Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 91
Found at i:3185384 original size:18 final size:18
Alignment explanation
Indices: 3185361--3185406 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
3185351 GACCGGTCAC
3185361 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
3185379 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
* *
3185397 TACTCGACCC
1 GACCCGACCC
3185407 ATTGACTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.13
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:3185428 original size:8 final size:8
Alignment explanation
Indices: 3185415--3185461 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
3185405 CCATTGACTC
3185415 GACCCGTT
1 GACCCGTT
3185423 GACCCGTT
1 GACCCGTT
3185431 GA-CCGTT
1 GACCCGTT
3185438 GACCGGCGTT
1 GACC--CGTT
3185448 GACCACTGTT
1 GACC-C-GTT
3185458 GACC
1 GACC
3185462 AAAACTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 7 0.21
8 11 0.32
9 1 0.03
10 15 0.44
ACGTcount: A:0.15, C:0.34, G:0.28, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:3185438 original size:15 final size:16
Alignment explanation
Indices: 3185418--3185451 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
3185408 TTGACTCGAC
3185418 CCGTTGACC-CGTTGA
1 CCGTTGACCGCGTTGA
3185433 CCGTTGACCGGCGTTGA
1 CCGTTGACC-GCGTTGA
3185450 CC
1 CC
3185452 ACTGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.12, C:0.35, G:0.29, T:0.24
Consensus pattern (16 bp):
CCGTTGACCGCGTTGA
Found at i:3186764 original size:18 final size:18
Alignment explanation
Indices: 3186738--3186773 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3186728 TCGAAAGGAC
*
3186738 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
3186756 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
3186774 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:3187988 original size:24 final size:24
Alignment explanation
Indices: 3187918--3188007 Score: 112
Period size: 23 Copynumber: 3.8 Consensus size: 24
3187908 TCCGACTTGA
* *
3187918 ATTCTGTTATGAT-CCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* *
3187941 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
3187964 ATTCTGATTTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
3187988 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
3188008 TTGAATTATG
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
23 31 0.55
24 25 0.45
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:3192448 original size:3 final size:3
Alignment explanation
Indices: 3192440--3192494 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
3192430 CAGTTTACTT
* * *
3192440 TTA TTA TTA TTTA TTA TTA TTA TTA TAA ATA TTA TTA TTG TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3192486 TTA TTA TTA
1 TTA TTA TTA
3192495 AATAAAATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3194328 original size:23 final size:26
Alignment explanation
Indices: 3194296--3194345 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
3194286 CCTTTTCTAA
*
3194296 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
3194319 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
3194345 T
1 T
3194346 TTTCTCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:3194872 original size:17 final size:18
Alignment explanation
Indices: 3194838--3194880 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3194828 TTTTCTTTCA
* *
3194838 ATTTTTTTATTACTTATT
1 ATTTTTATATTACATATT
3194856 ATTTTTATATTA-ATATT
1 ATTTTTATATTACATATT
*
3194873 TTTTTTAT
1 ATTTTTAT
3194881 TCAGGTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTTTATATTACATATT
Found at i:3199213 original size:14 final size:14
Alignment explanation
Indices: 3199194--3199264 Score: 74
Period size: 14 Copynumber: 5.1 Consensus size: 14
3199184 GCAAAGACAT
*
3199194 CAAAGAAAGAAAAA
1 CAAAGAAAAAAAAA
**
3199208 CAAAG-AAGGAAAA
1 CAAAGAAAAAAAAA
3199221 CAAAGAAAAAAAAGA
1 CAAAGAAAAAAAA-A
*
3199236 AAAAGAAAAAAGAAA
1 CAAAGAAAAAA-AAA
3199251 -AAAGAAAAAAAAA
1 CAAAGAAAAAAAAA
3199264 C
1 C
3199265 TTGAAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
13 15 0.31
14 20 0.41
15 12 0.24
16 2 0.04
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (14 bp):
CAAAGAAAAAAAAA
Found at i:3199220 original size:13 final size:13
Alignment explanation
Indices: 3199194--3199259 Score: 62
Period size: 13 Copynumber: 5.0 Consensus size: 13
3199184 GCAAAGACAT
3199194 CAAAGAAAGAAAAA
1 CAAAG-AAGAAAAA
*
3199208 CAAAGAAGGAAAA
1 CAAAGAAGAAAAA
*
3199221 CAAAGAAAAAAAA
1 CAAAGAAGAAAAA
*
3199234 GAAA-AAGAAAAAA
1 CAAAGAAG-AAAAA
* *
3199247 GAAAAAAGAAAAA
1 CAAAGAAGAAAAA
3199260 AAAACTTGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
12 2 0.04
13 35 0.78
14 8 0.18
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (13 bp):
CAAAGAAGAAAAA
Found at i:3199234 original size:9 final size:9
Alignment explanation
Indices: 3199216--3199262 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
3199206 AACAAAGAAG
*
3199216 GAAAACAAA
1 GAAAAAAAA
3199225 GAAAAAAAA
1 GAAAAAAAA
3199234 GAAAAAGAAA
1 GAAAAA-AAA
*
3199244 AAAGAAAAAA
1 GAA-AAAAAA
3199254 GAAAAAAAA
1 GAAAAAAAA
3199263 ACTTGAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 20 0.61
10 10 0.30
11 3 0.09
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:3199234 original size:22 final size:22
Alignment explanation
Indices: 3199199--3199262 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
3199189 GACATCAAAG
* *
3199199 AAAGAAAAACAAAGAAGGAA-AAC
1 AAAGAAAAA-AAAGAA-AAAGAAA
3199222 AAAGAAAAAAAAGAAAAAGAAA
1 AAAGAAAAAAAAGAAAAAGAAA
*
3199244 AAAGAAAAAAGAAAAAAAA
1 AAAGAAAAAA-AAGAAAAA
3199263 ACTTGAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 2 0.06
22 18 0.50
23 16 0.44
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAGAAAAAAAAGAAAAAGAAA
Found at i:3199245 original size:7 final size:7
Alignment explanation
Indices: 3199222--3199260 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
3199212 GAAGGAAAAC
3199222 AAAGAAA
1 AAAGAAA
*
3199229 AAAAAGAA
1 AAAGA-AA
3199237 AAAGAAA
1 AAAGAAA
3199244 AAAGAAA
1 AAAGAAA
3199251 AAAGAAA
1 AAAGAAA
3199258 AAA
1 AAA
3199261 AAACTTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 23 0.79
8 6 0.21
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:3199262 original size:32 final size:32
Alignment explanation
Indices: 3199199--3199263 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 32
3199189 GACATCAAAG
* * *
3199199 AAAGAAAAACAAAGAAGGAAAACAAAGAAAAA
1 AAAGAAAAACAAAGAAAGAAAAAAAAAAAAAA
* *
3199231 AAAGAAAAAGAAA-AAAGAAAAAAGAAAAAAA
1 AAAGAAAAACAAAGAAAGAAAAAAAAAAAAAA
3199262 AA
1 AA
3199264 CTTGAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (32 bp):
AAAGAAAAACAAAGAAAGAAAAAAAAAAAAAA
Found at i:3201656 original size:114 final size:113
Alignment explanation
Indices: 3201456--3201678 Score: 383
Period size: 114 Copynumber: 2.0 Consensus size: 113
3201446 GTGCCACGTT
3201456 CTCATAGTAGAAATAAGGAGACCCAATAGCTCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 CTCATAGTAGAAATAAGGAGACCCAATAGCTCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* * *
3201521 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 TTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTG
*
3201569 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGGGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGC-TCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* *
3201634 GTTCGGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
65 ATTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
3201679 CTGCATGATC
Statistics
Matches: 103, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
113 30 0.29
114 73 0.71
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.30
Consensus pattern (113 bp):
CTCATAGTAGAAATAAGGAGACCCAATAGCTCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
TTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTG
Found at i:3204609 original size:22 final size:22
Alignment explanation
Indices: 3204569--3204633 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
3204559 ATTTTTAATA
*
3204569 TATATTT-A-TTTTTAGTATTT
1 TATATTTAATTTTTTAATATTT
3204589 TA-ATTTTAATTTTTTAATATTT
1 TATA-TTTAATTTTTTAATATTT
3204611 TATATTTAATTTTTTGAATATTT
1 TATATTTAATTTTTT-AATATTT
3204634 AAATATTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
19 1 0.03
20 5 0.13
21 1 0.03
22 24 0.62
23 8 0.21
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (22 bp):
TATATTTAATTTTTTAATATTT
Found at i:3204639 original size:31 final size:30
Alignment explanation
Indices: 3204578--3204678 Score: 98
Period size: 31 Copynumber: 3.3 Consensus size: 30
3204568 ATATATTTAT
* **
3204578 TTTTAGTATTTTAA-TTTTAATTTTTTAATA
1 TTTTA-TATTTAAATTTTTAATTTTGAAATA
*
3204608 TTTTATATTTAATTTTTTGAATATTT-AAATA
1 TTTTATATTTAAATTTTT-AAT-TTTGAAATA
*
3204639 TTTTATAGTTAAATTTTTAATTTTGAAATAAA
1 TTTTATATTTAAATTTTTAATTTTGAAAT--A
3204671 TTTTATAT
1 TTTTATAT
3204679 ATTTTTTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
29 9 0.15
30 16 0.27
31 23 0.39
32 11 0.19
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (30 bp):
TTTTATATTTAAATTTTTAATTTTGAAATA
Found at i:3208223 original size:4 final size:4
Alignment explanation
Indices: 3208214--3208248 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
3208204 TTCAACTATG
3208214 TATT TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT
3208249 ACATGCATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:3222868 original size:17 final size:17
Alignment explanation
Indices: 3222846--3222886 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
3222836 AGGTTATACT
*
3222846 TTTCTTTCATCTCCATC
1 TTTCTTTCATCTCCATA
*
3222863 TTTCTTTCATCTTCATA
1 TTTCTTTCATCTCCATA
3222880 TTTCTTT
1 TTTCTTT
3222887 ATTTATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTCTTTCATCTCCATA
Found at i:3223557 original size:13 final size:13
Alignment explanation
Indices: 3223527--3223567 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
3223517 CATTATTATT
*
3223527 TTTTATTCA-GTA
1 TTTTATTCATTTA
*
3223539 -TTTATTTATTTA
1 TTTTATTCATTTA
3223551 TTTTATTCATTTA
1 TTTTATTCATTTA
3223564 TTTT
1 TTTT
3223568 CATTAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
11 7 0.29
12 2 0.08
13 15 0.62
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTTATTCATTTA
Found at i:3223743 original size:4 final size:4
Alignment explanation
Indices: 3223734--3223767 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
3223724 TTTTATTCAA
*
3223734 TATT TATT TATT TATT TATTT TATT CATT TATT T
1 TATT TATT TATT TATT TA-TT TATT TATT TATT T
3223768 TTATTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:3223756 original size:13 final size:13
Alignment explanation
Indices: 3223734--3223768 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
3223724 TTTTATTCAA
3223734 TATTTA-TTTATT
1 TATTTATTTTATT
3223746 TATTTATTTTATT
1 TATTTATTTTATT
*
3223759 CATTTATTTT
1 TATTTATTTT
3223769 TATTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (13 bp):
TATTTATTTTATT
Found at i:3223784 original size:25 final size:27
Alignment explanation
Indices: 3223716--3223780 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
3223706 TATTTTCTCA
3223716 TTATTAATTTTTATTCAATATTTATTTAT
1 TTATTAATTTTTATTC-A-ATTTATTTAT
*
3223745 TTATTTA-TTTTATTC-ATTTA-TT-T
1 TTATTAATTTTTATTCAATTTATTTAT
3223768 TTATTAATTTTTA
1 TTATTAATTTTTA
3223781 ATTCCCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
23 7 0.21
24 7 0.21
25 5 0.15
28 8 0.24
29 6 0.18
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (27 bp):
TTATTAATTTTTATTCAATTTATTTAT
Found at i:3228408 original size:19 final size:19
Alignment explanation
Indices: 3228384--3228434 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3228374 AAATGACCAA
*
3228384 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACGCGAACT
* *
3228403 CAAATTCGTAACGTGAACT
1 CAAATTCGCAACGCGAACT
*
3228422 CTAATTTCGCAAC
1 C-AAATTCGCAAC
3228435 AGAGGTTTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.25
Consensus pattern (19 bp):
CAAATTCGCAACGCGAACT
Found at i:3228539 original size:77 final size:77
Alignment explanation
Indices: 3228444--3228593 Score: 237
Period size: 77 Copynumber: 1.9 Consensus size: 77
3228434 CAGAGGTTTC
* * * * *
3228444 AAAATCGTAATGCGATTTTTAAATTCGTAACGCTAATTACTGATATAGGTAAACAGTACTATCGT
1 AAAATCGCAACGCGATTTTCAAATTCGCAACGCTAATTACTGATATAGGTAAACAGTACTATCGC
3228509 AACGCGAATAGT
66 AACGCGAATAGT
* *
3228521 AAAATCGCAACGCGATTTTCAAATTCGCAATGCTAATTACTGATATAGGTAAACAGTATTATCGC
1 AAAATCGCAACGCGATTTTCAAATTCGCAACGCTAATTACTGATATAGGTAAACAGTACTATCGC
3228586 AACGCGAA
66 AACGCGAA
3228594 ATTCGTAACG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 66 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (77 bp):
AAAATCGCAACGCGATTTTCAAATTCGCAACGCTAATTACTGATATAGGTAAACAGTACTATCGC
AACGCGAATAGT
Found at i:3228947 original size:20 final size:20
Alignment explanation
Indices: 3228898--3228947 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
3228888 TCGGTAATTA
*
3228898 GCGTTGCGAGTTTACTATTC
1 GCGTTGCGATTTTACTATTC
*
3228918 GCGTTGCGATTTTCCTATTC
1 GCGTTGCGATTTTACTATTC
*
3228938 GTGTTGCGAT
1 GCGTTGCGAT
3228948 AGTACTGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.20, G:0.26, T:0.42
Consensus pattern (20 bp):
GCGTTGCGATTTTACTATTC
Found at i:3228968 original size:77 final size:77
Alignment explanation
Indices: 3228857--3229007 Score: 221
Period size: 77 Copynumber: 2.0 Consensus size: 77
3228847 GAATTTAAAA
*
3228857 ATTCGCGTTACGATAGTACTATTTACCTAAATCGGTAATTAGCGTTGCGAGTTTACTATTCGCGT
1 ATTCGCGTTACGATAGTACTATGTACCTAAATCGGTAATTAGCGTTGCGAGTTTACTATTCGCGT
3228922 TGCGATTTTCCT
66 TGCGATTTTCCT
* * * * * * **
3228934 ATTCGTGTTGCGATAGTACTGTGTACCTATATCGGTAATTCGCGTTGCGATTTTTTTATTCGCGT
1 ATTCGCGTTACGATAGTACTATGTACCTAAATCGGTAATTAGCGTTGCGAGTTTACTATTCGCGT
3228999 TGCGATTTT
66 TGCGATTTT
3229008 GGAACCTGTG
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
77 65 1.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (77 bp):
ATTCGCGTTACGATAGTACTATGTACCTAAATCGGTAATTAGCGTTGCGAGTTTACTATTCGCGT
TGCGATTTTCCT
Found at i:3233399 original size:15 final size:15
Alignment explanation
Indices: 3233379--3233414 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3233369 TGGTTATGAC
*
3233379 TCATCGCTATCATCA
1 TCATCGCCATCATCA
3233394 TCATCGCCATCATCA
1 TCATCGCCATCATCA
3233409 TCATCG
1 TCATCG
3233415 TTGTCGTCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.36, G:0.08, T:0.31
Consensus pattern (15 bp):
TCATCGCCATCATCA
Found at i:3235537 original size:9 final size:9
Alignment explanation
Indices: 3235523--3235556 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3235513 TAAGTAAAAT
3235523 ATTAAATAA
1 ATTAAATAA
3235532 ATTAAAT-A
1 ATTAAATAA
*
3235540 CTTAAATAA
1 ATTAAATAA
3235549 ATTAAATA
1 ATTAAATA
3235557 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:3235555 original size:17 final size:17
Alignment explanation
Indices: 3235519--3235557 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3235509 TATATAAGTA
3235519 AAATA-TTAAATAAATT
1 AAATACTTAAATAAATT
3235535 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
3235552 AAATAC
1 AAATAC
3235558 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTTAAATAAATT
Found at i:3236677 original size:21 final size:21
Alignment explanation
Indices: 3236628--3236679 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3236618 ATATATATAG
* *
3236628 TTTAGAGTGTAGGGTTTAGGAT
1 TTTAG-GTTTAGGGTTTAGAAT
* *
3236650 GTAAGGTTTAGGGTTTAGAAT
1 TTTAGGTTTAGGGTTTAGAAT
3236671 TTTAGGTTT
1 TTTAGGTTT
3236680 TGAGATTGAG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (21 bp):
TTTAGGTTTAGGGTTTAGAAT
Found at i:3236693 original size:21 final size:23
Alignment explanation
Indices: 3236669--3236716 Score: 75
Period size: 21 Copynumber: 2.2 Consensus size: 23
3236659 AGGGTTTAGA
3236669 ATTTTAGG-TTTTGAGA-TTGAG
1 ATTTTAGGTTTTTGAGATTTGAG
3236690 A-TTTAGGTTTTTGAGATTTGAG
1 ATTTTAGGTTTTTGAGATTTGAG
3236712 ATTTT
1 ATTTT
3236717 TATATTTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.25
21 9 0.38
22 6 0.25
23 3 0.12
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (23 bp):
ATTTTAGGTTTTTGAGATTTGAG
Found at i:3237177 original size:4 final size:4
Alignment explanation
Indices: 3237168--3237194 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3237158 TCAAAATGTT
3237168 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
3237195 GATTATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:3237224 original size:30 final size:30
Alignment explanation
Indices: 3237190--3237247 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
3237180 TTTATTTATT
3237190 TATTTGATTATTAT-ATTAACTATAATATAA
1 TATTTGATTATT-TGATTAACTATAATATAA
3237220 TATTTGATTATTTGATTAACTATAATAT
1 TATTTGATTATTTGATTAACTATAATAT
3237248 TTATTTAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (30 bp):
TATTTGATTATTTGATTAACTATAATATAA
Found at i:3237493 original size:15 final size:15
Alignment explanation
Indices: 3237473--3237503 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3237463 CACATGTTGT
3237473 TAACATTTGACAGAA
1 TAACATTTGACAGAA
3237488 TAACATTTGACAGAA
1 TAACATTTGACAGAA
3237503 T
1 T
3237504 TGATAATGTG
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:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (15 bp):
TAACATTTGACAGAA
Found at i:3237884 original size:32 final size:33
Alignment explanation
Indices: 3237841--3237919 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 33
3237831 AAAAAAAATG
*
3237841 AAGTTAAGATAAAGTTTAAAA-ATAT-TTTTTT
1 AAGTTAAGATAAAGTTTAAAAGAAATATTTTTT
* *
3237872 AAAGTTATGATAAA-ATTAAAAGAAATATTTTTT
1 -AAGTTAAGATAAAGTTTAAAAGAAATATTTTTT
3237905 AAGTTAAGATAAAGT
1 AAGTTAAGATAAAGT
3237920 CAATTTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
31 6 0.15
32 27 0.69
33 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.39
Consensus pattern (33 bp):
AAGTTAAGATAAAGTTTAAAAGAAATATTTTTT
Found at i:3238801 original size:226 final size:228
Alignment explanation
Indices: 3238402--3238882 Score: 858
Period size: 226 Copynumber: 2.1 Consensus size: 228
3238392 GTAAAGTATC
* * * *
3238402 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTGTT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTGGT
* *
3238467 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTG
66 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAAATAAAATAATTTTG
3238532 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
3238597 GAAACATAAATTACATAACTTT-AAAAAAG-TA
196 GAAACATAAATTACATAACTTTAAAAAAAGATA
*
3238628 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAACATATTTATTATTATATTTGGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTGGT
*
3238693 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAAATAAAATAATTTTT
66 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAAATAAAATAATTTTG
3238758 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
3238823 GAAACATAAATTACATAACTTTAAAAAAAGTATA
196 GAAACATAAATTACATAACTTTAAAAAAAG-ATA
*
3238857 TATCATTTTTATAAAAGTGTTCATAC
1 TATCATTTTTATAAAAGTGTCCATAC
3238883 GTATAAAAGT
Statistics
Matches: 243, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
226 209 0.86
227 7 0.03
229 27 0.11
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTGGT
TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAAATAAAATAATTTTG
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
GAAACATAAATTACATAACTTTAAAAAAAGATA
Found at i:3239305 original size:179 final size:181
Alignment explanation
Indices: 3238951--3239423 Score: 684
Period size: 180 Copynumber: 2.6 Consensus size: 181
3238941 TCGATCCAAA
* * * * * *
3238951 TAAAAAAAGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACTGGTATA-GAAATG
1 TAAAAAAAATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGT-TACAAAATG
* * * * *
3239015 ATAAAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACAC
65 ATAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACAC
*
3239080 TTCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTT
130 TTCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTT
* *
3239132 T-TAAAAAATATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTTACAAAATGA
1 TAAAAAAAATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTTACAAAATGA
* * *
3239196 TAAAACCGGTAAAACGTTACCAGATATATTGAAAGTGTCGATACTTT-GTATAAGGATCGACACT
66 TAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACT
* ** *
3239260 TTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTT
131 TCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTT
*
3239311 TAAAAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGG-TATCAAAAT
1 TAAAAAAA-ATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTTA-CAAAAT
*
3239375 GATAAAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
64 GATAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
3239424 CGTAAGTACG
Statistics
Matches: 262, Mismatches: 26, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
179 65 0.25
180 100 0.38
181 97 0.37
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (181 bp):
TAAAAAAAATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTTACAAAATGA
TAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACT
TCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTT
Found at i:3239367 original size:20 final size:19
Alignment explanation
Indices: 3239344--3239390 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
3239334 CGATATAACA
3239344 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
3239364 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
3239384 GGTAAAA
1 GGTAAAA
3239391 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:3239392 original size:17 final size:19
Alignment explanation
Indices: 3239353--3239395 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
3239343 AGGTAAAAAT
3239353 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
3239373 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
3239390 ATGATA
1 ATGATA
3239396 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:3239405 original size:181 final size:180
Alignment explanation
Indices: 3238951--3239423 Score: 691
Period size: 181 Copynumber: 2.6 Consensus size: 180
3238941 TCGATCCAAA
* * * *
3238951 TAAAAAAAGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACTGGTAT-AGAAATG
1 TAAAAAAA-TATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCA-AAATG
* * * * *
3239015 ATAAAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACAC
64 ATAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACAC
*
3239080 TTCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTT
129 TTCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTT
* *
3239132 TTAAAAAATATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGT-TACAAAATGA
1 TAAAAAAATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAT-CAAAATGA
* * *
3239196 TAAAACCGGTAAAACGTTACCAGATATATTGAAAGTGTCGATACTTT-GTATAAGGATCGACACT
65 TAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACT
* ** *
3239260 TTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTT
130 TCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTT
*
3239311 TAAAAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATG
1 T-AAAAAA-ATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATG
*
3239376 ATAAAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
64 ATAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
3239424 CGTAAGTACG
Statistics
Matches: 263, Mismatches: 24, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
179 64 0.24
180 93 0.35
181 105 0.40
182 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (180 bp):
TAAAAAAATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
AAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTT
CGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTT
Found at i:3241614 original size:21 final size:21
Alignment explanation
Indices: 3241590--3241633 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3241580 AAGACAATCA
3241590 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
3241611 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
3241632 AG
1 AG
3241634 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:3241709 original size:33 final size:33
Alignment explanation
Indices: 3241667--3241732 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3241657 AAATAGATGG
*
3241667 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
3241700 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
3241733 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:3243546 original size:19 final size:19
Alignment explanation
Indices: 3243522--3243570 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
3243512 AATGTAGGGT
3243522 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
3243541 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
3243560 TATTTTTGTAT
1 TAATTTTGTAT
3243571 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:3244635 original size:198 final size:198
Alignment explanation
Indices: 3243689--3245050 Score: 2498
Period size: 198 Copynumber: 6.9 Consensus size: 198
3243679 CAATATGGCC
*
3243689 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
3243754 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACC-GTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
* *
3243818 GAATATGTCTAAATAATGTGTCGACACTATTTAGTTTGTGTCGATA-TTTTGTTCCAGAATGAAT
130 GAATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
3243882 GGAA
195 GGAA
3243886 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
3243951 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
3244016 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACT-TTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
3244081 GGAA
195 GGAA
*
3244085 AACAGGGTACAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
3244150 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
3244215 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACT-TTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
3244280 GGAA
195 GGAA
3244284 AACAGGGTGCAACCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
3244347 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
3244412 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
3244477 GAA
196 GAA
* *
3244480 AACAGGGTGCAACCATATAGTATCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
3244545 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
3244610 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
3244675 GAA
196 GAA
*
3244678 AACAAGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
** *
3244743 CAAAAGTATAATGTAATATGTTTTTTTTCAATCTAACCGGTACAAGTATACCGATTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
* *
3244808 AATATGTCTAAATAATGAGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
3244873 GAA
196 GAA
* * *
3244876 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAATTTTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
3244941 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
3245006 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTTGATA
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATA
3245051 CTAATTTAAA
Statistics
Matches: 1135, Mismatches: 25, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
196 122 0.11
197 226 0.20
198 539 0.47
199 248 0.22
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
GAA
Found at i:3246548 original size:3 final size:3
Alignment explanation
Indices: 3246528--3246608 Score: 90
Period size: 3 Copynumber: 27.0 Consensus size: 3
3246518 TGAAGCTGAC
* * * * * * *
3246528 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GAC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
3246576 GAC GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
3246609 CCAAACAAGT
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:3246563 original size:36 final size:36
Alignment explanation
Indices: 3246516--3246592 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
3246506 GGTCGCAGAA
*
3246516 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* *
3246552 GATGAAGCTGACGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
3246588 GATGA
1 GATGA
3246593 TGATGATGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.09, G:0.34, T:0.21
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:3247832 original size:16 final size:16
Alignment explanation
Indices: 3247800--3247833 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3247790 TATCCACAAC
* *
3247800 AAAGTGTCGATTTAAA
1 AAAGTGTCGACTGAAA
3247816 AAAGTGTCGACTGAAA
1 AAAGTGTCGACTGAAA
3247832 AA
1 AA
3247834 TGTAATAGAC
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:0.47, C:0.09, G:0.21, T:0.24
Consensus pattern (16 bp):
AAAGTGTCGACTGAAA
Found at i:3248224 original size:21 final size:21
Alignment explanation
Indices: 3248198--3248268 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
3248188 TAAAAATATG
3248198 ATGTAATAGGTAGCGCTTATA
1 ATGTAATAGGTAGCGCTTATA
* *
3248219 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTAGCG-CT-TATA
* *
3248242 ATGTAATAGGTAGTGGTTATA
1 ATGTAATAGGTAGCGCTTATA
*
3248263 TTGTAA
1 ATGTAA
3248269 AGTATCTATC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
21 23 0.55
22 2 0.05
23 17 0.40
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.39
Consensus pattern (21 bp):
ATGTAATAGGTAGCGCTTATA
Found at i:3248245 original size:23 final size:22
Alignment explanation
Indices: 3248193--3248254 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
3248183 ATAGGTAAAA
*
3248193 ATATGATGTAATAGGTAGCGCT
1 ATATAATGTAATAGGTAGCGCT
* *
3248215 -TATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCG-CT
3248237 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
3248255 TGGTTATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 17 0.50
22 1 0.03
23 16 0.47
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (22 bp):
ATATAATGTAATAGGTAGCGCT
Found at i:3248261 original size:23 final size:23
Alignment explanation
Indices: 3248193--3248263 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
3248183 ATAGGTAAAA
* * *
3248193 ATATGATGTAATAGGTAG-CGCT
1 ATATAATGTAATAGGTAGTGGTT
*
3248215 -TATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GGTT
3248237 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGGTT
3248260 ATAT
1 ATAT
3248264 TGTAAAGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
21 15 0.38
22 1 0.03
23 23 0.57
24 1 0.03
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGGTT
Found at i:3251450 original size:25 final size:25
Alignment explanation
Indices: 3251422--3251486 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
3251412 TTATCATTAA
3251422 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
3251447 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
3251472 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
3251487 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:3251857 original size:23 final size:23
Alignment explanation
Indices: 3251826--3251898 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
3251816 ATAGGTAAAA
*
3251826 ATATGATGTAATAGGTAGCTC-TT
1 ATATAATGTAATAGGTAG-TCGTT
*
3251849 ATATAATGTAATAAGT-GTCGTTT
1 ATATAATGTAATAGGTAGTCG-TT
*
3251872 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTCGTT
3251895 ATAT
1 ATAT
3251899 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
21 2 0.05
22 1 0.02
23 37 0.86
24 3 0.07
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTCGTT
Found at i:3252210 original size:25 final size:25
Alignment explanation
Indices: 3252172--3252221 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3252162 AAATCAATTA
*
3252172 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
3252197 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
3252222 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:3252941 original size:39 final size:39
Alignment explanation
Indices: 3252898--3252984 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
3252888 TCCGATGCTC
*
3252898 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
3252937 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
3252976 ATCAAAATC
1 ATCAAAATC
3252985 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:3253436 original size:23 final size:23
Alignment explanation
Indices: 3253405--3253477 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
3253395 ATAGGTAAAA
*
3253405 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
3253428 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
3253451 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
3253474 ATAT
1 ATAT
3253478 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:3253502 original size:46 final size:45
Alignment explanation
Indices: 3253405--3253502 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
3253395 ATAGGTAAAA
* * *
3253405 ATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATAT-ATGTAATATCTATCCTTT
* *
3253451 ATATAATGTAATAGGTAGTGGTTATAT-TGTAAAGTATCTATCCTTT
1 ATATAATGTAATAGGTAGCGCTTATATATGT-AA-TATCTATCCTTT
*
3253497 TTATAA
1 ATATAA
3253503 AAGTGTCCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 3 0.07
45 2 0.05
46 39 0.89
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (45 bp):
ATATAATGTAATAGGTAGCGCTTATATATGTAATATCTATCCTTT
Found at i:3253866 original size:23 final size:23
Alignment explanation
Indices: 3253835--3253907 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
3253825 ATAGGTAAAA
*
3253835 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
3253858 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
3253881 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
3253904 ATAT
1 ATAT
3253908 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:3253932 original size:46 final size:45
Alignment explanation
Indices: 3253835--3253932 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
3253825 ATAGGTAAAA
* * *
3253835 ATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATAT-ATGTAATATCTATCCTTT
* *
3253881 ATATAATGTAATAGGTAGTGGTTATAT-TGTAAAGTATCTATCCTTT
1 ATATAATGTAATAGGTAGCGCTTATATATGT-AA-TATCTATCCTTT
*
3253927 TTATAA
1 ATATAA
3253933 AAGTGTCCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 3 0.07
45 2 0.05
46 39 0.89
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (45 bp):
ATATAATGTAATAGGTAGCGCTTATATATGTAATATCTATCCTTT
Found at i:3254011 original size:430 final size:430
Alignment explanation
Indices: 3253203--3254687 Score: 2819
Period size: 430 Copynumber: 3.5 Consensus size: 430
3253193 GTTAATGTTG
* *
3253203 TTAAATT-TAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
*
3253267 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATA
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
3253332 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
131 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
3253397 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTATATAATGTAA
196 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTATATAATGTAA
3253462 TAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
261 TAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
3253527 GGAAAACATTAATTTAAGGTTATCCTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
326 GGAAAACATTAATTTAAGGTTATCCTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
3253592 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
391 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
*
3253632 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAACTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
3253697 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
3253762 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
131 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
3253827 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTATATAATGTAA
196 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTATATAATGTAA
3253892 TAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
261 TAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
3253957 GGAAAACATTAATTTAAGGTTATCCTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
326 GGAAAACATTAATTTAAGGTTATCCTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
3254022 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
391 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
3254062 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
3254127 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
* *
3254192 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGAAAACTTTCAATATAAT
131 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
* *
3254257 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAA
196 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTATATAATGTAA
* ** *
3254322 TAGGTAGTGATTATATTGTAAAGTATCTATATTTTTTATAAAAGTGTTCATACTTTTTTCACTGT
261 TAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
* *
3254387 GGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGC
326 GGAAAACATTAATTTAAGGTTATCCTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
3254452 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
391 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
*
3254492 TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
*
3254557 ATAAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
3254622 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
131 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
3254687 A
196 A
3254688 TAATGTAATA
Statistics
Matches: 1036, Mismatches: 19, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
429 7 0.01
430 1029 0.99
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (430 bp):
TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTATATAATGTAA
TAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
GGAAAACATTAATTTAAGGTTATCCTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
Found at i:3254296 original size:23 final size:23
Alignment explanation
Indices: 3254265--3254337 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
3254255 ATAGGTAAAA
* *
3254265 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGATT
*
3254288 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGATT
*
3254311 ATATAATGTAATAGGTAGTGATT
1 ATATAATGTAATAGGTAGCGATT
3254334 ATAT
1 ATAT
3254338 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGATT
Found at i:3257788 original size:37 final size:37
Alignment explanation
Indices: 3257734--3257804 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
3257724 ATGCGGACAT
3257734 TATTTGACTAGTCAGTAGTTTCAGAGGGAAGTTTCAG
1 TATTTGACTAGTCAGTAGTTTCAGAGGGAAGTTTCAG
*
3257771 TATTTGACTAGTTAGTAGTTTCAGAGGGAAGTTT
1 TATTTGACTAGTCAGTAGTTTCAGAGGGAAGTTT
3257805 TACTGATATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (37 bp):
TATTTGACTAGTCAGTAGTTTCAGAGGGAAGTTTCAG
Found at i:3257839 original size:37 final size:39
Alignment explanation
Indices: 3257798--3257874 Score: 104
Period size: 41 Copynumber: 2.0 Consensus size: 39
3257788 GTTTCAGAGG
*
3257798 GAAGTTTTACTG-AT-ATCTTAATTTAAGGTTAAGGAAT
1 GAAGTTTTACTGTATAATCATAATTTAAGGTTAAGGAAT
*
3257835 GAAGTTTTGCTGTATGACATCATAATTTAAGGTTAAGGAA
1 GAAGTTTTACTGTAT-A-ATCATAATTTAAGGTTAAGGAA
3257875 CGACACTACG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 11 0.32
38 2 0.06
41 21 0.62
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (39 bp):
GAAGTTTTACTGTATAATCATAATTTAAGGTTAAGGAAT
Found at i:3259689 original size:2 final size:2
Alignment explanation
Indices: 3259682--3259711 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3259672 CATTGATTTA
3259682 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3259712 GGTCATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3267215 original size:18 final size:21
Alignment explanation
Indices: 3267155--3267217 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
3267145 TACAAGTACA
* *
3267155 TATACAATGATCATAACATGA-
1 TATACAAT-ATCATAAAATCAT
3267176 TA-ACAATATCATAAAATCAT
1 TATACAATATCATAAAATCAT
3267196 TATACAATAT-A-AAAAT-AT
1 TATACAATATCATAAAATCAT
3267214 TATA
1 TATA
3267218 AAAATAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.16
19 15 0.39
20 8 0.21
21 9 0.24
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.32
Consensus pattern (21 bp):
TATACAATATCATAAAATCAT
Found at i:3267463 original size:15 final size:13
Alignment explanation
Indices: 3267406--3267457 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 13
3267396 TTTTTTTTTG
3267406 TAAAAAATTACATAT
1 TAAAAAA-TA-ATAT
3267421 TAAATAAATAATATT
1 TAAA-AAATAATA-T
3267436 TAATAAAATAATAT
1 TAA-AAAATAATAT
3267450 TAAAAAAT
1 TAAAAAAT
3267458 TAAATAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.15
14 7 0.21
15 18 0.53
16 4 0.12
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
TAAAAAATAATAT
Found at i:3268351 original size:31 final size:31
Alignment explanation
Indices: 3268293--3268353 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
3268283 ATCATATCTT
*
3268293 AATTAAATAAAAACGAAAGTGATCATATATG
1 AATTAAATAAAAACGAAAGTGAACATATATG
*
3268324 AATTAAATAAAAA-TAAAGGTGAACATATAT
1 AATTAAATAAAAACGAAA-GTGAACATATAT
3268354 TATGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.57, C:0.05, G:0.11, T:0.26
Consensus pattern (31 bp):
AATTAAATAAAAACGAAAGTGAACATATATG
Found at i:3286272 original size:29 final size:28
Alignment explanation
Indices: 3286221--3286278 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
3286211 TAAAAATAAC
* *
3286221 AAAAAAATATTTTTTTATATTAATATTTA
1 AAAAAAATATTCTATTATATTAAT-TTTA
3286250 AAAAAAATACTTCTATTAT-TTAATTTTA
1 AAAAAAATA-TTCTATTATATTAATTTTA
3286278 A
1 A
3286279 TTCCAATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 5 0.19
29 14 0.54
30 7 0.27
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (28 bp):
AAAAAAATATTCTATTATATTAATTTTA
Found at i:3287868 original size:81 final size:81
Alignment explanation
Indices: 3287755--3288406 Score: 950
Period size: 81 Copynumber: 8.1 Consensus size: 81
3287745 AGGCATTTCG
* * * * *
3287755 TCTTTTACCCAAAGGAATTTAGCCTTTCATCTAACTTGCATGATTGACACATTCCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACATTTCTGCCAAATGC
*
3287820 ACAGCTAGGCCATTGA
66 ACAGCTAGGCCATTAA
**
3287836 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTCACATAATTGACACATTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACATTTCTGCCAAATGC
*
3287901 AAAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * *
3287917 TCTTTTACTCAAAGGTATTTAATCTTTCATCTAA-GTGACATAATTGACACCTTTCTACCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTG-CATAATTGACACATTTCTGCCAAATG
*
3287981 CACAACTAGGCCATTAA
65 CACAGCTAGGCCATTAA
* *
3287998 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACACATTTATGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACATTTCTGCCAAATGC
* *
3288063 ACAACTAGGTCATTAA
66 ACAGCTAGGCCATTAA
* * * *
3288079 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAA-TTGGCATAATTAATACCTTTCTGTCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTT-GCATAATTGACACATTTCTGCCAAATG
3288143 CACAGCTAGGCCATTAA
65 CACAGCTAGGCCATTAA
* * *
3288160 TCTTTTACTCAAAGGTATTTAATCTTTCATCTAACTAGCATAATTAACACATTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACATTTCTGCCAAATGC
3288225 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
3288241 TATTTTACTCAAAGGTATTTAACCTTTCATCTAAC-TGCATAATTGACACCTTTCTACCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACATTTCTGCCAAATGC
* **
3288305 ACAACTATACCATTAA
66 ACAGCTAGGCCATTAA
* *
3288321 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACATTTCTGCCAAATGC
* *
3288386 ACAGATAGGACATTAA
66 ACAGCTAGGCCATTAA
3288402 TCTTT
1 TCTTT
3288407 CATTTTAAAA
Statistics
Matches: 510, Mismatches: 56, Indels: 10
0.89 0.10 0.02
Matches are distributed among these distances:
80 73 0.14
81 435 0.85
82 2 0.00
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACATTTCTGCCAAATGC
ACAGCTAGGCCATTAA
Found at i:3290789 original size:31 final size:31
Alignment explanation
Indices: 3290754--3290813 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3290744 AACTTAAAAG
* *
3290754 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
3290785 AGTTTTACAATATTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
3290814 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:3291342 original size:21 final size:21
Alignment explanation
Indices: 3291291--3291362 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
3291281 TAATTAAAAT
3291291 AAATATAAATAT-TAATAATATA
1 AAAT-TAAATATAT-ATAATATA
* * *
3291313 TAAA-AAAATGTATATGATATA
1 -AAATTAAATATATATAATATA
*
3291334 AAATTAAATATCTATAATATA
1 AAATTAAATATATATAATATA
*
3291355 ATATTAAA
1 AAATTAAA
3291363 AAATTAATAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
20 3 0.08
21 32 0.82
22 1 0.03
23 3 0.08
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (21 bp):
AAATTAAATATATATAATATA
Found at i:3291369 original size:64 final size:62
Alignment explanation
Indices: 3291313--3291496 Score: 210
Period size: 64 Copynumber: 2.8 Consensus size: 62
3291303 TAATAATATA
3291313 TAAAAAAATGTATATGATATAAAATTAAATATCTATAATATAATATTAAAAAATTAATAATTAAT
1 TAAAAAAAT-TA-AT-AT-TAAAATT-AATATCTATAATATAATATT-AAAAATTAATAATTAA-
3291378 TTAT
59 TTAT
* *
3291382 TTAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAAAATTAATATTTAATTTAT
1 TAAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAAAATTAATAATTAA-TTAT
* * *
3291445 T-TAAAAATTAATATTAATATTAAAATCAAATATAATATAATA-TAAAAATTAA
1 TAAAAAAATTAATATTAAAATTAATATC---TATAATATAATATTAAAAATTAA
3291497 ATATAAACCC
Statistics
Matches: 107, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
62 23 0.21
63 21 0.20
64 30 0.28
65 19 0.18
66 2 0.02
67 2 0.02
68 2 0.02
69 8 0.07
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (62 bp):
TAAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAAAATTAATAATTAATTAT
Found at i:3291387 original size:23 final size:23
Alignment explanation
Indices: 3291356--3291399 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
3291346 TATAATATAA
3291356 TATT-AAAAAATTAATAATTAATT
1 TATTAAAAAAATTAAT-ATTAATT
*
3291379 TATTTAAAAAATTAATATTAA
1 TATTAAAAAAATTAATATTAA
3291400 AATTAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATTAAAAAAATTAATATTAATT
Found at i:3291452 original size:23 final size:26
Alignment explanation
Indices: 3291391--3291460 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 26
3291381 TTTAAAAAAT
3291391 TAATATT-AAAATTAATATCTATAATA
1 TAATATTAAAAATTAATAT-TATAATA
3291417 TAATATTAAAAATTAATATT-TAAT-
1 TAATATTAAAAATTAATATTATAATA
*
3291441 TTAT-TTAAAAATTAATATTA
1 TAATATTAAAAATTAATATTA
3291461 ATATTAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
23 15 0.37
24 3 0.07
25 4 0.10
26 8 0.20
27 11 0.27
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
TAATATTAAAAATTAATATTATAATA
Found at i:3291470 original size:41 final size:41
Alignment explanation
Indices: 3291412--3291502 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
3291402 TTAATATCTA
* * * *
3291412 TAATATAATATTAAAAATTAATATTTAAT-TTATTTAAAAAT
1 TAATATAATATTAAAAATCAA-ATATAATATAATATAAAAAT
3291453 TAATATTAATATT-AAAATCAAATATAATATAATATAAAAAT
1 TAATA-TAATATTAAAAATCAAATATAATATAATATAAAAAT
3291494 TAAATATAA
1 T-AATATAA
3291503 ACCCTCTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
40 6 0.14
41 26 0.60
42 11 0.26
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (41 bp):
TAATATAATATTAAAAATCAAATATAATATAATATAAAAAT
Found at i:3291475 original size:23 final size:23
Alignment explanation
Indices: 3291449--3291502 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
3291439 ATTTATTTAA
*
3291449 AAAT-TAATATTAATATTAAAATC
1 AAATATAATA-TAATATAAAAATC
*
3291472 AAATATAATATAATATAAAAATT
1 AAATATAATATAATATAAAAATC
3291495 AAATATAA
1 AAATATAA
3291503 ACCCTCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
AAATATAATATAATATAAAAATC
Found at i:3298182 original size:23 final size:23
Alignment explanation
Indices: 3298156--3298209 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
3298146 AATTAAATAA
*
3298156 TTATTTTAATGTA-TTTATAAAA-T
1 TTATTTAAAT-TATTTTA-AAAATT
3298179 TTATATTAAATTATTTTAAAAATT
1 TTAT-TTAAATTATTTTAAAAATT
3298203 TTATTTA
1 TTATTTA
3298210 CAATATTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTATTTAAATTATTTTAAAAATT
Found at i:3303201 original size:20 final size:19
Alignment explanation
Indices: 3303173--3303215 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3303163 AGATAAAATT
*
3303173 AAATTATTAATAATATATAA
1 AAATAATTAAT-ATATATAA
*
3303193 AAATAATTAATTTATATAA
1 AAATAATTAATATATATAA
3303212 AAAT
1 AAAT
3303216 TTAAAATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATAATTAATATATATAA
Found at i:3303935 original size:2 final size:2
Alignment explanation
Indices: 3303930--3303960 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3303920 TTTTTTTAAT
3303930 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 T
3303961 TATTTTAATG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3305067 original size:21 final size:21
Alignment explanation
Indices: 3305043--3305086 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3305033 AAAGAGAGAA
*
3305043 ATATAC-GAGCAAATTACAAGC
1 ATATACGGAGCAAATCA-AAGC
*
3305064 ATATTCGGAGCAAATCAAAGC
1 ATATACGGAGCAAATCAAAGC
3305085 AT
1 AT
3305087 TCTTTTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.20
Consensus pattern (21 bp):
ATATACGGAGCAAATCAAAGC
Found at i:3305742 original size:13 final size:14
Alignment explanation
Indices: 3305714--3305781 Score: 63
Period size: 16 Copynumber: 4.9 Consensus size: 14
3305704 TTTATCTTGA
*
3305714 TATTATTTCTTGTTT
1 TATTATTTATT-TTT
3305729 TATTATTT-TTTTT
1 TATTATTTATTTTT
*
3305742 TA--ATTT-TTTCT
1 TATTATTTATTTTT
3305753 TATTATTTATTACTTT
1 TATTATTTATT--TTT
3305769 TATTATTTATTTT
1 TATTATTTATTTT
3305782 CTATATTTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
11 10 0.22
13 9 0.20
14 6 0.13
15 8 0.17
16 13 0.28
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.75
Consensus pattern (14 bp):
TATTATTTATTTTT
Found at i:3305769 original size:21 final size:21
Alignment explanation
Indices: 3305716--3305775 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
3305706 TATCTTGATA
* *
3305716 TTATTTCTTGTTTTATTATTTT
1 TTATTACTT-TTTTATTATTAT
* * *
3305738 TTTTTAATTTTTTCTTATTAT
1 TTATTACTTTTTTATTATTAT
3305759 TTATTACTTTTATTATT
1 TTATTACTTTT-TTATT
3305776 TATTTTCTAT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (21 bp):
TTATTACTTTTTTATTATTAT
Found at i:3305788 original size:16 final size:15
Alignment explanation
Indices: 3305747--3305788 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
3305737 TTTTTTAATT
3305747 TTTTCTTATTATTTA
1 TTTTCTTATTATTTA
3305762 TTACTT-TTATTATTTA
1 TT--TTCTTATTATTTA
3305778 TTTTCTATATT
1 TTTTCT-TATT
3305789 TTGTTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.09
15 3 0.13
16 16 0.70
17 2 0.09
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTCTTATTATTTA
Found at i:3305882 original size:11 final size:12
Alignment explanation
Indices: 3305847--3305886 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
3305837 CTATTCTTAT
3305847 TATTATTACTAT-
1 TATT-TTACTATA
3305859 TATTTTACTATA
1 TATTTTACTATA
3305871 TATTTTACATATA
1 TATTTTAC-TATA
3305884 TAT
1 TAT
3305887 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.27
12 12 0.46
13 7 0.27
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTTTACTATA
Found at i:3305884 original size:2 final size:2
Alignment explanation
Indices: 3305879--3305952 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
3305869 TATATTTTAC
3305879 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3305921 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3305953 TTCCCCTATT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3306005 original size:2 final size:2
Alignment explanation
Indices: 3306000--3306038 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3305990 TTACATTTAC
3306000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3306039 TTTATTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3306277 original size:14 final size:14
Alignment explanation
Indices: 3306234--3306309 Score: 59
Period size: 14 Copynumber: 5.1 Consensus size: 14
3306224 CTGATTTTCT
*
3306234 TTTTCTTTACCTTCA
1 TTTTCTTTA-CTTTA
3306249 TTTT-TTATA-TTTA
1 TTTTCTT-TACTTTA
3306262 TTTTCTTTACTTTA
1 TTTTCTTTACTTTA
3306276 TTTAT-TTTACTTACTA
1 TTT-TCTTTACTT--TA
3306292 GTTTATCTTTACTTTA
1 -TTT-TCTTTACTTTA
3306308 TT
1 TT
3306310 CTTTTTGACC
Statistics
Matches: 52, Mismatches: 1, Indels: 16
0.75 0.01 0.23
Matches are distributed among these distances:
13 9 0.17
14 18 0.35
15 9 0.17
16 4 0.08
17 5 0.10
18 7 0.13
ACGTcount: A:0.18, C:0.13, G:0.01, T:0.67
Consensus pattern (14 bp):
TTTTCTTTACTTTA
Found at i:3306302 original size:18 final size:15
Alignment explanation
Indices: 3306258--3306309 Score: 63
Period size: 14 Copynumber: 3.4 Consensus size: 15
3306248 ATTTTTTATA
3306258 TTTATTT-TCTTTAC
1 TTTATTTATCTTTAC
3306272 TTTATTTAT-TTTAC
1 TTTATTTATCTTTAC
3306286 TTACTAGTTTATCTTTAC
1 TT--TA-TTTATCTTTAC
3306304 TTTATT
1 TTTATT
3306310 CTTTTTGACC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
14 14 0.42
15 3 0.09
16 4 0.12
17 5 0.15
18 7 0.21
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTATTTATCTTTAC
Found at i:3310493 original size:98 final size:98
Alignment explanation
Indices: 3310234--3310474 Score: 355
Period size: 95 Copynumber: 2.5 Consensus size: 98
3310224 TTATGATATT
* * *
3310234 ATATATATACAATAAATCTTAAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGG
1 ATATATATACAAT-GATCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
*
3310299 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
65 ATAAGATTCAGCTAGCCTGATAAAGGCGATTATA
**
3310333 ATATATAATA-AA-G--CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAACTTTATGG
1 ATATAT-ATACAATGATCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
*
3310394 ATAATATTCAGCTAGCCTGATAAAGGCGATTATA
65 ATAAGATTCAGCTAGCCTGATAAAGGCGATTATA
* *
3310428 ATATATATACAATGATATTGAGTTGTCCCTATAGAGCAATTGGTTAA
1 ATATATATACAATGATCTTGAGTTGTCCCTCTAGAGCAATTGGTTAA
3310475 GTGTCTTGGC
Statistics
Matches: 128, Mismatches: 9, Indels: 11
0.86 0.06 0.07
Matches are distributed among these distances:
94 3 0.02
95 84 0.66
96 1 0.01
98 29 0.23
99 8 0.06
100 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (98 bp):
ATATATATACAATGATCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGA
TAAGATTCAGCTAGCCTGATAAAGGCGATTATA
Found at i:3311824 original size:36 final size:36
Alignment explanation
Indices: 3311771--3311851 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
3311761 TAATTTACTC
* *
3311771 AAAACAAAATTTTGTCTCTCTTGAAACATTTTCTCTT
1 AAAAC-AAATTTTGTCTCTCTTGAAACAGTTTCCCTT
* *
3311808 AAAACAAATTTTGTCTCTTTTGAGACAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAAACAGTTTCCCTT
*
3311844 GAAACAAA
1 AAAACAAA
3311852 AACTTTGAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
36 34 0.87
37 5 0.13
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.38
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAAACAGTTTCCCTT
Found at i:3311972 original size:36 final size:37
Alignment explanation
Indices: 3311864--3312027 Score: 109
Period size: 36 Copynumber: 4.5 Consensus size: 37
3311854 CTTTGAATCT
* * * * * *
3311864 GTTTTCCTTGAAAC-AAATTTCGTCTCCCTTGAGATA
1 GTTTCCCTTAAAACAAAATTTTGTCTCTCTTGAAACA
** * * * * *
3311900 GTTTCTTTTAGAACAAAGTTTTGGCTCTCTTTAGACA
1 GTTTCCCTTAAAACAAAATTTTGTCTCTCTTGAAACA
* * *
3311937 ATTTCTCTTAAAACAAAA-TTTGTCTCTCTTGAGACA
1 GTTTCCCTTAAAACAAAATTTTGTCTCTCTTGAAACA
* * ** *
3311973 ATTTCCCTT-GAATTAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTAAAACAAAATTTTGTCTCTCTTGAAACA
*
3312009 GTTTCCCTTGAAACAAAAT
1 GTTTCCCTTAAAACAAAAT
3312028 CTATGAATCT
Statistics
Matches: 100, Mismatches: 25, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
35 5 0.05
36 59 0.59
37 36 0.36
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (37 bp):
GTTTCCCTTAAAACAAAATTTTGTCTCTCTTGAAACA
Found at i:3312023 original size:72 final size:74
Alignment explanation
Indices: 3311864--3312027 Score: 183
Period size: 72 Copynumber: 2.3 Consensus size: 74
3311854 CTTTGAATCT
* * * **
3311864 GTTTTCCTTGAAAC-AAATTTCGTCTCCCTTGAGATAGTTTCTTTTAGAACAAAGTTTTGGCTCT
1 GTTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAATTTCCCTTAGAACAAAGTTTTGGCTCT
*
3311928 CTTTAGACA
66 CTTGAGACA
* * * * * *
3311937 ATTTCTCTTAAAACAAAATTT-GTCTCTCTTGAGACAATTTCCCTT-GAATTAAA-TTTTGTCTC
1 GTTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAATTTCCCTTAGAA-CAAAGTTTTGGCTC
3311999 TCTTGAGACA
65 TCTTGAGACA
3312009 GTTTCCCTTGAAACAAAAT
1 GTTTCCCTTGAAACAAAAT
3312028 CTATGAATCT
Statistics
Matches: 74, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
72 36 0.49
73 32 0.43
74 6 0.08
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (74 bp):
GTTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAATTTCCCTTAGAACAAAGTTTTGGCTCT
CTTGAGACA
Found at i:3312053 original size:138 final size:139
Alignment explanation
Indices: 3311901--3312161 Score: 337
Period size: 138 Copynumber: 1.9 Consensus size: 139
3311891 CTTGAGATAG
* * ** *
3311901 TTTCTTTTAGAACAAAGTTTTGGCTCTCTTTAGACAATTTCTCTTAAAAC-AAAATTTGTCTCTC
1 TTTCATTTAGAACAAA-TTTCGGCTCTCTCGAGACAATTTCTCTTAAAACTAAAATTTATCTCTC
**
3311965 TTGAGACAATTTCCCTTGAATTAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCT
65 TTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCT
3312030 ATGAATCTGT
130 ATGAATCTGT
* * * * ** *
3312040 TTTCATTTA-AACAAATTTCGTCTCTCTCGAGACATTTTCTTTTAGAACTAAGTTTTATCTCTTT
1 TTTCATTTAGAACAAATTTCGGCTCTCTCGAGACAATTTCTCTTAAAACTAAAATTTATCTCTCT
* * * *
3312104 TGAGACAGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA
66 TGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
3312162 CCAACCTTTG
Statistics
Matches: 103, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
137 26 0.25
138 69 0.67
139 8 0.08
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (139 bp):
TTTCATTTAGAACAAATTTCGGCTCTCTCGAGACAATTTCTCTTAAAACTAAAATTTATCTCTCT
TGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTA
TGAATCTGT
Found at i:3312081 original size:174 final size:174
Alignment explanation
Indices: 3311771--3312161 Score: 532
Period size: 174 Copynumber: 2.2 Consensus size: 174
3311761 TAATTTACTC
* * * *
3311771 AAAACAAAATTTTGTCTCTCTTGAAACATTTTCTCTTAAAACAAATTTTGTCTCTTTTGAGACAG
1 AAAACAAAA-TTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * * *
3311836 TTTCCCTTGAAACAAAAACTTTGAATCTGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGATAG
65 TTTCCCTTGAAACAAAAACTATGAATCTGTTTTCATTGAAACAAATTTCGTCTCCCTCGAGACAG
* *
3311901 TTTCTTTTAGAACAAAGTTTTGGCTCTCTTT-AGACAATTTCTCTT
130 TTTCTTTTAGAACAAAGTTTTAGCTCT-TTTGAGACAATTTCCCTT
* **
3311946 AAAACAAAATTTGTCTCTCTTGAGACAATTTCCCTTGAATTAAATTTTGTCTCTCTTGAGACAGT
1 AAAACAAAATTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGT
* * * *
3312011 TTCCCTTGAAACAAAATCTATGAATCTGTTTTCATTTAAACAAATTTCGTCTCTCTCGAGACATT
66 TTCCCTTGAAACAAAAACTATGAATCTGTTTTCATTGAAACAAATTTCGTCTCCCTCGAGACAGT
* * *
3312076 TTCTTTTAGAACTAAGTTTTATCTCTTTTGAGACAGTTTCCCTT
131 TTCTTTTAGAACAAAGTTTTAGCTCTTTTGAGACAATTTCCCTT
* ** * *
3312120 GAAACAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA
1 AAAACAAAATTTGTCTCTCTTGAGACAATTTCTCTTGAAACA
3312162 CCAACCTTTG
Statistics
Matches: 187, Mismatches: 28, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
173 3 0.02
174 175 0.94
175 9 0.05
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.41
Consensus pattern (174 bp):
AAAACAAAATTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGT
TTCCCTTGAAACAAAAACTATGAATCTGTTTTCATTGAAACAAATTTCGTCTCCCTCGAGACAGT
TTCTTTTAGAACAAAGTTTTAGCTCTTTTGAGACAATTTCCCTT
Found at i:3312137 original size:36 final size:36
Alignment explanation
Indices: 3312089--3312161 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
3312079 TTTTAGAACT
*
3312089 AAGTTTTATCTCTTTTGAGACAGTTTCCCTTGAAAC
1 AAGTTTTATCTCTCTTGAGACAGTTTCCCTTGAAAC
* * *
3312125 AAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAAC
1 AAGTTTTATCTCTCTTGAGACAGTTTCCCTTGAAAC
3312161 A
1 A
3312162 CCAACCTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (36 bp):
AAGTTTTATCTCTCTTGAGACAGTTTCCCTTGAAAC
Found at i:3312519 original size:18 final size:18
Alignment explanation
Indices: 3312496--3312534 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3312486 ATCACTCTCA
*
3312496 ACATTGTATTTGAACTCT
1 ACATTGTATTTCAACTCT
3312514 ACATTGTATTTCAACTCT
1 ACATTGTATTTCAACTCT
3312532 ACA
1 ACA
3312535 ACAGAGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.41
Consensus pattern (18 bp):
ACATTGTATTTCAACTCT
Found at i:3313838 original size:9 final size:9
Alignment explanation
Indices: 3313824--3313887 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
3313814 TGATAATTTC
3313824 TTTTTTTAT
1 TTTTTTTAT
3313833 TTTTTTTATT
1 TTTTTTTA-T
3313843 TTTTTCTTAT
1 TTTTT-TTAT
* *
3313853 TATTTATTAC
1 T-TTTTTTAT
*
3313863 TTTTATTAT
1 TTTTTTTAT
* *
3313872 TTATTTTCT
1 TTTTTTTAT
3313881 TTTTTTT
1 TTTTTTT
3313888 TTGTTTTGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
9 27 0.60
10 12 0.27
11 6 0.13
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:3313867 original size:36 final size:36
Alignment explanation
Indices: 3313800--3313869 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
3313790 AATTTAGTCC
* *
3313800 TTTTATTTTTATCTTGATAATTTCTTTTTTTATTTT
1 TTTTATTTTTATCTTGATAATTTATTCTTTTATTTT
* *
3313836 TTTTATTTTTTTCTT-ATTATTTATTACTTTTATT
1 TTTTATTTTTATCTTGATAATTTATT-CTTTTATT
3313870 ATTTATTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 8 0.28
36 21 0.72
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.76
Consensus pattern (36 bp):
TTTTATTTTTATCTTGATAATTTATTCTTTTATTTT
Found at i:3313999 original size:2 final size:2
Alignment explanation
Indices: 3313992--3314033 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3313982 ACATATACCC
3313992 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3314034 CCCCTATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3314293 original size:33 final size:34
Alignment explanation
Indices: 3314245--3314329 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 34
3314235 TTTTGACTAA
3314245 TATTTTC-TTTATTTTTTCT-ATTTTAC-TTATCTT
1 TATTTTCATTT-TTTTTTCTGATTTT-CTTTATCTT
* * *
3314278 TGTTTTCATTTTTTTTCCTGATTTTCTTTTTCTT
1 TATTTTCATTTTTTTTTCTGATTTTCTTTATCTT
*
3314312 TATTTT-ATTTTATTTTCT
1 TATTTTCATTTTTTTTTCT
3314330 TTACTTTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
33 24 0.56
34 19 0.44
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.74
Consensus pattern (34 bp):
TATTTTCATTTTTTTTTCTGATTTTCTTTATCTT
Found at i:3314327 original size:19 final size:19
Alignment explanation
Indices: 3314245--3314345 Score: 68
Period size: 19 Copynumber: 5.3 Consensus size: 19
3314235 TTTTGACTAA
*
3314245 TATTTTCTTTATTTT-TTC
1 TATTTTCTTTATTTTATTT
*
3314263 TATTTTAC-TTATCTTTGTTT
1 TATTTT-CTTTAT-TTTATTT
* *
3314283 TCATTTT-TTT-TCCTGATTT
1 T-ATTTTCTTTAT-TTTATTT
*
3314302 TCTTTTTCTTTATTTTATTT
1 T-ATTTTCTTTATTTTATTT
*
3314322 TATTTTCTTTACTTTA-TT
1 TATTTTCTTTATTTTATTT
3314340 TATTTT
1 TATTTT
3314346 ACTTACTAGT
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
18 18 0.27
19 29 0.43
20 14 0.21
21 6 0.09
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (19 bp):
TATTTTCTTTATTTTATTT
Found at i:3314364 original size:18 final size:15
Alignment explanation
Indices: 3314310--3314371 Score: 67
Period size: 14 Copynumber: 4.1 Consensus size: 15
3314300 TTTCTTTTTC
*
3314310 TTTAT-TTTATTTTA
1 TTTATCTTTACTTTA
3314324 TTT-TCTTTACTTTA
1 TTTATCTTTACTTTA
3314338 TTTAT-TTTACTTACTA
1 TTTATCTTTACTT--TA
3314354 GTTTATCTTTACTTTA
1 -TTTATCTTTACTTTA
3314370 TT
1 TT
3314372 CTTTTTGACC
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
13 1 0.02
14 21 0.51
15 3 0.07
16 4 0.10
17 5 0.12
18 7 0.17
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTATCTTTACTTTA
Found at i:3314624 original size:38 final size:38
Alignment explanation
Indices: 3314552--3314625 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
3314542 GTAATGGGGT
*
3314552 GAGGGGGAGATAAAGTAGTAGGTTGCTCCTAACGGGAC
1 GAGGGGGAGATAAAGTAGTAGGTTGCTCCCAACGGGAC
* *
3314590 GAGGGGGAGGTAAGGTAGTAGGTTGC-CCACAACGGG
1 GAGGGGGAGATAAAGTAGTAGGTTGCTCC-CAACGGG
3314626 TTGAGAGCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 2 0.06
38 30 0.94
ACGTcount: A:0.27, C:0.14, G:0.43, T:0.16
Consensus pattern (38 bp):
GAGGGGGAGATAAAGTAGTAGGTTGCTCCCAACGGGAC
Found at i:3317745 original size:62 final size:62
Alignment explanation
Indices: 3317676--3317798 Score: 246
Period size: 62 Copynumber: 2.0 Consensus size: 62
3317666 GGAAATCGGT
3317676 AAGTTATTTTTCTTAAATTTGTAGGTTTTAAACCGGCCTTAGTTTAAGATTTACTAGTGGGG
1 AAGTTATTTTTCTTAAATTTGTAGGTTTTAAACCGGCCTTAGTTTAAGATTTACTAGTGGGG
3317738 AAGTTATTTTTCTTAAATTTGTAGGTTTTAAACCGGCCTTAGTTTAAGATTTACTAGTGGG
1 AAGTTATTTTTCTTAAATTTGTAGGTTTTAAACCGGCCTTAGTTTAAGATTTACTAGTGGG
3317799 TATTAAGTAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (62 bp):
AAGTTATTTTTCTTAAATTTGTAGGTTTTAAACCGGCCTTAGTTTAAGATTTACTAGTGGGG
Found at i:3320795 original size:29 final size:29
Alignment explanation
Indices: 3320755--3320813 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3320745 TATTTATAAG
3320755 AGAATATTTATGTAAATTTGGGATATTTA
1 AGAATATTTATGTAAATTTGGGATATTTA
3320784 AGAATATTTATGTAAATTTGGGATATTTA
1 AGAATATTTATGTAAATTTGGGATATTTA
3320813 A
1 A
3320814 TCTTGGTGTT
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:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (29 bp):
AGAATATTTATGTAAATTTGGGATATTTA
Found at i:3321133 original size:2 final size:2
Alignment explanation
Indices: 3321126--3321152 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3321116 TCAAGTTACC
3321126 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
3321153 ATGATAAAGG
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:3324238 original size:2 final size:2
Alignment explanation
Indices: 3324231--3324291 Score: 95
Period size: 2 Copynumber: 30.5 Consensus size: 2
3324221 AGAATCAGAT
* * *
3324231 TA TA TA TA TA TA CA CA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3324273 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
3324292 GTATGTATGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3324548 original size:2 final size:2
Alignment explanation
Indices: 3324536--3324607 Score: 128
Period size: 2 Copynumber: 36.0 Consensus size: 2
3324526 AAAATTTTTA
3324536 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3324579 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3324608 GTTTTCGTCC
Statistics
Matches: 68, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.01
2 65 0.96
3 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3325887 original size:7 final size:7
Alignment explanation
Indices: 3325877--3325910 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
3325867 ATGTAAATTT
3325877 AAAATAC
1 AAAATAC
3325884 AAAATAC
1 AAAATAC
3325891 AAAATAC
1 AAAATAC
3325898 AAAATAC
1 AAAATAC
3325905 AAAATA
1 AAAATA
3325911 TTAAATATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.74, C:0.12, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAATAC
Found at i:3329150 original size:16 final size:16
Alignment explanation
Indices: 3329129--3329181 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
3329119 AAGAAATTTA
*
3329129 TTTTTATGTTAGTATT
1 TTTTTATGTTAATATT
*
3329145 TTTTTAAATAGTTATTATT
1 TTTTT--AT-GTTAATATT
*
3329164 TTTTTATATTAATATT
1 TTTTTATGTTAATATT
3329180 TT
1 TT
3329182 ATGTAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 14 0.45
17 2 0.06
18 2 0.06
19 13 0.42
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
TTTTTATGTTAATATT
Found at i:3329180 original size:35 final size:35
Alignment explanation
Indices: 3329129--3329195 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
3329119 AAGAAATTTA
* * *
3329129 TTTTTATGTTAGTATTTT-TTTAAATAGTTATTATT
1 TTTTTATATTAATATTTTATGTAAATA-TTATTATT
3329164 TTTTTATATTAATATTTTATGTAAATATTATT
1 TTTTTATATTAATATTTTATGTAAATATTATT
3329196 TTATTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 21 0.75
36 7 0.25
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (35 bp):
TTTTTATATTAATATTTTATGTAAATATTATTATT
Found at i:3329214 original size:15 final size:16
Alignment explanation
Indices: 3329173--3329212 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3329163 TTTTTTATAT
3329173 TAATATTTTATGTAAA
1 TAATATTTTATGTAAA
*
3329189 TATTATTTTAT-TAAAA
1 TAATATTTTATGT-AAA
3329205 TAATATTT
1 TAATATTT
3329213 ATATAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TAATATTTTATGTAAA
Found at i:3331016 original size:21 final size:21
Alignment explanation
Indices: 3330996--3331064 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
3330986 ATCTCCGCAG
*
3330996 GGTTACATTCCGAGCCCG-CA
1 GGTTACATTCCTAGCCCGCCA
3331016 GGGTTACATTCCTAGCCCGCCA
1 -GGTTACATTCCTAGCCCGCCA
*
3331038 GGTTACATGCCTAGCCCGCCA
1 GGTTACATTCCTAGCCCGCCA
3331059 GGTTAC
1 GGTTAC
3331065 TAGCCCGCAG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 43 0.96
22 2 0.04
ACGTcount: A:0.19, C:0.35, G:0.25, T:0.22
Consensus pattern (21 bp):
GGTTACATTCCTAGCCCGCCA
Found at i:3331698 original size:34 final size:33
Alignment explanation
Indices: 3331594--3331698 Score: 124
Period size: 33 Copynumber: 3.2 Consensus size: 33
3331584 ATAAATGTTT
*
3331594 TTAAAATACAAA-TATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
3331627 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
3331659 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
3331694 TTAAA
1 TTAAA
3331699 TTTCAACTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
32 3 0.05
33 35 0.57
34 22 0.36
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:3332451 original size:125 final size:125
Alignment explanation
Indices: 3332078--3332796 Score: 1310
Period size: 125 Copynumber: 5.8 Consensus size: 125
3332068 TTTAAGTTAT
*
3332078 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
* *
3332143 GCGTCCCGGAAACGCGCCTTCACGTGAATAGTG-AATAATAGGTACTGATATATCTAGTG
66 GCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
3332202 TCCCCGAGGGACATGAATGACATAATAGGGCAATG---ATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
3332264 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTG
66 GCG-CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
3332325 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
3332390 GCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTG
66 GCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
3332450 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
3332515 GCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
3332575 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
3332640 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAAT--GTACTG--ATATCTAGTG
66 GCG-CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
3332697 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
3332762 GCGCCCCGTGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
3332797 CCGATTATAG
Statistics
Matches: 583, Mismatches: 6, Indels: 15
0.97 0.01 0.02
Matches are distributed among these distances:
121 61 0.10
122 106 0.18
123 60 0.10
124 40 0.07
125 249 0.43
126 67 0.11
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (125 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:3332763 original size:372 final size:370
Alignment explanation
Indices: 3332078--3332796 Score: 1325
Period size: 372 Copynumber: 1.9 Consensus size: 370
3332068 TTTAAGTTAT
*
3332078 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
3332143 GCGTCCCGGAAACGCGCCTTCACGTGAATAGTGAATAATAGGTACTGATATATCTAGTGTCCCCG
66 GCGCCCCGGAAACGCGCCTTCACGTGAATAGTGAATAATAGGTACTGATATATCTAGTGTCCCCG
3332208 AGGGACATGAATGACATAATAGGGCAATGATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCG
131 AGGGACATGAATGACATAATAGGGCAATGATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCG
3332273 GGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTGTCCCCGAGGGACA
196 GGAACGCGCCTTCACGTGAATAGTGAAATAG-AGGTACTGA-ATATCTAGTGTCCCCGAGGGACA
3332338 TGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCGGGAAC
259 TGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCGGGAAC
3332403 GCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTG
324 GCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTG
3332450 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
3332515 GCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCC
66 GCGCCCCGGAAACGCGCCTTCACGTGAATAGTG-AATAATAGGTACTGATATATCTAGTGTCCCC
3332580 GAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCC
130 GAGGGACATGAATGACATAATAGGGCAATG---ATATTCTCTGACGAAATAATGGAAGGCGCGCC
*
3332645 CCCGGGAACGCGCCTTCACGTGAATAGTGAAATA-ATGTACTG-ATATCTAGTGTCCCCGAGGGA
192 CCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGAGGTACTGAATATCTAGTGTCCCCGAGGGA
*
3332708 CATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCGTGA
257 CATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCGGGA
3332773 ACGCGCCTTCACGTGAATAGTGAA
322 ACGCGCCTTCACGTGAATAGTGAA
3332797 CCGATTATAG
Statistics
Matches: 338, Mismatches: 5, Indels: 8
0.96 0.01 0.02
Matches are distributed among these distances:
372 204 0.60
373 61 0.18
374 7 0.02
376 66 0.20
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (370 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCGGAAACGCGCCTTCACGTGAATAGTGAATAATAGGTACTGATATATCTAGTGTCCCCG
AGGGACATGAATGACATAATAGGGCAATGATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCG
GGAACGCGCCTTCACGTGAATAGTGAAATAGAGGTACTGAATATCTAGTGTCCCCGAGGGACATG
AATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCGGGAACGC
GCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTG
Found at i:3332877 original size:8 final size:8
Alignment explanation
Indices: 3332864--3332903 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
3332854 TCACAATCTT
3332864 TCAAATTC
1 TCAAATTC
3332872 TCAAATTC
1 TCAAATTC
* *
3332880 CCAAACTC
1 TCAAATTC
3332888 T-AAATTC
1 TCAAATTC
3332895 TCAAATTC
1 TCAAATTC
3332903 T
1 T
3332904 GAAAATGAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.35
Consensus pattern (8 bp):
TCAAATTC
Found at i:3335962 original size:23 final size:23
Alignment explanation
Indices: 3335924--3335981 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
3335914 TAGTTATAAT
3335924 TTTTACAT--TATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
3335945 TTTTACATAATATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
3335968 TTTTACATAATATA
1 TTTTACATAATATA
3335982 TTATTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (23 bp):
TTTTACATAATATAATCGAAACA
Found at i:3341441 original size:27 final size:31
Alignment explanation
Indices: 3341368--3341435 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
3341358 CAAGAAAGAT
*
3341368 AATTAATGATAATTTATTTAGACAAAATAACA
1 AATT-ATGATAATTTATATAGACAAAATAACA
3341400 AATTATGATAATTTATATAGACAAAATAACA
1 AATTATGATAATTTATATAGACAAAATAACA
3341431 AATTA
1 AATTA
3341436 AATTTAGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (31 bp):
AATTATGATAATTTATATAGACAAAATAACA
Found at i:3341771 original size:194 final size:200
Alignment explanation
Indices: 3341409--3341819 Score: 519
Period size: 194 Copynumber: 2.1 Consensus size: 200
3341399 AAATTATGAT
* * * *
3341409 AATTTATATAGACAAAATAACAAATTAAATTTAGTTAAAATAAAAAAATTTATGTCAAATTTATT
1 AATTTATTTAGTCACAATAAC-AATTAAATTTAGTCAAAATAAAAAAATTTATGTCAAATTTATT
* * * *
3341474 TAGTTAAAATATTTTATCAAAACAACAAATTATGACAAATTTAAATAGTTATAATAACAAATTAT
65 TAGTTAAAATATTTTATCAAAACAACAAATTATGACAAATTTAAATAATAAAAAAAACAAATTAT
* * *
3341539 AATAAATATTAATTTCTCAATATAAAAAGTTATGACAAATAATA-TTTTTTCACAATAATCAATT
130 AACAAATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTTTTTTCACAATAAACAATT
3341603 ATAACA
195 ATAACA
*
3341609 AATTTATTTAGTCACAATAAC-ATTAAATTTAGTCAAAAT-AAAAAA-TTATGTTAAATTTATTT
1 AATTTATTTAGTCACAATAACAATTAAATTTAGTCAAAATAAAAAAATTTATGTCAAATTTATTT
* * * * * * * * ** *
3341671 TG-T-CATTATTTTCTCAAAATAACAACTTTTGACCAATTTATTTAATAAAAAAAACAATTTATA
66 AGTTAAAATATTTTATCAAAACAACAAATTATGACAAATTTAAATAATAAAAAAAACAAATTATA
* * * *
3341734 ACAAATATTAATTTTTCATTATAAAAAATTGTGACAAATAATATTTTTTTCACAATAAACAATTG
131 ACAAATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTTTTTTCACAATAAACAATTA
3341799 TAACA
196 TAACA
*
3341804 AAATTATTTAGTCACA
1 AATTTATTTAGTCACA
3341820 GTAAAAAAGT
Statistics
Matches: 182, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
194 84 0.46
195 40 0.22
196 17 0.09
197 6 0.03
198 17 0.09
200 18 0.10
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (200 bp):
AATTTATTTAGTCACAATAACAATTAAATTTAGTCAAAATAAAAAAATTTATGTCAAATTTATTT
AGTTAAAATATTTTATCAAAACAACAAATTATGACAAATTTAAATAATAAAAAAAACAAATTATA
ACAAATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTTTTTTCACAATAAACAATTA
TAACA
Done.