Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008526.1 Hibiscus syriacus cultivar Beakdansim tig00111398_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: 3043201
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 12
Found at i:1974312 original size:3 final size:3
Alignment explanation
Indices: 1974304--1974388 Score: 98
Period size: 3 Copynumber: 28.3 Consensus size: 3
1974294 ATATTAATTG
* * * * * * *
1974304 ATT ATT ATT ATT ATT ATT ATT ATA ATA ATA ATA ATA ATA ATA ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1974352 ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1974389 AATATATTAA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:1975858 original size:13 final size:13
Alignment explanation
Indices: 1975842--1975881 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
1975832 ATATAATAAA
1975842 TAAATATTTATTT
1 TAAATATTTATTT
*
1975855 TAAATAAATTATTT
1 TAAAT-ATTTATTT
1975869 T-AATATTTATTT
1 TAAATATTTATTT
1975881 T
1 T
1975882 TCAATATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:1978246 original size:31 final size:31
Alignment explanation
Indices: 1978208--1978335 Score: 123
Period size: 31 Copynumber: 4.1 Consensus size: 31
1978198 GAACCTTGGT
* *
1978208 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
1978239 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * *
1978270 TACTGTCTATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGTA
* * * *
1978301 ATTCTGTCCATATGTTCTGTAGAACATAGGTA
1 A-ACTGTCCATATGTCCCGAAGAACATAGGTA
1978333 AAC
1 AAC
1978336 CCTCGACTCT
Statistics
Matches: 75, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
30 1 0.01
31 50 0.67
32 23 0.31
33 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:1982482 original size:24 final size:22
Alignment explanation
Indices: 1982442--1982518 Score: 67
Period size: 24 Copynumber: 3.6 Consensus size: 22
1982432 GTGCAATTAA
1982442 TGCATCGATGCA---TAAGGAG
1 TGCATCGATGCACTGTAAGGAG
1982461 TGCATCGATGCACATGTTAAGG-G
1 TGCATCGATGCAC-TG-TAAGGAG
* *
1982484 ATGCATCGATTCACTGT-A-GAA
1 -TGCATCGATGCACTGTAAGGAG
1982505 TGCATCGATGCACT
1 TGCATCGATGCACT
1982519 TCAAGGGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 12 0.25
20 14 0.29
21 1 0.02
22 1 0.02
23 3 0.06
24 17 0.35
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTAAGGAG
Found at i:1983765 original size:22 final size:23
Alignment explanation
Indices: 1983737--1983779 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1983727 GTGACATAAT
1983737 CTACGTG-CTATGTGAAAATGAA
1 CTACGTGTCTATGTGAAAATGAA
*
1983759 CTACGTGTTTATGTGAAAATG
1 CTACGTGTCTATGTGAAAATG
1983780 TGAAATGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (23 bp):
CTACGTGTCTATGTGAAAATGAA
Found at i:1984025 original size:23 final size:23
Alignment explanation
Indices: 1983990--1984057 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1983980 AATCTTATAT
1983990 GGCACTTCAGTGCATTTCTACGC
1 GGCACTTCAGTGCATTTCTACGC
* * * *
1984013 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCAGTGCATTTCTACGC
*
1984036 GGCACTTCAGTGCATTTATACG
1 GGCACTTCAGTGCATTTCTACG
1984058 AGTTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (23 bp):
GGCACTTCAGTGCATTTCTACGC
Found at i:1993150 original size:27 final size:27
Alignment explanation
Indices: 1993095--1993151 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
1993085 CACTAACCTT
* *
1993095 AATAATAATAATAATAATAGTTTTATA
1 AATAATAATAATAATAATAATTTGATA
1993122 AATAATAATAA-AA-AATTAATTTGACTA
1 AATAATAATAATAATAA-TAATTTGA-TA
1993149 AAT
1 AAT
1993152 CATTCATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 2 0.08
26 8 0.31
27 16 0.62
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (27 bp):
AATAATAATAATAATAATAATTTGATA
Found at i:1993984 original size:19 final size:19
Alignment explanation
Indices: 1993917--1993990 Score: 51
Period size: 19 Copynumber: 3.8 Consensus size: 19
1993907 TTGTATGAAG
* *
1993917 TAAATATAA-ATAAAATTT
1 TAAATTTAACATAAAAATT
* * **
1993935 TAAAATGAACATAAAAAAAA
1 TAAATTTAACAT-AAAAATT
1993955 TAAATAATTAACATAAAAATT
1 TAAAT--TTAACATAAAAATT
*
1993976 TAAATTTAAAATAAA
1 TAAATTTAACATAAA
1993991 TACGTACCTA
Statistics
Matches: 41, Mismatches: 11, Indels: 7
0.69 0.19 0.12
Matches are distributed among these distances:
18 6 0.15
19 11 0.27
20 8 0.20
21 10 0.24
22 6 0.15
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (19 bp):
TAAATTTAACATAAAAATT
Found at i:1995295 original size:31 final size:31
Alignment explanation
Indices: 1995201--1995295 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 31
1995191 TTTTTAATTA
*
1995201 TAATCGAAATTATTATTAATTATATAAATTTT
1 TAATTGAAATTATTATTAATTAT-TAAATTTT
* * *
1995233 AAATTAAAACTTA-TACTAA-TA-T-AATATTT
1 TAATTGAAA-TTATTATTAATTATTAAAT-TTT
1995262 TAATTGAAATTATTATTAATTATTAAATTTT
1 TAATTGAAATTATTATTAATTATTAAATTTT
1995293 TAA
1 TAA
1995296 AATAAATAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
28 6 0.12
29 16 0.32
30 2 0.04
31 9 0.18
32 14 0.28
33 3 0.06
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.48
Consensus pattern (31 bp):
TAATTGAAATTATTATTAATTATTAAATTTT
Found at i:1996015 original size:2 final size:2
Alignment explanation
Indices: 1996010--1996036 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1996000 TAAAAAAATA
1996010 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 A
1996037 AAGTAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1996147 original size:28 final size:32
Alignment explanation
Indices: 1996115--1996174 Score: 74
Period size: 34 Copynumber: 1.9 Consensus size: 32
1996105 TATTGATTAA
1996115 AAATA-AAAAA-TT-AA-TTTGATATAAATAT
1 AAATACAAAAATTTAAAGTTTGATATAAATAT
1996143 AAATACTAAAAATTTGAAAGTTTGATATAAAT
1 AAATAC-AAAAATTT-AAAGTTTGATATAAAT
1996175 GAATTAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
28 5 0.19
30 5 0.19
31 2 0.08
33 2 0.08
34 12 0.46
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.35
Consensus pattern (32 bp):
AAATACAAAAATTTAAAGTTTGATATAAATAT
Found at i:2000743 original size:60 final size:60
Alignment explanation
Indices: 2000650--2000772 Score: 169
Period size: 60 Copynumber: 2.0 Consensus size: 60
2000640 GTATATACAT
* *
2000650 ATAGTTCGGAATGAAATTGGAATGTTAAAAAAGTTTGAGGACTAATTTAGAATGA-AGGTC
1 ATAGTTCGGAATGAAATTGAAATGTTAAAAAAGTTTAAGGACTAATTTAGAATGATA-GTC
* * *
2000710 ATAGTTCGAGGATGAACTTGAAATGTT-CAAAAGTTTAAGGACTAATTTAGAATGATAGTC
1 ATAGTTCG-GAATGAAATTGAAATGTTAAAAAAGTTTAAGGACTAATTTAGAATGATAGTC
2000770 ATA
1 ATA
2000773 ATTTAAGGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
60 40 0.71
61 16 0.29
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.31
Consensus pattern (60 bp):
ATAGTTCGGAATGAAATTGAAATGTTAAAAAAGTTTAAGGACTAATTTAGAATGATAGTC
Found at i:2000802 original size:60 final size:60
Alignment explanation
Indices: 2000660--2000841 Score: 167
Period size: 60 Copynumber: 3.0 Consensus size: 60
2000650 ATAGTTCGGA
* * * * * *
2000660 ATGAAATTGGAATGTTAAAAAAGTTTGAGGACTAATTTAGAATGA-AGGTCATAGTTCGAGG
1 ATGAACTTGAAATGTT-CAAAAGTTTAAGGACTAATTTAGAATGATA-GTCATAATTTGAGG
*
2000721 ATGAACTTGAAATGTTCAAAAGTTTAAGGACTAATTTAGAATGATAGTCATAATTTAAGG
1 ATGAACTTGAAATGTTCAAAAGTTTAAGGACTAATTTAGAATGATAGTCATAATTTGAGG
* * * * *
2000781 ATGCAA-TTGGAACAT-TT-AAAAGTTTAGGGAGC-AATTTAAAATAATGGTCATACTTTGAGG
1 ATG-AACTT-GAA-ATGTTCAAAAGTTTAAGGA-CTAATTTAGAATGATAGTCATAATTTGAGG
2000841 A
1 A
2000842 GATATGAATG
Statistics
Matches: 103, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
60 78 0.76
61 23 0.22
62 2 0.02
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (60 bp):
ATGAACTTGAAATGTTCAAAAGTTTAAGGACTAATTTAGAATGATAGTCATAATTTGAGG
Found at i:2016403 original size:17 final size:17
Alignment explanation
Indices: 2016377--2016439 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
2016367 ACAATTATTT
2016377 AAAT-TAAAAATATATA
1 AAATATAAAAATATATA
2016393 AAATATAAAAAT-TATTA
1 AAATATAAAAATATA-TA
* ** * *
2016410 AGATAT-TCAATACATT
1 AAATATAAAAATATATA
2016426 AAATATAAAAATAT
1 AAATATAAAAATAT
2016440 TACAAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 7
0.68 0.18 0.14
Matches are distributed among these distances:
16 15 0.44
17 19 0.56
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (17 bp):
AAATATAAAAATATATA
Found at i:2016439 original size:24 final size:25
Alignment explanation
Indices: 2016401--2016468 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 25
2016391 TAAAATATAA
*
2016401 AAATTATT-AAGATATTCAATACATT
1 AAATTATTAAAAATATTCAATA-ATT
2016426 AAA-TA-TAAAAATATTACAA-AATT
1 AAATTATTAAAAATATT-CAATAATT
2016449 AAATTATTAAAAA-A-TCAATA
1 AAATTATTAAAAATATTCAATA
2016469 TAAGAATCAC
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
22 3 0.08
23 9 0.24
24 13 0.35
25 12 0.32
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.34
Consensus pattern (25 bp):
AAATTATTAAAAATATTCAATAATT
Found at i:2018118 original size:37 final size:38
Alignment explanation
Indices: 2018033--2018119 Score: 101
Period size: 37 Copynumber: 2.3 Consensus size: 38
2018023 ATTAAACATT
*
2018033 TTTTATATTTTTAATTTTATAAAAAATATTATATAAATA
1 TTTTATA-ATTTAATTTTATAAAAAATATTATATAAATA
*
2018072 --TTATGAATTTAATTTTTTAAAGAAA-A-TATATAAATA
1 TTTTAT-AATTTAATTTTATAAA-AAATATTATATAAATA
2018108 TTTTATAATTTA
1 TTTTATAATTTA
2018120 TAATATTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
36 10 0.24
37 24 0.57
38 8 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (38 bp):
TTTTATAATTTAATTTTATAAAAAATATTATATAAATA
Found at i:2018139 original size:18 final size:17
Alignment explanation
Indices: 2018094--2018142 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
2018084 TTTTTTAAAG
*
2018094 AAAATATATAAATATTTT
1 AAAATATAT-AATATTAT
* *
2018112 ATAATTTATAATATTAT
1 AAAATATATAATATTAT
2018129 ACAAATATATAATA
1 A-AAATATATAATA
2018143 AGGACAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATATATAATATTAT
Found at i:2018636 original size:2 final size:2
Alignment explanation
Indices: 2018629--2018660 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2018619 TTTCTTGTTA
2018629 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2018661 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2024670 original size:2 final size:2
Alignment explanation
Indices: 2024663--2024701 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
2024653 AATATTTGCT
2024663 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2024702 TTTCATACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2025213 original size:21 final size:20
Alignment explanation
Indices: 2025129--2025213 Score: 73
Period size: 20 Copynumber: 4.2 Consensus size: 20
2025119 AAATAACCAA
*
2025129 CAAATTCGCAACGCGAA-CTC
1 CAAATTCGCAACGC-AATTTC
* * *
2025149 CAATTTCGCAACACAGTTTC
1 CAAATTCGCAACGCAATTTC
* *
2025169 CAAATTCGCAAAGCGATTCTC
1 CAAATTCGCAACGCAATT-TC
*
2025190 CAAATTCGCAACGCTAATTAC
1 CAAATTCGCAACGC-AATTTC
2025211 CAA
1 CAA
2025214 TATAGGTAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
19 1 0.02
20 27 0.54
21 19 0.38
22 3 0.06
ACGTcount: A:0.35, C:0.31, G:0.12, T:0.22
Consensus pattern (20 bp):
CAAATTCGCAACGCAATTTC
Found at i:2025261 original size:58 final size:58
Alignment explanation
Indices: 2025190--2025313 Score: 230
Period size: 58 Copynumber: 2.1 Consensus size: 58
2025180 AGCGATTCTC
*
2025190 CAAATTCGCAACGCTAATTACCAATATAGGTAAACACAACTATTCGCAACTCAGTTTT
1 CAAATTCGCAACGCTAATTACCAATATAGGTAAACACAACTATTCACAACTCAGTTTT
*
2025248 CAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCACAACTCAGTTTT
1 CAAATTCGCAACGCTAATTACCAATATAGGTAAACACAACTATTCACAACTCAGTTTT
2025306 CAAATTCG
1 CAAATTCG
2025314 AAACTTAGTT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 64 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.27
Consensus pattern (58 bp):
CAAATTCGCAACGCTAATTACCAATATAGGTAAACACAACTATTCACAACTCAGTTTT
Found at i:2025318 original size:20 final size:20
Alignment explanation
Indices: 2025295--2025333 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2025285 AACTATTCAC
2025295 AACTCAGTTTTCAAATTCGA
1 AACTCAGTTTTCAAATTCGA
*
2025315 AACTTAGTTTTCAAATTCG
1 AACTCAGTTTTCAAATTCG
2025334 TAACGCGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (20 bp):
AACTCAGTTTTCAAATTCGA
Found at i:2025831 original size:58 final size:58
Alignment explanation
Indices: 2025738--2025872 Score: 207
Period size: 58 Copynumber: 2.3 Consensus size: 58
2025728 CAAAATTGGC
* * * *
2025738 TAATTCGTGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACTTATATCGG
1 TAATTCGCGTTGCGAATTTGAAAACTGAGTGGCGAATAGTTGTGTTTACCTATATCGA
*
2025796 TAATTCGCGTTGCGAATTTGAAAACTGAGTGGCGAATAGTTGTGTTTACCTATATTGA
1 TAATTCGCGTTGCGAATTTGAAAACTGAGTGGCGAATAGTTGTGTTTACCTATATCGA
* *
2025854 TAATTAGCGTTACGAATTT
1 TAATTCGCGTTGCGAATTT
2025873 CGAGAATCGC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 70 1.00
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (58 bp):
TAATTCGCGTTGCGAATTTGAAAACTGAGTGGCGAATAGTTGTGTTTACCTATATCGA
Found at i:2025950 original size:20 final size:21
Alignment explanation
Indices: 2025860--2025976 Score: 150
Period size: 21 Copynumber: 5.7 Consensus size: 21
2025850 TTGATAATTA
* *
2025860 GCGTTACGAATTTCGAGAATC
1 GCGTTGCGAATTTGGAGAATC
2025881 GCGTTGCGAATTTGGAGAATC
1 GCGTTGCGAATTTGGAGAATC
2025902 GCGTTGCGAATTTGGAGAATC
1 GCGTTGCGAATTTGGAGAATC
2025923 GCGTTGCGAATTTGGA-AA-C
1 GCGTTGCGAATTTGGAGAATC
* * *
2025942 TGTGTTGCGAAATTGGAG-TTC
1 -GCGTTGCGAATTTGGAGAATC
*
2025963 GTGTTGCGAATTTG
1 GCGTTGCGAATTTG
2025977 TTGGTTATTT
Statistics
Matches: 87, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
19 1 0.01
20 29 0.33
21 57 0.66
ACGTcount: A:0.23, C:0.14, G:0.32, T:0.32
Consensus pattern (21 bp):
GCGTTGCGAATTTGGAGAATC
Found at i:2026167 original size:2 final size:2
Alignment explanation
Indices: 2026160--2026191 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2026150 CTAAGATTTA
2026160 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
2026192 TCAAATATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2033825 original size:24 final size:24
Alignment explanation
Indices: 2033774--2033872 Score: 103
Period size: 24 Copynumber: 4.1 Consensus size: 24
2033764 CAAAATTTAG
* * *
2033774 GTCAAGTATTAGATTAGAATCCAA
1 GTCAAGTATCAGATCAGAATACAA
*
2033798 GTCAAGTATCAGATCAGAATACAC
1 GTCAAGTATCAGATCAGAATACAA
* *
2033822 GTC-AGATATCATATCAGAATTA-AT
1 GTCAAG-TATCAGATCAGAA-TACAA
*
2033846 GTCAAGTATCAGATCAGAATTCAA
1 GTCAAGTATCAGATCAGAATACAA
2033870 GTC
1 GTC
2033873 GAAAATCATA
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
23 3 0.05
24 55 0.89
25 4 0.06
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATACAA
Found at i:2033880 original size:24 final size:23
Alignment explanation
Indices: 2033754--2033872 Score: 96
Period size: 24 Copynumber: 5.0 Consensus size: 23
2033744 ATTCATATAA
* * * *
2033754 AATATCACATCAAAATTTAGGTC
1 AATATCAGATCAGAATTCAAGTC
* * *
2033777 AAGTATTAGATTAGAATCCAAGTC
1 AA-TATCAGATCAGAATTCAAGTC
* *
2033801 AAGTATCAGATCAGAATACACGTC
1 AA-TATCAGATCAGAATTCAAGTC
*
2033825 AGATATCATATCAGAATT-AATGTC
1 A-ATATCAGATCAGAATTCAA-GTC
2033849 AAGTATCAGATCAGAATTCAAGTC
1 AA-TATCAGATCAGAATTCAAGTC
2033873 GAAAATCATA
Statistics
Matches: 76, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
23 4 0.05
24 69 0.91
25 3 0.04
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (23 bp):
AATATCAGATCAGAATTCAAGTC
Found at i:2038279 original size:2 final size:2
Alignment explanation
Indices: 2038272--2038304 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2038262 TTTTTAAAAC
2038272 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2038305 CCCCCATCCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2038537 original size:24 final size:24
Alignment explanation
Indices: 2038510--2038663 Score: 112
Period size: 24 Copynumber: 6.4 Consensus size: 24
2038500 ATCAAAGCAT
2038510 AATTCATGTCAAATATCATATCAA
1 AATTCATGTCAAATATCATATCAA
* * * * * * *
2038534 AATTTAGGTCAAGTATTAGATTAG
1 AATTCATGTCAAATATCATATCAA
* * * *
2038558 AATCCAAGTCAAGTATCATATCAG
1 AATTCATGTCAAATATCATATCAA
* *
2038582 AATACATGTCAGATATCATATCAA
1 AATTCATGTCAAATATCATATCAA
* * * *
2038606 AATCCATGTCAAGTATCAGATCAG
1 AATTCATGTCAAATATCATATCAA
* *
2038630 AATTCAAGTCGAAA-ATCATATAAA
1 AATTCATGTC-AAATATCATATCAA
2038654 ATATTCATGT
1 A-ATTCATGT
2038664 GAGTAGGGAA
Statistics
Matches: 98, Mismatches: 30, Indels: 3
0.75 0.23 0.02
Matches are distributed among these distances:
24 89 0.91
25 9 0.09
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.31
Consensus pattern (24 bp):
AATTCATGTCAAATATCATATCAA
Found at i:2038648 original size:48 final size:47
Alignment explanation
Indices: 2038558--2038655 Score: 126
Period size: 48 Copynumber: 2.1 Consensus size: 47
2038548 ATTAGATTAG
* * *
2038558 AATCCAAGTCAAGTATCATATCAGAATACATGTCAGATATCATATCAA
1 AATCCAAGTCAAGTATCAGATCAGAATACAAGTCAGAAATCATAT-AA
* *
2038606 AATCCATGTCAAGTATCAGATCAGAATTCAAGTC-GAAAATCATATAA
1 AATCCAAGTCAAGTATCAGATCAGAATACAAGTCAG-AAATCATATAA
2038653 AAT
1 AAT
2038656 ATTCATGTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
47 6 0.14
48 38 0.86
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (47 bp):
AATCCAAGTCAAGTATCAGATCAGAATACAAGTCAGAAATCATATAA
Found at i:2038648 original size:72 final size:72
Alignment explanation
Indices: 2038514--2038650 Score: 186
Period size: 72 Copynumber: 1.9 Consensus size: 72
2038504 AAGCATAATT
** * * *
2038514 CATGTCAAATATCATATCAAAATTTAGGTCAAGTATTAGATTAGAATCCAAGTCAAGTATCATAT
1 CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGAATCATAT
2038579 CAGAATA
66 CAGAATA
* * *
2038586 CATGTCAGATATCATATCAAAATCCATGTCAAGTATCAGATCAGAATTCAAGTCGAA-AATCATA
1 CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTC-AAGAATCATA
2038650 T
65 T
2038651 AAAATATTCA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
72 54 0.96
73 2 0.04
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.29
Consensus pattern (72 bp):
CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGAATCATAT
CAGAATA
Found at i:2059476 original size:22 final size:25
Alignment explanation
Indices: 2059437--2059483 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 25
2059427 TTATATACAT
*
2059437 TTTCATATGAAAATAAATT-ATATA
1 TTTCATATGAAAAGAAATTAATATA
2059461 TTTCAT-T-AAAAGAAATTAATATA
1 TTTCATATGAAAAGAAATTAATATA
2059484 ATTAAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 6 0.29
24 6 0.29
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (25 bp):
TTTCATATGAAAAGAAATTAATATA
Found at i:2061682 original size:18 final size:18
Alignment explanation
Indices: 2061659--2061693 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2061649 GTGTCCGAAG
2061659 CGTGAGATTCGTCTGAAA
1 CGTGAGATTCGTCTGAAA
2061677 CGTGAGATTCGTCTGAA
1 CGTGAGATTCGTCTGAA
2061694 GCAAGTTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (18 bp):
CGTGAGATTCGTCTGAAA
Found at i:2064543 original size:172 final size:173
Alignment explanation
Indices: 2064248--2064606 Score: 569
Period size: 172 Copynumber: 2.1 Consensus size: 173
2064238 CATCAAATAT
*
2064248 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTTGCAATTTAATCACTAAATT
1 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
*
2064313 TATAAATTCTTTCAAATTTAACCAATTAAGCATATTAATACTAAATTCAAGCATAGTATACCAAC
66 TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
* * *
2064378 TTTTTATAATTTACTCTAATTTCTTAAATTCCTCAAATTTTGC
131 TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
* * *
2064421 AAAACGATCCCTAATTACTATTTGGTTCTCAACATTTTCAAAGTTAGCAATTTAATC-CATAAAT
1 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCAC-TAAAT
* * *
2064485 TT-TAAATTCTTTCTAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATAGCAA
65 TTATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAA
* *
2064549 CTTTTAATAATTTACTCTTATTCCTTAAATTCCTTAAATTTTAC
130 CTTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
*
2064593 AAAATGGTCCCTAA
1 AAAATGATCCCTAA
2064607 AACTTTACAA
Statistics
Matches: 170, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
172 110 0.65
173 60 0.35
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (173 bp):
AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
Found at i:2064851 original size:30 final size:30
Alignment explanation
Indices: 2064817--2064877 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2064807 CTATGCTTTG
2064817 TGATCAATCTCCCTCTCAAGCTCTCACTGC
1 TGATCAATCTCCCTCTCAAGCTCTCACTGC
2064847 TGATCAATCTCCCTCTCAAGCTCTCACTGC
1 TGATCAATCTCCCTCTCAAGCTCTCACTGC
2064877 T
1 T
2064878 TCTGTAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.20, C:0.39, G:0.10, T:0.31
Consensus pattern (30 bp):
TGATCAATCTCCCTCTCAAGCTCTCACTGC
Found at i:2065079 original size:23 final size:23
Alignment explanation
Indices: 2065053--2065096 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2065043 AGTTGCATGC
2065053 CCCCCACATGCAGACGTGCAGGA
1 CCCCCACATGCAGACGTGCAGGA
*
2065076 CCCCCACATGCAGATGTGCAG
1 CCCCCACATGCAGACGTGCAG
2065097 CCTTGCAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.39, G:0.25, T:0.11
Consensus pattern (23 bp):
CCCCCACATGCAGACGTGCAGGA
Found at i:2065141 original size:22 final size:22
Alignment explanation
Indices: 2065113--2065166 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
2065103 AGGACCCAGG
2065113 ACCCGTGATTTCTCCTTGCAGA
1 ACCCGTGATTTCTCCTTGCAGA
* *
2065135 ACCCGTGCTCTCTCCTTGCAGA
1 ACCCGTGATTTCTCCTTGCAGA
2065157 ACCCGTGATT
1 ACCCGTGATT
2065167 CTCACGTCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.17, C:0.35, G:0.19, T:0.30
Consensus pattern (22 bp):
ACCCGTGATTTCTCCTTGCAGA
Found at i:2066089 original size:20 final size:21
Alignment explanation
Indices: 2066058--2066111 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
2066048 GATTCTTGAC
2066058 AATCGCAATGCGATTTT-CAT
1 AATCGCAATGCGATTTTCCAT
* *
2066078 ATTCGCATTGCGATTTTCCAT
1 AATCGCAATGCGATTTTCCAT
*
2066099 AATCGCAACGCGA
1 AATCGCAATGCGA
2066112 ATATAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (21 bp):
AATCGCAATGCGATTTTCCAT
Found at i:2066124 original size:20 final size:20
Alignment explanation
Indices: 2066099--2066150 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2066089 GATTTTCCAT
* *
2066099 AATCGCAACGCGAATATAAA
1 AATCGCAACGCGAACACAAA
*
2066119 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACAAA
2066139 AATCGCAACGCG
1 AATCGCAACGCG
2066151 TATCCGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.27, G:0.17, T:0.12
Consensus pattern (20 bp):
AATCGCAACGCGAACACAAA
Found at i:2066160 original size:20 final size:20
Alignment explanation
Indices: 2066118--2066327 Score: 237
Period size: 20 Copynumber: 10.5 Consensus size: 20
2066108 GCGAATATAA
* *
2066118 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2066138 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2066158 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
2066178 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
2066198 AAATCGCAATGCGTATCTGT
1 AAATCGCAACGCGTATCCGT
*
2066218 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2066238 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
2066258 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
2066278 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
2066298 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
2066318 AAATCACAAC
1 AAATCGCAAC
2066328 ACTGAAATTT
Statistics
Matches: 164, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.01
20 161 0.98
21 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2067059 original size:24 final size:24
Alignment explanation
Indices: 2067020--2067066 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2067010 AAATTTGGTC
2067020 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2067044 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2067067 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2067258 original size:12 final size:12
Alignment explanation
Indices: 2067241--2067265 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2067231 ATATAATCCT
2067241 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2067253 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2067265 G
1 G
2067266 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2069604 original size:33 final size:34
Alignment explanation
Indices: 2069551--2069697 Score: 181
Period size: 33 Copynumber: 4.2 Consensus size: 34
2069541 CGGATATTAC
* * *
2069551 AATCGCAACGAGAGAATCGCAATAC-GAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGGAAATGAA
*
2069584 AATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGGAAATGAA
2069618 AATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAA
1 AATCGCAA--C--AA-GAAAATCGCAATGCGGAAATGAA
* *
2069656 AATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGGAAATGAA
2069690 AATCGCAA
1 AATCGCAA
2069698 TGCGAAATGA
Statistics
Matches: 100, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
33 34 0.34
34 32 0.32
36 2 0.02
38 18 0.18
39 14 0.14
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.13
Consensus pattern (34 bp):
AATCGCAACAAGAAAATCGCAATGCGGAAATGAA
Found at i:2069632 original size:53 final size:50
Alignment explanation
Indices: 2069551--2069801 Score: 244
Period size: 53 Copynumber: 4.8 Consensus size: 50
2069541 CGGATATTAC
* * *
2069551 AATCGCAACGAGAGAATCGCAATACGAAATGAAAATCCCAA-C-AA-GAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAAGCAAATGAA
2069598 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAAAATCGCAATGCGAAATGAAAATCGCAA-GC-AAATGAA
*
2069656 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGC-GAAATGAAAATCGCAA-GC-AAATGAA
* * *
2069709 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA-C-GA-GAG
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAAGCAAATGAA
2069756 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAA--C-G--A-GAAAATCGCAATGCGAAATGAAAATCGCA
2069802 TTGCGATTCT
Statistics
Matches: 179, Mismatches: 7, Indels: 30
0.83 0.03 0.14
Matches are distributed among these distances:
47 18 0.10
48 1 0.01
49 2 0.01
50 3 0.02
52 31 0.17
53 108 0.60
55 2 0.01
56 1 0.01
57 2 0.01
58 11 0.06
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (50 bp):
AATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAAGCAAATGAA
Found at i:2069652 original size:72 final size:72
Alignment explanation
Indices: 2069565--2069798 Score: 286
Period size: 72 Copynumber: 3.3 Consensus size: 72
2069555 GCAACGAGAG
*
2069565 AATCGCAATACGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
2069630 AAATGAA
66 AAATGAA
* * *
2069637 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
2069702 AAATGAA
66 AAATGAA
* * * * * * *
2069709 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAAAATCGCAA--C-G--A-GAGAATCGCAATG
1 AATCGCAATGCGA-AAT-GAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATG
2069766 CGGAAATGAA
64 C-GAAATGAA
2069776 AATCGCAATGCGAAATGAAAATC
1 AATCGCAATGCGAAATGAAAATC
2069799 GCATTGCGAT
Statistics
Matches: 140, Mismatches: 18, Indels: 14
0.81 0.10 0.08
Matches are distributed among these distances:
65 1 0.01
66 19 0.14
67 20 0.14
69 1 0.01
70 1 0.01
72 89 0.64
73 8 0.06
74 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:2069728 original size:14 final size:14
Alignment explanation
Indices: 2069709--2069763 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2069699 GCGAAATGAA
2069709 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2069723 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2069742 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2069756 AATCGCAA
1 AATCGCAA
2069764 TGCGGAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2069732 original size:33 final size:33
Alignment explanation
Indices: 2069690--2069783 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
2069680 CGGAAATGAA
2069690 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
2069723 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
2069756 AATCGCAATGCGGAAATGAAAATCGCAA
1 AATCGCAATGC-GAAATGAAAATCGCAA
2069784 TGCGAAATGA
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 44 0.73
34 16 0.27
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:2069746 original size:86 final size:89
Alignment explanation
Indices: 2069595--2069801 Score: 357
Period size: 86 Copynumber: 2.3 Consensus size: 89
2069585 ATCCCAACAA
2069595 GAAAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATC
1 GAAAATCGCAATGC-GAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAAATGAAAATC
2069660 GCAACGAGAGAATCGCAATGCGGAAAT
63 GCAACGAGAGAATCGCAATGCGGAAAT
*
2069687 GAAAATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAAATGAAAATCGCA
1 GAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAAATGAAAATCGCA
2069749 ACGAGAGAATCGCAATGCGGAAAT
66 ACGAGAGAATCGCAATGCGGAAAT
2069773 GAAAATCGCAATGCGAAATGAAAATCGCA
1 GAAAATCGCAATGCGAAATGAAAATCGCA
2069802 TTGCGATTCT
Statistics
Matches: 114, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
86 81 0.71
87 1 0.01
89 2 0.02
91 16 0.14
92 14 0.12
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.14
Consensus pattern (89 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAAATGAAAATCGCA
ACGAGAGAATCGCAATGCGGAAAT
Found at i:2069841 original size:53 final size:52
Alignment explanation
Indices: 2069778--2069893 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
2069768 GAAATGAAAA
*
2069778 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
2069830 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
2069883 TCGCATTGCGA
1 TCGCATTGCGA
2069894 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:2069856 original size:19 final size:19
Alignment explanation
Indices: 2069816--2069903 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
2069806 GATTCTCTCG
2069816 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2069836 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2069855 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2069869 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2069888 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2069904 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2070013 original size:14 final size:14
Alignment explanation
Indices: 2069994--2070030 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2069984 CATCAATTAC
2069994 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2070008 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2070022 ACAAATCAA
1 ACAAATCAA
2070031 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2071465 original size:21 final size:21
Alignment explanation
Indices: 2071435--2071493 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
2071425 GTGAATCGGG
2071435 CTCTTGAATGGTGGGAGTGAC
1 CTCTTGAATGGTGGGAGTGAC
* * ** *
2071456 CTCTTCAATGATGACAGTGGC
1 CTCTTGAATGGTGGGAGTGAC
*
2071477 CTCTTGAACGGTGGGAG
1 CTCTTGAATGGTGGGAG
2071494 GGGACTCTCG
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.34, T:0.27
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGTGAC
Found at i:2072086 original size:33 final size:33
Alignment explanation
Indices: 2071992--2072124 Score: 131
Period size: 33 Copynumber: 3.9 Consensus size: 33
2071982 ACGCGAAATG
*
2071992 AGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACC
1 AGAATCGCAACGCGAAACCAAAATCGCAA--CG--A-C
* * **
2072030 AAAATCACAACGCGAAATGAAAATCGCAACGAC
1 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
* * *
2072063 AGAATCGCAATGCGAAACCAAAATCGTAACGAG
1 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
**
2072096 AGAATCGCAACGCGAAATGAAAATCGCAA
1 AGAATCGCAACGCGAAACCAAAATCGCAA
2072125 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
33 52 0.66
34 1 0.01
36 2 0.03
38 24 0.30
ACGTcount: A:0.48, C:0.24, G:0.19, T:0.09
Consensus pattern (33 bp):
AGAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2072121 original size:52 final size:52
Alignment explanation
Indices: 2071991--2072129 Score: 147
Period size: 52 Copynumber: 2.7 Consensus size: 52
2071981 AACGCGAAAT
* * * *
2071991 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCACAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCACAACGA
* ** * **
2072043 GA-AAT-GAAAATCGCAACGACAGAATCGCAATGCGAAACCAAAATCGTAACGA
1 GAGAATCGCAACGCGAAACGA-A-AATCGCAATGCGAAACCAAAATCACAACGA
*
2072095 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
2072130 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 43 0.63
53 4 0.06
54 9 0.13
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.09
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCACAACGA
Found at i:2072122 original size:19 final size:19
Alignment explanation
Indices: 2071957--2072129 Score: 123
Period size: 19 Copynumber: 9.6 Consensus size: 19
2071947 TAGTTTACTT
* *
2071957 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
2071977 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
2071996 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
2072015 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
2072034 TCACAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2072053 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
* **
2072067 TCGCAATGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
* *
2072086 TCGTAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
2072100 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2072119 TCGCAATGCGA
1 TCGCAACGCGA
2072130 TTTTGGTTTC
Statistics
Matches: 122, Mismatches: 21, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
14 16 0.13
15 1 0.01
16 7 0.06
17 6 0.05
18 1 0.01
19 79 0.65
20 12 0.10
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2072160 original size:14 final size:14
Alignment explanation
Indices: 2072141--2072199 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
2072131 TTTGGTTTCG
2072141 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
2072155 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
2072172 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
2072188 CGTTGCGATTTT
1 CGTTGCGATTTT
2072200 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2072167 original size:33 final size:33
Alignment explanation
Indices: 2072125--2072248 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
2072115 AAAATCGCAA
*
2072125 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
2072158 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
2072191 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
2072224 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
2072249 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2072179 original size:19 final size:18
Alignment explanation
Indices: 2072125--2072216 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
2072115 AAAATCGCAA
2072125 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
2072144 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
2072158 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
2072177 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
2072191 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
2072210 TGCGATT
1 TGCGATT
2072217 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:2072226 original size:14 final size:14
Alignment explanation
Indices: 2072174--2072230 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2072164 TTTGGTTTCG
*
2072174 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
2072188 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2072207 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2072221 CGTTGCGATT
1 CGTTGCGATT
2072231 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2072507 original size:93 final size:93
Alignment explanation
Indices: 2072346--2072661 Score: 614
Period size: 93 Copynumber: 3.4 Consensus size: 93
2072336 TCAGGGTATT
2072346 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
2072411 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
2072439 AATTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
2072504 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
2072532 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
2072597 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
2072625 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
2072662 AAGCAATCTA
Statistics
Matches: 220, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 220 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:2074392 original size:20 final size:20
Alignment explanation
Indices: 2074361--2074457 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
2074351 TTTTGGTTGA
2074361 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
2074381 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
2074401 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
2074420 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
2074435 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
2074455 AAT
1 AAT
2074458 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:2074413 original size:21 final size:21
Alignment explanation
Indices: 2074359--2074423 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
2074349 TCTTTTGGTT
2074359 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
2074380 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
2074400 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
2074421 GAA
1 GAA
2074424 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:2074427 original size:14 final size:14
Alignment explanation
Indices: 2074408--2074464 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2074398 GAGAAATGAA
2074408 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2074422 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2074441 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2074455 AATCGCAACG
1 AATCGCAACG
2074465 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2074440 original size:33 final size:33
Alignment explanation
Indices: 2074359--2074481 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
2074349 TCTTTTGGTT
*
2074359 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
2074400 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2074433 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2074466 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2074482 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2074517 original size:14 final size:14
Alignment explanation
Indices: 2074498--2074554 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2074488 TTTGGTTTCG
2074498 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2074512 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2074531 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2074545 CGTTGCGATT
1 CGTTGCGATT
2074555 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2074530 original size:33 final size:33
Alignment explanation
Indices: 2074482--2074561 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
2074472 AAAATCGCAA
**
2074482 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2074515 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2074548 TGCGATTTTCATTT
1 TGCGATTTTCATTT
2074562 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2074567 original size:21 final size:21
Alignment explanation
Indices: 2074542--2074621 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
2074532 GTTGCGATTC
2074542 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
2074563 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
2074584 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
2074605 TCTCGTTGCGACTTTTC
1 TCTCGTTGCGA-TTTTC
2074622 TGCAAATTGA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
20 6 0.12
21 32 0.65
22 11 0.22
ACGTcount: A:0.14, C:0.21, G:0.16, T:0.49
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:2074737 original size:33 final size:33
Alignment explanation
Indices: 2074695--2074765 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2074685 AATACTAACT
2074695 TGAAAATCGCAACGAGAGAATAGCAACACGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACACGAAA
* * *
2074728 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACACGAAA
2074761 TGAAA
1 TGAAA
2074766 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACACGAAA
Found at i:2075174 original size:20 final size:20
Alignment explanation
Indices: 2075149--2075296 Score: 199
Period size: 20 Copynumber: 7.4 Consensus size: 20
2075139 AAAAATCGCA
2075149 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* *
2075169 TTGCGATATACGGATACGCA
1 TTGCGATTTACGGATACGCG
2075189 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
*
2075209 TTGCGATTTACGGATACACG
1 TTGCGATTTACGGATACGCG
2075229 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* *
2075249 TTGCGATTTATGTG-TTCGCG
1 TTGCGATTTACG-GATACGCG
* ** *
2075269 TTGCGATTTTCATATTCGCG
1 TTGCGATTTACGGATACGCG
2075289 TTGCGATT
1 TTGCGATT
2075297 ATGGAAAATC
Statistics
Matches: 114, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
20 113 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
TTGCGATTTACGGATACGCG
Found at i:2075314 original size:21 final size:20
Alignment explanation
Indices: 2075290--2075337 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2075280 ATATTCGCGT
2075290 TGCGATTATGGAAAATCGCAA
1 TGCGATTAT-GAAAATCGCAA
* *
2075311 TGCGAATATGAAAATCGCAT
1 TGCGATTATGAAAATCGCAA
2075331 TGCGATT
1 TGCGATT
2075338 GTCAAGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (20 bp):
TGCGATTATGAAAATCGCAA
Found at i:2087527 original size:21 final size:22
Alignment explanation
Indices: 2087487--2087539 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2087477 TTTTCCATAA
* *
2087487 TGCTACATGGGTATCGATAC-CC
1 TGCTACA-GTGTACCGATACTCC
*
2087509 TGCTACAGTGTACCGATACTCT
1 TGCTACAGTGTACCGATACTCC
2087531 TGCTACAGT
1 TGCTACAGT
2087540 AATTTCGTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (22 bp):
TGCTACAGTGTACCGATACTCC
Found at i:2088004 original size:28 final size:28
Alignment explanation
Indices: 2087982--2088079 Score: 187
Period size: 28 Copynumber: 3.5 Consensus size: 28
2087972 CACTTAACCT
2087982 TTGTAACATGTCATCTTGTACTTACCAA
1 TTGTAACATGTCATCTTGTACTTACCAA
2088010 TTGTAACATGTCATCTTGTACTTACCAA
1 TTGTAACATGTCATCTTGTACTTACCAA
2088038 TTGTAACATGTCATCTTGTACTTACCAA
1 TTGTAACATGTCATCTTGTACTTACCAA
*
2088066 TTGTAACATATCAT
1 TTGTAACATGTCAT
2088080 ATAATACATT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
28 69 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (28 bp):
TTGTAACATGTCATCTTGTACTTACCAA
Found at i:2088313 original size:31 final size:31
Alignment explanation
Indices: 2088270--2088370 Score: 159
Period size: 31 Copynumber: 3.3 Consensus size: 31
2088260 GCTCATATAA
*
2088270 TAATATGTCCATATGTCCCGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
*
2088301 TAA-CTTGTCCATATGTCCCAAAGAACATAGG
1 TAATC-TGTCCATATGTCCCGAAGAACATAGG
*
2088332 TAATCTATCCATATGTCCCGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
2088363 TAATCTGT
1 TAATCTGT
2088371 AACATATATA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
31 62 0.98
32 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (31 bp):
TAATCTGTCCATATGTCCCGAAGAACATAGG
Found at i:2088583 original size:31 final size:31
Alignment explanation
Indices: 2088545--2088667 Score: 201
Period size: 31 Copynumber: 4.0 Consensus size: 31
2088535 CCCGAAGGAC
* * *
2088545 CAGTCCATATGTCCCAAAGAACCTAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2088576 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2088607 CAGTCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2088638 CAATCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
2088668 CCCTTGACTA
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 86 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2091185 original size:30 final size:30
Alignment explanation
Indices: 2091116--2091173 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
2091106 AATTTAAGAT
2091116 AAAATGTTTTTGGACTTGAATTGAATTTGC
1 AAAATGTTTTTGGACTTGAATTGAATTTGC
*
2091146 AAAATGTTTTTGGATTTGAATTGAATTT
1 AAAATGTTTTTGGACTTGAATTGAATTT
2091174 ATTCAAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTGC
Found at i:2091270 original size:8 final size:8
Alignment explanation
Indices: 2091257--2091364 Score: 62
Period size: 8 Copynumber: 15.0 Consensus size: 8
2091247 GGTGTCAAAG
2091257 TGCATCCA
1 TGCATCCA
2091265 TGCATCCA
1 TGCATCCA
*
2091273 TGCATCCC
1 TGCATCCA
*
2091281 TGCA---G
1 TGCATCCA
2091286 TGCATCCA
1 TGCATCCA
*
2091294 TGCATCCC
1 TGCATCCA
2091302 TGCA---A
1 TGCATCCA
2091307 TGCATCCA
1 TGCATCCA
2091315 TGCAT-C-
1 TGCATCCA
*
2091321 TGCA-CTAA
1 TGCATC-CA
*
2091329 TGCATCGA
1 TGCATCCA
2091337 TGCAT-CA
1 TGCATCCA
2091344 TGCA---A
1 TGCATCCA
*
2091349 TGTATCCA
1 TGCATCCA
2091357 TGCATCCA
1 TGCATCCA
2091365 AACATCGAAT
Statistics
Matches: 77, Mismatches: 10, Indels: 26
0.68 0.09 0.23
Matches are distributed among these distances:
5 12 0.16
6 4 0.05
7 6 0.08
8 54 0.70
9 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (8 bp):
TGCATCCA
Found at i:2091333 original size:22 final size:20
Alignment explanation
Indices: 2091264--2091458 Score: 118
Period size: 21 Copynumber: 9.8 Consensus size: 20
2091254 AAGTGCATCC
*
2091264 ATGCATCCATGCATCCCTGCA
1 ATGCATCCATGCAT-CATGCA
* *
2091285 GTGCATCCATGCATCCCTGCA
1 ATGCATCCATGCAT-CATGCA
2091306 ATGCATCCATGCATC-TGCACTA
1 ATGCATCCATGCATCATG--C-A
*
2091328 ATGCATCGATGCATCATGCA
1 ATGCATCCATGCATCATGCA
*
2091348 ATGTATCCATGCATC---CA
1 ATGCATCCATGCATCATGCA
* * *
2091365 A-ACATCGAATGCA--AT-TA
1 ATGCATC-CATGCATCATGCA
* * * *
2091382 GTGCATCGATGCATCTTGCT
1 ATGCATCCATGCATCATGCA
* * *
2091402 ATGCATCGATGCATCCTTGCC
1 ATGCATCCATGCAT-CATGCA
* *
2091423 ATGCATCGATGCATCATGCC
1 ATGCATCCATGCATCATGCA
2091443 ATGCATCCATGCATCA
1 ATGCATCCATGCATCA
2091459 AGGCTGCAAC
Statistics
Matches: 143, Mismatches: 19, Indels: 25
0.76 0.10 0.13
Matches are distributed among these distances:
16 3 0.02
17 14 0.10
18 4 0.03
19 3 0.02
20 48 0.34
21 54 0.38
22 15 0.10
23 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (20 bp):
ATGCATCCATGCATCATGCA
Found at i:2091408 original size:20 final size:20
Alignment explanation
Indices: 2091383--2091457 Score: 114
Period size: 20 Copynumber: 3.7 Consensus size: 20
2091373 ATGCAATTAG
*
2091383 TGCATCGATGCATCTTGCTA
1 TGCATCGATGCATCTTGCCA
2091403 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCAT-CTTGCCA
*
2091424 TGCATCGATGCATCATGCCA
1 TGCATCGATGCATCTTGCCA
*
2091444 TGCATCCATGCATC
1 TGCATCGATGCATC
2091458 AAGGCTGCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
20 32 0.63
21 19 0.37
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (20 bp):
TGCATCGATGCATCTTGCCA
Found at i:2091860 original size:34 final size:32
Alignment explanation
Indices: 2091821--2091890 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
2091811 TTTTGTAAAG
* *
2091821 GGGAAAGGTTCTAGATTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGATTAGCCCG-G-AAAAACTA
*
2091855 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGATTAGCCCGGAAAAACTA
2091887 GGGA
1 GGGA
2091891 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGATTAGCCCGGAAAAACTA
Found at i:2092890 original size:14 final size:15
Alignment explanation
Indices: 2092865--2092893 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2092855 TGATGGTAAA
2092865 GGAAGATGAAGAAAG
1 GGAAGATGAAGAAAG
2092880 GGAAGAT-AAGAAAG
1 GGAAGATGAAGAAAG
2092894 AGGTAGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.38, T:0.07
Consensus pattern (15 bp):
GGAAGATGAAGAAAG
Found at i:2094750 original size:30 final size:30
Alignment explanation
Indices: 2094679--2094738 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2094669 ACAATTTAAG
2094679 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
2094709 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
2094739 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:2094835 original size:8 final size:8
Alignment explanation
Indices: 2094822--2094929 Score: 62
Period size: 8 Copynumber: 15.0 Consensus size: 8
2094812 GGTGTCAAAG
2094822 TGCATCCA
1 TGCATCCA
2094830 TGCATCCA
1 TGCATCCA
*
2094838 TGCATCCC
1 TGCATCCA
*
2094846 TGCA---G
1 TGCATCCA
2094851 TGCATCCA
1 TGCATCCA
*
2094859 TGCATCCC
1 TGCATCCA
2094867 TGCA---A
1 TGCATCCA
2094872 TGCATCCA
1 TGCATCCA
2094880 TGCAT-C-
1 TGCATCCA
*
2094886 TGCA-CTAA
1 TGCATC-CA
*
2094894 TGCATCGA
1 TGCATCCA
2094902 TGCAT-CA
1 TGCATCCA
2094909 TGCA---A
1 TGCATCCA
*
2094914 TGCATTCA
1 TGCATCCA
2094922 TGCATCCA
1 TGCATCCA
2094930 AAAATCGAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 26
0.69 0.08 0.23
Matches are distributed among these distances:
5 13 0.17
6 4 0.05
7 6 0.08
8 54 0.69
9 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (8 bp):
TGCATCCA
Found at i:2094854 original size:21 final size:21
Alignment explanation
Indices: 2094829--2094928 Score: 116
Period size: 21 Copynumber: 4.8 Consensus size: 21
2094819 AAGTGCATCC
2094829 ATGCATCCATGCATCCCTGCA
1 ATGCATCCATGCATCCCTGCA
*
2094850 GTGCATCCATGCATCCCTGCA
1 ATGCATCCATGCATCCCTGCA
2094871 ATGCATCCATGCAT--CTGCACTA
1 ATGCATCCATGCATCCCTG--C-A
* *
2094893 ATGCATCGATGCAT-CATGCA
1 ATGCATCCATGCATCCCTGCA
*
2094913 ATGCATTCATGCATCC
1 ATGCATCCATGCATCC
2094929 AAAAATCGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
19 3 0.04
20 13 0.19
21 36 0.53
22 14 0.21
23 2 0.03
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (21 bp):
ATGCATCCATGCATCCCTGCA
Found at i:2094917 original size:20 final size:20
Alignment explanation
Indices: 2094829--2095023 Score: 109
Period size: 21 Copynumber: 9.8 Consensus size: 20
2094819 AAGTGCATCC
*
2094829 ATGCATCCATGCATCCCTGCA
1 ATGCATCCATGCAT-CATGCA
* *
2094850 GTGCATCCATGCATCCCTGCA
1 ATGCATCCATGCAT-CATGCA
2094871 ATGCATCCATGCATC-TGCACTA
1 ATGCATCCATGCATCATG--C-A
*
2094893 ATGCATCGATGCATCATGCA
1 ATGCATCCATGCATCATGCA
*
2094913 ATGCATTCATGCATC---CA
1 ATGCATCCATGCATCATGCA
** * *
2094930 A-AAATCGAATGCA--AT-TA
1 ATGCATC-CATGCATCATGCA
* * * *
2094947 GTGCATCGATGCATCTTGCT
1 ATGCATCCATGCATCATGCA
* * *
2094967 ATGCATCGATGCATCCTTGCC
1 ATGCATCCATGCAT-CATGCA
* *
2094988 ATGCATCCATGCATCCTGCC
1 ATGCATCCATGCATCATGCA
2095008 ATGCATCCATGCATCA
1 ATGCATCCATGCATCA
2095024 AGGCTGCAAC
Statistics
Matches: 140, Mismatches: 22, Indels: 25
0.75 0.12 0.13
Matches are distributed among these distances:
16 2 0.01
17 14 0.10
18 3 0.02
19 3 0.02
20 48 0.34
21 53 0.38
22 15 0.11
23 2 0.01
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (20 bp):
ATGCATCCATGCATCATGCA
Found at i:2095426 original size:34 final size:32
Alignment explanation
Indices: 2095387--2095456 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
2095377 TTTTGTAAAG
* * *
2095387 GGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
2095421 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
2095453 GGGA
1 GGGA
2095457 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:2107723 original size:20 final size:20
Alignment explanation
Indices: 2107698--2107738 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2107688 GTTTTAGCTG
2107698 GATCCTACATAGATGCTTAT
1 GATCCTACATAGATGCTTAT
2107718 GATCCTACATAGATGCTTAT
1 GATCCTACATAGATGCTTAT
2107738 G
1 G
2107739 TTTTCTAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (20 bp):
GATCCTACATAGATGCTTAT
Found at i:2118409 original size:13 final size:14
Alignment explanation
Indices: 2118383--2118415 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2118373 TTTAAAACTA
2118383 TAAAAGTAT-TTTT
1 TAAAAGTATATTTT
*
2118396 TAAAATTATATTTT
1 TAAAAGTATATTTT
2118410 TAAAAG
1 TAAAAG
2118416 ATTCTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (14 bp):
TAAAAGTATATTTT
Found at i:2118411 original size:14 final size:13
Alignment explanation
Indices: 2118383--2118424 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2118373 TTTAAAACTA
2118383 TAAAAGTATTTTT
1 TAAAAGTATTTTT
*
2118396 TAAAATTATATTTT
1 TAAAAGTAT-TTTT
2118410 TAAAAG-ATTCTTT
1 TAAAAGTATT-TTT
2118423 TA
1 TA
2118425 TAAATCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 1 0.04
13 15 0.60
14 9 0.36
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (13 bp):
TAAAAGTATTTTT
Found at i:2125124 original size:20 final size:20
Alignment explanation
Indices: 2125099--2125230 Score: 115
Period size: 20 Copynumber: 6.5 Consensus size: 20
2125089 TGGGAAAATT
2125099 GCAATGCGATACTGACTATC
1 GCAATGCGATACTGACTATC
*
2125119 GCAATGCGATACTTACTATC
1 GCAATGCGATACTGACTATC
* *
2125139 GCAATGCGATAAT-ACAAAATC
1 GCAATGCGATACTGAC--TATC
* * *
2125160 GCAACGAGATACTGACTTTC
1 GCAATGCGATACTGACTATC
* * *
2125180 GCAACGCGATTCTGACTTTC
1 GCAATGCGATACTGACTATC
* *
2125200 GCAACGCGATAAT-ACATAATC
1 GCAATGCGATACTGAC-T-ATC
2125221 GCAATGCGAT
1 GCAATGCGAT
2125231 TTTCAAAGCG
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 63 0.68
21 24 0.26
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
GCAATGCGATACTGACTATC
Found at i:2125140 original size:61 final size:61
Alignment explanation
Indices: 2125106--2125224 Score: 175
Period size: 61 Copynumber: 2.0 Consensus size: 61
2125096 ATTGCAATGC
* * *
2125106 GATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATACAAAATCGCAACGA
1 GATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAAATCGCAACGA
* * * *
2125167 GATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATACATAATCGCAA
1 GATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAAATCGCAA
2125225 TGCGATTTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (61 bp):
GATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAAATCGCAACGA
Found at i:2125426 original size:22 final size:22
Alignment explanation
Indices: 2125398--2125441 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2125388 CACTCTCTCA
2125398 CCCATCTCCGACAAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
* *
2125420 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
2125442 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:2125739 original size:20 final size:20
Alignment explanation
Indices: 2125685--2125743 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2125675 GCGATTCTCT
**
2125685 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
2125705 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
2125725 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
2125744 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2125934 original size:25 final size:24
Alignment explanation
Indices: 2125880--2125934 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
2125870 TGTTTATTAT
* *
2125880 TGTTTTTGGTATATCTTCATAGTG
1 TGTTTTTGGTATATCTACATAGTA
*
2125904 TAGTTTTTGGTATATCTAACTTAGTA
1 T-GTTTTTGGTATATCT-ACATAGTA
2125930 TGTTT
1 TGTTT
2125935 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 19 0.73
26 6 0.23
ACGTcount: A:0.20, C:0.07, G:0.18, T:0.55
Consensus pattern (24 bp):
TGTTTTTGGTATATCTACATAGTA
Found at i:2127084 original size:18 final size:18
Alignment explanation
Indices: 2127063--2127107 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2127053 TCCATTTCGG
*
2127063 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
2127081 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2127099 GAGCCATCA
1 GAGCCATCA
2127108 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2127643 original size:19 final size:20
Alignment explanation
Indices: 2127589--2127655 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
2127579 TAGTTTACTT
* *
2127589 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2127609 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
2127629 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
2127648 TCGCAACG
1 TCGCAACG
2127656 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2127663 original size:14 final size:14
Alignment explanation
Indices: 2127644--2127716 Score: 92
Period size: 14 Copynumber: 4.9 Consensus size: 14
2127634 ATGCGAAATG
2127644 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2127658 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
2127677 AAAATCGCAACGAC
1 AAAATCGCAACGAC
2127691 AAAATCGCAACGAC
1 AAAATCGCAACGAC
2127705 AAAATCGCAACG
1 AAAATCGCAACG
2127717 CGAAATGAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 36 0.69
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 10 0.19
ACGTcount: A:0.49, C:0.25, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2127670 original size:33 final size:33
Alignment explanation
Indices: 2127628--2127700 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
2127618 GGAAATGGCT
2127628 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2127661 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2127694 ATCGCAA
1 ATCGCAA
2127701 CGACAAAATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2127713 original size:47 final size:47
Alignment explanation
Indices: 2127644--2127733 Score: 171
Period size: 47 Copynumber: 1.9 Consensus size: 47
2127634 ATGCGAAATG
*
2127644 AAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGACAAAATCGCAACGCGAAATGAAAATCGCAACGAC
2127691 AAAATCGCAACGACAAAATCGCAACGCGAAATGAAAATCGCAA
1 AAAATCGCAACGACAAAATCGCAACGCGAAATGAAAATCGCAA
2127734 TGCGATTTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.50, C:0.23, G:0.17, T:0.10
Consensus pattern (47 bp):
AAAATCGCAACGACAAAATCGCAACGCGAAATGAAAATCGCAACGAC
Found at i:2127769 original size:14 final size:14
Alignment explanation
Indices: 2127750--2127807 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2127740 TTGTGTTTCG
2127750 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2127764 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2127780 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
2127796 CGTTGCGATTTT
1 CGTTGCGATTTT
2127808 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2127788 original size:32 final size:33
Alignment explanation
Indices: 2127745--2127823 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
2127735 GCGATTTGTG
*
2127745 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
2127777 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
2127810 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
2127824 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 26 0.58
33 19 0.42
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:2127859 original size:21 final size:20
Alignment explanation
Indices: 2127810--2127864 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
2127800 GCGATTTTCA
*
2127810 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
* *
2127830 TTCCGCGTTGCGATAGTCATT
1 TTTCGCGTTGCGATAGCCA-T
2127851 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
2127865 TTTAAGTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:2129706 original size:340 final size:340
Alignment explanation
Indices: 2129086--2129765 Score: 1342
Period size: 340 Copynumber: 2.0 Consensus size: 340
2129076 TCCCATCCCT
2129086 GAAGATAATAGTGTATGACAGCATGATAAATTACATATCACTGTCTGATTTGAGAGATATGATCA
1 GAAGATAATAGTGTATGACAGCATGATAAATTACATATCACTGTCTGATTTGAGAGATATGATCA
2129151 AAGGATGGAGCTCTCATTTGGCTAAATTCTTGGATGGGATTAATTATTGGACTCATTCTGGACAC
66 AAGGATGGAGCTCTCATTTGGCTAAATTCTTGGATGGGATTAATTATTGGACTCATTCTGGACAC
2129216 AAGAAGCCAAAGAAGTTCAATGTCACAGTTGTCAGAGACGAGACCGCGCCACAACAATCGCCGGG
131 AAGAAGCCAAAGAAGTTCAATGTCACAGTTGTCAGAGACGAGACCGCGCCACAACAATCGCCGGG
2129281 AGCCAGAGGGGATTGTGGTCCTCTCGTATGCTTGTGCTTGGCGCGTTTGACGACGGGAAGCACAG
196 AGCCAGAGGGGATTGTGGTCCTCTCGTATGCTTGTGCTTGGCGCGTTTGACGACGGGAAGCACAG
2129346 AGTTTCTACCTCCCACCGATAGAGATAGAGCTGCAGTAGGCTTGTGGTTTCGGCATTATATGGCT
261 AGTTTCTACCTCCCACCGATAGAGATAGAGCTGCAGTAGGCTTGTGGTTTCGGCATTATATGGCT
2129411 AGAGCAATATATTCG
326 AGAGCAATATATTCG
2129426 GAAGATAATAGTGTATGACAGCATGATAAATTACATATCACTGTCTGATTTGAGAGATATGATCA
1 GAAGATAATAGTGTATGACAGCATGATAAATTACATATCACTGTCTGATTTGAGAGATATGATCA
2129491 AAGGATGGAGCTCTCATTTGGCTAAATTCTTGGATGGGATTAATTATTGGACTCATTCTGGACAC
66 AAGGATGGAGCTCTCATTTGGCTAAATTCTTGGATGGGATTAATTATTGGACTCATTCTGGACAC
2129556 AAGAAGCCAAAGAAGTTCAATGTCACAGTTGTCAGAGACGAGACCGCGCCACAACAATCGCCGGG
131 AAGAAGCCAAAGAAGTTCAATGTCACAGTTGTCAGAGACGAGACCGCGCCACAACAATCGCCGGG
*
2129621 AGCCAGAGGGGATTGTGGTCCTCTCGTATGCTTGTGCTTGGCGTGTTTGACGACGGGAAGCACAG
196 AGCCAGAGGGGATTGTGGTCCTCTCGTATGCTTGTGCTTGGCGCGTTTGACGACGGGAAGCACAG
*
2129686 AGTTTCTACCTCCCACCGATAGAGATAGAGCTGCAGTAGGCTTGTGGTTTCGGTATTATATGGCT
261 AGTTTCTACCTCCCACCGATAGAGATAGAGCTGCAGTAGGCTTGTGGTTTCGGCATTATATGGCT
2129751 AGAGCAATATATTCG
326 AGAGCAATATATTCG
2129766 AGACGCTGCC
Statistics
Matches: 338, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
340 338 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (340 bp):
GAAGATAATAGTGTATGACAGCATGATAAATTACATATCACTGTCTGATTTGAGAGATATGATCA
AAGGATGGAGCTCTCATTTGGCTAAATTCTTGGATGGGATTAATTATTGGACTCATTCTGGACAC
AAGAAGCCAAAGAAGTTCAATGTCACAGTTGTCAGAGACGAGACCGCGCCACAACAATCGCCGGG
AGCCAGAGGGGATTGTGGTCCTCTCGTATGCTTGTGCTTGGCGCGTTTGACGACGGGAAGCACAG
AGTTTCTACCTCCCACCGATAGAGATAGAGCTGCAGTAGGCTTGTGGTTTCGGCATTATATGGCT
AGAGCAATATATTCG
Found at i:2130107 original size:14 final size:15
Alignment explanation
Indices: 2130072--2130109 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
2130062 TGATTGTTTA
2130072 ATTGATTTGTAAAAG
1 ATTGATTTGTAAAAG
*
2130087 ATT-ATTTGTAAATG
1 ATTGATTTGTAAAAG
2130101 -TTGATTTGT
1 ATTGATTTGT
2130110 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 16 0.76
15 3 0.14
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (15 bp):
ATTGATTTGTAAAAG
Found at i:2130270 original size:19 final size:19
Alignment explanation
Indices: 2130246--2130294 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
2130236 ATCGCAACGA
*
2130246 GAAAATCGGAATACGAAAT
1 GAAAATCGCAATACGAAAT
*
2130265 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATACGAAAT
2130284 GAAAATCGCAA
1 GAAAATCGCAA
2130295 CGAGAAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.51, C:0.14, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATACGAAAT
Found at i:2130301 original size:19 final size:19
Alignment explanation
Indices: 2130260--2130301 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2130250 ATCGGAATAC
* *
2130260 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGA
2130279 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
2130298 GAAA
1 GAAA
2130302 ATCACAATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.14, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:2130427 original size:20 final size:20
Alignment explanation
Indices: 2130381--2130427 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2130371 TCATTTCGAA
*
2130381 TTGCGATAGCCAGTTTTGTG
1 TTGCGATAGCCAGTTTTGCG
*
2130401 TTACGATAGCCA-TTTTCGCG
1 TTGCGATAGCCAGTTTT-GCG
2130421 TTGCGAT
1 TTGCGAT
2130428 TTCCCCGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGATAGCCAGTTTTGCG
Found at i:2130666 original size:20 final size:20
Alignment explanation
Indices: 2130641--2130708 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
2130631 TTGAAGATGA
2130641 TTGCGATTTTTAGAATCTCG
1 TTGCGATTTTTAGAATCTCG
*** *
2130661 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTTAGAATCTCG
**
2130681 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-TAGAATCTCG
2130702 TTGCGAT
1 TTGCGAT
2130709 AGTCAGTATC
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 23 0.62
21 14 0.38
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGCGATTTTTAGAATCTCG
Found at i:2130705 original size:41 final size:40
Alignment explanation
Indices: 2130640--2130731 Score: 121
Period size: 41 Copynumber: 2.3 Consensus size: 40
2130630 TTTGAAGATG
*
2130640 ATTGCGATTTTTAGAATCTCGTTGCGAAAGTCAGAATCTC
1 ATTGCGATTTTTAGAATCTCGTTGCGAAAGTCAGAATCGC
* ** * *
2130680 GTTGCGATTTTGTATTATCTCGTTGCGATAGTCAGTATCGC
1 ATTGCGATTTT-TAGAATCTCGTTGCGAAAGTCAGAATCGC
2130721 ATTGCGATTTT
1 ATTGCGATTTT
2130732 CCAAATTCGC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 10 0.23
41 34 0.77
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (40 bp):
ATTGCGATTTTTAGAATCTCGTTGCGAAAGTCAGAATCGC
Found at i:2130761 original size:20 final size:21
Alignment explanation
Indices: 2130717--2130768 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2130707 ATAGTCAGTA
*
2130717 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
2130738 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
2130758 TCGCATTGCGA
1 TCGCATTGCGA
2130769 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:2131580 original size:24 final size:24
Alignment explanation
Indices: 2131553--2131606 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2131543 GTATTCGAAA
*
2131553 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
2131577 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
2131601 TTTGAT
1 TTTGAT
2131607 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:2133754 original size:33 final size:33
Alignment explanation
Indices: 2133712--2133835 Score: 187
Period size: 33 Copynumber: 3.8 Consensus size: 33
2133702 AATTACTATC
2133712 GCAATGCGAAATGAAAATCGCAACGAGAGAATT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATT
** *
2133745 GCAATGCGAAATGAAAATCGCAACGCTA-ATTT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATT
* *
2133777 CGCAATGCGAAATGAAAATCGCAACGAGGGAATC
1 -GCAATGCGAAATGAAAATCGCAACGAGAGAATT
2133811 GCAATGCGAAATGAAAATCGCAACG
1 GCAATGCGAAATGAAAATCGCAACG
2133836 CGAATTTAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
32 3 0.04
33 76 0.94
34 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
GCAATGCGAAATGAAAATCGCAACGAGAGAATT
Found at i:2133816 original size:66 final size:66
Alignment explanation
Indices: 2133710--2133842 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
2133700 GAAATTACTA
* *
2133710 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATTGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
2133775 T
66 T
*
2133776 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
2133841 T
66 T
2133842 T
1 T
2133843 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:2133857 original size:19 final size:19
Alignment explanation
Indices: 2133835--2133876 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2133825 AAATCGCAAC
*
2133835 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCATT
* *
2133854 GCGATTTTCATTTCGCATT
1 GCGAATTTAATTTCGCATT
2133873 GCGA
1 GCGA
2133877 TAGTACTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCATT
Found at i:2134003 original size:14 final size:14
Alignment explanation
Indices: 2133984--2134020 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2133974 CATCAATTAA
2133984 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2133998 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2134012 ACAAATCAA
1 ACAAATCAA
2134021 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2135442 original size:21 final size:21
Alignment explanation
Indices: 2135376--2135442 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2135366 GTGAATCGGG
*
2135376 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2135396 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2135418 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2135439 CTCT
1 CTCT
2135443 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2135461 original size:42 final size:41
Alignment explanation
Indices: 2135376--2135498 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
2135366 GTGAATCGGG
* * * *
2135376 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
2135418 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
2135460 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
2135499 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:2135832 original size:93 final size:89
Alignment explanation
Indices: 2135716--2135898 Score: 296
Period size: 93 Copynumber: 2.0 Consensus size: 89
2135706 ATTTCAAACT
*
2135716 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGTTTAGC
2135781 AGAATTGGCAGCAACCGAATAAATTTAC
62 AGAATTGGCAGCAACCGAATAAATTTAC
*
2135809 TTCAACCAAAAGACAACAA-AAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAGT
1 TTCAACCAAAAGACAA-AACAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAGA
2135873 ATTGGCAGCAACCGAATAAATTTAC
65 ATTGGCAGCAACCGAATAAATTTAC
2135898 T
1 T
2135899 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
89 42 0.48
93 43 0.49
94 2 0.02
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (89 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAGAA
TTGGCAGCAACCGAATAAATTTAC
Found at i:2136280 original size:21 final size:21
Alignment explanation
Indices: 2136256--2136330 Score: 52
Period size: 21 Copynumber: 3.7 Consensus size: 21
2136246 GTGACGGGAT
2136256 AGGTGATGGCTCTCGTTGTAG
1 AGGTGATGGCTCTCGTTGTAG
* ** *
2136277 AGGTGTATAG-TCGGGTTG-ATC
1 AGGTG-ATGGCTCTCGTTGTA-G
*
2136298 AGGTGATGGCTCT-G-GGT-G
1 AGGTGATGGCTCTCGTTGTAG
2136316 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
2136331 AAGTGGAGGA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
18 13 0.32
19 2 0.05
20 5 0.12
21 18 0.44
22 3 0.07
ACGTcount: A:0.15, C:0.13, G:0.41, T:0.31
Consensus pattern (21 bp):
AGGTGATGGCTCTCGTTGTAG
Found at i:2137632 original size:20 final size:19
Alignment explanation
Indices: 2137586--2137623 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2137576 TCTTTTGGTT
2137586 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
2137605 GATAATGAGAATCGCAACG
1 GA-AATGAAAATCGCAACG
2137624 CGGAAATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.47, C:0.16, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:2137664 original size:19 final size:18
Alignment explanation
Indices: 2137642--2137708 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 18
2137632 ACTATCGCAA
*
2137642 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCGCGT
2137661 TGCGATTTTTATTTCGCGT
1 TGCGA-TTTTATTTCGCGT
*
2137680 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTT-CGCGT
2137700 TGCGATTTT
1 TGCGATTTT
2137709 CATTCTCGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 1 0.02
19 26 0.62
20 15 0.36
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Done.