATAC ACATAT
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* *
255871 ACATAT ACATAC ACATAT ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* *
255919 ACATAC ACATAC ACATATAC ATATAC ACATAC ACATAC ACATAC ACATAT
1 ACATAC ACATAC AC--ATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * *
255969 ACATAT ACATAT ACATAT ACATAC ACATAC ACAT-- ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
256015 ACATAC ACATAC ACATAC ACATAC ACAT-- ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
*
256061 ACATAC ACATAC ATATAC ATACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC --ACATAC ACATAC ACATAC ACATAC ACATAC
256111 ACATAC ATACATAC ACATAC ACAT-- ACATAC ACATAC ACATAC ACATAC
1 ACATAC --ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
*
256159 ACATAT ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
256207 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
256255 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
256303 ACATAC AC-TAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
256350 ACATAC ACATAC ACAT-- ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
256396 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
256444 ACATAC ACATAC A
1 ACATAC ACATAC A
256457 TACATACATA
Statistics
Matches: 762, Mismatches: 33, Indels: 40
0.91 0.04 0.05
Matches are distributed among these distances:
4 24 0.03
5 10 0.01
6 712 0.93
8 16 0.02
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (6 bp):
ACATAC
Found at i:256528 original size:2 final size:2
Alignment explanation
Indices: 256521--257580 Score: 364
Period size: 2 Copynumber: 530.0 Consensus size: 2
256511 ACTAAAACTT
256521 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
256563 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
256604 TA TA TA -A TA TA TA TA TA TA TA TA TA TA CT- TA GT- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA
* * * * *
256645 CT- TA TA CTT TA TA TT TA AA CTA TA TA -A T- TT TA CA TA TA TA
1 -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * * *
256685 TA -A TT TA TA T- TA -A AA AA TA TA TA T- TT TA TA AA TA GT- TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA T-A
* * * * *
256724 -A TA GT- TCA TA TA TA AA CA CTA GTA TA CA TGG TA TA TA -A TT TA
1 TA TA -TA T-A TA TA TA TA TA -TA -TA TA TA T-A TA TA TA TA TA TA
* * *
256766 TA CA TA -A TA TA TA TA GT- TA TA TA TA TA TA AA TA TA AA GTA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
256808 TA GTT TA TA TA TA TA GTT TA TA T- TA TA TA TA TA TA TA CT- TA
1 TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * *
256849 TA CTT TA TA TG TA TA TA TA TA TA TA CTT TA GTC TT TA TA -A T-
1 TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA
* *
256890 TA TA CTT TA TA TA TA TA -A TA TA CT- TA TA CTT TA TA TA CTA TA
1 TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA -TA TA
* * * * * *
256932 TA TG TA TA TA TA CTT TA TA CTA -A AA CTT TA TA CA TA CA TA TA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
* * * * * * *
256974 TA TG TA TA TA AA CTT TA TA GTT TA TA TG TA TA CT- TT TA CTT TA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA
* *
257017 TA GTT TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
257060 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
257102 TA TA TA TA CA TA CT- TA TGC TT TA CA TG TA TA TA TA CT- TA TA
1 TA TA TA TA TA TA -TA TA T-A TA TA TA TA TA TA TA TA -TA TA TA
* * * *
257143 TA T- TT TGG TA TT TA TA -A T- TA TA CTT TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
257184 -A T- TCA TA GTT TA TA TA TA T- TA TA TA CTT TA TA TT TA AA CTA
1 TA TA T-A TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
* * * * *
257225 TA TA -A AA TA TA TA -A TT TA TA CA TA GTG TA TA TA -A TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * ** * *
257265 -A T- TA TA CA TA -A TA TA TA AA TA TA -A GC TG TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
257303 AA TA TA -A T- TCA TA TA TA AA CTA TA TA -A TT TA TA T- TA -A TA
1 TA TA TA TA TA T-A TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * * *
257342 AA CTA TA TA CTT TA TA CA TA -A TA TA TA -A AA TT TA TA TA TA GTA
1 TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * * *
257385 TA TGA TA -A TA TA AA TA TA AA CTA TA TA GTT TA TA TA CA TA GTT
1 TA T-A TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA
* ** *
257428 TA TA TA TA CA -A TA TA TA TA CC T- TA TA TA TA CA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
257467 GTT TA TA TA TA GTT TA TA T- TA -A TA AA CTA TA TA GTT TA TA CA
1 -TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * *
257509 TA -A TA TA CA TA GTT TA TA TA TA GTA TA TA -A TA -A TA TA AA TA
1 TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
*
257550 TA AA CTA TA -A TA TA TA TA TA TA TA TA T- TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
257581 ATTGTTTCAA
Statistics
Matches: 776, Mismatches: 167, Indels: 230
0.66 0.14 0.20
Matches are distributed among these distances:
1 58 0.07
2 657 0.85
3 61 0.08
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:257425 original size:13 final size:13
Alignment explanation
Indices: 257409--257433 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
257399 TATAAACTAT
257409 ATAGTTTATATAC
1 ATAGTTTATATAC
257422 ATAGTTTATATA
1 ATAGTTTATATA
257434 TACAATATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
ATAGTTTATATAC
Found at i:257696 original size:3 final size:3
Alignment explanation
Indices: 257688--257743 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
257678 TTTCGTCTCG
* *
257688 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTAA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
*
257734 ATA TT- TTA TT
1 TTA TTA TTA TT
257744 GTTTTTATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:261486 original size:55 final size:55
Alignment explanation
Indices: 261422--261563 Score: 214
Period size: 55 Copynumber: 2.6 Consensus size: 55
261412 ACATTCAAGT
* * *
261422 GATTCATGAAGAAGGACGTCCGATGAATGAAGAAATTTGAACCTGATTGAAGAAC
1 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTGAAGAAC
* *
261477 GATTCATGAAGATGGACATCCGATGAATGAAGAAATCTGAAACTGATTGAAGACC
1 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTGAAGAAC
*
261532 GATCCATGAAGAAAGG-CATCCGATGAATGAAG
1 GATTCATGAAG-AAGGACATCCGATGAATGAAG
261564 TTTGAAGTTG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
55 76 0.96
56 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.20
Consensus pattern (55 bp):
GATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTGAAGAAC
Found at i:264235 original size:27 final size:26
Alignment explanation
Indices: 264205--264270 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
264195 TAATCTTTAG
*
264205 TTCTTTGAATATTGAATGAATTAAAGA
1 TTCTTTGAATATTCAA-GAATTAAAGA
* *
264232 TTCTTTTAATTATTCAAGAATTATAGA
1 TTCTTTGAA-TATTCAAGAATTAAAGA
264259 TT-TTTGACATAT
1 TTCTTTGA-ATAT
264271 GGCAAGATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
26 7 0.21
27 20 0.61
28 6 0.18
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (26 bp):
TTCTTTGAATATTCAAGAATTAAAGA
Found at i:264907 original size:1 final size:1
Alignment explanation
Indices: 264901--264940 Score: 62
Period size: 1 Copynumber: 40.0 Consensus size: 1
264891 CAATCATAAC
* *
264901 AAAAAAAAAAAACAAAAAAAAAAAAAAAGAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
264941 GGGACGATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.95, C:0.03, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:264922 original size:16 final size:16
Alignment explanation
Indices: 264901--264940 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
264891 CAATCATAAC
264901 AAAAAAAAAAAACAAA
1 AAAAAAAAAAAACAAA
*
264917 AAAAAAAAAAAAGAAA
1 AAAAAAAAAAAACAAA
264933 AAAAAAAA
1 AAAAAAAA
264941 GGGACGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.95, C:0.03, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAACAAA
Found at i:266012 original size:32 final size:32
Alignment explanation
Indices: 265976--266049 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
265966 GCATCGTTAA
* *
265976 AGATTCAACAACAAATGTTGGGGCATATTTGG
1 AGATTCAACAACAAATATTGGGGCATATATGG
***
266008 AGATTCAACATTGAATATTGGGGCATATATGG
1 AGATTCAACAACAAATATTGGGGCATATATGG
*
266040 GGATTCAACA
1 AGATTCAACA
266050 TCCTGATGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.28
Consensus pattern (32 bp):
AGATTCAACAACAAATATTGGGGCATATATGG
Found at i:266337 original size:43 final size:43
Alignment explanation
Indices: 266275--266403 Score: 141
Period size: 43 Copynumber: 3.0 Consensus size: 43
266265 ACGAAGGCAC
* * * **
266275 CATCCACGATTTTAACTCCACGATGGAGGATATCGTACCGATG
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
* * *
266318 GATCCACGATTTCAACTCCACGACAGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
* * * * *
266361 CATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
266404 ATCAACATTC
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
Found at i:266686 original size:41 final size:41
Alignment explanation
Indices: 266615--266695 Score: 92
Period size: 41 Copynumber: 2.0 Consensus size: 41
266605 AACTCCAACA
* * *
266615 GTAAGTCTTCCGAGCAGATGCTTAAATCCTTCGGGTCATCT
1 GTAAGCCTTCCGAGCAGATGCATAAATCCTTCGGGCCATCT
* * *
266656 GTAAGCCTTTCGAGCAAGATG-ATAAGTCCTTTGGGCCATC
1 GTAAGCCTTCCGAGC-AGATGCATAAATCCTTCGGGCCATC
266696 CATAAGACCT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
41 28 0.85
42 5 0.15
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (41 bp):
GTAAGCCTTCCGAGCAGATGCATAAATCCTTCGGGCCATCT
Found at i:266971 original size:133 final size:133
Alignment explanation
Indices: 266709--267174 Score: 718
Period size: 133 Copynumber: 3.5 Consensus size: 133
266699 AAGACCTTTG
* *
266709 GAAGAAGCGGAACAGATTCATCTCTTTCAAGATTTGATATTCCCTGAGTGACAACGGAACAAGTC
1 GAAGAAGCGGAACA-AATCATCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTC
* *
266774 TATCATGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCATCCTGATCTGATATTCCC
65 TACCATGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCATCCAGATCTGATATTCCC
266839 TTAA
130 TTAA
* * * *
266843 GAAGAAGCGGAACAAATCATTTTTTTCAAGACTTGATATTCCCTGAGTGACAGCGAAACAAGTCT
1 GAAGAAGCGGAACAAATCATCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCT
* *
266908 ACCATGATTCAATCTTCACTGAGTAACAGCGGAATGGATCAACTCATCCAGATCTGATATTCCCT
66 ACCATGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCATCCAGATCTGATATTCCCT
*
266973 TCA
131 TAA
* * * * * *
266976 GAAGATGTGGAACATATCATTCTCTTTCAAGATTTGATATTCCCCGAGTAACAGCGGAATAAGTC
1 GAAGAAGCGGAACAAATCA-TCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTC
*
267041 TACCA-GATTCAATCTTCCCTGAGTGACAACGGAATGGATCAACTCATCCAGATCTGATATTCCC
65 TACCATGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCATCCAGATCTGATATTCCC
*
267105 TTTA
130 TTAA
*
267109 GAAGAAGCAGAACAAATCACTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTC
1 GAAGAAGCGGAACAAATCA-TCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTC
267174 T
65 T
267175 TGCCACGATT
Statistics
Matches: 298, Mismatches: 33, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
133 241 0.81
134 57 0.19
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (133 bp):
GAAGAAGCGGAACAAATCATCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCT
ACCATGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCATCCAGATCTGATATTCCCT
TAA
Found at i:267271 original size:112 final size:110
Alignment explanation
Indices: 267073--267411 Score: 516
Period size: 112 Copynumber: 3.0 Consensus size: 110
267063 GTGACAACGG
* * * * *
267073 AATGGATCAACTCATCCAGATCTGATATTCCCTTTAGAAGAAGCAGAACAAATCACTCTCTTTCA
1 AATGGATCAACT-TTCCAGATCTGATATTCCC-TCAGAAGAAGCGGAACAGATCCCTCTCTTTCA
*
267138 AGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTGCCACGATTT
64 AGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTGCCA-GATTC
267186 AATGGATCAACTTTCCTAGATCTGATATTCCCTCAGAAGAAGCGGAACAGATCCCTCTCTTTCAA
1 AATGGATCAACTTTCC-AGATCTGATATTCCCTCAGAAGAAGCGGAACAGATCCCTCTCTTTCAA
267251 GATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTGCCATGATTC
65 GATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTGCCA-GATTC
* *
267298 AATGGATCAACTTTCCCAGATCTGATATTCCCTCAGAAGAAGCGGAACAGATCCGTCTATTTCAA
1 AATGGATCAACTTT-CCAGATCTGATATTCCCTCAGAAGAAGCGGAACAGATCCCTCTCTTTCAA
* ** *
267363 GATTTGATATTCCATGAGTGACAATGGAACAAGTCTTCCCAGATTC
65 GATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTGCCAGATTC
267409 AAT
1 AAT
267412 CTTCCCTGAA
Statistics
Matches: 211, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
111 8 0.04
112 174 0.82
113 29 0.14
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (110 bp):
AATGGATCAACTTTCCAGATCTGATATTCCCTCAGAAGAAGCGGAACAGATCCCTCTCTTTCAAG
ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTGCCAGATTC
Found at i:267618 original size:3 final size:3
Alignment explanation
Indices: 267610--267658 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
267600 TTTCGTCTCG
* *
267610 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTAA TTA CTA TTA ATA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
267654 TTA TT
1 TTA TT
267659 GTTTTTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 32 0.82
4 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:275763 original size:54 final size:54
Alignment explanation
Indices: 275639--275800 Score: 281
Period size: 54 Copynumber: 3.0 Consensus size: 54
275629 CTAAGTGCCA
* * *
275639 AAATGGAAATTCACAAACTCATTATGAATTCCATGGA-TGCAAACATAGTGCCG
1 AAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACATAGTGTCG
275692 AAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACATAGTGTCG
1 AAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACATAGTGTCG
*
275746 AAATGGTAATTCACAAACTCATTATGAATTCCATGGGTTGCACACATAGTGTCG
1 AAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACATAGTGTCG
275800 A
1 A
275801 TAGTACACAT
Statistics
Matches: 104, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 36 0.35
54 68 0.65
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (54 bp):
AAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACATAGTGTCG
Found at i:276927 original size:25 final size:24
Alignment explanation
Indices: 276890--276940 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
276880 TAATTGACCA
276890 CATTTAATCAAATCACTTAAAAAAT
1 CATTTAATCAAATCAC-TAAAAAAT
* * * *
276915 CATTTTATTAAATTACTAATAAAT
1 CATTTAATCAAATCACTAAAAAAT
276939 CA
1 CA
276941 CTAATCTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (24 bp):
CATTTAATCAAATCACTAAAAAAT
Found at i:282779 original size:23 final size:23
Alignment explanation
Indices: 282753--282804 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
282743 GCACTCAACA
*
282753 CAATTTAATTTTCCAAGACATTT
1 CAATTTAATTTTCCAAGACATAT
** * *
282776 CAATCCACTTTTCCACGACATAT
1 CAATTTAATTTTCCAAGACATAT
282799 CAATTT
1 CAATTT
282805 GCTACAATAC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (23 bp):
CAATTTAATTTTCCAAGACATAT
Found at i:289043 original size:52 final size:52
Alignment explanation
Indices: 288925--289032 Score: 180
Period size: 52 Copynumber: 2.1 Consensus size: 52
288915 GTTAATATTT
* * *
288925 CCCCACTTAATCATTAAATATCCCCCCAAAATTTTTATTTTGTTCTTATATA
1 CCCCACTTACTCACTAAATATCCCCCCAAAATGTTTATTTTGTTCTTATATA
*
288977 CCCCACTTACTCACTAAATATCCCCCCAAAATGTTTATTTTGTTCTTATCTA
1 CCCCACTTACTCACTAAATATCCCCCCAAAATGTTTATTTTGTTCTTATATA
289029 CCCC
1 CCCC
289033 GCTTTTTCAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.28, C:0.31, G:0.03, T:0.39
Consensus pattern (52 bp):
CCCCACTTACTCACTAAATATCCCCCCAAAATGTTTATTTTGTTCTTATATA
Found at i:291555 original size:20 final size:20
Alignment explanation
Indices: 291530--291572 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
291520 TCTAAGAGCT
291530 CATTTAGGACCATATAGATG
1 CATTTAGGACCATATAGATG
* *
291550 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
291570 CAT
1 CAT
291573 GTGGTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:293855 original size:54 final size:54
Alignment explanation
Indices: 293792--294084 Score: 344
Period size: 54 Copynumber: 5.4 Consensus size: 54
293782 ATAAGTTCAT
* *
293792 TGGGGTGCACA-TATAGTGCCGATACGGT-ATATCATAAACATATTATGAATTTCG
1 TGGGTTGCACACT-TAGTGCCGATACGGTCGT-TCATAAACATATTATGAATTTCG
* * *
293846 TGGGTTGCACACTTAGTGCCGATATGGT-GTTCATAAACTTATAATGAA-TTCTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTC-G
* * * *
293899 TGGGTTGCACACTTAGTGTCGATACGATCGTTCATAAACATATTATGAATTCCA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCG
* * * * *
293953 TGTGTTGCACACTTAGTGTCAATACGGTCGTTCATAAACATATTATAAATTTCT
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCG
* * * * *
294007 TGGATTGCATACTTAGTGTCGATACGGTCGTTTATAAACATATTATG-AGTTCTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTC-G
294061 TGGGTTGCACACTTAGTGCCGATA
1 TGGGTTGCACACTTAGTGCCGATA
294085 ATACACATAG
Statistics
Matches: 205, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
52 3 0.01
53 46 0.22
54 153 0.75
55 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (54 bp):
TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCG
Found at i:298258 original size:54 final size:54
Alignment explanation
Indices: 298182--298640 Score: 555
Period size: 54 Copynumber: 8.5 Consensus size: 54
298172 TTTTCACAAC
* * * *
298182 ATTAT-AAGTTCGTTGGGGTGCACACGTAGTGCCGATACGATCGTTCATAAACAT
1 ATTATGAATTTCG-TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACAT
* *
298236 ATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATACAGTCGTTCATAAACTT
1 ATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACAT
* * * * ** *
298290 ATTTTGAATTTCTTAGGTTACACACTTAGTGTTGATGCGGTCGTTCATAAACAT
1 ATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACAT
** * * * *
298344 ATTATGAATTTTATGGCTTGCAAACTTAGTGTCGATACGGTTGTTCATAAACAT
1 ATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACAT
* * * *
298398 ATTATGAATTTTGTAGGTTGCACACTTAGTGCCAATACGGTCATTCATAAACAT
1 ATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACAT
* * * *
298452 ATTATGAATTTTGTGGGTTGCGCACTTAGTGCTGATACAGTCGTTCATAAACAT
1 ATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACAT
* * * *
298506 ATTATGAATTTCGTAGGTTGCACACTTAGTGTCAATATGGTCGTTCATAAACAT
1 ATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACAT
* * * *
298560 ATTATGAATTTCTTTGGTTGTACACTTAGTGTCGATACGGTCGTTCATAAA-AT
1 ATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACAT
*
298613 ATTATGAATTAT-GTGGGTTGTACACTTA
1 ATTATGAATT-TCGTGGGTTGCACACTTA
298641 ATGTCAATAG
Statistics
Matches: 349, Mismatches: 54, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
53 26 0.07
54 317 0.91
55 6 0.02
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (54 bp):
ATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACAT
Found at i:301901 original size:53 final size:54
Alignment explanation
Indices: 301821--301985 Score: 262
Period size: 54 Copynumber: 3.1 Consensus size: 54
301811 GTTGCACCTA
*
301821 AGTGTCGAAATGGTAATTCACAAACTCATTATGAATTCCATGGA-TGCATACAT
1 AGTGTCGAAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACAT
* *
301874 AGTGTTGAAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACATAT
1 AGTGTCGAAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACAT
* *
301928 AGTGTCAAAATGGTAATTCACAAACTCATTATGAATTCCATGTG-TTGCACACAA
1 AGTGTCGAAATGGTAATTCACAAACTCATTATGAATTCCATG-GATTGCACACAT
301982 AGTG
1 AGTG
301986 CCGATAGTAC
Statistics
Matches: 103, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
53 43 0.42
54 59 0.57
55 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (54 bp):
AGTGTCGAAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACAT
Found at i:303815 original size:22 final size:22
Alignment explanation
Indices: 303787--303849 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
303777 AATAACATTT
*
303787 ATGATAAATATCATATATATTC
1 ATGATAAACATCATATATATTC
*
303809 ATGATAAACATAATATATATTC
1 ATGATAAACATCATATATATTC
303831 ATGATAAACATCATATATA
1 ATGATAAACATCATATATA
303850 ATAACTAGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.37
Consensus pattern (22 bp):
ATGATAAACATCATATATATTC
Found at i:312027 original size:18 final size:18
Alignment explanation
Indices: 312000--312044 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
311990 AAATACTCTC
312000 TTTTACTTTATTCCTTTA
1 TTTTACTTTATTCCTTTA
*
312018 TTTTATTTTATTCCTTTA
1 TTTTACTTTATTCCTTTA
312036 TTTTTACTT
1 -TTTTACTT
312045 ATCTCTCCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTACTTTATTCCTTTA
Found at i:313787 original size:3 final size:3
Alignment explanation
Indices: 313779--313828 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
313769 TTCTCGTAGC
313779 ATA ATA ATA ATA 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 ATA ATA ATA ATA
313827 AT
1 AT
313829 GTATTAAGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:319133 original size:4 final size:4
Alignment explanation
Indices: 319126--319150 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
319116 CATAAAATGC
319126 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
319151 AGCATTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:323660 original size:261 final size:256
Alignment explanation
Indices: 323102--323902 Score: 864
Period size: 261 Copynumber: 3.1 Consensus size: 256
323092 TGACCACAAA
* * *
323102 GATGTTTTTATATGATATTTGT--GAAAATGAGAAAGT-ATTTTTCAAAGTTTCTCATTTAATAT
1 GATGTTTTCATATGATATTTGTAAAAAAATGAGAAAGTGA-TTTTCAAAGTTTCTCATTTAATCT
* *
323164 TTTCAG-AAATGAAATTTTTGAAAAGTAAGAACA-CAATTTCCAAAGTTTCTTACCTAGTGAATT
65 TTTCTGAAAATGAAATTTTT-AAAAGTAAGAA-AGCAATTTCCAAAGTTTCTTACCTAGTAAATT
* * * * * * *
323227 ATTTCCAAAACTAGTAAGTCCTTTGGGACATCAATAAGTCTTCCGAACCTGATGAATAGATCCTC
128 ATTTCCAAAATTAGTAAGTCCTCT-GGCCATCAGTAAGTCTTCCGAGCCTGATG-ATAAACCCT-
* * * * **
323292 TAGGTTATCTGTAAGTCTTCCGAGCAAGATGATAAGACCTCT-GAGCTATCTATAAGATTGATAA
190 TGGGTTATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTCTAG-GCTATCTATAAGATT-TTGG
323356 GCAT
253 GCAT
* * ** * *
323360 GACGTTTTCATATTATATTTAAAAAGATAAAT-A-AAAGTGATTTTCCAAGTGTCTCATTTAATC
1 GATGTTTTCATATGATATTTGTAAA-A-AAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATC
*
323423 TTTTCTGAAAATGAAATTTTTAAAATGTAAGAAAGCAACTTCCAAAGTTTCTTACCTAGTAAATT
64 TTTTCTGAAAATGAAATTTTTAAAA-GTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAATT
* * * *
323488 ATTTCCAAAATTAGTAAGTACACTAGGCCATTAGTAAGTCATCCGAGCCTGATGATTAAACCCTA
128 ATTTCCAAAATTAGTAAGTCCTCT-GGCCATCAGTAAGTCTTCCGAGCCTGATGA-TAAACCCT-
* * *
323553 TGGGTTATCTTTAAGTCTTTTGAGCAAGATGATAAGTCCTCTAGGCCATCTATAAGACTTTTGGG
190 TGGGTTATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTCTAGGCTATCTATAAGA-TTTTGGG
323618 CAT
254 CAT
* * *
323621 GATGTTTTCATATGAAATTTGTAAAAAAATGAGAAAGTGATTTTTAAAGTTTCTCATTTATTCTT
1 GATGTTTTCATATGATATTTGTAAAAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATCTT
* * * * * *
323686 TTTTGAAAATGAAATTTTTTAGAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTTGTAGACTAT
66 TTCTGAAAATGAAA-TTTTTAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAATTAT
* * * * * * *
323751 TTCCAAAATTAGTAAGTCCTCTGAGCTATCAGTAAATCTTTCGAGCCTGATGATAATCTCTCGAG
130 TTCCAAAATTAGTAAGTCCTCTG-GCCATCAGTAAGTCTTCCGAGCCTGATGATAAACCCTTGGG
* * * * * *
323816 TCAACTGTAAGTCATTCAACCAAGATGATAAGTCCGT-TAGGCTATCTATAATATCTTTGGGCAT
194 TTATCTGTAAGTCTTTCGAGCAAGATGATAAGTCC-TCTAGGCTATCTATAAGAT-TTTGGGCAT
* *
323880 GATTTTTTCATATGACATTTGTA
1 GATGTTTTCATATGATATTTGTA
323903 GGGGGAAATA
Statistics
Matches: 454, Mismatches: 72, Indels: 33
0.81 0.13 0.06
Matches are distributed among these distances:
258 18 0.04
259 78 0.17
260 47 0.10
261 296 0.65
262 15 0.03
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Consensus pattern (256 bp):
GATGTTTTCATATGATATTTGTAAAAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATCTT
TTCTGAAAATGAAATTTTTAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAATTATT
TCCAAAATTAGTAAGTCCTCTGGCCATCAGTAAGTCTTCCGAGCCTGATGATAAACCCTTGGGTT
ATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTCTAGGCTATCTATAAGATTTTGGGCAT
Found at i:325700 original size:15 final size:16
Alignment explanation
Indices: 325671--325705 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
325661 AAATAAATAA
325671 AAAATAATAAAAAGAT
1 AAAATAATAAAAAGAT
325687 AAAATAAT-AAAAGAT
1 AAAATAATAAAAAGAT
325702 AAAA
1 AAAA
325706 AGGGAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (16 bp):
AAAATAATAAAAAGAT
Found at i:325706 original size:16 final size:17
Alignment explanation
Indices: 325670--325706 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
325660 TAAATAAATA
325670 AAAAATAATAAAAAGAT
1 AAAAATAATAAAAAGAT
325687 -AAAATAAT-AAAAGAT
1 AAAAATAATAAAAAGAT
325702 AAAAA
1 AAAAA
325707 GGGAGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (17 bp):
AAAAATAATAAAAAGAT
Found at i:325716 original size:41 final size:39
Alignment explanation
Indices: 325670--325760 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 39
325660 TAAATAAATA
*
325670 AAAAATAATAA-AAAGATAAAATAATA-AAAGATAAAAAGGG
1 AAAAATAATAATAAAGATAAAATAAAATAAAGAT---AAGGG
325710 AGAAAATAA-AATAAAGATAAAATAAAATAAAGATAAGGG
1 A-AAAATAATAATAAAGATAAAATAAAATAAAGATAAGGG
325749 AAAAATAATAAT
1 AAAAATAATAAT
325761 GAAAAAAACA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
38 7 0.15
39 9 0.20
40 3 0.07
41 21 0.46
42 6 0.13
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.16
Consensus pattern (39 bp):
AAAAATAATAATAAAGATAAAATAAAATAAAGATAAGGG
Found at i:325722 original size:5 final size:5
Alignment explanation
Indices: 325712--325784 Score: 51
Period size: 5 Copynumber: 13.8 Consensus size: 5
325702 AAAAAGGGAG
*
325712 AAAAT AAAAT AAAGAT AAAAT AAAAT AAAGAT AAGGGA- AAAAT AATAAT
1 AAAAT AAAAT AAA-AT AAAAT AAAAT AAA-AT AA--AAT AAAAT AA-AAT
* *
325761 GAAA- AAAAC AAAAGT AAAAT AAAA
1 AAAAT AAAAT AAAA-T AAAAT AAAA
325785 ATACTCACAA
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
4 4 0.07
5 31 0.56
6 19 0.35
7 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.10, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:325731 original size:11 final size:10
Alignment explanation
Indices: 325712--325784 Score: 51
Period size: 11 Copynumber: 6.9 Consensus size: 10
325702 AAAAAGGGAG
325712 AAAATAAAAT
1 AAAATAAAAT
325722 AAAGATAAAAT
1 AAA-ATAAAAT
325733 AAAATAAAGAT
1 AAAATAAA-AT
*
325744 AAGGGA-AAAAT
1 AA--AATAAAAT
*
325755 AATAATGAAA-
1 AA-AATAAAAT
*
325765 AAAACAAAAGT
1 AAAATAAAA-T
325776 AAAATAAAA
1 AAAATAAAA
325785 ATACTCACAA
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
9 5 0.10
10 11 0.22
11 29 0.59
12 3 0.06
13 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.10, T:0.15
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:325733 original size:16 final size:16
Alignment explanation
Indices: 325712--325745 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
325702 AAAAAGGGAG
325712 AAAATAAAATAAAGAT
1 AAAATAAAATAAAGAT
325728 AAAATAAAATAAAGAT
1 AAAATAAAATAAAGAT
325744 AA
1 AA
325746 GGGAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (16 bp):
AAAATAAAATAAAGAT
Found at i:325915 original size:9 final size:9
Alignment explanation
Indices: 325903--325946 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
325893 CCAAAAAGAA
*
325903 AAAAATATT
1 AAAAATAAT
*
325912 AAAAATATT
1 AAAAATAAT
325921 AAAAAATAAT
1 -AAAAATAAT
325931 AAAAATAAT
1 AAAAATAAT
325940 AAAAATA
1 AAAAATA
325947 GAAGAATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
9 25 0.76
10 8 0.24
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (9 bp):
AAAAATAAT
Found at i:325924 original size:19 final size:19
Alignment explanation
Indices: 325902--325944 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
325892 GCCAAAAAGA
* *
325902 AAAAAATATTAAAAATATT
1 AAAAAATAATAAAAATAAT
325921 AAAAAATAATAAAAATAAT
1 AAAAAATAATAAAAATAAT
325940 AAAAA
1 AAAAA
325945 TAGAAGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAAATAATAAAAATAAT
Found at i:328745 original size:6 final size:6
Alignment explanation
Indices: 328722--328784 Score: 69
Period size: 6 Copynumber: 10.7 Consensus size: 6
328712 ACCCACCTTA
*
328722 TTTTC- TTTTC- TCTTCT TTTTCT TTTTCT TTTTCT CTTTT-T CTTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT -TTTTCT -TTTTCT
*
328769 TTTCCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTT
328785 TATTTCAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
5 9 0.18
6 37 0.73
7 5 0.10
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:328771 original size:25 final size:24
Alignment explanation
Indices: 328722--328790 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 24
328712 ACCCACCTTA
*
328722 TTTTC-TTTTCTC-TTCTTTTTCT
1 TTTTCTTTTTCTCTTTTTTTTTCT
328744 TTTTCTTTTTCTCTTTTTCTTTTCT
1 TTTTCTTTTTCTCTTTTT-TTTTCT
* *
328769 TTTCCTTTTTCT-TTTTTATTTC
1 TTTTCTTTTTCTCTTTTTTTTTC
328791 AATTTAGGGC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 5 0.12
23 11 0.27
24 8 0.20
25 17 0.41
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTCTTTTTCTCTTTTTTTTTCT
Found at i:340825 original size:13 final size:13
Alignment explanation
Indices: 340807--340831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
340797 GTTAACTGAT
340807 TTTAAAGAATTGG
1 TTTAAAGAATTGG
340820 TTTAAAGAATTG
1 TTTAAAGAATTG
340832 ATGAATAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (13 bp):
TTTAAAGAATTGG
Found at i:341378 original size:19 final size:19
Alignment explanation
Indices: 341354--341393 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
341344 GTTAGTACAA
341354 TACTAACATATGTAATCGT
1 TACTAACATATGTAATCGT
341373 TACTAACATATGTAATCGT
1 TACTAACATATGTAATCGT
341392 TA
1 TA
341394 TGAATTGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TACTAACATATGTAATCGT
Found at i:342054 original size:20 final size:20
Alignment explanation
Indices: 342026--342068 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
342016 TATATTAGGC
* *
342026 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
*
342046 TATTTTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
342066 TAT
1 TAT
342069 GGAATAATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.58
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:342137 original size:46 final size:45
Alignment explanation
Indices: 342080--342172 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 45
342070 GAATAATGTC
* *
342080 AAGTGTATTGGTAAAATAAGCTTACGAGCTTAT-GGTATTAAATGGT
1 AAGTATATTGGTAAAATAAGCTTACCAGCTTATAGG-A-TAAATGGT
342126 AAGTATATTGGTAAAATAAGCTTACCAGCTTATAGGATAAATGGT
1 AAGTATATTGGTAAAATAAGCTTACCAGCTTATAGGATAAATGGT
342171 AA
1 AA
342173 AAGATTTTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
45 10 0.23
46 32 0.73
47 2 0.05
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.32
Consensus pattern (45 bp):
AAGTATATTGGTAAAATAAGCTTACCAGCTTATAGGATAAATGGT
Found at i:354535 original size:123 final size:122
Alignment explanation
Indices: 354305--354537 Score: 276
Period size: 123 Copynumber: 1.9 Consensus size: 122
354295 TATAATCTTA
****
354305 AATTCTTAACTATAAAAATATATATTTTATTATTTTTCTTAATTTATCGAATATATTTTTTTGGT
1 AATTCTTAACTATAAAAATATATA-TTTATTATTTTTCTTAATTTATCGAATATATTTTTAAAAT
* * * * * *
354370 TTAAAGTAGGTGAAGTTTATTATTGAAGTTAAGAATATATATTTAAAATATATGTTTG
65 TTAAAGTAGATAAAATTTAATATTGAAGTTAAGAAAAAATATTTAAAATATATGTTTG
*
354428 AATTCTTAACTATAAAAATATATA-TTATT-TTTTTCTTAATTTATTGAATATATATTTTAAAAT
1 AATTCTTAACTATAAAAATATATATTTATTATTTTTCTTAATTTATCGAATATAT-TTTTAAAAT
*
354491 ATTATAAG-A-ATAAAATTTAAATATTTAAGTTAAGATAAAAATATTTA
65 -TTA-AAGTAGATAAAATTT-AATATTGAAGTTAAGA-AAAAATATTTA
354538 TAGTTAAGAA
Statistics
Matches: 93, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
120 23 0.25
121 16 0.17
122 18 0.19
123 36 0.39
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (122 bp):
AATTCTTAACTATAAAAATATATATTTATTATTTTTCTTAATTTATCGAATATATTTTTAAAATT
TAAAGTAGATAAAATTTAATATTGAAGTTAAGAAAAAATATTTAAAATATATGTTTG
Found at i:358578 original size:21 final size:21
Alignment explanation
Indices: 358552--358613 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
358542 AGTAAAAAAT
358552 AATAATAATAATTTAGGTAAA
1 AATAATAATAATTTAGGTAAA
*
358573 AATAATAATAATTTAGATAAA
1 AATAATAATAATTTAGGTAAA
* *
358594 AATAATAATATTTTAAGTAA
1 AATAATAATAATTTAGGTAA
358614 TTTAATAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (21 bp):
AATAATAATAATTTAGGTAAA
Found at i:358578 original size:24 final size:24
Alignment explanation
Indices: 358546--358603 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 24
358536 GTTTTAAGTA
*
358546 AAAAATAATAATAATAATTTAGGT
1 AAAAATAATAATAATAATTTAGAT
358570 --AAA-AATAATAATAATTTAGAT
1 AAAAATAATAATAATAATTTAGAT
358591 AAAAATAATAATA
1 AAAAATAATAATA
358604 TTTTAAGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 17 0.57
22 3 0.10
23 3 0.10
24 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (24 bp):
AAAAATAATAATAATAATTTAGAT
Found at i:367912 original size:18 final size:21
Alignment explanation
Indices: 367867--367912 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
367857 CTCTTATGGG
*
367867 GAGTATCGATACTCTACCCTT
1 GAGTATCGATACTCTACCCAT
367888 G-GTATCGATA-T-T-CCCAT
1 GAGTATCGATACTCTACCCAT
367905 GAGTATCG
1 GAGTATCG
367913 GTACCAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 5 0.22
18 7 0.30
19 1 0.04
20 9 0.39
21 1 0.04
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (21 bp):
GAGTATCGATACTCTACCCAT
Found at i:368972 original size:14 final size:15
Alignment explanation
Indices: 368947--368975 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
368937 GTCCATTCGA
368947 ATAAACCCAAAACTC
1 ATAAACCCAAAACTC
368962 ATAAA-CCAAAACTC
1 ATAAACCCAAAACTC
368976 GAGGCGTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.31, G:0.00, T:0.14
Consensus pattern (15 bp):
ATAAACCCAAAACTC
Found at i:375697 original size:51 final size:52
Alignment explanation
Indices: 375640--375748 Score: 125
Period size: 51 Copynumber: 2.1 Consensus size: 52
375630 AACAGTAGCT
* * *
375640 AAAATGCAAGAAAAT-AAAAT-TTAGTAGTTAAATAAGAAA-TAAATAGTGACC
1 AAAATGC-A-AAAATGAAAATAATAGTAGCTAAATAAGAAATTAAAAAGTGACC
* * *
375691 AAAATGCAAAAATGAAAATAATAGTAGCTAAATCAGAAATTAAAAAGTTACT
1 AAAATGCAAAAATGAAAATAATAGTAGCTAAATAAGAAATTAAAAAGTGACC
375743 AAAATG
1 AAAATG
375749 AATAAATTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
49 5 0.10
50 6 0.12
51 23 0.47
52 15 0.31
ACGTcount: A:0.58, C:0.06, G:0.13, T:0.23
Consensus pattern (52 bp):
AAAATGCAAAAATGAAAATAATAGTAGCTAAATAAGAAATTAAAAAGTGACC
Found at i:377356 original size:58 final size:58
Alignment explanation
Indices: 377226--377426 Score: 222
Period size: 58 Copynumber: 3.4 Consensus size: 58
377216 GTAAGACGTG
* * *
377226 GCTGATTCGAAGTGTTGTGAATCGAGCACATGAAATGTAATCCCCTCTAGTGGGGCATT
1 GCTGATTCGAAGTGTTGTGAATCGAGCA-AAGAAATGTAAACCCCTCTGGTGGGGCATT
* ** * **
377285 GCTAATTCGAAGTGTCATGAATCGAGCAAAGAAATGTAAACCCCTCTGGTGGTGTGTT
1 GCTGATTCGAAGTGTTGTGAATCGAGCAAAGAAATGTAAACCCCTCTGGTGGGGCATT
* * * * *
377343 GTTGATTCAAAGTGTTGTGAATCGAGTAAAGAAATGTTAACCCCTCTGGTGGGGCATC
1 GCTGATTCGAAGTGTTGTGAATCGAGCAAAGAAATGTAAACCCCTCTGGTGGGGCATT
* * * **
377401 ACTGATTCAAAATGACGTGAATCGAG
1 GCTGATTCGAAGTGTTGTGAATCGAG
377427 TGAAGGAAAT
Statistics
Matches: 117, Mismatches: 25, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
58 92 0.79
59 25 0.21
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (58 bp):
GCTGATTCGAAGTGTTGTGAATCGAGCAAAGAAATGTAAACCCCTCTGGTGGGGCATT
Found at i:377525 original size:41 final size:41
Alignment explanation
Indices: 377461--377567 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
377451 GGCCGAAGGT
* * * *
377461 CTTATGGATGGCCCAAATAACTTA-TCATCTTGCTCAAAAGA
1 CTTAT-GATGGCCCGAATGACTTACACATCATGCTCAAAAGA
**
377502 CTTATAGATGGCCCGAATGACTTACACATCATGCTTGAAAGA
1 CTTAT-GATGGCCCGAATGACTTACACATCATGCTCAAAAGA
*
377544 CTTACTGATGGCCCGAAGGACTTA
1 CTTA-TGATGGCCCGAATGACTTA
377568 AGCTGATTCG
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 21 0.38
42 34 0.61
43 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (41 bp):
CTTATGATGGCCCGAATGACTTACACATCATGCTCAAAAGA
Found at i:377835 original size:286 final size:284
Alignment explanation
Indices: 377289--377853 Score: 764
Period size: 286 Copynumber: 2.0 Consensus size: 284
377279 GGCATTGCTA
* * *
377289 ATTCGAAGTGTCATGAATCGAGCAAAGAAATGTAAACCCCTCTGGTGGTGTGTTGTTGATTCAAA
1 ATTCGAAGTGTCATGAATCGACCAAAGAAATGTAAACCCCTCTAGTGGTGGGTTGTTGATTCAAA
* * * * *
377354 GTGTTGTGAATCGAGTAAAGAAATGTTAACCCCTCTGGTGGGGCATCACTGATTCAAAATGACGT
66 GTATCGTGAATCAAGAAAAGAAATGTTAACCCCTCTAGTGGGGCATCACTGATTCAAAATGACGT
* * *
377419 GAATCGAGTGAAGGAAATGTTGAAAACACCCTGGCCGAAGGTCTTATGGATGGCCCAAATAACTT
131 GAATCGAGTGAAGGAAATGTGGAAAACACCCTGGCCGAAGGTCTTATAGATGGCCCAAAGAACTT
* * * * * * *
377484 ATCATCTTGCTCAAAAGACTTATAGATGGCCCGAATGACTTACACATCATGCTTGAAAGACTTAC
196 ATCATCCTGCTCAAAAGACTTAGAGATGACCCAAAGGACTTACACATCATGCTCGAAAAACTTAC
377549 TGATGGCCCGAAGGACTTAAGCTG
261 TGATGGCCCGAAGGACTTAAGCTG
* * * *
377573 ATTCGAAGTGTTATGAATCGAACCATAGGAAATTTTAACCCCTCTAGTGG-GGGATTGTTGATTC
1 ATTCGAAGTGTCATGAATCG-ACCA-AAGAAATGTAAACCCCTCTAGTGGTGGG-TTGTTGATTC
*
377637 GAAA-TATCGTGAATCAAGCAAAAGAAATGTTAACCCCTCTAGTGGGGCATCACTGATTCGAAAT
63 -AAAGTATCGTGAATCAAG-AAAAGAAATGTTAACCCCTCTAGTGGGGCATCACTGATTCAAAAT
* *
377701 GTA-GTGAAT-GAGTGAAGGAAATGTGGAAAACATCCT-GCCTGAAGGTCTTATAGATGGCCCGA
126 G-ACGTGAATCGAGTGAAGGAAATGTGGAAAACACCCTGGCC-GAAGGTCTTATAGATGGCCCAA
* * *
377763 AGAACTTATCATCCTGCTCGAAAGACTTAGAGATGACCCAAAGGATTTA-AGTATCATGCTCGAA
189 AGAACTTATCATCCTGCTCAAAAGACTTAGAGATGACCCAAAGGACTTACA-CATCATGCTCGAA
377827 AAACTTACTGATGGCCCGAAGGACTTA
253 AAACTTACTGATGGCCCGAAGGACTTA
377854 CTCACCAAGA
Statistics
Matches: 245, Mismatches: 28, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
284 19 0.08
285 9 0.04
286 164 0.67
287 52 0.21
288 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (284 bp):
ATTCGAAGTGTCATGAATCGACCAAAGAAATGTAAACCCCTCTAGTGGTGGGTTGTTGATTCAAA
GTATCGTGAATCAAGAAAAGAAATGTTAACCCCTCTAGTGGGGCATCACTGATTCAAAATGACGT
GAATCGAGTGAAGGAAATGTGGAAAACACCCTGGCCGAAGGTCTTATAGATGGCCCAAAGAACTT
ATCATCCTGCTCAAAAGACTTAGAGATGACCCAAAGGACTTACACATCATGCTCGAAAAACTTAC
TGATGGCCCGAAGGACTTAAGCTG
Found at i:379369 original size:28 final size:28
Alignment explanation
Indices: 379337--379393 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
379327 GATAAAATGC
* *
379337 TTAGGCTGACTTGGGAAGGTAATGTGTT
1 TTAGGCTAACTTGGGAAGATAATGTGTT
* * *
379365 TTAGGTTAATTTGGGGAGATAATGTGTT
1 TTAGGCTAACTTGGGAAGATAATGTGTT
379393 T
1 T
379394 CAAGTTAGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.23, C:0.04, G:0.33, T:0.40
Consensus pattern (28 bp):
TTAGGCTAACTTGGGAAGATAATGTGTT
Found at i:379400 original size:28 final size:28
Alignment explanation
Indices: 379347--379400 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
379337 TTAGGCTGAC
* * *
379347 TTGGGAAGGTAATGTGTTTTAGGTTAAT
1 TTGGGAAGATAATGTGTTTCAAGTTAAT
*
379375 TTGGGGAGATAATGTGTTTCAAGTTA
1 TTGGGAAGATAATGTGTTTCAAGTTA
379401 GCTTCTTGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.26, C:0.02, G:0.31, T:0.41
Consensus pattern (28 bp):
TTGGGAAGATAATGTGTTTCAAGTTAAT
Found at i:379886 original size:4 final size:4
Alignment explanation
Indices: 379870--379951 Score: 77
Period size: 4 Copynumber: 21.8 Consensus size: 4
379860 TTTTATCGGT
*
379870 TTTC TTT- TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTTT TTTC TTT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC
* * *
379917 TTTG TTT- TTTC CTTC -TTC TTT- TTT- ATTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
379952 TCTATCTTTA
Statistics
Matches: 67, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
3 17 0.25
4 47 0.70
5 3 0.04
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:379890 original size:8 final size:8
Alignment explanation
Indices: 379870--379951 Score: 77
Period size: 7 Copynumber: 10.9 Consensus size: 8
379860 TTTTATCGGT
379870 TTTCTTT-
1 TTTCTTTC
379877 TTTCTTTC
1 TTTCTTTC
379885 TTTCTTTC
1 TTTCTTTC
379893 TTTCTTTC
1 TTTCTTTC
*
379901 TTTCTTTTT
1 TTTC-TTTC
379910 TTTCTTT-
1 TTTCTTTC
*
379917 TTTGTTT-
1 TTTCTTTC
*
379924 TTTCCTTC
1 TTTCTTTC
379932 -TTCTTT-
1 TTTCTTTC
*
379938 TTT-ATTC
1 TTTCTTTC
379945 TTTCTTT
1 TTTCTTT
379952 TCTATCTTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
6 2 0.03
7 28 0.45
8 25 0.40
9 7 0.11
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.79
Consensus pattern (8 bp):
TTTCTTTC
Found at i:379946 original size:40 final size:40
Alignment explanation
Indices: 379869--379954 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 40
379859 ATTTTATCGG
* *
379869 TTTTCTTTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTT
1 TTTTCTTTTTTCTTTCTTTCCTTCTTTCTTTCTTTCTTTC
* *
379909 TTTTCTTTTTTGTTT-TTTCCTTC-TTCTTTTTTATTCTTTC
1 TTTTCTTTTTTCTTTCTTTCCTTCTTTC-TTTCT-TTCTTTC
379949 TTTTCT
1 TTTTCT
379955 ATCTTTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
38 3 0.08
39 11 0.28
40 26 0.65
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.79
Consensus pattern (40 bp):
TTTTCTTTTTTCTTTCTTTCCTTCTTTCTTTCTTTCTTTC
Found at i:381338 original size:14 final size:15
Alignment explanation
Indices: 381316--381352 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
381306 GTAAATACAA
*
381316 AGATGCAAAAATGGG
1 AGATGCAAAAATGCG
381331 AG-TGC-AAAATGCG
1 AGATGCAAAAATGCG
381344 AGATGCAAA
1 AGATGCAAA
381353 TGCAACAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 9 0.47
14 6 0.32
15 4 0.21
ACGTcount: A:0.46, C:0.11, G:0.30, T:0.14
Consensus pattern (15 bp):
AGATGCAAAAATGCG
Found at i:383800 original size:26 final size:25
Alignment explanation
Indices: 383755--383826 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 25
383745 ACTTAATTTT
*
383755 AAAAAATAAATCAACGATAATAA-AAA
1 AAAAAATAAAACAAC-ATAA-AATAAA
*
383781 AAAAAGTGAAAACAACATAAAATAAA
1 AAAAAAT-AAAACAACATAAAATAAA
383807 AAAAAATAAAACAAACATAA
1 AAAAAATAAAAC-AACATAA
383827 GTACAAGGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 7 0.17
26 26 0.65
27 7 0.17
ACGTcount: A:0.75, C:0.08, G:0.04, T:0.12
Consensus pattern (25 bp):
AAAAAATAAAACAACATAAAATAAA
Found at i:383950 original size:51 final size:51
Alignment explanation
Indices: 383853--383983 Score: 142
Period size: 51 Copynumber: 2.6 Consensus size: 51
383843 GCATAAAATA
* * * *
383853 AAAT-AATAGTGACTAAAATACAAGAAAATAAAATTTAGTAGTTAAATAAG
1 AAATAAATAGTGACTAAAATGCAAGAAATTAAAATATAGTAGCTAAATAAG
* * *
383903 AAATAAATATTGACCAAAATGCAA-AAATTAAAATAATAGTAGCTAAATCAG
1 AAATAAATAGTGACTAAAATGCAAGAAATTAAAAT-ATAGTAGCTAAATAAG
* *
383954 AAATTAAAAAGTGACTAAAATG-AATAAATT
1 AAA-TAAATAGTGACTAAAATGCAAGAAATT
383984 GCAAATATCA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
50 13 0.19
51 34 0.51
52 20 0.30
ACGTcount: A:0.58, C:0.06, G:0.11, T:0.25
Consensus pattern (51 bp):
AAATAAATAGTGACTAAAATGCAAGAAATTAAAATATAGTAGCTAAATAAG
Found at i:384122 original size:33 final size:32
Alignment explanation
Indices: 384063--384127 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
384053 TAAAAACTAA
** *
384063 TGACTAAATTCGAATAAATCAGAATAATAATAG
1 TGACTAAATTAAAATAAATCAAAATAA-AATAG
384096 TGACTAAATTAAAATAAAAT-AAAATAAAATAG
1 TGACTAAATTAAAAT-AAATCAAAATAAAATAG
384128 AATGATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 5 0.18
33 19 0.68
34 4 0.14
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.26
Consensus pattern (32 bp):
TGACTAAATTAAAATAAATCAAAATAAAATAG
Found at i:394068 original size:22 final size:22
Alignment explanation
Indices: 394043--394095 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
394033 AAGTGCCTCG
394043 GCACTGATACGAAAGTGCATTA
1 GCACTGATACGAAAGTGCATTA
* *
394065 GCACTAATACGGAAGTGCATTA
1 GCACTGATACGAAAGTGCATTA
394087 GCACTGATA
1 GCACTGATA
394096 TACTAAAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (22 bp):
GCACTGATACGAAAGTGCATTA
Found at i:395130 original size:21 final size:21
Alignment explanation
Indices: 395053--395134 Score: 92
Period size: 21 Copynumber: 3.9 Consensus size: 21
395043 TAAGCCTTCA
* * *
395053 GTATGAATATCAGTTCATCTG
1 GTATGGATACCAGTTCATCCG
* **
395074 GTATAGATACCAACTCATCCG
1 GTATGGATACCAGTTCATCCG
* *
395095 ATATGGATACTAGTTCATCCG
1 GTATGGATACCAGTTCATCCG
395116 GTATGGATACCAGTTCATC
1 GTATGGATACCAGTTCATC
395135 TAGTATCGAA
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (21 bp):
GTATGGATACCAGTTCATCCG
Found at i:395148 original size:21 final size:21
Alignment explanation
Indices: 395106--395148 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
395096 TATGGATACT
* * *
395106 AGTTCATCCGGTATGGATACC
1 AGTTCATCCAGTATCGAAACC
*
395127 AGTTCATCTAGTATCGAAACC
1 AGTTCATCCAGTATCGAAACC
395148 A
1 A
395149 ATACTCTGGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (21 bp):
AGTTCATCCAGTATCGAAACC
Found at i:396805 original size:43 final size:43
Alignment explanation
Indices: 396757--396842 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
396747 CAGTAATTTT
396757 AAATTTATGATTAGATGTATTGATAATGATTTCTTATAAATAA
1 AAATTTATGATTAGATGTATTGATAATGATTTCTTATAAATAA
396800 AAATTTATGATTAGATGTATTGATAATGATTTCTTATAAATAA
1 AAATTTATGATTAGATGTATTGATAATGATTTCTTATAAATAA
396843 GATTAAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (43 bp):
AAATTTATGATTAGATGTATTGATAATGATTTCTTATAAATAA
Found at i:403686 original size:13 final size:13
Alignment explanation
Indices: 403668--403715 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
403658 TTAAATGATA
*
403668 AATAAAAAATTAC
1 AATAAAAAACTAC
* *
403681 AATAAAAAAGTCC
1 AATAAAAAACTAC
*
403694 AATAAACAACTAC
1 AATAAAAAACTAC
403707 AATAAAAAA
1 AATAAAAAA
403716 GTACTAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.69, C:0.12, G:0.02, T:0.17
Consensus pattern (13 bp):
AATAAAAAACTAC
Found at i:403728 original size:26 final size:26
Alignment explanation
Indices: 403668--403717 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
403658 TTAAATGATA
* *
403668 AATAAAAAATTACAATAAAAAAGTCC
1 AATAAACAACTACAATAAAAAAGTCC
403694 AATAAACAACTACAATAAAAAAGT
1 AATAAACAACTACAATAAAAAAGT
403718 ACTAAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.66, C:0.12, G:0.04, T:0.18
Consensus pattern (26 bp):
AATAAACAACTACAATAAAAAAGTCC
Found at i:404179 original size:32 final size:32
Alignment explanation
Indices: 404134--404199 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
404124 AGCCTCCAGA
* * *
404134 GGGTCATATAACTATGTGACGGTGGCGGCGGC
1 GGGTCATAAAACTAGGTGAAGGTGGCGGCGGC
*
404166 GGGTCATAAAACTAGGTGAAGGTGGCGGTGGC
1 GGGTCATAAAACTAGGTGAAGGTGGCGGCGGC
404198 GG
1 GG
404200 TGGCGGTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.21, C:0.15, G:0.44, T:0.20
Consensus pattern (32 bp):
GGGTCATAAAACTAGGTGAAGGTGGCGGCGGC
Found at i:407604 original size:14 final size:14
Alignment explanation
Indices: 407585--407619 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
407575 TTTTTTACTT
407585 TTTTTAATAGAACA
1 TTTTTAATAGAACA
* *
407599 TTTTTAATGGAATA
1 TTTTTAATAGAACA
407613 TTTTTAA
1 TTTTTAA
407620 AAATCAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (14 bp):
TTTTTAATAGAACA
Found at i:410619 original size:21 final size:23
Alignment explanation
Indices: 410575--410622 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
410565 GAAAAAATCC
410575 GAGGAAGAAGCTTCAGCATCGAAG
1 GAGGAAGAAGCTTCAG-ATCGAAG
*
410599 GAGGAAGAAGC-TCAG-TTGAAG
1 GAGGAAGAAGCTTCAGATCGAAG
410620 GAG
1 GAG
410623 AGCCTAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 8 0.35
23 4 0.17
24 11 0.48
ACGTcount: A:0.38, C:0.12, G:0.38, T:0.12
Consensus pattern (23 bp):
GAGGAAGAAGCTTCAGATCGAAG
Found at i:413239 original size:2 final size:2
Alignment explanation
Indices: 413232--413256 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
413222 AAATTTATTA
413232 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
413257 ATAATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:413365 original size:36 final size:36
Alignment explanation
Indices: 413313--413385 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
413303 TACTAAACCA
413313 TCCCCGTTTAACATAAACGGTTTTTCCCCGTCCCCG
1 TCCCCGTTTAACATAAACGGTTTTTCCCCGTCCCCG
**
413349 TCCCCGTTTAGTATAAACGGTTTTTCCCCGTCCCCG
1 TCCCCGTTTAACATAAACGGTTTTTCCCCGTCCCCG
413385 T
1 T
413386 TTAATTCAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.15, C:0.37, G:0.15, T:0.33
Consensus pattern (36 bp):
TCCCCGTTTAACATAAACGGTTTTTCCCCGTCCCCG
Found at i:416086 original size:19 final size:21
Alignment explanation
Indices: 416059--416101 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
416049 TTTTCCTTCG
*
416059 AAAGCAAAATTGG-ATTTTGA
1 AAAGCAAAAATGGAATTTTGA
416079 AAAG-AAAAATGGAATTTTGA
1 AAAGCAAAAATGGAATTTTGA
416099 AAA
1 AAA
416102 ATGATTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.53, C:0.02, G:0.19, T:0.26
Consensus pattern (21 bp):
AAAGCAAAAATGGAATTTTGA
Found at i:420600 original size:23 final size:23
Alignment explanation
Indices: 420570--420618 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
420560 TGGTGGTTGG
*
420570 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
420593 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
420616 TTT
1 TTT
420619 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:442433 original size:11 final size:11
Alignment explanation
Indices: 442417--442447 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
442407 ATGGAATATG
442417 GTAAATAAACA
1 GTAAATAAACA
442428 GTAAATAAACA
1 GTAAATAAACA
*
442439 GCAAATAAA
1 GTAAATAAA
442448 ATGAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.16
Consensus pattern (11 bp):
GTAAATAAACA
Found at i:443782 original size:33 final size:33
Alignment explanation
Indices: 443745--443825 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
443735 AGTCTTACTT
*
443745 GGACTCAAGATGC-TTCGTTTTAGTGTTTCAATA
1 GGACTCAA-ATACGTTCGTTTTAGTGTTTCAATA
*
443778 GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAATACGTTCGTTTTAGTGTTTCAATA
**
443811 AAACTCAAATACGTT
1 GGACTCAAATACGTT
443826 GATTTATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 3 0.07
33 40 0.93
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (33 bp):
GGACTCAAATACGTTCGTTTTAGTGTTTCAATA
Found at i:443826 original size:33 final size:33
Alignment explanation
Indices: 443761--443826 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
443751 AAGATGCTTC
**
443761 GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
1 GTTTTAGTGTTTCAATAAAACTCAAATACGTTG
443794 GTTTTAGTGTTTCAATAAAACTCAAATACGTTG
1 GTTTTAGTGTTTCAATAAAACTCAAATACGTTG
443827 ATTTATTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (33 bp):
GTTTTAGTGTTTCAATAAAACTCAAATACGTTG
Found at i:453444 original size:39 final size:35
Alignment explanation
Indices: 453401--453493 Score: 96
Period size: 39 Copynumber: 2.5 Consensus size: 35
453391 AATATGAAAT
* *
453401 AATTTAATAAATTAAAAATTTAGAATGTTATGGTAGTAA
1 AATTTAA-AAATTATAAATTTAGAAT-TT-TAG-AGTAA
* * *
453440 AATTTAAGAAATGATGAATTTAGAATTTTAGAGTGA
1 AATTTAA-AAATTATAAATTTAGAATTTTAGAGTAA
453476 AATTTAAAAATTATAAAT
1 AATTTAAAAATTATAAAT
453494 AAACATTTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
35 9 0.20
36 11 0.24
37 2 0.04
38 2 0.04
39 22 0.48
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (35 bp):
AATTTAAAAATTATAAATTTAGAATTTTAGAGTAA
Found at i:455234 original size:56 final size:55
Alignment explanation
Indices: 455138--455247 Score: 145
Period size: 56 Copynumber: 2.0 Consensus size: 55
455128 AATTTTTGAA
*
455138 AATATATATATTATATAGTTTTGAAAACGGTATTCGAATATATATAT-ATATATG
1 AATATATATATTATATAGTTTTGAAAACGATATTCGAATATATATATAATATATG
*
455192 AATATATATATATATTATAGTTTTGAAAAC-AT-TTTGAAAATATATATATAATATAT
1 AATATATATAT-TA-TATAGTTTTGAAAACGATATTCG--AATATATATATAATATAT
455248 AATTTTTGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
54 14 0.29
55 3 0.06
56 26 0.53
57 6 0.12
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (55 bp):
AATATATATATTATATAGTTTTGAAAACGATATTCGAATATATATATAATATATG
Found at i:455235 original size:54 final size:54
Alignment explanation
Indices: 455138--455241 Score: 149
Period size: 54 Copynumber: 1.9 Consensus size: 54
455128 AATTTTTGAA
* *
455138 AATATATATATTATATAGTTTTGAAAACGGTATTCGAATATATATATATATATG
1 AATATATATATTATATAGTTTTGAAAACGATATTCGAAAATATATATATATATG
*
455192 AATATATATATATATTATAGTTTTGAAAAC-AT-TTTGAAAATATATATATA
1 AATATATATAT-TA-TATAGTTTTGAAAACGATATTCGAAAATATATATATA
455242 ATATATAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
54 27 0.60
55 3 0.07
56 15 0.33
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (54 bp):
AATATATATATTATATAGTTTTGAAAACGATATTCGAAAATATATATATATATG
Found at i:455273 original size:26 final size:28
Alignment explanation
Indices: 455223--455313 Score: 150
Period size: 28 Copynumber: 3.3 Consensus size: 28
455213 TTTGAAAACA
*
455223 TTTTGAAAATATATATATAATATATAAT
1 TTTTGAAAATATATATATAATATATAGT
455251 TTTTGAAAATATATATATAATATATAGT
1 TTTTGAAAATATATATATAATATATAGT
*
455279 TTTTGAAAACATAT-T-TAATATATAGT
1 TTTTGAAAATATATATATAATATATAGT
455305 TTTTGAAAA
1 TTTTGAAAA
455314 CATTTTGAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
26 20 0.33
27 1 0.02
28 40 0.66
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (28 bp):
TTTTGAAAATATATATATAATATATAGT
Found at i:455299 original size:37 final size:36
Alignment explanation
Indices: 455289--455364 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 36
455279 TTTTGAAAAC
* *
455289 ATATTTAATATATAGTTTTTGAAAACATTTTGAATAT
1 ATATATAATATATAGTTTTTGAAAA-ATTATGAATAT
455326 ATATATAATATATAGTTTTTGAAAAATATAT-AATAT
1 ATATATAATATATAGTTTTTGAAAAAT-TATGAATAT
455362 ATA
1 ATA
455365 GTTTTTTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 10 0.28
37 26 0.72
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (36 bp):
ATATATAATATATAGTTTTTGAAAAATTATGAATAT
Found at i:455324 original size:26 final size:26
Alignment explanation
Indices: 455223--455328 Score: 133
Period size: 28 Copynumber: 3.9 Consensus size: 26
455213 TTTGAAAACA
* *
455223 TTTTGAAAATATATATATAATATATAAT
1 TTTTGAAAACATAT-T-TAATATATAGT
*
455251 TTTTGAAAATATATATATAATATATAGT
1 TTTTGAAAACATAT-T-TAATATATAGT
455279 TTTTGAAAACATATTTAATATATAGT
1 TTTTGAAAACATATTTAATATATAGT
455305 TTTTGAAAACAT-TTTGAATATATA
1 TTTTGAAAACATATTT-AATATATA
455329 TATAATATAT
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
25 3 0.04
26 31 0.41
27 1 0.01
28 40 0.53
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (26 bp):
TTTTGAAAACATATTTAATATATAGT
Found at i:455334 original size:63 final size:65
Alignment explanation
Indices: 455249--455411 Score: 241
Period size: 63 Copynumber: 2.6 Consensus size: 65
455239 ATAATATATA
*
455249 ATTTTTGAAAATATATATATAATATATAGTTTTTGAAAACATATTTAATATATAG-TTTTTGAAA
1 ATTTTTG--AATATATATATAATATATAGTTTTTGAAAACATATATAATATATAGTTTTTTGAAA
455313 AC
64 AC
455315 A-TTTTGAATATATATATAATATATAGTTTTTGAAAA-ATATATAATATATAGTTTTTTGAAAAC
1 ATTTTTGAATATATATATAATATATAGTTTTTGAAAACATATATAATATATAGTTTTTTGAAAAC
*
455378 ATTTTTTAA-ATATATATAATATA-A--TTTTGAAAAC
1 ATTTTTGAATATATATATAATATATAGTTTTTGAAAAC
455412 GTTTTAGAAA
Statistics
Matches: 92, Mismatches: 2, Indels: 11
0.88 0.02 0.10
Matches are distributed among these distances:
60 9 0.10
62 15 0.16
63 56 0.61
64 6 0.07
65 5 0.05
66 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (65 bp):
ATTTTTGAATATATATATAATATATAGTTTTTGAAAACATATATAATATATAGTTTTTTGAAAAC
Found at i:455354 original size:25 final size:26
Alignment explanation
Indices: 455316--455376 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 26
455306 TTTGAAAACA
*
455316 TTTTGAATATATATATAATATATAG-T
1 TTTTGAA-AAATATATAATATATAGTT
455342 TTTTGAAAAATATATAATATATAGTT
1 TTTTGAAAAATATATAATATATAGTT
455368 TTTTGAAAA
1 TTTTGAAAA
455377 CATTTTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
25 16 0.48
26 17 0.52
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (26 bp):
TTTTGAAAAATATATAATATATAGTT
Found at i:455363 original size:27 final size:28
Alignment explanation
Indices: 455321--455393 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
455311 AAACATTTTG
455321 AATATATATATAATATATAG-TTTTTGAAA
1 AATATAT-TA-AATATATAGTTTTTTGAAA
455350 AATATA-T-AATATATAGTTTTTTGAAA
1 AATATATTAAATATATAGTTTTTTGAAA
* *
455376 ACATTTTTTAAATATATA
1 A-ATATATTAAATATATA
455394 TAATATAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
25 9 0.24
26 10 0.26
27 4 0.11
28 1 0.03
29 14 0.37
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (28 bp):
AATATATTAAATATATAGTTTTTTGAAA
Found at i:467194 original size:15 final size:14
Alignment explanation
Indices: 467170--467204 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
467160 ATAAAATAAT
467170 TAAAATCAAATACA
1 TAAAATCAAATACA
467184 TAAATATCAAATACA
1 TAAA-ATCAAATACA
*
467199 AAAAAT
1 TAAAAT
467205 ATTTATTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAAATCAAATACA
Found at i:470996 original size:30 final size:31
Alignment explanation
Indices: 470933--471001 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 31
470923 CTTTTAAAAC
* **
470933 TTGCAATACAGTCCCCCAACATTTAGAGTGT
1 TTGCAATACAATCCCCCAACATTTAGACCGT
* *
470964 TTGTAATACAAT-CCCCAACATTTAGTCCGT
1 TTGCAATACAATCCCCCAACATTTAGACCGT
470994 TTGCAATA
1 TTGCAATA
471002 TGGTCCCCGA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (31 bp):
TTGCAATACAATCCCCCAACATTTAGACCGT
Found at i:472307 original size:31 final size:31
Alignment explanation
Indices: 472272--472339 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
472262 CGGATACGTC
*
472272 GGGGACCATATTGCAAA-TAGACTAAATGTTG
1 GGGGACCATATTACAAACT-GACTAAATGTTG
***
472303 GGGGATTGTATTACAAACTGACTAAATGTTG
1 GGGGACCATATTACAAACTGACTAAATGTTG
*
472334 AGGGAC
1 GGGGAC
472340 TGTATTGTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (31 bp):
GGGGACCATATTACAAACTGACTAAATGTTG
Found at i:484665 original size:18 final size:20
Alignment explanation
Indices: 484634--484674 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
484624 TATTTTTTAA
484634 AAAGAAAACAC-AAACTTTG
1 AAAGAAAACACAAAACTTTG
*
484653 AAAG-AAACCCAAAACTTTG
1 AAAGAAAACACAAAACTTTG
484672 AAA
1 AAA
484675 ATCTTCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.59, C:0.17, G:0.10, T:0.15
Consensus pattern (20 bp):
AAAGAAAACACAAAACTTTG
Found at i:484986 original size:2 final size:2
Alignment explanation
Indices: 484979--485003 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
484969 TTTCTTTTTA
484979 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
485004 ATTTTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:486457 original size:17 final size:17
Alignment explanation
Indices: 486412--486458 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
486402 CTTTAAAAAG
**
486412 TTTATAATTATTTTACTT
1 TTTAT-ATTATTTTAAGT
*
486430 TTTA-ATAATTTTAAGT
1 TTTATATTATTTTAAGT
486446 TTTATATTATTTT
1 TTTATATTATTTT
486459 TAAAGATTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 13 0.54
17 7 0.29
18 4 0.17
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (17 bp):
TTTATATTATTTTAAGT
Found at i:493519 original size:10 final size:10
Alignment explanation
Indices: 493506--493544 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
493496 CGTCTCGGCT
*
493506 CGGCTCGACA
1 CGGCACGACA
493516 CGGCACGACA
1 CGGCACGACA
*
493526 TGGCACGACA
1 CGGCACGACA
*
493536 CGACACGAC
1 CGGCACGAC
493545 TCAGCTCGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.28, C:0.38, G:0.28, T:0.05
Consensus pattern (10 bp):
CGGCACGACA
Found at i:493869 original size:22 final size:22
Alignment explanation
Indices: 493844--493898 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
493834 TCAGGAGTTA
* *
493844 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
493866 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
493888 CGGGAGTTATA
1 CAGGAGTTATA
493899 ACAACTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:494582 original size:23 final size:25
Alignment explanation
Indices: 494546--494591 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
494536 GTTTATTACT
* *
494546 TTTTTATTTCATTTTAT-TTTTTCC
1 TTTTGATTTCATTTAATGTTTTTCC
494570 TTTTGATTT-ATTTAATGTTTTT
1 TTTTGATTTCATTTAATGTTTTT
494592 TTATTTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTTGATTTCATTTAATGTTTTTCC
Found at i:494627 original size:29 final size:28
Alignment explanation
Indices: 494587--494645 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
494577 TTATTTAATG
* *
494587 TTTTTTTATTTTCTTTATTTTCTTATTAT
1 TTTTTTTATTTTCCTTATTTTCAT-TTAT
* *
494616 TTTTTTTCTTTTCCTTCTTTTCATTTAT
1 TTTTTTTATTTTCCTTATTTTCATTTAT
494644 TT
1 TT
494646 AATATTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (28 bp):
TTTTTTTATTTTCCTTATTTTCATTTAT
Found at i:494654 original size:11 final size:11
Alignment explanation
Indices: 494638--494662 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
494628 CCTTCTTTTC
494638 ATTTATTTAAT
1 ATTTATTTAAT
494649 ATTTATTTAAT
1 ATTTATTTAAT
494660 ATT
1 ATT
494663 CATTATCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTTATTTAAT
Found at i:495255 original size:33 final size:33
Alignment explanation
Indices: 495213--495288 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
495203 TCATTTTTTG
*
495213 TCTTAATTTTGCCTGAATTCCCATAATACTCCT
1 TCTTAATTTTGCCTGAATTCCCATAATACCCCT
*
495246 TCTTAATTTTGCCTGAATTCCCGTAATACCCCT
1 TCTTAATTTTGCCTGAATTCCCATAATACCCCT
* *
495279 CCTAAATTTT
1 TCTTAATTTT
495289 ATGATTCTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.24, C:0.28, G:0.07, T:0.42
Consensus pattern (33 bp):
TCTTAATTTTGCCTGAATTCCCATAATACCCCT
Found at i:496282 original size:28 final size:28
Alignment explanation
Indices: 496250--496315 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
496240 CTGACTTAAT
496250 GACATAATGTTTTAAATACTAGTTCGAA
1 GACATAATGTTTTAAATACTAGTTCGAA
* * *
496278 GACATAATGTTTTAAGTATTAGTTCGAT
1 GACATAATGTTTTAAATACTAGTTCGAA
496306 GACATAATGT
1 GACATAATGT
496316 GAACAAATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (28 bp):
GACATAATGTTTTAAATACTAGTTCGAA
Found at i:503976 original size:92 final size:90
Alignment explanation
Indices: 503743--504021 Score: 396
Period size: 91 Copynumber: 3.1 Consensus size: 90
503733 AGTTCATCGA
* * * *
503743 TTTTTAGAAAGTATATCGCGAAACGGATACAACTATAGATTTCATCGCAAAGATGAAAATTCCAC
1 TTTTTAGAAAATATATCGTGAAACGGATACAACGATAGATTTCATCGCAAAGATGAACATTCC-C
503808 TGAATGGTTCACTTATTATTTTTACT
65 TGAATGGTTCACTTATTATTTTTACT
** * *
503834 TTTTTTTAAAATATATCGTGAAACGAATACAACGATAGATTTCATTGCAAAGATGAACATTCCCT
1 TTTTTAGAAAATATATCGTGAAACGGATACAACGATAGATTTCATCGCAAAGATGAACATTCCC-
* *
503899 TGAATGGTTCATTTATTATGTTTACT
65 TGAATGGTTCACTTATTATTTTTACT
*
503925 CTTTTTAGAAAATATATCGTGAAACGGATACAAAGATAGATTTCATCGCAAAGATGAACATTCTC
1 -TTTTTAGAAAATATATCGTGAAACGGATACAACGATAGATTTCATCGCAAAGATGAACATTC-C
* * *
503990 CTAAATTGTTCACTTATTGTTTTTACT
64 CTGAATGGTTCACTTATTATTTTTACT
504017 TTTTT
1 TTTTT
504022 TTTGTCTCAA
Statistics
Matches: 165, Mismatches: 20, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
90 1 0.01
91 84 0.51
92 78 0.47
93 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (90 bp):
TTTTTAGAAAATATATCGTGAAACGGATACAACGATAGATTTCATCGCAAAGATGAACATTCCCT
GAATGGTTCACTTATTATTTTTACT
Found at i:504022 original size:92 final size:91
Alignment explanation
Indices: 503743--504022 Score: 400
Period size: 92 Copynumber: 3.1 Consensus size: 91
503733 AGTTCATCGA
* * * *
503743 TTTTTAGAAAGTATATCGCGAAACGGATACAACTATAGATTTCATCGCAAAGATGAAAATTCCAC
1 TTTTTAGAAAATATATCGTGAAACGGATACAACGATAGATTTCATCGCAAAGATGAACATTCC-C
503808 TGAATGGTTCACTTATTATTTTTACTT
65 TGAATGGTTCACTTATTATTTTTACTT
* * *
503835 TTTTT-TAAAATATATCGTGAAACGAATACAACGATAGATTTCATTGCAAAGATGAACATTCCCT
1 TTTTTAGAAAATATATCGTGAAACGGATACAACGATAGATTTCATCGCAAAGATGAACATTCCC-
* * *
503899 TGAATGGTTCATTTATTATGTTTACTC
65 TGAATGGTTCACTTATTATTTTTACTT
*
503926 TTTTTAGAAAATATATCGTGAAACGGATACAAAGATAGATTTCATCGCAAAGATGAACATTCTCC
1 TTTTTAGAAAATATATCGTGAAACGGATACAACGATAGATTTCATCGCAAAGATGAACATTC-CC
* * *
503991 TAAATTGTTCACTTATTGTTTTTACTT
65 TGAATGGTTCACTTATTATTTTTACTT
504018 TTTTT
1 TTTTT
504023 TTGTCTCAAA
Statistics
Matches: 165, Mismatches: 20, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
90 1 0.01
91 79 0.48
92 83 0.50
93 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (91 bp):
TTTTTAGAAAATATATCGTGAAACGGATACAACGATAGATTTCATCGCAAAGATGAACATTCCCT
GAATGGTTCACTTATTATTTTTACTT
Found at i:504912 original size:22 final size:22
Alignment explanation
Indices: 504884--504926 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
504874 CACAGTTAGC
504884 CGTTTAATCTTTTACCCAAAGG
1 CGTTTAATCTTTTACCCAAAGG
*
504906 CGTTTAATCTTTTACCTAAAG
1 CGTTTAATCTTTTACCCAAAG
504927 ACATTTAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.40
Consensus pattern (22 bp):
CGTTTAATCTTTTACCCAAAGG
Found at i:504912 original size:83 final size:81
Alignment explanation
Indices: 504737--504912 Score: 280
Period size: 83 Copynumber: 2.1 Consensus size: 81
504727 TCTTTCCTCT
* *
504737 AAAGGCATTTAACATTTCATCCAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGC
1 AAAGGCATTTAACATTTCATCCAACTTGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAGCC
504802 ATTTAATCTTTTACCC
66 ATTTAATCTTTTACCC
* *
504818 AAAGACATTTAACATTTTTCATCTAACTTGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAG
1 AAAGGCATTTAACA--TTTCATCCAACTTGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAG
*
504883 CCGTTTAATCTTTTACCC
64 CCATTTAATCTTTTACCC
*
504901 AAAGGCGTTTAA
1 AAAGGCATTTAA
504913 TCTTTTACCT
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
81 13 0.15
83 73 0.85
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (81 bp):
AAAGGCATTTAACATTTCATCCAACTTGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAGCC
ATTTAATCTTTTACCC
Found at i:504933 original size:22 final size:22
Alignment explanation
Indices: 504886--504939 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
504876 CAGTTAGCCG
* *
504886 TTTAATCTTTTACCCAAAGGCG
1 TTTAATCTTTTACCCAAAGACA
*
504908 TTTAATCTTTTACCTAAAGACA
1 TTTAATCTTTTACCCAAAGACA
*
504930 TTTAACCTTT
1 TTTAATCTTT
504940 CATCTAACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (22 bp):
TTTAATCTTTTACCCAAAGACA
Found at i:504984 original size:103 final size:104
Alignment explanation
Indices: 504798--505020 Score: 376
Period size: 103 Copynumber: 2.1 Consensus size: 104
504788 ATGCACAGTT
*
504798 AGGCATTTAATCTTTTACCCAAAGACATTTAACATTTTTCATCTAACTTGCATGATTGGCACCTT
1 AGGCATTTAATCTTTTACCCAAAGACATTTAACA-CTTTCATCTAACTTGCATGATTGGCACCTT
*
504863 TCTGCCAAATGCACAGTTAGCCGTTTAATCTTTTACCCAA
65 TCTACCAAATGCACAGTTAGCCGTTTAATCTTTTACCCAA
* *
504903 AGGCGTTTAATCTTTTACCTAAAGACATTTAAC-CTTTCATCTAACTTGCATGATTGGCACCTTT
1 AGGCATTTAATCTTTTACCCAAAGACATTTAACACTTTCATCTAACTTGCATGATTGGCACCTTT
*
504967 CTACCAAATGCACAGTTAGGCGTTTAATCTTTTACCCAA
66 CTACCAAATGCACAGTTAGCCGTTTAATCTTTTACCCAA
*
505006 AGGCATTTAACCTTT
1 AGGCATTTAATCTTT
505021 CATCTAACTT
Statistics
Matches: 111, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
103 80 0.72
105 31 0.28
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (104 bp):
AGGCATTTAATCTTTTACCCAAAGACATTTAACACTTTCATCTAACTTGCATGATTGGCACCTTT
CTACCAAATGCACAGTTAGCCGTTTAATCTTTTACCCAA
Found at i:505045 original size:81 final size:81
Alignment explanation
Indices: 504903--505081 Score: 304
Period size: 81 Copynumber: 2.2 Consensus size: 81
504893 TTTTACCCAA
* * *
504903 AGGCGTTTAATCTTTTACCTAAAGACATTTAACCTTTCATCTAACTTGCATGATTGGCACCTTTC
1 AGGCGTTTAATCTTTTACCCAAAGACATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTC
504968 TACCAAATGCACAGTT
66 TACCAAATGCACAGTT
*
504984 AGGCGTTTAATCTTTTACCCAAAGGCATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTC
1 AGGCGTTTAATCTTTTACCCAAAGACATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTC
*
505049 TACGAAATGCACAGTT
66 TACCAAATGCACAGTT
*
505065 AGACGTTTAATCTTTTA
1 AGGCGTTTAATCTTTTA
505082 TTTTAAAACA
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 92 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (81 bp):
AGGCGTTTAATCTTTTACCCAAAGACATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTC
TACCAAATGCACAGTT
Found at i:510820 original size:82 final size:81
Alignment explanation
Indices: 510680--510895 Score: 297
Period size: 82 Copynumber: 2.7 Consensus size: 81
510670 TCTTTCCTCT
* ** * * * *
510680 AAAGGCATTTAACCTTTTGTCTAACTTGCTTTATTAGCACATTTCTACCAAATGCACAGTTAGTC
1 AAAGGAATTTAACCTTTCATCTAACTTGCATGATTAGCACATTTCTACCAAATACACAGTTAGAC
*
510745 ATTTAATCTTTTACCC
66 ATTTAATCTTTTACAC
* *
510761 AAAGGTATTTAACCTTGTCATCTAACTTGCATGATTGGCACATTTCTACCAAATACACAGTTAGA
1 AAAGGAATTTAACCTT-TCATCTAACTTGCATGATTAGCACATTTCTACCAAATACACAGTTAGA
*
510826 CGTTTAATCTTTTACAC
65 CATTTAATCTTTTACAC
* * *
510843 AAAGGAATTTAACTTTTCATCTAACTTGCATGATTAGCACCTTTCTTCCAAAT
1 AAAGGAATTTAACCTTTCATCTAACTTGCATGATTAGCACATTTCTACCAAAT
510896 GCATTGTAAT
Statistics
Matches: 119, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
81 49 0.41
82 70 0.59
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.38
Consensus pattern (81 bp):
AAAGGAATTTAACCTTTCATCTAACTTGCATGATTAGCACATTTCTACCAAATACACAGTTAGAC
ATTTAATCTTTTACAC
Found at i:512254 original size:56 final size:56
Alignment explanation
Indices: 512169--512391 Score: 285
Period size: 56 Copynumber: 4.0 Consensus size: 56
512159 CAAATGATAT
*
512169 TGTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATATT-T-TATGGGCAC
1 TGTGTTTGCAAAAACTAAGAAATTCATAATAAGTTTATGAAT-TTCTGTATGGGCAC
* *
512224 TGTGTTTGCAAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAC
1 TGTGTTTGC-AAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCAC
* * * * * * *
512281 TATCTATGCAAAAACTAAGAAATTCATAATAAATTTATAAATTTCTGTTTGGGAAC
1 TGTGTTTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCAC
*
512337 TGT-ATT-CAAAAACTAAGAAATTCATAATAAGTTTATGAATTT-TCGTATGGGCAC
1 TGTGTTTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCT-GTATGGGCAC
512391 T
1 T
512392 ACGTGTGCAA
Statistics
Matches: 145, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
53 1 0.01
54 43 0.30
55 11 0.08
56 76 0.52
57 14 0.10
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (56 bp):
TGTGTTTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCAC
Found at i:512401 original size:110 final size:113
Alignment explanation
Indices: 512172--512402 Score: 330
Period size: 110 Copynumber: 2.1 Consensus size: 113
512162 ATGATATTGT
* * * *
512172 GTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATATTTTATGGGCACTGTGTTTGCAAAA
1 GTGTGCAAAAACTAAGAAATTCATAATAAATTTATAAATATTTTATGGGAACTGTGATTGCAAAA
*
512237 AACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATC
66 AACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTATC
* *
512285 -TATGCAAAAACTAAGAAATTCATAATAAATTTATAAAT-TTCTGTTTGGGAACTGT-ATT-C-A
1 GTGTGCAAAAACTAAGAAATTCATAATAAATTTATAAATATT-T-TATGGGAACTGTGATTGCAA
*
512345 AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTA-C
64 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTATC
512394 GTGTGCAAA
1 GTGTGCAAA
512403 CTACAGAGTT
Statistics
Matches: 106, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
109 1 0.01
110 54 0.51
111 3 0.03
112 38 0.36
113 10 0.09
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (113 bp):
GTGTGCAAAAACTAAGAAATTCATAATAAATTTATAAATATTTTATGGGAACTGTGATTGCAAAA
AACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTATC
Done.