Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008964.1 Hibiscus syriacus cultivar Beakdansim tig00112305_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: 2156694
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 6 of 11
Found at i:997127 original size:117 final size:112
Alignment explanation
Indices: 996917--997225 Score: 423
Period size: 117 Copynumber: 2.8 Consensus size: 112
996907 AAGCGTTGGA
996917 TTGAACAAGTTCTTCTCATTATGAACTTCTTCT-CTCTTGTTGGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTC-T-TTGGATGAGTTCTTCTCATTATGAA
996981 CTCTTCACTGAAAATGTTGATCCACCTCTTTCTGTGATGAAATCGAACCAAGG
64 CTCTTCACTGAAAATGTTGATCCACCTCTTTCTGTGATGAAATCG-A--AA-G
*
997034 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTCTTTGGATGAGTTCTTCTCATTATGAAC
* * * *
997099 TCTTCACTGAAAATGTTGATCCATCTCTTTCTGTGATGGATTTGAAAG
65 TCTTCACTGAAAATGTTGATCCACCTCTTTCTGTGATGAAATCGAAAG
* * *
997147 --GAACAAGTTCTTCTCATTATGAAC-T-TTATCCT-TTAGGATGAGTTCTTCTCATTATGAGCT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCTTTGGATGAGTTCTTCTCATTATGAACT
* *
997207 CTCCATTGAAAATGTTGAT
66 CTTCACTGAAAATGTTGAT
997226 GCAAAGTTGA
Statistics
Matches: 179, Mismatches: 11, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
107 42 0.23
108 4 0.02
109 2 0.01
110 1 0.01
111 24 0.13
113 1 0.01
114 2 0.01
116 1 0.01
117 97 0.54
118 2 0.01
119 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (112 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCTTTGGATGAGTTCTTCTCATTATGAACT
CTTCACTGAAAATGTTGATCCACCTCTTTCTGTGATGAAATCGAAAG
Found at i:997244 original size:87 final size:89
Alignment explanation
Indices: 997147--997316 Score: 238
Period size: 91 Copynumber: 1.9 Consensus size: 89
997137 GATTTGAAAG
*
997147 GAACAAGTTCTTCTCATTATGAACTT-TATC-CTT-TAGGATGAGTTCTTCTCATTATGAGCTCT
1 GAACAAGTTCTTCTCATTATGAACTTCT-TCTCTTCTAGGATGAGTTCTTCTCATTATGAACTCT
*
997209 CCATTGAAAATGTTGATGCAAAGTT
65 CCACTGAAAATGTTGATGCAAAGTT
**
997234 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCGTTTGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTC-TCTTC-TAGGATGAGTTCTTCTCATTATGAACTC
* *
997299 TTCACTGGAAATGTTGAT
64 TCCACTGAAAATGTTGAT
997317 CCCTCAAGCG
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
87 28 0.39
88 1 0.01
89 3 0.04
91 40 0.56
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (89 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTCTTCTAGGATGAGTTCTTCTCATTATGAACTCTC
CACTGAAAATGTTGATGCAAAGTT
Found at i:997477 original size:136 final size:136
Alignment explanation
Indices: 997234--997582 Score: 556
Period size: 136 Copynumber: 2.6 Consensus size: 136
997224 ATGCAAAGTT
* * * **
997234 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTC-GTTTGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * ** * * *
997298 CTTCACTGGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTTATGAATCGAGTGA
66 CTCCATTGGAAATACTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGA
997363 TAGGTC
131 TAGGTC
997369 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* *
997434 CTCCATTGGAAATACTGATCCTTCAAGCAAGGTGTCACTGATTCAAAATGTCATGAATCTAGTGA
66 CTCCATTGGAAATACTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGA
997499 TAGGTC
131 TAGGTC
997505 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
*
997570 CTCAATTGGAAAT
66 CTCCATTGGAAAT
997583 GCTGGTTCAC
Statistics
Matches: 198, Mismatches: 15, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
135 33 0.17
136 165 0.83
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGGAAATACTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGA
TAGGTC
Found at i:998474 original size:7 final size:7
Alignment explanation
Indices: 998464--998537 Score: 51
Period size: 8 Copynumber: 10.0 Consensus size: 7
998454 CCTTTTTCTC
998464 TTTTTAT
1 TTTTTAT
998471 TTTTTCAT
1 TTTTT-AT
*
998479 TTCTT-T
1 TTTTTAT
*
998485 TTTTCAT
1 TTTTTAT
*
998492 TTTTCAT
1 TTTTTAT
*
998499 TTTTTTT
1 TTTTTAT
998506 CTTTTTCAT
1 -TTTTT-AT
998515 TTTTTCAT
1 TTTTT-AT
*
998523 TTTTCAT
1 TTTTTAT
998530 CTTTTTAT
1 -TTTTTAT
998538 CTGTTCTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
6 4 0.07
7 20 0.37
8 29 0.54
9 1 0.02
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAT
Found at i:998487 original size:20 final size:20
Alignment explanation
Indices: 998458--998516 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
998448 AACCCTCCTT
*
998458 TTTCTCTTTTT-ATTTTTTCA
1 TTTCTTTTTTTCA-TTTTTCA
998478 TTTCTTTTTTTCATTTTTCA
1 TTTCTTTTTTTCATTTTTCA
998498 --T-TTTTTTTC-TTTTTCA
1 TTTCTTTTTTTCATTTTTCA
998514 TTT
1 TTT
998517 TTTCATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 7 0.20
17 8 0.23
18 2 0.06
20 17 0.49
21 1 0.03
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTCTTTTTTTCATTTTTCA
Found at i:998535 original size:31 final size:30
Alignment explanation
Indices: 998470--998535 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 30
998460 TCTCTTTTTA
* *
998470 TTTTTTCATTTCTTTTTTTCATTTTTCATT
1 TTTTTTCATTTCATTTTTTCATTTTTCATC
*
998500 TTTTTTCTTTTTCATTTTTTCATTTTTCATC
1 TTTTTTC-ATTTCATTTTTTCATTTTTCATC
998531 TTTTT
1 TTTTT
998536 ATCTGTTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (30 bp):
TTTTTTCATTTCATTTTTTCATTTTTCATC
Found at i:998549 original size:31 final size:31
Alignment explanation
Indices: 998479--998550 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
998469 ATTTTTTCAT
* *
998479 TTCTTTTTTTCATTTTTCATTTTTTTTCTTT
1 TTCTTTTTTTCATTTTTCATTTTTTATCTTG
*
998510 TTCATTTTTTCATTTTTCATCTTTTTATC-TG
1 TTCTTTTTTTCATTTTTCAT-TTTTTATCTTG
998541 TTCTTTTTTT
1 TTCTTTTTTT
998551 TTCTTCAAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 29 0.81
32 7 0.19
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.76
Consensus pattern (31 bp):
TTCTTTTTTTCATTTTTCATTTTTTATCTTG
Found at i:1011700 original size:3 final size:3
Alignment explanation
Indices: 1011692--1011731 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1011682 ATATTAATTA
1011692 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1011732 TTTATAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1013837 original size:26 final size:28
Alignment explanation
Indices: 1013793--1013844 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
1013783 ATGTTTTCTA
1013793 ATTTTCAAAAAACTAAAAA-TGAAAACT
1 ATTTTCAAAAAACTAAAAATTGAAAACT
*
1013820 ATTTTCTAAAAAC-AAAAATTGAAAA
1 ATTTTCAAAAAACTAAAAATTGAAAA
1013845 TAAAAATAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.60, C:0.10, G:0.04, T:0.27
Consensus pattern (28 bp):
ATTTTCAAAAAACTAAAAATTGAAAACT
Found at i:1022037 original size:30 final size:30
Alignment explanation
Indices: 1021990--1022075 Score: 120
Period size: 30 Copynumber: 2.9 Consensus size: 30
1021980 CAGGGAACAA
*
1021990 GGGATGATGGG-GTTGGTGTTGAAAAAAAT
1 GGGATGGTGGGTGTTGGTGTTGAAAAAAAT
*
1022019 GTGATGGTGGGTGTTGGTGTTGAAAAAAAT
1 GGGATGGTGGGTGTTGGTGTTGAAAAAAAT
* **
1022049 GGGGTGGTAAGTGTTGGTGTTGAAAAA
1 GGGATGGTGGGTGTTGGTGTTGAAAAA
1022076 TGGTGTTTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
29 9 0.18
30 41 0.82
ACGTcount: A:0.28, C:0.00, G:0.42, T:0.30
Consensus pattern (30 bp):
GGGATGGTGGGTGTTGGTGTTGAAAAAAAT
Found at i:1025710 original size:19 final size:20
Alignment explanation
Indices: 1025686--1025735 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1025676 GATAAATTTA
*
1025686 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
1025705 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
1025726 TT-ATAATTTT
1 TTAATAATTTT
1025736 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:1025712 original size:31 final size:31
Alignment explanation
Indices: 1025672--1025739 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1025662 TTTTATAGTA
*
1025672 TTTAGATAAATTTATTAA-TAATTTTATAATCT
1 TTTA-ATAAATTTAATAAGT-ATTTTATAATCT
*
1025704 TTTAATAAATTTAATAAGTATTTTATAATTT
1 TTTAATAAATTTAATAAGTATTTTATAATCT
1025735 TTTAA
1 TTTAA
1025740 ACTTTATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTAATAAATTTAATAAGTATTTTATAATCT
Found at i:1026485 original size:11 final size:10
Alignment explanation
Indices: 1026465--1026578 Score: 58
Period size: 10 Copynumber: 11.0 Consensus size: 10
1026455 AATAAAGTTA
*
1026465 AAAAAATTAT
1 AAAATATTAT
1026475 AAAATACTTAT
1 AAAATA-TTAT
*
1026486 TAAAT-TTATT
1 AAAATATTA-T
*
1026496 AAAAGATTAT
1 AAAATATTAT
1026506 AAAATTATTA-
1 AAAA-TATTAT
1026516 ATAAAT-TTATT
1 A-AAATATTA-T
*
1026527 AAAAGATTAT
1 AAAATATTAT
1026537 AAAATTATTA-
1 AAAA-TATTAT
1026547 ATAAAT-TTATT
1 A-AAATATTA-T
* *
1026558 TAAATACTAT
1 AAAATATTAT
1026568 AAAATAATTAT
1 AAAAT-ATTAT
1026579 TATATTATCG
Statistics
Matches: 79, Mismatches: 11, Indels: 27
0.68 0.09 0.23
Matches are distributed among these distances:
9 9 0.11
10 35 0.44
11 35 0.44
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (10 bp):
AAAATATTAT
Found at i:1026508 original size:19 final size:19
Alignment explanation
Indices: 1026467--1026547 Score: 61
Period size: 19 Copynumber: 4.6 Consensus size: 19
1026457 TAAAGTTAAA
*
1026467 AAAATTA-TAAAATACTTATT
1 AAAATTATTAAAAGA-TTA-T
*
1026487 AAATTTATTAAAAGATTAT
1 AAAATTATTAAAAGATTAT
1026506 AAAATTATT-----A--AT
1 AAAATTATTAAAAGATTAT
*
1026518 AAATTTATTAAAAGATTAT
1 AAAATTATTAAAAGATTAT
1026537 AAAATTATTAA
1 AAAATTATTAA
1026548 TAAATTTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
12 10 0.21
14 1 0.02
17 1 0.02
19 21 0.44
20 9 0.19
21 6 0.12
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (19 bp):
AAAATTATTAAAAGATTAT
Found at i:1026508 original size:31 final size:31
Alignment explanation
Indices: 1026465--1026577 Score: 156
Period size: 31 Copynumber: 3.6 Consensus size: 31
1026455 AATAAAGTTA
* *
1026465 AAAAAATTATAAAA-TACTTATTAAATTTATT
1 AAAAGATTATAAAATTA-TTAATAAATTTATT
1026496 AAAAGATTATAAAATTATTAATAAATTTATT
1 AAAAGATTATAAAATTATTAATAAATTTATT
1026527 AAAAGATTATAAAATTATTAATAAATTTATT
1 AAAAGATTATAAAATTATTAATAAATTTATT
* * * *
1026558 TAAATACTATAAAATAATTA
1 AAAAGATTATAAAATTATTA
1026578 TTATATTATC
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
31 73 0.97
32 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (31 bp):
AAAAGATTATAAAATTATTAATAAATTTATT
Found at i:1029349 original size:22 final size:22
Alignment explanation
Indices: 1029324--1029390 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 22
1029314 TTCCTAAATA
1029324 AAATAATCAAACTAAAAATCTT
1 AAATAATCAAACTAAAAATCTT
* * * *
1029346 AAATAA--AGAGTAATAA--TA
1 AAATAATCAAACTAAAAATCTT
*
1029364 AAATAATCAAACTAAAAATCCT
1 AAATAATCAAACTAAAAATCTT
1029386 AAATA
1 AAATA
1029391 TAAAAAAATT
Statistics
Matches: 32, Mismatches: 9, Indels: 8
0.65 0.18 0.16
Matches are distributed among these distances:
18 7 0.22
20 14 0.44
22 11 0.34
ACGTcount: A:0.63, C:0.10, G:0.03, T:0.24
Consensus pattern (22 bp):
AAATAATCAAACTAAAAATCTT
Found at i:1029769 original size:13 final size:13
Alignment explanation
Indices: 1029751--1029775 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1029741 TGACCCAATC
1029751 GACCCGTTGATTT
1 GACCCGTTGATTT
1029764 GACCCGTTGATT
1 GACCCGTTGATT
1029776 GTTAACTTTG
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:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (13 bp):
GACCCGTTGATTT
Found at i:1031026 original size:37 final size:37
Alignment explanation
Indices: 1030955--1031055 Score: 112
Period size: 37 Copynumber: 2.7 Consensus size: 37
1030945 TATTGACTTA
*
1030955 TTCATCCATTAGGATGATAAATCCAATTACCGACTGG
1 TTCATCCATTAGGATGATAAATCCAACTACCGACTGG
* ** *
1030992 TTCATCTATTAGGATGATAAATTTAACTATCGACTGG
1 TTCATCCATTAGGATGATAAATCCAACTACCGACTGG
* * * *
1031029 TTTATCCCACTAGGATGGTAAACCCAA
1 TTCAT-CCATTAGGATGATAAATCCAA
1031056 TAACTGTATG
Statistics
Matches: 51, Mismatches: 12, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
37 36 0.71
38 15 0.29
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (37 bp):
TTCATCCATTAGGATGATAAATCCAACTACCGACTGG
Found at i:1031796 original size:11 final size:11
Alignment explanation
Indices: 1031780--1031808 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1031770 AAGCAATCCA
1031780 TATATTTTCAT
1 TATATTTTCAT
1031791 TATATTTTCAT
1 TATATTTTCAT
1031802 TATATTT
1 TATATTT
1031809 ATTAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (11 bp):
TATATTTTCAT
Found at i:1034408 original size:20 final size:20
Alignment explanation
Indices: 1034385--1034450 Score: 123
Period size: 20 Copynumber: 3.3 Consensus size: 20
1034375 AATCTGTAAA
1034385 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
1034405 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
1034425 TCGCAACACATAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
1034445 TCGCAA
1 TCGCAA
1034451 AGCGCGTTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.44, C:0.26, G:0.14, T:0.17
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:1034623 original size:22 final size:22
Alignment explanation
Indices: 1034605--1034652 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1034595 CTACGACAAC
*
1034605 ATCCGTCCCCATCTCCGACGAA
1 ATCCATCCCCATCTCCGACGAA
*
1034627 ATCCATCCCCATCTCCGGCGAA
1 ATCCATCCCCATCTCCGACGAA
1034649 ATCC
1 ATCC
1034653 GTCTATCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.46, G:0.12, T:0.19
Consensus pattern (22 bp):
ATCCATCCCCATCTCCGACGAA
Found at i:1035064 original size:20 final size:19
Alignment explanation
Indices: 1035021--1035074 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1035011 AAATCGCAAC
1035021 GCGATTTTAGTTTCGAGTT
1 GCGATTTTAGTTTCGAGTT
* * *
1035040 ACGATTTTCATTTTCGCGTT
1 GCGATTTT-AGTTTCGAGTT
1035060 GCGATTTTAAGTTTC
1 GCGATTTT-AGTTTC
1035075 AGAAACTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.48
Consensus pattern (19 bp):
GCGATTTTAGTTTCGAGTT
Found at i:1036769 original size:21 final size:21
Alignment explanation
Indices: 1036742--1036791 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1036732 GTTAGGGGAG
* *
1036742 TTACGTGATGAGGTCCATGCT
1 TTACGTGAGGAGGTCCATACT
* *
1036763 TTGCGTGAGGAGGTCGATACT
1 TTACGTGAGGAGGTCCATACT
1036784 TTACGTGA
1 TTACGTGA
1036792 AGACGATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (21 bp):
TTACGTGAGGAGGTCCATACT
Found at i:1036832 original size:21 final size:21
Alignment explanation
Indices: 1036808--1036857 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1036798 TGGTGCATGG
1036808 CGTGATGAGGTACA-GTCTTTA
1 CGTGATGAGGTACAGGT-TTTA
* *
1036829 CGTGGTGAGGTAGAGGTTTTA
1 CGTGATGAGGTACAGGTTTTA
*
1036850 CGCGATGA
1 CGTGATGA
1036858 CAATGGTGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.22, C:0.12, G:0.36, T:0.30
Consensus pattern (21 bp):
CGTGATGAGGTACAGGTTTTA
Found at i:1037283 original size:20 final size:20
Alignment explanation
Indices: 1037273--1037314 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1037263 TTGCAACGGG
*
1037273 AATCTGTAAATCGCAATGCA
1 AATCTGTAAATCGCAACGCA
*
1037293 AATCTGTAAATCGCAACACA
1 AATCTGTAAATCGCAACGCA
1037313 AA
1 AA
1037315 AGTCAAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.21
Consensus pattern (20 bp):
AATCTGTAAATCGCAACGCA
Found at i:1037341 original size:20 final size:20
Alignment explanation
Indices: 1037318--1037388 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
1037308 ACACAAAAGT
*
1037318 CAAATTCGCAATGCGATTTC
1 CAAATTCGCAATGTGATTTC
1037338 CAAATTCGCAATGTGATTTC
1 CAAATTCGCAATGTGATTTC
* * *
1037358 CAAATTTGCAACGTGATTTA
1 CAAATTCGCAATGTGATTTC
*
1037378 TAAATTCGCAA
1 CAAATTCGCAA
1037389 CACTGAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (20 bp):
CAAATTCGCAATGTGATTTC
Found at i:1037431 original size:20 final size:20
Alignment explanation
Indices: 1037408--1037450 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1037398 TCAAATTTGT
*
1037408 AACTCTATTTCTGAATTCGC
1 AACTCGATTTCTGAATTCGC
*
1037428 AACTCGATTTTTGAATTCGC
1 AACTCGATTTCTGAATTCGC
1037448 AAC
1 AAC
1037451 ACGAATTTTA
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:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (20 bp):
AACTCGATTTCTGAATTCGC
Found at i:1037459 original size:20 final size:20
Alignment explanation
Indices: 1037414--1037463 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1037404 TTGTAACTCT
*
1037414 ATTTCTGAATTCGCAACTCGA
1 ATTT-TGAATTCGCAACACGA
*
1037435 TTTTTGAATTCGCAACACGA
1 ATTTTGAATTCGCAACACGA
1037455 ATTTT-AATT
1 ATTTTGAATT
1037464 TCGCCACATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 4 0.15
20 19 0.73
21 3 0.12
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (20 bp):
ATTTTGAATTCGCAACACGA
Found at i:1037466 original size:20 final size:19
Alignment explanation
Indices: 1037423--1037490 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
1037413 TATTTCTGAA
*
1037423 TTCGCAACTCGATTTTTGAA-
1 TTCGCAACACGA-TTTT-AAT
1037443 TTCGCAACACGAATTTTAAT
1 TTCGCAACACG-ATTTTAAT
* * *
1037463 TTCGCCACATG-TTTTATT
1 TTCGCAACACGATTTTAAT
1037481 TTCGCAACAC
1 TTCGCAACAC
1037491 AAATGTTTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
18 14 0.35
19 2 0.05
20 23 0.57
21 1 0.03
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (19 bp):
TTCGCAACACGATTTTAAT
Found at i:1038278 original size:12 final size:12
Alignment explanation
Indices: 1038257--1038290 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1038247 ACCACATTTC
*
1038257 CAATACCAAACA
1 CAATATCAAACA
1038269 CAATATCAAACA
1 CAATATCAAACA
*
1038281 CAATCTCAAA
1 CAATATCAAA
1038291 ACCCACAACC
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:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1038467 original size:24 final size:24
Alignment explanation
Indices: 1038416--1038469 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1038406 GTATTCGAAA
* **
1038416 TTTGATCTTGGTCAATTCTTGGAC
1 TTTGATCTTGGTCAATACTCAGAC
*
1038440 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACTCAGAC
1038464 TTTGAT
1 TTTGAT
1038470 GATATTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.15, G:0.19, T:0.46
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCAGAC
Found at i:1041079 original size:20 final size:20
Alignment explanation
Indices: 1041056--1041099 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1041046 AATCACAACA
*
1041056 CGAATTTGACTTTCACTTTG
1 CGAATTTGACTTTCACGTTG
*
1041076 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCACGTTG
1041096 CGAA
1 CGAA
1041100 AGTGTACCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
CGAATTTGACTTTCACGTTG
Found at i:1041210 original size:25 final size:25
Alignment explanation
Indices: 1041170--1041219 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1041160 AAATCAATTA
* *
1041170 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATAGGTACATTATTTG
1041195 AACATTGTTATAGGTACATTATTTG
1 AACATTGTTATAGGTACATTATTTG
1041220 GAAAATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (25 bp):
AACATTGTTATAGGTACATTATTTG
Found at i:1043258 original size:13 final size:14
Alignment explanation
Indices: 1043240--1043272 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
1043230 CTCCAATTAA
1043240 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
1043253 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1043267 ACAAAT
1 ACAAAT
1043273 ACATCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1044653 original size:21 final size:21
Alignment explanation
Indices: 1044624--1044693 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
1044614 GTGAATCGGG
*
1044624 CTCTCGAACGGTGGGAGAGAC
1 CTCTTGAACGGTGGGAGAGAC
* ** *
1044645 CTCTTGAACGATGACAGTGAC
1 CTCTTGAACGGTGGGAGAGAC
* *
1044666 CTCTTGAACAGTGGGAGAGGC
1 CTCTTGAACGGTGGGAGAGAC
1044687 CTCTTGA
1 CTCTTGA
1044694 CCGACATATC
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.24, C:0.23, G:0.31, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGAGAC
Found at i:1045439 original size:15 final size:16
Alignment explanation
Indices: 1045407--1045442 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1045397 AAATCATTGA
1045407 AAAATTATATAGAAAT
1 AAAATTATATAGAAAT
*
1045423 AAAATTATGTA-AAAT
1 AAAATTATATAGAAAT
1045438 AAAAT
1 AAAAT
1045443 GCCTTCCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
AAAATTATATAGAAAT
Found at i:1046388 original size:24 final size:24
Alignment explanation
Indices: 1046361--1046417 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
1046351 AGTGGAGCCG
*
1046361 AAATTTATATTGAAATTCAAACTC
1 AAATTTAAATTGAAATTCAAACTC
*
1046385 AAATTTAAATTTAAATTCAAACTC
1 AAATTTAAATTGAAATTCAAACTC
*
1046409 CAA-TTAAAT
1 AAATTTAAAT
1046418 ATTAAATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 6 0.20
24 24 0.80
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATTTAAATTGAAATTCAAACTC
Found at i:1046422 original size:24 final size:25
Alignment explanation
Indices: 1046367--1046424 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 25
1046357 GCCGAAATTT
1046367 ATATTGAAATTCAAACTCAAATTTAA
1 ATATT-AAATTCAAACTCAAATTTAA
*
1046393 AT-TTAAATTCAAACTCCAA-TTAA
1 ATATTAAATTCAAACTCAAATTTAA
1046416 ATATTAAAT
1 ATATTAAAT
1046425 GAATTTGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 6 0.20
24 20 0.67
25 2 0.07
26 2 0.07
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (25 bp):
ATATTAAATTCAAACTCAAATTTAA
Found at i:1046819 original size:25 final size:25
Alignment explanation
Indices: 1046791--1046840 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1046781 CATTATTTTC
*
1046791 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1046816 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1046841 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:1047027 original size:29 final size:29
Alignment explanation
Indices: 1046985--1047042 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1046975 TTGCAACGCA
*
1046985 AAAGTAAAATTCGCGTTGCGATTGTTGCG
1 AAAGTAAAATTCGCATTGCGATTGTTGCG
* * *
1047014 AAAGTCAAATTCGCATTGCGCTTTTTGCG
1 AAAGTAAAATTCGCATTGCGATTGTTGCG
1047043 TTGCGAACTT
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:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (29 bp):
AAAGTAAAATTCGCATTGCGATTGTTGCG
Found at i:1049612 original size:24 final size:24
Alignment explanation
Indices: 1049585--1049638 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1049575 CTGAAACATC
*
1049585 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
1049609 ATCAAAGTCCGGGTATTGACCGAG
1 ATCAAAATCCGAGTATTGACCAAG
1049633 ATCAAA
1 ATCAAA
1049639 TTTTGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1050461 original size:20 final size:20
Alignment explanation
Indices: 1050414--1050505 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
1050404 CAGAAATGAG
*
1050414 TTGCGAATTTG-AAATTCAGTG
1 TTGCGAATTTGTAAA-TC-GTA
*
1050435 TTGCGAATTTGTAAATCGCA
1 TTGCGAATTTGTAAATCGTA
* * *
1050455 ATGCGAATTTGTAAATCATG
1 TTGCGAATTTGTAAATCGTA
*
1050475 TTGCGAATTTGGAAATCGTA
1 TTGCGAATTTGTAAATCGTA
1050495 TTGCGAATTTG
1 TTGCGAATTTG
1050506 ACTTCTGTGT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
20 44 0.73
21 13 0.22
22 3 0.05
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (20 bp):
TTGCGAATTTGTAAATCGTA
Found at i:1050477 original size:40 final size:41
Alignment explanation
Indices: 1050415--1050520 Score: 137
Period size: 40 Copynumber: 2.6 Consensus size: 41
1050405 AGAAATGAGT
*
1050415 TGCGAATTTGAAATTCAGTGTTGCGAATTTGTAAATCGCAA
1 TGCGAATTTGAAATTCAGTGTTGCGAATTTGGAAATCGCAA
* *
1050456 TGCGAATTTGTAAA-TCA-TGTTGCGAATTTGGAAATCGTAT
1 TGCGAATTTG-AAATTCAGTGTTGCGAATTTGGAAATCGCAA
* *
1050496 TGCGAATTTG-ACTTCTGTGTTGCGA
1 TGCGAATTTGAAATTCAGTGTTGCGA
1050521 TTTACAGATT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
38 1 0.02
39 2 0.04
40 38 0.67
41 13 0.23
42 3 0.05
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (41 bp):
TGCGAATTTGAAATTCAGTGTTGCGAATTTGGAAATCGCAA
Found at i:1050520 original size:20 final size:20
Alignment explanation
Indices: 1050385--1050505 Score: 102
Period size: 20 Copynumber: 6.0 Consensus size: 20
1050375 AAATTATATA
* **
1050385 GAAATCGAGTTGCGGAATTCA
1 GAAATCGTGTTGC-GAATTTG
*
1050406 GAAAT-GAGTTGCGAATTT-
1 GAAATCGTGTTGCGAATTTG
1050424 GAAATTCAGTGTTGCGAATTTG
1 GAAA-TC-GTGTTGCGAATTTG
* ***
1050446 TAAATCGCAATGCGAATTTG
1 GAAATCGTGTTGCGAATTTG
* *
1050466 TAAATCATGTTGCGAATTTG
1 GAAATCGTGTTGCGAATTTG
*
1050486 GAAATCGTATTGCGAATTTG
1 GAAATCGTGTTGCGAATTTG
1050506 ACTTCTGTGT
Statistics
Matches: 83, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.05
19 6 0.07
20 51 0.61
21 19 0.23
22 3 0.04
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (20 bp):
GAAATCGTGTTGCGAATTTG
Found at i:1050538 original size:20 final size:20
Alignment explanation
Indices: 1050515--1050580 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
1050505 GACTTCTGTG
*
1050515 TTGCGATTTACAGATTCGCA
1 TTGCGATTTACAAATTCGCA
*
1050535 TTGCGATTTACAAATTCGCG
1 TTGCGATTTACAAATTCGCA
*
1050555 TTGCGATTTACATATTCGCA
1 TTGCGATTTACAAATTCGCA
1050575 TTGCGA
1 TTGCGA
1050581 ATTTGGAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (20 bp):
TTGCGATTTACAAATTCGCA
Found at i:1050538 original size:40 final size:40
Alignment explanation
Indices: 1050494--1050585 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 40
1050484 TGGAAATCGT
*
1050494 ATTGCGAATTTGAC-TTCTGTGTTGCGATTTACAGATTCGC
1 ATTGCGAATTTGACATTC-GCGTTGCGATTTACAGATTCGC
*
1050534 ATTGCG-ATTT-ACAAATTCGCGTTGCGATTTACATATTCGC
1 ATTGCGAATTTGAC--ATTCGCGTTGCGATTTACAGATTCGC
1050574 ATTGCGAATTTG
1 ATTGCGAATTTG
1050586 GAAACTGAGT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
38 2 0.04
39 4 0.09
40 32 0.71
41 7 0.16
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (40 bp):
ATTGCGAATTTGACATTCGCGTTGCGATTTACAGATTCGC
Found at i:1050598 original size:40 final size:40
Alignment explanation
Indices: 1050514--1050600 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 40
1050504 TGACTTCTGT
* *
1050514 GTTGCGATTTACAGATTCGCATTGCGATTTACAAATTCGC
1 GTTGCGATTTACAGATTCGCATTGCGATTTACAAACTCGA
* **
1050554 GTTGCGATTTACATATTCGCATTGCGAATTTGGAAACT-GA
1 GTTGCGATTTACAGATTCGCATTGCG-ATTTACAAACTCGA
1050594 GTTGCGA
1 GTTGCGA
1050601 AATTGGAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 33 0.80
41 8 0.20
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.34
Consensus pattern (40 bp):
GTTGCGATTTACAGATTCGCATTGCGATTTACAAACTCGA
Found at i:1053576 original size:2 final size:2
Alignment explanation
Indices: 1053569--1053596 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1053559 CATCAAATTA
1053569 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
1053597 GGGGCAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1070806 original size:2 final size:2
Alignment explanation
Indices: 1070799--1070837 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1070789 TTTTAAACTT
1070799 TA TA 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 TA TA T
1070838 GTATGTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1072487 original size:15 final size:15
Alignment explanation
Indices: 1072467--1072496 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1072457 GATCTGTTTG
1072467 ATCAACTGAAAGGCA
1 ATCAACTGAAAGGCA
1072482 ATCAACTGAAAGGCA
1 ATCAACTGAAAGGCA
1072497 CAACAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (15 bp):
ATCAACTGAAAGGCA
Found at i:1078108 original size:16 final size:19
Alignment explanation
Indices: 1078062--1078109 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 19
1078052 TAAGAAATAA
1078062 GAGAAGAAAGAAAGGAAATG
1 GAGAAGAAAGAAAGGAAA-G
1078082 GAGAAGAAAGAAAGGAAAG
1 GAGAAGAAAGAAAGGAAAG
1078101 GAAGAAGAA
1 G-AGAAGAA
1078110 TAAAAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.02
Consensus pattern (19 bp):
GAGAAGAAAGAAAGGAAAG
Found at i:1078430 original size:21 final size:20
Alignment explanation
Indices: 1078396--1078436 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1078386 ATAGAATGTT
* *
1078396 ATTTTATGATTAATTGATTA
1 ATTTCATGATTAATTAATTA
1078416 ATTTCATGAATTAATTAATTA
1 ATTTCATG-ATTAATTAATTA
1078437 TAGGAAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (20 bp):
ATTTCATGATTAATTAATTA
Found at i:1083718 original size:40 final size:40
Alignment explanation
Indices: 1083663--1083784 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
1083653 TGCAGGTTTA
1083663 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1083703 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1083743 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1083783 TA
1 TA
1083785 GCACTACGGT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1083982 original size:47 final size:44
Alignment explanation
Indices: 1083888--1083999 Score: 152
Period size: 47 Copynumber: 2.5 Consensus size: 44
1083878 GTAACCATGC
* *
1083888 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGAA
* * *
1083932 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--T-AATGGCAAGTATATTGGAA
1083979 AAATAAGCTTACGAGCTTATG
1 AAATAAGCTTACGAGCTTATG
1084000 AGATAAATGG
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
44 22 0.37
46 1 0.02
47 37 0.62
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGAA
Found at i:1084491 original size:18 final size:18
Alignment explanation
Indices: 1084455--1084492 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1084445 TTTAAGAAAA
*
1084455 TAAATTTTAAATCGCTTT
1 TAAATTTTAAATAGCTTT
1084473 TAAATTTTGAAATAG-TTT
1 TAAATTTT-AAATAGCTTT
1084491 TA
1 TA
1084493 GAAAATACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (18 bp):
TAAATTTTAAATAGCTTT
Found at i:1085208 original size:54 final size:54
Alignment explanation
Indices: 1085066--1085427 Score: 476
Period size: 54 Copynumber: 6.7 Consensus size: 54
1085056 TTGCACGTGT
* * * * * * * ** *
1085066 AGTGCCGATACGATAATTCACAAACTTATTATGAATTACGTGGGGTGCACACAC
1 AGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
* * * * *
1085120 AGTGTCAATAC-GAAATTCACAAACTTATTATGAATTTCTTAAG-TGTCACACAT
1 AGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCTTAAGTTG-CACACAC
1085173 AGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
1 AGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
* *
1085227 AGTGTCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
1 AGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
* * *
1085281 AGTGCCAATACAAAAATTCATAAACGCATTGTGAATTTCTTAAGTTGCACACAA
1 AGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
*
1085335 AGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
1 AGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
*** *
1085389 AGTGCCAATATGGAAATTCATAAACTTATTATGAATTTC
1 AGTGCCAATACAAAAATTCATAAACTCATTATGAATTTC
1085428 GTGGGGTTGC
Statistics
Matches: 277, Mismatches: 28, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
52 2 0.01
53 42 0.15
54 231 0.83
55 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (54 bp):
AGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
Found at i:1085359 original size:162 final size:161
Alignment explanation
Indices: 1085066--1085449 Score: 527
Period size: 162 Copynumber: 2.4 Consensus size: 161
1085056 TTGCACGTGT
* * * * ** *
1085066 AGTGCCGATACGATAATTCACAAACTTATTATGAATTACGTGGGGTGCACACACAGTGTCAATAC
1 AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCGTAAGGTGCACACACAGTGCCAATAC
* ** *
1085131 GAAATTCACAAACTTATTATGAATTTCTTAAGTGTCACACATAGTGCCAATACAAAAATTCATAA
66 AAAATTCACAAACGCATTATGAATTTCTTAAGTGTCACACAAAGTGCCAATACAAAAATTCATAA
1085196 ACTCATTATGAATTTCTTAAGTTGCACACAC
131 ACTCATTATGAATTTCTTAAGTTGCACACAC
* * * *
1085227 AGTGTCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
1 AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCGTAAGGTGCACACACAGTGCCAATAC
* * *
1085292 AAAAATTCATAAACGCATTGTGAATTTCTTAAGT-TGCACACAAAGTGCCAATACAGAAATTCAT
66 -AAAATTCACAAACGCATTATGAATTTCTTAAGTGT-CACACAAAGTGCCAATACAAAAATTCAT
1085356 AAACTCATTATGAATTTCTTAAGTTGCACACAC
129 AAACTCATTATGAATTTCTTAAGTTGCACACAC
* * ** *
1085389 AGTGCCAATATGGAAATTCATAAACTTATTATGAATTTCGTGGGGTTGCACACATAGTGCC
1 AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCGTAAGG-TGCACACACAGTGCC
1085450 CATTCGGTAA
Statistics
Matches: 193, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
161 55 0.28
162 124 0.64
163 14 0.07
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (161 bp):
AGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCGTAAGGTGCACACACAGTGCCAATAC
AAAATTCACAAACGCATTATGAATTTCTTAAGTGTCACACAAAGTGCCAATACAAAAATTCATAA
ACTCATTATGAATTTCTTAAGTTGCACACAC
Found at i:1088019 original size:17 final size:17
Alignment explanation
Indices: 1087997--1088101 Score: 88
Period size: 17 Copynumber: 6.1 Consensus size: 17
1087987 AATTAAGATT
*
1087997 TAGTTTAATAAATGAAC
1 TAGTTTAATCAATGAAC
* * *
1088014 TAGTTTGATGAATAAAC
1 TAGTTTAATCAATGAAC
*
1088031 TAGTTTAATTAATGAAC
1 TAGTTTAATCAATGAAC
* *
1088048 TAACTTTATTCAATGAAC
1 T-AGTTTAATCAATGAAC
*
1088066 T--TGTAATCTTGAATGAAC
1 TAGTTTAATC---AATGAAC
1088084 TAGTTTAATCAATGAAC
1 TAGTTTAATCAATGAAC
1088101 T
1 T
1088102 GCTTAGTTAA
Statistics
Matches: 70, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
15 5 0.07
17 37 0.53
18 22 0.31
20 6 0.09
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (17 bp):
TAGTTTAATCAATGAAC
Found at i:1090365 original size:2 final size:2
Alignment explanation
Indices: 1090360--1090388 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1090350 AATGATGTAT
1090360 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 T
1090389 TTAAAATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1090650 original size:14 final size:14
Alignment explanation
Indices: 1090631--1090657 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1090621 ACAAGAAGGG
1090631 AAATATGTATATAT
1 AAATATGTATATAT
1090645 AAATATGTATATA
1 AAATATGTATATA
1090658 AAAGTAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
AAATATGTATATAT
Found at i:1091768 original size:17 final size:17
Alignment explanation
Indices: 1091746--1091867 Score: 131
Period size: 17 Copynumber: 7.1 Consensus size: 17
1091736 AATTAAGAGT
*
1091746 TAGTTTAATAAATGAAC
1 TAGTTTAATTAATGAAC
* *
1091763 TAGTTTGATGAATGAAC
1 TAGTTTAATTAATGAAC
1091780 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
* *
1091797 TAACTTTATTTAATGAAC
1 T-AGTTTAATTAATGAAC
*
1091815 T--TGTAATCTTGAATGAAC
1 TAGTTTAA--TT-AATGAAC
*
1091833 TAGTTTCATTAATGAAC
1 TAGTTTAATTAATGAAC
1091850 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
1091867 T
1 T
1091868 GCTTAGTTAA
Statistics
Matches: 88, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
15 3 0.03
17 57 0.65
18 25 0.28
20 3 0.03
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:1091880 original size:17 final size:17
Alignment explanation
Indices: 1091860--1091901 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1091850 TAGTTTAATT
* *
1091860 AATGAACTGCTTAGTTA
1 AATGAACTGCATAGCTA
*
1091877 AATGAAGTGCATAGCTA
1 AATGAACTGCATAGCTA
1091894 AATGAACT
1 AATGAACT
1091902 ACATGTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (17 bp):
AATGAACTGCATAGCTA
Found at i:1093186 original size:17 final size:17
Alignment explanation
Indices: 1093164--1093233 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
1093154 AATTAAGAGT
*
1093164 TAGTTTGATTAATGCAC
1 TAGTTTGATTAATGAAC
* *
1093181 TAGTTTAATAAATGAAC
1 TAGTTTGATTAATGAAC
1093198 TAGTTTGATTAATGAAC
1 TAGTTTGATTAATGAAC
*
1093215 TAACTTT-ATTAATGAAC
1 T-AGTTTGATTAATGAAC
1093232 TA
1 TA
1093234 AATGCATGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
16 1 0.02
17 41 0.89
18 4 0.09
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.40
Consensus pattern (17 bp):
TAGTTTGATTAATGAAC
Found at i:1093202 original size:34 final size:34
Alignment explanation
Indices: 1093164--1093233 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
1093154 AATTAAGAGT
* *
1093164 TAGTTTGATTAATGCACT-AGTTTAATAAATGAAC
1 TAGTTTGATTAATGAACTAACTTT-ATAAATGAAC
*
1093198 TAGTTTGATTAATGAACTAACTTTATTAATGAAC
1 TAGTTTGATTAATGAACTAACTTTATAAATGAAC
1093232 TA
1 TA
1093234 AATGCATGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 28 0.88
35 4 0.12
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.40
Consensus pattern (34 bp):
TAGTTTGATTAATGAACTAACTTTATAAATGAAC
Found at i:1095988 original size:10 final size:10
Alignment explanation
Indices: 1095973--1095998 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1095963 ATTCTTTAAA
1095973 CTTTTTCTTT
1 CTTTTTCTTT
1095983 CTTTTTCTTT
1 CTTTTTCTTT
1095993 CTTTTT
1 CTTTTT
1095999 TTTAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
CTTTTTCTTT
Found at i:1097308 original size:17 final size:17
Alignment explanation
Indices: 1097260--1097324 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 17
1097250 AATTAAGAGT
* *
1097260 TAGTTTGATTAATGCAC
1 TAGTTTTATTAATGAAC
*
1097277 T--TTTTAATAAATGAAC
1 TAGTTTT-ATTAATGAAC
1097293 TAGTTTTATTAATGAAC
1 TAGTTTTATTAATGAAC
**
1097310 TAACTTTATTAATGA
1 TAGTTTTATTAATGA
1097325 TCTAAATGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 3 0.08
16 9 0.23
17 23 0.59
18 4 0.10
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (17 bp):
TAGTTTTATTAATGAAC
Found at i:1097329 original size:17 final size:17
Alignment explanation
Indices: 1097286--1097329 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
1097276 CTTTTTAATA
**
1097286 AATGAACTAGTTTTATT
1 AATGAACTAACTTTATT
1097303 AATGAACTAACTTTATT
1 AATGAACTAACTTTATT
*
1097320 AATGATCTAA
1 AATGAACTAA
1097330 ATGCATGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (17 bp):
AATGAACTAACTTTATT
Found at i:1097405 original size:17 final size:17
Alignment explanation
Indices: 1097385--1097426 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1097375 ACTACTTCCC
1097385 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
* *
1097402 TAAATGCAATGCATGCT
1 TAAATGAAATACATGCT
*
1097419 TTAATGAA
1 TAAATGAA
1097427 CAACATACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:1104988 original size:14 final size:15
Alignment explanation
Indices: 1104965--1104997 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1104955 AAAAAATAAC
1104965 ATATTAAAT-AAATA
1 ATATTAAATAAAATA
*
1104979 ATATTTAATAAAATA
1 ATATTAAATAAAATA
1104994 ATAT
1 ATAT
1104998 GAGACAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATATTAAATAAAATA
Found at i:1110053 original size:46 final size:46
Alignment explanation
Indices: 1109986--1110579 Score: 595
Period size: 46 Copynumber: 12.6 Consensus size: 46
1109976 TAAGTGAAAT
* *
1109986 GCATGAAAGGATGTCATAAATGAAATGCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
* *
1110032 GCATGAAAGGATGTCATAAATGAAATGCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
*
1110078 CCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
* * *
1110124 GCATAAAAAGATGCCATTAATGAAATGCATGAAAGGATGCCA-TAA-
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATG-CATTAAG
** * *
1110169 --ATGAAATACATGACAGT--ATGCATTAAGGCATGAAAGGATGCCA-TAA-
1 GCATGAAA-GGATGCCA-TAAATG-A--AATGCATGAAAGGATG-CATTAAG
*
1110215 --ATGAAATGTATG--A-AACGATGCATTAATGCATGAAAGGATGCCATAAATGAAATG
1 GCATGAAA-GGATGCCATAA--ATG-A--AATGCATGAAAGGATG-CAT---T--AA-G
* *
1110269 CATGAAAGGATGCATTAAGGATGCCATAAATGAAATGCATGAACGGATGCATTAAG
1 ---G-CA---TG-A--AAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
*
1110325 GCATGAAAGGATGCCATAAATGAAATGCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
*
1110371 GCATGAAAGTATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
***
1110417 GCATGAAAGGATGTTGTAAATGAAAT-CATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
* *
1110462 GCATGAAATGATGCCATAAATGAAATGCATGAAAGGATGCATTAAT
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
* * *
1110508 GCATGAAAGGATGCCATAAATGAAATACATGAAATGATGCATTAAA
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
1110554 GCATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATGCCATAAATGAAAT
1110580 TAACGAATAA
Statistics
Matches: 480, Mismatches: 34, Indels: 68
0.82 0.06 0.12
Matches are distributed among these distances:
43 8 0.02
44 8 0.02
45 42 0.09
46 373 0.78
47 2 0.00
48 1 0.00
49 2 0.00
50 1 0.00
52 3 0.01
53 1 0.00
56 1 0.00
57 2 0.00
59 1 0.00
60 1 0.00
62 3 0.01
63 17 0.04
64 1 0.00
65 5 0.01
66 5 0.01
67 1 0.00
68 2 0.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
Found at i:1110154 original size:118 final size:116
Alignment explanation
Indices: 1110032--1110409 Score: 495
Period size: 118 Copynumber: 3.1 Consensus size: 116
1110022 ATGCATTAAG
*
1110032 GCATGAAAGGATGTCATAAATGAAATGCATGAAATGATGCATTAAGCCATGAAAGGATGCCATAA
1 GCATGAAAGGATGTCATAAATGAAATGCATGAAA-GATGCATTAAGGCATGAAAGGATGCCATAA
* *
1110097 ATGAAATGCATGAAAGGATGCATTAAGGCATAAAAAGATGCCATTAATGAAAT
65 ATGAAATGCATGAAACGATGCATTAAGGCAT-AAAAGATGCCATAAATGAAAT
* * *
1110150 GCATGAAAGGATGCCATAAATGAAATACATGACAGTATGCATTAAGGCATGAAAGGATGCCATAA
1 GCATGAAAGGATGTCATAAATGAAATGCATGAAAG-ATGCATTAAGGCATGAAAGGATGCCATAA
* * *
1110215 ATGAAATGTATGAAACGATGCATTAATGCATGAAAGGATGCCATAAATGAAAT
65 ATGAAATGCATGAAACGATGCATTAAGGCAT-AAAAGATGCCATAAATGAAAT
*
1110268 GCATGAAAGGATGCATTAAGGATGCCATAAATGAAATGCATGAACGGATGCATTAAGGCATGAAA
1 GCATGAAA-G--G-A-T---G-T--CATAAATGAAATGCATGAA-AGATGCATTAAGGCATGAAA
* *
1110333 GGATGCCATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGTATGCCATAAATGAAAT
54 GGATGCCATAAATGAAATGCATGAAACGATGCATTAAGGCATAAAAG-ATGCCATAAATGAAAT
1110397 GCATGAAAGGATG
1 GCATGAAAGGATG
1110410 CATTAAGGCA
Statistics
Matches: 227, Mismatches: 19, Indels: 25
0.84 0.07 0.09
Matches are distributed among these distances:
117 1 0.00
118 114 0.50
119 1 0.00
121 2 0.01
122 1 0.00
123 1 0.00
124 1 0.00
125 1 0.00
126 2 0.01
128 4 0.02
129 98 0.43
130 1 0.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (116 bp):
GCATGAAAGGATGTCATAAATGAAATGCATGAAAGATGCATTAAGGCATGAAAGGATGCCATAAA
TGAAATGCATGAAACGATGCATTAAGGCATAAAAGATGCCATAAATGAAAT
Found at i:1110155 original size:72 final size:72
Alignment explanation
Indices: 1110079--1110235 Score: 242
Period size: 72 Copynumber: 2.2 Consensus size: 72
1110069 TGCATTAAGC
* *
1110079 CATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATAAAAAGATGCCATTAA
1 CATGAAAGGATGCCATAAATGAAATACATGAAAGGATGCATTAAGGCATAAAAAGATGCCATAAA
1110144 TGAAATG
66 TGAAATG
* * * *
1110151 CATGAAAGGATGCCATAAATGAAATACATGACAGTATGCATTAAGGCATGAAAGGATGCCATAAA
1 CATGAAAGGATGCCATAAATGAAATACATGAAAGGATGCATTAAGGCATAAAAAGATGCCATAAA
1110216 TGAAATG
66 TGAAATG
* *
1110223 TATGAAACGATGC
1 CATGAAAGGATGC
1110236 ATTAATGCAT
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 77 1.00
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.21
Consensus pattern (72 bp):
CATGAAAGGATGCCATAAATGAAATACATGAAAGGATGCATTAAGGCATAAAAAGATGCCATAAA
TGAAATG
Found at i:1110302 original size:129 final size:127
Alignment explanation
Indices: 1110156--1110552 Score: 569
Period size: 129 Copynumber: 3.0 Consensus size: 127
1110146 AAATGCATGA
*
1110156 AAGGATGCCATAAATGAAATACATGACAGTATGCATTAAGGCATGAAAGGATGCCATAAATGAAA
1 AAGGATGCCATAAATGAAAT-CATGA-AGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAA
*
1110221 TGTATGAAACGATGCATTAATGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATT
64 TGCATGAAACGATGCATTAATGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATT
1110285 AAGGATGCCATAAATGAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAA
1 AAGGATGCCATAAATGAAAT-CATGAA-GGATGCATTAAGGCATGAAAGGATGCCATAAATGAAA
* * *
1110350 TGCATGAAATGATGCATTAAGGCATGAAAGTATGCCATAAATGAAATGCATGAAAGGATGCATT
64 TGCATGAAACGATGCATTAATGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATT
** *
1110414 AAGGCATGAAAGGATGTTGTAAATGAAATCATGAAAGGATGCATTAAGGCATGAAATGATGCCAT
1 AAGG-ATG---CCA-----TAAATGAAATCATG-AAGGATGCATTAAGGCATGAAAGGATGCCAT
* * *
1110479 AAATGAAATGCATGAAAGGATGCATTAATGCATGAAAGGATGCCATAAATGAAATACATGAAATG
56 AAATGAAATGCATGAAACGATGCATTAATGCATGAAAGGATGCCATAAATGAAATGCATGAAAGG
1110544 ATGCATT
121 ATGCATT
1110551 AA
1 AA
1110553 AGCATGAAAG
Statistics
Matches: 243, Mismatches: 14, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
128 1 0.00
129 125 0.51
130 3 0.01
133 1 0.00
137 101 0.42
138 12 0.05
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (127 bp):
AAGGATGCCATAAATGAAATCATGAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATG
CATGAAACGATGCATTAATGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATT
Found at i:1110494 original size:26 final size:26
Alignment explanation
Indices: 1109975--1110579 Score: 320
Period size: 26 Copynumber: 25.4 Consensus size: 26
1109965 AACTGAAGTT
* *
1109975 ATAAGTGAAATGCATGAAAGGATGTC
1 ATAAATGAAATGCATGAAAGGATGCC
*
1110001 ATAAATGAAATGCATGAAATGATG-C
1 ATAAATGAAATGCATGAAAGGATGCC
* *
1110026 AT---T--AAGGCATGAAAGGATGTC
1 ATAAATGAAATGCATGAAAGGATGCC
*
1110047 ATAAATGAAATGCATGAAATGATG-C
1 ATAAATGAAATGCATGAAAGGATGCC
1110072 AT---T--AA-GCCATGAAAGGATGCC
1 ATAAATGAAATG-CATGAAAGGATGCC
1110093 ATAAATGAAATGCATGAAAGGATG-C
1 ATAAATGAAATGCATGAAAGGATGCC
* * *
1110118 AT---T--AAGGCATAAAAAGATGCC
1 ATAAATGAAATGCATGAAAGGATGCC
*
1110139 ATTAATGAAATGCATGAAAGGATGCC
1 ATAAATGAAATGCATGAAAGGATGCC
* * *
1110165 ATAAATGAAATACATGACAGTATG-C
1 ATAAATGAAATGCATGAAAGGATGCC
*
1110190 AT---T--AAGGCATGAAAGGATGCC
1 ATAAATGAAATGCATGAAAGGATGCC
* *
1110211 ATAAATGAAATGTATGAAACGATG-C
1 ATAAATGAAATGCATGAAAGGATGCC
1110236 AT---T--AATGCATGAAAGGATGCC
1 ATAAATGAAATGCATGAAAGGATGCC
1110257 ATAAATGAAATGCATGAAAGGATG-C
1 ATAAATGAAATGCATGAAAGGATGCC
* * *
1110282 ATTAA-G-GATGCCAT-AAATGAAATG-C
1 ATAAATGAAATG-CATGAAA-G-GATGCC
*
1110307 ATGAACGGATGCATTAAGGCATGAAAGGATGCC
1 AT-AA---ATG-A--AATGCATGAAAGGATGCC
*
1110340 ATAAATGAAATGCATGAAATGATG-C
1 ATAAATGAAATGCATGAAAGGATGCC
* *
1110365 AT---T--AAGGCATGAAAGTATGCC
1 ATAAATGAAATGCATGAAAGGATGCC
1110386 ATAAATGAAATGCATGAAAGGATG-C
1 ATAAATGAAATGCATGAAAGGATGCC
* **
1110411 AT---T--AAGGCATGAAAGGATGTT
1 ATAAATGAAATGCATGAAAGGATGCC
*
1110432 GTAAATGAAAT-CATGAAAGGATG-C
1 ATAAATGAAATGCATGAAAGGATGCC
* ****
1110456 AT---T--AAGGCATGAAATGATGCC-
1 ATAAATGAAATGCATGAAA-GGATGCC
1110477 ATAAATGAAATGCATGAAAGGATG-C
1 ATAAATGAAATGCATGAAAGGATGCC
1110502 AT---T--AATGCATGAAAGGATGCC
1 ATAAATGAAATGCATGAAAGGATGCC
* *
1110523 ATAAATGAAATACATGAAATGATG-C
1 ATAAATGAAATGCATGAAAGGATGCC
1110548 AT---T-AAA-GCATGAAAGGATGCC
1 ATAAATGAAATGCATGAAAGGATGCC
1110569 ATAAATGAAAT
1 ATAAATGAAAT
1110580 TAACGAATAA
Statistics
Matches: 440, Mismatches: 60, Indels: 158
0.67 0.09 0.24
Matches are distributed among these distances:
19 3 0.01
20 128 0.29
21 32 0.07
22 9 0.02
23 6 0.01
24 16 0.04
25 53 0.12
26 169 0.38
27 1 0.00
28 1 0.00
29 4 0.01
30 1 0.00
32 5 0.01
33 7 0.02
34 5 0.01
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (26 bp):
ATAAATGAAATGCATGAAAGGATGCC
Found at i:1110573 original size:20 final size:20
Alignment explanation
Indices: 1110012--1110567 Score: 183
Period size: 20 Copynumber: 24.7 Consensus size: 20
1110002 TAAATGAAAT
* *
1110012 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAA
1110032 GCATGAAAGGATGTCATAAATGAAA
1 GCATGAAAGGATG-CAT---T-AAA
*
1110057 TGCATGAAATGATGCATT-AA
1 -GCATGAAAGGATGCATTAAA
1110077 GCCATGAAAGGATGCCATAAATGAAA
1 G-CATGAAAGGATG-CAT---T-AAA
*
1110103 TGCATGAAAGGATGCATTAAG
1 -GCATGAAAGGATGCATTAAA
* *
1110124 GCATAAAAAGATGCCATTAATGAAA
1 GCATGAAAGGATG-CA-T--T-AAA
1110149 TGCATGAAAGGATGCCATAAATGAAA
1 -GCATGAAAGGATG-CAT---T-AAA
* * * *
1110175 TACATGACAGTATGCATTAAG
1 -GCATGAAAGGATGCATTAAA
1110196 GCATGAAAGGATGCCATAAATGAAA
1 GCATGAAAGGATG-CAT---T-AAA
* * *
1110221 TGTATGAAACGATGCATTAAT
1 -GCATGAAAGGATGCATTAAA
1110242 GCATGAAAGGATGCCATAAATGAAA
1 GCATGAAAGGATG-CAT---T-AAA
1110267 TGCATGAAAGGATGCATT-AA
1 -GCATGAAAGGATGCATTAAA
* *
1110287 GGATGCCATAA--ATG-A--AAT
1 GCATG--A-AAGGATGCATTAAA
* *
1110305 GCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCATTAAA
1110325 GCATGAAAGGATGCCATAAATGAAA
1 GCATGAAAGGATG-CAT---T-AAA
* *
1110350 TGCATGAAATGATGCATTAAG
1 -GCATGAAAGGATGCATTAAA
*
1110371 GCATGAAAGTATGCCATAAATGAAA
1 GCATGAAAGGATG-CAT---T-AAA
*
1110396 TGCATGAAAGGATGCATTAAG
1 -GCATGAAAGGATGCATTAAA
*
1110417 GCATGAAAGGATG-TTGTAAA
1 GCATGAAAGGATGCAT-TAAA
*
1110437 TGAAATCATGAAAGGATGCATTAAG
1 -G----CATGAAAGGATGCATTAAA
*
1110462 GCATGAAATGATGCCATAAATGAAA
1 GCATGAAAGGATG-CAT---T-AAA
*
1110487 TGCATGAAAGGATGCATTAAT
1 -GCATGAAAGGATGCATTAAA
1110508 GCATGAAAGGATGCCATAAATGAAA
1 GCATGAAAGGATG-CAT---T-AAA
* *
1110533 TACATGAAATGATGCATTAAA
1 -GCATGAAAGGATGCATTAAA
1110554 GCATGAAAGGATGC
1 GCATGAAAGGATGC
1110568 CATAAATGAA
Statistics
Matches: 412, Mismatches: 51, Indels: 146
0.68 0.08 0.24
Matches are distributed among these distances:
15 1 0.00
16 1 0.00
17 3 0.01
18 6 0.01
19 7 0.02
20 139 0.34
21 43 0.10
22 12 0.03
24 10 0.02
25 59 0.14
26 130 0.32
27 1 0.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAA
Found at i:1114846 original size:21 final size:21
Alignment explanation
Indices: 1114822--1114862 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1114812 TAATTAAGAA
*
1114822 TCAAGGAGCTTTACTTCAAAG
1 TCAAGGAGCCTTACTTCAAAG
*
1114843 TCAAGGCGCCTTACTTCAAA
1 TCAAGGAGCCTTACTTCAAA
1114863 TCCATAGCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (21 bp):
TCAAGGAGCCTTACTTCAAAG
Found at i:1122479 original size:829 final size:828
Alignment explanation
Indices: 1120848--1122507 Score: 2946
Period size: 829 Copynumber: 2.0 Consensus size: 828
1120838 ACTTTGTGGA
1120848 AAAAAATTACACGATGTGTATGTTCTCTATACTTAGAAAATTTAGAAATTTTTTATGAAGGAACT
1 AAAAAATTACACGATGTGTATGTTCTCTATACTTAGAAAATTTAGAAATTTTTTATGAAGGAACT
1120913 CTAGTTAGTTTTGGCATTAAATATATATTGTGCTTAAAAGAAAAATCAAACAACTCCGTTATATG
66 CTAGTTAGTTTTGGCATTAAATATATATTGTGCTTAAAAGAAAAATCAAACAACTCCGTTATATG
*
1120978 AAATTATGAAAAAGCTTAGGCATAGCTGTAGAGGGACATTCCTCTATGTTGTGGTATTGCTTGAA
131 AAATTATGAAAAAGCTTAGGCATAGCTGTAGAGGGACATTCCTCTATGTTGTGGTATTGCCTGAA
1121043 ATTTCTTTAATAAATGGCATCCTCGCACATATGAGTGAATGAAAGTAGTCACGAGATGACTCTAC
196 ATTTCTTT-ATAAATGGCATCCTCGCACATATGAGTGAATGAAAGTAGTCACGAGATGACTCTAC
*
1121108 TTAACTAGCTCGGGGGTGGAAGGTATGCTCCCTTTCACCTATAGTGTGGAAGAGTATGTGTGATG
260 TTAACTAGCTCGGGGGCGGAAGGTATGCTCCCTTTCACCTATAGTGTGGAAGAGTATGTGTGATG
1121173 GGCTGACTCCCTTCGTAGCAGCATCTCTAAAAAAAGTTCAGAAAAATGGAGTAGTAAAAATGTGC
325 GGCTGACTCCCTTCGTAGCAGCATCTCTAAAAAAAGTTCAGAAAAATGGAG-AGTAAAAATGTGC
1121238 TTAATGAATAAGTAAATGCCTTGGAAAAAACTAGGGGACTTGAGTAGAAATTGTCTAAATTTGCT
389 TTAATGAATAAGTAAATGCCTTGGAAAAAACTAGGGGACTTGAGTAGAAATTGTCTAAATTTGCT
1121303 AAGTATAGATTGGATGAAATCACGCACACACACTACCACAAAGAATCTTGACCTAGGGAAAAGTA
454 AAGTATAGATTGGATGAAATCACGCACACACACTACCACAAAGAATCTTGACCTAGGGAAAAGTA
1121368 CTTGACTTCTTGATATGTCTAGCATGTTGAAGCCTAATGTTCTGAGGGTTGAAATTTAATTTTGT
519 CTTGACTTCTTGATATGTCTAGCATGTTGAAGCCTAATGTTCTGAGGGTTGAAATTTAATTTTGT
* *
1121433 CCTACTGTCTTATTGTTGAAAGTTGCCATGACATTCTGCTTATGTAACTGCTATCCATTGCTTGA
584 CATACTGTCTTATTGTTGAAAGTTGCCATGACATTCTGCTTATGTAACTGCTATCCATTACTTGA
* *
1121498 GGATAATTAATAGCTTAAGTTTGGGGGTGTATTAACTTCCTATAAAGGCTACTTTTATGGTCTTT
649 GGACAAGTAATAGCTTAAGTTTGGGGGTGTATTAACTTCCTATAAAGGCTACTTTTATGG-CTTT
*
1121563 TCACTTAAGTTATTGTTTATTTAAAAGCCCATTTTAGTCATTTAGGATCAGTAGTTGCATATAGT
713 TCACTTAAGTTATTATTTATTTAAAAGCCCATTTTAGTCATTTAGGATCAGTAGTTGCATATAGT
*
1121628 TGCATGTGTGGTGGTATTGTTTTTATTTCTTAATGGTGTTGTATGAGAGAAAG
778 TGCATGTGTGGTAGTATTG-TTTTATTTCTTAATGG-GTTGTATGAGAGAAAG
*
1121681 AAAAAATTACACGATGTGTATGTTCTCTATACTTAGAAAATTTAGAATTTTTTTATGAAGGAACT
1 AAAAAATTACACGATGTGTATGTTCTCTATACTTAGAAAATTTAGAAATTTTTTATGAAGGAACT
*
1121746 CTAGTTAGTTTTGGCATTAAAATATAGTATTGTGCTTAAAAGAAAAATCAAAACAAC-CCTTATA
66 CTAGTTAGTTTTGGCATT-AAATATA-TATTGTGCTTAAAAGAAAAATC-AAACAACTCCGT-TA
*
1121810 TATGAAATTATGAATAAATGCTTAGGCATAGCTGTAGAGGGGCATTCCTCTATGTTGTGGTA-TG
127 TATGAAATTATGAA-AAA-GCTTAGGCATAGCTGTAGAGGGACATTCCTCTATGTTGTGGTATTG
* *
1121874 CCTGAAATTTCTTT-T-AATGGCATCCTCGCGCATATGAGTGAATGAAAGTAGTCACGGGATGAC
190 CCTGAAATTTCTTTATAAATGGCATCCTCGCACATATGAGTGAATGAAAGTAGTCACGAGATGAC
1121937 TCTACTTAACTAGCTCGGGGGCGGAAGGTATGCTCCCTTTCACCTATAGTGTGGAAGAGTATGTG
255 TCTACTTAACTAGCTCGGGGGCGGAAGGTATGCTCCCTTTCACCTATAGTGTGGAAGAGTATGTG
1122002 TGATGGGCTGACTCCCTTCGTAGCAG-ATCTCTAAAAAAAGTTCAGAAAAAATGG-G-G-AAAAA
320 TGATGGGCTGACTCCCTTCGTAGCAGCATCTCTAAAAAAAGTTCAG-AAAAATGGAGAGTAAAAA
*
1122063 TGTGCTTAATGAATAAGTAAATGCCTTGGCAAAAACTA-GGGACTTGAGTAGAAATTGTCTAAAT
384 TGTGCTTAATGAATAAGTAAATGCCTTGGAAAAAACTAGGGGACTTGAGTAGAAATTGTCTAAAT
*
1122127 TTGCTAAGTATAGATTGGATGAAATCACGCACACACACTACCACAAAGAATCTTGACCTAGTGAA
449 TTGCTAAGTATAGATTGGATGAAATCACGCACACACACTACCACAAAGAATCTTGACCTAGGGAA
1122192 AAGTACTTGACTTCTTGATATGTCTAGCATGTTGAAGCCTAATGTTCTGAGGGTTGAAATTTAAT
514 AAGTACTTGACTTCTTGATATGTCTAGCATGTTGAAGCCTAATGTTCTGAGGGTTGAAATTTAAT
1122257 TTTGTCATACTGTCTTATTGTTGAAAGTTGCCATGACATTCTGCTTATGTAACTGCTATCCATTA
579 TTTGTCATACTGTCTTATTGTTGAAAGTTGCCATGACATTCTGCTTATGTAACTGCTATCCATTA
1122322 CTTGAGGACAAGTAATAGCTTAAGTTTGGGGGTGTATTAACTTCCTATAAAGGCTACTTTT-TGG
644 CTTGAGGACAAGTAATAGCTTAAGTTTGGGGGTGTATTAACTTCCTATAAAGGCTACTTTTATGG
*
1122386 -TTTTCACTTAAGTTATTATTTATTTAAAAGCCTATTTTAGTCATTTTAGGATCATGTAGTTGCA
709 CTTTTCACTTAAGTTATTATTTATTTAAAAGCCCATTTTAGTCA-TTTAGGATCA-GTAGTTGCA
* *
1122450 TATAGTTGCATGTGGTGGTATTGTTGTTTTATTTCTTAATGGGTTGTATGAGAGAAAG
772 TATAGTTGCATGT-GTGGTAGTATTGTTTTATTTCTTAATGGGTTGTATGAGAGAAAG
1122508 GTGCATTGTT
Statistics
Matches: 799, Mismatches: 18, Indels: 26
0.95 0.02 0.03
Matches are distributed among these distances:
826 41 0.05
827 26 0.03
828 41 0.05
829 286 0.36
830 42 0.05
831 1 0.00
833 102 0.13
834 151 0.19
835 26 0.03
836 23 0.03
837 18 0.02
838 42 0.05
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (828 bp):
AAAAAATTACACGATGTGTATGTTCTCTATACTTAGAAAATTTAGAAATTTTTTATGAAGGAACT
CTAGTTAGTTTTGGCATTAAATATATATTGTGCTTAAAAGAAAAATCAAACAACTCCGTTATATG
AAATTATGAAAAAGCTTAGGCATAGCTGTAGAGGGACATTCCTCTATGTTGTGGTATTGCCTGAA
ATTTCTTTATAAATGGCATCCTCGCACATATGAGTGAATGAAAGTAGTCACGAGATGACTCTACT
TAACTAGCTCGGGGGCGGAAGGTATGCTCCCTTTCACCTATAGTGTGGAAGAGTATGTGTGATGG
GCTGACTCCCTTCGTAGCAGCATCTCTAAAAAAAGTTCAGAAAAATGGAGAGTAAAAATGTGCTT
AATGAATAAGTAAATGCCTTGGAAAAAACTAGGGGACTTGAGTAGAAATTGTCTAAATTTGCTAA
GTATAGATTGGATGAAATCACGCACACACACTACCACAAAGAATCTTGACCTAGGGAAAAGTACT
TGACTTCTTGATATGTCTAGCATGTTGAAGCCTAATGTTCTGAGGGTTGAAATTTAATTTTGTCA
TACTGTCTTATTGTTGAAAGTTGCCATGACATTCTGCTTATGTAACTGCTATCCATTACTTGAGG
ACAAGTAATAGCTTAAGTTTGGGGGTGTATTAACTTCCTATAAAGGCTACTTTTATGGCTTTTCA
CTTAAGTTATTATTTATTTAAAAGCCCATTTTAGTCATTTAGGATCAGTAGTTGCATATAGTTGC
ATGTGTGGTAGTATTGTTTTATTTCTTAATGGGTTGTATGAGAGAAAG
Found at i:1125702 original size:23 final size:25
Alignment explanation
Indices: 1125663--1125708 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
1125653 ATCGTTACAG
1125663 GATAGCTTCTAAAGCCTGAAGAATA
1 GATAGCTTCTAAAGCCTGAAGAATA
1125688 GATAGC-T-TAAAGCCTGAAGAA
1 GATAGCTTCTAAAGCCTGAAGAA
1125709 ATATTCCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 14 0.67
24 1 0.05
25 6 0.29
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (25 bp):
GATAGCTTCTAAAGCCTGAAGAATA
Found at i:1127106 original size:26 final size:27
Alignment explanation
Indices: 1127056--1127107 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1127046 AATTTATATT
*
1127056 TTTAATCCTTAAACTTTTATAATTTAC
1 TTTAATCCCTAAACTTTTATAATTTAC
1127083 TTTAATCCCTAAA-TTTTCA-AATTTA
1 TTTAATCCCTAAACTTTT-ATAATTTA
1127108 TTTTTCCGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (27 bp):
TTTAATCCCTAAACTTTTATAATTTAC
Found at i:1127435 original size:7 final size:7
Alignment explanation
Indices: 1127423--1127448 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1127413 AAAGGACCGT
1127423 TTTTCTA
1 TTTTCTA
1127430 TTTTCTA
1 TTTTCTA
1127437 TTTTCTA
1 TTTTCTA
1127444 TTTTC
1 TTTTC
1127449 AATCGCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTCTA
Found at i:1132295 original size:2 final size:2
Alignment explanation
Indices: 1132288--1132333 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1132278 TGATTCTGTC
1132288 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
1132329 TA TA T
1 TA TA T
1132334 TAAAAAATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1132956 original size:30 final size:29
Alignment explanation
Indices: 1132917--1132974 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1132907 TTAACAAAAA
* *
1132917 TGATGATTTTGGAATATATTAATAGTCGGG
1 TGATCATTTTAGAAT-TATTAATAGTCGGG
* *
1132947 TGATCATTTTATAATTTTTAATAGTCGG
1 TGATCATTTTAGAATTATTAATAGTCGG
1132975 ATGACTCAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (29 bp):
TGATCATTTTAGAATTATTAATAGTCGGG
Found at i:1136418 original size:23 final size:23
Alignment explanation
Indices: 1136336--1136478 Score: 160
Period size: 23 Copynumber: 6.2 Consensus size: 23
1136326 TTATTTATTG
* * *
1136336 TTCACGAACATATTCTTTTAATG
1 TTCACGAACATGTTCGTTTAATA
* *
1136359 TTCACGAACATATTCGTTTAATG
1 TTCACGAACATGTTCGTTTAATA
1136382 TTCACGAACATGTTCGTTTAATA
1 TTCACGAACATGTTCGTTTAATA
* *
1136405 TTCACGAACTTGTTTGTTTATATA
1 TTCACGAACATGTTCGTTTA-ATA
* ** **
1136429 TTCACAAACATGTTTATTTAGCA
1 TTCACGAACATGTTCGTTTAATA
*
1136452 TTCACGAACATGTTCGTTTAGTA
1 TTCACGAACATGTTCGTTTAATA
1136475 TTCA
1 TTCA
1136479 TTTAGCATTT
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
23 85 0.81
24 20 0.19
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (23 bp):
TTCACGAACATGTTCGTTTAATA
Found at i:1138778 original size:35 final size:35
Alignment explanation
Indices: 1138739--1138812 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
1138729 TGTTATATAT
*
1138739 AATATAATAATGATTATTCATATGTGATCATATTA
1 AATATAATAATGATTATTCATAGGTGATCATATTA
1138774 AATATAATAATGATTATTCATAGGTGATCATATTA
1 AATATAATAATGATTATTCATAGGTGATCATATTA
1138809 AATA
1 AATA
1138813 AAAAAATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (35 bp):
AATATAATAATGATTATTCATAGGTGATCATATTA
Found at i:1139846 original size:2 final size:2
Alignment explanation
Indices: 1139841--1139870 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1139831 TTAAATTTAA
*
1139841 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1139871 TTTATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1139928 original size:26 final size:27
Alignment explanation
Indices: 1139895--1139961 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
1139885 TTTTCATCCT
***
1139895 CTTAAAATTTTATAAA-TTATTTTCTA
1 CTTAAAATTTTATAAATTTATCCCCTA
1139921 CTTAAAATTTTATAAATTTATCCCCTA
1 CTTAAAATTTTATAAATTTATCCCCTA
1139948 CTTAAAATTTTATA
1 CTTAAAATTTTATA
1139962 TGTGTCCCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
26 16 0.43
27 21 0.57
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (27 bp):
CTTAAAATTTTATAAATTTATCCCCTA
Found at i:1140787 original size:59 final size:58
Alignment explanation
Indices: 1140669--1140807 Score: 156
Period size: 59 Copynumber: 2.4 Consensus size: 58
1140659 GAACATATGA
* ** *
1140669 ATAGT-CGAGTGACCATTTTATAACTTTTAATAGTGGTAGACTCAACAAAGTAATGTCTT
1 ATAGTCCGAG-GACCA-TTTATAACTTTTAATAATGGTAGACTCAACAAAACAATATCTT
1140728 ATAGTCCGAGGACCATTTATAACTTTTAATAATCGG-ATGACTCAACAAAACAATATCTT
1 ATAGTCCGAGGACCATTTATAACTTTTAATAAT-GGTA-GACTCAACAAAACAATATCTT
* * * *
1140787 ATAATCAGAAGACTATTTATA
1 ATAGTCCGAGGACCATTTATA
1140808 TATTACCCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
58 18 0.26
59 47 0.68
60 4 0.06
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (58 bp):
ATAGTCCGAGGACCATTTATAACTTTTAATAATGGTAGACTCAACAAAACAATATCTT
Found at i:1141699 original size:2 final size:2
Alignment explanation
Indices: 1141692--1141817 Score: 252
Period size: 2 Copynumber: 63.0 Consensus size: 2
1141682 TTATGGCGTA
1141692 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1141734 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1141776 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1141818 ACACACACAT
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 124 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1141875 original size:2 final size:2
Alignment explanation
Indices: 1141826--1141856 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1141816 TCACACACAC
1141826 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 A
1141857 ATCTTGTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1147349 original size:3 final size:3
Alignment explanation
Indices: 1147343--1147368 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1147333 ATCACCATCA
1147343 TCG TCG TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TC
1147369 AGGAGCAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.31, T:0.35
Consensus pattern (3 bp):
TCG
Found at i:1149422 original size:8 final size:8
Alignment explanation
Indices: 1149405--1149434 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1149395 TAATTAAATA
*
1149405 AAATATTT
1 AAATAATT
1149413 AAATAATT
1 AAATAATT
1149421 AAATAATT
1 AAATAATT
1149429 AAATAA
1 AAATAA
1149435 AATACTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
AAATAATT
Found at i:1149437 original size:29 final size:31
Alignment explanation
Indices: 1149395--1149468 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 31
1149385 GCAAAAAAAT
* *
1149395 TAATTAAATAAAATATTTAA-ATAAT-TAAA
1 TAATTAAATAAAATATCTAATAAAATATAAA
1149424 TAATTAAATAAAATA-CTAATAAAATATAAA
1 TAATTAAATAAAATATCTAATAAAATATAAA
*
1149454 -AATAAAATAAAATAT
1 TAATTAAATAAAATAT
1149469 ACCTTAAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 3 0.08
29 32 0.82
30 4 0.10
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (31 bp):
TAATTAAATAAAATATCTAATAAAATATAAA
Found at i:1149443 original size:16 final size:15
Alignment explanation
Indices: 1149390--1149469 Score: 64
Period size: 13 Copynumber: 5.5 Consensus size: 15
1149380 TAACTGCAAA
1149390 AAAAT-TAATTAAAT
1 AAAATATAATTAAAT
1149404 AAAATAT--TTAAAT
1 AAAATATAATTAAAT
1149417 AATTAA-ATAATTAAAT
1 AA--AATATAATTAAAT
*
1149433 AAAATACTAATAAAAT
1 AAAATA-TAATTAAAT
* *
1149449 ATAA-A-AATAAAAT
1 AAAATATAATTAAAT
1149462 AAAATATA
1 AAAATATA
1149470 CCTTAAGTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
13 19 0.35
14 10 0.19
15 6 0.11
16 19 0.35
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATATAATTAAAT
Found at i:1149454 original size:18 final size:17
Alignment explanation
Indices: 1149431--1149469 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1149421 AAATAATTAA
*
1149431 ATAAAATACTAATAAAAT
1 ATAAAATA-AAATAAAAT
1149449 ATAAAAATAAAATAAAAT
1 AT-AAAATAAAATAAAAT
1149467 ATA
1 ATA
1149470 CCTTAAGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 12 0.63
19 6 0.32
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAATAAAATAAAAT
Found at i:1150595 original size:182 final size:181
Alignment explanation
Indices: 1150287--1150887 Score: 914
Period size: 182 Copynumber: 3.3 Consensus size: 181
1150277 GTCGATACAA
* * *
1150287 ATAAAAATGTATCGATCCATATCTATATAACAGGTAAAAATATGACAAAACTGGTCTCGAAATGA
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTC-AAATGA
* * *
1150352 CCAAACCGGTAAAGCACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACA
65 CAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACT
*
1150417 TTTGGAATTTAAAAGACAAGTAGTAATAGCGCCTATAAAGTGTCGATACTTT
130 TTTGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTT
* * * * **
1150469 CTAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAAAATCGGTCTCACGGTGA
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCA-AATGA
* * * *
1150534 CAAAACCGGTAAAGCGGTACCGGATATGTTAAAAGTGTCGATAGTTTAGTATAAGTATCGACACT
65 CAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACT
*
1150599 TTTGGAATTTAAAAGACAAGCAGTAATAGTGCCTATAAAGTGTCGATACTTT
130 TTTGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTT
1150651 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGA
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTC-AAATGA
* * * * * *
1150716 CAAAACTGGTAAAGCGTTACCAGATATGTTGAAAGTGTCGATACATTAATATAAATATCGAAACT
65 CAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACT
* *
1150781 TTTGGAATTTAAAAGAAAAGCAGTTATAGCGCCTATAAAGTGTCGATACTTT
130 TTTGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTT
* * *
1150833 ATAAAAACGTATCGATCCATAATAATATAACTGGTAAAAATATGACAAAACCGGT
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGT
1150888 AAAGCGATAC
Statistics
Matches: 378, Mismatches: 39, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
181 1 0.00
182 376 0.99
183 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (181 bp):
ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAATGAC
AAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
TTGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTT
Found at i:1153622 original size:24 final size:24
Alignment explanation
Indices: 1153595--1153660 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
1153585 AGCTCGTATA
1153595 AATTTGCACCGTAGTGCCACGTAG
1 AATTTGCACCGTAGTGCCACGTAG
** ** *
1153619 AATTTATACCAAAGTGCCGCGTAG
1 AATTTGCACCGTAGTGCCACGTAG
*
1153643 AA-ATGCACCGTAGTGCCA
1 AATTTGCACCGTAGTGCCA
1153661 TATAAGATTG
Statistics
Matches: 31, Mismatches: 11, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
23 10 0.32
24 21 0.68
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (24 bp):
AATTTGCACCGTAGTGCCACGTAG
Found at i:1153905 original size:17 final size:16
Alignment explanation
Indices: 1153879--1153912 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1153869 ACATGGTTAT
*
1153879 TATTCTTATACTTCATA
1 TATTCATATAC-TCATA
1153896 TATTCATATACTCATA
1 TATTCATATACTCATA
1153912 T
1 T
1153913 CATTGTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTCATATACTCATA
Found at i:1154101 original size:43 final size:41
Alignment explanation
Indices: 1154039--1154119 Score: 99
Period size: 43 Copynumber: 1.9 Consensus size: 41
1154029 TCCCATAAAC
** * *
1154039 ATATATATCATTTGATTCATGTCTTATTCTTATATCATCAT
1 ATATATATCATTTGATTCATCACTTAATCTCATATCATCAT
*
1154080 ATATATATCATCTATGTTTCATCACTTAATCTCATATCAT
1 ATATATATCAT-T-TGATTCATCACTTAATCTCATATCAT
1154120 ATAACATGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 11 0.33
42 1 0.03
43 21 0.64
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48
Consensus pattern (41 bp):
ATATATATCATTTGATTCATCACTTAATCTCATATCATCAT
Found at i:1154922 original size:13 final size:13
Alignment explanation
Indices: 1154904--1154940 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
1154894 ATTCCTTTAG
1154904 TTTTTCCAC-TAAC
1 TTTTTCC-CTTAAC
1154917 TTTTTCCCTTAAC
1 TTTTTCCCTTAAC
1154930 TTTTTCCCTTA
1 TTTTTCCCTTA
1154941 TTTATTCGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 1 0.04
13 22 0.96
ACGTcount: A:0.16, C:0.30, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTTTCCCTTAAC
Found at i:1159376 original size:24 final size:24
Alignment explanation
Indices: 1159349--1159414 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
1159339 AACTCGTATA
1159349 AATTTGCACCGTAGTGCCACGTAG
1 AATTTGCACCGTAGTGCCACGTAG
* **
1159373 AATTTGCACCGAAGTGCTGCGTAG
1 AATTTGCACCGTAGTGCCACGTAG
*
1159397 AA-ATGCACCGTAGTGCCA
1 AATTTGCACCGTAGTGCCA
1159415 TATAAGATTG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
23 12 0.34
24 23 0.66
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (24 bp):
AATTTGCACCGTAGTGCCACGTAG
Found at i:1159854 original size:43 final size:41
Alignment explanation
Indices: 1159792--1159872 Score: 99
Period size: 43 Copynumber: 1.9 Consensus size: 41
1159782 TCCCATAAAC
** * *
1159792 ATATATATCATTTGATTCATGTCTTATTCTTATATCATCAT
1 ATATATATCATTTGATTCATCACTTAATCTAATATCATCAT
*
1159833 ATATATATCATCTATGTTTCATCACTTAATCTAATATCAT
1 ATATATATCAT-T-TGATTCATCACTTAATCTAATATCAT
1159873 ATAACATGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 11 0.33
42 1 0.03
43 21 0.64
ACGTcount: A:0.32, C:0.16, G:0.04, T:0.48
Consensus pattern (41 bp):
ATATATATCATTTGATTCATCACTTAATCTAATATCATCAT
Found at i:1161507 original size:18 final size:18
Alignment explanation
Indices: 1161484--1161522 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1161474 GAAAAAATAT
1161484 GAAGAAGAAAAGATAGAG
1 GAAGAAGAAAAGATAGAG
*
1161502 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATAGAG
1161520 GAA
1 GAA
1161523 ATGAGGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.36, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATAGAG
Found at i:1164058 original size:201 final size:201
Alignment explanation
Indices: 1163545--1164507 Score: 1258
Period size: 201 Copynumber: 4.8 Consensus size: 201
1163535 GTAAATAGAT
* *
1163545 GTGTCAATACATTTATACAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * ** **
1163610 GGTAATTTTTCAATTTAACCGGTATAAATATACTTGTTTTATGAGAGAATAGGTTTACATAATGT
66 GGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGT
* * * * * *
1163675 ATCGACACTTGTGGAATTTGTGTCGATTCTTTTTGTCCAAAATGAATGCCCAAAAGAGGTACACG
131 ATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACGAGGTGCACG
1163740 CATAAA
196 CATAAA
* * *
1163746 ATGTCGATAC----ATAAAAAGTCTTGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * *
1163807 GGT-AATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCAACACAATG
66 GGTAAATTTT-CAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACATAATG
* * *
1163871 TATCGACACTTTTGAAATTTGTGTCAATACATTTTGTCCAGAATGAATGCCCAAACTAGGTGCAC
130 TATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACGAGGTGCAC
1163936 GCATAAA
195 GCATAAA
*
1163943 GTGTCGATACATTTATACAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * *
1164008 GGTAAATTTTCAATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGATCTACATAATGT
66 GGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGT
* *
1164073 ATCGACACTTGTTG-AATTTGTGTCGATACTTTTTTTCCAGAATGAATGCCCAAACTAGGTGCAC
131 ATCGACACTT-TTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACGAGGTGCAC
1164137 GCATAAA
195 GCATAAA
* * * * *
1164144 ATGTCGATAAATTTATAAAAAGTATCGATCTCAAAAATATCGAAACCTATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * * * **
1164209 GGTAAATTTCCAATATAACTGGTATAAATATACCGGTTTAATTAGAAAAGCGGTCAACATAATGT
66 GGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGT
* * * *
1164274 ATTGATACTTTTTAAATTTGTGTTGATACTTTTTGTCCAGAATGAATG-CC-AACGAGGTGCACG
131 ATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACGAGGTGCACG
1164337 CATAAA
196 CATAAA
* * * * * ** *
1164343 GTGTCAATACATTTAAAAAAAATATCGATCCCAAAAATATCAAAACTGATCATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * * **
1164408 GGTAAATTTACAATGTAACTGGTATAAATATACCGGTTTAATTAGAAAAGCGGTCAACATAATGT
66 GGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGT
* * * *
1164473 TTCGACAGTTTTTAAATTTGTATCGATATCTTTTT
131 ATCGACACTTTTGAAATTTGTGTCGATA-CTTTTT
1164508 AAATTTCGCG
Statistics
Matches: 676, Mismatches: 77, Indels: 19
0.88 0.10 0.02
Matches are distributed among these distances:
196 5 0.01
197 169 0.25
199 158 0.23
200 10 0.01
201 325 0.48
202 9 0.01
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (201 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGT
ATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACGAGGTGCACG
CATAAA
Found at i:1165170 original size:2 final size:2
Alignment explanation
Indices: 1165163--1165196 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1165153 ATGGGGAATG
1165163 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
1165197 GGATACTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1166038 original size:3 final size:3
Alignment explanation
Indices: 1166007--1166065 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
1165997 CAAGCGGTCA
* * * *
1166007 ATG AAG ATG ACG ATG AAG ATG AAG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1166055 ATG ATG ATG AT
1 ATG ATG ATG AT
1166066 CCAAACAAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.39, C:0.02, G:0.32, T:0.27
Consensus pattern (3 bp):
ATG
Found at i:1168893 original size:28 final size:26
Alignment explanation
Indices: 1168862--1168925 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 26
1168852 ATGTGATTAG
1168862 ATGAGAAATGAACATGAGATATACGAAT
1 ATGAGAAATG-ACATG-GATATACGAAT
* * *
1168890 ATGAATGAAATGATATGGTTATATGAAT
1 ATG-A-GAAATGACATGGATATACGAAT
1168918 ATGAGAAA
1 ATGAGAAA
1168926 AGGTATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
28 15 0.48
29 5 0.16
30 6 0.19
ACGTcount: A:0.48, C:0.03, G:0.22, T:0.27
Consensus pattern (26 bp):
ATGAGAAATGACATGGATATACGAAT
Found at i:1169128 original size:32 final size:32
Alignment explanation
Indices: 1169087--1169178 Score: 100
Period size: 32 Copynumber: 2.9 Consensus size: 32
1169077 AGTAGAGGGT
1169087 TTACCTATGTTTTACGGAACATATGGACAAAA
1 TTACCTATGTTTTACGGAACATATGGACAAAA
* **
1169119 TTACCTATGTCTTT-C-GAGACATATGGATAGTA
1 TTACCTATGT-TTTACGGA-ACATATGGACAAAA
* *
1169151 -TACCTATGTTCTAAGGAACATATGGACA
1 TTACCTATGTTTTACGGAACATATGGACA
1169179 GTTTACCTAG
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
30 2 0.04
31 21 0.42
32 24 0.48
33 3 0.06
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (32 bp):
TTACCTATGTTTTACGGAACATATGGACAAAA
Found at i:1169172 original size:31 final size:31
Alignment explanation
Indices: 1169088--1169211 Score: 97
Period size: 31 Copynumber: 4.0 Consensus size: 31
1169078 GTAGAGGGTT
* * **
1169088 TACCTATGTTTTACGGAACATATGGACAAAA
1 TACCTATGTTCTAAGGAACATATGGACAGTA
*** *
1169119 TTACCTATG-TCTTTCGAGACATATGGATAGTA
1 -TACCTATGTTCTAAGGA-ACATATGGACAGTA
*
1169151 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTAAGGAACATATGGACAGTA
* ** * *
1169182 TACCTAGGTTCTTCGGGACCTATGGACAGT
1 TACCTATGTTCTAAGGAACATATGGACAGT
1169212 TGTCGAGGTT
Statistics
Matches: 73, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
31 49 0.67
32 24 0.33
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAGTA
Found at i:1173906 original size:28 final size:26
Alignment explanation
Indices: 1173875--1173938 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 26
1173865 ATGTGATTAG
1173875 ATGAGAAATGAACATGAGATATACGAAT
1 ATGAGAAATG-ACATG-GATATACGAAT
* * *
1173903 ATGAATGAAATGATATGGTTATATGAAT
1 ATG-A-GAAATGACATGGATATACGAAT
1173931 ATGAGAAA
1 ATGAGAAA
1173939 AGGTATATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
28 15 0.48
29 5 0.16
30 6 0.19
ACGTcount: A:0.48, C:0.03, G:0.22, T:0.27
Consensus pattern (26 bp):
ATGAGAAATGACATGGATATACGAAT
Found at i:1174010 original size:13 final size:15
Alignment explanation
Indices: 1173994--1174025 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
1173984 ATAGGAAAGA
1173994 AATATGTG-ATATG-
1 AATATGTGAATATGT
1174007 AATATGTGAATATGT
1 AATATGTGAATATGT
1174022 AATA
1 AATA
1174026 GAGAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 5 0.29
15 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (15 bp):
AATATGTGAATATGT
Found at i:1174198 original size:20 final size:20
Alignment explanation
Indices: 1174173--1174219 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1174163 TTTTCCAATT
1174173 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
1174193 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATATGTAAA
1174213 TCGCAAC
1 TCGCAAC
1174220 ACAGAAGCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:1174236 original size:20 final size:19
Alignment explanation
Indices: 1174213--1174352 Score: 104
Period size: 20 Copynumber: 7.0 Consensus size: 19
1174203 AATTTGTAAA
*
1174213 TCGCAACACAGAAGCCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
1174233 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
*
1174253 TCGCAACACAAAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
* **
1174273 TCGTAATGCGAATTTGT-AAA-
1 TCGCAACACGAA---GTCAAAT
1174293 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
* *
1174313 TCGCAACGCGATAGCCAAAT
1 TCGCAACACGA-AGTCAAAT
*
1174333 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACG-AAGTCAAAT
1174353 GTTTTTACGC
Statistics
Matches: 96, Mismatches: 14, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
18 2 0.02
19 9 0.09
20 75 0.78
21 8 0.08
22 2 0.02
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.18
Consensus pattern (19 bp):
TCGCAACACGAAGTCAAAT
Found at i:1174237 original size:40 final size:40
Alignment explanation
Indices: 1174193--1174323 Score: 185
Period size: 40 Copynumber: 3.3 Consensus size: 40
1174183 AATATGTAAA
*
1174193 TCGCAACGCGAATTTGTAAATCGCAACACAGAAGCCAAAT
1 TCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAAT
* *
1174233 TCGCAACGCG-A-TAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAAT
* *
1174273 TCGTAATGCGAATTTGTAAATCGCAACACAGAAGTCAAAT
1 TCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAAT
1174313 TCGCAACGCGA
1 TCGCAACGCGA
1174324 TAGCCAAATT
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
38 3 0.04
39 4 0.05
40 64 0.82
41 4 0.05
42 3 0.04
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (40 bp):
TCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAAT
Found at i:1174286 original size:80 final size:80
Alignment explanation
Indices: 1174200--1174352 Score: 270
Period size: 80 Copynumber: 1.9 Consensus size: 80
1174190 AAATCGCAAC
*
1174200 GCGAATTTGTAAATCGCAACACAGAAGCCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAA
1 GCGAATTTGTAAATCGCAACACAGAAGCCAAATTCGCAACGCGATAGCCAAATTCGCAACACAAA
1174265 AGTCAAATTCGTAAT
66 AGTCAAATTCGTAAT
* * *
1174280 GCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGCCAAATTCGCAACGCGAA
1 GCGAATTTGTAAATCGCAACACAGAAGCCAAATTCGCAACGCGATAGCCAAATTCGCAACACAAA
1174345 AGTCAAAT
66 AGTCAAAT
1174353 GTTTTTACGC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.19
Consensus pattern (80 bp):
GCGAATTTGTAAATCGCAACACAGAAGCCAAATTCGCAACGCGATAGCCAAATTCGCAACACAAA
AGTCAAATTCGTAAT
Found at i:1174337 original size:40 final size:39
Alignment explanation
Indices: 1174213--1174352 Score: 158
Period size: 40 Copynumber: 3.5 Consensus size: 39
1174203 AATTTGTAAA
*
1174213 TCGCAACACAGAAGCCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACGCGATAG-CAAAT
* * * * *
1174253 TCGCAACACAAAAGTCAAATTCGTAATGCGAATTTGTAAA-
1 TCGCAACACAGAAGTCAAATTCGCAACGCG-A-TAGCAAAT
1174293 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGCCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACGCGATAG-CAAAT
*
1174333 TCGCAACGC-GAAAGTCAAAT
1 TCGCAACACAG-AAGTCAAAT
1174353 GTTTTTACGC
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
38 2 0.02
39 5 0.06
40 70 0.84
41 4 0.05
42 2 0.02
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.18
Consensus pattern (39 bp):
TCGCAACACAGAAGTCAAATTCGCAACGCGATAGCAAAT
Found at i:1174847 original size:14 final size:14
Alignment explanation
Indices: 1174805--1174850 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
1174795 AAGAAACCCT
*
1174805 AAATCGCAACACCA
1 AAATCGCAACACGA
*
1174819 AAACCGCAACACGA
1 AAATCGCAACACGA
*
1174833 AAATCGCAACGCGA
1 AAATCGCAACACGA
1174847 AAAT
1 AAAT
1174851 GAAAATCGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.50, C:0.30, G:0.13, T:0.07
Consensus pattern (14 bp):
AAATCGCAACACGA
Found at i:1177039 original size:21 final size:21
Alignment explanation
Indices: 1177021--1177096 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
1177011 AGTACCTCCT
1177021 ATCGTTCAAGAGGCCCCTCTC
1 ATCGTTCAAGAGGCCCCTCTC
* * *
1177042 ATC-ATCGAAGAAGCCCCTCCC
1 ATCGTTC-AAGAGGCCCCTCTC
* *
1177063 ACCGTTCAAGAGGCCCCTGTC
1 ATCGTTCAAGAGGCCCCTCTC
1177084 ATCGTTCAAGAGG
1 ATCGTTCAAGAGG
1177097 TCTCGCCCGC
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 2 0.05
21 40 0.91
22 2 0.05
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.20
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCTC
Found at i:1177045 original size:42 final size:42
Alignment explanation
Indices: 1176998--1177094 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
1176988 GATGCACCTA
* * *
1176998 TCATCATTCAAGAAGTACCTCCTATCGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAAGCACCTCCCACCGTTCAAGAGGCCCCTC
* *
1177040 TCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAAGCACCTCCCACCGTTCAAGAGGCCCCTC
*
1177082 TCATCGTTCAAGA
1 TCATCATTCAAGA
1177095 GGTCTCGCCC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 2 0.04
42 43 0.91
43 2 0.04
ACGTcount: A:0.26, C:0.35, G:0.16, T:0.23
Consensus pattern (42 bp):
TCATCATTCAAGAAGCACCTCCCACCGTTCAAGAGGCCCCTC
Found at i:1178542 original size:61 final size:62
Alignment explanation
Indices: 1178442--1178581 Score: 194
Period size: 66 Copynumber: 2.2 Consensus size: 62
1178432 TTTTACATTG
*
1178442 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
* * *
1178502 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA--TTTTT-CTTGATTAATTGATTTGT
1178567 A
62 A
1178568 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
1178582 GTTTCTAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
60 17 0.24
61 18 0.26
64 4 0.06
66 31 0.44
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.51
Consensus pattern (62 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
Found at i:1179015 original size:18 final size:18
Alignment explanation
Indices: 1178992--1179028 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1178982 CGAAATTTAT
1178992 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1179010 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1179028 A
1 A
1179029 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Done.