Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007884.1 Hibiscus syriacus cultivar Beakdansim tig00110264_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: 2814991
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 13
Found at i:2422987 original size:14 final size:14
Alignment explanation
Indices: 2422968--2422998 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2422958 AATGAACGTA
2422968 AACGAACACAAACG
1 AACGAACACAAACG
*
2422982 AACGAACATAAACG
1 AACGAACACAAACG
2422996 AAC
1 AAC
2422999 ATAACTGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.26, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:2423212 original size:14 final size:14
Alignment explanation
Indices: 2423195--2423274 Score: 108
Period size: 14 Copynumber: 5.7 Consensus size: 14
2423185 AACACTCATA
2423195 AACGAACATAAACG
1 AACGAACATAAACG
* *
2423209 AACGGACATAAATG
1 AACGAACATAAACG
2423223 AAC-AGACATAAACG
1 AACGA-ACATAAACG
*
2423237 AACGGACATAAACG
1 AACGAACATAAACG
*
2423251 AACGAACATAAATG
1 AACGAACATAAACG
2423265 AACGAACATA
1 AACGAACATA
2423275 TTACTGAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
14 57 1.00
ACGTcount: A:0.55, C:0.19, G:0.16, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:2423364 original size:40 final size:41
Alignment explanation
Indices: 2423316--2423395 Score: 126
Period size: 40 Copynumber: 1.9 Consensus size: 41
2423306 ACGTGCCCTC
2423316 TGTTCATGTTCGTTCATTTAAT-TAAACGAACACAAAATCT
1 TGTTCATGTTCGTTCATTTAATATAAACGAACACAAAATCT
*
2423356 TGTTCATGTTCGTTCATTTAATAAATAAACGAACATAAAA
1 TGTTCATGTTCGTTCATTTAAT--ATAAACGAACACAAAA
2423396 GAACTTCCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 22 0.61
43 14 0.39
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (41 bp):
TGTTCATGTTCGTTCATTTAATATAAACGAACACAAAATCT
Found at i:2424404 original size:31 final size:31
Alignment explanation
Indices: 2424366--2424459 Score: 136
Period size: 31 Copynumber: 3.0 Consensus size: 31
2424356 CCCGAAGGAC
* *
2424366 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
2424397 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
2424428 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
2424459 C
1 C
2424460 CCTCGACCCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 55 0.98
32 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:2424663 original size:23 final size:24
Alignment explanation
Indices: 2424637--2424683 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
2424627 ATATACTTGT
*
2424637 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
2424660 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
2424684 CAGGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:2425225 original size:21 final size:21
Alignment explanation
Indices: 2425195--2425238 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2425185 ATTCTGTCGT
* *
2425195 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2425216 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2425237 TT
1 TT
2425239 ACCCAGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2428273 original size:31 final size:31
Alignment explanation
Indices: 2428235--2428359 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
2428225 CCCGAAGGAC
* *
2428235 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
2428266 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
2428297 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
2428328 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
2428359 C
1 C
2428360 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:2428563 original size:23 final size:24
Alignment explanation
Indices: 2428537--2428583 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
2428527 ATATACTTGT
*
2428537 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
2428560 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
2428584 CAGGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:2429124 original size:21 final size:21
Alignment explanation
Indices: 2429094--2429137 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2429084 ATTCTGTCGT
* *
2429094 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2429115 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2429136 TT
1 TT
2429138 ACCCAGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2431731 original size:23 final size:23
Alignment explanation
Indices: 2431670--2431760 Score: 101
Period size: 23 Copynumber: 3.9 Consensus size: 23
2431660 GTCGAGGGTT
* *
2431670 CTATGTGGTCCTTCGGGACAAAAC
1 CTATGTGGTCATTCGGGAC-AACC
*
2431694 CTATGTGGTCCTTCGGGACAACC
1 CTATGTGGTCATTCGGGACAACC
* * *
2431717 CTATATAGTCATTCGGGATAACC
1 CTATGTGGTCATTCGGGACAACC
* *
2431740 CAATGTGGTCATTCGAGACAA
1 CTATGTGGTCATTCGGGACAA
2431761 TTATATGGTA
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
23 38 0.67
24 19 0.33
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.26
Consensus pattern (23 bp):
CTATGTGGTCATTCGGGACAACC
Found at i:2436890 original size:17 final size:19
Alignment explanation
Indices: 2436854--2436892 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2436844 TTAGTCCCAT
*
2436854 TTTTTTTACATATTATGAA
1 TTTTTTTACATATTACGAA
2436873 TTTTTTTA-ATATT-CGAA
1 TTTTTTTACATATTACGAA
2436890 TTT
1 TTT
2436893 GGTCCTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 5 0.26
19 8 0.42
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTTTTACATATTACGAA
Found at i:2438452 original size:19 final size:21
Alignment explanation
Indices: 2438428--2438469 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 21
2438418 TCCCACTAAC
2438428 TTTTTTTC-TTCATTTT-TTT
1 TTTTTTTCTTTCATTTTATTT
2438447 TTTTTTTCTTTCATTTTATTT
1 TTTTTTTCTTTCATTTTATTT
2438468 TT
1 TT
2438470 ATCATTTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.38
20 8 0.38
21 5 0.24
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTTTCTTTCATTTTATTT
Found at i:2440442 original size:15 final size:15
Alignment explanation
Indices: 2440422--2440455 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2440412 TCAAAAAAGC
2440422 AAAGAAAAAG-AAGAA
1 AAAGAAAAAGCAA-AA
2440437 AAAGAAAAAGCAAAA
1 AAAGAAAAAGCAAAA
2440452 AAAG
1 AAAG
2440456 GGACAATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGCAAAA
Found at i:2442133 original size:66 final size:65
Alignment explanation
Indices: 2442058--2442274 Score: 175
Period size: 66 Copynumber: 3.4 Consensus size: 65
2442048 TCATCTTTTG
2442058 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGTCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTT-ACAACGAATGGGTCATCCA
2442123 C
65 C
* * * * * * * ** *
2442124 GATTTCAACTTCATGACGAAGAATAT-C-GTGTCTA-CCAGCAACATT-CATC-TTTAGGT--T-
1 GATTTCAACTTCACGACGAAGGATATCCAAT-TCAAGGC-TCAAC-TTACAACGAATGGGTCATC
*
2442181 --G
63 CAC
* * *
2442182 GATTTCAACTTCACGCCGAAGGATATCCAATTCAAGGCTCAATTTTACAACGAATGGGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAA-CTTACAACGAATGGGTCATCCA
2442247 C
65 C
* *
2442248 GATTTCAACTTCACGACAAAAGATATC
1 GATTTCAACTTCACGACGAAGGATATC
2442275 GTGTGCACAA
Statistics
Matches: 109, Mismatches: 28, Indels: 28
0.66 0.17 0.17
Matches are distributed among these distances:
58 23 0.21
59 9 0.08
60 5 0.05
61 4 0.04
63 5 0.05
64 5 0.05
65 8 0.07
66 50 0.46
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (65 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTACAACGAATGGGTCATCCAC
Found at i:2442232 original size:124 final size:119
Alignment explanation
Indices: 2441934--2442340 Score: 496
Period size: 124 Copynumber: 3.3 Consensus size: 119
2441924 CTCGCTCAAG
* * * *
2441934 ATTGAATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGGAGGGGCTA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
* * * * *
2441999 TCCACGATTTTAACTTCACAACAAAGGATATCGTGCCCACCAGCAACGTTCATCTT
66 TCCACGATTTCAACTTCACGAC-AAGAATATCGTG-TCACCAGCAACATTCATCTT
*
2442055 -TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGTCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
*
2442119 TCCACGATTTCAACTTCATGACGAAGAATATCGTGTCTACCAGCAACATTCATCTTT
66 TCCACGATTTCAACTTCACGAC-AAGAATATCGTGTC-ACCAGCAACATTCATC-TT
* * *
2442176 AGGTTGGATTTCAACTTCACGCCGAAGGATATCCAATTCAAGGCTCAATTTTACAACGAATGGGC
1 A--TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGC
* * * * *
2442241 CATCCACGATTTCAACTTCACGACAAAAGATATCGTGTGCACAAGTAGA-ATCCCTCCATAT
64 CATCCACGATTTCAACTTCACGACAAGA-ATATCGTGT-CACCAGCA-ACATTCAT-C-T-T
2442302 ATTGGATTTCAACTTCAC-AGCGAAGGATATCCAATTCAA
1 ATTGGATTTCAACTTCACGA-CGAAGGATATCCAATTCAA
2442341 AGAAGGAGCG
Statistics
Matches: 251, Mismatches: 24, Indels: 19
0.85 0.08 0.06
Matches are distributed among these distances:
119 1 0.00
120 104 0.41
121 2 0.01
123 3 0.01
124 135 0.54
125 4 0.02
126 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (119 bp):
ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
TCCACGATTTCAACTTCACGACAAGAATATCGTGTCACCAGCAACATTCATCTT
Found at i:2444497 original size:29 final size:28
Alignment explanation
Indices: 2444464--2444519 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
2444454 AATGTAATTT
*
2444464 ATATATTTTTA-ATTATTTCGAATTTTAGC
1 ATATAATTTTAGA-TATTT-GAATTTTAGC
*
2444493 ATATAATTTTAGATATTTGTATTTTAG
1 ATATAATTTTAGATATTTGAATTTTAG
2444520 TCCTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.33
29 15 0.62
30 1 0.04
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (28 bp):
ATATAATTTTAGATATTTGAATTTTAGC
Found at i:2445011 original size:12 final size:13
Alignment explanation
Indices: 2444986--2445014 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2444976 TTTGTCTTAA
2444986 AAAATTATTTTTT
1 AAAATTATTTTTT
2444999 AAAATTA-TTTTT
1 AAAATTATTTTTT
2445011 AAAA
1 AAAA
2445015 GACGTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAATTATTTTTT
Found at i:2445237 original size:43 final size:43
Alignment explanation
Indices: 2445190--2445278 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
2445180 ATTTTTGGTT
* *
2445190 TAGTTTTGGAGGTTTGATTATTGGGATTTCAGTATTTTTACAG
1 TAGTTTGGGAGGGTTGATTATTGGGATTTCAGTATTTTTACAG
*
2445233 TAGTTTGGGAGGGTTGATTATTGGGATTTCAGTATTTTTACGG
1 TAGTTTGGGAGGGTTGATTATTGGGATTTCAGTATTTTTACAG
2445276 TAG
1 TAG
2445279 CATATGTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.20, C:0.04, G:0.29, T:0.46
Consensus pattern (43 bp):
TAGTTTGGGAGGGTTGATTATTGGGATTTCAGTATTTTTACAG
Found at i:2454966 original size:60 final size:59
Alignment explanation
Indices: 2454809--2454966 Score: 167
Period size: 60 Copynumber: 2.6 Consensus size: 59
2454799 CTATTCATCC
* * *
2454809 AAAGTTTAGGGATCAATTTAGAATGATGGTCATAGTTTGAGGATGAAATTATAACATTCA
1 AAAGTTTAAGGATCAATTTAGAAT-AAGGTCATAGTTTGAGGATGAAATTAGAACATTCA
* * * * **
2454869 CAAGTTTAAGGA-CTAATATAGAATAAGTGTCACAGTTTGGGGATGAAATTAGAATGTTCA
1 AAAGTTTAAGGATC-AATTTAGAATAAG-GTCATAGTTTGAGGATGAAATTAGAACATTCA
*
2454929 AAAGTTTAAGGATCAATTTA-AAGTAAAGATCATAGTTT
1 AAAGTTTAAGGATCAATTTAGAA-T-AAGGTCATAGTTT
2454967 AGGTACATAT
Statistics
Matches: 80, Mismatches: 13, Indels: 10
0.78 0.13 0.10
Matches are distributed among these distances:
59 5 0.06
60 71 0.89
61 4 0.05
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (59 bp):
AAAGTTTAAGGATCAATTTAGAATAAGGTCATAGTTTGAGGATGAAATTAGAACATTCA
Found at i:2457765 original size:2 final size:2
Alignment explanation
Indices: 2457753--2457788 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2457743 TCATACATAC
2457753 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2457789 CTTACTGTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2458307 original size:10 final size:10
Alignment explanation
Indices: 2458292--2458497 Score: 177
Period size: 10 Copynumber: 20.4 Consensus size: 10
2458282 GGTAAACGTG
2458292 TATACATATA
1 TATACATATA
2458302 TATACATATA
1 TATACATATA
2458312 TATACATATA
1 TATACATATA
2458322 TAT--ATATA
1 TATACATATA
*
2458330 TATACATACA
1 TATACATATA
2458340 TATACATACATA
1 TATACAT--ATA
*
2458352 TATACATACA
1 TATACATATA
*
2458362 TATATATATA
1 TATACATATA
**
2458372 TATATGTATA
1 TATACATATA
**
2458382 TATATGTATA
1 TATACATATA
*
2458392 CATACATATA
1 TATACATATA
2458402 TACATACATATA
1 T--ATACATATA
2458414 TACATACATATA
1 T--ATACATATA
**
2458426 TATATGTATA
1 TATACATATA
*
2458436 TATATATATA
1 TATACATATA
*
2458446 TATATATATA
1 TATACATATA
**
2458456 TATATGTATA
1 TATACATATA
*
2458466 TAT-C-TATG
1 TATACATATA
*
2458474 TATATATATA
1 TATACATATA
*
2458484 TATATATATA
1 TATACATATA
2458494 TATA
1 TATA
2458498 GAGAGAGAGA
Statistics
Matches: 170, Mismatches: 18, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
8 14 0.08
10 125 0.74
12 31 0.18
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (10 bp):
TATACATATA
Found at i:2458314 original size:4 final size:4
Alignment explanation
Indices: 2458292--2458497 Score: 223
Period size: 4 Copynumber: 51.5 Consensus size: 4
2458282 GGTAAACGTG
* * * * *
2458292 TATA CATA TATA TACA TATA TATA CATA TATA TATA TATA TACA TACA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * * *
2458340 TATA CATA CATA TATA CATA CATA TATA TATA TATA TGTA TATA TATG
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * * * *
2458388 TATA CATA CATA TATA CATA CATA TATA CATA CATA TATA TATG TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * *
2458436 TATA TATA TATA TATA TATA TATA TGTA TATA TCTA TGTA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
2458484 TATA TATA TATA TA
1 TATA TATA TATA TA
2458498 GAGAGAGAGA
Statistics
Matches: 173, Mismatches: 29, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 173 1.00
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (4 bp):
TATA
Found at i:2461381 original size:23 final size:23
Alignment explanation
Indices: 2461355--2461401 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2461345 ATCAATGTAT
2461355 TACTATGTAGATTTAGAACGTAA
1 TACTATGTAGATTTAGAACGTAA
2461378 TACTATGTAGATTTAGAACGTAA
1 TACTATGTAGATTTAGAACGTAA
2461401 T
1 T
2461402 CTCGTTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (23 bp):
TACTATGTAGATTTAGAACGTAA
Found at i:2462671 original size:11 final size:11
Alignment explanation
Indices: 2462646--2462679 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2462636 AAGGTAAAAC
*
2462646 TATTTTTTA-T
1 TATTTTATATT
2462656 TATTTTATATT
1 TATTTTATATT
2462667 TATTTTATATT
1 TATTTTATATT
2462678 TA
1 TA
2462680 ATTATTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TATTTTATATT
Found at i:2463683 original size:60 final size:59
Alignment explanation
Indices: 2463577--2463694 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 59
2463567 TATTTGACAT
* *
2463577 GATGCCTTCAAGTTCCAAGGGAGGCATTCAACTGCGAGCTTCTTCGACCTCAATGTCGA
1 GATGCCTTCAAGTTCCAAGGGAAGCATTCAACTGCGAGCTTCTTCGACCTAAATGTCGA
* * *
2463636 GATGCCTTCAAGTT-CAAGGGGAAAGCATTTAACTATC-AGCTTGTTCGACCTAAATGTCG
1 GATGCCTTCAAGTTCCAA-GGG-AAGCATTCAACT-GCGAGCTTCTTCGACCTAAATGTCG
2463695 GCATCATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
58 3 0.06
59 17 0.33
60 30 0.59
61 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (59 bp):
GATGCCTTCAAGTTCCAAGGGAAGCATTCAACTGCGAGCTTCTTCGACCTAAATGTCGA
Found at i:2468197 original size:19 final size:22
Alignment explanation
Indices: 2468145--2468197 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 22
2468135 TCTTAAATTA
2468145 ATAAATAACATACATATTAAAAT
1 ATAAATAA-ATACATATTAAAAT
2468168 ATAAACT-AATAC-TA-TAAAAT
1 ATAAA-TAAATACATATTAAAAT
2468188 -TAAATAAATA
1 ATAAATAAATA
2468198 AAACATTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 1 0.04
19 8 0.29
20 6 0.21
21 2 0.07
22 4 0.14
23 6 0.21
24 1 0.04
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAAATAAATACATATTAAAAT
Found at i:2479295 original size:129 final size:126
Alignment explanation
Indices: 2479100--2479410 Score: 313
Period size: 129 Copynumber: 2.4 Consensus size: 126
2479090 TGGCTCAATT
* * *
2479100 AGTTAGAAATTGAGATTAAAAAAACTTAAGGGCCTCAATTATAAAGTTAAGAAAGTGAGATTAAA
1 AGTTA-AAA-TGAGATT-AAAAAA-TTAAGGACCTCAATTATAAAGATAAAAAAGTGAGATTAAA
*** * * *
2479165 AAATTGTGGGTCTCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAACTTAAAAGCCTCGATTAT
62 AAATTACAGATCTCAATTATAAAGATAAAAAGTGAGATTGAAAAAAA-TTAAAA-CCTCAATTAT
2479230 AA
125 AA
* * *
2479232 AGTTAAAAGTGAGATTATAAAATTAAGGTCCTCAATTATAAAGGTAAAAAAG-G-GATTGAAAAA
1 AGTTAAAA-TGAGATTAAAAAATTAAGGACCTCAATTATAAAGATAAAAAAGTGAGATT-AAAAA
* * * * **
2479295 AGTTACAGATTTCAATTATAAAGATAAAAAGTTAGATTGAATAATATTAGGACCTCAATTATAA
64 A-TTACAGATCTCAATTATAAAGATAAAAAGTGAGATTGAAAAAAATTAAAACCTCAATTATAA
* *
2479359 AGGTGAAAATAAGATTTAAAAAATTAAGGACCT-AATTATAAAGATGAAAAAA
1 A-GTTAAAATGAGA-TTAAAAAATTAAGGACCTCAATTATAAAGAT-AAAAAA
2479411 TGGGGGCCCT
Statistics
Matches: 152, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
127 31 0.20
128 39 0.26
129 62 0.41
130 5 0.03
131 10 0.07
132 5 0.03
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (126 bp):
AGTTAAAATGAGATTAAAAAATTAAGGACCTCAATTATAAAGATAAAAAAGTGAGATTAAAAAAT
TACAGATCTCAATTATAAAGATAAAAAGTGAGATTGAAAAAAATTAAAACCTCAATTATAA
Found at i:2479353 original size:43 final size:43
Alignment explanation
Indices: 2479110--2479401 Score: 253
Period size: 43 Copynumber: 6.8 Consensus size: 43
2479100 AGTTAGAAAT
* * *
2479110 TGAGATTAAAAAAACTTAAGGGCCTCAATTATAAAGTTAAGAAAG
1 TGAGATTGAAAAAA-TTAAGGACCTCAATTATAAAGGTAA-AAAG
** **
2479155 TGAGATT-AAAAAATTGTGGGTCTCAATTATAAAGGTAAAAAG
1 TGAGATTGAAAAAATTAAGGACCTCAATTATAAAGGTAAAAAG
* * *
2479197 TGAGATTGAAAAAAACTTAA-AAGCCTCGATTATAAA-GTTAAAAG
1 TGAGATTG-AAAAAA-TTAAGGA-CCTCAATTATAAAGGTAAAAAG
* *
2479241 TGAGATT-ATAAAATTAAGGTCCTCAATTATAAAGGTAAAAAAG
1 TGAGATTGAAAAAATTAAGGACCTCAATTATAAAGGT-AAAAAG
** *
2479284 -G-GATTGAAAAAAGTTACA-GATTTCAATTATAAAGATAAAAAG
1 TGAGATTGAAAAAA-TTA-AGGACCTCAATTATAAAGGTAAAAAG
* * *
2479326 TTAGATTGAATAATATT-AGGACCTCAATTATAAAGGTGAAAA-
1 TGAGATTGAA-AAAATTAAGGACCTCAATTATAAAGGTAAAAAG
* *
2479368 TAAGATTTAAAAAATTAAGGACCT-AATTATAAAG
1 TGAGATTGAAAAAATTAAGGACCTCAATTATAAAG
2479402 ATGAAAAAAT
Statistics
Matches: 202, Mismatches: 30, Indels: 34
0.76 0.11 0.13
Matches are distributed among these distances:
41 35 0.17
42 46 0.23
43 62 0.31
44 36 0.18
45 23 0.11
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (43 bp):
TGAGATTGAAAAAATTAAGGACCTCAATTATAAAGGTAAAAAG
Found at i:2479918 original size:4 final size:4
Alignment explanation
Indices: 2479909--2479953 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
2479899 TTATTTTTAG
2479909 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
2479954 CATATTAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TAAT
Found at i:2480176 original size:24 final size:24
Alignment explanation
Indices: 2480130--2480176 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2480120 GACGGAGAGC
* * *
2480130 ATAAATGAACATGACATATAATTT
1 ATAAATAAACATGACAAACAATTT
2480154 ATAAATAAACATGACAAACAATT
1 ATAAATAAACATGACAAACAATT
2480177 AACTCATTTT
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:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (24 bp):
ATAAATAAACATGACAAACAATTT
Found at i:2488534 original size:2 final size:2
Alignment explanation
Indices: 2488527--2488553 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2488517 CTACACTTCA
2488527 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
2488554 ATTAGAGAAT
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:2499311 original size:83 final size:83
Alignment explanation
Indices: 2499109--2499351 Score: 350
Period size: 83 Copynumber: 3.0 Consensus size: 83
2499099 TGAAATATAT
*
2499109 GTTTAATA-TTTAAATTTAAAAGATATTATTATATGTTTAAATTTAGATATTAAAAGAG-TTTGG
1 GTTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAAGAGTTTTGG
** *
2499172 TTTAAGTAAAACTCTAAG
66 TTGGAGTAAAACTCTCAG
* *
2499190 G-TT-ATATTTTAAATTTAAAATATATTATTATCTGTTTAAATTTAGATATTAAAAAAGTTTTGG
1 GTTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAAGAGTTTTGG
2499253 TTGGAGTAAAACTCTCAG
66 TTGGAGTAAAACTCTCAG
* * * * * *
2499271 GTTTAACATTTTAAATTTAAAAGACACTATTATCTATTTAAAGTTAGATATTAAAAGAGTTTTAG
1 GTTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAAGAGTTTTGG
2499336 TTGGAGTAAAACTCTC
66 TTGGAGTAAAACTCTC
2499352 TCGAAATTCC
Statistics
Matches: 144, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
79 3 0.02
80 49 0.34
81 22 0.15
82 2 0.01
83 68 0.47
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.42
Consensus pattern (83 bp):
GTTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAAGAGTTTTGG
TTGGAGTAAAACTCTCAG
Found at i:2500168 original size:13 final size:13
Alignment explanation
Indices: 2500150--2500181 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2500140 CACCTAATTT
2500150 GTGATTTAGAACG
1 GTGATTTAGAACG
2500163 GTGATTTAGAACG
1 GTGATTTAGAACG
*
2500176 TTGATT
1 GTGATT
2500182 CCTACTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.28, T:0.38
Consensus pattern (13 bp):
GTGATTTAGAACG
Found at i:2500248 original size:21 final size:21
Alignment explanation
Indices: 2500222--2500270 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
2500212 ATGTTTATGG
2500222 TTGTAAACCATAACGAGAAAC
1 TTGTAAACCATAACGAGAAAC
2500243 TTGTAAACCATAACGAGAAAC
1 TTGTAAACCATAACGAGAAAC
2500264 TTGTAAA
1 TTGTAAA
2500271 ATTCTATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.22
Consensus pattern (21 bp):
TTGTAAACCATAACGAGAAAC
Found at i:2504376 original size:82 final size:82
Alignment explanation
Indices: 2504273--2504517 Score: 341
Period size: 83 Copynumber: 3.0 Consensus size: 82
2504263 GGAAATATAT
* * * * *
2504273 GTTTAATA-TTTAAATTTAAAATATATTACTATTTATTTATATTTATATATTAAAAGAGTTTGAT
1 GTTTAATATTTTAAATTTAAAATATATTATTATCTGTTTAAATTTAGATATTAAAAGAGTTTGAT
* *
2504337 TTGAGTAAAATTCTCAG
66 TGGAGTAAAACTCTCAG
* *
2504354 GTTTAATATTTTAAATTTAAAATATATTATTATCTGTTTAAATTTAGATATTAAAAGAATTTTGG
1 GTTTAATATTTTAAATTTAAAATATATTATTATCTGTTTAAATTTAGATATTAAAAG-AGTTTGA
2504419 TTGGAGTAAAACTCTCAG
65 TTGGAGTAAAACTCTCAG
* * *
2504437 ATTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATGAAAAGAGTTTTAG
1 GTTTAATATTTTAAATTTAAAATATATTATTATCTGTTTAAATTTAGATATTAAAAGAG-TTT-G
2504502 A-TGGAGTAAAACTCTC
64 ATTGGAGTAAAACTCTC
2504518 TCGAACTTCC
Statistics
Matches: 146, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
81 8 0.05
82 44 0.30
83 93 0.64
84 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (82 bp):
GTTTAATATTTTAAATTTAAAATATATTATTATCTGTTTAAATTTAGATATTAAAAGAGTTTGAT
TGGAGTAAAACTCTCAG
Found at i:2508655 original size:6 final size:6
Alignment explanation
Indices: 2508644--2508669 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2508634 CTCGCCACTC
2508644 CCGACG CCGACG CCGACG CCGACG CC
1 CCGACG CCGACG CCGACG CCGACG CC
2508670 CCAACCGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.54, G:0.31, T:0.00
Consensus pattern (6 bp):
CCGACG
Found at i:2512428 original size:48 final size:48
Alignment explanation
Indices: 2512365--2512935 Score: 381
Period size: 48 Copynumber: 11.8 Consensus size: 48
2512355 AACTGTAGGC
* * *
2512365 TGCTTTTGTTTAAGATGAT-TGAAGCTCTGATAACTTTTCGGAGGCTGA
1 TGCTGTTGTTGAAGATGATCAGAA-CTCTGATAACTTTTCGGAGGCTGA
** *
2512413 TGCTGTTGTTGAAGATGAAAAGAACTCTGATAAGTTTCTC-GAGGCGTG-
1 TGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTT-TCGGAGGC-TGA
* * *
2512461 TGCTGTTGTTGAAGATGATCAGAACTCAGAGAACTTTTTGGAGGCTGA
1 TGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTTTCGGAGGCTGA
* * *
2512509 TGCTGTTGTTGAAGATGATAAGAACTCTGATAA-TTTCCCCGTGGAGCCTGA
1 TGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTT--TC--GGAGGCTGA
* * * *
2512560 GGCTGTTGTTGAAGATGATCGGAACTCTGATAACTTTTCCGAGGCTGT
1 TGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTTTCGGAGGCTGA
* * * * **
2512608 TGCTGTTGTTGAAGATCATCAGAACCCTGATAACTTTCCCGAGGAGCCCA
1 TGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTTTCGGA-G-GCTGA
* * * ** *
2512658 -AC-GTTGTTGCAGGAGGTGATCAGAACTCTGATAACTTTCCTTAGGAC-AA
1 TGCTGTTGTTG-A--AGATGATCAGAACTCTGATAACTTTTCGGAGG-CTGA
* * * * * **
2512707 TGTTTTTGTTGAAGATGTTCAGAACTCTGATTACTTTCCTTAGGAC-GA
1 TGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTTTCGGAGG-CTGA
* * * * * **
2512755 AGTTTTTGTTGAAGATGATCAGAACTCTGACAACCTTCTC-GAGTTTGA
1 TGCTGTTGTTGAAGATGATCAGAACTCTGATAA-CTTTTCGGAGGCTGA
* ** * * ** **
2512803 TGCTGTTGCTGTTGTTGATCAGAACTCTGATAACTTTCCTTAGGAGGA
1 TGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTTTCGGAGGCTGA
* * * *
2512851 TGCT-TCTGTTGAAGATTATCAGAAATCTGATAA-TTTTCTCGAGACTGA
1 TGCTGT-TGTTGAAGATGATCAGAACTCTGATAACTTTTC-GGAGGCTGA
* * * *
2512899 TGCCGTTGTTGAAGACGACCAGAACTCTGAAAACTTT
1 TGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTT
2512936 CCTGATGATG
Statistics
Matches: 411, Mismatches: 87, Indels: 49
0.75 0.16 0.09
Matches are distributed among these distances:
47 15 0.04
48 298 0.73
49 20 0.05
50 6 0.01
51 69 0.17
52 3 0.01
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (48 bp):
TGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTTTCGGAGGCTGA
Found at i:2512604 original size:99 final size:98
Alignment explanation
Indices: 2512365--2512937 Score: 451
Period size: 96 Copynumber: 5.9 Consensus size: 98
2512355 AACTGTAGGC
* * * *
2512365 TGCTTTTGTTTAAGATGAT-TGAAGCTCTGATAACTTTTCGGAGGCTGATGCTGTTGTTGAAGAT
1 TGCTGTTGTTGAAGATGATCAGAA-CTCTGATAACTTTTCCGAGGCTGATGCTGTTGTTGAAGAT
** * * * * *
2512429 GAAAAGAACTCTGATAAGTTTCTCGAGGCG-TG-
65 GATCAGAACTCTGATAACTTTCCCGTGGAGCCGA
* * **
2512461 TGCTGTTGTTGAAGATGATCAGAACTCAGAGAACTTTTTGGAGGCTGATGCTGTTGTTGAAGATG
1 TGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTTTCCGAGGCTGATGCTGTTGTTGAAGATG
*
2512526 ATAAGAACTCTGATAA-TTTCCCCGTGGAGCCTGA
66 ATCAGAACTCTGATAACTTT-CCCGTGGAGCC-GA
* * * *
2512560 GGCTGTTGTTGAAGATGATCGGAACTCTGATAACTTTTCCGAGGCTGTTGCTGTTGTTGAAGATC
1 TGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTTTCCGAGGCTGATGCTGTTGTTGAAGATG
* * *
2512625 ATCAGAACCCTGATAACTTTCCCGAGGAGCCCA
66 ATCAGAACTCTGATAACTTTCCCGTGGAGCCGA
* * * * * *
2512658 -AC-GTTGTTGCAGGAGGTGATCAGAACTCTGATAAC-TTTCCTTAGGAC-AATGTTTTTGTTGA
1 TGCTGTTGTTG-A--AGATGATCAGAACTCTGATAACTTTTCC-GAGG-CTGATGCTGTTGTTGA
* * *
2512719 AGATGTTCAGAACTCTGATTACTTT-CCTTAGGA--CGA
61 AGATGATCAGAACTCTGATAACTTTCCCGT-GGAGCCGA
* * * * * ** * ** *
2512755 AGTTTTTGTTGAAGATGATCAGAACTCTGACAAC-CTTCTCGAGTTTGATGCTGTTGCTGTTGTT
1 TGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTTTC-CGAGGCTGATGCTGTTGTTGAAGAT
*
2512819 GATCAGAACTCTGATAACTTT-CCTTAGGAG--GA
65 GATCAGAACTCTGATAACTTTCCCGT-GGAGCCGA
* * * *
2512851 TGCT-TCTGTTGAAGATTATCAGAAATCTGATAA-TTTTCTCGAGACTGATGCCGTTGTTGAAGA
1 TGCTGT-TGTTGAAGATGATCAGAACTCTGATAACTTTTC-CGAGGCTGATGCTGTTGTTGAAGA
* * *
2512914 CGACCAGAACTCTGAAAACTTTCC
64 TGATCAGAACTCTGATAACTTTCC
2512938 TGATGATGTT
Statistics
Matches: 385, Mismatches: 72, Indels: 39
0.78 0.15 0.08
Matches are distributed among these distances:
95 4 0.01
96 214 0.56
97 9 0.02
98 10 0.03
99 144 0.37
100 4 0.01
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (98 bp):
TGCTGTTGTTGAAGATGATCAGAACTCTGATAACTTTTCCGAGGCTGATGCTGTTGTTGAAGATG
ATCAGAACTCTGATAACTTTCCCGTGGAGCCGA
Found at i:2514309 original size:2 final size:2
Alignment explanation
Indices: 2514302--2514334 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2514292 CTTTTTAAAT
2514302 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
2514335 GTACATTGGA
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:2515076 original size:3 final size:3
Alignment explanation
Indices: 2515068--2515119 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
2515058 TAGAATTTAG
2515068 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2515116 ATT A
1 ATT A
2515120 CAGTTTAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2516018 original size:48 final size:48
Alignment explanation
Indices: 2515927--2516024 Score: 117
Period size: 48 Copynumber: 2.0 Consensus size: 48
2515917 AACTCAAACT
* * * * *
2515927 TTCAAGAGTTTGATGTTGTTGTTGAAAATGATTAGGACTCTGATAACC
1 TTCAAGAGATTGATGTTGTAGTTGAAAATGATGAGAACCCTGATAACC
* *
2515975 TTCAAGAGATTGATGTTGTAGTTGAAGATGATCGA-AACCCTGATGACC
1 TTCAAGAGATTGATGTTGTAGTTGAAAATGAT-GAGAACCCTGATAACC
2516023 TT
1 TT
2516025 TTGAAAGTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 41 0.98
49 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (48 bp):
TTCAAGAGATTGATGTTGTAGTTGAAAATGATGAGAACCCTGATAACC
Found at i:2517693 original size:14 final size:15
Alignment explanation
Indices: 2517656--2517694 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
2517646 ATTGGGAGAA
*
2517656 TATTTTATGTAAAAG
1 TATTTTATTTAAAAG
2517671 TATTTTATTTAAAAG
1 TATTTTATTTAAAAG
2517686 TA-TTTATTT
1 TATTTTATTT
2517695 TTATTTCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (15 bp):
TATTTTATTTAAAAG
Found at i:2518230 original size:42 final size:42
Alignment explanation
Indices: 2518124--2518356 Score: 163
Period size: 42 Copynumber: 5.7 Consensus size: 42
2518114 ATTTATTAAA
* * * **
2518124 AAAAAAGCCACTAAAGTGCATGATTATTGCGATGTTTA-TA-
1 AAAAACGCCACTAAAGTGCATGACTATTGTGACATTTACTAC
* ** * * * *
2518164 AAAAACGTCGTTCATGTGCATGACTATTGTGGCATTTACTGC
1 AAAAACGCCACTAAAGTGCATGACTATTGTGACATTTACTAC
* * * *
2518206 AACAACGCCACTAAAGTGTATGACTATTATGACATTTATTAC
1 AAAAACGCCACTAAAGTGCATGACTATTGTGACATTTACTAC
* * * *
2518248 AAAAATGCCACTAAAGTGCATGACTATTGCGTCGTTTA-TA-
1 AAAAACGCCACTAAAGTGCATGACTATTGTGACATTTACTAC
** * * * *
2518288 AAAAAAACC-CTAAAGTGCATGAGTATTGCG-CGTTTATTAC
1 AAAAACGCCACTAAAGTGCATGACTATTGTGACATTTACTAC
* * *
2518328 AAAAAAGCCACTAAAGTGAATGATTATTG
1 AAAAACGCCACTAAAGTGCATGACTATTG
2518357 CGGTGTTTAT
Statistics
Matches: 152, Mismatches: 36, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
38 6 0.04
39 22 0.14
40 42 0.28
41 20 0.13
42 62 0.41
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (42 bp):
AAAAACGCCACTAAAGTGCATGACTATTGTGACATTTACTAC
Found at i:2518338 original size:80 final size:81
Alignment explanation
Indices: 2518240--2518398 Score: 223
Period size: 80 Copynumber: 2.0 Consensus size: 81
2518230 TATTATGACA
* *
2518240 TTTATTACAAAAATGCCACTAAAGTGCATGACTATTGC-GTCGTTTAT-AAAAAAAACCCTAAAG
1 TTTATTACAAAAAAGCCACTAAAGTGAATGACTATTGCGGT-GTTTATCAAAAAAAACCCTAAAG
2518303 TGCATGAGTATTGCGCG
65 TGCATGAGTATTGCGCG
* ** *
2518320 TTTATTACAAAAAAGCCACTAAAGTGAATGATTATTGCGGTGTTTATCAAAAATGACGCTAAAGT
1 TTTATTACAAAAAAGCCACTAAAGTGAATGACTATTGCGGTGTTTATCAAAAAAAACCCTAAAGT
* *
2518385 TCATGATTATTGCG
66 GCATGAGTATTGCG
2518399 ATGTTTTTGT
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
80 41 0.59
81 28 0.41
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (81 bp):
TTTATTACAAAAAAGCCACTAAAGTGAATGACTATTGCGGTGTTTATCAAAAAAAACCCTAAAGT
GCATGAGTATTGCGCG
Found at i:2518366 original size:42 final size:41
Alignment explanation
Indices: 2518124--2518404 Score: 196
Period size: 40 Copynumber: 6.9 Consensus size: 41
2518114 ATTTATTAAA
* *
2518124 AAAAAAGCCACTAAAGTGCATGATTATTGCGATGTTTATA-
1 AAAAAAGCCACTAAAGTGCATGACTATTGCGGTGTTTATAC
* * ** * * * ** *
2518164 AAAAACGTCGTTCATGTGCATGACTATTGTGGCATTTACTGC
1 AAAAAAGCCACTAAAGTGCATGACTATTGCGGTGTTTA-TAC
* * * ** ***
2518206 AACAACGCCACTAAAGTGTATGACTATTATGACATTTATTAC
1 AAAAAAGCCACTAAAGTGCATGACTATTGCGGTGTTTA-TAC
*
2518248 AAAAATGCCACTAAAGTGCATGACTATTGC-GTCGTTTATA-
1 AAAAAAGCCACTAAAGTGCATGACTATTGCGGT-GTTTATAC
* * *
2518288 AAAAAAACC-CTAAAGTGCATGAGTATTGC-GCGTTTATTAC
1 AAAAAAGCCACTAAAGTGCATGACTATTGCGGTGTTTA-TAC
* *
2518328 AAAAAAGCCACTAAAGTGAATGATTATTGCGGTGTTTAT-C
1 AAAAAAGCCACTAAAGTGCATGACTATTGCGGTGTTTATAC
* * * * * *
2518368 AAAAATGACGCTAAAGTTCATGATTATTGCGATGTTT
1 AAAAAAGCCACTAAAGTGCATGACTATTGCGGTGTTT
2518405 TTGTAGTAAA
Statistics
Matches: 189, Mismatches: 45, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
38 5 0.03
39 22 0.12
40 74 0.39
41 22 0.12
42 66 0.35
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (41 bp):
AAAAAAGCCACTAAAGTGCATGACTATTGCGGTGTTTATAC
Found at i:2521312 original size:15 final size:15
Alignment explanation
Indices: 2521292--2521335 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2521282 TTTATAAAAG
2521292 TTTTATTTTCTTTTC
1 TTTTATTTTCTTTTC
*
2521307 TTTTATTCTCTTTTC
1 TTTTATTTTCTTTTC
*
2521322 TTTTCACTTTCTTT
1 TTTT-ATTTTCTTT
2521336 ATTTTCTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTATTTTCTTTTC
Found at i:2521326 original size:25 final size:25
Alignment explanation
Indices: 2521292--2521346 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
2521282 TTTATAAAAG
*
2521292 TTTTATTTTC-TTTTCTTTTATTCTC
1 TTTTATTTTCACTTTC-TTTATTCTC
* *
2521317 TTTTCTTTTCACTTTCTTTATTTTC
1 TTTTATTTTCACTTTCTTTATTCTC
2521342 TTTTA
1 TTTTA
2521347 AGTTTTCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTATTTTCACTTTCTTTATTCTC
Found at i:2523188 original size:163 final size:163
Alignment explanation
Indices: 2522903--2523284 Score: 622
Period size: 163 Copynumber: 2.3 Consensus size: 163
2522893 AAAACATATT
* * *
2522903 TTTATTCAAAAACCATATTAATCCCTCCAACCAAACACTCCGTAATGTGTAGGTTCCCCAGAACC
1 TTTA-TCAAAAATCATATTATTCCCTCCAACC-AACACTCCATAATGTGTAGGTTCCCCAGAACC
* * * * *
2522968 ATACACCTACCTACACACTAAGTAAGGACTTACCCTGAGCCCAAAGCATAGGAGCCTGCAGTAAC
64 ATACACCCACCTACACACCAAGTAAGGACTTACCCTGAGCACAAAGCAGAAGAGCCTGCAGTAAC
*
2523033 GATAACTTCTTCCAACAACACCCT-CTCATAAAACA
129 GATAACTTCCTCCAACAACACCCTCCT-ATAAAACA
*
2523068 TTTATCAAAAATCATATTATTCCCTCCAACCAACACTCCATAATGTGTAGGTTCCCTAGAACCAT
1 TTTATCAAAAATCATATTATTCCCTCCAACCAACACTCCATAATGTGTAGGTTCCCCAGAACCAT
*
2523133 ACACCCACCTACACACCAAGTAAGGACTTACCCTGAGCACAAAGCAGAAGAGCCTGCAGTAACGG
66 ACACCCACCTACACACCAAGTAAGGACTTACCCTGAGCACAAAGCAGAAGAGCCTGCAGTAACGA
*
2523198 TAACTTCCTCCAACAACACCTTCCTATAAAACA
131 TAACTTCCTCCAACAACACCCTCCTATAAAACA
2523231 TTTATCAAAAATCATATTATTCCCTCCAACCAACACTCCATAATGTGTAGGTTC
1 TTTATCAAAAATCATATTATTCCCTCCAACCAACACTCCATAATGTGTAGGTTC
2523285 TTAGGTTCCA
Statistics
Matches: 204, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
163 173 0.85
164 27 0.13
165 4 0.02
ACGTcount: A:0.36, C:0.31, G:0.10, T:0.23
Consensus pattern (163 bp):
TTTATCAAAAATCATATTATTCCCTCCAACCAACACTCCATAATGTGTAGGTTCCCCAGAACCAT
ACACCCACCTACACACCAAGTAAGGACTTACCCTGAGCACAAAGCAGAAGAGCCTGCAGTAACGA
TAACTTCCTCCAACAACACCCTCCTATAAAACA
Found at i:2525915 original size:32 final size:32
Alignment explanation
Indices: 2525867--2525927 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
2525857 TAATGCCCGA
* * *
2525867 TCAACGTCGGTTAAAGTTCTGGTCAACTGTGG
1 TCAACGCCGGTCAAAGTTCCGGTCAACTGTGG
2525899 TCAACGCCGGTCAAAGTTCCGGTCAACTG
1 TCAACGCCGGTCAAAGTTCCGGTCAACTG
2525928 AGTTTAACGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (32 bp):
TCAACGCCGGTCAAAGTTCCGGTCAACTGTGG
Found at i:2529059 original size:13 final size:12
Alignment explanation
Indices: 2529035--2529106 Score: 58
Period size: 14 Copynumber: 5.6 Consensus size: 12
2529025 CCAAATATTG
2529035 AATAAT-AAAAT
1 AATAATAAAAAT
2529046 AATAAGTAAAAAT
1 AATAA-TAAAAAT
2529059 ATATAATAAAAATAT
1 A-ATAAT-AAAA-AT
*
2529074 ACATAAGAAAGATAT
1 A-ATAATAAA-A-AT
2529089 AATAATAAAAAT
1 AATAATAAAAAT
2529101 AA-AATA
1 AATAATA
2529107 TATATATATG
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
11 9 0.17
12 5 0.10
13 8 0.15
14 18 0.35
15 12 0.23
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (12 bp):
AATAATAAAAAT
Found at i:2529066 original size:28 final size:28
Alignment explanation
Indices: 2529005--2529101 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 28
2528995 TAAAAAAACG
* *
2529005 AATAAATATATACATAATAACCAAATAT-T
1 AATAAAAATATACATAAGAA--AAATATAT
2529034 GAATAATAAA-ATA-ATAAGTAAAAATATAT
1 -AATAA-AAATATACATAAG-AAAAATATAT
*
2529063 AATAAAAATATACATAAGAAAGATATAAT
1 AATAAAAATATACATAAGAAAAATAT-AT
2529092 AATAAAAATA
1 AATAAAAATA
2529102 AAATATATAT
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
27 3 0.05
28 21 0.36
29 22 0.38
30 10 0.17
31 2 0.03
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (28 bp):
AATAAAAATATACATAAGAAAAATATAT
Found at i:2529093 original size:29 final size:28
Alignment explanation
Indices: 2529005--2529106 Score: 86
Period size: 28 Copynumber: 3.5 Consensus size: 28
2528995 TAAAAAAACG
*
2529005 AATAAATATATACATAA-TAACCAAATAT-T
1 AATAAAAATATA-ATAAGTAA--AAATATAT
2529034 GAATAATAAA-ATAATAAGTAAAAATATAT
1 -AATAA-AAATATAATAAGTAAAAATATAT
*
2529063 AATAAAAATATACATAAG-AAAGATATAAT
1 AATAAAAATATA-ATAAGTAAAAATAT-AT
*
2529092 AATAAAAATAAAATA
1 AATAAAAATATAATA
2529107 TATATATATG
Statistics
Matches: 63, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 23 0.37
30 11 0.17
31 2 0.03
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (28 bp):
AATAAAAATATAATAAGTAAAAATATAT
Found at i:2529212 original size:26 final size:26
Alignment explanation
Indices: 2529181--2529231 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2529171 AATAATAGAG
2529181 AAATATA-ATAAATAGATAAAAAAATT
1 AAATATATATAAATA-ATAAAAAAATT
* *
2529207 AAATATATATATATAATAATAAAAT
1 AAATATATATAAATAATAAAAAAAT
2529232 ATATTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (26 bp):
AAATATATATAAATAATAAAAAAATT
Found at i:2531269 original size:105 final size:105
Alignment explanation
Indices: 2530948--2531829 Score: 1440
Period size: 105 Copynumber: 8.4 Consensus size: 105
2530938 GTATTGTTCC
* * * * * * *
2530948 GAGTCCAATATCCTCCGCTGTGAAGTTGAAACTGGTTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
* * * *
2531013 CTAACGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCCG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** *
2531054 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTCGGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAA
* *** *
2531119 TCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2531160 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
2531225 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2531265 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGCCTCTGACATTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
2531330 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2531370 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
2531435 CAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2531475 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGACATTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
2531540 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2531580 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
2531645 CAGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2531685 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
2531750 CAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2531790 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
2531830 GGTAAAACCT
Statistics
Matches: 726, Mismatches: 49, Indels: 3
0.93 0.06 0.00
Matches are distributed among these distances:
105 591 0.81
106 135 0.19
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2532605 original size:10 final size:11
Alignment explanation
Indices: 2532575--2532604 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
2532565 ACCCGTCTTA
2532575 TTTTTTTTTCT
1 TTTTTTTTTCT
2532586 TTTTTTTTTCT
1 TTTTTTTTTCT
2532597 TTTTTTTT
1 TTTTTTTT
2532605 CAACTTAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:2532757 original size:118 final size:115
Alignment explanation
Indices: 2532538--2532773 Score: 373
Period size: 118 Copynumber: 2.0 Consensus size: 115
2532528 TTGGTTGCAA
* * * * *
2532538 GACGCCCTTTGCGGGTTTTCATCTTGAACCCGTCTTATTTTTTTTTCTTTTTTTTTTCTTTTTTT
1 GACGCACTTTACGGGTTTTCATCTTGAACCCGTCTTATTTTCTCTTCTTTTTTTTTTCCTTTTTT
2532603 TTCAACTTAAGACGCCCTCTCGGGTTTTCATCCTAAGCGAAGTATTTCTT
66 TTCAACTTAAGACGCCCTCTCGGGTTTTCATCCTAAGCGAAGTATTTCTT
2532653 GACGCACTTTACGGGTTTTCATCTTGAACCCGTCTTATTTTCTCTTCTTTTGTTCTTTTTCCTTT
1 GACGCACTTTACGGGTTTTCATCTTGAACCCGTCTTATTTTCTCTTC-TTT-TT-TTTTTCCTTT
* * *
2532718 TTTTTCAACTTAGGACGCCCTCTGGGGTTTTCATCCTAAGCGAATTATTTCTT
63 TTTTTCAACTTAAGACGCCCTCTCGGGTTTTCATCCTAAGCGAAGTATTTCTT
2532771 GAC
1 GAC
2532774 CGCGTCCGAG
Statistics
Matches: 110, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
115 43 0.39
116 3 0.03
117 2 0.02
118 62 0.56
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.48
Consensus pattern (115 bp):
GACGCACTTTACGGGTTTTCATCTTGAACCCGTCTTATTTTCTCTTCTTTTTTTTTTCCTTTTTT
TTCAACTTAAGACGCCCTCTCGGGTTTTCATCCTAAGCGAAGTATTTCTT
Found at i:2543261 original size:13 final size:12
Alignment explanation
Indices: 2543237--2543308 Score: 58
Period size: 14 Copynumber: 5.6 Consensus size: 12
2543227 CCAAATATTG
2543237 AATAAT-AAAAT
1 AATAATAAAAAT
2543248 AATAAGTAAAAAT
1 AATAA-TAAAAAT
2543261 ATATAATAAAAATAT
1 A-ATAAT-AAAA-AT
*
2543276 ACATAAGAAAGATAT
1 A-ATAATAAA-A-AT
2543291 AATAATAAAAAT
1 AATAATAAAAAT
2543303 AA-AATA
1 AATAATA
2543309 TATATATATG
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
11 9 0.17
12 5 0.10
13 8 0.15
14 18 0.35
15 12 0.23
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (12 bp):
AATAATAAAAAT
Found at i:2543268 original size:28 final size:28
Alignment explanation
Indices: 2543207--2543303 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 28
2543197 TAAAAAAACG
* *
2543207 AATAAATATATACATAATAACCAAATAT-T
1 AATAAAAATATACATAAGAA--AAATATAT
2543236 GAATAATAAA-ATA-ATAAGTAAAAATATAT
1 -AATAA-AAATATACATAAG-AAAAATATAT
*
2543265 AATAAAAATATACATAAGAAAGATATAAT
1 AATAAAAATATACATAAGAAAAATAT-AT
2543294 AATAAAAATA
1 AATAAAAATA
2543304 AAATATATAT
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
27 3 0.05
28 21 0.36
29 22 0.38
30 10 0.17
31 2 0.03
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (28 bp):
AATAAAAATATACATAAGAAAAATATAT
Found at i:2543295 original size:29 final size:28
Alignment explanation
Indices: 2543207--2543308 Score: 86
Period size: 28 Copynumber: 3.5 Consensus size: 28
2543197 TAAAAAAACG
*
2543207 AATAAATATATACATAA-TAACCAAATAT-T
1 AATAAAAATATA-ATAAGTAA--AAATATAT
2543236 GAATAATAAA-ATAATAAGTAAAAATATAT
1 -AATAA-AAATATAATAAGTAAAAATATAT
*
2543265 AATAAAAATATACATAAG-AAAGATATAAT
1 AATAAAAATATA-ATAAGTAAAAATAT-AT
*
2543294 AATAAAAATAAAATA
1 AATAAAAATATAATA
2543309 TATATATATG
Statistics
Matches: 63, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 23 0.37
30 11 0.17
31 2 0.03
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (28 bp):
AATAAAAATATAATAAGTAAAAATATAT
Found at i:2545370 original size:2 final size:2
Alignment explanation
Indices: 2545363--2545391 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2545353 CTTTTTAAAT
2545363 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2545392 GTACATTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2546122 original size:3 final size:3
Alignment explanation
Indices: 2546114--2546204 Score: 157
Period size: 3 Copynumber: 30.3 Consensus size: 3
2546104 ATCAATTCGA
2546114 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
2546162 ATT ATT ATT ATC ATT ATT -TAT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT A
2546205 CAGTTTAAAT
Statistics
Matches: 84, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
2 1 0.01
3 82 0.98
4 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2548807 original size:31 final size:31
Alignment explanation
Indices: 2548755--2548815 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2548745 ATTTAAAAGA
* *
2548755 ATTTTATTTTTATTTTCATTTAAAAATATGT
1 ATTTTATGTTAATTTTCATTTAAAAATATGT
*
2548786 ATTTTATGTTAATATTT-ATTTAAAAGTATG
1 ATTTTATGTTAAT-TTTCATTTAAAAATATG
2548816 ACTAAATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (31 bp):
ATTTTATGTTAATTTTCATTTAAAAATATGT
Found at i:2548814 original size:27 final size:27
Alignment explanation
Indices: 2548737--2548814 Score: 68
Period size: 31 Copynumber: 2.7 Consensus size: 27
2548727 AAGTTGGGAG
* *
2548737 AATACTTTATTTAAAAGAATTTTATTTT
1 AATA-TTTATTTAAAAGTATTTTATGTT
*
2548765 TAT-TTTCATTTAAAAATATGTATTTTATGTT
1 AATATTT-ATTT--AAA-A-GTATTTTATGTT
2548796 AATATTTATTTAAAAGTAT
1 AATATTTATTTAAAAGTAT
2548815 GACTAAATTG
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
26 3 0.08
27 8 0.20
28 3 0.08
29 6 0.15
30 1 0.03
31 16 0.40
32 3 0.08
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (27 bp):
AATATTTATTTAAAAGTATTTTATGTT
Found at i:2550128 original size:131 final size:131
Alignment explanation
Indices: 2549894--2550129 Score: 301
Period size: 131 Copynumber: 1.8 Consensus size: 131
2549884 TAATTTCAAG
* * ** * * *
2549894 AGTGAAAACGATAATATCAAATTATTTACAATCGAGAATAAATGACATTTCGTGCACTAAAACAA
1 AGTGAAAACGATAATAGCAAATGAAATACAATCGAGAATAAATGACATCTCATACACTAAAACAA
* * * *
2549959 TCATTTATTACCCCAATTGAAATAAAGAGATATTACTATTTCGTCTTAAAATTCAATATCGATTC
66 TCATTTATCACCCCAATCGAAACAAAAAGATATTACTATTTCGTCTTAAAATTCAATATCGATTC
2550024 A
131 A
* * * * *
2550025 AGTGAAAACGATAATAGCTAATGAAATCCAATCGAGAATAAATGACCTCTCATACATTAAAGCAA
1 AGTGAAAACGATAATAGCAAATGAAATACAATCGAGAATAAATGACATCTCATACACTAAAACAA
* **
2550090 TCATTTATCACTCGGATCGAAACAAAAAGATATTACTATT
66 TCATTTATCACCCCAATCGAAACAAAAAGATATTACTATT
2550130 CTCAGTGTCG
Statistics
Matches: 86, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
131 86 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (131 bp):
AGTGAAAACGATAATAGCAAATGAAATACAATCGAGAATAAATGACATCTCATACACTAAAACAA
TCATTTATCACCCCAATCGAAACAAAAAGATATTACTATTTCGTCTTAAAATTCAATATCGATTC
A
Found at i:2552183 original size:3 final size:3
Alignment explanation
Indices: 2552175--2552220 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
2552165 TAAAATTAGT
*
2552175 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2552221 GATGATGATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2553848 original size:35 final size:35
Alignment explanation
Indices: 2553804--2553871 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
2553794 TTGGTCACAT
*
2553804 TTGAATGATGTTATTGTTGAAGATGGTCGAAACTC
1 TTGAATGATGTTATTGTTGAAGATGGTCAAAACTC
* *
2553839 TTGACTGATGTTGTTGTTGAAGATGGTCAAAAC
1 TTGAATGATGTTATTGTTGAAGATGGTCAAAAC
2553872 CCTTATGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.37
Consensus pattern (35 bp):
TTGAATGATGTTATTGTTGAAGATGGTCAAAACTC
Found at i:2553898 original size:47 final size:48
Alignment explanation
Indices: 2553841--2553957 Score: 148
Period size: 47 Copynumber: 2.5 Consensus size: 48
2553831 CGAAACTCTT
* * **
2553841 GACTGATGTTGTTGTTGAAGATGGTCAAAAC-CCTTATGA-TTTTTAAA
1 GACTGATGTTGTTGTTGAAGATGATCAAAACTCC-GATGACTTTCCAAA
* * *
2553888 GATTGATGTTGTTGTTGAAGATGATCGAAACTCCGATGACTTTCCCAA
1 GACTGATGTTGTTGTTGAAGATGATCAAAACTCCGATGACTTTCCAAA
2553936 GACTGATGTTGTTGTTGAAGAT
1 GACTGATGTTGTTGTTGAAGAT
2553958 TATCGGAACT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
47 32 0.53
48 28 0.47
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (48 bp):
GACTGATGTTGTTGTTGAAGATGATCAAAACTCCGATGACTTTCCAAA
Found at i:2557366 original size:64 final size:63
Alignment explanation
Indices: 2557317--2557440 Score: 198
Period size: 64 Copynumber: 2.0 Consensus size: 63
2557307 TGCACTAAGG
*
2557317 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AACAAGCCTGAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AAACCTGAGTGCATCGATGCATGG--
2557380 T
63 T
2557381 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCAT
2557441 AAAATGCATT
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
64 29 0.51
65 26 0.46
66 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCATGGT
Found at i:2560154 original size:20 final size:23
Alignment explanation
Indices: 2560097--2560142 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2560087 ATGCACTGCT
2560097 GAGTGCATCGATGCATATTCATG
1 GAGTGCATCGATGCATATTCATG
* *
2560120 GAGTGCATCGGTGCATCTTCATG
1 GAGTGCATCGATGCATATTCATG
2560143 ATTATCGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (23 bp):
GAGTGCATCGATGCATATTCATG
Found at i:2567749 original size:19 final size:19
Alignment explanation
Indices: 2567722--2567773 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
2567712 ACAAGCCTGA
*
2567722 GTGCATCGATGCATGGTCT
1 GTGCATCGATGCATGGTAT
*
2567741 GTGCCTCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
2567760 GTGCATCGATGCAT
1 GTGCATCGATGCAT
2567774 AAAATGCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:2567863 original size:20 final size:20
Alignment explanation
Indices: 2567838--2567875 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2567828 TTCGAAATGG
2567838 TGAGTGCATCGATGCATCAA
1 TGAGTGCATCGATGCATCAA
*
2567858 TGAGTGCATCGGTGCATC
1 TGAGTGCATCGATGCATC
2567876 CCTTTACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAGTGCATCGATGCATCAA
Found at i:2568730 original size:2 final size:2
Alignment explanation
Indices: 2568723--2568749 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2568713 TCATCATAAA
2568723 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
2568750 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2568964 original size:31 final size:31
Alignment explanation
Indices: 2568926--2568990 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
2568916 GAACCTCAGC
2568926 AACTGTCCATAGGTCTCGAAGAACCCAGGTA
1 AACTGTCCATAGGTCTCGAAGAACCCAGGTA
*
2568957 AACTGTCCATAGGTCTCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCTCGAAGAACCCAGGTA
2568988 AAC
1 AAC
2568991 CCTCGACTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.20
Consensus pattern (31 bp):
AACTGTCCATAGGTCTCGAAGAACCCAGGTA
Found at i:2569471 original size:19 final size:20
Alignment explanation
Indices: 2569443--2569487 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
2569433 TATTCACACC
*
2569443 TATCATTAACACATGCAACA
1 TATCAATAACACATGCAACA
*
2569463 -ATCAATAACACATGTAACA
1 TATCAATAACACATGCAACA
2569482 TATCAA
1 TATCAA
2569488 CCATATGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.49, C:0.22, G:0.04, T:0.24
Consensus pattern (20 bp):
TATCAATAACACATGCAACA
Found at i:2569814 original size:20 final size:23
Alignment explanation
Indices: 2569789--2569842 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 23
2569779 CCTTGAAGTT
2569789 CATCGATGCATTC-T-ACA-GTG
1 CATCGATGCATTCTTAACATGTG
2569809 CATCGATGCATTCTTTAACATGTG
1 CATCGATGCATTC-TTAACATGTG
2569833 CATCGATGCA
1 CATCGATGCA
2569843 CTACCCATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.43
22 1 0.03
23 3 0.10
24 13 0.43
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (23 bp):
CATCGATGCATTCTTAACATGTG
Found at i:2569984 original size:65 final size:64
Alignment explanation
Indices: 2569830--2569991 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 64
2569820 TCTTTAACAT
* * *
2569830 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCAATTTAAGGGG
1 GTGCATCGATGCACTTCCTATGCATCGATACACCAATCACATTCGATGTTTTCAATTTAAGGGG
* * ** * *
2569894 GTGCATCGATGCAC-TCCTAATGCATCGATGCACTAATTGCATTCGATGTTTTCATTTTTTAA-T
1 GTGCATCGATGCACTTCCT-ATGCATCGATACACCAATCACATTCGATGTTTTCA--ATTTAAGG
2569957 GG
63 GG
*
2569959 GTGCATCGATGCACTTCCTGTGCATCGATACAC
1 GTGCATCGATGCACTTCCTATGCATCGATACAC
2569992 ACTGAATAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
63 2 0.02
64 44 0.53
65 28 0.34
66 9 0.11
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCACTTCCTATGCATCGATACACCAATCACATTCGATGTTTTCAATTTAAGGGG
Found at i:2573286 original size:30 final size:29
Alignment explanation
Indices: 2573247--2573330 Score: 73
Period size: 31 Copynumber: 2.8 Consensus size: 29
2573237 GAAGGACCTA
*
2573247 TCCAGAGGTCATAAAGAACCTCA-AAAACTG
1 TCCATAGGTCAT-AAGAACCT-AGAAAACTG
* *
2573277 TCCATAGGTCCCTAAGAACCTAGGTAAACTG
1 TCCATAGGT-CATAAGAACCTA-GAAAACTG
2573308 TCCATAGGTC-TCGAAGAACCTAG
1 TCCATAGGTCAT--AAGAACCTAG
2573331 GTAAACCCTC
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
29 2 0.04
30 18 0.39
31 26 0.57
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (29 bp):
TCCATAGGTCATAAGAACCTAGAAAACTG
Found at i:2573309 original size:31 final size:31
Alignment explanation
Indices: 2573271--2573336 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
2573261 AGAACCTCAA
*
2573271 AAACTGTCCATAGGTCCCTAAGAACCTAGGT
1 AAACTGTCCATAGGTCCCGAAGAACCTAGGT
*
2573302 AAACTGTCCATAGGTCTCGAAGAACCTAGGT
1 AAACTGTCCATAGGTCCCGAAGAACCTAGGT
2573333 AAAC
1 AAAC
2573337 CCTCGACTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (31 bp):
AAACTGTCCATAGGTCCCGAAGAACCTAGGT
Found at i:2574155 original size:20 final size:22
Alignment explanation
Indices: 2574130--2574187 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
2574120 TTTCCCTTGA
2574130 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
2574150 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
2574173 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
2574188 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:2574262 original size:64 final size:64
Alignment explanation
Indices: 2574175--2574336 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 64
2574165 TCTTTAACAT
* * *
2574175 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCA-TTTT-AAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTGAA-GG
2574238 G
64 G
* * * * *
2574239 GTGCATCGATGTACTCCTAATGCATCGATGCACTAATTACATTCGATGTTTCCATTTTTGAATGG
1 GTGCATCGATGCACTCCT-ATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTGAAGGG
* *
2574304 GTACATCGATGCACTTCCTGTGCATCGATACAC
1 GTGCATCGATGCAC-TCCTATGCATCGATACAC
2574337 ACTGAATAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
63 2 0.02
64 44 0.54
65 30 0.37
66 6 0.07
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCACTCCTATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTGAAGGG
Found at i:2576981 original size:21 final size:21
Alignment explanation
Indices: 2576955--2577002 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2576945 TCCAAACCAT
2576955 AAGCAAGATCTGATGTTTCCA
1 AAGCAAGATCTGATGTTTCCA
*
2576976 AAGCAAGATCTGTTGTTTCCA
1 AAGCAAGATCTGATGTTTCCA
2576997 AAGCAA
1 AAGCAA
2577003 AAAATTGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (21 bp):
AAGCAAGATCTGATGTTTCCA
Found at i:2581295 original size:21 final size:21
Alignment explanation
Indices: 2581269--2581311 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2581259 TTTCTGGGTT
* *
2581269 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
2581290 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
2581311 A
1 A
2581312 CGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:2581424 original size:68 final size:69
Alignment explanation
Indices: 2581291--2581444 Score: 197
Period size: 69 Copynumber: 2.2 Consensus size: 69
2581281 ACCCATTCAA
* * *
2581291 GGGGAACCGATACCCCTTCAACGAAATGAATTTCCAGAATGCAAGAGGGGAATCGATACCCCCA-
1 GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCCAG
2581355 GGGG
66 GGGG
* * * *
2581359 GGGGAACCGATACCCCCTCATCGTATAA-GAAATTCCATAATGCTATAGGGGAACCGATA-CCCC
1 GGGGAACCGATACCCCCTCAACG-A-AATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCC
2581422 AGGGGG
64 AGGGGG
*
2581428 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
2581445 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
68 26 0.35
69 47 0.63
70 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCCAG
GGGG
Found at i:2581781 original size:29 final size:29
Alignment explanation
Indices: 2581747--2581818 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
2581737 CATATTATGA
** *
2581747 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAACGTAT
*
2581776 TACATGACATGAATTCATATTATACGTAT
1 TACATGACATGAATTCATATTAAACGTAT
2581805 TACATGACATGAAT
1 TACATGACATGAAT
2581819 ATACAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAACGTAT
Found at i:2581875 original size:30 final size:29
Alignment explanation
Indices: 2581832--2581909 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
2581822 CAGAAAAAGT
*
2581832 TATATGCACTATGTGATAAAGGTATGTAAA
1 TATATGC-CTATGTGATAAAGGTATGGAAA
* *
2581862 TGATATGCCTATGTGTTAAAGTTATGGAAA
1 T-ATATGCCTATGTGATAAAGGTATGGAAA
* *
2581892 TACTATGTCTACGTGATA
1 TA-TATGCCTATGTGATA
2581910 TGAACTACGG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 33 0.82
31 6 0.15
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.36
Consensus pattern (29 bp):
TATATGCCTATGTGATAAAGGTATGGAAA
Found at i:2582186 original size:22 final size:22
Alignment explanation
Indices: 2582112--2582178 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
2582102 TTATGGACAT
2582112 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2582134 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2582156 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2582178 A
1 A
2582179 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:2582950 original size:31 final size:31
Alignment explanation
Indices: 2582898--2582958 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2582888 ATTTAAAAGA
* *
2582898 ATTTTATTTTTATTTTCATTTAAAAATATGT
1 ATTTTATGTTAATTTTCATTTAAAAATATGT
*
2582929 ATTTTATGTTAATATTT-ATTTAAAAGTATG
1 ATTTTATGTTAAT-TTTCATTTAAAAATATG
2582959 ACTAAATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (31 bp):
ATTTTATGTTAATTTTCATTTAAAAATATGT
Found at i:2582957 original size:27 final size:27
Alignment explanation
Indices: 2582880--2582957 Score: 68
Period size: 31 Copynumber: 2.7 Consensus size: 27
2582870 AAGTTGGGAG
* *
2582880 AATACTTTATTTAAAAGAATTTTATTTT
1 AATA-TTTATTTAAAAGTATTTTATGTT
*
2582908 TAT-TTTCATTTAAAAATATGTATTTTATGTT
1 AATATTT-ATTT--AAA-A-GTATTTTATGTT
2582939 AATATTTATTTAAAAGTAT
1 AATATTTATTTAAAAGTAT
2582958 GACTAAATTG
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
26 3 0.08
27 8 0.20
28 3 0.08
29 6 0.15
30 1 0.03
31 16 0.40
32 3 0.08
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (27 bp):
AATATTTATTTAAAAGTATTTTATGTT
Found at i:2584274 original size:131 final size:131
Alignment explanation
Indices: 2584040--2584275 Score: 301
Period size: 131 Copynumber: 1.8 Consensus size: 131
2584030 TAATTTCAAG
* * ** * * *
2584040 AGTGAAAACGATAATATCAAATTATTTACAATCGAGAATAAATGACATTTCGTGCACTAAAACAA
1 AGTGAAAACGATAATAGCAAATGAAATACAATCGAGAATAAATGACATCTCATACACTAAAACAA
* * * *
2584105 TCATTTATTACCCCAATTGAAATAAAGAGATATTACTATTTCGTCTTAAAATTCAATATCGATTC
66 TCATTTATCACCCCAATCGAAACAAAAAGATATTACTATTTCGTCTTAAAATTCAATATCGATTC
2584170 A
131 A
* * * * *
2584171 AGTGAAAACGATAATAGCTAATGAAATCCAATCGAGAATAAATGACCTCTCATACATTAAAGCAA
1 AGTGAAAACGATAATAGCAAATGAAATACAATCGAGAATAAATGACATCTCATACACTAAAACAA
* **
2584236 TCATTTATCACTCGGATCGAAACAAAAAGATATTACTATT
66 TCATTTATCACCCCAATCGAAACAAAAAGATATTACTATT
2584276 CTCAGTGTCG
Statistics
Matches: 86, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
131 86 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (131 bp):
AGTGAAAACGATAATAGCAAATGAAATACAATCGAGAATAAATGACATCTCATACACTAAAACAA
TCATTTATCACCCCAATCGAAACAAAAAGATATTACTATTTCGTCTTAAAATTCAATATCGATTC
A
Found at i:2586330 original size:3 final size:3
Alignment explanation
Indices: 2586322--2586358 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2586312 TAAAATTAGT
*
2586322 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2586359 GATGATGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2586363 original size:3 final size:3
Alignment explanation
Indices: 2586357--2586400 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2586347 AATAATAATA
2586357 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
2586401 AATAGGACGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:2588017 original size:35 final size:35
Alignment explanation
Indices: 2587973--2588040 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
2587963 TTGGTCACAT
*
2587973 TTGAATGATGTTATTGTTGAAGATGGTCGAAACTC
1 TTGAATGATGTTATTGTTGAAGATGGTCAAAACTC
* *
2588008 TTGACTGATGTTGTTGTTGAAGATGGTCAAAAC
1 TTGAATGATGTTATTGTTGAAGATGGTCAAAAC
2588041 CCTTATGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.37
Consensus pattern (35 bp):
TTGAATGATGTTATTGTTGAAGATGGTCAAAACTC
Found at i:2588067 original size:47 final size:48
Alignment explanation
Indices: 2588010--2588126 Score: 148
Period size: 47 Copynumber: 2.5 Consensus size: 48
2588000 CGAAACTCTT
* * **
2588010 GACTGATGTTGTTGTTGAAGATGGTCAAAAC-CCTTATG-ATTTTTAAA
1 GACTGATGTTGTTGTTGAAGATGATCAAAACTCC-GATGAATTTCCAAA
* * *
2588057 GATTGATGTTGTTGTTGAAGATGATCGAAACTCCGATGAATTTCCCAA
1 GACTGATGTTGTTGTTGAAGATGATCAAAACTCCGATGAATTTCCAAA
2588105 GACTGATGTTGTTGTTGAAGAT
1 GACTGATGTTGTTGTTGAAGAT
2588127 TATCGGAACT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
47 31 0.52
48 29 0.48
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (48 bp):
GACTGATGTTGTTGTTGAAGATGATCAAAACTCCGATGAATTTCCAAA
Found at i:2591525 original size:64 final size:63
Alignment explanation
Indices: 2591476--2591599 Score: 189
Period size: 64 Copynumber: 2.0 Consensus size: 63
2591466 TGCACTAAGG
*
2591476 GTGCATCGATGCATAAAATACATTCGATG-TTTCA-AACAAGCCTGAGTGCATCGATGCATGGTC
1 GTGCATCGATGCATAAAATACATTCGATGTTTTCATAA-AAACCTGAGTGCATCGATGCATGG--
2591539 T
63 T
*
2591540 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCAT
1 GTGCATCGATGCATAAAATACATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCAT
2591600 AAAATGCATT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
64 28 0.50
65 26 0.46
66 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATACATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCATGGT
Found at i:2594298 original size:23 final size:22
Alignment explanation
Indices: 2594271--2594350 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 22
2594261 CACTGCTGAG
2594271 TGCATCGATGCACATTCATGGA
1 TGCATCGATGCACATTCATGGA
*
2594293 GTGCATCGGTGCATC-TTCAT-GA
1 -TGCATCGATGCA-CATTCATGGA
* * *
2594315 TGTATCGATGCAAATTCAAAGGA
1 TGCATCGATGCACATTC-ATGGA
*
2594338 TGCATCAATGCAC
1 TGCATCGATGCAC
2594351 TAGTGATAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
21 13 0.29
22 3 0.07
23 28 0.62
24 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACATTCATGGA
Found at i:2604442 original size:2 final size:2
Alignment explanation
Indices: 2604435--2604459 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2604425 ATACCATAAA
2604435 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
2604460 TATATATATC
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2604640 original size:30 final size:30
Alignment explanation
Indices: 2604601--2604690 Score: 78
Period size: 31 Copynumber: 2.9 Consensus size: 30
2604591 GAAAGACCTA
*
2604601 TCCAGAGGTCATAAAGAACCT-CG-ACAACTG
1 TCCATAGGTCAT-AAGAACCTACGTA-AACTG
* *
2604631 TCCATAGGTCCCTAAGAACCTAGGTAAACTG
1 TCCATAGGT-CATAAGAACCTACGTAAACTG
*
2604662 TCCATAGGTC-TCGAAGAACCTAGGTAAAC
1 TCCATAGGTCAT--AAGAACCTACGTAAAC
2604691 CCTCGACTCT
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
29 1 0.02
30 17 0.33
31 33 0.63
32 1 0.02
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (30 bp):
TCCATAGGTCATAAGAACCTACGTAAACTG
Found at i:2604664 original size:31 final size:31
Alignment explanation
Indices: 2604626--2604690 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
2604616 GAACCTCGAC
*
2604626 AACTGTCCATAGGTCCCTAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
*
2604657 AACTGTCCATAGGTCTCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
2604688 AAC
1 AAC
2604691 CCTCGACTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACCTAGGTA
Found at i:2605544 original size:24 final size:20
Alignment explanation
Indices: 2605487--2605524 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2605477 TTTCCATTGA
2605487 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
2605507 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
2605525 TTAACATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:2605610 original size:64 final size:64
Alignment explanation
Indices: 2605533--2605693 Score: 166
Period size: 64 Copynumber: 2.5 Consensus size: 64
2605523 CTTTAACATT
* *
2605533 TGCATCGATGCACTACACATGCATCGATACACCAATCACCTTCGATGTTTTCA-TTTT-AAGGGG
1 TGCATCGATGCACTACA-ATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTGAA-GGG
2605596 G
64 G
* * * *
2605597 TGCATCGATGCACTCCTAATGCATCGATGA-ACTAATTACATTCGATGTTTCCATTTTTGAATGG
1 TGCATCGATGCACTAC-AATGCATCGAT-ACACCAATCACATTCGATGTTTCCATTTTTGAAGGG
2605661 G
64 G
* * **
2605662 TACATCGATGCACTTCTTGTGCATCGATACAC
1 TGCATCGATGCACTAC-AATGCATCGATACAC
2605694 ACTGAATAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
64 45 0.55
65 35 0.43
66 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (64 bp):
TGCATCGATGCACTACAATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTGAAGGGG
Found at i:2608335 original size:21 final size:21
Alignment explanation
Indices: 2608309--2608358 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
2608299 TCCAAACCAT
2608309 AAGCAAGATCTGATGTTTCCA
1 AAGCAAGATCTGATGTTTCCA
*
2608330 AAGCAAGATCTGTTGTTTCCA
1 AAGCAAGATCTGATGTTTCCA
2608351 AAGCAAGA
1 AAGCAAGA
2608359 AATTGGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (21 bp):
AAGCAAGATCTGATGTTTCCA
Found at i:2609062 original size:31 final size:31
Alignment explanation
Indices: 2609027--2609085 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2609017 AACTTAAAAG
* *
2609027 AGTTTTGTAATACTGAAATTTAAATAATTTT
1 AGTTTTATAATAATGAAATTTAAATAATTTT
2609058 AGTTTTATAATAATGAAATTTAAATAAT
1 AGTTTTATAATAATGAAATTTAAATAAT
2609086 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (31 bp):
AGTTTTATAATAATGAAATTTAAATAATTTT
Found at i:2609134 original size:22 final size:22
Alignment explanation
Indices: 2609109--2609374 Score: 205
Period size: 22 Copynumber: 12.5 Consensus size: 22
2609099 ATAATAAATT
2609109 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
2609131 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
**
2609153 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
2609175 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** **
2609197 TTTTAAAATCCAT--AT-TTTA
1 TTTTAAAATAAATCAATCCATA
*** * *
2609216 AAAT-AAATCAATCCAT--AT-
1 TTTTAAAATAAATCAATCCATA
* * *
2609234 TTTAAAATAAATCAATCCAT--AT-
1 TTT--TA-AAATAAATCAATCCATA
2609256 TTTTAA-ATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
2609277 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
* *** *
2609299 TCTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
* *
2609321 TTTAAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
2609343 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
2609365 TTTTAAAATA
1 TTTTAAAATA
2609375 GATTTAAATA
Statistics
Matches: 196, Mismatches: 36, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
18 15 0.08
19 5 0.03
20 7 0.04
21 10 0.05
22 155 0.79
23 4 0.02
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:2609160 original size:44 final size:44
Alignment explanation
Indices: 2609109--2609374 Score: 352
Period size: 44 Copynumber: 6.2 Consensus size: 44
2609099 ATAATAAATT
*
2609109 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
**
2609153 TTTTAAAATAAAAT-TTTCCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAAT-AAATCAATCCATATTTTAAAATAAATCAATCCATA
2609197 -TTT----T-AA--AATCCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
*
2609233 TTTTAAAATAAATCAATCCATATTTTTAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
* * *** *
2609277 TTTTAAAATAAATCAATCTATATCTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
* *
2609321 TTTAAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
2609365 TTTTAAAATA
1 TTTTAAAATA
2609375 GATTTAAATA
Statistics
Matches: 191, Mismatches: 22, Indels: 18
0.83 0.10 0.08
Matches are distributed among these distances:
36 28 0.15
37 5 0.03
39 1 0.01
41 1 0.01
42 2 0.01
43 3 0.02
44 147 0.77
45 4 0.02
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.40
Consensus pattern (44 bp):
TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
Found at i:2609179 original size:66 final size:66
Alignment explanation
Indices: 2609109--2609374 Score: 345
Period size: 66 Copynumber: 4.2 Consensus size: 66
2609099 ATAATAAATT
**
2609109 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAAAT-TTTCCA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAAT-AAATCAATCCA
2609173 TA
65 TA
2609175 TTTTAAAATAAATCAATCCATATTTT---A-AAATC---C-ATATTTTAAAATAAATCAATCCAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCAT
2609232 A
66 A
* * *
2609233 TTTTAAAATAAATCAATCCATATTTTTAAATAAATCAATCCATATTTTAAAATAAATCAATCTAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCAT
2609298 A
66 A
* *** * *
2609299 TCTTAAAATAAATTTTTTCATATTTAAAAATAAATCAAT-TCATATTTTAAAATAAATCAATCCA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCT-ATATTTTAAAATAAATCAATCCA
2609363 TA
65 TA
2609365 TTTTAAAATA
1 TTTTAAAATA
2609375 GATTTAAATA
Statistics
Matches: 177, Mismatches: 13, Indels: 20
0.84 0.06 0.10
Matches are distributed among these distances:
57 4 0.02
58 44 0.25
59 1 0.01
61 1 0.01
62 10 0.06
63 1 0.01
65 1 0.01
66 115 0.65
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.40
Consensus pattern (66 bp):
TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCAT
A
Found at i:2609186 original size:80 final size:80
Alignment explanation
Indices: 2609114--2609364 Score: 261
Period size: 80 Copynumber: 3.0 Consensus size: 80
2609104 AAATTTTTTA
* **
2609114 AAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAAAT-TTTCCATATTT
1 AAATAAA--AATCCATATTTTAAAATAAATCAATCCATATTTTAAAAT-AAATCAATCCATATTT
2609178 TAAAATAAATCAATCCAT
63 TAAAATAAATCAATCCAT
** * *
2609196 ATTTTAAAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTTA
1 AAATAAAAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAA
2609261 AATAAATCAATCCATATTTT
66 AATAAATCAATCC--A---T
* * *** * * *
2609281 AAAATAAATCAATCTATATCTTAAAATAAATTTTTTCATATTTAAAAATAAATCAATTCATATTT
1 -AAATAAA--AATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTT
2609346 TAAAATAAATCAATCCAT
63 TAAAATAAATCAATCCAT
2609364 A
1 A
2609365 TTTTAAAATA
Statistics
Matches: 141, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
79 4 0.03
80 62 0.44
82 6 0.04
83 1 0.01
85 1 0.01
86 5 0.04
88 62 0.44
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (80 bp):
AAATAAAAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAA
AATAAATCAATCCAT
Found at i:2609208 original size:14 final size:14
Alignment explanation
Indices: 2609189--2609219 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2609179 AAAATAAATC
2609189 AATCCATATTTTAA
1 AATCCATATTTTAA
2609203 AATCCATATTTTAA
1 AATCCATATTTTAA
2609217 AAT
1 AAT
2609220 AAATCAATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (14 bp):
AATCCATATTTTAA
Found at i:2611446 original size:211 final size:207
Alignment explanation
Indices: 2610923--2611523 Score: 970
Period size: 199 Copynumber: 2.9 Consensus size: 207
2610913 TTTCAGAGTG
*
2610923 ACTGTTCATTCTCGGACGAACATGGTGTCAATATGTTGTAGAATGGTTAAAGGTCTCCTCTCAAA
1 ACTGTTCATTCTCGGACGAACATGGTGTCAATATGTTGTAGAATGGTTAAATGTCTCCTCTCAAA
*
2610988 CTTATCATCTTTGATCAGCTTCATTGCTTCGCTGCTATCAACTTCAAGTATCACTTGCTTCTCGC
66 CTTATCATCTTTGATCAGCTTCACTGCTTCGCTGCTATCAACTTCAAGTATCACTTGCTTCTCGC
* *
2611053 CTGCTTTCCAGTCTGTTCGAAGTCC-CTAGAGTATTTCCCATAATTCTGATTCCAGTGGGGATAA
131 CTGCTTTCCAGGCTGTTCGAAGTCCTC-AGAGTATGTCCCATAATTCTGATTCCAGTGGGGATAA
**
2611117 GAAGTTCCTCGTG
195 GAAGTTCCTCGCC
*
2611130 ACTGTTCATTCTC-G--G-----GGTGTCAATATGTTGTAGAATGGCTAAATGTCTCCTCTCAAA
1 ACTGTTCATTCTCGGACGAACATGGTGTCAATATGTTGTAGAATGGTTAAATGTCTCCTCTCAAA
2611187 CTTATCATCTTTGATCAGCTTCACTGCTTCGCTGCTATCAACTTCAAGTATCACTTGCTTCTCGC
66 CTTATCATCTTTGATCAGCTTCACTGCTTCGCTGCTATCAACTTCAAGTATCACTTGCTTCTCGC
*
2611252 CTGCTTTCCAGGCTGTTCGAAGTCCATCGAGTATGTATGTACCATAATTCTGATTCCAGTGGGGA
131 CTGCTTTCCAGGCTGTTCGAAGTCC-TC-AG-A-GTATGTCCCATAATTCTGATTCCAGTGGGGA
2611317 TAAGAAGTTCCTCGCC
192 TAAGAAGTTCCTCGCC
* *
2611333 ACTGTTCATTCTCGGACGAACATGGTGTCAATATATTGTAGAATGTTTAAATGTCTCCTCTCAAA
1 ACTGTTCATTCTCGGACGAACATGGTGTCAATATGTTGTAGAATGGTTAAATGTCTCCTCTCAAA
*
2611398 CGTATCATCTTTGATCAGCTTCACTGCTTCGCTGCTATCAACTTCAAGTATCACTTGCTTCTCGC
66 CTTATCATCTTTGATCAGCTTCACTGCTTCGCTGCTATCAACTTCAAGTATCACTTGCTTCTCGC
*
2611463 CTGCTTTCCAGGCTGTTCGAAGTCCCTC-GAGTATGTCCCATAATTCTGATACCAGTGGGGA
131 CTGCTTTCCAGGCTGTTCGAAGT-CCTCAGAGTATGTCCCATAATTCTGATTCCAGTGGGGA
2611524 GCAGTAATAT
Statistics
Matches: 366, Mismatches: 15, Indels: 26
0.90 0.04 0.06
Matches are distributed among these distances:
199 128 0.35
201 3 0.01
202 1 0.00
203 56 0.15
204 2 0.01
206 2 0.01
207 42 0.11
208 1 0.00
209 1 0.00
211 128 0.35
212 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (207 bp):
ACTGTTCATTCTCGGACGAACATGGTGTCAATATGTTGTAGAATGGTTAAATGTCTCCTCTCAAA
CTTATCATCTTTGATCAGCTTCACTGCTTCGCTGCTATCAACTTCAAGTATCACTTGCTTCTCGC
CTGCTTTCCAGGCTGTTCGAAGTCCTCAGAGTATGTCCCATAATTCTGATTCCAGTGGGGATAAG
AAGTTCCTCGCC
Found at i:2612493 original size:31 final size:29
Alignment explanation
Indices: 2612452--2612516 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
2612442 GGGTAGAAGC
* *
2612452 AAAAAAAAGGAAAAATTAATGACAAAAGGA
1 AAAAAAAAGGAAAAAGTAA-AACAAAAGGA
* *
2612482 AAAAAAGAAGGAGAAAGTAAAAGAAAAGGA
1 AAAAAA-AAGGAAAAAGTAAAACAAAAGGA
2612512 AAAAA
1 AAAAA
2612517 GAAAATTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.72, C:0.02, G:0.20, T:0.06
Consensus pattern (29 bp):
AAAAAAAAGGAAAAAGTAAAACAAAAGGA
Found at i:2614071 original size:42 final size:42
Alignment explanation
Indices: 2614004--2614084 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
2613994 TTGTGGCATT
* *
2614004 TATTACAAAAACGCCACTAAGGTGCATGACTATAGCGGTTTC
1 TATTACAAAAACACCACTAAAGTGCATGACTATAGCGGTTTC
* * * *
2614046 TATTACAAAAACATCGCTAAAGTGCATGATTATTGCGGT
1 TATTACAAAAACACCACTAAAGTGCATGACTATAGCGGT
2614085 GTTTATCTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (42 bp):
TATTACAAAAACACCACTAAAGTGCATGACTATAGCGGTTTC
Found at i:2614363 original size:27 final size:28
Alignment explanation
Indices: 2614333--2614388 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
2614323 ATATTATTAT
2614333 AATT-AATTTATAT-ATTTTCTTTAAAAA
1 AATTAAATTTATATAATTTT-TTTAAAAA
*
2614360 AATTAAATTTATATAATTTTTTTACAAA
1 AATTAAATTTATATAATTTTTTTAAAAA
2614388 A
1 A
2614389 TTGAAAAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 4 0.15
28 17 0.65
29 5 0.19
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (28 bp):
AATTAAATTTATATAATTTTTTTAAAAA
Found at i:2614959 original size:81 final size:81
Alignment explanation
Indices: 2614766--2614985 Score: 273
Period size: 82 Copynumber: 2.7 Consensus size: 81
2614756 CAAACGGGGC
* ** * *
2614766 CTAAAGTGCATGACTATTGCGGTGTTTATTGCAAAAACGTCACTAAAGTGCATGACTATTGTGGT
1 CTAAAGTGCATGACTATTGTGGCATTTA-T--AAAAACGCCGCTAAAGTGCATGACTATTGTGGT
* *
2614831 GTTTATTACAAAAATGTCA
63 GTTTATCACAAAAATGCCA
**
2614850 CTAAAGTGCATGACTATTGTGGTGTTTATAAAAAACGCCGCTAAAGTGCATGACTATTGTGGCT-
1 CTAAAGTGCATGACTATTGTGGCATTTAT-AAAAACGCCGCTAAAGTGCATGACTATTGTGG-TG
2614914 TTTATCA-AAAAATGCCA
64 TTTATCACAAAAATGCCA
* * *
2614931 CTAAATTGTATGATTATTGTGGCATTTATAAAAACGCCGCTAAAGTGCATGACTA
1 CTAAAGTGCATGACTATTGTGGCATTTATAAAAACGCCGCTAAAGTGCATGACTA
2614986 CTGCGGCGTT
Statistics
Matches: 124, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
80 26 0.21
81 33 0.27
82 36 0.29
83 2 0.02
84 27 0.22
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (81 bp):
CTAAAGTGCATGACTATTGTGGCATTTATAAAAACGCCGCTAAAGTGCATGACTATTGTGGTGTT
TATCACAAAAATGCCA
Found at i:2615050 original size:42 final size:41
Alignment explanation
Indices: 2614766--2615054 Score: 271
Period size: 42 Copynumber: 7.0 Consensus size: 41
2614756 CAAACGGGGC
* * * *
2614766 CTAAAGTGCATGACTATTGCGGTGTTTATTGCAAAAACGTCA
1 CTAAAGTGCATGACTATTGTGGTGTTTATT-AAAAAACGCCG
* * *
2614808 CTAAAGTGCATGACTATTGTGGTGTTTATTACAAAAATGTCA
1 CTAAAGTGCATGACTATTGTGGTGTTTATTA-AAAAACGCCG
2614850 CTAAAGTGCATGACTATTGTGGTGTTTA-TAAAAAACGCCG
1 CTAAAGTGCATGACTATTGTGGTGTTTATTAAAAAACGCCG
* * *
2614890 CTAAAGTGCATGACTATTGTGGCT-TTTATCAAAAAATGCCA
1 CTAAAGTGCATGACTATTGTGG-TGTTTATTAAAAAACGCCG
* * * **
2614931 CTAAATTGTATGATTATTGTGGCATTTA-T-AAAAACGCCG
1 CTAAAGTGCATGACTATTGTGGTGTTTATTAAAAAACGCCG
* * * * * *
2614970 CTAAAGTGCATGACTACTGCGGCGTTTTTGTAATAAACACCG
1 CTAAAGTGCATGACTATTGTGGTGTTTAT-TAAAAAACGCCG
* * * * *
2615012 CTAAGGTGAATGACTATTGCGGTATTTATTACAAAAACACCG
1 CTAAAGTGCATGACTATTGTGGTGTTTATTA-AAAAACGCCG
2615054 C
1 C
2615055 CTTATAAGAG
Statistics
Matches: 207, Mismatches: 32, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
39 29 0.14
40 33 0.16
41 38 0.18
42 107 0.52
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (41 bp):
CTAAAGTGCATGACTATTGTGGTGTTTATTAAAAAACGCCG
Found at i:2620776 original size:14 final size:14
Alignment explanation
Indices: 2620759--2620789 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2620749 GATGGATATA
2620759 TATCGTATAATTCT
1 TATCGTATAATTCT
2620773 TATCGTATAATTCT
1 TATCGTATAATTCT
2620787 TAT
1 TAT
2620790 ATATTGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (14 bp):
TATCGTATAATTCT
Found at i:2623379 original size:19 final size:20
Alignment explanation
Indices: 2623355--2623396 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2623345 GAATTTGAAA
2623355 TTAAG-AGTATCTCTTATTT
1 TTAAGAAGTATCTCTTATTT
* *
2623374 TTAAGAATTATCTTTTATTT
1 TTAAGAAGTATCTCTTATTT
2623394 TTA
1 TTA
2623397 GGATTAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (20 bp):
TTAAGAAGTATCTCTTATTT
Found at i:2623391 original size:20 final size:20
Alignment explanation
Indices: 2623362--2623432 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
2623352 AAATTAAGAG
*
2623362 TATCTCTTATTTTTAAGAAT
1 TATCTTTTATTTTTAAGAAT
*
2623382 TATCTTTTATTTTT-AGGAT
1 TATCTTTTATTTTTAAGAAT
**
2623401 TAAGTTTGAATATTTTTCAAGAAT
1 TATCTTT---TATTTTT-AAGAAT
2623425 TATCTTTT
1 TATCTTTT
2623433 GTTATTTCTT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
19 9 0.23
20 13 0.33
21 1 0.03
22 7 0.18
24 9 0.23
ACGTcount: A:0.28, C:0.07, G:0.08, T:0.56
Consensus pattern (20 bp):
TATCTTTTATTTTTAAGAAT
Found at i:2627370 original size:3 final size:3
Alignment explanation
Indices: 2627362--2627401 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2627352 GATTATGCTT
2627362 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2627402 CTTAAGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2629461 original size:32 final size:32
Alignment explanation
Indices: 2629415--2629508 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 32
2629405 AACGAAATAA
* * *
2629415 ATTTATTCAAAATAAAAATTTGTCTCAAATTT
1 ATTTAATCAAAATAAAAATTTCTCACAAATTT
** * *
2629447 ATTTTGTCAAAATAAAAAATTCTGACAAATTT
1 ATTTAATCAAAATAAAAATTTCTCACAAATTT
* * *
2629479 ATTTAATCAAAATAATAATTTATAACAAAT
1 ATTTAATCAAAATAAAAATTTCTCACAAAT
2629509 ATTAATTTCT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (32 bp):
ATTTAATCAAAATAAAAATTTCTCACAAATTT
Found at i:2629603 original size:185 final size:188
Alignment explanation
Indices: 2629291--2629781 Score: 604
Period size: 198 Copynumber: 2.6 Consensus size: 188
2629281 GGATTTCGAT
* * *
2629291 ATTTATTTAGTCATAATAACAATTTATAACAATTATTAATTTCTCAATATAAAAAATT-TGACAA
1 ATTTATTTAATCAAAATAACAATTTATAACAAATATTAATTTCTC-ATATAAAAAATTGTGACAA
* * *
2629355 AAAATATTCTTTCATAATAACAAATTGTAACAAATTTATTTAGTTACAATAACGAAATAAATTTA
65 ATAATATTCTTTCACAATAACAAATTGTAACAAAATTATTTAGTTACAATAACGAAATAAATTTA
* *
2629420 TTCAAAATAAA-AATT-TGTCTCAA-A-T-T-TATTTTGTCAAAATAAAAAATTCTGACAA
130 GTCAAAATAAATAATTATGTC-AAATATTCTATATTTTGTCAAAAT-AAAAATTCTGACAA
* *
2629475 ATTTATTTAATCAAAATAATAATTTATAACAAATATTAATTTCTCATCATAAAGAATTGTGACAA
1 ATTTATTTAATCAAAATAACAATTTATAACAAATATTAATTTCTCAT-ATAAAAAATTGTGACAA
* * **
2629540 GTAATATTCTTTCACAATAACAAATTGTAACAAAATGATTTA-TTCACAATAAC-ACGTTAAATT
65 ATAATATTCTTTCACAATAACAAATTGTAACAAAATTATTTAGTT-ACAATAACGA-AATAAATT
* * *
2629603 TAGTCAAAGTAAATAGTTATGTCAAATTTATTTCGTCTCAATATTTTGTCAAAATAAAAATTGTG
128 TAGTCAAAATAAATAATTATGTCAAA--TA--T--TCT--ATATTTTGTCAAAATAAAAATTCTG
2629668 ACAA
185 ACAA
* *
2629672 ATTTATTTAATCAAAATAACAATTTGTAACAAATATTAATTTCTCATTTATAAAAAAATGTGACA
1 ATTTATTTAATCAAAATAACAATTTATAACAAATATTAATTTCTCA--TATAAAAAATTGTGACA
2629737 AATAATATTCTTTCACAATAACAAATTGTAACAAAATTATTTAGT
64 AATAATATTCTTTCACAATAACAAATTGTAACAAAATTATTTAGT
2629782 CGGAGTAAAA
Statistics
Matches: 263, Mismatches: 23, Indels: 27
0.84 0.07 0.09
Matches are distributed among these distances:
183 2 0.01
184 53 0.20
185 68 0.26
186 5 0.02
187 4 0.02
189 1 0.00
194 1 0.00
195 1 0.00
197 57 0.22
198 69 0.26
199 2 0.01
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (188 bp):
ATTTATTTAATCAAAATAACAATTTATAACAAATATTAATTTCTCATATAAAAAATTGTGACAAA
TAATATTCTTTCACAATAACAAATTGTAACAAAATTATTTAGTTACAATAACGAAATAAATTTAG
TCAAAATAAATAATTATGTCAAATATTCTATATTTTGTCAAAATAAAAATTCTGACAA
Found at i:2641602 original size:13 final size:13
Alignment explanation
Indices: 2641584--2641608 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2641574 GTTCAACAAT
2641584 ATGATAACATCCA
1 ATGATAACATCCA
2641597 ATGATAACATCC
1 ATGATAACATCC
2641609 CATATGATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (13 bp):
ATGATAACATCCA
Done.