Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007979.1 Hibiscus syriacus cultivar Beakdansim tig00110418_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: 2767453
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 13
Found at i:1044527 original size:26 final size:26
Alignment explanation
Indices: 1044498--1044770 Score: 204
Period size: 26 Copynumber: 11.5 Consensus size: 26
1044488 CACATTAACA
1044498 CATCCATTT-ATGCATTTTAATTATGG
1 CATCC-TTTCATGCATTTTAATTATGG
1044524 CATCCTTTCATGCATTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTATGG
*
1044550 CATCCTTTCATG------ACTTAT-G
1 CATCCTTTCATGCATTTTAATTATGG
*
1044569 CATTCTTTCATGCATTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTATGG
*
1044595 CATCCTTTCATGC--CTT-A--AT-G
1 CATCCTTTCATGCATTTTAATTATGG
*
1044615 CATCATTTCATGCATTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTATGG
* *
1044641 AATCCTTTCATGCATTTTAATTATGA
1 CATCCTTTCATGCATTTTAATTATGG
* * *
1044667 CATCCTTTCATTC--CTTAATGAT--
1 CATCCTTTCATGCATTTTAATTATGG
** * *
1044689 --TTATGTCATGCATTTTAATTATTG
1 CATCCTTTCATGCATTTTAATTATGG
*
1044713 CAT-CTTTCATGC--CTT-A--AT-G
1 CATCCTTTCATGCATTTTAATTATGG
*
1044732 CATCCTTTCATGCATTTTAACTATGG
1 CATCCTTTCATGCATTTTAATTATGG
*
1044758 CATCCTTTAATGC
1 CATCCTTTCATGC
1044771 CTTAATGCAT
Statistics
Matches: 195, Mismatches: 25, Indels: 54
0.71 0.09 0.20
Matches are distributed among these distances:
19 16 0.08
20 36 0.18
21 2 0.01
22 12 0.06
23 5 0.03
24 9 0.05
25 19 0.10
26 96 0.49
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.45
Consensus pattern (26 bp):
CATCCTTTCATGCATTTTAATTATGG
Found at i:1044583 original size:45 final size:45
Alignment explanation
Indices: 1044518--1044652 Score: 209
Period size: 45 Copynumber: 3.0 Consensus size: 45
1044508 TGCATTTTAA
*
1044518 TTATGGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGAC
1 TTAT-GCATTCTTTCATGCATTTTAATTATGGCATCCTTTCATGAC
*
1044564 TTATGCATTCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
1 TTATGCATTCTTTCATGCATTTTAATTATGGCATCCTTTCATGAC
*
1044609 TTAATGCA-TCATTTCATGCATTTTAATTATGGAATCCTTTCATG
1 TT-ATGCATTC-TTTCATGCATTTTAATTATGGCATCCTTTCATG
1044653 CATTTTAATT
Statistics
Matches: 84, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
45 43 0.51
46 41 0.49
ACGTcount: A:0.23, C:0.20, G:0.12, T:0.45
Consensus pattern (45 bp):
TTATGCATTCTTTCATGCATTTTAATTATGGCATCCTTTCATGAC
Found at i:1044633 original size:46 final size:44
Alignment explanation
Indices: 1044518--1044653 Score: 209
Period size: 46 Copynumber: 3.0 Consensus size: 44
1044508 TGCATTTTAA
*
1044518 TTATGGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGAC
1 TTAT-GCAT-CTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
1044564 TTATGCATTCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
1 TTATGCA-TCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
*
1044609 TTAATGCATCATTTCATGCATTTTAATTATGGAATCCTTTCATGC
1 TT-ATGCATC-TTTCATGCATTTTAATTATGGCATCCTTTCATGC
1044654 ATTTTAATTA
Statistics
Matches: 85, Mismatches: 2, Indels: 6
0.91 0.02 0.06
Matches are distributed among these distances:
45 42 0.49
46 43 0.51
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.45
Consensus pattern (44 bp):
TTATGCATCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
Found at i:1044698 original size:72 final size:71
Alignment explanation
Indices: 1044572--1044724 Score: 227
Period size: 72 Copynumber: 2.1 Consensus size: 71
1044562 ACTTATGCAT
* *
1044572 TCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATT
1 TCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCATGTCATGCATTTTAATT
1044637 ATGGAA
66 ATGGAA
* *
1044643 TCCTTTCATGCATTTTAATTATGACATCCTTTCATTCCTTAATG-ATTTATGTCATGCATTTTAA
1 T-CTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCA-TCATGTCATGCATTTTAA
* *
1044707 TTATTGCA
64 TTATGGAA
1044715 TCTTTCATGC
1 TCTTTCATGC
1044725 CTTAATGCAT
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
71 11 0.15
72 63 0.85
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.47
Consensus pattern (71 bp):
TCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCATGTCATGCATTTTAATT
ATGGAA
Found at i:1044720 original size:117 final size:117
Alignment explanation
Indices: 1044502--1044770 Score: 411
Period size: 117 Copynumber: 2.3 Consensus size: 117
1044492 TTAACACATC
*
1044502 CATTT-ATGCATTTTAATTATGGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGACTT
1 CATTTCATGCATTTTAATTATGGCATCCTTTCATGCATTTTAATTATGACATCCTTTCATGACTT
1044566 ATGCATTCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCAT
66 ATGCATTCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCAT
* **
1044618 CATTTCATGCATTTTAATTATGGAATCCTTTCATGCATTTTAATTATGACATCCTTTCATTCCTT
1 CATTTCATGCATTTTAATTATGGCATCCTTTCATGCATTTTAATTATGACATCCTTTCATGACTT
*
1044683 AATG-ATT-TATGTCATGCATTTTAATTATTGCAT-CTTTCATGCCTTAATGCAT
66 -ATGCATTCT-T-TCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCAT
* * *
1044735 CCTTTCATGCATTTTAACTATGGCATCCTTTAATGC
1 CATTTCATGCATTTTAATTATGGCATCCTTTCATGC
1044771 CTTAATGCAT
Statistics
Matches: 140, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
116 6 0.04
117 110 0.79
118 24 0.17
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (117 bp):
CATTTCATGCATTTTAATTATGGCATCCTTTCATGCATTTTAATTATGACATCCTTTCATGACTT
ATGCATTCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCAT
Found at i:1044741 original size:20 final size:20
Alignment explanation
Indices: 1044711--1044790 Score: 72
Period size: 20 Copynumber: 3.8 Consensus size: 20
1044701 TTTTAATTAT
1044711 TGCAT-CTTTCATGCCTTAA
1 TGCATCCTTTCATGCCTTAA
*
1044730 TGCATCCTTTCATGCATTTTAACTA
1 TGCATCCTTTCATGC--CTT-A--A
*
1044755 TGGCATCCTTTAATGCCTTAA
1 T-GCATCCTTTCATGCCTTAA
*
1044776 TGCATCATTTCATGC
1 TGCATCCTTTCATGC
1044791 ATTTTCATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
19 5 0.10
20 21 0.43
21 2 0.04
22 2 0.04
23 2 0.04
24 2 0.04
25 2 0.04
26 13 0.27
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.41
Consensus pattern (20 bp):
TGCATCCTTTCATGCCTTAA
Found at i:1044803 original size:46 final size:46
Alignment explanation
Indices: 1044646--1044803 Score: 212
Period size: 46 Copynumber: 3.5 Consensus size: 46
1044636 TATGGAATCC
* * *
1044646 TTTCATGCATTTTAATTATGACATCCTTTCATTCCTTAATG-ATTTA
1 TTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCA-TCA
* * *
1044692 TGTCATGCATTTTAATTATTGCAT-CTTTCATGCCTTAATGCATCC
1 TTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCA
* *
1044737 TTTCATGCATTTTAACTATGGCATCCTTTAATGCCTTAATGCATCA
1 TTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCA
*
1044783 TTTCATGCATTTTCATTATGG
1 TTTCATGCATTTTAATTATGG
1044804 ATTCGATTTA
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
45 37 0.38
46 60 0.62
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (46 bp):
TTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCA
Found at i:1045263 original size:19 final size:19
Alignment explanation
Indices: 1045194--1045265 Score: 58
Period size: 19 Copynumber: 3.6 Consensus size: 19
1045184 TGGCTCCTCA
**
1045194 GTATCGATACCCCTACCATG
1 GTATCGATA-CCCTATTATG
1045214 GTATCGATACTACC-ATTCTATG
1 GTATCGATAC--CCTA-T-TATG
1045236 GTA-CTGATACCCTATTATG
1 GTATC-GATACCCTATTATG
1045255 GTATCGATACC
1 GTATCGATACC
1045266 ATTTTTATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
19 14 0.33
20 14 0.33
21 4 0.09
22 11 0.26
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (19 bp):
GTATCGATACCCTATTATG
Found at i:1045314 original size:20 final size:20
Alignment explanation
Indices: 1045289--1045358 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
1045279 ATTTTGAAAT
1045289 GGTATCGATA-CCTTCATTTC
1 GGTATCGATACCCTTC-TTTC
*
1045309 GGTATCGATACTCCCTCTTT-
1 GGTATCGATAC-CCTTCTTTC
1045329 GGTATCGATACTCCTTC-TTC
1 GGTATCGATAC-CCTTCTTTC
1045349 GGTATCGATA
1 GGTATCGATA
1045359 TTAATTGAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.04
20 36 0.80
21 3 0.07
22 4 0.09
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.39
Consensus pattern (20 bp):
GGTATCGATACCCTTCTTTC
Found at i:1056318 original size:64 final size:63
Alignment explanation
Indices: 1056250--1056479 Score: 221
Period size: 64 Copynumber: 3.6 Consensus size: 63
1056240 TTGGAACACT
* ***
1056250 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
1056314 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * * * *
1056378 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAAT-TC
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATAGC
*
1056441 A
63 C
* *
1056442 TCGATGCATCGATGCATGGACTGATGCATCGGTGCATG
1 T-GATGCATCGATGCATGGAGTG-TGCATCGATGCATG
1056480 CCTTTGAATA
Statistics
Matches: 138, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
63 4 0.03
64 70 0.51
65 64 0.46
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:1056402 original size:19 final size:19
Alignment explanation
Indices: 1056378--1056428 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1056368 GAAAATATTC
1056378 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1056397 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1056416 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1056429 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1056470 original size:65 final size:64
Alignment explanation
Indices: 1056272--1056479 Score: 230
Period size: 65 Copynumber: 3.2 Consensus size: 64
1056262 GCACCAAGTG
* *
1056272 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGG-CTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGGAC-TG
1056336 -
64 A
*
1056336 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGACT
1056398 GA
63 GA
* * * *
1056400 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGACT
1056464 GA
63 GA
*
1056466 TGCATCGGTGCATG
1 TGCATCGATGCATG
1056480 CCTTTGAATA
Statistics
Matches: 125, Mismatches: 8, Indels: 21
0.81 0.05 0.14
Matches are distributed among these distances:
63 10 0.08
64 46 0.37
65 65 0.52
66 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGACTGA
Found at i:1062545 original size:30 final size:30
Alignment explanation
Indices: 1062466--1062537 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
1062456 ATTGATGCAT
* *
1062466 TTCTAACATCTGCATGGGATAAATTCCCCA
1 TTCTCACATATGCATGGGATAAATTCCCCA
*
1062496 TTCTCACATATGCATGGGATAAATTTCCCA
1 TTCTCACATATGCATGGGATAAATTCCCCA
*
1062526 TTCTGACATATG
1 TTCTCACATATG
1062538 TTTGGGATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (30 bp):
TTCTCACATATGCATGGGATAAATTCCCCA
Found at i:1063885 original size:20 final size:21
Alignment explanation
Indices: 1063862--1063900 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1063852 GTTTTCAAAG
1063862 TTTTGAG-GTTATTTTAAATT
1 TTTTGAGTGTTATTTTAAATT
* *
1063882 TTTTGTGTTTTATTTTAAA
1 TTTTGAGTGTTATTTTAAA
1063901 AATATATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (21 bp):
TTTTGAGTGTTATTTTAAATT
Found at i:1065494 original size:3 final size:3
Alignment explanation
Indices: 1065486--1065523 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1065476 AATGGATCAC
1065486 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1065524 TGACAGGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1069786 original size:30 final size:32
Alignment explanation
Indices: 1069745--1069803 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
1069735 AAGAAAATAA
*
1069745 ATAAATAAAAT-ATAA-AAAAAGTATATATGT
1 ATAAATAAAATAATAATAAAAAATATATATGT
*
1069775 ATAAGTAAAATAATAATAAAAAATATATA
1 ATAAATAAAATAATAATAAAAAATATATA
1069804 AACAATAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 10 0.40
31 4 0.16
32 11 0.44
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (32 bp):
ATAAATAAAATAATAATAAAAAATATATATGT
Found at i:1072016 original size:108 final size:107
Alignment explanation
Indices: 1071759--1072066 Score: 487
Period size: 108 Copynumber: 2.9 Consensus size: 107
1071749 TGGAACTGGT
*
1071759 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT--C
1 AAATTG-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGC
* * * *
1071822 -CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGG
65 ACGATATCC-TCGTTGTGGAGTTGAAATCGGCTCCAAAATTGGG
1071865 AAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCA
1 AAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCA
* *
1071930 CGATATCCTCGTCGTGGAGTTGAAATCGGCTCTAAAATTGGG
66 CGATATCCTCGTTGTGGAGTTGAAATCGGCTCCAAAATTGGG
*
1071972 AAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGC
1 AAATTGTT-GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGC
1072037 ACGATATCCTCCGTTGTGGAGTTGAAATCG
65 ACGATATCCT-CGTTGTGGAGTTGAAATCG
1072067 TGGATGTTTG
Statistics
Matches: 188, Mismatches: 9, Indels: 7
0.92 0.04 0.03
Matches are distributed among these distances:
105 54 0.29
106 6 0.03
107 37 0.20
108 73 0.39
109 18 0.10
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (107 bp):
AAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCA
CGATATCCTCGTTGTGGAGTTGAAATCGGCTCCAAAATTGGG
Found at i:1083627 original size:2 final size:2
Alignment explanation
Indices: 1083620--1083654 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1083610 ATGATAAAAC
1083620 AT AT AT AT AT 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 AT AT AT AT AT A
1083655 ATTAATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1086652 original size:15 final size:12
Alignment explanation
Indices: 1086620--1086648 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1086610 TTTTTAAAAA
1086620 TAAAATATTATT
1 TAAAATATTATT
1086632 TAAAATATTATT
1 TAAAATATTATT
1086644 TAAAA
1 TAAAA
1086649 AAATTGAATA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:1099267 original size:19 final size:19
Alignment explanation
Indices: 1099245--1099283 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1099235 TAAAGAGAAT
*
1099245 AAAATAAAAGGAAAAAATA
1 AAAATAAAAGAAAAAAATA
*
1099264 AAAATAAAATAAAAAAATA
1 AAAATAAAAGAAAAAAATA
1099283 A
1 A
1099284 GATAAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (19 bp):
AAAATAAAAGAAAAAAATA
Found at i:1099288 original size:24 final size:26
Alignment explanation
Indices: 1099222--1099298 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 26
1099212 CAAGGTAAAG
*
1099222 AAAACAAATAAGATAAAGAGAATAAAAT
1 AAAAGAAATAAGAT-AAGA-AATAAAAT
1099250 AAAAGGAAA-AA-ATAA-AAATAAAAT
1 AAAA-GAAATAAGATAAGAAATAAAAT
1099274 AAAA-AAATAAGATAAGAAA-AAAAT
1 AAAAGAAATAAGATAAGAAATAAAAT
1099298 A
1 A
1099299 GTAAAGTAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
22 3 0.07
23 2 0.05
24 22 0.50
25 4 0.09
26 2 0.05
27 2 0.05
28 6 0.14
29 3 0.07
ACGTcount: A:0.77, C:0.01, G:0.09, T:0.13
Consensus pattern (26 bp):
AAAAGAAATAAGATAAGAAATAAAAT
Found at i:1099345 original size:2 final size:2
Alignment explanation
Indices: 1099340--1099375 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1099330 AAAAAAGAAA
1099340 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
1099376 CAAAGTATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1099525 original size:41 final size:40
Alignment explanation
Indices: 1099460--1099537 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
1099450 TCACTTCACC
* *
1099460 GAAAGTGGGGGGCTTTAGTCAGAAATAAGA-AAAAAAGAG
1 GAAAGTGGGGGACTTTAGTCAGAAATAAAACAAAAAAGAG
*
1099499 GAAAGTGGGAGAGACTTTAGTTAGAAATAAAACAAAAAA
1 GAAAGTGGG-G-GACTTTAGTCAGAAATAAAACAAAAAA
1099538 TGGGCTCTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 9 0.27
40 1 0.03
41 17 0.52
42 6 0.18
ACGTcount: A:0.50, C:0.05, G:0.28, T:0.17
Consensus pattern (40 bp):
GAAAGTGGGGGACTTTAGTCAGAAATAAAACAAAAAAGAG
Found at i:1099652 original size:23 final size:22
Alignment explanation
Indices: 1099610--1099654 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1099600 TATTTTTTTT
* *
1099610 AAAATAATATAATAATAAATAA
1 AAAATAAAATAATAAAAAATAA
1099632 AAAATGAAAATAATAAAAAATAA
1 AAAAT-AAAATAATAAAAAATAA
1099655 TATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (22 bp):
AAAATAAAATAATAAAAAATAA
Found at i:1100630 original size:18 final size:18
Alignment explanation
Indices: 1100607--1100648 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1100597 TTGACCGGTT
*
1100607 TTGACCCGACCCGGCCCG
1 TTGACCCGACCCGACCCG
*
1100625 TTGACCCGACTCGACCCG
1 TTGACCCGACCCGACCCG
1100643 TTGACC
1 TTGACC
1100649 GTTGACCGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.45, G:0.24, T:0.17
Consensus pattern (18 bp):
TTGACCCGACCCGACCCG
Found at i:1101274 original size:20 final size:20
Alignment explanation
Indices: 1101236--1101274 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1101226 GGTTTTCGCT
*
1101236 TATTATTTAAATAATATTTA
1 TATTATTTAAATAAGATTTA
* *
1101256 TATTATTTATATTAGATTT
1 TATTATTTAAATAAGATTT
1101275 CCAATATGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TATTATTTAAATAAGATTTA
Found at i:1101710 original size:42 final size:41
Alignment explanation
Indices: 1101663--1101867 Score: 268
Period size: 42 Copynumber: 4.8 Consensus size: 41
1101653 GAAGTATTAT
*
1101663 CAGGTCCCTTTGTTGTGTGCGAAGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
*
1101705 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTGC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
*
1101747 CAGGTCCCTTTGCTGTGTGCAAGGGCAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTCC
*
1101789 CAGGTCCCTTTGCTGTGTGCAAGGATAAACCTTACAGCTTTCC
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAG-TTTCC
* * *
1101832 TAGG-CTCCTCTGCTTTGTGCACAGGTTAAGCCTTAC
1 CAGGTC-CCTTTGCTGTGTGCA-AGG-TAAGCCTTAC
1101868 TGGTGTATAG
Statistics
Matches: 147, Mismatches: 11, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
41 4 0.03
42 110 0.75
43 21 0.14
44 12 0.08
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTCC
Found at i:1109103 original size:42 final size:41
Alignment explanation
Indices: 1109044--1109248 Score: 241
Period size: 42 Copynumber: 4.8 Consensus size: 41
1109034 GAAGTATTAT
*
1109044 CAGGTCCCTTTGCTGTGTGCGAAGGTAATCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
* *
1109086 CAGGTCCCTTTGCTGTGTGTGAAGGTAAGCCTTACAGTTTGC
1 CAGGTCCCTTTGCTGTGTG-CAAGGTAAGCCTTACAGTTTCC
* *
1109128 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTCC
* *
1109170 CAGGTCCCTTTGTTGTGTGCAAGGATAAACCTTACAGTTTTCC
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAG-TTTCC
* * *
1109213 TAGG-CTCCTCTGCTTTGTGCACAGGTTAAGCCTTAC
1 CAGGTC-CCTTTGCTGTGTGCA-AGG-TAAGCCTTAC
1109249 TGGTGTATAG
Statistics
Matches: 142, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
41 4 0.03
42 106 0.75
43 20 0.14
44 12 0.08
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTCC
Found at i:1109815 original size:17 final size:18
Alignment explanation
Indices: 1109782--1109817 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1109772 ATATATACGT
*
1109782 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
1109800 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
1109817 A
1 A
1109818 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:1110236 original size:35 final size:35
Alignment explanation
Indices: 1110197--1110268 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1110187 TTAAAAAACC
1110197 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1110232 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1110267 CT
1 CT
1110269 TCTTTTTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:1112269 original size:16 final size:16
Alignment explanation
Indices: 1112248--1112278 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1112238 AATACTGATA
1112248 TTGAATCTAATATTGT
1 TTGAATCTAATATTGT
*
1112264 TTGAATGTAATATTG
1 TTGAATCTAATATTG
1112279 ATACGAGTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.48
Consensus pattern (16 bp):
TTGAATCTAATATTGT
Found at i:1122368 original size:66 final size:67
Alignment explanation
Indices: 1122260--1122399 Score: 201
Period size: 66 Copynumber: 2.1 Consensus size: 67
1122250 TTAAAGAGCT
* * * * *
1122260 GATCCATGACCCCCTGAATGAAAACCTTACATATATGCAGTAATAACTTCCTATATTACATTGAG
1 GATCCATGA-CCCCGGAACGAAAACCTTAAATATATGCAGTAATAACTTCCTAAATTACAATGAG
1122325 ATC
65 ATC
*
1122328 GATCCATGA-CCCGGAACGAAAACCTTAAATATTTGCAGTAATAACTTCCTAAATTACAATGAGA
1 GATCCATGACCCCGGAACGAAAACCTTAAATATATGCAGTAATAACTTCCTAAATTACAATGAGA
*
1122392 TG
66 TC
1122394 GATCCA
1 GATCCA
1122400 ACACTTCAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
66 56 0.86
68 9 0.14
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (67 bp):
GATCCATGACCCCGGAACGAAAACCTTAAATATATGCAGTAATAACTTCCTAAATTACAATGAGA
TC
Found at i:1127193 original size:18 final size:17
Alignment explanation
Indices: 1127170--1127203 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1127160 ATGCTTTGAC
1127170 AAACATGCTAATTAAAAT
1 AAACATGC-AATTAAAAT
*
1127188 AAACATTCAATTAAAA
1 AAACATGCAATTAAAA
1127204 AATGAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.26
Consensus pattern (17 bp):
AAACATGCAATTAAAAT
Found at i:1129869 original size:3 final size:3
Alignment explanation
Indices: 1129856--1129897 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1129846 TATTTATTGT
*
1129856 ATA ACA 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
1129898 TATTTGAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1135338 original size:26 final size:24
Alignment explanation
Indices: 1135307--1135382 Score: 64
Period size: 26 Copynumber: 3.0 Consensus size: 24
1135297 TTTTAGTTGA
1135307 AAATTTAATACTTTTTAAATAATTT
1 AAATTTAATA-TTTTTAAATAATTT
*
1135332 AATATTTTTATATTTTT-AATAATTT
1 AA-A-TTTAATATTTTTAAATAATTT
* * *
1135357 TAAGTTATTAATTTATTAAATAATTT
1 AAATTTAAT-ATTT-TTAAATAATTT
1135383 TTATGACTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
23 3 0.07
24 5 0.12
25 13 0.32
26 14 0.34
27 6 0.15
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (24 bp):
AAATTTAATATTTTTAAATAATTT
Found at i:1135341 original size:9 final size:9
Alignment explanation
Indices: 1135310--1135359 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
1135300 TAGTTGAAAA
1135310 TTTAATACTT
1 TTTAATA-TT
*
1135320 TTTAA-ATAA
1 TTTAATAT-T
1135329 TTTAATATT
1 TTTAATATT
1135338 TTT-ATATT
1 TTTAATATT
*
1135346 TTTAATAAT
1 TTTAATATT
1135355 TTTAA
1 TTTAA
1135360 GTTATTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
8 9 0.26
9 18 0.53
10 7 0.21
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTAATATT
Found at i:1136470 original size:5 final size:5
Alignment explanation
Indices: 1136460--1136508 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
1136450 ATCCGTCCGT
* ** *
1136460 CTCGG CTCGG CTCGG CACTA CTCGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
1136509 AGTCGTGGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.06, C:0.41, G:0.35, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:1142340 original size:6 final size:6
Alignment explanation
Indices: 1142329--1142353 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1142319 ACGGCTCGGC
1142329 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
1142354 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:1161871 original size:23 final size:23
Alignment explanation
Indices: 1161841--1161891 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1161831 TTTTCAATAA
*
1161841 ATATGCCTTAATTACACATTTTC
1 ATATGCCTTAATGACACATTTTC
* *
1161864 ATATGCCTTTATGGCACATTTTC
1 ATATGCCTTAATGACACATTTTC
*
1161887 TTATG
1 ATATG
1161892 TTTTTTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (23 bp):
ATATGCCTTAATGACACATTTTC
Found at i:1167067 original size:29 final size:29
Alignment explanation
Indices: 1167032--1167090 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1167022 ATTTTCACAT
1167032 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1167061 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1167090 A
1 A
1167091 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:1172917 original size:3 final size:3
Alignment explanation
Indices: 1172911--1172935 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1172901 AATAATAATA
1172911 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1172936 CAAATTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1178330 original size:3 final size:3
Alignment explanation
Indices: 1178324--1178400 Score: 84
Period size: 3 Copynumber: 25.7 Consensus size: 3
1178314 CTAATTTTTT
** **
1178324 TTA TTA TTA TTA TTA TTA AAA TTA AAA TTA TTA TTA TTA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* *
1178373 ATA TTA TTA TTA -TA TTA TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1178401 TACAAACAGT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
2 2 0.03
3 56 0.93
4 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1178353 original size:24 final size:25
Alignment explanation
Indices: 1178325--1178395 Score: 110
Period size: 24 Copynumber: 2.9 Consensus size: 25
1178315 TAATTTTTTT
*
1178325 TATTATTATTATTATTAAAATTAAA
1 TATTATTATTATTATTATAATTAAA
*
1178350 -ATTATTATTATTATTATTATTAAA
1 TATTATTATTATTATTATAATTAAA
1178374 TATTATTATTA-TATTATAATTA
1 TATTATTATTATTATTATAATTA
1178396 TTATTTACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 32 0.76
25 10 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTATTATTATTATTATAATTAAA
Found at i:1178360 original size:30 final size:31
Alignment explanation
Indices: 1178324--1178400 Score: 113
Period size: 30 Copynumber: 2.5 Consensus size: 31
1178314 CTAATTTTTT
1178324 TTATTATTATTATTATTAAA-ATTAAAATTA
1 TTATTATTATTATTATTAAATATTAAAATTA
**
1178354 TTATTATTATTATTATTAAATATTATTATTA
1 TTATTATTATTATTATTAAATATTAAAATTA
*
1178385 -TATTATAATTATTATT
1 TTATTATTATTATTATT
1178401 TACAAACAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 35 0.81
31 8 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
TTATTATTATTATTATTAAATATTAAAATTA
Found at i:1178443 original size:26 final size:26
Alignment explanation
Indices: 1178407--1178461 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
1178397 TATTTACAAA
*
1178407 CAGTTACAAACAAAACAGGACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
*
1178433 CAGTTACAAACAAACCAGAACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
1178459 CAG
1 CAG
1178462 ACCAATCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.33, G:0.18, T:0.07
Consensus pattern (26 bp):
CAGTTACAAACAAAACAGAACCGGCC
Found at i:1180488 original size:20 final size:21
Alignment explanation
Indices: 1180459--1180510 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1180449 AGAAATGAAA
1180459 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
*
1180479 AATTCTTTTATTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
1180501 -ATT-ATTTATT
1 AATTCATTTATT
1180511 ATTTTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 18 0.64
21 3 0.11
22 7 0.25
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:1182575 original size:7 final size:7
Alignment explanation
Indices: 1182543--1182581 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
1182533 TCATACATCC
*
1182543 TTTTTCA
1 TTTTGCA
1182550 TTTTGCA
1 TTTTGCA
1182557 TCTTTGCA
1 T-TTTGCA
*
1182565 TTTTTCA
1 TTTTGCA
1182572 TTTTGCA
1 TTTTGCA
1182579 TTT
1 TTT
1182582 ATACTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 21 0.75
8 7 0.25
ACGTcount: A:0.13, C:0.15, G:0.08, T:0.64
Consensus pattern (7 bp):
TTTTGCA
Found at i:1182578 original size:14 final size:14
Alignment explanation
Indices: 1182543--1182581 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
1182533 TCATACATCC
*
1182543 TTTTTCATTTTGCA
1 TTTTGCATTTTGCA
*
1182557 TCTTTGCATTTTTCA
1 T-TTTGCATTTTGCA
1182572 TTTTGCATTT
1 TTTTGCATTT
1182582 ATACTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.13, C:0.15, G:0.08, T:0.64
Consensus pattern (14 bp):
TTTTGCATTTTGCA
Found at i:1185169 original size:13 final size:12
Alignment explanation
Indices: 1185151--1185183 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1185141 TCCAGCAAAG
1185151 AAAGAAGAAAAAA
1 AAAGAA-AAAAAA
1185164 AAAG-AAAAAAA
1 AAAGAAAAAAAA
1185175 AAAGAAAAA
1 AAAGAAAAA
1185184 GGAAAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.53
12 5 0.26
13 4 0.21
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:1185169 original size:17 final size:17
Alignment explanation
Indices: 1185147--1185189 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1185137 CTCATCCAGC
*
1185147 AAAGAAAGAAGAAAA-AA
1 AAAGAAA-AAAAAAAGAA
1185164 AAAGAAAAAAAAAAGAA
1 AAAGAAAAAAAAAAGAA
1185181 AAAGGAAAA
1 AAA-GAAAA
1185190 TTGAATCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 6 0.26
17 12 0.52
18 5 0.22
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAAAAAGAA
Found at i:1185174 original size:11 final size:11
Alignment explanation
Indices: 1185158--1185183 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1185148 AAGAAAGAAG
1185158 AAAAAAAAAGA
1 AAAAAAAAAGA
1185169 AAAAAAAAAGA
1 AAAAAAAAAGA
1185180 AAAA
1 AAAA
1185184 GGAAAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:1189694 original size:55 final size:54
Alignment explanation
Indices: 1189628--1189744 Score: 182
Period size: 55 Copynumber: 2.1 Consensus size: 54
1189618 ACTTCAATGA
* *
1189628 TTACGAACATCTGAGCAGAAGCCACA-AAAAAGGATGAATGTATTGTCAAAATGTT
1 TTACGAACATCTGAGCAGAAGCCACAGAAAAA-GATGAATGCACTGTC-AAATGTT
*
1189683 TTACGAACATCTGAGCAGAAGCCACAGGAAAAGATGAATGCACTGTCAAATGTT
1 TTACGAACATCTGAGCAGAAGCCACAGAAAAAGATGAATGCACTGTCAAATGTT
1189737 TTACGAAC
1 TTACGAAC
1189745 CTGTTATTCT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
54 15 0.26
55 39 0.67
56 4 0.07
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (54 bp):
TTACGAACATCTGAGCAGAAGCCACAGAAAAAGATGAATGCACTGTCAAATGTT
Found at i:1190139 original size:22 final size:22
Alignment explanation
Indices: 1190111--1190165 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1190101 ATCTACATTC
*
1190111 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
1190133 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
1190155 TTCAAAGATGA
1 TTCAAAGATGA
1190166 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:1190941 original size:76 final size:76
Alignment explanation
Indices: 1190841--1191479 Score: 1172
Period size: 76 Copynumber: 8.4 Consensus size: 76
1190831 ACTATTTCCC
*
1190841 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1190906 AAGCCTTCGGG
66 AAGCCTTCGGG
1190917 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1190982 AAGCCTTCGGG
66 AAGCCTTCGGG
* *
1190993 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTAGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1191058 AAGCCTTCGGG
66 AAGCCTTCGGG
* *
1191069 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAATAGCCTTCGAGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1191134 AAGCCTTCGGG
66 AAGCCTTCGGG
*
1191145 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1191210 AAGCCTTCGGG
66 AAGCCTTCGGG
1191221 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1191286 AAGCCTTCGGG
66 AAGCCTTCGGG
1191297 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1191362 AAGCCTTCGGG
66 AAGCCTTCGGG
*
1191373 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
1191438 AAACCTT-GGG
66 AAGCCTTCGGG
* *
1191448 ATCATCTGTAAGTCATGCAGTGCATGATGTTT
1 -TCATCTGTAAGTCCTTCAGTGCATGATGTTT
1191480 TTAAGACCTC
Statistics
Matches: 547, Mismatches: 15, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
75 3 0.01
76 544 0.99
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTCGGG
Found at i:1191629 original size:3 final size:3
Alignment explanation
Indices: 1191623--1191701 Score: 81
Period size: 3 Copynumber: 26.7 Consensus size: 3
1191613 CTAATTTTTT
** ** *
1191623 TTA TTA TTA TTA TTA AAA TTA AAA TTA TTA TTA TTA TTA TTAA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
*
1191669 TTA TTA TTA -TA TTA TTA -TA TTA TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1191702 TACAAACAGT
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
2 4 0.07
3 55 0.90
4 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1191661 original size:27 final size:27
Alignment explanation
Indices: 1191623--1191696 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
1191613 CTAATTTTTT
1191623 TTATTATTATTATTAAAATTAAAATTA
1 TTATTATTATTATTAAAATTAAAATTA
**
1191650 TTATTATTATTATTAAATATTATTATTA
1 TTATTATTATTATTAAA-ATTAAAATTA
*
1191678 -TATTATTA-TATTATAATTA
1 TTATTATTATTATTAAAATTA
1191697 TTATTTACAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 4 0.09
26 6 0.14
27 25 0.58
28 8 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTATTATTATTATTAAAATTAAAATTA
Found at i:1191744 original size:26 final size:26
Alignment explanation
Indices: 1191708--1191762 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
1191698 TATTTACAAA
* *
1191708 CAGTTACAAACAAAACTGGACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
*
1191734 CAGTTACAAACAAACCAGAACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
1191760 CAG
1 CAG
1191763 ACTAACCAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.33, G:0.18, T:0.09
Consensus pattern (26 bp):
CAGTTACAAACAAAACAGAACCGGCC
Found at i:1197140 original size:20 final size:20
Alignment explanation
Indices: 1197117--1197177 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
1197107 CGTTAATTCT
1197117 AAAATCGCGTTGCGAATTTC
1 AAAATCGCGTTGCGAATTTC
** **
1197137 AAAA-CTAAGTTGCGAATCTGG
1 AAAATC-GCGTTGCGAAT-TTC
1197158 AAAATTCGCGTTGCGAATTT
1 AAAA-TCGCGTTGCGAATTT
1197178 GGAAACTGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 7
0.68 0.16 0.16
Matches are distributed among these distances:
19 1 0.03
20 13 0.43
21 6 0.20
22 9 0.30
23 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (20 bp):
AAAATCGCGTTGCGAATTTC
Found at i:1197184 original size:42 final size:40
Alignment explanation
Indices: 1197116--1197218 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 40
1197106 ACGTTAATTC
*
1197116 TAAAA-TCGCGTTGCGAATTTCAAAACTAAGTTGCG-AAT
1 TAAAATTCGCGTTGCGAATTTGAAAACTAAGTTGCGAAAT
* **
1197154 CTGGAAAATTCGCGTTGCGAATTTGGAAACTGTGTTGCGAAAT
1 -T--AAAATTCGCGTTGCGAATTTGAAAACTAAGTTGCGAAAT
* *
1197197 TAGAGTTCGCGTTGCGAATTTG
1 TAAAATTCGCGTTGCGAATTTG
1197219 TTGGTTATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
39 1 0.02
40 19 0.35
41 4 0.07
42 27 0.50
43 3 0.06
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (40 bp):
TAAAATTCGCGTTGCGAATTTGAAAACTAAGTTGCGAAAT
Found at i:1197192 original size:20 final size:20
Alignment explanation
Indices: 1197125--1197194 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
1197115 CTAAAATCGC
** *
1197125 GTTGCGAATTTCAAAACTAA
1 GTTGCGAATTTGGAAACTGA
* * *
1197145 GTTGCGAATCTGGAAAATTCGC
1 GTTGCGAATTTGG-AAACT-GA
*
1197167 GTTGCGAATTTGGAAACTGT
1 GTTGCGAATTTGGAAACTGA
1197187 GTTGCGAA
1 GTTGCGAA
1197195 ATTAGAGTTC
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 19 0.49
21 8 0.21
22 12 0.31
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (20 bp):
GTTGCGAATTTGGAAACTGA
Found at i:1200120 original size:36 final size:36
Alignment explanation
Indices: 1200079--1200151 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
1200069 AAAGTACATC
*
1200079 ACCTCAAGTCCTTCATTAAAATACTTCCTTAAACCT
1 ACCTCAAGTACTTCATTAAAATACTTCCTTAAACCT
*
1200115 ACCTCAAGTACTTCATTAAAATATTTCCTTAAACCT
1 ACCTCAAGTACTTCATTAAAATACTTCCTTAAACCT
1200151 A
1 A
1200152 AATGGAGGAA
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:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (36 bp):
ACCTCAAGTACTTCATTAAAATACTTCCTTAAACCT
Found at i:1202399 original size:29 final size:29
Alignment explanation
Indices: 1202354--1202411 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1202344 GTGTTGGCCG
* *
1202354 TAGGTCGTCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
1202383 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
1202412 AAGAGACTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.34, G:0.28, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:1202464 original size:10 final size:10
Alignment explanation
Indices: 1202451--1202501 Score: 50
Period size: 10 Copynumber: 4.7 Consensus size: 10
1202441 ACACGCTGGG
1202451 CATCCGAGGC
1 CATCCGAGGC
1202461 CATCCGACCGAGGC
1 CAT-C--C-GAGGC
1202475 CATCCGAGAG-
1 CATCCGAG-GC
1202485 CATCCGAGGC
1 CATCCGAGGC
1202495 CATCCGA
1 CATCCGA
1202502 CCGAGGCCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
9 1 0.03
10 21 0.60
11 3 0.09
13 2 0.06
14 8 0.23
ACGTcount: A:0.24, C:0.39, G:0.27, T:0.10
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:1202473 original size:14 final size:14
Alignment explanation
Indices: 1202454--1202520 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
1202444 CGCTGGGCAT
1202454 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
1202468 CCGAGGCCATCCGAGAGCA
1 CCGAGGCCATCC----G-A
1202487 TCCGAGGCCATCCGA
1 -CCGAGGCCATCCGA
1202502 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
1202516 ACGAG
1 CCGAG
1202521 TTATGCGAGG
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
14 30 0.65
15 1 0.02
16 1 0.02
18 1 0.02
19 1 0.02
20 12 0.26
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:1202488 original size:34 final size:34
Alignment explanation
Indices: 1202450--1202515 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
1202440 AACACGCTGG
1202450 GCATCCGAGGCCATCCGACCGAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGACCGAGGCCATCCGAGA
1202484 GCATCCGAGGCCATCCGACCGAGGCCATCCGA
1 GCATCCGAGGCCATCCGACCGAGGCCATCCGA
1202516 ACGAGTTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.23, C:0.39, G:0.29, T:0.09
Consensus pattern (34 bp):
GCATCCGAGGCCATCCGACCGAGGCCATCCGAGA
Found at i:1202515 original size:10 final size:10
Alignment explanation
Indices: 1202468--1202501 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1202458 GGCCATCCGA
1202468 CCGAGGCCAT
1 CCGAGGCCAT
1202478 CCGAGAG-CAT
1 CCGAG-GCCAT
1202488 CCGAGGCCAT
1 CCGAGGCCAT
1202498 CCGA
1 CCGA
1202502 CCGAGGCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 1 0.05
10 20 0.91
11 1 0.05
ACGTcount: A:0.24, C:0.38, G:0.29, T:0.09
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:1202559 original size:33 final size:33
Alignment explanation
Indices: 1202502--1202586 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 33
1202492 GGCCATCCGA
* * * * *
1202502 CCGAGGCCATCCGAACGAGTTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1202535 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
*
1202568 CCGAGGGAAACCGAGCGAG
1 CCGAGGGCAACCGAGCGAG
1202587 GGTAGGTCGC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.27, C:0.26, G:0.38, T:0.09
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:1202622 original size:29 final size:29
Alignment explanation
Indices: 1202590--1202645 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1202580 GAGCGAGGGT
1202590 AGGTCGCCCGAAGGGCATGGCGACCTACA
1 AGGTCGCCCGAAGGGCATGGCGACCTACA
*
1202619 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGAAGGGCATGGCGACCTA
1202646 TGTGTTGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.38, T:0.11
Consensus pattern (29 bp):
AGGTCGCCCGAAGGGCATGGCGACCTACA
Found at i:1203417 original size:47 final size:49
Alignment explanation
Indices: 1203317--1203422 Score: 148
Period size: 47 Copynumber: 2.2 Consensus size: 49
1203307 ATATTAAGAT
* *
1203317 TTTTTTTTCAAAAAACAAATTATTAATAATATTAATATTTATGTGTCGA
1 TTTTTTTTAAAAAAACAAATTATTAATAATATTAACATTTATGTGTCGA
* *
1203366 --TTTTTAAAAAAAATAAATTATTAATAATATTAACATTTATGT-T-GA
1 TTTTTTTTAAAAAAACAAATTATTAATAATATTAACATTTATGTGTCGA
1203411 TTTTTTTTAAAA
1 TTTTTTTTAAAA
1203423 TGCAATATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
45 2 0.04
46 1 0.02
47 47 0.94
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (49 bp):
TTTTTTTTAAAAAAACAAATTATTAATAATATTAACATTTATGTGTCGA
Found at i:1206991 original size:28 final size:28
Alignment explanation
Indices: 1206934--1206991 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
1206924 CTTTCATCCT
*
1206934 CCTAAAATTTTATAAGTTCAAATTCGTC
1 CCTAAAATTTTATAAGTTCAAATTCATC
* *
1206962 CCTAGAATTTTATAAGTTCAAATTTATC
1 CCTAAAATTTTATAAGTTCAAATTCATC
1206990 CC
1 CC
1206992 CTAATATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (28 bp):
CCTAAAATTTTATAAGTTCAAATTCATC
Found at i:1208257 original size:3 final size:3
Alignment explanation
Indices: 1208243--1208274 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1208233 TACCATTTAA
*
1208243 AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1208275 AAAACTCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:1210769 original size:20 final size:20
Alignment explanation
Indices: 1210740--1210783 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1210730 TCGTTTAATC
1210740 GTTCTAGTACTGACATGGCA
1 GTTCTAGTACTGACATGGCA
*
1210760 GTTCTGGTACTGACATGGCA
1 GTTCTAGTACTGACATGGCA
1210780 GTTC
1 GTTC
1210784 ACGGTGTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.32
Consensus pattern (20 bp):
GTTCTAGTACTGACATGGCA
Found at i:1211520 original size:28 final size:29
Alignment explanation
Indices: 1211443--1211524 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 29
1211433 ATTTAAGTAT
1211443 TTAAAGTATTTTTTGTCAAAATAAATACC
1 TTAAAGTATTTTTTGTCAAAATAAATACC
* * * **
1211472 TAAAATTATATTTTTAATCAAAATAGGTA-C
1 TTAAAGTAT-TTTTT-GTCAAAATAAATACC
*
1211502 TTAAAGTATTTTATGTCAAAATA
1 TTAAAGTATTTTTTGTCAAAATA
1211525 TGCACCTAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
28 8 0.19
29 11 0.26
30 13 0.31
31 10 0.24
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (29 bp):
TTAAAGTATTTTTTGTCAAAATAAATACC
Found at i:1211534 original size:28 final size:28
Alignment explanation
Indices: 1211444--1211539 Score: 84
Period size: 28 Copynumber: 3.3 Consensus size: 28
1211434 TTTAAGTATT
*
1211444 TAAAGTATTTTTTGTCAAAATAAATACC
1 TAAAGTATTTTTTGTCAAAATAAGTACC
* * * *
1211472 TAAAATTATATTTTTAATCAAAATAGGTACT
1 T-AAAGTAT-TTTTT-GTCAAAATAAGTACC
* * *
1211503 TAAAGTATTTTATGTCAAAATATGCACC
1 TAAAGTATTTTTTGTCAAAATAAGTACC
*
1211531 TAAACTATT
1 TAAAGTATT
1211540 CAAAATTTTC
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
28 20 0.38
29 10 0.19
30 11 0.21
31 12 0.23
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (28 bp):
TAAAGTATTTTTTGTCAAAATAAGTACC
Found at i:1212756 original size:10 final size:10
Alignment explanation
Indices: 1212743--1212782 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
1212733 TAACTTTCAA
1212743 TAAATTTTAT
1 TAAATTTTAT
1212753 TAAATTTTAT
1 TAAATTTTAT
*
1212763 TAAATTATAT
1 TAAATTTTAT
1212773 TAAAATTTTA
1 T-AAATTTTA
1212783 ATTTGTAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 20 0.74
11 7 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TAAATTTTAT
Found at i:1213472 original size:28 final size:28
Alignment explanation
Indices: 1213440--1213493 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1213430 TCCGATGTAG
*
1213440 TCAGATTTGTTCGAATCTTTATTTTGCA
1 TCAGATTTGTTCGAATCTTTAGTTTGCA
* *
1213468 TCAGATTTGTTTGTATCTTTAGTTTG
1 TCAGATTTGTTCGAATCTTTAGTTTG
1213494 TTCGAGCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.19, C:0.11, G:0.17, T:0.54
Consensus pattern (28 bp):
TCAGATTTGTTCGAATCTTTAGTTTGCA
Found at i:1217446 original size:18 final size:18
Alignment explanation
Indices: 1217425--1217467 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
1217415 TAATAATGAG
1217425 TTATTATAAAATATATTT
1 TTATTATAAAATATATTT
*
1217443 TTATTAT-AATTATATTT
1 TTATTATAAAATATATTT
1217460 TTATTATA
1 TTATTATA
1217468 GTTTAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATAAAATATATTT
Found at i:1218381 original size:14 final size:13
Alignment explanation
Indices: 1218362--1218392 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
1218352 ATTGGGTTTA
1218362 AAATATCAATAATT
1 AAATATCAATAA-T
1218376 AAATATCAATAAT
1 AAATATCAATAAT
1218389 AAAT
1 AAAT
1218393 TAATTTAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATCAATAAT
Found at i:1219663 original size:2 final size:2
Alignment explanation
Indices: 1219656--1219690 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1219646 GGATTTAATT
1219656 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1219691 GAGTATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1220356 original size:24 final size:24
Alignment explanation
Indices: 1220310--1220389 Score: 76
Period size: 24 Copynumber: 3.3 Consensus size: 24
1220300 TATTTGTTAT
*
1220310 TTTTAAACATTTTGTTTAATTATTTA
1 TTTTAAA-A-TTTATTTAATTATTTA
*
1220336 TTTTAAAATTTATTTAGTTATTTA
1 TTTTAAAATTTATTTAATTATTTA
* *
1220360 TTTTGAAA-TTCTTTAA-TATTT-
1 TTTTAAAATTTATTTAATTATTTA
1220381 TTATTAAAA
1 TT-TTAAAA
1220390 CACTGAATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.04
22 10 0.21
23 6 0.13
24 21 0.45
25 1 0.02
26 7 0.15
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTTAAAATTTATTTAATTATTTA
Found at i:1222843 original size:131 final size:132
Alignment explanation
Indices: 1222608--1222870 Score: 424
Period size: 131 Copynumber: 2.0 Consensus size: 132
1222598 CAATTTCGAG
* *
1222608 TTTGATTTTGAAACTTGGTTTGAGCTTTAACTCCCTTAATAAGTTTGGCTCGGTAATTGCACTCC
1 TTTGATTTTGAAACTTGGTTTAAGCTTTAACTACCTTAATAAGTTTGGCTCGGTAATTGCACTCC
* * *
1222673 TAATTGTAACAATTTTCTTGTTGAAATTTCGTGACATGCATGTAGATTTATGCAACAATTATGCT
66 TAATTGTAACAATTTTCCTGATGAAAATTCGTGACATGCATGTAGATTTATGCAACAATTATGCT
1222738 TC
131 TC
*
1222740 TTTGATTTTGAAACTTGGTTTAAG-TTTCAACTACTTTAA-AAGTTTGGCTCGGTAATTGCACTC
1 TTTGATTTTGAAACTTGGTTTAAGCTTT-AACTACCTTAATAAGTTTGGCTCGGTAATTGCACTC
*
1222803 CTAATTGTAACAATTTTCCTGATGAAAATTCGT-AGCATGCATGTAGATTTATGCAACAATTGTG
65 CTAATTGTAACAATTTTCCTGATGAAAATTCGTGA-CATGCATGTAGATTTATGCAACAATTATG
1222867 CTTC
129 CTTC
1222871 AGTTGAACAA
Statistics
Matches: 122, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
130 1 0.01
131 89 0.73
132 32 0.26
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.41
Consensus pattern (132 bp):
TTTGATTTTGAAACTTGGTTTAAGCTTTAACTACCTTAATAAGTTTGGCTCGGTAATTGCACTCC
TAATTGTAACAATTTTCCTGATGAAAATTCGTGACATGCATGTAGATTTATGCAACAATTATGCT
TC
Found at i:1223286 original size:23 final size:23
Alignment explanation
Indices: 1223259--1223331 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
1223249 TTTAATTTAC
1223259 TTTAAATAATTTATATTTAAAAT
1 TTTAAATAATTTATATTTAAAAT
* * *
1223282 TTTAACTAATTTATAATT-ATAT
1 TTTAAATAATTTATATTTAAAAT
* * * *
1223304 GTTAAATACTTTAAAATTTAAATT
1 TTTAAATAATTT-ATATTTAAAAT
1223328 TTTA
1 TTTA
1223332 TATTAGTGGT
Statistics
Matches: 37, Mismatches: 11, Indels: 3
0.73 0.22 0.06
Matches are distributed among these distances:
22 12 0.32
23 20 0.54
24 5 0.14
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (23 bp):
TTTAAATAATTTATATTTAAAAT
Found at i:1223321 original size:29 final size:28
Alignment explanation
Indices: 1223264--1223327 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
1223254 TTTACTTTAA
*
1223264 ATAATTTATATTTAAAATTTTAACTAATTT
1 ATAA-TTATATTTAAAACTTTAAC-AATTT
1223294 ATAATTATATGTTAAATACTTTAA-AATTT
1 ATAATTATAT-TTAAA-ACTTTAACAATTT
1223323 A-AATT
1 ATAATT
1223328 TTTATATTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
28 4 0.13
29 12 0.39
30 9 0.29
31 6 0.19
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (28 bp):
ATAATTATATTTAAAACTTTAACAATTT
Found at i:1229794 original size:15 final size:15
Alignment explanation
Indices: 1229774--1229804 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1229764 ATCCCTGTAA
1229774 AGACGATACTCACTC
1 AGACGATACTCACTC
1229789 AGACGATACTCACTC
1 AGACGATACTCACTC
1229804 A
1 A
1229805 TCAGTGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.32, G:0.13, T:0.19
Consensus pattern (15 bp):
AGACGATACTCACTC
Found at i:1229951 original size:30 final size:31
Alignment explanation
Indices: 1229890--1229953 Score: 85
Period size: 32 Copynumber: 2.1 Consensus size: 31
1229880 AATCCTCTAT
* *
1229890 TAGTTTCTCTCAAACACTAATAATCTTTTACC
1 TAGTTTCTCTCAAACACCAAGAA-CTTTTACC
*
1229922 TAGTTTCTCTCGAACACCAAGAA-TTTTACC
1 TAGTTTCTCTCAAACACCAAGAACTTTTACC
1229952 TA
1 TA
1229954 AGAAATGGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 9 0.31
32 20 0.69
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (31 bp):
TAGTTTCTCTCAAACACCAAGAACTTTTACC
Found at i:1238934 original size:17 final size:18
Alignment explanation
Indices: 1238912--1238958 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1238902 TATAGAATTG
*
1238912 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
1238929 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
1238947 GATTCCAATTCC
1 GATTCCAATTCC
1238959 CTCAGAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.32
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:1239216 original size:20 final size:20
Alignment explanation
Indices: 1239191--1239248 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1239181 ACACAGAAGT
*
1239191 CAAATTCGCAACGCGATAGC
1 CAAATTCGCAACGCGAAAGC
* * * *
1239211 CAAATTTGCAACACAAAAGT
1 CAAATTCGCAACGCGAAAGC
*
1239231 CAAATTCGCAAAGCGAAA
1 CAAATTCGCAACGCGAAA
1239249 CACACTATTA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.16
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGC
Found at i:1239376 original size:22 final size:22
Alignment explanation
Indices: 1239351--1239408 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
1239341 TCACTCTCTA
*
1239351 CGACGACATCCATCCCCATCTC
1 CGACGAAATCCATCCCCATCTC
* * *
1239373 CGACGAAATTCGTCCGCATCTC
1 CGACGAAATCCATCCCCATCTC
* *
1239395 CGGCGAAATTCATC
1 CGACGAAATCCATC
1239409 TATCTCCATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.21
Consensus pattern (22 bp):
CGACGAAATCCATCCCCATCTC
Found at i:1242350 original size:23 final size:23
Alignment explanation
Indices: 1242324--1242368 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1242314 CACCACAGCT
*
1242324 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
1242347 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1242369 ATATAATGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1242557 original size:147 final size:148
Alignment explanation
Indices: 1242336--1242648 Score: 558
Period size: 147 Copynumber: 2.1 Consensus size: 148
1242326 TATAAATGCA
* *
1242336 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGCTGTCCATAAGGACCACATATAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1242400 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
1242465 CCAAAGAATAT-ATATATC
130 CCAAAGAATATAATATATC
1242483 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1242548 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
1242613 CAAAGAATATACATATGTC
131 CAAAGAATATA-ATATATC
*
1242632 TCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
1242649 CCCTCTACCC
Statistics
Matches: 159, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
146 1 0.01
147 136 0.86
149 22 0.14
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (148 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATAATATATC
Found at i:1243236 original size:64 final size:63
Alignment explanation
Indices: 1243103--1243259 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
1243093 TAATGAGGGT
* * * ** *
1243103 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
1243167 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
1243229 G
63 G
*
1243230 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
1243260 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:1249376 original size:23 final size:23
Alignment explanation
Indices: 1249350--1249394 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1249340 CACCACAGCT
* *
1249350 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCG
* *
1249373 CGTAGAATTACACCGTAGTGCC
1 CGTAGAAATACACCGAAGTGCC
1249395 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCG
Found at i:1249632 original size:149 final size:149
Alignment explanation
Indices: 1249362--1249676 Score: 542
Period size: 149 Copynumber: 2.1 Consensus size: 149
1249352 TATAAATGCA
*
1249362 CCGAAGTG-CCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATAA
1 CCGAAG-GACCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
* *
1249426 TTCCTTAAGGATCATATACATATACTAGGGACCAAGTATGTGTCTTTCAAAACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGACCAAGTATATGTCTTTCAAAACTTCACACATGTT
*
1249491 CCAAAGAATATATATATATC
130 CCAAAGAATATACATATATC
*
1249511 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
* *
1249576 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATATGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGACCAAGTATATGTCTTTCAAAACTTCACACATGTTC
*
1249641 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
1249660 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
1249677 CCCTCTACCC
Statistics
Matches: 157, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
148 1 0.01
149 156 0.99
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGACCAAGTATATGTCTTTCAAAACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:1250251 original size:64 final size:64
Alignment explanation
Indices: 1250129--1250285 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 64
1250119 TAATGAGGGT
* *
1250129 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTTTTACTGGG
1 ATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGATGTTCTATTTTTACTGGG
* * * **
1250193 ATGCATCGATGCA-TGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCACT-ACTGATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTTTTACTG
*
1250256 AG
63 GG
* **
1250258 -TGCATCGATGCATTACCAATGCATCGAT
1 ATGCATCGATGCACTACTGATGCATCGAT
1250286 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
63 1 0.01
64 65 0.82
65 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGATGTTCTATTTTTACTGGG
Found at i:1251342 original size:21 final size:22
Alignment explanation
Indices: 1251318--1251363 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
1251308 CTCATCATCG
*
1251318 AAGAAG-CCCCT-TCCACCGTTC
1 AAGAAGACCCCTGT-CAACGTTC
1251339 AAG-AGACCCCTGTCAACGTTC
1 AAGAAGACCCCTGTCAACGTTC
1251360 AAGA
1 AAGA
1251364 GGTCCCGCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
20 2 0.10
21 18 0.86
22 1 0.05
ACGTcount: A:0.30, C:0.35, G:0.17, T:0.17
Consensus pattern (22 bp):
AAGAAGACCCCTGTCAACGTTC
Found at i:1252794 original size:69 final size:67
Alignment explanation
Indices: 1252713--1252889 Score: 247
Period size: 67 Copynumber: 2.6 Consensus size: 67
1252703 TGGGGTTCAC
1252713 TTTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAA-TTGATGAGGAAATA
1 TTTTTTTGCTTGTTTAATTGAATTTGT--A---AAAGTTGATTTGTTTAATTTGATGAGGAAATA
1252776 AGAATTA
61 AGAATTA
* *
1252783 -TTTTTTGCTTGTTTAATTG-ATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAAT
1 TTTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAAT
1252846 TA
66 TA
1252848 TTTTTTTGCTTGTTTAAATTG-ATTTGTAAAAGTTGATTTGTT
1 TTTTTTTGCTTGTTT-AATTGAATTTGTAAAAGTTGATTTGTT
1252890 GTTTTAAATT
Statistics
Matches: 101, Mismatches: 2, Indels: 11
0.89 0.02 0.10
Matches are distributed among these distances:
64 17 0.17
65 19 0.19
66 14 0.14
67 27 0.27
68 4 0.04
69 20 0.20
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (67 bp):
TTTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAAT
TA
Found at i:1253378 original size:18 final size:18
Alignment explanation
Indices: 1253355--1253390 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1253345 AAGCCGGTTG
*
1253355 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1253373 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1253391 CCTTTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1254345 original size:24 final size:24
Alignment explanation
Indices: 1254300--1254346 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1254290 ATTTATAGTG
* * *
1254300 AAGCTGAAATTTATATTGAAATTT
1 AAGCTCAAATTGAAATTGAAATTT
*
1254324 AAGCTCAAATTGAAATTTAAATT
1 AAGCTCAAATTGAAATTGAAATT
1254347 CAAACTTCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (24 bp):
AAGCTCAAATTGAAATTGAAATTT
Found at i:1254349 original size:18 final size:18
Alignment explanation
Indices: 1254314--1254350 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1254304 TGAAATTTAT
*
1254314 ATTGAAATTTAAGCTCAA
1 ATTGAAATTTAAACTCAA
*
1254332 ATTGAAATTTAAATTCAA
1 ATTGAAATTTAAACTCAA
1254350 A
1 A
1254351 CTTCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (18 bp):
ATTGAAATTTAAACTCAA
Found at i:1254754 original size:25 final size:25
Alignment explanation
Indices: 1254726--1254777 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1254716 AACATTATTT
*
1254726 TTCAAATAATGTACCCATAACAATG
1 TTCAAATAATGTACCCACAACAATG
*
1254751 TTCAAATAATGTACTCACAACAATG
1 TTCAAATAATGTACCCACAACAATG
1254776 TT
1 TT
1254778 TAATTGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (25 bp):
TTCAAATAATGTACCCACAACAATG
Found at i:1254899 original size:34 final size:34
Alignment explanation
Indices: 1254856--1254937 Score: 128
Period size: 34 Copynumber: 2.4 Consensus size: 34
1254846 CTTTCGCAAC
*
1254856 GCGAAAGTAAAATTCGCAACGCGAAATAAGCGTT
1 GCGAAAGTAAAATTCGCAACGCGAAATAAGCATT
*
1254890 GCGAAAGTAAAATTCGCAACGCGAAATAAGTATT
1 GCGAAAGTAAAATTCGCAACGCGAAATAAGCATT
* *
1254924 GCGATAGTCAAATT
1 GCGAAAGTAAAATT
1254938 TGCGTTGCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (34 bp):
GCGAAAGTAAAATTCGCAACGCGAAATAAGCATT
Found at i:1255300 original size:18 final size:18
Alignment explanation
Indices: 1255277--1255312 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1255267 AAGCCGGTTG
*
1255277 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1255295 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1255313 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1257601 original size:24 final size:24
Alignment explanation
Indices: 1257567--1257620 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1257557 CCATCACATC
1257567 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
1257591 ATCAAAGTCCGGGTATTGACTAAG
1 ATCAAAATCCGAGTATTGACCAAG
1257615 ATCAAA
1 ATCAAA
1257621 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:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1257767 original size:12 final size:12
Alignment explanation
Indices: 1257746--1257779 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1257736 GGTTGTGGGT
*
1257746 TTTGAGATTGTG
1 TTTGATATTGTG
1257758 TTTGATATTGTG
1 TTTGATATTGTG
*
1257770 TTTGTTATTG
1 TTTGATATTG
1257780 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1258396 original size:16 final size:15
Alignment explanation
Indices: 1258374--1258412 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1258364 GAAATCATTG
1258374 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
1258390 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
1258405 AAAAATTA
1 AAAAATTA
1258413 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:1258573 original size:18 final size:18
Alignment explanation
Indices: 1258550--1258595 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
1258540 AAAACATTTG
1258550 TGTTGCGAAACTAAAACC
1 TGTTGCGAAACTAAAACC
1258568 TGTTGCGAAACTAAAACC
1 TGTTGCGAAACTAAAACC
1258586 TGTTGCGAAA
1 TGTTGCGAAA
1258596 TTTAATTCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (18 bp):
TGTTGCGAAACTAAAACC
Found at i:1258647 original size:19 final size:20
Alignment explanation
Indices: 1258606--1258661 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
1258596 TTTAATTCGT
* * *
1258606 GTTGCGAATTCGAAAATCTA
1 GTTGTGAATTTGAAATTCTA
1258626 GTTGTGAATTTGAAATTC-A
1 GTTGTGAATTTGAAATTCTA
1258645 GTTGTGAATTTGAAATT
1 GTTGTGAATTTGAAATT
1258662 TCGCGTTGCG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.39
Consensus pattern (20 bp):
GTTGTGAATTTGAAATTCTA
Found at i:1258691 original size:20 final size:20
Alignment explanation
Indices: 1258666--1258736 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
1258656 GAAATTTCGC
1258666 GTTGCGAATTTAACTTTTGT
1 GTTGCGAATTTAACTTTTGT
* * * *
1258686 GTTGCGAATTTGACTATCGA
1 GTTGCGAATTTAACTTTTGT
* *
1258706 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTAACTTTTGT
1258726 GTTGCG-ATTTA
1 GTTGCGAATTTA
1258737 CAGATTCGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 4 0.10
20 38 0.90
ACGTcount: A:0.20, C:0.13, G:0.24, T:0.44
Consensus pattern (20 bp):
GTTGCGAATTTAACTTTTGT
Found at i:1258750 original size:40 final size:41
Alignment explanation
Indices: 1258661--1258758 Score: 112
Period size: 40 Copynumber: 2.4 Consensus size: 41
1258651 AATTTGAAAT
* * * *
1258661 TTCGCGTTGCGAATTTAACTTTTGTGTTGCGAATTTGACTA
1 TTCGAGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACGA
1258702 -TCGAGTTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACAGA
1 TTCGAGTTGCGAATTTGACTTCTGTGTTGCGAATTTGAC-GA
* *
1258741 TTCGTGTTGCGAAATTGA
1 TTCGAGTTGCGAATTTGA
1258759 AAACTGGGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.04
39 5 0.10
40 42 0.86
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.41
Consensus pattern (41 bp):
TTCGAGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACGA
Found at i:1261304 original size:2 final size:2
Alignment explanation
Indices: 1261299--1261331 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1261289 GAATAATTAA
1261299 AT AT AT AT 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 AT AT AT AT A
1261332 GAATATGTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1261413 original size:34 final size:36
Alignment explanation
Indices: 1261369--1261470 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
1261359 TTTCGTCCTA
1261369 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
1261404 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
1261439 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
1261471 GTTCTACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 30 0.48
35 3 0.05
37 29 0.47
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:1261920 original size:2 final size:2
Alignment explanation
Indices: 1261915--1261945 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1261905 TTATTAGTGT
*
1261915 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1261946 TTCCTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1262077 original size:16 final size:18
Alignment explanation
Indices: 1262056--1262090 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1262046 TTTACTCATT
1262056 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
1262072 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
1262090 T
1 T
1262091 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:1265361 original size:20 final size:22
Alignment explanation
Indices: 1265303--1265372 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 22
1265293 CAAAAAGGGC
1265303 AAAAA-GAAAAAAGA-AAATAAGCA
1 AAAAAGGAAAAAA-ACAAA-AA-CA
*
1265326 AAAAAGGAAAAAAACAAGAACA
1 AAAAAGGAAAAAAACAAAAACA
* *
1265348 AAAAA-G-AAAGAACAAAAATA
1 AAAAAGGAAAAAAACAAAAACA
1265368 AAAAA
1 AAAAA
1265373 AGGGACAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 16 0.39
21 1 0.02
22 7 0.17
23 8 0.20
24 9 0.22
ACGTcount: A:0.80, C:0.06, G:0.11, T:0.03
Consensus pattern (22 bp):
AAAAAGGAAAAAAACAAAAACA
Found at i:1266030 original size:22 final size:22
Alignment explanation
Indices: 1266005--1266053 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1265995 CCATCAATCT
*
1266005 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
1266027 TTTGAGCATCAAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
1266049 TTTGA
1 TTTGA
1266054 CCAAACACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (22 bp):
TTTGAGCATCAAATGTCAAACC
Found at i:1267017 original size:36 final size:36
Alignment explanation
Indices: 1266974--1267043 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
1266964 ACTAGAATAG
*
1266974 TTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAA
1 TTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAA
* *
1267010 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCCCTTGAGACAATTTCCCTTGAAACA
1267044 TAAACATTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAA
Found at i:1267106 original size:36 final size:36
Alignment explanation
Indices: 1267059--1267285 Score: 227
Period size: 37 Copynumber: 6.4 Consensus size: 36
1267049 ATTGAAAACA
* * *
1267059 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1267095 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
* * *
1267132 TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA-G
* * * *
1267161 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
** * *
1267197 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
* *
1267234 TTTCTCTTGAAACAAATTTTGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1267270 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
1267286 ATCTTTGAAT
Statistics
Matches: 157, Mismatches: 23, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.01
29 19 0.12
30 2 0.01
35 1 0.01
36 66 0.42
37 67 0.43
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:1267156 original size:102 final size:100
Alignment explanation
Indices: 1266978--1267249 Score: 364
Period size: 102 Copynumber: 2.7 Consensus size: 100
1266968 GAATAGTTTT
* *
1266978 GTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
*
1267043 ATAAACATTGAAAACATTTCCCTTGAAATAAATTTC
66 A-AAACATTGAAAACATTTCCCTTGAAACAAATTTC
* *
1267079 GTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
1 GTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
* * ** * *
1267144 CAAAATATTTGAATATGTTTTCTTTGAAACAAATTTC
65 CAAAACA-TTGAAAACATTTCCCTTGAAACAAATTTC
* ** * *
1267181 GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1 GTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1267246 CAAA
65 CAAA
1267250 TTTTGTCTAT
Statistics
Matches: 150, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
101 31 0.21
102 119 0.79
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (100 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
AAAACATTGAAAACATTTCCCTTGAAACAAATTTC
Found at i:1267228 original size:37 final size:36
Alignment explanation
Indices: 1267162--1267285 Score: 169
Period size: 36 Copynumber: 3.4 Consensus size: 36
1267152 TTGAATATGT
* *
1267162 TTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
1267197 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
1267234 TTTCTCTTGAAACAAATTTTGTCTATCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
1267270 TTTCCCTTGAAACAAA
1 TTTCTCTTGAAACAAA
1267286 ATCTTTGAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
35 5 0.06
36 42 0.54
37 31 0.40
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:1267251 original size:138 final size:139
Alignment explanation
Indices: 1267079--1267336 Score: 410
Period size: 138 Copynumber: 1.9 Consensus size: 139
1267069 AATAAATTTC
* *
1267079 GTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAA
* * ** *
1267144 CAAAATATTTGAATATGTTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAA
66 CAAAATATTTGAATATATTTCCCCTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAA
1267209 CTAAGTTTT
131 CTAAGTTTT
*
1267218 GTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAA
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAA
* * *
1267282 CAAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTT
66 CAAAATATTTGAATATATTTCCCCTAAAACAAATTTCGTCTCCCTTGAGACAGTT
1267337 ACTCTTGAAA
Statistics
Matches: 108, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
138 81 0.75
139 27 0.25
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (139 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAA
CAAAATATTTGAATATATTTCCCCTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAA
CTAAGTTTT
Done.