Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008199.1 Hibiscus syriacus cultivar Beakdansim tig00110819_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: 2638622
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:2016259 original size:18 final size:18
Alignment explanation
Indices: 2016238--2016274 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2016228 GTAATTGGAG
2016238 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
2016256 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
2016274 T
1 T
2016275 ATATATTTCG
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:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:2016282 original size:24 final size:24
Alignment explanation
Indices: 2016230--2016276 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2016220 TTTCATATGT
* *
2016230 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
2016254 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
2016277 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:2016576 original size:39 final size:39
Alignment explanation
Indices: 2016533--2016619 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
2016523 TCCGATGCTC
*
2016533 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
2016572 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
2016611 ATCAAAATC
1 ATCAAAATC
2016620 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:2017050 original size:23 final size:23
Alignment explanation
Indices: 2017019--2017082 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2017009 ATAGGTAAAC
*
2017019 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
2017042 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
2017065 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2017083 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:2017089 original size:23 final size:23
Alignment explanation
Indices: 2017019--2017091 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
2017009 ATAGGTAAAC
* **
2017019 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
2017042 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
2017065 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
2017088 ATAT
1 ATAT
2017092 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:2020024 original size:17 final size:17
Alignment explanation
Indices: 2019997--2020029 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
2019987 CACTTTAATA
2019997 TCATATAATA-TGATTC
1 TCATATAATATTGATTC
2020013 TCATATTAATATTGATT
1 TCATA-TAATATTGATT
2020030 GTTCCCCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (17 bp):
TCATATAATATTGATTC
Found at i:2022153 original size:2 final size:2
Alignment explanation
Indices: 2022146--2022170 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2022136 CAACAGTTAA
2022146 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2022171 AATGAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2024264 original size:39 final size:39
Alignment explanation
Indices: 2024210--2024285 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
2024200 CATTCGATCT
* *
2024210 CAAACACAAGGTTAGTGATGATCGTAAGATGGATGCCAA
1 CAAACACAAGATTAGTGATGATCATAAGATGGATGCCAA
2024249 CAAACACAAGATTAGTGATGATCATAAGATGGATGCC
1 CAAACACAAGATTAGTGATGATCATAAGATGGATGCC
2024286 TTCTCACCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (39 bp):
CAAACACAAGATTAGTGATGATCATAAGATGGATGCCAA
Found at i:2025076 original size:54 final size:54
Alignment explanation
Indices: 2024994--2025111 Score: 191
Period size: 54 Copynumber: 2.2 Consensus size: 54
2024984 AATTGGTGTT
* *
2024994 GACCTGAACCTAAATTAGACCTGAAAATTGTGGATCCGAACCCGACCTAAGAAC
1 GACCTGAACCCAAATTAGACCTGAAAATTGTGGATCCAAACCCGACCTAAGAAC
* * *
2025048 GACCTGAACCCGAATTGGACCTGGAAATTGTGGATCCAAACCCGACCTAAGAAC
1 GACCTGAACCCAAATTAGACCTGAAAATTGTGGATCCAAACCCGACCTAAGAAC
2025102 GACCTGAACC
1 GACCTGAACC
2025112 GAAAATATGA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (54 bp):
GACCTGAACCCAAATTAGACCTGAAAATTGTGGATCCAAACCCGACCTAAGAAC
Found at i:2025251 original size:16 final size:16
Alignment explanation
Indices: 2025232--2025262 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2025222 TGAATCTGAC
2025232 CTGTTTTTAACCTAAT
1 CTGTTTTTAACCTAAT
2025248 CTGTTTTTAACCTAA
1 CTGTTTTTAACCTAA
2025263 CCTATAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (16 bp):
CTGTTTTTAACCTAAT
Found at i:2025480 original size:13 final size:13
Alignment explanation
Indices: 2025464--2025490 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2025454 GACCTATTAT
2025464 ATAAAATTATTTA
1 ATAAAATTATTTA
2025477 ATAAAATTATTTA
1 ATAAAATTATTTA
2025490 A
1 A
2025491 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:2025552 original size:14 final size:14
Alignment explanation
Indices: 2025530--2025576 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
2025520 TGCAAAGGAA
*
2025530 AATTAATATAGTTT
1 AATTTATATAGTTT
2025544 AATTTATATA----
1 AATTTATATAGTTT
2025554 AA-TTATATAGTTT
1 AATTTATATAGTTT
2025567 AATTTATATA
1 AATTTATATA
2025577 AAAAATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:2025563 original size:23 final size:24
Alignment explanation
Indices: 2025529--2025578 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
2025519 ATGCAAAGGA
2025529 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
2025553 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
2025576 AAA
1 AAA
2025579 AAATAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:2027577 original size:30 final size:30
Alignment explanation
Indices: 2027541--2027600 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
2027531 TTCCAACGAG
2027541 TAGGAACATCCAATACTAACTTACCAGATA
1 TAGGAACATCCAATACTAACTTACCAGATA
2027571 TAGGAACATCCAATACTAACTTACCAGATA
1 TAGGAACATCCAATACTAACTTACCAGATA
2027601 AAGAAGAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.23
Consensus pattern (30 bp):
TAGGAACATCCAATACTAACTTACCAGATA
Found at i:2028815 original size:102 final size:102
Alignment explanation
Indices: 2028634--2028832 Score: 344
Period size: 102 Copynumber: 2.0 Consensus size: 102
2028624 AACAACCAAC
* * *
2028634 AGTAGCTACAAATTAAACAATTTATTTAAATTGTAAATAAAGGCAGCTAATAACCTTATAAAAAC
1 AGTAACTACAAATTAAACAATTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAAAAAC
*
2028699 AATCTGAATGAACAACCAACAACACTAACAAATCAAT
66 AATCTGAATGAACAACCAACAACACAAACAAATCAAT
* *
2028736 AGTAACTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAAAAGC
1 AGTAACTACAAATTAAACAATTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAAAAAC
2028801 AATCTGAATGAACAACCAACAACACAAACAAA
66 AATCTGAATGAACAACCAACAACACAAACAAA
2028833 GACTATAGAG
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 91 1.00
ACGTcount: A:0.51, C:0.18, G:0.09, T:0.23
Consensus pattern (102 bp):
AGTAACTACAAATTAAACAATTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAAAAAC
AATCTGAATGAACAACCAACAACACAAACAAATCAAT
Found at i:2029116 original size:6 final size:6
Alignment explanation
Indices: 2029105--2029175 Score: 65
Period size: 6 Copynumber: 12.0 Consensus size: 6
2029095 AGGGTTTTTA
* * *
2029105 GGTTTG GGTTTG GATTTG GGTTTTG GGTTTG GG-TTC GGTTT- GGTTCG
1 GGTTTG GGTTTG GGTTTG GG-TTTG GGTTTG GGTTTG GGTTTG GGTTTG
* * *
2029152 TGTTTG GGTTCG GGTTTA GGTTTG
1 GGTTTG GGTTTG GGTTTG GGTTTG
2029176 AGTACAGGTT
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
5 8 0.16
6 37 0.73
7 6 0.12
ACGTcount: A:0.03, C:0.04, G:0.44, T:0.49
Consensus pattern (6 bp):
GGTTTG
Found at i:2029135 original size:13 final size:13
Alignment explanation
Indices: 2029100--2029139 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
2029090 TGATTAGGGT
*
2029100 TTTTAGGTTTGGG
1 TTTTGGGTTTGGG
*
2029113 -TTTGGATTTGGG
1 TTTTGGGTTTGGG
2029125 TTTTGGGTTTGGG
1 TTTTGGGTTTGGG
2029138 TT
1 TT
2029140 CGGTTTGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.05, C:0.00, G:0.40, T:0.55
Consensus pattern (13 bp):
TTTTGGGTTTGGG
Found at i:2029163 original size:12 final size:11
Alignment explanation
Indices: 2029105--2029164 Score: 59
Period size: 11 Copynumber: 5.2 Consensus size: 11
2029095 AGGGTTTTTA
*
2029105 GGTTTGGGTTT
1 GGTTTGGGTTC
*
2029116 GGATTTGGGTTTTG
1 GG-TTTGGG--TTC
2029130 GGTTTGGGTTC
1 GGTTTGGGTTC
2029141 GGTTT-GGTTC
1 GGTTTGGGTTC
2029151 GTGTTTGGGTTC
1 G-GTTTGGGTTC
2029163 GG
1 GG
2029165 GTTTAGGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
10 6 0.14
11 14 0.33
12 12 0.29
13 6 0.14
14 4 0.10
ACGTcount: A:0.02, C:0.05, G:0.45, T:0.48
Consensus pattern (11 bp):
GGTTTGGGTTC
Found at i:2029647 original size:18 final size:18
Alignment explanation
Indices: 2029613--2029657 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
2029603 TATGAACTTA
2029613 TAGAGAGAAAACAAAGAAT
1 TAGAGAG-AAACAAAGAAT
* * *
2029632 TTGAGAGAAACGAAGAGT
1 TAGAGAGAAACAAAGAAT
2029650 TAGAGAGA
1 TAGAGAGA
2029658 GAGAGAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.53, C:0.04, G:0.29, T:0.13
Consensus pattern (18 bp):
TAGAGAGAAACAAAGAAT
Found at i:2029936 original size:16 final size:15
Alignment explanation
Indices: 2029895--2029948 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 15
2029885 TAGTTTTTAT
2029895 TAATTAACTATT-T-A
1 TAATTAA-TATTATAA
2029909 TAATTAATATTATAA
1 TAATTAATATTATAA
*
2029924 TAATT-ATA-TATTA
1 TAATTAATATTATAA
2029937 TAATTAATATTA
1 TAATTAATATTA
2029949 ATATTAACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
13 13 0.37
14 14 0.40
15 8 0.23
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTAATATTATAA
Found at i:2029943 original size:28 final size:31
Alignment explanation
Indices: 2029906--2029971 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 31
2029896 AATTAACTAT
2029906 TTATAATTAATATT-ATAATAA-TTATA-TA
1 TTATAATTAATATTAATAATAACTTATATTA
*
2029934 TTATAATTAATATTAATATTAACTTATATTA
1 TTATAATTAATATTAATAATAACTTATATTA
*
2029965 ATATAAT
1 TTATAAT
2029972 ATAGTTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 14 0.42
29 6 0.18
30 5 0.15
31 8 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (31 bp):
TTATAATTAATATTAATAATAACTTATATTA
Found at i:2029967 original size:50 final size:51
Alignment explanation
Indices: 2029906--2030002 Score: 128
Period size: 50 Copynumber: 1.9 Consensus size: 51
2029896 AATTAACTAT
*
2029906 TTATAATTAATATTATAATAA-TTAT-ATATTATAATTAATATTAATATTAAC
1 TTATAATTAATATAAT-ATAATTTATAAT-TTATAATTAATATTAATATTAAC
* *
2029957 TTAT-ATTAATATAATATAGTTTATAATTTGTAATTAATATTAATAT
1 TTATAATTAATATAATATAATTTATAATTTATAATTAATATTAATAT
2030003 AAAATATAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
49 3 0.07
50 32 0.78
51 6 0.15
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (51 bp):
TTATAATTAATATAATATAATTTATAATTTATAATTAATATTAATATTAAC
Found at i:2030027 original size:31 final size:29
Alignment explanation
Indices: 2029988--2030114 Score: 114
Period size: 31 Copynumber: 4.1 Consensus size: 29
2029978 TATAATTTGT
2029988 AATTAATATTAATATAAAATATAGTCTATA
1 AATTAATATTAATATAAAATATAGT-TATA
*
2030018 ACATTAATATTAATATAAACTATAGGTTATA
1 A-ATTAATATTAATATAAAATATA-GTTATA
* *
2030049 AATTATATAGTATAGTTTATAAACTATAGTTAATA
1 AATTA-ATA-T-TA--ATATAAAATATAGTT-ATA
2030084 TAATTAATATTAATAT--AATATAGTTTATA
1 -AATTAATATTAATATAAAATATAG-TTATA
2030113 AA
1 AA
2030115 CCATATACTA
Statistics
Matches: 83, Mismatches: 4, Indels: 22
0.76 0.04 0.20
Matches are distributed among these distances:
28 2 0.02
29 9 0.11
30 7 0.08
31 32 0.39
32 3 0.04
33 4 0.05
34 4 0.05
35 17 0.20
36 5 0.06
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (29 bp):
AATTAATATTAATATAAAATATAGTTATA
Found at i:2030040 original size:24 final size:25
Alignment explanation
Indices: 2029995--2030041 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
2029985 TGTAATTAAT
**
2029995 ATTAATATAAAATATAGTCTATAAC
1 ATTAATATAAAATATAAACTATAAC
*
2030020 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
2030042 GGTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAC
Found at i:2030068 original size:14 final size:14
Alignment explanation
Indices: 2030051--2030112 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
2030041 AGGTTATAAA
*
2030051 TTATATAGTATAGT
1 TTATATAATATAGT
2030065 TTATA-AACTATAGT
1 TTATATAA-TATAGT
*
2030079 TAATATAATTAATA-T
1 TTATATAA-T-ATAGT
*
2030094 TAATATAATATAGT
1 TTATATAATATAGT
2030108 TTATA
1 TTATA
2030113 AACCATATAC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
13 4 0.10
14 21 0.52
15 12 0.30
16 3 0.08
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (14 bp):
TTATATAATATAGT
Found at i:2030152 original size:65 final size:64
Alignment explanation
Indices: 2029959--2030162 Score: 209
Period size: 65 Copynumber: 3.1 Consensus size: 64
2029949 ATATTAACTT
* * * *
2029959 ATATTAATATAATATAGTTTATAATTTGTA-ATTAATATTAATATAAAATATAGTCTATAA-CAT
1 ATATTAATATAATATAGTTTATAAATTATATACT-ATATTAATATAAAATATAGT-TA-AATAAT
2030022 TA
63 TA
* * *
2030024 ATATTAATATAAACTATAGGTTATAAATTATATAGTATAGTT--TATAAACTATAGTTAATATAA
1 ATATTAATAT-AA-TATAGTTTATAAATTATATACTATA-TTAATATAAAATATAGTTAA-ATAA
2030087 TTA
62 TTA
** *
2030090 ATATTAATATAATATAGTTTATAAACCATATACTATATTAATATAAATTATAGTTAAGATAATTA
1 ATATTAATATAATATAGTTTATAAATTATATACTATATTAATATAAAATATAGTTAA-ATAATTA
*
2030155 ACATTAAT
1 ATATTAAT
2030163 GTAAACTATA
Statistics
Matches: 118, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
63 2 0.02
64 22 0.19
65 44 0.37
66 28 0.24
67 18 0.15
68 4 0.03
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (64 bp):
ATATTAATATAATATAGTTTATAAATTATATACTATATTAATATAAAATATAGTTAAATAATTA
Found at i:2030208 original size:21 final size:21
Alignment explanation
Indices: 2030182--2030257 Score: 116
Period size: 21 Copynumber: 3.6 Consensus size: 21
2030172 ATAGTACATT
2030182 AATATAAACTATAGTTTATAA
1 AATATAAACTATAGTTTATAA
2030203 AATATAAACTATAGTTTATAA
1 AATATAAACTATAGTTTATAA
* * *
2030224 ATTATATACTATAGGTTATAA
1 AATATAAACTATAGTTTATAA
*
2030245 AGTATAAACTATA
1 AATATAAACTATA
2030258 TAGTACACTA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (21 bp):
AATATAAACTATAGTTTATAA
Found at i:2030421 original size:35 final size:37
Alignment explanation
Indices: 2030382--2030458 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
2030372 ATATATATTG
*
2030382 TATATAGTTTA-A-ACATACATGTACTATAAGTTACA
1 TATATAGTTTACATACATACATATACTATAAGTTACA
** *
2030417 TATATAGTTTACATGTATACATATACTATAGGTTACA
1 TATATAGTTTACATACATACATATACTATAAGTTACA
2030454 TATAT
1 TATAT
2030459 TAACTATTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 11 0.31
36 1 0.03
37 24 0.67
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.40
Consensus pattern (37 bp):
TATATAGTTTACATACATACATATACTATAAGTTACA
Found at i:2030640 original size:35 final size:36
Alignment explanation
Indices: 2030601--2030674 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
2030591 TATACTATAC
*
2030601 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
**
2030636 ATAGTTTACATGTATACATATACTATAAGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
2030673 AT
1 AT
2030675 TAACTATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 7 0.21
37 27 0.79
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:2030876 original size:2 final size:2
Alignment explanation
Indices: 2030871--2031060 Score: 130
Period size: 2 Copynumber: 97.5 Consensus size: 2
2030861 TTATGCATAG
2030871 TA 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 TA TA
* * * * * * *
2030912 TA CT- TA TA T- TA GT- TA TA CA TA CA CA CA CA CA CA TA TA TA TA
1 TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2030953 TA TA CTA TA T- TA -A TA TA AA T- TA TA -A TA TA TA AA CTA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * * *
2030993 T- TT TA TA TA -A TT TA TA CA TA TA TA GTT TA TA TA CA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
2031034 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 T
2031061 TAATATAAAT
Statistics
Matches: 154, Mismatches: 19, Indels: 30
0.76 0.09 0.15
Matches are distributed among these distances:
1 10 0.06
2 138 0.90
3 6 0.04
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2031100 original size:98 final size:99
Alignment explanation
Indices: 2030944--2031127 Score: 300
Period size: 98 Copynumber: 1.9 Consensus size: 99
2030934 ACACACACAC
*
2030944 ATATATATATATACTATATTAATATAAATTATAATATATAAACTATATATTTTATATAATTTATA
1 ATATATATATATACTATATTAATATAAATAATAATATATAAACTATATATTTTATATAATTTATA
*
2031009 CATATATAGTTTATATACATACATATATATATAT
66 CATATATAATTTATATACATACATATATATATAT
* * *
2031043 ATATATATATATA-TATATTAATATAAATAATATTTTATAAATTATATACTTTT-TATAATTTAT
1 ATATATATATATACTATATTAATATAAATAATAATATATAAACTATATA-TTTTATATAATTTAT
2031106 ACATATATAATTTATATACATA
65 ACATATATAATTTATATACATA
2031128 GTTCACATAA
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
98 62 0.78
99 17 0.22
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (99 bp):
ATATATATATATACTATATTAATATAAATAATAATATATAAACTATATATTTTATATAATTTATA
CATATATAATTTATATACATACATATATATATAT
Found at i:2031151 original size:98 final size:98
Alignment explanation
Indices: 2030925--2031155 Score: 281
Period size: 98 Copynumber: 2.4 Consensus size: 98
2030915 TTATATTAGT
* * * * *
2030925 TATACATACACACACACACATATATATATATA-CTATATTAATATAAATTATAATATATAAACTA
1 TATACATACATACATAAACATATATATATATATATATATTAATATAAATAATAATATATAAACTA
*
2030989 TATATTTTATATAATTTATACATATATAGTTTA
66 TATATTTTATATAATTTATACATATATAATTTA
* * * * * *
2031022 TATACATACATATATATATATATATATATATATATATATTAATATAAATAATATTTTATAAATTA
1 TATACATACATACATAAACATATATATATATATATATATTAATATAAATAATAATATATAAACTA
2031087 TATACTTTT-TATAATTTATACATATATAATTTA
66 TATA-TTTTATATAATTTATACATATATAATTTA
**
2031120 TATACATAGTTCACATAAACATA-AT-TCATATATATA
1 TATACATACAT-ACATAAACATATATAT-ATATATATA
2031156 GCTTATAATA
Statistics
Matches: 114, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
97 28 0.25
98 74 0.65
99 12 0.11
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (98 bp):
TATACATACATACATAAACATATATATATATATATATATTAATATAAATAATAATATATAAACTA
TATATTTTATATAATTTATACATATATAATTTA
Found at i:2031176 original size:21 final size:19
Alignment explanation
Indices: 2031149--2031201 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 19
2031139 CATAATTCAT
*
2031149 ATATATAGCTTATAATAATA
1 ATATATAGTTTATAAT-ATA
2031169 ATTATATAGTTTATAATATA
1 A-TATATAGTTTATAATATA
2031189 A-ATATAGTTTATA
1 ATATATAGTTTATA
2031202 TACAAACTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 12 0.39
20 5 0.16
21 14 0.45
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (19 bp):
ATATATAGTTTATAATATA
Found at i:2031890 original size:16 final size:16
Alignment explanation
Indices: 2031869--2031922 Score: 99
Period size: 16 Copynumber: 3.4 Consensus size: 16
2031859 CTTCGTACCT
2031869 GAACTGGCATCGATCC
1 GAACTGGCATCGATCC
2031885 GAACTGGCATCGATCC
1 GAACTGGCATCGATCC
*
2031901 GAACTGGAATCGATCC
1 GAACTGGCATCGATCC
2031917 GAACTG
1 GAACTG
2031923 AAAATGACCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (16 bp):
GAACTGGCATCGATCC
Found at i:2036119 original size:4 final size:4
Alignment explanation
Indices: 2036110--2036153 Score: 52
Period size: 4 Copynumber: 10.0 Consensus size: 4
2036100 ACTTTCTCAA
2036110 ATTT ATTT ATCTTT ATTT ATTT ATTT ATCTTT ATTT ATTT ATTT
1 ATTT ATTT A--TTT ATTT ATTT ATTT A--TTT ATTT ATTT ATTT
2036154 TCTCAATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
4 28 0.78
6 8 0.22
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:2036129 original size:14 final size:14
Alignment explanation
Indices: 2036110--2036151 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
2036100 ACTTTCTCAA
2036110 ATTTATTTATCTT-T
1 ATTTATTTAT-TTAT
2036124 ATTTATTTATTTAT
1 ATTTATTTATTTAT
*
2036138 CTTTATTTATTTAT
1 ATTTATTTATTTAT
2036152 TTTCTCAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 2 0.08
14 24 0.92
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTATTTATTTAT
Found at i:2036131 original size:18 final size:18
Alignment explanation
Indices: 2036110--2036153 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
2036100 ACTTTCTCAA
2036110 ATTTATTTATCTTTATTT
1 ATTTATTTATCTTTATTT
2036128 ATTTATTTATCTTTATTT
1 ATTTATTTATCTTTATTT
2036146 ATTTATTT
1 ATTTATTT
2036154 TCTCAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTATTTATCTTTATTT
Found at i:2036164 original size:18 final size:18
Alignment explanation
Indices: 2036075--2036164 Score: 50
Period size: 18 Copynumber: 5.3 Consensus size: 18
2036065 AAATTTAACT
* *
2036075 TTTTATTTATTTTTTTAA
1 TTTTATTTATTTTCTCAA
*
2036093 TTTTCA--TACTTTCTCAA
1 TTTT-ATTTATTTTCTCAA
* *
2036110 ATTTATTTATCTT-T--A
1 TTTTATTTATTTTCTCAA
**
2036125 -TTTATTTATTTATCTTTA
1 TTTTATTTATTT-TCTCAA
2036143 -TTTATTTATTTTCTCAA
1 TTTTATTTATTTTCTCAA
2036160 TTTTA
1 TTTTA
2036165 AAAAAATAGT
Statistics
Matches: 55, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
14 10 0.18
15 2 0.04
16 2 0.04
17 16 0.29
18 24 0.44
19 1 0.02
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTATTTATTTTCTCAA
Found at i:2036192 original size:8 final size:8
Alignment explanation
Indices: 2036174--2036216 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
2036164 AAAAAAATAG
2036174 TTTTTTA-
1 TTTTTTAT
2036181 TTTTTTAT
1 TTTTTTAT
2036189 TTTTTTAT
1 TTTTTTAT
*
2036197 TTTTTCTCT
1 TTTTT-TAT
2036206 TTTTTATAT
1 TTTTT-TAT
2036215 TT
1 TT
2036217 ATATATTTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
7 7 0.23
8 13 0.42
9 11 0.35
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTAT
Found at i:2036192 original size:15 final size:16
Alignment explanation
Indices: 2036174--2036212 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
2036164 AAAAAAATAG
2036174 TTTTTTATTTTTTAT-
1 TTTTTTATTTTTTATC
*
2036189 TTTTTTATTTTTTCTC
1 TTTTTTATTTTTTATC
2036205 TTTTTTAT
1 TTTTTTAT
2036213 ATTTATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTATTTTTTATC
Found at i:2036778 original size:50 final size:50
Alignment explanation
Indices: 2036719--2036824 Score: 203
Period size: 50 Copynumber: 2.1 Consensus size: 50
2036709 TTTAATATTA
2036719 AATTATAAAAATGAAAAAATATTAAATATATTTTTATTTTATTATACTTTT
1 AATT-TAAAAATGAAAAAATATTAAATATATTTTTATTTTATTATACTTTT
2036770 AATTTAAAAATGAAAAAATATTAAATATATTTTTATTTTATTATACTTTT
1 AATTTAAAAATGAAAAAATATTAAATATATTTTTATTTTATTATACTTTT
2036820 AATTT
1 AATTT
2036825 TTTAATTGAT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 51 0.93
51 4 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (50 bp):
AATTTAAAAATGAAAAAATATTAAATATATTTTTATTTTATTATACTTTT
Found at i:2037373 original size:31 final size:31
Alignment explanation
Indices: 2037338--2037424 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
2037328 TGGGCTTCTA
2037338 ATAAAATA-CTAATTCAACCCTTAAACTTTAG
1 ATAAAATATC-AATTCAACCCTTAAACTTTAG
* * * *
2037369 ATAAAATATCAATTTAACCTTTGATCTTTAG
1 ATAAAATATCAATTCAACCCTTAAACTTTAG
* *
2037400 AT-AAATAATCAATTTAACCCCTAAA
1 ATAAAAT-ATCAATTCAACCCTTAAA
2037425 TTTGATCAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
30 4 0.09
31 41 0.89
32 1 0.02
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.34
Consensus pattern (31 bp):
ATAAAATATCAATTCAACCCTTAAACTTTAG
Found at i:2040073 original size:26 final size:26
Alignment explanation
Indices: 2040009--2040062 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
2039999 AAAAATTAAA
2040009 TTTAAGACATTTAAATTGTAATTTAT
1 TTTAAGACATTTAAATTGTAATTTAT
2040035 TTTAAGACATTTAAATTGTAATTTAT
1 TTTAAGACATTTAAATTGTAATTTAT
2040061 TT
1 TT
2040063 ATATATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (26 bp):
TTTAAGACATTTAAATTGTAATTTAT
Found at i:2040786 original size:7 final size:7
Alignment explanation
Indices: 2040774--2040800 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2040764 ACGCCTCTCT
2040774 GTCCACA
1 GTCCACA
2040781 GTCCACA
1 GTCCACA
2040788 GTCCACA
1 GTCCACA
2040795 GTCCAC
1 GTCCAC
2040801 CCATTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.44, G:0.15, T:0.15
Consensus pattern (7 bp):
GTCCACA
Found at i:2042686 original size:28 final size:28
Alignment explanation
Indices: 2042646--2042741 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
2042636 TGACTTGAAT
2042646 TCATTATTTATCTATTTTTTTAAAAAAA
1 TCATTATTTATCTATTTTTTTAAAAAAA
*
2042674 TCATTATTTATCTTTTTTTTTAAAAAAAA
1 TCATTATTTATCTATTTTTTT-AAAAAAA
**
2042703 TCATTATTTATCT-TTTTTTT--TTAAA
1 TCATTATTTATCTATTTTTTTAAAAAAA
2042728 TCATTATTTATCTA
1 TCATTATTTATCTA
2042742 AAATTAAAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.25
28 27 0.43
29 20 0.32
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (28 bp):
TCATTATTTATCTATTTTTTTAAAAAAA
Found at i:2042702 original size:29 final size:28
Alignment explanation
Indices: 2042646--2042740 Score: 142
Period size: 29 Copynumber: 3.5 Consensus size: 28
2042636 TGACTTGAAT
*
2042646 TCATTATTTATCTATTTTTTTAAAAAAA
1 TCATTATTTATCTTTTTTTTTAAAAAAA
2042674 TCATTATTTATCTTTTTTTTTAAAAAAAA
1 TCATTATTTATCTTTTTTTTT-AAAAAAA
*
2042703 TCATTATTTATCTTTTTTTTT---TAAA
1 TCATTATTTATCTTTTTTTTTAAAAAAA
2042728 TCATTATTTATCT
1 TCATTATTTATCT
2042741 AAAATTAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.25
28 20 0.31
29 28 0.44
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (28 bp):
TCATTATTTATCTTTTTTTTTAAAAAAA
Found at i:2043633 original size:33 final size:33
Alignment explanation
Indices: 2043591--2043657 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
2043581 CGGTCCACCC
2043591 GGGCCTTATACAGACTTACAGAGGTATAGGTGT
1 GGGCCTTATACAGACTTACAGAGGTATAGGTGT
2043624 GGGCCTTATACAGACTTACAGAGGTATAGGTGT
1 GGGCCTTATACAGACTTACAGAGGTATAGGTGT
2043657 G
1 G
2043658 TGCTAATTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (33 bp):
GGGCCTTATACAGACTTACAGAGGTATAGGTGT
Found at i:2051341 original size:3 final size:3
Alignment explanation
Indices: 2051299--2051323 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2051289 TTTCTAAATC
2051299 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
2051324 TGTTTTCTTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2051661 original size:15 final size:15
Alignment explanation
Indices: 2051633--2051673 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
2051623 CTTAATGTAG
2051633 ATAAACATAT-TTTAT
1 ATAAA-ATATATTTAT
2051648 ATAAAATATATTTAT
1 ATAAAATATATTTAT
*
2051663 A-AAAATTTATT
1 ATAAAATATATT
2051674 CAACAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
ATAAAATATATTTAT
Found at i:2053101 original size:2 final size:2
Alignment explanation
Indices: 2053059--2053083 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2053049 AATTTTAGTA
2053059 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2053084 AAAAGAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2056258 original size:39 final size:39
Alignment explanation
Indices: 2056180--2056261 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
2056170 TTTTCACCCT
* *
2056180 AAACCTGACCCGACCCGACCCGAACAGTACATTTAAAAA
1 AAACCCGACCCGACCCGACCCGAACAGTAAATTTAAAAA
*
2056219 AAACCCGACCCGACCCGACCCGAACCCG-AAATTTTAAAAA
1 AAACCCGACCCGACCCGACCCGAA-CAGTAAA-TTTAAAAA
2056259 AAA
1 AAA
2056262 AATCCGACCC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 25 0.66
40 13 0.34
ACGTcount: A:0.43, C:0.34, G:0.12, T:0.11
Consensus pattern (39 bp):
AAACCCGACCCGACCCGACCCGAACAGTAAATTTAAAAA
Found at i:2060668 original size:477 final size:477
Alignment explanation
Indices: 2059774--2060729 Score: 1894
Period size: 477 Copynumber: 2.0 Consensus size: 477
2059764 TGATAAAATC
2059774 ATCATTGATGTTATGCTTTTGTTTTCTTTATTTTTTAAGATAATAGTAATATTAATATGATATTT
1 ATCATTGATGTTATGCTTTTGTTTTCTTTATTTTTTAAGATAATAGTAATATTAATATGATATTT
2059839 TTTTTAATTATAAACTTTTCATGTAATTTTATTTCTATATTAATAATAACATGTATCATTTTTTA
66 TTTTTAATTATAAACTTTTCATGTAATTTTATTTCTATATTAATAATAACATGTATCATTTTTTA
2059904 AATAAACTAACATTTTATGATAAGATAATGATACATACTATCACCTTATTGTTCAAATAAAAATA
131 AATAAACTAACATTTTATGATAAGATAATGATACATACTATCACCTTATTGTTCAAATAAAAATA
2059969 TGTCAAATACAATGTCAGGGGTTTTAATATCACCCTCTAAAAATTATCGAAATAACACTTTCAAT
196 TGTCAAATACAATGTCAGGGGTTTTAATATCACCCTCTAAAAATTATCGAAATAACACTTTCAAT
2060034 ATCATAGGCGAATGCACACCACGTCAGTTACGTATTCTTAAAAACACATATGACAGGACACGTTA
261 ATCATAGGCGAATGCACACCACGTCAGTTACGTATTCTTAAAAACACATATGACAGGACACGTTA
2060099 TTGAATGAGATAAAATACAAATTAAACAAATTTTATCCAAAGAAGAACACCCACGACACGTATAA
326 TTGAATGAGATAAAATACAAATTAAACAAATTTTATCCAAAGAAGAACACCCACGACACGTATAA
2060164 GAAATATGTATTAATACAAATATAGTGATAGTGGCATTTGATAATGTATATGTACATATTTTATC
391 GAAATATGTATTAATACAAATATAGTGATAGTGGCATTTGATAATGTATATGTACATATTTTATC
2060229 TTTAATCACTCAATGAATACAT
456 TTTAATCACTCAATGAATACAT
2060251 ATCATTGATGTTATGCTTTTGTTTTCTTTATTTTTTAAGATAATAGTAATATTAATATGATATTT
1 ATCATTGATGTTATGCTTTTGTTTTCTTTATTTTTTAAGATAATAGTAATATTAATATGATATTT
2060316 TTTTTAATTATAAACTTTTCATGTAATTTTATTTCTATATTAATAATAACATGTATCATTTTTTA
66 TTTTTAATTATAAACTTTTCATGTAATTTTATTTCTATATTAATAATAACATGTATCATTTTTTA
2060381 AATAAACTAACATTTTATGATAAGATAATGATACATACTATCACCTTATTGTTCAAATAAAAATA
131 AATAAACTAACATTTTATGATAAGATAATGATACATACTATCACCTTATTGTTCAAATAAAAATA
2060446 TGTCAAATACAATGTCAGGGGTTTTAATATCACCCTCTAAAAATTATCGAAATAACACTTTCAAT
196 TGTCAAATACAATGTCAGGGGTTTTAATATCACCCTCTAAAAATTATCGAAATAACACTTTCAAT
*
2060511 ATCATAGGCGAATGCACACTACGTCAGTTACGTATTCTTAAAAACACATATGACAGGACACGTTA
261 ATCATAGGCGAATGCACACCACGTCAGTTACGTATTCTTAAAAACACATATGACAGGACACGTTA
2060576 TTGAATGAGATAAAATACAAATTAAACAAATTTTATCCAAAGAAGAACACCCACGACACGTATAA
326 TTGAATGAGATAAAATACAAATTAAACAAATTTTATCCAAAGAAGAACACCCACGACACGTATAA
*
2060641 GAAATATGTATTAATACAAATATAGTGATAGTGGCATTTGATAATGTATATGTATATATTTTATC
391 GAAATATGTATTAATACAAATATAGTGATAGTGGCATTTGATAATGTATATGTACATATTTTATC
2060706 TTTAATCACTCAATGAATACAT
456 TTTAATCACTCAATGAATACAT
2060728 AT
1 AT
2060730 TTAAATGTTA
Statistics
Matches: 477, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
477 477 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (477 bp):
ATCATTGATGTTATGCTTTTGTTTTCTTTATTTTTTAAGATAATAGTAATATTAATATGATATTT
TTTTTAATTATAAACTTTTCATGTAATTTTATTTCTATATTAATAATAACATGTATCATTTTTTA
AATAAACTAACATTTTATGATAAGATAATGATACATACTATCACCTTATTGTTCAAATAAAAATA
TGTCAAATACAATGTCAGGGGTTTTAATATCACCCTCTAAAAATTATCGAAATAACACTTTCAAT
ATCATAGGCGAATGCACACCACGTCAGTTACGTATTCTTAAAAACACATATGACAGGACACGTTA
TTGAATGAGATAAAATACAAATTAAACAAATTTTATCCAAAGAAGAACACCCACGACACGTATAA
GAAATATGTATTAATACAAATATAGTGATAGTGGCATTTGATAATGTATATGTACATATTTTATC
TTTAATCACTCAATGAATACAT
Found at i:2061908 original size:21 final size:19
Alignment explanation
Indices: 2061894--2062086 Score: 113
Period size: 19 Copynumber: 9.9 Consensus size: 19
2061884 TCCAAGTTCG
2061894 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
*
2061913 TGTTGCGATTTTCCAAA-T
1 CGTTGCGATTTTCCAAATT
* * **
2061931 --TTACGGTAGTCCAAATT
1 CGTTGCGATTTTCCAAATT
* ** *
2061948 TGTTGCGATAGTCCAAGTT
1 CGTTGCGATTTTCCAAATT
** * *
2061967 CACGTTGCGATAGTCGAAGTT
1 --CGTTGCGATTTTCCAAATT
2061988 CGCGTTGCGATTTTCCAAATT
1 --CGTTGCGATTTTCCAAATT
* * *
2062009 CGTTGCGATATTCGAAGTT
1 CGTTGCGATTTTCCAAATT
2062028 CACGTTGCGATTTTCCAAATT
1 --CGTTGCGATTTTCCAAATT
** *
2062049 CGTTGCGATAGTCCAAGTT
1 CGTTGCGATTTTCCAAATT
*
2062068 CACGCTGCGATTTTCCAAA
1 --CGTTGCGATTTTCCAAA
2062087 CTCGCAACGA
Statistics
Matches: 137, Mismatches: 28, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
16 11 0.08
17 1 0.01
18 1 0.01
19 62 0.45
21 62 0.45
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:2061919 original size:19 final size:19
Alignment explanation
Indices: 2061875--2062064 Score: 116
Period size: 21 Copynumber: 9.7 Consensus size: 19
2061865 CAACGCGATT
* *
2061875 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATATTCCAAATT--CG
* *
2061896 TTGCGATTTTCCAAATTTG
1 TTGCGATATTCCAAATTCG
*
2061915 TTGCGATTTTCCAAA-T--
1 TTGCGATATTCCAAATTCG
* * * *
2061931 TTACGGTAGTCCAAATTTG
1 TTGCGATATTCCAAATTCG
* *
2061950 TTGCGATAGTCCAAGTTCACG
1 TTGCGATATTCCAAATT--CG
* * *
2061971 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATATTCCAAATT--CG
*
2061992 TTGCGATTTTCCAAATTCG
1 TTGCGATATTCCAAATTCG
* *
2062011 TTGCGATATTCGAAGTTCACG
1 TTGCGATATTCCAAATT--CG
*
2062032 TTGCGATTTTCCAAATTCG
1 TTGCGATATTCCAAATTCG
*
2062051 TTGCGATAGTCCAA
1 TTGCGATATTCCAA
2062065 GTTCACGCTG
Statistics
Matches: 136, Mismatches: 26, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
16 11 0.08
17 1 0.01
18 1 0.01
19 60 0.44
21 63 0.46
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (19 bp):
TTGCGATATTCCAAATTCG
Found at i:2062013 original size:40 final size:40
Alignment explanation
Indices: 2061969--2062086 Score: 200
Period size: 40 Copynumber: 3.0 Consensus size: 40
2061959 TCCAAGTTCA
*
2061969 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCACGTTGCGATTTTCCAAATT
*
2062009 CGTTGCGATATTCGAAGTTCACGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCACGTTGCGATTTTCCAAATT
* *
2062049 CGTTGCGATAGTCCAAGTTCACGCTGCGATTTTCCAAA
1 CGTTGCGATAGTCGAAGTTCACGTTGCGATTTTCCAAA
2062087 CTCGCAACGA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (40 bp):
CGTTGCGATAGTCGAAGTTCACGTTGCGATTTTCCAAATT
Found at i:2062531 original size:19 final size:19
Alignment explanation
Indices: 2062504--2062560 Score: 96
Period size: 19 Copynumber: 3.0 Consensus size: 19
2062494 ACGTTTTTCA
*
2062504 AACTCTCGCAACACATTTT
1 AACTATCGCAACACATTTT
2062523 AACTATCGCAACACATTTT
1 AACTATCGCAACACATTTT
*
2062542 AACTATCACAACACATTTT
1 AACTATCGCAACACATTTT
2062561 TCAAAATCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.32
Consensus pattern (19 bp):
AACTATCGCAACACATTTT
Found at i:2073650 original size:13 final size:13
Alignment explanation
Indices: 2073634--2073689 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
2073624 TACAGCATAA
2073634 ATTTATATTATAT
1 ATTTATATTATAT
2073647 ATTTATA-TATATT
1 ATTTATATTATA-T
* *
2073660 ATATATATAATAT
1 ATTTATATTATAT
2073673 ATTATATATCTATAT
1 ATT-TATAT-TATAT
2073688 AT
1 AT
2073690 ATAATTTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 4 0.11
13 17 0.49
14 8 0.23
15 6 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTATATTATAT
Found at i:2073655 original size:2 final size:2
Alignment explanation
Indices: 2073637--2073692 Score: 66
Period size: 2 Copynumber: 30.0 Consensus size: 2
2073627 AGCATAAATT
*
2073637 TA TA T- TA TA TA TT TA TA TA TA T- TA TA TA TA TA -A TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2073675 TA TA TA TC TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
2073693 ATTTATACAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
1 4 0.09
2 42 0.91
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2073666 original size:26 final size:26
Alignment explanation
Indices: 2073637--2073692 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
2073627 AGCATAAATT
*
2073637 TATATTATATATT-TATATATATTATA
1 TATATAATATATTATATATATA-TATA
*
2073663 TATATAATATATTATATATCTATATA
1 TATATAATATATTATATATATATATA
2073689 TATA
1 TATA
2073693 ATTTATACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 20 0.74
27 7 0.26
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
TATATAATATATTATATATATATATA
Found at i:2073672 original size:24 final size:24
Alignment explanation
Indices: 2073634--2073694 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
2073624 TACAGCATAA
2073634 ATTTATAT-TAT-ATAT-TTATAT
1 ATTTATATATATAATATATTATAT
2073655 ATATTATATATATAATATATTATAT
1 AT-TTATATATATAATATATTATAT
*
2073680 ATCTATATATATAAT
1 ATTTATATATATAAT
2073695 TTATACATCT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
21 2 0.06
22 6 0.17
23 3 0.09
24 16 0.46
25 8 0.23
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTTATATATATAATATATTATAT
Found at i:2080573 original size:16 final size:17
Alignment explanation
Indices: 2080545--2080589 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
2080535 TTGGACACTA
2080545 TTATATTAATTTC-AGT
1 TTATATTAATTTCTAGT
2080561 TTAT-TTAACTTTCTAGT
1 TTATATTAA-TTTCTAGT
*
2080578 TTAAATTAATTT
1 TTATATTAATTT
2080590 TTATGATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 4 0.16
16 8 0.32
17 9 0.36
18 4 0.16
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.58
Consensus pattern (17 bp):
TTATATTAATTTCTAGT
Found at i:2097338 original size:20 final size:19
Alignment explanation
Indices: 2097312--2097357 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
2097302 TATGTTATGG
2097312 ATTGAGAGGAAAAGAAGAGA
1 ATTGAGAGGAAAA-AAGAGA
* *
2097332 TTTGAGA-GAAGAAAGAGA
1 ATTGAGAGGAAAAAAGAGA
2097350 ATTGAGAG
1 ATTGAGAG
2097358 ATAAGAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 12 0.55
19 4 0.18
20 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (19 bp):
ATTGAGAGGAAAAAAGAGA
Found at i:2104506 original size:3 final size:3
Alignment explanation
Indices: 2104498--2104554 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
2104488 TATATTAAAA
2104498 AAT AAT AAT -AT AAT AAT AAT -AT AAT AAT AAT -AT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* *
2104541 ATT AAT AGT AAT AA
1 AAT AAT AAT AAT AA
2104555 ATATAAAGGG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 6 0.13
3 37 0.80
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2104514 original size:11 final size:11
Alignment explanation
Indices: 2104498--2104557 Score: 86
Period size: 11 Copynumber: 5.4 Consensus size: 11
2104488 TATATTAAAA
2104498 AATAATAATAT
1 AATAATAATAT
2104509 AATAATAATAT
1 AATAATAATAT
2104520 AATAATAATAT
1 AATAATAATAT
2104531 AATAATAAATATT
1 AATAAT-AATA-T
*
2104544 AATAGTAATA-
1 AATAATAATAT
2104554 AATA
1 AATA
2104558 TAAAGGGGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
10 4 0.09
11 28 0.61
12 8 0.17
13 6 0.13
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
AATAATAATAT
Found at i:2104982 original size:38 final size:39
Alignment explanation
Indices: 2104936--2105012 Score: 147
Period size: 38 Copynumber: 2.0 Consensus size: 39
2104926 TGATTTGAAA
2104936 GTAAGCTTCAGAAAACAGAGAGAAAA-CCGAAGCGATTT
1 GTAAGCTTCAGAAAACAGAGAGAAAATCCGAAGCGATTT
2104974 GTAAGCTTCAGAAAACAGAGAGAAAATCCGAAGCGATTT
1 GTAAGCTTCAGAAAACAGAGAGAAAATCCGAAGCGATTT
2105013 AAGTACCTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 26 0.68
39 12 0.32
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (39 bp):
GTAAGCTTCAGAAAACAGAGAGAAAATCCGAAGCGATTT
Found at i:2107296 original size:19 final size:20
Alignment explanation
Indices: 2107272--2107318 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
2107262 AAAGTTCGCT
*
2107272 AAAATATAAAAAT-AAAACG
1 AAAATATAAAAATAAAAACA
2107291 AAAATA-AAAAATAAAAACA
1 AAAATATAAAAATAAAAACA
2107310 AAAATATAA
1 AAAATATAA
2107319 CGAAATGAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 6 0.24
19 17 0.68
20 2 0.08
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (20 bp):
AAAATATAAAAATAAAAACA
Found at i:2112502 original size:21 final size:22
Alignment explanation
Indices: 2112469--2112509 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2112459 GGTTAAAATA
2112469 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
2112491 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
2112510 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:2112980 original size:12 final size:12
Alignment explanation
Indices: 2112965--2112994 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2112955 AAAAGTATGC
2112965 GAAAAATAGAGA
1 GAAAAATAGAGA
*
2112977 GAAAACTAGAGA
1 GAAAAATAGAGA
2112989 GAAAAA
1 GAAAAA
2112995 GAAGATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:2113216 original size:76 final size:76
Alignment explanation
Indices: 2113136--2113281 Score: 215
Period size: 76 Copynumber: 1.9 Consensus size: 76
2113126 CTAAAATACC
* * *
2113136 TAAAA-AAAATAATATAATATTCTATATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAAT
1 TAAAATAAAA-AA-ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAAT
2113199 ACAAAGAAAGAGA
64 ACAAAGAAAGAGA
* *
2113212 TAAAATATAAAAATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATAC
1 TAAAATAAAAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAC
2113277 AAAGA
66 AAAGA
2113282 TAAAATATAA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
75 25 0.40
76 35 0.56
77 3 0.05
ACGTcount: A:0.59, C:0.11, G:0.03, T:0.27
Consensus pattern (76 bp):
TAAAATAAAAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAC
AAAGAAAGAGA
Found at i:2117217 original size:2 final size:2
Alignment explanation
Indices: 2117210--2117242 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2117200 TGTTAACTTG
2117210 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 T
2117243 CAAACTCAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2121050 original size:28 final size:28
Alignment explanation
Indices: 2121016--2121069 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
2121006 ATAAATTGTG
2121016 GAAAATTAAAGTACTTCGTTTGGTGGAT
1 GAAAATTAAAGTACTTCGTTTGGTGGAT
*
2121044 GAAAATTAAAGTACTTTGTTTGGTGG
1 GAAAATTAAAGTACTTCGTTTGGTGG
2121070 GAGGGCAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (28 bp):
GAAAATTAAAGTACTTCGTTTGGTGGAT
Found at i:2124842 original size:142 final size:142
Alignment explanation
Indices: 2124586--2124868 Score: 530
Period size: 142 Copynumber: 2.0 Consensus size: 142
2124576 ATGTTGGGGG
*
2124586 AAATCTGAGTTAGATATGTATCTTGAAGCACCTTGTGAAAAAAGAGATGATGAGGCTTTTGATAT
1 AAATCTGAGTTAGATATGTATCTTGAAGCACCTCGTGAAAAAAGAGATGATGAGGCTTTTGATAT
2124651 TTTGAAATGGTGGAGTCTTAAGAGTAATGCATATAAGGTTTTGGCATTAATGGCAAAGGATATTC
66 TTTGAAATGGTGGAGTCTTAAGAGTAATGCATATAAGGTTTTGGCATTAATGGCAAAGGATATTC
2124716 TTGCTATACCAA
131 TTGCTATACCAA
2124728 AAATCTGAGTTAGATATGTATCTTGAAGCACCTCGTGAAAAAAGAGATGATGAGGCTTTTGATAT
1 AAATCTGAGTTAGATATGTATCTTGAAGCACCTCGTGAAAAAAGAGATGATGAGGCTTTTGATAT
* *
2124793 TTTGAAATGGTGGAGTCTTAAGAGTAATGCATATAAGGTTTTGGTATTAATGGCGAAGGATATTC
66 TTTGAAATGGTGGAGTCTTAAGAGTAATGCATATAAGGTTTTGGCATTAATGGCAAAGGATATTC
*
2124858 TTGTTATACCA
131 TTGCTATACCA
2124869 GTTTCGACAG
Statistics
Matches: 137, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 137 1.00
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.34
Consensus pattern (142 bp):
AAATCTGAGTTAGATATGTATCTTGAAGCACCTCGTGAAAAAAGAGATGATGAGGCTTTTGATAT
TTTGAAATGGTGGAGTCTTAAGAGTAATGCATATAAGGTTTTGGCATTAATGGCAAAGGATATTC
TTGCTATACCAA
Found at i:2126598 original size:23 final size:23
Alignment explanation
Indices: 2126572--2126632 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
2126562 CAGTTCATAT
*
2126572 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
2126595 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
2126618 AATTGCACCGTAGTG
1 AATTGCACCGAAGTG
2126633 TCATATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:2126786 original size:103 final size:102
Alignment explanation
Indices: 2126651--2126867 Score: 389
Period size: 103 Copynumber: 2.1 Consensus size: 102
2126641 TAATGTCCAT
*
2126651 AAGGACCACATATCATCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAG
1 AAGGACCACATATCATCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAG
*
2126716 ACCTCACACATGTTCCAAAGAATACATATATGCCCCG
66 ACCTCACACATGTTCCAAAGAATACATATATACCCCG
*
2126753 AATGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCA-TCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
2126818 GACCTCACACATGTTCCAAAGAATACATATATATCCCG
65 GACCTCACACATGTTCCAAAGAATACATATATACCCCG
2126856 AAGGACCACATA
1 AAGGACCACATA
2126868 GACCCTCTAC
Statistics
Matches: 109, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
102 14 0.13
103 95 0.87
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (102 bp):
AAGGACCACATATCATCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAG
ACCTCACACATGTTCCAAAGAATACATATATACCCCG
Found at i:2127388 original size:19 final size:20
Alignment explanation
Indices: 2127351--2127388 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2127341 TTTTTCATTA
*
2127351 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
2127371 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
2127389 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:2127440 original size:21 final size:21
Alignment explanation
Indices: 2127416--2127458 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2127406 TCATATTCAT
* *
2127416 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
2127437 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
2127458 T
1 T
2127459 AGCCCATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:2131323 original size:23 final size:21
Alignment explanation
Indices: 2131279--2131354 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 21
2131269 GTGGGGGGGT
2131279 ATCGATTCCCTCAAGGAGGGA
1 ATCGATTCCCTCAAGGAGGGA
2131300 ATCGATTCCCATTCAAAGGA-GGA
1 ATCGATTCCC--TC-AAGGAGGGA
* * * *
2131323 ATCGGTTCCCTTATGG-GGGT
1 ATCGATTCCCTCAAGGAGGGA
2131343 ATCGATTCCCTC
1 ATCGATTCCCTC
2131355 TGCCAAATGT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 15 0.33
21 11 0.24
23 14 0.31
24 5 0.11
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (21 bp):
ATCGATTCCCTCAAGGAGGGA
Found at i:2139448 original size:2 final size:2
Alignment explanation
Indices: 2139436--2139471 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2139426 GAGAATTGAA
* *
2139436 AT AT AT GT AT AT AT AT GT 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
2139472 TCCTATACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2139451 original size:10 final size:10
Alignment explanation
Indices: 2139436--2139471 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
2139426 GAGAATTGAA
2139436 ATATATGTAT
1 ATATATGTAT
2139446 ATATATGTAT
1 ATATATGTAT
*
2139456 ATATATATAT
1 ATATATGTAT
2139466 ATATAT
1 ATATAT
2139472 TCCTATACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (10 bp):
ATATATGTAT
Found at i:2155942 original size:20 final size:20
Alignment explanation
Indices: 2155917--2155962 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2155907 TTTCTGAGTG
*
2155917 ATGTTGGAGAACTCTTTCAC
1 ATGTTGGACAACTCTTTCAC
2155937 ATGTTGGACAACTCTTTCAC
1 ATGTTGGACAACTCTTTCAC
2155957 ATGTTG
1 ATGTTG
2155963 AATAACTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (20 bp):
ATGTTGGACAACTCTTTCAC
Found at i:2155969 original size:20 final size:20
Alignment explanation
Indices: 2155926--2155969 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2155916 GATGTTGGAG
*
2155926 AACTCTTTCACATGTTGGAC
1 AACTCTTTCACATGTTGAAC
*
2155946 AACTCTTTCACATGTTGAAT
1 AACTCTTTCACATGTTGAAC
2155966 AACT
1 AACT
2155970 TTCATTACTG
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:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (20 bp):
AACTCTTTCACATGTTGAAC
Found at i:2156446 original size:22 final size:23
Alignment explanation
Indices: 2156398--2156446 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
2156388 AATTAAAGTG
2156398 TGACTATAATAGCTACTAAAAAATT
1 TGACTATAATAGCTACT--AAAATT
*
2156423 TGACTATAATATCTACT-AAATT
1 TGACTATAATAGCTACTAAAATT
2156445 TG
1 TG
2156447 TGTGAAGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
25 16 0.70
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (23 bp):
TGACTATAATAGCTACTAAAATT
Found at i:2158477 original size:21 final size:21
Alignment explanation
Indices: 2158451--2158491 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
2158441 TTGTAAGTTG
2158451 GTGGAAGCATGGTATGCTATA
1 GTGGAAGCATGGTATGCTATA
2158472 GTGGAAGCATGGTATGCTAT
1 GTGGAAGCATGGTATGCTAT
2158492 TATTAACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.10, G:0.34, T:0.29
Consensus pattern (21 bp):
GTGGAAGCATGGTATGCTATA
Found at i:2161187 original size:29 final size:29
Alignment explanation
Indices: 2161145--2161202 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
2161135 CAGTACCGGG
2161145 GGTAGGTCGCCATGCACGCCCAGCGACCT
1 GGTAGGTCGCCATGCACGCCCAGCGACCT
* *
2161174 GGTAGGTCGCCATGCATGCCCTGCGACCT
1 GGTAGGTCGCCATGCACGCCCAGCGACCT
2161203 ACCTCAACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.16, C:0.36, G:0.31, T:0.17
Consensus pattern (29 bp):
GGTAGGTCGCCATGCACGCCCAGCGACCT
Found at i:2161226 original size:10 final size:10
Alignment explanation
Indices: 2161213--2161323 Score: 63
Period size: 10 Copynumber: 11.1 Consensus size: 10
2161203 ACCTCAACCT
2161213 CCATGCACGC
1 CCATGCACGC
2161223 CCATGCACGC
1 CCATGCACGC
*
2161233 CCA-ACGAC-C
1 CCATGC-ACGC
*
2161242 TCCATGCATGC
1 -CCATGCACGC
*
2161253 CCAGGCACGC
1 CCATGCACGC
*
2161263 CCA-ACGAC-C
1 CCATGC-ACGC
*
2161272 TCCATGCACGG
1 -CCATGCACGC
2161283 CCATGCACGC
1 CCATGCACGC
*
2161293 CCA-ACGAC-C
1 CCATGC-ACGC
*
2161302 TCCATGCACGG
1 -CCATGCACGC
2161313 CCATGCACGC
1 CCATGCACGC
2161323 C
1 C
2161324 GGAGGTCACC
Statistics
Matches: 76, Mismatches: 13, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
9 6 0.08
10 66 0.87
11 4 0.05
ACGTcount: A:0.23, C:0.48, G:0.20, T:0.10
Consensus pattern (10 bp):
CCATGCACGC
Found at i:2161243 original size:30 final size:30
Alignment explanation
Indices: 2161209--2161323 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
2161199 ACCTACCTCA
2161209 ACCTCCATGCACGCCCATGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
* *
2161239 ACCTCCATGCATGCCCAGGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
*
2161269 ACCTCCATGCACGGCCATGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
*
2161299 ACCTCCATGCACGGCCATGCACGCC
1 ACCTCCATGCACGCCCATGCACGCC
2161324 GGAGGTCACC
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 80 1.00
ACGTcount: A:0.23, C:0.48, G:0.19, T:0.10
Consensus pattern (30 bp):
ACCTCCATGCACGCCCATGCACGCCCAACG
Found at i:2161584 original size:14 final size:14
Alignment explanation
Indices: 2161565--2161605 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
2161555 TTAATTATGT
2161565 ATGATTTGATAGTA
1 ATGATTTGATAGTA
2161579 ATGA-TT--TAGTA
1 ATGATTTGATAGTA
2161590 ATGATTTGATAGTA
1 ATGATTTGATAGTA
2161604 AT
1 AT
2161606 AATGAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 9 0.38
12 2 0.08
13 2 0.08
14 11 0.46
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.44
Consensus pattern (14 bp):
ATGATTTGATAGTA
Found at i:2161654 original size:11 final size:11
Alignment explanation
Indices: 2161638--2161706 Score: 50
Period size: 11 Copynumber: 7.1 Consensus size: 11
2161628 TATGATTTGA
2161638 TAGTAATGATT
1 TAGTAATGATT
2161649 TAGTAATGATT
1 TAGTAATGATT
*
2161660 T-GATGATGATT
1 TAG-TAATGATT
2161671 TA--AAT-A-T
1 TAGTAATGATT
2161678 T--TAATGATT
1 TAGTAATGATT
2161687 T-G--ATGATT
1 TAGTAATGATT
2161695 TAGTAATGATT
1 TAGTAATGATT
2161706 T
1 T
2161707 GATAATATCA
Statistics
Matches: 47, Mismatches: 2, Indels: 18
0.70 0.03 0.27
Matches are distributed among these distances:
7 5 0.11
8 9 0.19
9 5 0.11
10 1 0.02
11 27 0.57
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:2161679 original size:19 final size:21
Alignment explanation
Indices: 2161643--2161685 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
2161633 TTTGATAGTA
*
2161643 ATGATTTAGTAATGATTTGATG
1 ATGATTTAG-AATGATTTAATG
2161665 ATGATTTA-AAT-ATTTAATG
1 ATGATTTAGAATGATTTAATG
2161684 AT
1 AT
2161686 TTGATGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
20 3 0.15
22 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (21 bp):
ATGATTTAGAATGATTTAATG
Found at i:2161754 original size:26 final size:26
Alignment explanation
Indices: 2161698--2161889 Score: 159
Period size: 26 Copynumber: 7.6 Consensus size: 26
2161688 GATGATTTAG
*
2161698 TAATGATTTGATAAT-ATCAAATTATAG
1 TAATGATTTGATAATAATC--ATTATAA
2161725 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
2161751 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
2161777 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
2161800 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
2161823 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
2161849 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* *
2161875 AAATGATTTAATAAT
1 TAATGATTTGATAAT
2161890 GATTTAAATA
Statistics
Matches: 136, Mismatches: 18, Indels: 23
0.77 0.10 0.13
Matches are distributed among these distances:
21 4 0.03
22 3 0.02
23 12 0.09
24 7 0.05
25 8 0.06
26 82 0.60
27 17 0.12
28 3 0.02
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.43
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:2161765 original size:37 final size:36
Alignment explanation
Indices: 2161722--2161895 Score: 115
Period size: 37 Copynumber: 5.1 Consensus size: 36
2161712 TATCAAATTA
* *
2161722 TAGTAATGAT-TTGATAATAATCATTATAATAATGATT
1 TAGTAATAATATT-ATAAAAATCATT-TAATAATGATT
*
2161759 TAGTAATAATCATTATAAAAATGATTTAATAATGA-T
1 TAGTAATAAT-ATTATAAAAATCATTTAATAATGATT
* *
2161795 T--T-A-AATATT-T---AATGA-TT--TGATGATT
1 TAGTAATAATATTATAAAAATCATTTAATAATGATT
* * *
2161820 TAGTAATGAT-TTGATAATAATCATTATAGTAATGATT
1 TAGTAATAATATT-ATAAAAATCATT-TAATAATGATT
*
2161857 TAGTAATAATCATTATAAAAATGATTTAATAATGATT
1 TAGTAATAAT-ATTATAAAAATCATTTAATAATGATT
2161894 TA
1 TA
2161896 AATATTTAAT
Statistics
Matches: 108, Mismatches: 11, Indels: 36
0.70 0.07 0.23
Matches are distributed among these distances:
24 5 0.05
25 2 0.02
26 2 0.02
27 6 0.06
28 3 0.03
29 2 0.02
30 2 0.02
31 3 0.03
32 3 0.03
33 5 0.05
34 2 0.02
35 1 0.01
36 2 0.02
37 46 0.43
38 20 0.19
39 4 0.04
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.43
Consensus pattern (36 bp):
TAGTAATAATATTATAAAAATCATTTAATAATGATT
Found at i:2161782 original size:98 final size:95
Alignment explanation
Indices: 2161680--2161956 Score: 324
Period size: 98 Copynumber: 2.8 Consensus size: 95
2161670 TTAAATATTT
* *
2161680 AATGATTTGATGATTTAGTAATGATTTGATAATATCA-AATTATAGTAATGATTTGATAATAATC
1 AATGATTTAATGATTTA--AAT-ATTTAATAATATCATAATT-TAGTAATGATTTGATAATAATC
2161744 ATTATAATAATGATTTAGTAATAATCATTATAAA
62 ATTATAATAATGATTTAGTAATAATCATTATAAA
* * * *
2161778 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
1 AATGA-TT--TAATGATTTAAATATTTAATAATATCATAATTTAGTAATGATTTGATAATAATCA
*
2161843 TTATAGTAATGATTTAGTAATAATCATTATAAA
63 TTATAATAATGATTTAGTAATAATCATTATAAA
* * * *
2161876 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAAT-ATCA
1 AATGA-TT--TAATGATTTAAATATTTAATAATATCATAATTTAGTAATGATTTGATAATAATC-
*
2161940 AATTATAGTAATGATTT
62 -ATTATAATAATGATTT
2161957 GATAATTATT
Statistics
Matches: 166, Mismatches: 7, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
97 3 0.02
98 130 0.78
99 24 0.14
101 9 0.05
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.44
Consensus pattern (95 bp):
AATGATTTAATGATTTAAATATTTAATAATATCATAATTTAGTAATGATTTGATAATAATCATTA
TAATAATGATTTAGTAATAATCATTATAAA
Found at i:2161800 original size:125 final size:124
Alignment explanation
Indices: 2161653--2161889 Score: 397
Period size: 125 Copynumber: 1.9 Consensus size: 124
2161643 ATGATTTAGT
* *
2161653 AATGATTTGATGATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAAT-ATCA
1 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATC-
* *
2161717 AATTATAGTAATGATTT-GATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAA
65 -ATTATAGTAATGATTTAG-TAATAATCATTATAAAAATGATTTAATAATAATCATTATAAA
2161778 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
1 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
2161843 TTATAGTAATGATTTAGTAATAATCATTATAAAAATGATTTAATAAT
66 TTATAGTAATGATTTAGTAATAATCATTATAAAAATGATTTAATAAT
2161890 GATTTAAATA
Statistics
Matches: 106, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
124 44 0.42
125 59 0.56
126 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (124 bp):
AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
TTATAGTAATGATTTAGTAATAATCATTATAAAAATGATTTAATAATAATCATTATAAA
Found at i:2161896 original size:11 final size:12
Alignment explanation
Indices: 2161718--2161893 Score: 101
Period size: 12 Copynumber: 14.2 Consensus size: 12
2161708 ATAATATCAA
*
2161718 ATTATAGTAATG
1 ATTATAATAATG
*
2161730 ATTTGATAATAATC
1 A-TT-ATAATAATG
2161744 ATTATAATAATG
1 ATTATAATAATG
*
2161756 ATTTAGTAATAATC
1 A-TTA-TAATAATG
*
2161770 ATTATAAAAATG
1 ATTATAATAATG
2161782 ATT-TAATAATG
1 ATTATAATAATG
* *
2161793 ATT-TAAATATTTA
1 ATTAT-AATA-ATG
* * *
2161806 ATGAT-TTGATG
1 ATTATAATAATG
*
2161817 ATT-TAGTAATG
1 ATTATAATAATG
*
2161828 ATTTGATAATAATC
1 A-TT-ATAATAATG
*
2161842 ATTATAGTAATG
1 ATTATAATAATG
*
2161854 ATTTAGTAATAATC
1 A-TTA-TAATAATG
*
2161868 ATTATAAAAATG
1 ATTATAATAATG
2161880 ATT-TAATAATG
1 ATTATAATAATG
2161891 ATT
1 ATT
2161894 TAAATATTTA
Statistics
Matches: 125, Mismatches: 26, Indels: 27
0.70 0.15 0.15
Matches are distributed among these distances:
10 1 0.01
11 29 0.23
12 43 0.34
13 21 0.17
14 31 0.25
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.43
Consensus pattern (12 bp):
ATTATAATAATG
Found at i:2162083 original size:14 final size:14
Alignment explanation
Indices: 2162064--2162105 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
2162054 TTTAAATATT
2162064 TAATGATTTGATAC
1 TAATGATTTGATAC
2162078 TAATGA-TT--TAC
1 TAATGATTTGATAC
*
2162089 TAATTATTTGATAC
1 TAATGATTTGATAC
2162103 TAA
1 TAA
2162106 ACATCATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
11 8 0.33
12 2 0.08
13 2 0.08
14 12 0.50
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (14 bp):
TAATGATTTGATAC
Found at i:2164263 original size:15 final size:14
Alignment explanation
Indices: 2164240--2164270 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
2164230 TACAACACTA
2164240 AACTTTAATATAAT
1 AACTTTAATATAAT
2164254 AACTTATAATATAAT
1 AACTT-TAATATAAT
2164269 AA
1 AA
2164271 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:2164278 original size:16 final size:16
Alignment explanation
Indices: 2164245--2164291 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
2164235 CACTAAACTT
*
2164245 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
2164260 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
2164276 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
2164292 ACTTTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:2164667 original size:16 final size:18
Alignment explanation
Indices: 2164638--2164676 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
2164628 ACTAATTAAC
*
2164638 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
2164656 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
2164672 ATTTA
1 ATTTA
2164677 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:2164720 original size:16 final size:16
Alignment explanation
Indices: 2164682--2164731 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
2164672 ATTTACCTTA
2164682 TCTCCCTTT-CTTC-T
1 TCTCCCTTTCCTTCTT
**
2164696 TCTTACTTTCCTTCTT
1 TCTCCCTTTCCTTCTT
*
2164712 TCTCCCTTTCTTTCTT
1 TCTCCCTTTCCTTCTT
2164728 TCTC
1 TCTC
2164732 GGCTGCAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 7 0.24
15 4 0.14
16 18 0.62
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (16 bp):
TCTCCCTTTCCTTCTT
Found at i:2164941 original size:48 final size:49
Alignment explanation
Indices: 2164889--2165003 Score: 159
Period size: 49 Copynumber: 2.4 Consensus size: 49
2164879 TAGGATCACA
*
2164889 TGGCATGC-TGTAGGCATGCAGC-GGGAGCAGGAGCACGTGAAG-TTATCT
1 TGGCATGCATGCA-GCATGCAGCGGGGAGCAGGAGCACGTGAAGTTTAT-T
2164937 TGGCATGCATGCAGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTTATT
1 TGGCATGCATGCAGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTTATT
*
2164986 TGGC-TGCATG-TGCATGCA
1 TGGCATGCATGCAGCATGCA
2165004 TGGTCTCGGG
Statistics
Matches: 62, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
47 7 0.11
48 23 0.37
49 28 0.45
50 4 0.06
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (49 bp):
TGGCATGCATGCAGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTTATT
Found at i:2165220 original size:29 final size:29
Alignment explanation
Indices: 2165117--2165211 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
2165107 GCCAATAGAG
* **
2165117 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
2165146 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
2165175 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
2165204 AGGTCGCC
1 AGGTCGCC
2165212 CCGGCGTCCA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:2165314 original size:50 final size:50
Alignment explanation
Indices: 2165238--2165354 Score: 172
Period size: 50 Copynumber: 2.4 Consensus size: 50
2165228 CCCGAGACCA
2165238 TGCATG-C-ACATGCA-GCCAAATAAACTTCACGTGCTCCTGCTCCCCGC
1 TGCATGCCTACATGCATGCCAAATAAACTTCACGTGCTCCTGCTCCCCGC
*
2165285 TGCATGCCTGCATGCATGCCAAGAT-AACTTCACGTGCTCCTGCTCCCCGC
1 TGCATGCCTACATGCATGCCAA-ATAAACTTCACGTGCTCCTGCTCCCCGC
*
2165335 TGCTTGCCTACA-GCATGCCA
1 TGCATGCCTACATGCATGCCA
2165355 TGTGATCCTA
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
47 6 0.10
48 1 0.02
49 14 0.22
50 40 0.63
51 2 0.03
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (50 bp):
TGCATGCCTACATGCATGCCAAATAAACTTCACGTGCTCCTGCTCCCCGC
Found at i:2165765 original size:46 final size:48
Alignment explanation
Indices: 2165703--2165794 Score: 129
Period size: 46 Copynumber: 2.0 Consensus size: 48
2165693 TTCTATAGTT
2165703 AAAAAATAATTAATTAGTTTGTT-TT-GTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTT-TTGTTAGTTAAATAGTTAAGTTATATAA
*
2165748 AAAAAATTATTTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATAT
2165795 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
45 8 0.20
46 15 0.37
47 3 0.07
48 7 0.17
49 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATATAA
Found at i:2165870 original size:32 final size:32
Alignment explanation
Indices: 2165832--2165907 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 32
2165822 TTAGTTAGTA
2165832 AGTTTATTAGTAG-TATA-TTATAATGAAAAAAT
1 AGTTTATTAGTAGTTATAGTTAT-AT-AAAAAAT
*
2165864 AGTTTATTAGTTAGTTTTAGTTATATAAAAAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAAAT
*
2165897 ATTTTATTAGT
1 AGTTTATTAGT
2165908 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.28
33 19 0.49
34 5 0.13
35 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (32 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAAAT
Found at i:2165978 original size:16 final size:16
Alignment explanation
Indices: 2165946--2165992 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
2165936 TTTAAAAAGT
*
2165946 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
2165962 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
2165978 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
2165993 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:2165987 original size:15 final size:14
Alignment explanation
Indices: 2165967--2165997 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
2165957 GTTTATTAGT
2165967 TTATTATATTATAAG
1 TTATTATATTA-AAG
2165982 TTATTATATTAAAG
1 TTATTATATTAAAG
2165996 TT
1 TT
2165998 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:2168150 original size:14 final size:14
Alignment explanation
Indices: 2168131--2168172 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
2168121 ACAATGATGT
*
2168131 TTAGTATCAAATAA
1 TTAGTATCAAATCA
2168145 TTAG--T-AAATCA
1 TTAGTATCAAATCA
2168156 TTAGTATCAAATCA
1 TTAGTATCAAATCA
2168170 TTA
1 TTA
2168173 AATATTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
11 9 0.38
12 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (14 bp):
TTAGTATCAAATCA
Found at i:2168304 original size:27 final size:27
Alignment explanation
Indices: 2168274--2168536 Score: 103
Period size: 26 Copynumber: 9.7 Consensus size: 27
2168264 ATTAGTAATA
2168274 ATTATCAAATCATTACTATAATTTGAT
1 ATTATCAAATCATTACTATAATTTGAT
*
2168301 ATTATCAAATCATTACTAAATCAAATCATTAAAT
1 ATTATCAAATCATTACT--AT--AAT--TT-GAT
* * *
2168335 ATT-T-AAATCATTATTAAATCATTTTATAAT
1 ATTATCAAATCATTACT--AT-A-ATT-TGAT
2168365 GATTATACTAAATCATTACTATAA--TGATT
1 -ATTAT-C-AAATCATTACTATAATTTGA-T
2168394 ATTATCAAATCATTAC--T-A----A-
1 ATTATCAAATCATTACTATAATTTGAT
* * * **
2168413 ATCATCAAATCATTA-AATATTTAAAT
1 ATTATCAAATCATTACTATAATTTGAT
* **
2168439 CATTATTAAATCATTTTTATAA--TGATT
1 -ATTATCAAATCATTACTATAATTTGA-T
*
2168466 ATTA-CTAAATCATTATTATAA--TGATT
1 ATTATC-AAATCATTACTATAATTTGA-T
2168492 ATTATCAAATCATTACTATAATTTGAT
1 ATTATCAAATCATTACTATAATTTGAT
2168519 ATTATCAAATCATTACTA
1 ATTATCAAATCATTACTA
2168537 AATCATCAAA
Statistics
Matches: 187, Mismatches: 19, Indels: 60
0.70 0.07 0.23
Matches are distributed among these distances:
19 14 0.07
20 1 0.01
21 1 0.01
23 1 0.01
24 1 0.01
25 1 0.01
26 52 0.28
27 51 0.27
28 13 0.07
29 3 0.02
30 4 0.02
31 8 0.04
32 17 0.09
33 5 0.03
34 5 0.03
35 10 0.05
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (27 bp):
ATTATCAAATCATTACTATAATTTGAT
Found at i:2168321 original size:11 final size:11
Alignment explanation
Indices: 2168307--2168417 Score: 50
Period size: 11 Copynumber: 9.6 Consensus size: 11
2168297 TGATATTATC
2168307 AAATCATTACT
1 AAATCATTACT
* *
2168318 AAATCAAATCATT
1 AAATC--ATTACT
2168331 AAAT-ATT--T
1 AAATCATTACT
*
2168339 AAATCATTATT
1 AAATCATTACT
*
2168350 AAATCATT-TT
1 AAATCATTACT
*
2168360 ATAATGATTATACT
1 A-AATCA-T-TACT
2168374 AAATCATTACT
1 AAATCATTACT
* *
2168385 ATAATGATTATTAT
1 A-AATCATTA--CT
2168399 CAAATCATTACT
1 -AAATCATTACT
2168411 AAATCAT
1 AAATCAT
2168418 CAAATCATTA
Statistics
Matches: 77, Mismatches: 10, Indels: 26
0.68 0.09 0.23
Matches are distributed among these distances:
8 5 0.06
9 3 0.04
10 5 0.06
11 30 0.39
12 10 0.13
13 13 0.17
14 10 0.13
15 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.41
Consensus pattern (11 bp):
AAATCATTACT
Found at i:2168325 original size:43 final size:43
Alignment explanation
Indices: 2168277--2168416 Score: 110
Period size: 43 Copynumber: 3.1 Consensus size: 43
2168267 AGTAATAATT
2168277 ATCAAATCATTACTATAATTTGATATTATCAAATCATTACTAA
1 ATCAAATCATTACTATAATTTGATATTATCAAATCATTACTAA
* * *
2168320 ATCAAATCATTA-AAT-ATTTAAATCATTATTAAATCATTTTA-TAATGA
1 ATCAAATCATTACTATAATTT-GAT-ATTATCAAATCA--TTACT-A--A
2168367 TTATACTAAATCATTACTATAA--TGATTATTATCAAATCATTACTAA
1 --AT-C-AAATCATTACTATAATTTGA-TATTATCAAATCATTACTAA
2168413 ATCA
1 ATCA
2168417 TCAAATCATT
Statistics
Matches: 76, Mismatches: 6, Indels: 31
0.67 0.05 0.27
Matches are distributed among these distances:
41 4 0.05
42 5 0.07
43 24 0.32
44 3 0.04
45 4 0.05
46 1 0.01
47 1 0.01
48 4 0.05
49 3 0.04
50 13 0.17
51 11 0.14
52 2 0.03
53 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (43 bp):
ATCAAATCATTACTATAATTTGATATTATCAAATCATTACTAA
Found at i:2168352 original size:19 final size:19
Alignment explanation
Indices: 2168328--2168454 Score: 54
Period size: 19 Copynumber: 6.6 Consensus size: 19
2168318 AAATCAAATC
2168328 ATTAAATATTTAAATCATT
1 ATTAAATATTTAAATCATT
* * *
2168347 ATTAAATCATTT-TATAATG
1 ATTAAAT-ATTTAAATCATT
*
2168366 ATT--ATA-CTAAATCATT
1 ATTAAATATTTAAATCATT
2168382 ACTATAATGATTATTATCAAATCATT
1 A-T-TAA--A-TATT-T-AAATCATT
* *
2168408 ACTAAATCA-TCAAATC---
1 ATTAAAT-ATTTAAATCATT
2168424 ATTAAATATTTAAATCATT
1 ATTAAATATTTAAATCATT
2168443 ATTAAATCATTT
1 ATTAAAT-ATTT
2168455 TTATAATGAT
Statistics
Matches: 78, Mismatches: 12, Indels: 35
0.62 0.10 0.28
Matches are distributed among these distances:
15 2 0.03
16 18 0.23
17 3 0.04
18 1 0.01
19 26 0.33
20 8 0.10
21 2 0.03
22 3 0.04
23 2 0.03
24 3 0.04
25 1 0.01
26 9 0.12
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTAAATATTTAAATCATT
Found at i:2168410 original size:26 final size:26
Alignment explanation
Indices: 2168344--2168536 Score: 151
Period size: 26 Copynumber: 7.7 Consensus size: 26
2168334 TATTTAAATC
* *
2168344 ATTATTAAATCATT-TTATAATGATT
1 ATTATCAAATCATTACTATAATGATT
2168369 A-TA-CTAAATCATTACTATAATGATT
1 ATTATC-AAATCATTACTATAATGATT
* *
2168394 ATTATCAAATCATTACTA-AATCATCAA
1 ATTATCAAATCATTACTATAATGAT--T
* * *
2168421 ATCATTAAAT-ATT--TA-AATCATT
1 ATTATCAAATCATTACTATAATGATT
**
2168443 A-T-T-AAATCATTTTTATAATGATT
1 ATTATCAAATCATTACTATAATGATT
*
2168466 ATTA-CTAAATCATTATTATAATGATT
1 ATTATC-AAATCATTACTATAATGATT
2168492 ATTATCAAATCATTACTATAATTTGA-T
1 ATTATCAAATCATTACTATAA--TGATT
2168519 ATTATCAAATCATTACTA
1 ATTATCAAATCATTACTA
2168537 AATCATCAAA
Statistics
Matches: 140, Mismatches: 11, Indels: 32
0.77 0.06 0.17
Matches are distributed among these distances:
19 4 0.03
20 4 0.03
22 3 0.02
23 7 0.05
24 19 0.14
25 17 0.12
26 54 0.39
27 29 0.21
28 3 0.02
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (26 bp):
ATTATCAAATCATTACTATAATGATT
Found at i:2168414 original size:61 final size:60
Alignment explanation
Indices: 2168339--2168542 Score: 198
Period size: 61 Copynumber: 3.3 Consensus size: 60
2168329 TTAAATATTT
*
2168339 AAATCATTATTAAATCATTTTATAATGATTATACTAAATCATTACTATAATGATTATTATC
1 AAATCATTACTAAATCATTTTATAATGATTATA-TAAATCATTACTATAATGATTATTATC
*** * * * * * * *
2168400 AAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTA-AATCATTTTTAT-
1 AAATCATTACTAAATCATTTTAT-AATGATTATATAAATCATTACTATAATGATTATTATC
*
2168459 AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATTTGA-TATTA
1 AA--ATCATTACTAAATCATT-TTATAATGATTA-TAT-AAATCATTACTATAA--TGATTATTA
2168523 TC
59 TC
2168525 AAATCATTACTAAATCAT
1 AAATCATTACTAAATCAT
2168543 CAAATCATTA
Statistics
Matches: 110, Mismatches: 23, Indels: 17
0.73 0.15 0.11
Matches are distributed among these distances:
59 2 0.02
60 10 0.09
61 51 0.46
62 10 0.09
63 11 0.10
64 17 0.15
65 5 0.05
66 4 0.04
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (60 bp):
AAATCATTACTAAATCATTTTATAATGATTATATAAATCATTACTATAATGATTATTATC
Found at i:2168450 original size:46 final size:46
Alignment explanation
Indices: 2168301--2168453 Score: 140
Period size: 46 Copynumber: 3.3 Consensus size: 46
2168291 ATAATTTGAT
2168301 ATTATCAAATCATTACT-AA--ATCAAATCATTAAATATTTAAATC
1 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
* * * *
2168344 ATTATTAAATCATTTTA-TAATGATTATACTAAATCATT-ACTA--TAATGATT
1 ATTATCAAATCA--TTACTAA--ATCAT-C-AAATCATTAAATATTTAA--ATC
2168394 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
1 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
*
2168440 ATTATTAAATCATT
1 ATTATCAAATCATT
2168454 TTTATAATGA
Statistics
Matches: 87, Mismatches: 8, Indels: 27
0.71 0.07 0.22
Matches are distributed among these distances:
43 11 0.13
44 1 0.01
45 12 0.14
46 19 0.22
47 5 0.06
48 9 0.10
49 5 0.06
50 17 0.20
51 8 0.09
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (46 bp):
ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
Found at i:2168507 original size:37 final size:37
Alignment explanation
Indices: 2168434--2168509 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 37
2168424 ATTAAATATT
* * *
2168434 TAAATCATTATTAAATCATTTTTATAATGATTATTAC
1 TAAATCATTATTAAATCATTATTATAATAATCATTAC
* *
2168471 TAAATCATTATTATAATGATTATTATCA-AATCATTAC
1 TAAATCATTATTA-AATCATTATTATAATAATCATTAC
2168508 TA
1 TA
2168510 TAATTTGATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
37 22 0.67
38 11 0.33
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (37 bp):
TAAATCATTATTAAATCATTATTATAATAATCATTAC
Found at i:2168538 original size:125 final size:122
Alignment explanation
Indices: 2168344--2168578 Score: 384
Period size: 125 Copynumber: 1.9 Consensus size: 122
2168334 TATTTAAATC
*
2168344 ATTATTAAATCATTTTATAATGATTATACTAAATCATTACTATAATGATTATTATCAAATCATTA
1 ATTACTAAATCATTTTATAATGATTATACTAAATCATTACTATAATGATTATTATCAAATCATTA
* *
2168409 CTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATT
66 CTAAATCATCAAATCATTAAATATTTAAATCATCATCAAATCATTTTTATAATGATT
2168466 ATTACTAAATCATTATTATAATGATTATTA-TCAAATCATTACTATAATTTGA-TATTATCAAAT
1 ATTACTAAATCATT-TTATAATGATTA-TACT-AAATCATTACTATAA--TGATTATTATCAAAT
2168529 CATTACTAAATCATCAAATCATTAAATATTTAAATCATCATCAAATCATT
61 CATTACTAAATCATCAAATCATTAAATATTTAAATCATCATCAAATCATT
2168579 ACTAAATCAT
Statistics
Matches: 105, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
122 13 0.12
123 13 0.12
124 17 0.16
125 59 0.56
126 3 0.03
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (122 bp):
ATTACTAAATCATTTTATAATGATTATACTAAATCATTACTATAATGATTATTATCAAATCATTA
CTAAATCATCAAATCATTAAATATTTAAATCATCATCAAATCATTTTTATAATGATT
Found at i:2168539 original size:11 final size:11
Alignment explanation
Indices: 2168525--2168593 Score: 50
Period size: 11 Copynumber: 7.1 Consensus size: 11
2168515 TGATATTATC
2168525 AAATCATTACT
1 AAATCATTACT
2168536 AAATCA-T-C-
1 AAATCATTACT
2168544 AAATCA-T--T
1 AAATCATTACT
2168552 AAAT-ATT--T
1 AAATCATTACT
*
2168560 AAATCATCA-T
1 AAATCATTACT
2168570 CAAATCATTACT
1 -AAATCATTACT
2168582 AAATCATTACT
1 AAATCATTACT
2168593 A
1 A
2168594 TCAAATCATA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
7 1 0.02
8 17 0.34
9 3 0.06
10 2 0.04
11 26 0.52
12 1 0.02
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATCATTACT
Found at i:2168551 original size:98 final size:95
Alignment explanation
Indices: 2168280--2168509 Score: 317
Period size: 98 Copynumber: 2.4 Consensus size: 95
2168270 AATAATTATC
*
2168280 AAATCATTACTATAATTTGA-TATTATCAAATCATTACT-AA--ATCAAATCATTAAATATTTAA
1 AAATCATTACTATAA--TGATTATTATCAAATCATTACTAAATCATCAAATCATCAAATATTTAA
*
2168341 ATCATTATTAAATCA-TTTTATAATGATTATACT
64 ATC--TATCAAATCATTTTTATAATGATTATACT
*
2168374 AAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAAT
1 AAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATCAAATATTTAAAT
*
2168439 CATTATTAAATCATTTTTATAATGATTATTACT
66 C--TATCAAATCATTTTTATAATGATTA-TACT
*
2168472 AAATCATTATTATAATGATTATTATCAAATCATTACTA
1 AAATCATTACTATAATGATTATTATCAAATCATTACTA
2168510 TAATTTGATA
Statistics
Matches: 129, Mismatches: 1, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
92 3 0.02
93 18 0.14
94 17 0.13
96 36 0.28
97 14 0.11
98 41 0.32
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (95 bp):
AAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATCAAATATTTAAAT
CTATCAAATCATTTTTATAATGATTATACT
Found at i:2168555 original size:27 final size:22
Alignment explanation
Indices: 2168522--2168602 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 22
2168512 ATTTGATATT
2168522 ATCAAATCATTACTAAATCATC
1 ATCAAATCATTACTAAATCATC
2168544 AAATCATTAAAT-ATT--TAAATCATC
1 --ATC---AAATCATTACTAAATCATC
2168568 ATCAAATCATTACTAAATCATTAC
1 ATCAAATCATTACTAAATCA-T-C
2168592 TATCAAATCAT
1 -ATCAAATCAT
2168603 ACATAATTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 17
0.74 0.00 0.26
Matches are distributed among these distances:
19 4 0.08
20 3 0.06
22 10 0.21
23 1 0.02
24 13 0.27
25 10 0.21
26 3 0.06
27 4 0.08
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.35
Consensus pattern (22 bp):
ATCAAATCATTACTAAATCATC
Found at i:2168568 original size:19 final size:21
Alignment explanation
Indices: 2168546--2168602 Score: 55
Period size: 25 Copynumber: 2.6 Consensus size: 21
2168536 AAATCATCAA
*
2168546 ATCATTAAAT-ATT-TAAATC
1 ATCATCAAATCATTATAAATC
2168565 ATCATCAAATCATTACTAAATC
1 ATCATCAAATCATTA-TAAATC
2168587 ATTACTATCAAATCAT
1 A-T-C-ATCAAATCAT
2168603 ACATAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 9 0.29
20 3 0.10
22 7 0.23
23 1 0.03
24 1 0.03
25 10 0.32
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.37
Consensus pattern (21 bp):
ATCATCAAATCATTATAAATC
Done.