Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 11 of 322
Found at i:2782517 original size:16 final size:16
Alignment explanation
Indices: 2782493--2782535 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
2782483 ATTTTATTAC
2782493 TATTA-TTATTATATT
1 TATTATTTATTATATT
*
2782508 TATTATTTATTGTATT
1 TATTATTTATTATATT
2782524 TATTATTTATTA
1 TATTATTTATTA
2782536 GCATTAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TATTATTTATTATATT
Found at i:2782546 original size:19 final size:16
Alignment explanation
Indices: 2782505--2782550 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 16
2782495 TTATTATTAT
*
2782505 ATTTATTATTTATTGT
1 ATTTATTATTTATTGC
2782521 ATTTATTATTTATTAGC
1 ATTTATTATTTATT-GC
2782538 ATTAGTATTATTT
1 ATT--TATTATTT
2782551 TTACTTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 14 0.54
17 4 0.15
19 8 0.31
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (16 bp):
ATTTATTATTTATTGC
Found at i:2783030 original size:23 final size:22
Alignment explanation
Indices: 2782993--2783044 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
2782983 TTTTAACACT
*
2782993 ATATTATGTATATATATATTTTA
1 ATATTATGTACATAT-TATTTTA
* *
2783016 ATGTTATGTACATATTTTTTTA
1 ATATTATGTACATATTATTTTA
2783038 ATATTAT
1 ATATTAT
2783045 ATTTTTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (22 bp):
ATATTATGTACATATTATTTTA
Found at i:2783048 original size:16 final size:16
Alignment explanation
Indices: 2783031--2783060 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2783021 ATGTACATAT
2783031 TTTTTTA-ATATTATA
1 TTTTTTATATATTATA
2783046 TTTTTTATATATTAT
1 TTTTTTATATATTAT
2783061 TATGTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTTATATATTATA
Found at i:2783539 original size:19 final size:19
Alignment explanation
Indices: 2783490--2783543 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
2783480 CGTTTTCAAT
*
2783490 ATATTGTATATAT-TTTTA
1 ATATAGTATATATGTTTTA
*
2783508 ATCTAGTATTATATGTTTTA
1 ATATAGTA-TATATGTTTTA
2783528 TATATA-TATATATGTT
1 -ATATAGTATATATGTT
2783544 CCCCACTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 6 0.20
19 13 0.43
20 7 0.23
21 4 0.13
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (19 bp):
ATATAGTATATATGTTTTA
Found at i:2798503 original size:18 final size:18
Alignment explanation
Indices: 2798480--2798515 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2798470 GATGCTGGTG
2798480 TTGCCTTGTTGTAAGGGT
1 TTGCCTTGTTGTAAGGGT
2798498 TTGCCTTGTTGTAAGGGT
1 TTGCCTTGTTGTAAGGGT
2798516 GAGGGACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.33, T:0.44
Consensus pattern (18 bp):
TTGCCTTGTTGTAAGGGT
Found at i:2799959 original size:30 final size:30
Alignment explanation
Indices: 2799923--2799983 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2799913 TGCTTTTCAT
2799923 TGCAGCAATGCATGAATCTTGAAAGCAAAC
1 TGCAGCAATGCATGAATCTTGAAAGCAAAC
2799953 TGCAGCAATGCATGAATCTTGAAAGCAAAC
1 TGCAGCAATGCATGAATCTTGAAAGCAAAC
2799983 T
1 T
2799984 TATAGCAAAC
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:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (30 bp):
TGCAGCAATGCATGAATCTTGAAAGCAAAC
Found at i:2806548 original size:68 final size:69
Alignment explanation
Indices: 2806420--2806557 Score: 217
Period size: 68 Copynumber: 2.0 Consensus size: 69
2806410 ATAATTCACC
* *
2806420 CTCCAATAATTGCCTGCTATATATACCATATAACCATTGCCAAATATATACACCCCTGTAAACAT
1 CTCCAATAATTGCCTGCTATATATACCA-ATAACCATCGCCAAATAAATACACCCCTGTAAACAT
2806485 GGAGT
65 GGAGT
*
2806490 CTCCAATAATTGCTTGCTATATATACC-ATAACCATCGCCAAATAAATAC-CCCACTGTAAACAT
1 CTCCAATAATTGCCTGCTATATATACCAATAACCATCGCCAAATAAATACACCC-CTGTAAACAT
2806553 GGAGT
65 GGAGT
2806558 GGACCTCTGA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
67 3 0.05
68 35 0.55
70 26 0.41
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.28
Consensus pattern (69 bp):
CTCCAATAATTGCCTGCTATATATACCAATAACCATCGCCAAATAAATACACCCCTGTAAACATG
GAGT
Found at i:2807557 original size:22 final size:23
Alignment explanation
Indices: 2807530--2807575 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
2807520 CGTTTAGCCC
*
2807530 AACAAATCAAAGCCCCAA-CCCA
1 AACAAATCAAAGCCCAAATCCCA
*
2807552 AACAAATCAAGGCCCAAATCCCA
1 AACAAATCAAAGCCCAAATCCCA
2807575 A
1 A
2807576 GTTAAGCCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.50, C:0.37, G:0.07, T:0.07
Consensus pattern (23 bp):
AACAAATCAAAGCCCAAATCCCA
Found at i:2809382 original size:24 final size:24
Alignment explanation
Indices: 2809355--2809400 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2809345 ATTATTTAAA
2809355 TTATCATTATAATTATTATTTTCG
1 TTATCATTATAATTATTATTTTCG
* * *
2809379 TTATCATTGTCATTTTTATTTT
1 TTATCATTATAATTATTATTTT
2809401 GCCATGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.04, T:0.63
Consensus pattern (24 bp):
TTATCATTATAATTATTATTTTCG
Found at i:2819552 original size:17 final size:17
Alignment explanation
Indices: 2819519--2819552 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
2819509 TTTAATTAAG
2819519 TAAATTATTAAAAATTA
1 TAAATTATTAAAAATTA
2819536 TAAA-TATTAAAATATTA
1 TAAATTATTAAAA-ATTA
2819553 GATAATAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTATTAAAAATTA
Found at i:2829732 original size:14 final size:15
Alignment explanation
Indices: 2829706--2829736 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2829696 TCCAGGTTCA
2829706 TCAACACATTTTTCT
1 TCAACACATTTTTCT
2829721 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
2829735 TC
1 TC
2829737 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:2840296 original size:26 final size:27
Alignment explanation
Indices: 2840265--2840335 Score: 92
Period size: 26 Copynumber: 2.6 Consensus size: 27
2840255 TGATTATATA
*
2840265 TAAAAATTCAAAAAAAATTAAAAT-AG
1 TAAAAATTCAAAAAAAATAAAAATAAG
2840291 TAAAAAATTC-AAAAAAATAAAAATAAG
1 T-AAAAATTCAAAAAAAATAAAAATAAG
*
2840318 TAAGAATTCAAAATAAAA
1 TAAAAATTCAAAA-AAAA
2840336 ATTATAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 21 0.54
27 14 0.36
28 4 0.10
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.21
Consensus pattern (27 bp):
TAAAAATTCAAAAAAAATAAAAATAAG
Found at i:2840298 original size:27 final size:27
Alignment explanation
Indices: 2840266--2840352 Score: 90
Period size: 26 Copynumber: 3.2 Consensus size: 27
2840256 GATTATATAT
2840266 AAAAATTCAAAAAAAATTAAAATAGTA
1 AAAAATTCAAAAAAAATTAAAATAGTA
*
2840293 AAAAATTC-AAAAAAATAAAAATAAGT-
1 AAAAATTCAAAAAAAATTAAAAT-AGTA
* *
2840319 AAGAATTCAAAATAAAAATTATAAA-AATA
1 AAAAATTC-AAA-AAAAATTA-AAATAGTA
2840348 AAAAA
1 AAAAA
2840353 ATGATGAGAG
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
26 20 0.41
27 11 0.22
28 4 0.08
29 11 0.22
30 3 0.06
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.21
Consensus pattern (27 bp):
AAAAATTCAAAAAAAATTAAAATAGTA
Found at i:2848152 original size:27 final size:27
Alignment explanation
Indices: 2848095--2848155 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
2848085 TGGGTGTATC
* *
2848095 GCCTATCAGATAGGCACAACCAGTGCC
1 GCCTATCAGATAGGCACAACCAGTACA
* **
2848122 GCCTATCAGATAGGCACGATTAGTACA
1 GCCTATCAGATAGGCACAACCAGTACA
2848149 GCCTATC
1 GCCTATC
2848156 TGACACCCTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (27 bp):
GCCTATCAGATAGGCACAACCAGTACA
Found at i:2849399 original size:21 final size:18
Alignment explanation
Indices: 2849332--2849393 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
2849322 TGTGAAAATG
2849332 ATATAAACATATTAATAT-
1 ATATAAA-ATATTAATATA
*
2849350 AT-CAAAAT-TT-ATATA
1 ATATAAAATATTAATATA
*
2849365 ATATAAATTATTAATATA
1 ATATAAAATATTAATATA
2849383 ATAATAAAATA
1 AT-ATAAAATA
2849394 GTTTAAAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
14 4 0.11
15 4 0.11
16 6 0.17
17 5 0.14
18 9 0.26
19 7 0.20
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAAAATATTAATATA
Found at i:2854695 original size:16 final size:16
Alignment explanation
Indices: 2854676--2854709 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2854666 TACATGCAAT
*
2854676 ACATGTCACATTAGAC
1 ACATGTCACATTAAAC
*
2854692 ACATGTGACATTAAAC
1 ACATGTCACATTAAAC
2854708 AC
1 AC
2854710 CAGTAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (16 bp):
ACATGTCACATTAAAC
Found at i:2860279 original size:16 final size:16
Alignment explanation
Indices: 2860244--2860297 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
2860234 AAAAAATATG
* * *
2860244 TTTTCTATCATTTTAG
1 TTTTCTATCCTTCTAA
2860260 TTTTCTATCCCTTC-AA
1 TTTTCTAT-CCTTCTAA
*
2860276 TTTTTTATCCTTCTAA
1 TTTTCTATCCTTCTAA
2860292 TTTTCT
1 TTTTCT
2860298 TTTCACTCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 5 0.16
16 23 0.74
17 3 0.10
ACGTcount: A:0.17, C:0.20, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTTCTATCCTTCTAA
Found at i:2865996 original size:15 final size:15
Alignment explanation
Indices: 2865976--2866006 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2865966 GTCATGTAAG
2865976 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
2865991 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
2866006 T
1 T
2866007 ATATTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:2866198 original size:17 final size:17
Alignment explanation
Indices: 2866165--2866203 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
2866155 TAAGCTTTTG
2866165 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
2866182 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
2866199 ATTTT
1 ATTTT
2866204 CCACAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:2870337 original size:15 final size:15
Alignment explanation
Indices: 2870317--2870347 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2870307 GTCATGTAAA
2870317 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
2870332 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
2870347 T
1 T
2870348 ATATTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:2870538 original size:17 final size:17
Alignment explanation
Indices: 2870505--2870543 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
2870495 TAAGCTTTTG
2870505 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
2870522 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
2870539 ATTTT
1 ATTTT
2870544 CCACACCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:2872399 original size:14 final size:15
Alignment explanation
Indices: 2872374--2872403 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2872364 CCAGGTTCAC
2872374 CAACACATTTTTCTT
1 CAACACATTTTTCTT
2872389 CAACA-ATTTTTCTT
1 CAACACATTTTTCTT
2872403 C
1 C
2872404 CCATTTCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (15 bp):
CAACACATTTTTCTT
Found at i:2882387 original size:16 final size:16
Alignment explanation
Indices: 2882362--2882413 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
2882352 AAAAGTTATG
2882362 TTTTTCATCCTTCTAA
1 TTTTTCATCCTTCTAA
* * *
2882378 TTTTTTATCCCTCCAA
1 TTTTTCATCCTTCTAA
* *
2882394 TTTTTCATGCTTTTAA
1 TTTTTCATCCTTCTAA
2882410 TTTT
1 TTTT
2882414 CTTTTCACTC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.17, C:0.21, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTTCATCCTTCTAA
Found at i:2882996 original size:14 final size:15
Alignment explanation
Indices: 2882970--2883000 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2882960 TCTAGGTTCA
2882970 TCAACACATTTTTCT
1 TCAACACATTTTTCT
2882985 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
2882999 TC
1 TC
2883001 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:2883771 original size:11 final size:11
Alignment explanation
Indices: 2883751--2883793 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
2883741 TTAGAATATA
*
2883751 CCCATTCCTTG
1 CCCATACCTTG
2883762 CCCATACCTTG
1 CCCATACCTTG
*
2883773 CCCATACC-TA
1 CCCATACCTTG
2883783 CCCATACCTTG
1 CCCATACCTTG
2883794 GAAAGATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.19, C:0.47, G:0.07, T:0.28
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:2884355 original size:18 final size:18
Alignment explanation
Indices: 2884332--2884404 Score: 101
Period size: 18 Copynumber: 4.1 Consensus size: 18
2884322 CATGTATGAC
*
2884332 ACTATTCACGTATACGGT
1 ACTATTCACGTATACAGT
*
2884350 ACTATTCACATATACAGT
1 ACTATTCACGTATACAGT
* *
2884368 ACTATTTATGTATACAGT
1 ACTATTCACGTATACAGT
*
2884386 ACTGTTCACGTATACAGT
1 ACTATTCACGTATACAGT
2884404 A
1 A
2884405 GTTAGGATTG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (18 bp):
ACTATTCACGTATACAGT
Found at i:2884734 original size:14 final size:14
Alignment explanation
Indices: 2884715--2884749 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
2884705 TACACTGGAA
2884715 GAAAAGTTTCTAAC
1 GAAAAGTTTCTAAC
2884729 GAAAAGTTTCTAAC
1 GAAAAGTTTCTAAC
2884743 GAAAAGT
1 GAAAAGT
2884750 CTTGAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (14 bp):
GAAAAGTTTCTAAC
Found at i:2888471 original size:11 final size:11
Alignment explanation
Indices: 2888451--2888504 Score: 65
Period size: 11 Copynumber: 5.0 Consensus size: 11
2888441 TTAGAATATA
*
2888451 CCCATTCCTTG
1 CCCATACCTTG
2888462 CCCATACCTTG
1 CCCATACCTTG
*
2888473 CCCATACCTTT
1 CCCATACCTTG
* *
2888484 TCCATACC-TA
1 CCCATACCTTG
2888494 CCCATACCTTG
1 CCCATACCTTG
2888505 GAAAGGTCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
10 8 0.22
11 28 0.78
ACGTcount: A:0.19, C:0.44, G:0.06, T:0.31
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:2889172 original size:29 final size:29
Alignment explanation
Indices: 2889135--2889193 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2889125 TGACAATGTA
2889135 TGAGAAGAAAAATATATGTGGATGTAGTG
1 TGAGAAGAAAAATATATGTGGATGTAGTG
2889164 TGAGAAGAAAAATATATGTGGATGTAGTG
1 TGAGAAGAAAAATATATGTGGATGTAGTG
2889193 T
1 T
2889194 TCAAAATCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.29
Consensus pattern (29 bp):
TGAGAAGAAAAATATATGTGGATGTAGTG
Found at i:2891303 original size:23 final size:23
Alignment explanation
Indices: 2891277--2891322 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2891267 ACATGGTCTG
2891277 CCACATTGGCCGATCACACAGCC
1 CCACATTGGCCGATCACACAGCC
2891300 CCACATTGGCCGATCACACAGCC
1 CCACATTGGCCGATCACACAGCC
2891323 ATGTGTCGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.43, G:0.17, T:0.13
Consensus pattern (23 bp):
CCACATTGGCCGATCACACAGCC
Found at i:2892797 original size:151 final size:151
Alignment explanation
Indices: 2892523--2892824 Score: 577
Period size: 151 Copynumber: 2.0 Consensus size: 151
2892513 CGTTGGCATC
2892523 GACATGAATAGACCAAAGTCAGTGACATCTCCGTCTGCAGGGTATTTCACCGATGAAGGTGAGTT
1 GACATGAATAGACCAAAGTCAGTGACATCTCCGTCTGCAGGGTATTTCACCGATGAAGGTGAGTT
*
2892588 CAAAAATCTCAGCCTTAAGTTTTAGTCATGGGATTCTCTTGACTGCTTAATTCGTTTGGTATCTA
66 CAAAAATCTCAGCCTTAAGTATTAGTCATGGGATTCTCTTGACTGCTTAATTCGTTTGGTATCTA
2892653 GAAAGCTAAGTCAAAAAAGTT
131 GAAAGCTAAGTCAAAAAAGTT
*
2892674 GACATGAATAGACCAAAGTCAGTGACATCTCCGTCTGCAGGGTATTTCACCGATTAAGGTGAGTT
1 GACATGAATAGACCAAAGTCAGTGACATCTCCGTCTGCAGGGTATTTCACCGATGAAGGTGAGTT
2892739 CAAAAATCTCAGCCTTAAGTATTAGTCATGGGATTCTCTTGACTGCTTAATTCGTTTGGTATCTA
66 CAAAAATCTCAGCCTTAAGTATTAGTCATGGGATTCTCTTGACTGCTTAATTCGTTTGGTATCTA
*
2892804 GCAAGCTAAGTCAAAAAAGTT
131 GAAAGCTAAGTCAAAAAAGTT
2892825 TAGCGATGAA
Statistics
Matches: 148, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
151 148 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (151 bp):
GACATGAATAGACCAAAGTCAGTGACATCTCCGTCTGCAGGGTATTTCACCGATGAAGGTGAGTT
CAAAAATCTCAGCCTTAAGTATTAGTCATGGGATTCTCTTGACTGCTTAATTCGTTTGGTATCTA
GAAAGCTAAGTCAAAAAAGTT
Found at i:2893561 original size:51 final size:51
Alignment explanation
Indices: 2893502--2893605 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
2893492 TAAAAACAGT
* *
2893502 AAGAAAAAGTTAAAATAAGAATAGAGATTTATTAAATGTTAAGGCCTGGTC
1 AAGAAAAAGTTAAAATAAGAATAGAGATTTATTAAATGTTAAAGCCTAGTC
*
2893553 AAGAAAAAGTTAAAATAAGAATAGAGGTTTATTAAATGTTAAAGCCTAGTC
1 AAGAAAAAGTTAAAATAAGAATAGAGATTTATTAAATGTTAAAGCCTAGTC
2893604 AA
1 AA
2893606 CGAAGGACAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (51 bp):
AAGAAAAAGTTAAAATAAGAATAGAGATTTATTAAATGTTAAAGCCTAGTC
Found at i:2897890 original size:87 final size:87
Alignment explanation
Indices: 2897741--2897911 Score: 272
Period size: 87 Copynumber: 2.0 Consensus size: 87
2897731 TTTTTTCAGC
2897741 AGTGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAA-C
1 AGTGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAATC
*
2897805 CTATTAAATTGCATACTTCACGT
66 C-ACTAAATTGCATACTTCACGT
* * * **
2897828 AGTGTTAATGGATTGATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGTCTGCCGAATC
1 AGTGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAATC
2897893 CACTAAATTGCATACTTCA
66 CACTAAATTGCATACTTCA
2897912 AGTGAAGAAC
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
87 75 0.97
88 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (87 bp):
AGTGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAATC
CACTAAATTGCATACTTCACGT
Found at i:2898262 original size:153 final size:153
Alignment explanation
Indices: 2897981--2898282 Score: 453
Period size: 153 Copynumber: 2.0 Consensus size: 153
2897971 TTTAAGCATC
** * *
2897981 TTGCAATTTGACAATCCAAGAAACTGAAGCTTCGAAAGTCGAGTAAGAGATGCGGGTATGCTGAT
1 TTGCAATTTGACAATCCAAGAAACCCAAGCTTCGAAAGTCCAGTAAGAGATGCAGGTATGCTGAT
* *
2898046 GAAATTGTTATCACTAAGACCAAGATGTACCAAAGAGGATAGACCAGAAATATAACTTTGAATAT
66 GAAATTGTTATCACTAAGACCAAGATGTACCAAAGAGGATAGACCAGAAATATAACGTGGAATAT
* *
2898111 CTGCTTCACCAAGAGTGCACATG
131 CTCCTTCACAAAGAGTGCACATG
*
2898134 TTGCAATTTGACAA-CTCAAGAAACCCAAGCTTCGAGAGTCCAGTAAGAGATGCAGGTATGCTGA
1 TTGCAATTTGACAATC-CAAGAAACCCAAGCTTCGAAAGTCCAGTAAGAGATGCAGGTATGCTGA
* * ** *
2898198 TGAAGTTGTTATCACTAAGATCAAGATGTTTCAAAGAGGATAGACCAGAAATATCACGTGGAATA
65 TGAAATTGTTATCACTAAGACCAAGATGTACCAAAGAGGATAGACCAGAAATATAACGTGGAATA
*
2898263 TCTCCTTCACAAAGATTGCA
130 TCTCCTTCACAAAGAGTGCA
2898283 ATCCCTTAGA
Statistics
Matches: 133, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
152 1 0.01
153 132 0.99
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.25
Consensus pattern (153 bp):
TTGCAATTTGACAATCCAAGAAACCCAAGCTTCGAAAGTCCAGTAAGAGATGCAGGTATGCTGAT
GAAATTGTTATCACTAAGACCAAGATGTACCAAAGAGGATAGACCAGAAATATAACGTGGAATAT
CTCCTTCACAAAGAGTGCACATG
Found at i:2899521 original size:20 final size:21
Alignment explanation
Indices: 2899492--2899532 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2899482 AAAATATATT
*
2899492 TTCCATTCAA-TTTTCCATCC
1 TTCCACTCAAGTTTTCCATCC
2899512 TTCCACTCAAGTTTTCCATCC
1 TTCCACTCAAGTTTTCCATCC
2899533 CCTCAGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.20, C:0.37, G:0.02, T:0.41
Consensus pattern (21 bp):
TTCCACTCAAGTTTTCCATCC
Found at i:2900148 original size:14 final size:15
Alignment explanation
Indices: 2900122--2900152 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2900112 TCCAGGTTCA
2900122 TCAACACATTTTTCT
1 TCAACACATTTTTCT
2900137 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
2900151 TC
1 TC
2900153 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:2902954 original size:20 final size:20
Alignment explanation
Indices: 2902929--2902971 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2902919 GAGATTCCAT
2902929 TCCAATTTTAGTTGGAAGAC
1 TCCAATTTTAGTTGGAAGAC
2902949 TCCAATTTTAGTTGGAAGAC
1 TCCAATTTTAGTTGGAAGAC
2902969 TCC
1 TCC
2902972 TAAGTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (20 bp):
TCCAATTTTAGTTGGAAGAC
Found at i:2904630 original size:7 final size:7
Alignment explanation
Indices: 2904618--2904649 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
2904608 TCTACCACAC
2904618 AAAAATA
1 AAAAATA
2904625 AAAAATA
1 AAAAATA
2904632 AAAAATA
1 AAAAATA
2904639 AAAAATA
1 AAAAATA
2904646 AAAA
1 AAAA
2904650 CCCAAAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:2915918 original size:29 final size:29
Alignment explanation
Indices: 2915846--2915909 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
2915836 CTTATTTAAA
*
2915846 TAAAAT-ACGATGGAAAATAAAATAAAAG
1 TAAAATCACGATAGAAAATAAAATAAAAG
2915874 TAAAATCACGATAGAAAATAAAATAAAAG
1 TAAAATCACGATAGAAAATAAAATAAAAG
2915903 TAAAATC
1 TAAAATC
2915910 CATATAGAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 6 0.18
29 28 0.82
ACGTcount: A:0.64, C:0.06, G:0.11, T:0.19
Consensus pattern (29 bp):
TAAAATCACGATAGAAAATAAAATAAAAG
Found at i:2916165 original size:5 final size:5
Alignment explanation
Indices: 2916155--2916186 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
2916145 TTGTGTGTTC
2916155 TTTAT TTTAT TTTA- TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
2916187 TCACAACGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:2916174 original size:14 final size:14
Alignment explanation
Indices: 2916155--2916185 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2916145 TTGTGTGTTC
2916155 TTTATTTTATTTTA
1 TTTATTTTATTTTA
2916169 TTTATTTTATTTTA
1 TTTATTTTATTTTA
2916183 TTT
1 TTT
2916186 TTCACAACGA
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:2918223 original size:18 final size:18
Alignment explanation
Indices: 2918200--2918235 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2918190 AAATCTCTTC
2918200 TTCAAGGAAGCCATTGAG
1 TTCAAGGAAGCCATTGAG
2918218 TTCAAGGAAGCCATTGAG
1 TTCAAGGAAGCCATTGAG
2918236 ATATGCAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (18 bp):
TTCAAGGAAGCCATTGAG
Found at i:2932547 original size:57 final size:59
Alignment explanation
Indices: 2932478--2932592 Score: 180
Period size: 57 Copynumber: 2.0 Consensus size: 59
2932468 GTGCCCACTG
*
2932478 ACCGATCTCGCACACATAGTGCTCGGTT-GAAGAACTCGCACACACAGTGCCT-TAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTCTAATT
* * *
2932535 ACCGATTTCGCACACATAGTGCTCGGTTAAAAGAATTTGCACACACAGTGCCTCTAAT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTCTAAT
2932593 CATCCGCACA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 27 0.52
58 21 0.40
59 4 0.08
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (59 bp):
ACCGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTCTAATT
Found at i:2937371 original size:12 final size:11
Alignment explanation
Indices: 2937321--2937388 Score: 55
Period size: 12 Copynumber: 5.7 Consensus size: 11
2937311 ATTGAGTCCA
2937321 TTTATTTTATT
1 TTTATTTTATT
*
2937332 TTATTTTATTATT
1 TT-TATT-TTATT
* *
2937345 TTTGGTTTTAGT
1 TTT-ATTTTATT
2937357 TTTATTTCTATT
1 TTTATTT-TATT
2937369 TTTATGTTTATT
1 TTTAT-TTTATT
*
2937381 GTTATTTT
1 TTTATTTT
2937389 CTTAGACTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
11 8 0.17
12 27 0.59
13 11 0.24
ACGTcount: A:0.16, C:0.01, G:0.07, T:0.75
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:2937378 original size:24 final size:23
Alignment explanation
Indices: 2937320--2937388 Score: 70
Period size: 26 Copynumber: 2.9 Consensus size: 23
2937310 CATTGAGTCC
2937320 ATTTAT-TTTATTTTATTTTATT
1 ATTTATGTTTATTTTATTTTATT
*
2937342 ATTTTTGGTTTTAGTTTTATTTCTATT
1 ATTTAT-G-TTTA-TTTTATTT-TATT
2937369 -TTTATGTTTATTGTTATTTT
1 ATTTATGTTTATT-TTATTTT
2937389 CTTAGACTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
22 5 0.13
23 3 0.08
24 10 0.26
25 5 0.13
26 12 0.31
27 4 0.10
ACGTcount: A:0.17, C:0.01, G:0.07, T:0.74
Consensus pattern (23 bp):
ATTTATGTTTATTTTATTTTATT
Found at i:2937389 original size:25 final size:24
Alignment explanation
Indices: 2937321--2937390 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
2937311 ATTGAGTCCA
*
2937321 TTTAT-TTTATTTTATTTTATTATT
1 TTTATGTTTATTTTATTTT-CTATT
*
2937345 TTT-GGTTTTAGTTTTA-TTTCTATT
1 TTTATG-TTTA-TTTTATTTTCTATT
2937369 TTTATGTTTATTGTTATTTTCT
1 TTTATGTTTATT-TTATTTTCT
2937391 TAGACTTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
23 2 0.05
24 17 0.46
25 13 0.35
26 5 0.14
ACGTcount: A:0.16, C:0.03, G:0.07, T:0.74
Consensus pattern (24 bp):
TTTATGTTTATTTTATTTTCTATT
Found at i:2949721 original size:29 final size:29
Alignment explanation
Indices: 2949679--2949738 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
2949669 ATTTCTTTTG
2949679 TTGAGAGGACATTTGCTCCTCCATAACTC
1 TTGAGAGGACATTTGCTCCTCCATAACTC
2949708 TTGAGAGGACATTTGCTCCTCCATAACTC
1 TTGAGAGGACATTTGCTCCTCCATAACTC
2949737 TT
1 TT
2949739 ATTCTCTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (29 bp):
TTGAGAGGACATTTGCTCCTCCATAACTC
Found at i:2951385 original size:39 final size:39
Alignment explanation
Indices: 2951327--2951401 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
2951317 TGAATTTTAA
* *
2951327 CTCGATTGGCATTAGTATTTTTGCATATGATGAAATTAG
1 CTCGATTGGCATCAATATTTTTGCATATGATGAAATTAG
2951366 CTCGATTGGCATCAATATTTTTGCATATGATGAAAT
1 CTCGATTGGCATCAATATTTTTGCATATGATGAAAT
2951402 CCATTCTAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (39 bp):
CTCGATTGGCATCAATATTTTTGCATATGATGAAATTAG
Found at i:2953336 original size:21 final size:21
Alignment explanation
Indices: 2953304--2953344 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2953294 AGGCTCGAGG
2953304 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
2953325 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
2953345 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:2962003 original size:23 final size:23
Alignment explanation
Indices: 2961977--2962074 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
2961967 ATAAGTGCCA
2961977 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
2962000 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
2962023 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
2962045 CACTGAAATGTAGCCGAAGTTAC
1 CACTGATATGTAGCCGAAGCTAC
2962068 CACTGAT
1 CACTGAT
2962075 CAATAACACT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 20 0.29
23 48 0.71
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:2962042 original size:45 final size:45
Alignment explanation
Indices: 2961984--2962072 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
2961974 CCACACTGAT
* *
2961984 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
*
2962029 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGTTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
2962073 ATCAATAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.20
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:2964706 original size:12 final size:12
Alignment explanation
Indices: 2964689--2964718 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2964679 ACAGTCGAAA
*
2964689 ACAGATGCAAAT
1 ACAGATACAAAT
2964701 ACAGATACAAAT
1 ACAGATACAAAT
2964713 ACAGAT
1 ACAGAT
2964719 TTGAGCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (12 bp):
ACAGATACAAAT
Found at i:2973295 original size:14 final size:14
Alignment explanation
Indices: 2973276--2973305 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2973266 ATAATCTTTA
*
2973276 AATTTTTTATATTT
1 AATTTTTTAAATTT
2973290 AATTTTTTAAATTT
1 AATTTTTTAAATTT
2973304 AA
1 AA
2973306 AAATTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATTTTTTAAATTT
Found at i:2976601 original size:12 final size:12
Alignment explanation
Indices: 2976584--2976609 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2976574 AAGTGTGCCT
2976584 TCGAAAGACATC
1 TCGAAAGACATC
2976596 TCGAAAGACATC
1 TCGAAAGACATC
2976608 TC
1 TC
2976610 ATCGCATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.19
Consensus pattern (12 bp):
TCGAAAGACATC
Found at i:2981016 original size:2 final size:2
Alignment explanation
Indices: 2981009--2981039 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2980999 AAGAGTTAAA
2981009 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2981040 ACTAAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2983384 original size:3 final size:3
Alignment explanation
Indices: 2983378--2983639 Score: 98
Period size: 3 Copynumber: 87.0 Consensus size: 3
2983368 GATGAAAACG
** * *
2983378 ATA ATA ATA ATA ATA ATA ATA ATA CCA ACA ACGA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA
** **
2983423 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACGTA AGTAA ATA CGA A-A AGG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A--TA A-T-A ATA ATA ATA ATA
* * * * *
2983471 A-A ATA TATA AT- GTA AT- ATA A-A TTA ATTA GT- TTA ATA AT- ATG
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA
* * * * * *
2983512 ATG ATA ATA ATA GTG ATA AT- ACA ATA ACA ATA ATA A-A GTGGA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT--A ATA
* *
2983556 ATAA ATA ATA ATA ATA CATTA AGA ATA ATA ATA AT- ATA CTA ATA ATA
1 AT-A ATA ATA ATA ATA -A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
2983603 ACA ATA ATA GAAA ATA ATA ATA AAA ATA ATA AAA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
2983640 CAAAAAATAT
Statistics
Matches: 196, Mismatches: 39, Indels: 48
0.69 0.14 0.17
Matches are distributed among these distances:
2 18 0.09
3 153 0.78
4 17 0.09
5 8 0.04
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:2983562 original size:25 final size:26
Alignment explanation
Indices: 2983515--2983571 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
2983505 TAATATGATG
*
2983515 ATAATAATAGTGATAATACAATAACA
1 ATAATAATAGTGAAAATACAATAACA
*
2983541 ATAATAA-AGTGGAAAATA-AATAATA
1 ATAATAATAGT-GAAAATACAATAACA
2983566 ATAATA
1 ATAATA
2983572 CATTAAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.61, C:0.04, G:0.09, T:0.26
Consensus pattern (26 bp):
ATAATAATAGTGAAAATACAATAACA
Found at i:2983584 original size:20 final size:20
Alignment explanation
Indices: 2983559--2983611 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2983549 GTGGAAAATA
*
2983559 AATAATAATAATACATTAAG
1 AATAATAATAATACACTAAG
* *
2983579 AATAATAATAATATACTAAT
1 AATAATAATAATACACTAAG
*
2983599 AATAACAATAATA
1 AATAATAATAATA
2983612 GAAAATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (20 bp):
AATAATAATAATACACTAAG
Found at i:2983599 original size:17 final size:17
Alignment explanation
Indices: 2983555--2983639 Score: 70
Period size: 17 Copynumber: 5.1 Consensus size: 17
2983545 TAAAGTGGAA
2983555 AATA-AATAATAATAAT
1 AATATAATAATAATAAT
*
2983571 ACAT-TAAGAATAATAAT
1 A-ATATAATAATAATAAT
* *
2983588 AATATACTAATAATAAC
1 AATATAATAATAATAAT
*
2983605 AATAATAGAAAATAATAAT
1 AAT-ATA-ATAATAATAAT
*
2983624 AA-A-AATAATAAAAAT
1 AATATAATAATAATAAT
2983639 A
1 A
2983640 CAAAAAATAT
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
15 10 0.18
16 4 0.07
17 28 0.51
18 3 0.05
19 10 0.18
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (17 bp):
AATATAATAATAATAAT
Found at i:2983623 original size:22 final size:21
Alignment explanation
Indices: 2983558--2983639 Score: 74
Period size: 23 Copynumber: 3.7 Consensus size: 21
2983548 AGTGGAAAAT
* *
2983558 AAATAATAATAATACATTAAGAA
1 AAATAATAAAAATA-A-TAATAA
* *
2983581 TAATAATAATATACTAATAATAA
1 AAATAATAA-A-AATAATAATAA
*
2983604 CAATAATAGAAAATAATAATAA
1 AAATAATA-AAAATAATAATAA
2983626 AAATAATAAAAATA
1 AAATAATAAAAATA
2983640 CAAAAAATAT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 6 0.12
22 17 0.35
23 21 0.43
24 2 0.04
25 3 0.06
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATAATAAAAATAATAATAA
Found at i:2983645 original size:9 final size:9
Alignment explanation
Indices: 2983558--2983658 Score: 53
Period size: 9 Copynumber: 10.7 Consensus size: 9
2983548 AGTGGAAAAT
2983558 AAATAATAA
1 AAATAATAA
*
2983567 TAATACATTAA
1 AAATA-A-TAA
*
2983578 GAATAATAA
1 AAATAATAA
* *
2983587 TAAT-ATAC
1 AAATAATAA
*
2983595 TAATAATAA
1 AAATAATAA
*
2983604 CAATAATAGAAA
1 AAATAAT---AA
2983616 ATAATAATAA
1 A-AATAATAA
2983626 AAATAATAA
1 AAATAATAA
2983635 AAATACA-AA
1 AAATA-ATAA
* *
2983644 AAATATTGA
1 AAATAATAA
2983653 AAATAA
1 AAATAA
2983659 AATAGCAAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
8 7 0.10
9 45 0.62
10 6 0.08
11 7 0.10
12 2 0.03
13 6 0.08
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (9 bp):
AAATAATAA
Found at i:2986589 original size:35 final size:36
Alignment explanation
Indices: 2986550--2986619 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
2986540 CACACGCACA
2986550 TGTGT-CTCAAATATAAACTCAGTGAGTCACACACC
1 TGTGTACTCAAATATAAACTCAGTGAGTCACACACC
* * * *
2986585 TGTGTGACTCTAATATGAACTCGGTGAGTTACACA
1 TGTGT-ACTCAAATATAAACTCAGTGAGTCACACA
2986620 GCCTAGACAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 5 0.17
37 24 0.83
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (36 bp):
TGTGTACTCAAATATAAACTCAGTGAGTCACACACC
Found at i:2996805 original size:15 final size:17
Alignment explanation
Indices: 2996771--2996807 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
2996761 AGAAAAATAT
2996771 ATTTTCTATCCCTTCAA
1 ATTTTCTATCCCTTCAA
*
2996788 ATTTTC-AT-CCTTCCA
1 ATTTTCTATCCCTTCAA
2996803 ATTTT
1 ATTTT
2996808 TTTCACTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 11 0.58
16 2 0.11
17 6 0.32
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTCTATCCCTTCAA
Found at i:3009777 original size:22 final size:22
Alignment explanation
Indices: 3009749--3009793 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3009739 TAAGTATACT
3009749 AGAACTCTAATTTATTCTAAAC
1 AGAACTCTAATTTATTCTAAAC
3009771 AGAACTCTAATTTATTCTAAAC
1 AGAACTCTAATTTATTCTAAAC
3009793 A
1 A
3009794 AGAAGTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (22 bp):
AGAACTCTAATTTATTCTAAAC
Found at i:3016051 original size:18 final size:18
Alignment explanation
Indices: 3016024--3016097 Score: 85
Period size: 18 Copynumber: 4.1 Consensus size: 18
3016014 TACGACCATT
*
3016024 TATGGCACTATTCACGTA
1 TATGGTACTATTCACGTA
* *
3016042 TATGGAACTATTCATGTA
1 TATGGTACTATTCACGTA
* *
3016060 TACGGTACTATTTACGTA
1 TATGGTACTATTCACGTA
* *
3016078 TATAGTACTGTTCACGTA
1 TATGGTACTATTCACGTA
3016096 TA
1 TA
3016098 CAGTAGTTGG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (18 bp):
TATGGTACTATTCACGTA
Found at i:3032425 original size:27 final size:27
Alignment explanation
Indices: 3032386--3032440 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
3032376 ATGTTAGACA
3032386 CATGCCTGATTTGAAGAAGAATCTCAT
1 CATGCCTGATTTGAAGAAGAATCTCAT
* * *
3032413 CATGCTTGGTTTGAGGAAGAATCTCAT
1 CATGCCTGATTTGAAGAAGAATCTCAT
3032440 C
1 C
3032441 TCTTTAGGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (27 bp):
CATGCCTGATTTGAAGAAGAATCTCAT
Found at i:3035110 original size:31 final size:32
Alignment explanation
Indices: 3035041--3035111 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 32
3035031 GATTCAGTGT
*
3035041 AATTATATAAATGAAACTTTAATTGTGATTCG
1 AATTATATAAATGAAACTTTAATTGTGACTCG
* *
3035073 AA-TATATACATGAAACTTTAATTTTGACTC-
1 AATTATATAAATGAAACTTTAATTGTGACTCG
3035103 AATTATATA
1 AATTATATA
3035112 TATATATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 2 0.06
31 31 0.89
32 2 0.06
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.41
Consensus pattern (32 bp):
AATTATATAAATGAAACTTTAATTGTGACTCG
Found at i:3038037 original size:17 final size:16
Alignment explanation
Indices: 3037994--3038039 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
3037984 TGGTTTATTG
*
3037994 ATTTTAGTCATTTGTT
1 ATTTTAGTTATTTGTT
**
3038010 ATTTTTCTTATTTGTTT
1 ATTTTAGTTATTTG-TT
3038027 ATTTTAGTTATTT
1 ATTTTAGTTATTT
3038040 AAAGTTCCTC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.17, C:0.04, G:0.09, T:0.70
Consensus pattern (16 bp):
ATTTTAGTTATTTGTT
Found at i:3039326 original size:53 final size:53
Alignment explanation
Indices: 3039263--3039370 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
3039253 TGCCATATCC
3039263 TTGACCAGAAATTGTCATACCCTCTCGGAGAAAACAATGGAAGGTGTTGGAAT
1 TTGACCAGAAATTGTCATACCCTCTCGGAGAAAACAATGGAAGGTGTTGGAAT
3039316 TTGACCAGAAATTGTCATACCCTCTCGGAGAAAACAATGGAAGGTGTTGGAAT
1 TTGACCAGAAATTGTCATACCCTCTCGGAGAAAACAATGGAAGGTGTTGGAAT
3039369 TT
1 TT
3039371 TGGACAAGAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (53 bp):
TTGACCAGAAATTGTCATACCCTCTCGGAGAAAACAATGGAAGGTGTTGGAAT
Found at i:3039534 original size:37 final size:38
Alignment explanation
Indices: 3039479--3039558 Score: 153
Period size: 37 Copynumber: 2.1 Consensus size: 38
3039469 ATGTAAGGAA
3039479 ATTAGAGAGTATTTAATGATGAATTCTAATGAATTTTT
1 ATTAGAGAGTATTTAATGATGAATTCTAATGAATTTTT
3039517 ATTA-AGAGTATTTAATGATGAATTCTAATGAATTTTT
1 ATTAGAGAGTATTTAATGATGAATTCTAATGAATTTTT
3039554 ATTAG
1 ATTAG
3039559 CATTGAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 37 0.90
38 4 0.10
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.45
Consensus pattern (38 bp):
ATTAGAGAGTATTTAATGATGAATTCTAATGAATTTTT
Found at i:3046636 original size:11 final size:12
Alignment explanation
Indices: 3046609--3046668 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
3046599 CTTCAAAAAG
* *
3046609 AAATAAAAGACA
1 AAATAAAATAAA
*
3046621 AAATAAAAT-TA
1 AAATAAAATAAA
3046632 AAATAAAATAAA
1 AAATAAAATAAA
3046644 AAAT-AAATATAA
1 AAATAAAATA-AA
* *
3046656 TAGTAAAATAAA
1 AAATAAAATAAA
3046668 A
1 A
3046669 GGGCTCAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 15 0.38
12 19 0.49
13 5 0.13
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:3052086 original size:30 final size:30
Alignment explanation
Indices: 3052051--3052108 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
3052041 CATGGCCATG
* *
3052051 ACACACGGGCGTATGG-TCTACCCGTGTGTC
1 ACACACAGGCATATGGATC-ACCCGTGTGTC
*
3052081 ACACACAGGCATGTGGATCACCCGTGTG
1 ACACACAGGCATATGGATCACCCGTGTG
3052109 GAAGTGCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (30 bp):
ACACACAGGCATATGGATCACCCGTGTGTC
Found at i:3059787 original size:18 final size:18
Alignment explanation
Indices: 3059764--3059892 Score: 150
Period size: 18 Copynumber: 7.2 Consensus size: 18
3059754 CCCAACTACT
*
3059764 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* *
3059782 GTATACATGAATAGTATC
1 GTATACGTGAATAGTACC
* **
3059800 GTATACGCGAATAGTGTC
1 GTATACGTGAATAGTACC
* *
3059818 GTATACATGAATAGTGCC
1 GTATACGTGAATAGTACC
*
3059836 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
3059854 ATATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
* *
3059872 GTATACATGAATAGTATC
1 GTATACGTGAATAGTACC
3059890 GTA
1 GTA
3059893 AACGGTCGTA
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 94 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:3063524 original size:13 final size:13
Alignment explanation
Indices: 3063473--3063524 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
3063463 TTAAACCAAT
* *
3063473 CTTTTAAAAAACA
1 CTTTTCAAAAGCA
*
3063486 CTTCTCAAAAGCA
1 CTTTTCAAAAGCA
* *
3063499 CTTTTCCATAGCA
1 CTTTTCAAAAGCA
3063512 CTTTTCAAAAGCA
1 CTTTTCAAAAGCA
3063525 TTGTTAAACG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (13 bp):
CTTTTCAAAAGCA
Found at i:3066711 original size:11 final size:11
Alignment explanation
Indices: 3066695--3066719 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3066685 GTAAAATTTT
3066695 AAATTAAAATA
1 AAATTAAAATA
3066706 AAATTAAAATA
1 AAATTAAAATA
3066717 AAA
1 AAA
3066720 ATTTCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATTAAAATA
Found at i:3069578 original size:837 final size:837
Alignment explanation
Indices: 3067964--3069638 Score: 3305
Period size: 837 Copynumber: 2.0 Consensus size: 837
3067954 AGGTGTGATT
3067964 GGACCACCTATTAAAACGCTTTATTCAATGAAAAATAAATTTGGTTTAGGTAAAAAAATAAAAAG
1 GGACCACCTATTAAAACGCTTTATTCAATGAAAAATAAATTTGGTTTAGGTAAAAAAATAAAAAG
3068029 AAATGGGTTCGGAAGTTGATTACGCATGAGGAAGGGTTAGCACCCTCATTACGCCCAAAAACTGG
66 AAATGGGTTCGGAAGTTGATTACGCATGAGGAAGGGTTAGCACCCTCATTACGCCCAAAAACTGG
3068094 TACCAAATTGATTTGCTTCTGTCCTTGTAAAAAATTTAAAGGAAAAGATTTTCCGAAGTATGATT
131 TACCAAATTGATTTGCTTCTGTCCTTGTAAAAAATTTAAAGGAAAAGATTTTCCGAAGTATGATT
3068159 TTTCTTAAAAATGTTTGAATAGCTCAAATTAGCGGTCAAAAATCTCTCGTTCCAAGGACATGCAG
196 TTTCTTAAAAATGTTTGAATAGCTCAAATTAGCGGTCAAAAATCTCTCGTTCCAAGGACATGCAG
3068224 TTTCATACCCAGTACGATTGGATATGATCCCTTATACCTTTAAGGTACGATCGATCTTCGACTTT
261 TTTCATACCCAGTACGATTGGATATGATCCCTTATACCTTTAAGGTACGATCGATCTTCGACTTT
*
3068289 TGAAAAATTCGTGCATTAAAATTATAAAAGGTTATCTAAATATTTGGTTCACCGGAAAAGTCATA
326 TGAAAAATTCGTGCATTAAAATCATAAAAGGTTATCTAAATATTTGGTTCACCGGAAAAGTCATA
3068354 CCCAGTACGATTGAGCACGATTTTCCGAATTCCCCAAATATTAGATATTACCTTATTTCAAAAAT
391 CCCAGTACGATTGAGCACGATTTTCCGAATTCCCCAAATATTAGATATTACCTTATTTCAAAAAT
3068419 TTTGAATAACAGAAAATTGAAAATTTGCTCAAAAAACACGTTTATTTGCATAAAAACTTGGGATA
456 TTTGAATAACAGAAAATTGAAAATTTGCTCAAAAAACACGTTTATTTGCATAAAAACTTGGGATA
3068484 CATGTTCATTGAAATTGTTATTACAAAATACACAGTTCAAATCAAATTATATATGAAATATTTAA
521 CATGTTCATTGAAATTGTTATTACAAAATACACAGTTCAAATCAAATTATATATGAAATATTTAA
3068549 TACACAAATCCATTCAAAAATTGATAATTCTCATGATAATTTAAATAATGTATTAAAGATGAAGG
586 TACACAAATCCATTCAAAAATTGATAATTCTCATGATAATTTAAATAATGTATTAAAGATGAAGG
3068614 AATGACAATACATGATATAAAATTATGTACAAAAGAAATTTATGAAACATGTATATACAAGTAAA
651 AATGACAATACATGATATAAAATTATGTACAAAAGAAATTTATGAAACATGTATATACAAGTAAA
3068679 AATTGGATATAATTATTTGTAAAAAAAATGAAATTAATAATGTATGAAAGAAACAAAGTAAACAT
716 AATTGGATATAATTATTTGTAAAAAAAATGAAATTAATAATGTATGAAAGAAACAAAGTAAACAT
3068744 ATAAGTATATAAGTAACAAAATATATATATATATAATAATGCATAAGGATAATATGA
781 ATAAGTATATAAGTAACAAAATATATATATATATAATAATGCATAAGGATAATATGA
3068801 GGACCACCTATTAAAACGCTTTATTCAATGAAAAATAAATTTGGTTTAGGTAAAAAAATAAAAAG
1 GGACCACCTATTAAAACGCTTTATTCAATGAAAAATAAATTTGGTTTAGGTAAAAAAATAAAAAG
3068866 AAATGGGTTCGGAAGTTGATTACGCATGAGGAAGGGTTAGCACCCTCATTACGCCCAAAAACTGG
66 AAATGGGTTCGGAAGTTGATTACGCATGAGGAAGGGTTAGCACCCTCATTACGCCCAAAAACTGG
3068931 TACCAAATTGATTTGCTTCTGTCCTTGTAAAAAATTTAAAGGAAAAGATTTTCCGAAGTATGATT
131 TACCAAATTGATTTGCTTCTGTCCTTGTAAAAAATTTAAAGGAAAAGATTTTCCGAAGTATGATT
3068996 TTTCTTAAAAATGTTTGAATAGCTCAAATTAGCGGTCAAAAATCTCTCGTTCCAAGGACATGCAG
196 TTTCTTAAAAATGTTTGAATAGCTCAAATTAGCGGTCAAAAATCTCTCGTTCCAAGGACATGCAG
3069061 TTTCATACCCAGTACGATTGGATATGATCCCTTATACCTTTAAGGTACGATCGATCTTCGACTTT
261 TTTCATACCCAGTACGATTGGATATGATCCCTTATACCTTTAAGGTACGATCGATCTTCGACTTT
3069126 TGAAAAATTCGTGCATTAAAATCATAAAAGGTTATCTAAATATTTGGTTCACCGGAAAAGTCATA
326 TGAAAAATTCGTGCATTAAAATCATAAAAGGTTATCTAAATATTTGGTTCACCGGAAAAGTCATA
* * *
3069191 CCCAGTACGATTGAGCACGATTTTCCGAATTCTCCAAATATTAGATATTACCTTATTTCAGAATT
391 CCCAGTACGATTGAGCACGATTTTCCGAATTCCCCAAATATTAGATATTACCTTATTTCAAAAAT
3069256 TTTGAATAACAGAAAATTGAAAATTTGCTCAAAAAACACGTTTATTTGCATAAAAACTTGGGATA
456 TTTGAATAACAGAAAATTGAAAATTTGCTCAAAAAACACGTTTATTTGCATAAAAACTTGGGATA
3069321 CATGTTCATTGAAATTGTTATTACAAAATACACAGTTCAAATCAAATTATATATGAAATATTTAA
521 CATGTTCATTGAAATTGTTATTACAAAATACACAGTTCAAATCAAATTATATATGAAATATTTAA
3069386 TACACAAATCCATTCAAAAATTGATAATTCTCATGATAATTTAAATAATGTATTAAAGATGAAGG
586 TACACAAATCCATTCAAAAATTGATAATTCTCATGATAATTTAAATAATGTATTAAAGATGAAGG
*
3069451 AATGACAATACATGATATAAAATTATGTACACAAGAAATTTATGAAACATGTATATACAAGTAAA
651 AATGACAATACATGATATAAAATTATGTACAAAAGAAATTTATGAAACATGTATATACAAGTAAA
3069516 AATTGGATATAATTATTTGTAAAAAAAATGAAATTAATAATGTATGAAAGAAACAAAGTAAACAT
716 AATTGGATATAATTATTTGTAAAAAAAATGAAATTAATAATGTATGAAAGAAACAAAGTAAACAT
3069581 ATAAGTATATAAGTAACAAAATATATATATATATAATAATGCATAAGGATAATATGA
781 ATAAGTATATAAGTAACAAAATATATATATATATAATAATGCATAAGGATAATATGA
3069638 G
1 G
3069639 AGTGTGTACA
Statistics
Matches: 833, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
837 833 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (837 bp):
GGACCACCTATTAAAACGCTTTATTCAATGAAAAATAAATTTGGTTTAGGTAAAAAAATAAAAAG
AAATGGGTTCGGAAGTTGATTACGCATGAGGAAGGGTTAGCACCCTCATTACGCCCAAAAACTGG
TACCAAATTGATTTGCTTCTGTCCTTGTAAAAAATTTAAAGGAAAAGATTTTCCGAAGTATGATT
TTTCTTAAAAATGTTTGAATAGCTCAAATTAGCGGTCAAAAATCTCTCGTTCCAAGGACATGCAG
TTTCATACCCAGTACGATTGGATATGATCCCTTATACCTTTAAGGTACGATCGATCTTCGACTTT
TGAAAAATTCGTGCATTAAAATCATAAAAGGTTATCTAAATATTTGGTTCACCGGAAAAGTCATA
CCCAGTACGATTGAGCACGATTTTCCGAATTCCCCAAATATTAGATATTACCTTATTTCAAAAAT
TTTGAATAACAGAAAATTGAAAATTTGCTCAAAAAACACGTTTATTTGCATAAAAACTTGGGATA
CATGTTCATTGAAATTGTTATTACAAAATACACAGTTCAAATCAAATTATATATGAAATATTTAA
TACACAAATCCATTCAAAAATTGATAATTCTCATGATAATTTAAATAATGTATTAAAGATGAAGG
AATGACAATACATGATATAAAATTATGTACAAAAGAAATTTATGAAACATGTATATACAAGTAAA
AATTGGATATAATTATTTGTAAAAAAAATGAAATTAATAATGTATGAAAGAAACAAAGTAAACAT
ATAAGTATATAAGTAACAAAATATATATATATATAATAATGCATAAGGATAATATGA
Found at i:3070506 original size:782 final size:782
Alignment explanation
Indices: 3069003--3070570 Score: 3109
Period size: 782 Copynumber: 2.0 Consensus size: 782
3068993 ATTTTTCTTA
3069003 AAAATGTTTGAATAGCTCAAATTAGCGGTCAAAAATCTCTCGTTCCAAGGACATGCAGTTTCATA
1 AAAATGTTTGAATAGCTCAAATTAGCGGTCAAAAATCTCTCGTTCCAAGGACATGCAGTTTCATA
3069068 CCCAGTACGATTGGATATGATCCCTTATACCTTTAAGGTACGATCGATCTTCGACTTTTGAAAAA
66 CCCAGTACGATTGGATATGATCCCTTATACCTTTAAGGTACGATCGATCTTCGACTTTTGAAAAA
3069133 TTCGTGCATTAAAATCATAAAAGGTTATCTAAATATTTGGTTCACCGGAAAAGTCATACCCAGTA
131 TTCGTGCATTAAAATCATAAAAGGTTATCTAAATATTTGGTTCACCGGAAAAGTCATACCCAGTA
*
3069198 CGATTGAGCACGATTTTCCGAATTCTCCAAATATTAGATATTACCTTATTTCAGAATTTTTGAAT
196 CGATTGAGCACGATTTTCCGAATTCCCCAAATATTAGATATTACCTTATTTCAGAATTTTTGAAT
3069263 AACAGAAAATTGAAAATTTGCTCAAAAAACACGTTTATTTGCATAAAAACTTGGGATACATGTTC
261 AACAGAAAATTGAAAATTTGCTCAAAAAACACGTTTATTTGCATAAAAACTTGGGATACATGTTC
3069328 ATTGAAATTGTTATTACAAAATACACAGTTCAAATCAAATTATATATGAAATATTTAATACACAA
326 ATTGAAATTGTTATTACAAAATACACAGTTCAAATCAAATTATATATGAAATATTTAATACACAA
3069393 ATCCATTCAAAAATTGATAATTCTCATGATAATTTAAATAATGTATTAAAGATGAAGGAATGACA
391 ATCCATTCAAAAATTGATAATTCTCATGATAATTTAAATAATGTATTAAAGATGAAGGAATGACA
*
3069458 ATACATGATATAAAATTATGTACACAAGAAATTTATGAAACATGTATATACAAGTAAAAATTGGA
456 ATACATGATATAAAATTATGTACAAAAGAAATTTATGAAACATGTATATACAAGTAAAAATTGGA
3069523 TATAATTATTTGTAAAAAAAATGAAATTAATAATGTATGAAAGAAACAAAGTAAACATATAAGTA
521 TATAATTATTTGTAAAAAAAATGAAATTAATAATGTATGAAAGAAACAAAGTAAACATATAAGTA
3069588 TATAAGTAACAAAATATATATATATATAATAATGCATAAGGATAATATGAGAGTGTGTACAATAA
586 TATAAGTAACAAAATATATATATATATAATAATGCATAAGGATAATATGAGAGTGTGTACAATAA
3069653 ATAAGTGGTATGATTAAAAACATGGTTCCCAAAAGAAATATATTGTACATATAAATATCTTTAAA
651 ATAAGTGGTATGATTAAAAACATGGTTCCCAAAAGAAATATATTGTACATATAAATATCTTTAAA
3069718 GTAGGTTCTACACATAAAAAAAAATATTTATATGAAGATATATGAGAATAATAATATGTATCATA
716 GTAGGTTCTACACATAAAAAAAAATATTTATATGAAGATATATGAGAATAATAATATGTATCATA
3069783 GT
781 GT
3069785 AAAATGTTTGAATAGCTCAAATTAGCGGTCAAAAATCTCTCGTTCCAAGGACATGCAGTTTCATA
1 AAAATGTTTGAATAGCTCAAATTAGCGGTCAAAAATCTCTCGTTCCAAGGACATGCAGTTTCATA
3069850 CCCAGTACGATTGGATATGATCCCTTATACCTTTAAGGTACGATCGATCTTCGACTTTTGAAAAA
66 CCCAGTACGATTGGATATGATCCCTTATACCTTTAAGGTACGATCGATCTTCGACTTTTGAAAAA
*
3069915 TTCGTGCATTAAAATTATAAAAGGTTATCTAAATATTTGGTTCACCGGAAAAGTCATACCCAGTA
131 TTCGTGCATTAAAATCATAAAAGGTTATCTAAATATTTGGTTCACCGGAAAAGTCATACCCAGTA
3069980 CGATTGAGCACGATTTTCCGAATTCCCCAAATATTAGATATTACCTTATTTCAGAATTTTTGAAT
196 CGATTGAGCACGATTTTCCGAATTCCCCAAATATTAGATATTACCTTATTTCAGAATTTTTGAAT
3070045 AACAGAAAATTGAAAATTTGCTCAAAAAACACGTTTATTTGCATAAAAACTTGGGATACATGTTC
261 AACAGAAAATTGAAAATTTGCTCAAAAAACACGTTTATTTGCATAAAAACTTGGGATACATGTTC
3070110 ATTGAAATTGTTATTACAAAATACACAGTTCAAATCAAATTATATATGAAATATTTAATACACAA
326 ATTGAAATTGTTATTACAAAATACACAGTTCAAATCAAATTATATATGAAATATTTAATACACAA
3070175 ATCCATTCAAAAATTGATAATTCTCATGATAATTTAAATAATGTATTAAAGATGAAGGAATGACA
391 ATCCATTCAAAAATTGATAATTCTCATGATAATTTAAATAATGTATTAAAGATGAAGGAATGACA
3070240 ATACATGATATAAAATTATGTACAAAAGAAATTTATGAAACATGTATATACAAGTAAAAATTGGA
456 ATACATGATATAAAATTATGTACAAAAGAAATTTATGAAACATGTATATACAAGTAAAAATTGGA
3070305 TATAATTATTTGTAAAAAAAATGAAATTAATAATGTATGAAAGAAACAAAGTAAACATATAAGTA
521 TATAATTATTTGTAAAAAAAATGAAATTAATAATGTATGAAAGAAACAAAGTAAACATATAAGTA
3070370 TATAAGTAACAAAATATATATATATATAATAATGCATAAGGATAATATGAGAGTGTGTACAATAA
586 TATAAGTAACAAAATATATATATATATAATAATGCATAAGGATAATATGAGAGTGTGTACAATAA
3070435 ATAAGTGGTATGATTAAAAACATGGTTCCCAAAAGAAATATATTGTACATATAAATATCTTTAAA
651 ATAAGTGGTATGATTAAAAACATGGTTCCCAAAAGAAATATATTGTACATATAAATATCTTTAAA
3070500 GTAGGTTCTACACATAAAAAAAAATATTTATATGAAGATATATGAGAATAATAATATGTATCATA
716 GTAGGTTCTACACATAAAAAAAAATATTTATATGAAGATATATGAGAATAATAATATGTATCATA
3070565 GT
781 GT
3070567 AAAA
1 AAAA
3070571 AATAATTTAA
Statistics
Matches: 783, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
782 783 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (782 bp):
AAAATGTTTGAATAGCTCAAATTAGCGGTCAAAAATCTCTCGTTCCAAGGACATGCAGTTTCATA
CCCAGTACGATTGGATATGATCCCTTATACCTTTAAGGTACGATCGATCTTCGACTTTTGAAAAA
TTCGTGCATTAAAATCATAAAAGGTTATCTAAATATTTGGTTCACCGGAAAAGTCATACCCAGTA
CGATTGAGCACGATTTTCCGAATTCCCCAAATATTAGATATTACCTTATTTCAGAATTTTTGAAT
AACAGAAAATTGAAAATTTGCTCAAAAAACACGTTTATTTGCATAAAAACTTGGGATACATGTTC
ATTGAAATTGTTATTACAAAATACACAGTTCAAATCAAATTATATATGAAATATTTAATACACAA
ATCCATTCAAAAATTGATAATTCTCATGATAATTTAAATAATGTATTAAAGATGAAGGAATGACA
ATACATGATATAAAATTATGTACAAAAGAAATTTATGAAACATGTATATACAAGTAAAAATTGGA
TATAATTATTTGTAAAAAAAATGAAATTAATAATGTATGAAAGAAACAAAGTAAACATATAAGTA
TATAAGTAACAAAATATATATATATATAATAATGCATAAGGATAATATGAGAGTGTGTACAATAA
ATAAGTGGTATGATTAAAAACATGGTTCCCAAAAGAAATATATTGTACATATAAATATCTTTAAA
GTAGGTTCTACACATAAAAAAAAATATTTATATGAAGATATATGAGAATAATAATATGTATCATA
GT
Found at i:3074533 original size:16 final size:16
Alignment explanation
Indices: 3074512--3074543 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3074502 CTCATGGTGC
*
3074512 TTATAAAAAGTTATAT
1 TTATAAAAAATTATAT
3074528 TTATAAAAAATTATAT
1 TTATAAAAAATTATAT
3074544 AAATAGCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
TTATAAAAAATTATAT
Found at i:3082200 original size:20 final size:20
Alignment explanation
Indices: 3082175--3082221 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
3082165 CCTGGCGTTG
3082175 TTCTGGCACGTTCCAGAAGC
1 TTCTGGCACGTTCCAGAAGC
3082195 TTCTGGCACGTTCCAGAAGC
1 TTCTGGCACGTTCCAGAAGC
3082215 TTCTGGC
1 TTCTGGC
3082222 TTGTGTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.17, C:0.30, G:0.26, T:0.28
Consensus pattern (20 bp):
TTCTGGCACGTTCCAGAAGC
Found at i:3088390 original size:14 final size:15
Alignment explanation
Indices: 3088364--3088394 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3088354 TCCAGGTTCA
3088364 TCAACACATTTTTCT
1 TCAACACATTTTTCT
3088379 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
3088393 TC
1 TC
3088395 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:3096883 original size:13 final size:13
Alignment explanation
Indices: 3096865--3096889 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3096855 ATTTACAAGA
3096865 TTACATAATCAAT
1 TTACATAATCAAT
3096878 TTACATAATCAA
1 TTACATAATCAA
3096890 ATCTAAACTA
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
TTACATAATCAAT
Found at i:3104272 original size:21 final size:21
Alignment explanation
Indices: 3104248--3104301 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
3104238 ATACTATTAT
* *
3104248 TATATTTATTTTTATTCCTAG
1 TATATTTATTTTTAATACTAG
* *
3104269 TATATTTATTATTAATATTAG
1 TATATTTATTTTTAATACTAG
*
3104290 TATATGTATTTT
1 TATATTTATTTT
3104302 GTTATACGCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.61
Consensus pattern (21 bp):
TATATTTATTTTTAATACTAG
Found at i:3108701 original size:28 final size:28
Alignment explanation
Indices: 3108662--3108719 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
3108652 TGGTTCTGTG
3108662 ATATAAATCTTGGATATGGAGAGAGATT
1 ATATAAATCTTGGATATGGAGAGAGATT
* *
3108690 ATATAAATCTTGGATATGGATAGATATT
1 ATATAAATCTTGGATATGGAGAGAGATT
3108718 AT
1 AT
3108720 CCGACCTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (28 bp):
ATATAAATCTTGGATATGGAGAGAGATT
Found at i:3109923 original size:26 final size:26
Alignment explanation
Indices: 3109894--3109975 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
3109884 TGATACAAAT
3109894 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
3109920 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
3109946 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
3109972 TGAT
1 TGAT
3109976 GAATTAAATG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.30, C:0.05, G:0.27, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:3122537 original size:22 final size:21
Alignment explanation
Indices: 3122502--3122578 Score: 61
Period size: 22 Copynumber: 3.7 Consensus size: 21
3122492 AAAAGGTATC
* *
3122502 TACAAATTAAATCTATAAGAT
1 TACAAATCATATCTATAAGAT
*
3122523 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TATAAGAT
* *
3122546 TGCATATCATATC--TAAGAT
1 TACAAATCATATCTATAAGAT
*
3122565 TGC-AATCATATCTA
1 TACAAATCATATCTA
3122579 AGATTGTATC
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
18 8 0.17
19 9 0.20
21 3 0.07
22 17 0.37
23 9 0.20
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (21 bp):
TACAAATCATATCTATAAGAT
Found at i:3122594 original size:35 final size:37
Alignment explanation
Indices: 3122531--3122609 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
3122521 ATTACAAAAT
3122531 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTG
3122567 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGATATCATATCTAAGATTG
3122602 CATATCAT
1 CATATCAT
3122610 TGAAGATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 22 0.55
36 8 0.20
37 10 0.25
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTG
Found at i:3122607 original size:14 final size:15
Alignment explanation
Indices: 3122552--3122607 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
3122542 AGATTGCATA
3122552 TCATATCTAAGATTG
1 TCATATCTAAGATTG
3122567 CAATCATATCTAAGATTG
1 ---TCATATCTAAGATTG
3122585 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
3122602 -CATATC
1 TCATATC
3122608 ATTGAAGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 6 0.16
17 16 0.43
18 15 0.41
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:3122617 original size:17 final size:19
Alignment explanation
Indices: 3122538--3122609 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
3122528 AATCATATCT
3122538 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
3122557 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
3122575 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
3122592 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
3122610 TGAAGATTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:3123081 original size:44 final size:45
Alignment explanation
Indices: 3122969--3123162 Score: 282
Period size: 45 Copynumber: 4.3 Consensus size: 45
3122959 TTATATCTAC
*
3122969 TATCTTTGATCTGCTCCCCGTCTAATATAGAGACGCCAAATCTGT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* * *
3123014 TATCTTTGATCTGCTCCCTGTCTAATACAGAGACACCAAATCTGC
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* *
3123059 T-TCTTTAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* * *
3123103 TATCTCTGATTTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* *
3123148 CATCTTGGATCTGCT
1 TATCTTTGATCTGCT
3123163 TCGATGTAAA
Statistics
Matches: 132, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
44 39 0.30
45 93 0.70
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (45 bp):
TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
Found at i:3123090 original size:89 final size:89
Alignment explanation
Indices: 3122971--3123146 Score: 280
Period size: 89 Copynumber: 2.0 Consensus size: 89
3122961 ATATCTACTA
* * * *
3122971 TCTTTGATCTGCTCCCCGTCTAATATAGAGACGCCAAATCTGTTATCTTTGATCTGCTCCCTGTC
1 TCTTTAATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTCTGATCTGCTCCCCGTC
3123036 TAATACAGAGACACCAAATCTGCT
66 TAATACAGAGACACCAAATCTGCT
* *
3123060 TCTTTAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTCTGATTTGCTCCCCGTC
1 TCTTTAATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTCTGATCTGCTCCCCGTC
**
3123125 TAATACAGAGATGCCAAATCTG
66 TAATACAGAGACACCAAATCTG
3123147 TCATCTTGGA
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 79 1.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (89 bp):
TCTTTAATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTCTGATCTGCTCCCCGTC
TAATACAGAGACACCAAATCTGCT
Found at i:3123305 original size:78 final size:78
Alignment explanation
Indices: 3123176--3123470 Score: 443
Period size: 78 Copynumber: 3.8 Consensus size: 78
3123166 ATGTAAACAC
* **
3123176 ATGAAGGTCAGATCTACTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTATCCGTCTAATACAGAGATGCCAAATCATCT
3123241 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* *
3123254 ATGAAGGTCCA-ATCTGTTATGTCTTCGATCTGCTATTCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTATCCGTCTAATACAGAGATGCCAAATCATC
3123318 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* *
3123332 ATGAAGGTCCA-ATCTGTTATGTCTTCGATCTGCTATTCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTATCCGTCTAATACAGAGATGCCAAATCATC
3123396 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* * **
3123410 ATGAAGGTCAGATCTGCTATGTCTTCGATTTGCT-TCCCGTCGAATATGGAGATGCCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTAT-CCGTCTAATACAGAGATGCCAAATC
3123471 TGTTTCTTCG
Statistics
Matches: 203, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
77 3 0.01
78 198 0.98
79 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTATCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:3123631 original size:287 final size:287
Alignment explanation
Indices: 3123264--3123863 Score: 1031
Period size: 287 Copynumber: 2.1 Consensus size: 287
3123254 ATGAAGGTCC
* *** *
3123264 AATCTGTTATGTCTTCGATCTGCTATTCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCT
1 AATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAACCATCTTGGATCTGCT
* **
3123329 TCAATGAAGGTCCAATCTGTTATGTCTTCGATCTGCTATTCGTCTAATACAGAGATGCCAAATCA
66 TCAATGAAAGTCCAATCTGTTATGTCTTCGATCTGCTACCCGTCTAATACAGAGATGCCAAATCA
*
3123394 TCTTGGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCGATTTGCT-TCCCGTCGAATATG
131 TCTTGGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCT-CCGTCGAATATG
* * * *
3123458 GAGATGCCAAATCTGTTTCTTCGATTTGTTCTCTGATAGTACAGAGATGCGAAATCATCGTAGAT
195 GAGATGCCAAATATGTTTCTTCGATTTGTTCTCTGAAAGTAAAGAGATGCCAAATCATCGTAGAT
*
3123523 CTGCTTCAGCGTAAACACGTGAAAGCCA
260 CTGCGTCAGCGTAAACACGTGAAAGCCA
*
3123551 AATCTGCTATGTCTTCGATTTGCTCCCCGTCTAATACAGAGATGCCAAACCATCTTGGATCTGCT
1 AATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAACCATCTTGGATCTGCT
*
3123616 TCAATGAAAGTCCAATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCA
66 TCAATGAAAGTCCAATCTGTTATGTCTTCGATCTGCTACCCGTCTAATACAGAGATGCCAAATCA
3123681 TCTTGGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGG
131 TCTTGGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGG
*
3123746 AGATGCCAAATATGTTTCTTCGATTTGTTCTCTGAAAGTAAAGAGATGCCAAATCATCTTAGATC
196 AGATGCCAAATATGTTTCTTCGATTTGTTCTCTGAAAGTAAAGAGATGCCAAATCATCGTAGATC
3123811 TGCGTCAGCGTAAACACGTGAAAGCCA
261 TGCGTCAGCGTAAACACGTGAAAGCCA
3123838 AATCTGCTATGTCTTCGATCTGCTCC
1 AATCTGCTATGTCTTCGATCTGCTCC
3123864 TTGTAAACGC
Statistics
Matches: 294, Mismatches: 18, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
287 293 1.00
288 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (287 bp):
AATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAACCATCTTGGATCTGCT
TCAATGAAAGTCCAATCTGTTATGTCTTCGATCTGCTACCCGTCTAATACAGAGATGCCAAATCA
TCTTGGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGG
AGATGCCAAATATGTTTCTTCGATTTGTTCTCTGAAAGTAAAGAGATGCCAAATCATCGTAGATC
TGCGTCAGCGTAAACACGTGAAAGCCA
Found at i:3123756 original size:78 final size:78
Alignment explanation
Indices: 3123542--3123756 Score: 326
Period size: 78 Copynumber: 2.8 Consensus size: 78
3123532 CGTAAACACG
* *
3123542 TGAAAG-CCAAATCTGCTATGTCTTCGATTTGCTCCCCGTCTAATACAGAGATGCCAAACCATCT
1 TGAAAGTCC-AATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
3123606 TGGATCTGCTTCAA
65 TGGATCTGCTTCAA
*
3123620 TGAAAGTCCAATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTT
1 TGAAAGTCCAATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTT
3123685 GGATCTGCTTCAA
66 GGATCTGCTTCAA
* * * **
3123698 TGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAAT
1 TGAAAGTCCA-ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAAT
3123757 ATGTTTCTTC
Statistics
Matches: 126, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
77 2 0.02
78 122 0.97
79 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (78 bp):
TGAAAGTCCAATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTT
GGATCTGCTTCAA
Found at i:3124100 original size:220 final size:220
Alignment explanation
Indices: 3123699--3124288 Score: 950
Period size: 220 Copynumber: 2.7 Consensus size: 220
3123689 CTGCTTCAAT
* *
3123699 GAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATATGTTTC
1 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
* * *
3123764 TTCGATTTGTTCTCTGAAAGTAAAGAGATGCCAAATCATCTTAGATCTGCGTCAGCGTAAACACG
66 TTCGATTTGTTCTCTGAAAGTACAGAGATTCCAAATCATCTTAGATCTGCTTCAGCGTAAACACG
* *
3123829 TGAAAGCCAAATCTGCTATGTCTTCGATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTG
131 TGAAAGCCAAATCTGCTATGTCTTCGATATGCTCATTGTAAACGCAAGGATGCCAAATCATCTTG
3123894 GATCTACTTCGATGTGAAAACATCC
196 GATCTACTTCGATGTGAAAACATCC
3123919 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
1 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
* *
3123984 TTCGATTTGTTCTCTGAAAGTACAGAGATTCCAAATCATCTTAGATCTGCTTCAGTGTAAACATG
66 TTCGATTTGTTCTCTGAAAGTACAGAGATTCCAAATCATCTTAGATCTGCTTCAGCGTAAACACG
* *
3124049 TGAAAGCCAAATCTGCTATGTCTTCGATATGCTCATTGTCAACGTAAGGATGCCAAATCATCTTG
131 TGAAAGCCAAATCTGCTATGTCTTCGATATGCTCATTGTAAACGCAAGGATGCCAAATCATCTTG
3124114 GATCTACTTCGATGTGAAAACATCC
196 GATCTACTTCGATGTGAAAACATCC
* * *
3124139 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTTTCTGTTGAATATGGAGATGCCAAATCTGTTTC
1 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
* * * * *
3124204 TTTGATTTGTTCTCT-AACAATACAGAGATGT-TAAATCATCTTGGATCCGCTTCAGCGTAAACA
66 TTCGATTTGTTCTCTGAA-AGTACAGAGAT-TCCAAATCATCTTAGATCTGCTTCAGCGTAAACA
* * *
3124267 CCTGAAGGTCAAATCTGCTATG
129 CGTGAAAGCCAAATCTGCTATG
3124289 CTTTAGCCTG
Statistics
Matches: 344, Mismatches: 24, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
219 2 0.01
220 341 0.99
221 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (220 bp):
GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
TTCGATTTGTTCTCTGAAAGTACAGAGATTCCAAATCATCTTAGATCTGCTTCAGCGTAAACACG
TGAAAGCCAAATCTGCTATGTCTTCGATATGCTCATTGTAAACGCAAGGATGCCAAATCATCTTG
GATCTACTTCGATGTGAAAACATCC
Found at i:3127019 original size:290 final size:287
Alignment explanation
Indices: 3126473--3127050 Score: 1005
Period size: 290 Copynumber: 2.0 Consensus size: 287
3126463 TCATTTTTAG
3126473 TTGCCTATTCTGGGTATTTACGATCTCTCACATATCGCAATATATCCTGATACCAAGGGTTATCA
1 TTGCCTATTCTGGGTATTTACGATCTCTCACATATCGCAATATATCCTGATACCAAGGGTTATCA
*
3126538 TCCTTTTCTTCTTCCTCAATGTTACAACAGCAAGCTGGAGCCTCAAAGATACTCATCTGTATAGG
66 TCCTTTTCTTCTTCCTCAATGTTACAACAGCAAGCTGGAGCCTCAAAGATACTCATCTGAATAGG
3126603 TCACATCTCATCCTCTTTATTTACTTTAATCATTGAAGCCAAGGTTGCTAGAGCATCTGCCATCT
131 TCACATCTCATCCTCTTTATTTACTTTAATCATTGAAGCCAAGGTTGCTAGAGCATCTGCCATCT
3126668 GGTTTTCATCTCGTGGGATATAATTGAAAGTGATGTCATCGAACTCTAAAAGTAACCCCAAAACT
196 GGTTTTCATCTCGTGGGATATAATTGAAAGTGATGTCATCGAACTCTAAAAGTAACCCCAAAACT
*
3126733 ACCTTTCGATAATTGATCAATTTAGGA
261 ACCTTTCGATAATTGATCAATATAGGA
3126760 TTGCCTATTCTGGGTATTTACGATCTCTCACATATCGCAATATATCCTGATACCAAGGGTTATCA
1 TTGCCTATTCTGGGTATTTACGATCTCTCACATATCGCAATATATCCTGATACCAAGGGTTATCA
* * ** * *
3126825 TCCTTTTCTTCTTCCTCAATGTTGCGACAGTGAGCTGGAGCCTCGAAGATACTCATCTGAATGGG
66 TCCTTTTCTTCTTCCTCAATGTTACAACAGCAAGCTGGAGCCTCAAAGATACTCATCTGAATAGG
* *
3126890 TCTCATCTCCTCCTCCTCTTTATTTACTTTAATCATTGAAGCCAAGGTTGCTAGAGCATCTGCCA
131 TCACA--T-CTCATCCTCTTTATTTACTTTAATCATTGAAGCCAAGGTTGCTAGAGCATCTGCCA
*
3126955 TCTGGTTTTCATCTCGTGGGATATAATTGAAAGTGATGTCATCGAACTCCT-CAAGTAACCCCAA
193 TCTGGTTTTCATCTCGTGGGATATAATTGAAAGTGATGTCATCGAACT-CTAAAAGTAACCCCAA
*
3127019 AACTACCTTTTGATAATTGATCAATATAGGA
257 AACTACCTTTCGATAATTGATCAATATAGGA
3127050 T
1 T
3127051 CCCTTGTCTC
Statistics
Matches: 275, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
287 127 0.46
289 1 0.00
290 145 0.53
291 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (287 bp):
TTGCCTATTCTGGGTATTTACGATCTCTCACATATCGCAATATATCCTGATACCAAGGGTTATCA
TCCTTTTCTTCTTCCTCAATGTTACAACAGCAAGCTGGAGCCTCAAAGATACTCATCTGAATAGG
TCACATCTCATCCTCTTTATTTACTTTAATCATTGAAGCCAAGGTTGCTAGAGCATCTGCCATCT
GGTTTTCATCTCGTGGGATATAATTGAAAGTGATGTCATCGAACTCTAAAAGTAACCCCAAAACT
ACCTTTCGATAATTGATCAATATAGGA
Found at i:3131274 original size:16 final size:16
Alignment explanation
Indices: 3131253--3131284 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3131243 GAGTTACCGA
3131253 TTCATTTATCAGATAT
1 TTCATTTATCAGATAT
*
3131269 TTCATTTATCCGATAT
1 TTCATTTATCAGATAT
3131285 CTTTTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (16 bp):
TTCATTTATCAGATAT
Found at i:3135461 original size:18 final size:19
Alignment explanation
Indices: 3135423--3135461 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3135413 TGGTTCAAGC
*
3135423 TTTCAATCTCATATATCAA
1 TTTCAATCTCACATATCAA
*
3135442 TTTCAAT-TCACATTTCAA
1 TTTCAATCTCACATATCAA
3135460 TT
1 TT
3135462 CTTAGTTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCACATATCAA
Found at i:3135913 original size:51 final size:53
Alignment explanation
Indices: 3135799--3135922 Score: 153
Period size: 51 Copynumber: 2.4 Consensus size: 53
3135789 CTAGAACAGT
* * *
3135799 AACAGTAACAGTAGCAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGG
1 AACAGTAACAGTAACAGTAAGGTACACAGAGTACCTCATCGGAACAAATCCGA
* * * * * *
3135852 AACAGTAACAGTAATAGTAAGGTAC-GA-AGTGCCTCTTCGGAACGAATCTGA
1 AACAGTAACAGTAACAGTAAGGTACACAGAGTACCTCATCGGAACAAATCCGA
3135903 AACAGTAACAGTAACAGTAA
1 AACAGTAACAGTAACAGTAA
3135923 CAGAACAGTA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
51 38 0.62
52 1 0.02
53 22 0.36
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (53 bp):
AACAGTAACAGTAACAGTAAGGTACACAGAGTACCTCATCGGAACAAATCCGA
Found at i:3135914 original size:6 final size:6
Alignment explanation
Indices: 3135903--3135935 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
3135893 ACGAATCTGA
3135903 AACAGT AACAGT AACAGT AACAG- AACAGT AACA
1 AACAGT AACAGT AACAGT AACAGT AACAGT AACA
3135936 ATATCCGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.55, C:0.18, G:0.15, T:0.12
Consensus pattern (6 bp):
AACAGT
Found at i:3135982 original size:45 final size:45
Alignment explanation
Indices: 3135926--3136057 Score: 255
Period size: 45 Copynumber: 2.9 Consensus size: 45
3135916 ACAGTAACAG
*
3135926 AACAGTAACAATATCCGACACACAAAGTGCCGAATCGGTAACGGT
1 AACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACGGT
3135971 AACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACGGT
1 AACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACGGT
3136016 AACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAAC
1 AACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAAC
3136058 AGTAGTAGTA
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 86 1.00
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (45 bp):
AACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACGGT
Found at i:3136492 original size:15 final size:16
Alignment explanation
Indices: 3136455--3136504 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
3136445 CAATACACAT
3136455 TTCAATT-AA-TCATAA
1 TTCAATTCAATTCA-AA
* *
3136470 TTCCATTCCATTC-AA
1 TTCAATTCAATTCAAA
3136485 TTCAATTCAATTCAAA
1 TTCAATTCAATTCAAA
3136501 TTCA
1 TTCA
3136505 CTTTTCCACT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 19 0.68
16 7 0.25
17 2 0.07
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (16 bp):
TTCAATTCAATTCAAA
Found at i:3136815 original size:5 final size:6
Alignment explanation
Indices: 3136770--3136815 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
3136760 ACTTTTCCAA
* *
3136770 TCAATT T-ACATT TTAATT TTAATT TCAATT TCAATT TCAA-T TCAAT
1 TCAATT TCA-ATT TCAATT TCAATT TCAATT TCAATT TCAATT TCAAT
3136816 AACAATTCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
5 6 0.17
6 29 0.81
7 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (6 bp):
TCAATT
Found at i:3141147 original size:17 final size:18
Alignment explanation
Indices: 3141125--3141159 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3141115 GATATGATAC
*
3141125 TAAAAT-TATTAAAAAAT
1 TAAAATATATAAAAAAAT
3141142 TAAAATATATAAAAAAAT
1 TAAAATATATAAAAAAAT
3141160 CAGGGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:3141440 original size:23 final size:23
Alignment explanation
Indices: 3141415--3141457 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3141405 AAGGTATCTA
*
3141415 AAAATTAAATC-TCTAAGATTAC
1 AAAATCAAATCTTCTAAGATTAC
*
3141437 AAAATCATATCTTCTAAGATT
1 AAAATCAAATCTTCTAAGATT
3141458 GCATATCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.35
Consensus pattern (23 bp):
AAAATCAAATCTTCTAAGATTAC
Found at i:3141485 original size:18 final size:19
Alignment explanation
Indices: 3141449--3141503 Score: 103
Period size: 18 Copynumber: 2.9 Consensus size: 19
3141439 AATCATATCT
3141449 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
3141468 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
3141486 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
3141504 TGAAGATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 18 0.51
19 17 0.49
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:3141659 original size:21 final size:20
Alignment explanation
Indices: 3141622--3141660 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3141612 TTGGACTTCA
**
3141622 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
3141642 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
3141661 TCTGGGCCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:3159358 original size:7 final size:7
Alignment explanation
Indices: 3159337--3159378 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
3159327 TTATTTTGTT
3159337 TTATTTA
1 TTATTTA
*
3159344 GT-TTTA
1 TTATTTA
3159350 TTATTTA
1 TTATTTA
3159357 TTATTTA
1 TTATTTA
3159364 TTATTTA
1 TTATTTA
3159371 TT-TTTA
1 TTATTTA
3159377 TT
1 TT
3159379 TTATTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
6 11 0.34
7 21 0.66
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (7 bp):
TTATTTA
Found at i:3161938 original size:21 final size:21
Alignment explanation
Indices: 3161914--3161977 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
3161904 TTTATAGATG
*
3161914 CCTCTGTTTTCTATTGAAAAT
1 CCTCTGTTTTCTTTTGAAAAT
* *
3161935 CCTCTATTTTCTTTTGGAAAT
1 CCTCTGTTTTCTTTTGAAAAT
*
3161956 CCTCTGTTCTCTTTTGAAAAT
1 CCTCTGTTTTCTTTTGAAAAT
3161977 C
1 C
3161978 AACAGTTTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.20, C:0.22, G:0.09, T:0.48
Consensus pattern (21 bp):
CCTCTGTTTTCTTTTGAAAAT
Found at i:3165152 original size:11 final size:11
Alignment explanation
Indices: 3165136--3165169 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
3165126 ATGCCAAATT
3165136 ATCAAGAATAA
1 ATCAAGAATAA
*
3165147 ATCAAGAACAA
1 ATCAAGAATAA
3165158 ATCAAGAATAA
1 ATCAAGAATAA
3165169 A
1 A
3165170 ACTAAATGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.65, C:0.12, G:0.09, T:0.15
Consensus pattern (11 bp):
ATCAAGAATAA
Found at i:3179270 original size:27 final size:26
Alignment explanation
Indices: 3179233--3179347 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
3179223 AGCATGGCTG
* *
3179233 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
3179259 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
3179287 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
3179314 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
3179341 CCAGAAC
1 CCAGAAC
3179348 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:3179292 original size:54 final size:54
Alignment explanation
Indices: 3179233--3179347 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
3179223 AGCATGGCTG
*
3179233 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
3179287 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
3179341 CCAGAAC
1 CCAGAAC
3179348 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:3180585 original size:26 final size:26
Alignment explanation
Indices: 3180556--3180657 Score: 177
Period size: 26 Copynumber: 3.9 Consensus size: 26
3180546 ATTCTTTAAT
3180556 AAACATTTACCTAACCCATTATCATG
1 AAACATTTACCTAACCCATTATCATG
3180582 AAACATTTACCTAACCCATTATCATG
1 AAACATTTACCTAACCCATTATCATG
*
3180608 AAACATTTACCTAACCTATTATCATG
1 AAACATTTACCTAACCCATTATCATG
* *
3180634 GAACATTTACCTAACCTATTATCA
1 AAACATTTACCTAACCCATTATCA
3180658 ATTTGTATCA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.32
Consensus pattern (26 bp):
AAACATTTACCTAACCCATTATCATG
Found at i:3186526 original size:18 final size:18
Alignment explanation
Indices: 3186500--3186534 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3186490 ACGTTGCAGT
3186500 CCAACTAGATTTTAAGTG
1 CCAACTAGATTTTAAGTG
*
3186518 CCAATTAGATTTTAAGT
1 CCAACTAGATTTTAAGT
3186535 ATATCTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (18 bp):
CCAACTAGATTTTAAGTG
Found at i:3191828 original size:36 final size:36
Alignment explanation
Indices: 3191781--3191853 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
3191771 ACTCTTTGTT
3191781 TGGACTAGTATACTAATCGATTCTCGATCCAATCAG
1 TGGACTAGTATACTAATCGATTCTCGATCCAATCAG
3191817 TGGACTAGTATACTAATCGATTCTCGATCCAATCAG
1 TGGACTAGTATACTAATCGATTCTCGATCCAATCAG
3191853 T
1 T
3191854 CAGACCAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (36 bp):
TGGACTAGTATACTAATCGATTCTCGATCCAATCAG
Found at i:3195122 original size:13 final size:13
Alignment explanation
Indices: 3195104--3195128 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3195094 GAGTATTAAA
3195104 TACTTATATCTAG
1 TACTTATATCTAG
3195117 TACTTATATCTA
1 TACTTATATCTA
3195129 ATGCATATTC
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:0.32, C:0.16, G:0.04, T:0.48
Consensus pattern (13 bp):
TACTTATATCTAG
Found at i:3196233 original size:86 final size:84
Alignment explanation
Indices: 3196079--3196248 Score: 322
Period size: 86 Copynumber: 2.0 Consensus size: 84
3196069 ACAATCTACA
3196079 ACGTTTTCCGTTCTTTAGATTTTTCCCTAACAATTTTTCTTCCCATCTCTTTCAACAAATCATGC
1 ACGTTTTCCGTTCTTTAGATTTTTCCCTAACAATTTTTCTTCCCATCTCTTTCAACAAATCATGC
3196144 ATCCACAAATATTTGTTGT
66 ATCCACAAATATTTGTTGT
3196163 ACGTTTTCCAGGTTCTTTAGATTTTTCCCTAACAATTTTTCTTCCCATCTCTTTCAACAAATCAT
1 ACGTTTTCC--GTTCTTTAGATTTTTCCCTAACAATTTTTCTTCCCATCTCTTTCAACAAATCAT
3196228 GCATCCACAAATATTTGTTGT
64 GCATCCACAAATATTTGTTGT
3196249 CTTTGACTTT
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
84 9 0.11
86 75 0.89
ACGTcount: A:0.24, C:0.25, G:0.08, T:0.44
Consensus pattern (84 bp):
ACGTTTTCCGTTCTTTAGATTTTTCCCTAACAATTTTTCTTCCCATCTCTTTCAACAAATCATGC
ATCCACAAATATTTGTTGT
Found at i:3204152 original size:18 final size:18
Alignment explanation
Indices: 3204126--3204200 Score: 96
Period size: 18 Copynumber: 4.2 Consensus size: 18
3204116 TACGACCGTT
*
3204126 TACGGTACTATTCATGTA
1 TACGGTACTATTCACGTA
* *
3204144 TATGGTACTATTCACTTA
1 TACGGTACTATTCACGTA
**
3204162 TACAATACTATTCACGTA
1 TACGGTACTATTCACGTA
*
3204180 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
3204198 TAC
1 TAC
3204201 AGTAGTTGGG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:3204181 original size:36 final size:36
Alignment explanation
Indices: 3204131--3204201 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
3204121 CCGTTTACGG
* * *
3204131 TACTATTCATGTATATGGTACTATTCACTTATACAA
1 TACTATTCACGTATACGGTACTATTCACGTATACAA
*
3204167 TACTATTCACGTATACGGTACTGTTCACGTATACA
1 TACTATTCACGTATACGGTACTATTCACGTATACA
3204202 GTAGTTGGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (36 bp):
TACTATTCACGTATACGGTACTATTCACGTATACAA
Found at i:3209412 original size:153 final size:153
Alignment explanation
Indices: 3209131--3209432 Score: 408
Period size: 153 Copynumber: 2.0 Consensus size: 153
3209121 TTTAAGCATC
* * * * * *
3209131 TTGCAATTTACCAATGCAAGAAACTAAAGCTTGGAGAGTCTAGTAAGAGATGCAGGTATGTTGAT
1 TTGCAATTTACCAACGCAAGAAACCAAAGCTTCGAGAGTCCAATAAGAGATGCAGGTATGCTGAT
* * * *
3209196 GAAATTGTTAACACTAAGATTAAGATGTACCAAAGAGGATAGACCAGAAATATAACTTTGAATAT
66 GAAATTGTTAACACTAAGATCAAGATCTACCAAAGAGGATAGACCAGAAATATAACGTGGAATAT
* *
3209261 CTGCTTCACCAAGAGTGCACATG
131 CTCCTTCACAAAGAGTGCACATG
* * *
3209284 TTGCAATTTGA-CAACGTAAGAAACCCAAGCTTCGAGAGTCCAATAAGAGATGCAGGTATGCTGC
1 TTGCAATTT-ACCAACGCAAGAAACCAAAGCTTCGAGAGTCCAATAAGAGATGCAGGTATGCTGA
* ** *
3209348 TGAAATTGTTACCACTAAGATCAAGATCTGTCAAAGAGGATAGACCAGAAATATCACGTGGAATA
65 TGAAATTGTTAACACTAAGATCAAGATCTACCAAAGAGGATAGACCAGAAATATAACGTGGAATA
*
3209413 TCTCCTTCACAAAGATTGCA
130 TCTCCTTCACAAAGAGTGCA
3209433 GTCCCTTAGA
Statistics
Matches: 128, Mismatches: 20, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
153 127 0.99
154 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (153 bp):
TTGCAATTTACCAACGCAAGAAACCAAAGCTTCGAGAGTCCAATAAGAGATGCAGGTATGCTGAT
GAAATTGTTAACACTAAGATCAAGATCTACCAAAGAGGATAGACCAGAAATATAACGTGGAATAT
CTCCTTCACAAAGAGTGCACATG
Done.